http://hdl.handle.net/10023/52 2013-05-25T20:51:24Z 2013-05-25T20:51:24Z Reeks, Judith Anne Graham, Shirley Liu, Huanting White, Malcolm F Naismith, Jim http://hdl.handle.net/10023/3550 2013-05-24T11:01:02Z 2013-05-01T00:00:00Z

Abstract: The Cascade complex for CRISPR-mediated antiviral immunity uses CRISPR RNA (crRNA) to target invading DNA species from mobile elements such as viruses, leading to their destruction. The core of the Cascade effector complex consists of the Cas5 and Cas7 subunits, which are widely conserved in prokaryotes. Cas7 binds crRNA and forms the helical backbone of Cascade. Many archaea encode a version of the Cascade complex (denoted Type I-A) that includes a Csa5 (or small) subunit, which interacts weakly with the core proteins. Here, we report the crystal structure of the Csa5 protein from Sulfolobus solfataricus. Csa5 comprises a conserved α-helical domain with a small insertion consisting of a weakly conserved β-strand domain. In the crystal, the Csa5 monomers have multimerized into infinite helical threads. At each interface is a strictly conserved intersubunit salt bridge, deletion of which disrupts multimerization. Structural analysis indicates a shared evolutionary history among the small subunits of the CRISPR effector complexes. The same α-helical domain is found in the C-terminal domain of Cse2 (from Type I-E Cascade), while the N-terminal domain of Cse2 is found in Cmr5 of the CMR (Type III-B) effector complex. As Cmr5 shares no match with Csa5, two possibilities present themselves: selective domain loss from an ancestral Cse2 to create two new subfamilies or domain fusion of two separate families to create a new Cse2 family. A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes. Description: This work was funded by a grant from the Biotechnology and Biological Sciences Research Council (BBSRC) (REF: BB/G011400/1) to M.F.W. and J.H.N. and a BBSRC-funded studentship to J.R.

2013-05-01T00:00:00Z Reeks, Judith Anne Graham, Shirley Liu, Huanting White, Malcolm F Naismith, Jim The Cascade complex for CRISPR-mediated antiviral immunity uses CRISPR RNA (crRNA) to target invading DNA species from mobile elements such as viruses, leading to their destruction. The core of the Cascade effector complex consists of the Cas5 and Cas7 subunits, which are widely conserved in prokaryotes. Cas7 binds crRNA and forms the helical backbone of Cascade. Many archaea encode a version of the Cascade complex (denoted Type I-A) that includes a Csa5 (or small) subunit, which interacts weakly with the core proteins. Here, we report the crystal structure of the Csa5 protein from Sulfolobus solfataricus. Csa5 comprises a conserved α-helical domain with a small insertion consisting of a weakly conserved β-strand domain. In the crystal, the Csa5 monomers have multimerized into infinite helical threads. At each interface is a strictly conserved intersubunit salt bridge, deletion of which disrupts multimerization. Structural analysis indicates a shared evolutionary history among the small subunits of the CRISPR effector complexes. The same α-helical domain is found in the C-terminal domain of Cse2 (from Type I-E Cascade), while the N-terminal domain of Cse2 is found in Cmr5 of the CMR (Type III-B) effector complex. As Cmr5 shares no match with Csa5, two possibilities present themselves: selective domain loss from an ancestral Cse2 to create two new subfamilies or domain fusion of two separate families to create a new Cse2 family. A definitive answer awaits structural studies of further small subunits from other CRISPR effector complexes. Moynie, Lucile Leckie, Stuart M. McMahon, Stephen A. Duthie, Fraser G. Koehnke, Alessa Taylor, James W. Alphey, Magnus S. Brenk, Ruth Smith, Andrew D. Naismith, James H. http://hdl.handle.net/10023/3510 2013-05-03T13:01:03Z 2013-01-23T00:00:00Z

Abstract: Fatty acid biosynthesis is an essential component of metabolism in both eukaryotes and prokaryotes. The fatty acid biosynthetic pathway of Gram-negative bacteria is an established therapeutic target. Two homologous enzymes FabA and FabZ catalyze a key step in fatty acid biosynthesis; both dehydrate hydroxyacyl fatty acids that are coupled via a phosphopantetheine to an acyl carrier protein (ACP). The resulting trans-2-enoyl-ACP is further polymerized in a processive manner. FabA, however, carries out a second reaction involving isomerization of trans-2-enoyl fatty acid to cis-3-enoyl fatty acid. We have solved the structure of Pseudomonas aeruginosa FabA with a substrate allowing detailed molecular insight into the interactions of the active site. This has allowed a detailed examination of the factors governing the second catalytic step. We have also determined the structure of FabA in complex with small molecules (so-called fragments). These small molecules occupy distinct regions of the active site and form the basis for a rational inhibitor design program. (C) 2012 Elsevier Ltd. All rights reserved.

2013-01-23T00:00:00Z Moynie, Lucile Leckie, Stuart M. McMahon, Stephen A. Duthie, Fraser G. Koehnke, Alessa Taylor, James W. Alphey, Magnus S. Brenk, Ruth Smith, Andrew D. Naismith, James H. Fatty acid biosynthesis is an essential component of metabolism in both eukaryotes and prokaryotes. The fatty acid biosynthetic pathway of Gram-negative bacteria is an established therapeutic target. Two homologous enzymes FabA and FabZ catalyze a key step in fatty acid biosynthesis; both dehydrate hydroxyacyl fatty acids that are coupled via a phosphopantetheine to an acyl carrier protein (ACP). The resulting trans-2-enoyl-ACP is further polymerized in a processive manner. FabA, however, carries out a second reaction involving isomerization of trans-2-enoyl fatty acid to cis-3-enoyl fatty acid. We have solved the structure of Pseudomonas aeruginosa FabA with a substrate allowing detailed molecular insight into the interactions of the active site. This has allowed a detailed examination of the factors governing the second catalytic step. We have also determined the structure of FabA in complex with small molecules (so-called fragments). These small molecules occupy distinct regions of the active site and form the basis for a rational inhibitor design program. (C) 2012 Elsevier Ltd. All rights reserved. Collett, Christopher J. Massey, Richard S. Maguire, Oliver R. Batsanov, Andrei S. O'Donoghue, AnnMarie C. Smith, Andrew D. http://hdl.handle.net/10023/3509 2013-05-03T12:31:02Z 2013-01-01T00:00:00Z

Abstract: The in situ observation, isolation and reversible formation of intermediate 3-(hydroxybenzyl) azolium salts derived from NHC addition to a range of substituted benzaldehydes is probed. Equilibrium constants for the formation of these 3-(hydroxybenzyl) azolium salts, as well as rate constants of hydrogen-deuterium exchange (k(ex)) at C(alpha) of these intermediates for a range of N-aryl triazolinylidenes is reported. These combined studies give insight into the preference of N-pentafluorophenyl NHCs to participate in benzoin and Stetter reaction processes.

2013-01-01T00:00:00Z Collett, Christopher J. Massey, Richard S. Maguire, Oliver R. Batsanov, Andrei S. O'Donoghue, AnnMarie C. Smith, Andrew D. The in situ observation, isolation and reversible formation of intermediate 3-(hydroxybenzyl) azolium salts derived from NHC addition to a range of substituted benzaldehydes is probed. Equilibrium constants for the formation of these 3-(hydroxybenzyl) azolium salts, as well as rate constants of hydrogen-deuterium exchange (k(ex)) at C(alpha) of these intermediates for a range of N-aryl triazolinylidenes is reported. These combined studies give insight into the preference of N-pentafluorophenyl NHCs to participate in benzoin and Stetter reaction processes. Hua, Guoxiong Slawin, Alexandra M. Z. Randall, Rebecca A. M. Cordes, David B. Crawford, Luke Buehl, Michael Woollins, J. Derek http://hdl.handle.net/10023/3508 2013-05-03T12:01:02Z 2013-01-01T00:00:00Z

Abstract: Four-membered ring [PhP(Se)(mu-Se)](2) (Woollins' reagent, WR) reacts with disodium alkenyl-diols followed by in situ ring-closure reaction with appropriate dibromoalkanes affording a series of unusual nine-to fifteen-membered organoselenophosphorus macrocycles bearing the O-P-Se-C-n-Se-P-O or O-P-Se-C-n-O-P-Se linkage.

2013-01-01T00:00:00Z Hua, Guoxiong Slawin, Alexandra M. Z. Randall, Rebecca A. M. Cordes, David B. Crawford, Luke Buehl, Michael Woollins, J. Derek Four-membered ring [PhP(Se)(mu-Se)](2) (Woollins' reagent, WR) reacts with disodium alkenyl-diols followed by in situ ring-closure reaction with appropriate dibromoalkanes affording a series of unusual nine-to fifteen-membered organoselenophosphorus macrocycles bearing the O-P-Se-C-n-Se-P-O or O-P-Se-C-n-O-P-Se linkage. Nasomjai, Pitak O'Hagan, David Slawin, Alexandra M. Z. http://hdl.handle.net/10023/3444 2013-05-12T04:10:23Z 2009-07-27T00:00:00Z

Abstract: The synthesis of phosphonate analogues of ribose-1-phosphate and 5-fluoro-5-deoxyribose-1-phosphate is described. Preparations of both the alpha- and beta-phosphonate anomers are reported for the ribose and 5-fluoro-5-deoxyribose series and a synthesis of the corresponding cyclic phostones of each alpha-ribose is also reported. These compounds have been prepared as tools to probe the details of fluorometabolism in S. cattleya.

2009-07-27T00:00:00Z Nasomjai, Pitak O'Hagan, David Slawin, Alexandra M. Z. The synthesis of phosphonate analogues of ribose-1-phosphate and 5-fluoro-5-deoxyribose-1-phosphate is described. Preparations of both the alpha- and beta-phosphonate anomers are reported for the ribose and 5-fluoro-5-deoxyribose series and a synthesis of the corresponding cyclic phostones of each alpha-ribose is also reported. These compounds have been prepared as tools to probe the details of fluorometabolism in S. cattleya. Brunet, Vincent A. Slawin, Alexandra M. Z. O'Hagan, David http://hdl.handle.net/10023/3443 2013-05-12T04:10:18Z 2009-11-05T00:00:00Z

Abstract: A three step route to single diastereoisomers of the vicinal trifluoromethyl motif is described. The route starts from either syn- or anti-alpha,beta-epoxy alcohols and takes a direct approach in that each of the three steps introduces a fluorine atom in a regio- and stereospecific manner. Starting from either the syn- or the anti-alpha,beta-epoxy alcohol, stereospecific reactions generate two separate diastereoisomeric series of this motif. The route is a significant improvement on an earlier six step strategy.

2009-11-05T00:00:00Z Brunet, Vincent A. Slawin, Alexandra M. Z. O'Hagan, David A three step route to single diastereoisomers of the vicinal trifluoromethyl motif is described. The route starts from either syn- or anti-alpha,beta-epoxy alcohols and takes a direct approach in that each of the three steps introduces a fluorine atom in a regio- and stereospecific manner. Starting from either the syn- or the anti-alpha,beta-epoxy alcohol, stereospecific reactions generate two separate diastereoisomeric series of this motif. The route is a significant improvement on an earlier six step strategy. McMahon, Stephen Walsh, MA Ching, RTY Carter, Lester Dorward, M Johnson, Kenneth Alan Liu, Huanting Oke, Muse Block Jr, C Kennedy, MW Latiff, AA Cooper, A Taylor, Garry Lindsay White, Malcolm Frederick Naismith, James Henderson http://hdl.handle.net/10023/3437 2013-05-12T02:01:33Z 2006-11-01T00:00:00Z

Abstract: Ranasmurfin, a previously uncharacterized similar to 13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 angstrom with P2(1) symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 angstrom, beta = 93.3 degrees. Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution.

2006-11-01T00:00:00Z McMahon, Stephen Walsh, MA Ching, RTY Carter, Lester Dorward, M Johnson, Kenneth Alan Liu, Huanting Oke, Muse Block Jr, C Kennedy, MW Latiff, AA Cooper, A Taylor, Garry Lindsay White, Malcolm Frederick Naismith, James Henderson Ranasmurfin, a previously uncharacterized similar to 13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 angstrom with P2(1) symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 angstrom, beta = 93.3 degrees. Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution. Patabendige, Chami Nilasha Kahakachchi Azad, Abul Kalam Connor, Paul Alexander Rolle, Aurélie Irvine, John Thomas Sirr http://hdl.handle.net/10023/3426 2013-05-13T12:31:04Z 2013-03-21T00:00:00Z

Abstract: Lanthanide cuprates of formula Ln2CuO4 exist in two principal forms, T and T′ which are renowned for their exhibition at low temperatures of hole and electronic types of superconductivity, respectively. These structures differ primarily in the arrangement of oxygen between the perovskite layers and also in nature of the copper oxygen planes. The Cu-O distance in the T structure (~1.90 Å) is much shorter than the T′ (1.97Å), reflecting a transition between partial Cu+ and partial Cu3+ character. In seeking to find compositions that bridge these two structure/electron carrier types, we observed the transition from a T structure to a T′ type structure, resulting in the metastable form T″ with slightly larger volume but similar character to T′. This transition from T to T″ is associated with 5% increase in a and a 5% decrease in c parameters of the tetragonal unit cells, which results in disintegration of ceramic bodies. Description: This work was supported by EPSRC

2013-03-21T00:00:00Z Patabendige, Chami Nilasha Kahakachchi Azad, Abul Kalam Connor, Paul Alexander Rolle, Aurélie Irvine, John Thomas Sirr Lanthanide cuprates of formula Ln2CuO4 exist in two principal forms, T and T′ which are renowned for their exhibition at low temperatures of hole and electronic types of superconductivity, respectively. These structures differ primarily in the arrangement of oxygen between the perovskite layers and also in nature of the copper oxygen planes. The Cu-O distance in the T structure (~1.90 Å) is much shorter than the T′ (1.97Å), reflecting a transition between partial Cu+ and partial Cu3+ character. In seeking to find compositions that bridge these two structure/electron carrier types, we observed the transition from a T structure to a T′ type structure, resulting in the metastable form T″ with slightly larger volume but similar character to T′. This transition from T to T″ is associated with 5% increase in a and a 5% decrease in c parameters of the tetragonal unit cells, which results in disintegration of ceramic bodies. Lan, Rong Irvine, John T. S. Tao, Shanwen http://hdl.handle.net/10023/3425 2013-03-26T14:01:01Z 2013-01-29T00:00:00Z

Abstract: The N equivalent to Nbond (225 kcal mol(-1)) in dinitrogen is one of the strongest bonds in chemistry therefore artificial synthesis of ammonia under mild conditions is a significant challenge. Based on current knowledge, only bacteria and some plants can synthesise ammonia from air and water at ambient temperature and pressure. Here, for the first time, we report artificial ammonia synthesis bypassing N-2 separation and H-2 production stages. A maximum ammonia production rate of 1.14 x 10(-5) mol m(-2) s(-1) has been achieved when a voltage of 1.6 V was applied. Potentially this can provide an alternative route for the mass production of the basic chemical ammonia under mild conditions. Considering climate change and the depletion of fossil fuels used for synthesis of ammonia by conventional methods, this is a renewable and sustainable chemical synthesis process for future.

2013-01-29T00:00:00Z Lan, Rong Irvine, John T. S. Tao, Shanwen The N equivalent to Nbond (225 kcal mol(-1)) in dinitrogen is one of the strongest bonds in chemistry therefore artificial synthesis of ammonia under mild conditions is a significant challenge. Based on current knowledge, only bacteria and some plants can synthesise ammonia from air and water at ambient temperature and pressure. Here, for the first time, we report artificial ammonia synthesis bypassing N-2 separation and H-2 production stages. A maximum ammonia production rate of 1.14 x 10(-5) mol m(-2) s(-1) has been achieved when a voltage of 1.6 V was applied. Potentially this can provide an alternative route for the mass production of the basic chemical ammonia under mild conditions. Considering climate change and the depletion of fossil fuels used for synthesis of ammonia by conventional methods, this is a renewable and sustainable chemical synthesis process for future. Buehl, Michael Knight, Fergus Ross Kristkova, Anezka Ondik, Irina Malkina, Olga Randall, Rebecca Amy Michele Slawin, Alexandra Martha Zoya Woollins, J Derek http://hdl.handle.net/10023/3424 2013-05-12T04:36:59Z 2013-01-01T00:00:00Z

Abstract: Across the bay: J(125Te,125Te) spin–spin coupling is a highly sensitive probe into the electronic and geometric structure of 1,8-peri-substituted naphthalene tellurium derivatives. The coupling is related to the onset of multicenter bonding in these systems.

2013-01-01T00:00:00Z Buehl, Michael Knight, Fergus Ross Kristkova, Anezka Ondik, Irina Malkina, Olga Randall, Rebecca Amy Michele Slawin, Alexandra Martha Zoya Woollins, J Derek Across the bay: J(125Te,125Te) spin–spin coupling is a highly sensitive probe into the electronic and geometric structure of 1,8-peri-substituted naphthalene tellurium derivatives. The coupling is related to the onset of multicenter bonding in these systems. Surgenor, Brian A. Buehl, Michael Slawin, Alexandra M. Z. Woollins, J. Derek Kilian, Petr http://hdl.handle.net/10023/3423 2013-05-12T04:36:52Z 2012-10-01T00:00:00Z 2012-10-01T00:00:00Z Surgenor, Brian A. Buehl, Michael Slawin, Alexandra M. Z. Woollins, J. Derek Kilian, Petr Konrad, Tina Maria Durrani, Jamie Cobley, Christopher J. Clarke, Matt http://hdl.handle.net/10023/3422 2013-03-26T12:01:03Z 2013-01-01T00:00:00Z

Abstract: Using a family of novel mononuclear and dinuclear palladium complexes of phanephos ligands, the simultaneous control of regioselectivity and enantioselectivity in the hydroxycarbonylation and alkoxycarbonylation of styrene derivatives has been realised for the first time.

2013-01-01T00:00:00Z Konrad, Tina Maria Durrani, Jamie Cobley, Christopher J. Clarke, Matt Using a family of novel mononuclear and dinuclear palladium complexes of phanephos ligands, the simultaneous control of regioselectivity and enantioselectivity in the hydroxycarbonylation and alkoxycarbonylation of styrene derivatives has been realised for the first time. Makiyi, Edward F. Frade, Raquel F. M. Lebl, Tomas Jaffray, Ellis G. Cobb, Susan E. Harvey, Alan L. Slawin, Alexandra M. Z. Hay, Ronald T. Westwood, Nicholas J. http://hdl.handle.net/10023/3420 2013-05-12T04:10:20Z 2009-11-01T00:00:00Z

Abstract: The isolation, identification and total synthesis of two plant-derived inhibitors of the NF-kappa B signaling pathway from the iso-seco-tanapartholide family of natural products is described. A key step in the efficient reaction sequence is a late-stage oxidative cleavage reaction that was carried out in the absence of protecting groups to give the natural products directly. A detailed comparison of the synthetic material with samples of the natural products proved informative. Biological studies on synthetic material confirmed that these compounds act late in the NF-kappa B signaling pathway. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

2009-11-01T00:00:00Z Makiyi, Edward F. Frade, Raquel F. M. Lebl, Tomas Jaffray, Ellis G. Cobb, Susan E. Harvey, Alan L. Slawin, Alexandra M. Z. Hay, Ronald T. Westwood, Nicholas J. The isolation, identification and total synthesis of two plant-derived inhibitors of the NF-kappa B signaling pathway from the iso-seco-tanapartholide family of natural products is described. A key step in the efficient reaction sequence is a late-stage oxidative cleavage reaction that was carried out in the absence of protecting groups to give the natural products directly. A detailed comparison of the synthetic material with samples of the natural products proved informative. Biological studies on synthetic material confirmed that these compounds act late in the NF-kappa B signaling pathway. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) Zhou, Linna Stewart, Gavin Rideau, Emeline Westwood, Nicholas James Smith, Terry K http://hdl.handle.net/10023/3359 2013-05-12T04:36:57Z 2013-02-14T00:00:00Z

Abstract: Recently, the World Health Organization approved the nifurtimox–eflornithine combination therapy for the treatment of human African trypanosomiasis, renewing interest in nitroheterocycle therapies for this and associated diseases. In this study, we have synthesized a series of novel 5-nitro-2-furancarboxylamides that show potent trypanocidal activity, 1000-fold more potent than nifurtimox against in vitro Trypanosoma brucei with very low cytotoxicity against human HeLa cells. More importantly, the most potent analogue showed very limited cross-resistance to nifurtimox-resistant cells and vice versa. This implies that our novel, relatively easy to synthesize and therefore cheap, 5-nitro-2-furancarboxylamides are targeting a different, but still essential, biochemical process to those targeted by nifurtimox or its metabolites in the parasites. The significant increase in potency (smaller dose probably required) has the potential for greatly reducing unwanted side effects and also reducing the likelihood of drug resistance. Collectively, these findings have important implications for the future therapeutic treatment of African sleeping sickness.

2013-02-14T00:00:00Z Zhou, Linna Stewart, Gavin Rideau, Emeline Westwood, Nicholas James Smith, Terry K Recently, the World Health Organization approved the nifurtimox–eflornithine combination therapy for the treatment of human African trypanosomiasis, renewing interest in nitroheterocycle therapies for this and associated diseases. In this study, we have synthesized a series of novel 5-nitro-2-furancarboxylamides that show potent trypanocidal activity, 1000-fold more potent than nifurtimox against in vitro Trypanosoma brucei with very low cytotoxicity against human HeLa cells. More importantly, the most potent analogue showed very limited cross-resistance to nifurtimox-resistant cells and vice versa. This implies that our novel, relatively easy to synthesize and therefore cheap, 5-nitro-2-furancarboxylamides are targeting a different, but still essential, biochemical process to those targeted by nifurtimox or its metabolites in the parasites. The significant increase in potency (smaller dose probably required) has the potential for greatly reducing unwanted side effects and also reducing the likelihood of drug resistance. Collectively, these findings have important implications for the future therapeutic treatment of African sleeping sickness. Fuentes García, José Antonio Phillips, Scott D. Clarke, Matthew L. http://hdl.handle.net/10023/3353 2013-02-11T16:31:05Z 2012-12-10T00:00:00Z

Abstract: Enantioselective hydrogenation of ketones is a key reaction in organic chemistry. In the past, we have attempted to deal with some unsolved challenges in this arena by introducing chiral tridentate phosphine-diamine/Ru catalysts. New catalysts and new applications are presented here, including the synthesis of phosphine-amino-alcohol P,N,OH ligands derived from (R,S)-1-amino-2-indanol, (S,S)-1-amino-2-indanol and a new chiral P,N,N ligand derived from (R,R)-1,2-diphenylethylenediamine. Ruthenium pre-catalysts of type [RuCl2(L)(DMSO)] were isolated and then examined in the hydrogenation of ketones. While the new P,N,OH ligand based catalysts are poor, the new P,N,N system gives up to 98% e.e. on substrates that do not react at all with most catalysts. A preliminary attempt at realising a new delta lactone synthesis by organocatalytic Michael addition between acetophenone and acrylonitrile, followed by asymmetric hydrogenation of the nitrile functionalised ketone is challenging in part due to the Michael addition chemistry, but also since Noyori pressure hydrogenation catalysts gave massively reduced reactivity relative to their performance for other acetophenone derivatives. The Ru phosphine-diamine system allowed quantitative conversion and around 50% e.e. The product can be converted into a delta lactone by treatment with KOH with complete retention of enantiomeric excess. This approach potentially offers access to this class of chiral molecules in three steps from the extremely cheap building blocks acrylonitrile and methyl-ketones; we encourage researchers to improve on our efforts in this potentially useful but currently flawed process.

2012-12-10T00:00:00Z Fuentes García, José Antonio Phillips, Scott D. Clarke, Matthew L. Enantioselective hydrogenation of ketones is a key reaction in organic chemistry. In the past, we have attempted to deal with some unsolved challenges in this arena by introducing chiral tridentate phosphine-diamine/Ru catalysts. New catalysts and new applications are presented here, including the synthesis of phosphine-amino-alcohol P,N,OH ligands derived from (R,S)-1-amino-2-indanol, (S,S)-1-amino-2-indanol and a new chiral P,N,N ligand derived from (R,R)-1,2-diphenylethylenediamine. Ruthenium pre-catalysts of type [RuCl2(L)(DMSO)] were isolated and then examined in the hydrogenation of ketones. While the new P,N,OH ligand based catalysts are poor, the new P,N,N system gives up to 98% e.e. on substrates that do not react at all with most catalysts. A preliminary attempt at realising a new delta lactone synthesis by organocatalytic Michael addition between acetophenone and acrylonitrile, followed by asymmetric hydrogenation of the nitrile functionalised ketone is challenging in part due to the Michael addition chemistry, but also since Noyori pressure hydrogenation catalysts gave massively reduced reactivity relative to their performance for other acetophenone derivatives. The Ru phosphine-diamine system allowed quantitative conversion and around 50% e.e. The product can be converted into a delta lactone by treatment with KOH with complete retention of enantiomeric excess. This approach potentially offers access to this class of chiral molecules in three steps from the extremely cheap building blocks acrylonitrile and methyl-ketones; we encourage researchers to improve on our efforts in this potentially useful but currently flawed process. Moynie, Lucile Schnell, Robert McMahon, Stephen A. Sandalova, Tatyana Abdelli Boulkeroua, Wassila Schmidberger, Jason W. Alphey, Magnus Cukier, Cyprian Duthie, Fraser Kopec, Jolanta Liu, Huanting Jacewicz, Agata Hunter, William N. Naismith, James H. Schneider, Gunter http://hdl.handle.net/10023/3352 2013-05-07T14:38:46Z 2013-01-01T00:00:00Z

Abstract: Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

2013-01-01T00:00:00Z Moynie, Lucile Schnell, Robert McMahon, Stephen A. Sandalova, Tatyana Abdelli Boulkeroua, Wassila Schmidberger, Jason W. Alphey, Magnus Cukier, Cyprian Duthie, Fraser Kopec, Jolanta Liu, Huanting Jacewicz, Agata Hunter, William N. Naismith, James H. Schneider, Gunter Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns. Heaslip, Aoife T. Leung, Jacqueline M. Carey, Kimberly L. Catti, Federica Warshaw, David M. Westwood, Nicholas J. Ballif, Bryan A. Ward, Gary E. http://hdl.handle.net/10023/3351 2013-05-12T04:33:58Z 2010-01-15T00:00:00Z

Abstract: Toxoplasma gondii is an obligate intracellular parasite that enters cells by a process of active penetration. Host cell penetration and parasite motility are driven by a myosin motor complex consisting of four known proteins: TgMyoA, an unconventional Class XIV myosin; TgMLC1, a myosin light chain; and two membrane-associated proteins, TgGAP45 and TgGAP50. Little is known about how the activity of the myosin motor complex is regulated. Here, we show that treatment of parasites with a recently identified small-molecule inhibitor of invasion and motility results in a rapid and irreversible change in the electrophoretic mobility of TgMLC1. While the precise nature of the TgMLC1 modification has not yet been established, it was mapped to the peptide Val46-Arg59. To determine if the TgMLC1 modification is responsible for the motility defect observed in parasites after compound treatment, the activity of myosin motor complexes from control and compound-treated parasites was compared in an in vitro motility assay. TgMyoA motor complexes containing the modified TgMLC1 showed significantly decreased motor activity compared to control complexes. This change in motor activity likely accounts for the motility defects seen in the parasites after compound treatment and provides the first evidence, in any species, that the mechanical activity of Class XIV myosins can be modulated by posttranslational modifications to their associated light chains.

2010-01-15T00:00:00Z Heaslip, Aoife T. Leung, Jacqueline M. Carey, Kimberly L. Catti, Federica Warshaw, David M. Westwood, Nicholas J. Ballif, Bryan A. Ward, Gary E. Toxoplasma gondii is an obligate intracellular parasite that enters cells by a process of active penetration. Host cell penetration and parasite motility are driven by a myosin motor complex consisting of four known proteins: TgMyoA, an unconventional Class XIV myosin; TgMLC1, a myosin light chain; and two membrane-associated proteins, TgGAP45 and TgGAP50. Little is known about how the activity of the myosin motor complex is regulated. Here, we show that treatment of parasites with a recently identified small-molecule inhibitor of invasion and motility results in a rapid and irreversible change in the electrophoretic mobility of TgMLC1. While the precise nature of the TgMLC1 modification has not yet been established, it was mapped to the peptide Val46-Arg59. To determine if the TgMLC1 modification is responsible for the motility defect observed in parasites after compound treatment, the activity of myosin motor complexes from control and compound-treated parasites was compared in an in vitro motility assay. TgMyoA motor complexes containing the modified TgMLC1 showed significantly decreased motor activity compared to control complexes. This change in motor activity likely accounts for the motility defects seen in the parasites after compound treatment and provides the first evidence, in any species, that the mechanical activity of Class XIV myosins can be modulated by posttranslational modifications to their associated light chains. Parkin, John David Hähner, Georg http://hdl.handle.net/10023/3339 2013-04-24T14:01:02Z 2013-02-15T00:00:00Z

Abstract: A method for the simultaneous calibration of the spring constants of all flexural modes of microcantilevers is presented. It is based on a flow of gas from a microchannel that interacts with the microcantilever. The gas flow causes a measurable shift in the resonance frequencies of thermal noise spectra of the flexural modes. From the magnitude of the frequency shifts of the individual modes the spring constants can be determined with high accuracy and precision. The method is non-invasive and does not risk damage to the cantilever. Experimental data is presented for several V-shaped and rectangular cantilevers with nominal fundamental spring constants in the range of 0.03-1.75 N/m. The spring constants of the fundamental modes compare favorably to those obtained using the Sader method. The higher modes of oscillation are readily calibrated with experimental uncertainties of 5-10%.

2013-02-15T00:00:00Z Parkin, John David Hähner, Georg A method for the simultaneous calibration of the spring constants of all flexural modes of microcantilevers is presented. It is based on a flow of gas from a microchannel that interacts with the microcantilever. The gas flow causes a measurable shift in the resonance frequencies of thermal noise spectra of the flexural modes. From the magnitude of the frequency shifts of the individual modes the spring constants can be determined with high accuracy and precision. The method is non-invasive and does not risk damage to the cantilever. Experimental data is presented for several V-shaped and rectangular cantilevers with nominal fundamental spring constants in the range of 0.03-1.75 N/m. The spring constants of the fundamental modes compare favorably to those obtained using the Sader method. The higher modes of oscillation are readily calibrated with experimental uncertainties of 5-10%. Launay, Guillaume G. Slawin, Alexandra M. Z. O'Hagan, David http://hdl.handle.net/10023/3333 2013-05-12T04:10:08Z 2010-04-26T00:00:00Z

Abstract: The Prins reaction was investigated using BF3 center dot OEt2 as a Lewis acid. It has been recently demonstrated, that if BF3 center dot OEt2 is used in stoichiometric amounts then these reactions generate fluorinated products where the BF3 center dot OEt2 contributes fluoride ion to quench the intermediate carbocations. In this study oxa- and aza-Prins reactions for the synthesis of 4-fluoro-pyrans and -piperidines were investigated. The products were obtained in good yields, but only with moderate diastereoselectivity. These Prins fluorination reactions can be accelerated under microwave conditions. The study extends the Prins fluorination methodology for the generation of the C-F bond in heterocycles.

2010-04-26T00:00:00Z Launay, Guillaume G. Slawin, Alexandra M. Z. O'Hagan, David The Prins reaction was investigated using BF3 center dot OEt2 as a Lewis acid. It has been recently demonstrated, that if BF3 center dot OEt2 is used in stoichiometric amounts then these reactions generate fluorinated products where the BF3 center dot OEt2 contributes fluoride ion to quench the intermediate carbocations. In this study oxa- and aza-Prins reactions for the synthesis of 4-fluoro-pyrans and -piperidines were investigated. The products were obtained in good yields, but only with moderate diastereoselectivity. These Prins fluorination reactions can be accelerated under microwave conditions. The study extends the Prins fluorination methodology for the generation of the C-F bond in heterocycles. Lamberti, Marina Fortman, George C. Poater, Albert Broggi, Julie Slawin, Alexandra M. Z. Cavallo, Luigi Nolan, Steven P. http://hdl.handle.net/10023/3313 2013-05-12T04:10:51Z 2012-01-23T00:00:00Z

Abstract: The performance of 16-electron ruthenium complexes with the general formula Cp*Ru(L)X (in which L = phosphine or N-heterocyclic carbene ligand; X = Cl or OCH2CF3) was explored in azide−alkyne cycloaddition reactions that afford the 1,2,3- triazole products. The scope of the Cp*Ru(PiPr3)Cl precatalyst was investigated for terminal alkynes leading to new 1,5-disubstituted 1,2,3-triazoles in high yields. Mechanistic studies were conducted and revealed a number of proposed intermediates. Cp*Ru- (PiPr3)(η2-HCCPh)Cl was observed and characterized by 1H, 13C, and 31P NMR at temperatures between 273 and 213 K. A rare example of N,N-κ2-phosphazide complex, Cp*Ru(κ2-iPr3PN3Bn)Cl, was fully characterized, and a single-crystal X-ray diffraction structure was obtained. DFT calculations describe a complete map of the catalytic reactivity with phenylacetylene and/or benzylazide.

2012-01-23T00:00:00Z Lamberti, Marina Fortman, George C. Poater, Albert Broggi, Julie Slawin, Alexandra M. Z. Cavallo, Luigi Nolan, Steven P. The performance of 16-electron ruthenium complexes with the general formula Cp*Ru(L)X (in which L = phosphine or N-heterocyclic carbene ligand; X = Cl or OCH2CF3) was explored in azide−alkyne cycloaddition reactions that afford the 1,2,3- triazole products. The scope of the Cp*Ru(PiPr3)Cl precatalyst was investigated for terminal alkynes leading to new 1,5-disubstituted 1,2,3-triazoles in high yields. Mechanistic studies were conducted and revealed a number of proposed intermediates. Cp*Ru- (PiPr3)(η2-HCCPh)Cl was observed and characterized by 1H, 13C, and 31P NMR at temperatures between 273 and 213 K. A rare example of N,N-κ2-phosphazide complex, Cp*Ru(κ2-iPr3PN3Bn)Cl, was fully characterized, and a single-crystal X-ray diffraction structure was obtained. DFT calculations describe a complete map of the catalytic reactivity with phenylacetylene and/or benzylazide. Zhou, Wuzong Yu, Fengjiao Greer, Heather Frances Jiang, Zheng Edwards, Peter P. http://hdl.handle.net/10023/3304 2012-12-17T11:31:02Z 2012-09-01T00:00:00Z

Abstract: Scanning electron microscopy and high-resolution transmission electron microscopy have been used to investigate non-classic crystal growth of catalytic nanoparticles, such as zeolites, perovskites, metal and alloy particles. Growth mechanisms of some crystals with novel morphologies, for example, BiOBr flower-like particles and ZnO twin-crystals, have also been studied. A development of sampling method for soot particles inside a candle flame allows us to reveal all four well-known carbon forms, amorphous, graphitic, fullerenic and nanodiamond particles. This article demonstrates that electron microscopy is a powerful tool to study the microstructures of small particles, giving us more freedom to develop new materials.

2012-09-01T00:00:00Z Zhou, Wuzong Yu, Fengjiao Greer, Heather Frances Jiang, Zheng Edwards, Peter P. Scanning electron microscopy and high-resolution transmission electron microscopy have been used to investigate non-classic crystal growth of catalytic nanoparticles, such as zeolites, perovskites, metal and alloy particles. Growth mechanisms of some crystals with novel morphologies, for example, BiOBr flower-like particles and ZnO twin-crystals, have also been studied. A development of sampling method for soot particles inside a candle flame allows us to reveal all four well-known carbon forms, amorphous, graphitic, fullerenic and nanodiamond particles. This article demonstrates that electron microscopy is a powerful tool to study the microstructures of small particles, giving us more freedom to develop new materials. Zhu, Xiaofeng Yan, Xuan Carter, Lester G. Liu, Huanting Graham, Shirley Coote, Peter J. Naismith, James http://hdl.handle.net/10023/3302 2013-05-12T04:36:35Z 2012-06-01T00:00:00Z

Abstract: The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 angstrom resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that chargecharge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection.

2012-06-01T00:00:00Z Zhu, Xiaofeng Yan, Xuan Carter, Lester G. Liu, Huanting Graham, Shirley Coote, Peter J. Naismith, James The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 angstrom resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that chargecharge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection. Knight, Fergus Ross Randall, Rebecca Amy Michele Wakefield, Lucy Slawin, Alexandra Martha Zoya Woollins, J Derek http://hdl.handle.net/10023/3299 2013-01-07T16:36:57Z 2012-11-08T00:00:00Z

Abstract: Six silver(I) coordination complexes have been prepared and structurally characterised. Mixed chalcogen-donor acenaphthene ligands L1–L3 [Acenap(EPh)(E'Ph)] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te) were independently treated with silver(I) salts (AgBF4/AgOTf). In order to keep the number of variables to a minimum, all reactions were carried out using a 1:1 ratio of Ag/L and run in dichloromethane. The nature of the donor atoms, the coordinating ability of the respective counter-anion and the type of solvent used in recrystallisation, all affect the structural architecture of the final silver(I) complex, generating monomeric, silver(I) complexes {[AgBF4(L)2] (1 L = L1; 2 L = L2; 3 L = L3), [AgOTf(L)3] (4 L = L1; 5 L = L3), [AgBF4(L)3] (2a L = L1; 3a L = L3)} and a 1D polymeric chain {[AgOTf(L3)]n 6}. The organic acenaphthene ligands L1-L3 adopt a number of ligation modes (bis-monodentate μ2-η2-bridging, quasi-chelating combining monodentate and η6-E(phenyl)-Ag(I) and classical monodentate coordination) with the central silver atom at the centre of a tetrahedral or trigonal planar coordination geometry in each case. The importance of weak interactions in the formation of metal-organic structures is also highlighted by the number of short non-covalent contacts present within each complex.

2012-11-08T00:00:00Z Knight, Fergus Ross Randall, Rebecca Amy Michele Wakefield, Lucy Slawin, Alexandra Martha Zoya Woollins, J Derek Six silver(I) coordination complexes have been prepared and structurally characterised. Mixed chalcogen-donor acenaphthene ligands L1–L3 [Acenap(EPh)(E'Ph)] (Acenap = acenaphthene-5,6-diyl; E/E' = S, Se, Te) were independently treated with silver(I) salts (AgBF4/AgOTf). In order to keep the number of variables to a minimum, all reactions were carried out using a 1:1 ratio of Ag/L and run in dichloromethane. The nature of the donor atoms, the coordinating ability of the respective counter-anion and the type of solvent used in recrystallisation, all affect the structural architecture of the final silver(I) complex, generating monomeric, silver(I) complexes {[AgBF4(L)2] (1 L = L1; 2 L = L2; 3 L = L3), [AgOTf(L)3] (4 L = L1; 5 L = L3), [AgBF4(L)3] (2a L = L1; 3a L = L3)} and a 1D polymeric chain {[AgOTf(L3)]n 6}. The organic acenaphthene ligands L1-L3 adopt a number of ligation modes (bis-monodentate μ2-η2-bridging, quasi-chelating combining monodentate and η6-E(phenyl)-Ag(I) and classical monodentate coordination) with the central silver atom at the centre of a tetrahedral or trigonal planar coordination geometry in each case. The importance of weak interactions in the formation of metal-organic structures is also highlighted by the number of short non-covalent contacts present within each complex. Hagelueken, Gregor Huang, Hexian Harlos, Karl Clarke, Bradley R. Whitfield, Chris Naismith, James H. http://hdl.handle.net/10023/3298 2013-05-12T04:36:54Z 2012-10-01T00:00:00Z

Abstract: WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 angstrom and most only to 8 angstrom) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 angstrom resolution were non-isomorphous with a lower (3.5 angstrom) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 angstrom resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 angstrom resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 angstrom resolution electron density yielded a successful molecular-replacement solution of the 3.0 angstrom resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 angstrom resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations.

2012-10-01T00:00:00Z Hagelueken, Gregor Huang, Hexian Harlos, Karl Clarke, Bradley R. Whitfield, Chris Naismith, James H. WbdD is a bifunctional kinase/methyltransferase that is responsible for regulation of lipopolysaccharide O antigen polysaccharide chain length in Escherichia coli serotype O9a. Solving the crystal structure of this protein proved to be a challenge because the available crystals belonging to space group I23 only diffracted to low resolution (>95% of the crystals diffracted to resolution lower than 4 angstrom and most only to 8 angstrom) and were non-isomorphous, with changes in unit-cell dimensions of greater than 10%. Data from a serendipitously found single native crystal that diffracted to 3.0 angstrom resolution were non-isomorphous with a lower (3.5 angstrom) resolution selenomethionine data set. Here, a strategy for improving poor (3.5 angstrom resolution) initial phases by density modification and cross-crystal averaging with an additional 4.2 angstrom resolution data set to build a crude model of WbdD is desribed. Using this crude model as a mask to cut out the 3.5 angstrom resolution electron density yielded a successful molecular-replacement solution of the 3.0 angstrom resolution data set. The resulting map was used to build a complete model of WbdD. The hydration status of individual crystals appears to underpin the variable diffraction quality of WbdD crystals. After the initial structure had been solved, methods to control the hydration status of WbdD were developed and it was thus possible to routinely obtain high-resolution diffraction (to better than 2.5 angstrom resolution). This novel and facile crystal-dehydration protocol may be useful for similar challenging situations. Illingworth, Robert S. Botting, Catherine H. Grimes, Graeme R. Bickmore, Wendy A. Eskeland, Ragnhild http://hdl.handle.net/10023/3297 2013-05-12T04:36:51Z 2012-04-09T00:00:00Z

Abstract: The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner.

2012-04-09T00:00:00Z Illingworth, Robert S. Botting, Catherine H. Grimes, Graeme R. Bickmore, Wendy A. Eskeland, Ragnhild The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner. Pirrie, Lisa McCarthy, Anna R. Major, Louise L. Morkunaite, Vaida Zubriene, Asta Matulis, Daumantas Lain, Sonia Lebl, Tomas Westwood, Nicholas J. http://hdl.handle.net/10023/3293 2012-12-14T11:31:01Z 2012-10-01T00:00:00Z

Abstract: The search for potent and selective sirtuin inhibitors continues as chemical tools of this type are of use in helping to assign the function of this interesting class of deacetylases. Here we describe SAR studies starting from the unselective sirtuin inhibitor tenovin-6. These studies identify a sub-micromolar inhibitor that has increased selectivity for SIRT2 over SIRT1 compared to tenovin-6. In addition, a H-1-NMR-based method is developed and used to validate further this class of sirtuin inhibitors. A thermal shift analysis of SIRT2 in the presence of tenovin-6, -43, a control tenovin and the known SIRT2 inhibitor AGK2 is also presented.

2012-10-01T00:00:00Z Pirrie, Lisa McCarthy, Anna R. Major, Louise L. Morkunaite, Vaida Zubriene, Asta Matulis, Daumantas Lain, Sonia Lebl, Tomas Westwood, Nicholas J. The search for potent and selective sirtuin inhibitors continues as chemical tools of this type are of use in helping to assign the function of this interesting class of deacetylases. Here we describe SAR studies starting from the unselective sirtuin inhibitor tenovin-6. These studies identify a sub-micromolar inhibitor that has increased selectivity for SIRT2 over SIRT1 compared to tenovin-6. In addition, a H-1-NMR-based method is developed and used to validate further this class of sirtuin inhibitors. A thermal shift analysis of SIRT2 in the presence of tenovin-6, -43, a control tenovin and the known SIRT2 inhibitor AGK2 is also presented. Hagelueken, Gregor Huang, Hexian Clarke, Bradley R. Lebl, Tomas Whitfield, Chris Naismith, James H. http://hdl.handle.net/10023/3292 2012-12-14T11:01:01Z 2012-11-01T00:00:00Z

Abstract: The Escherichia coli serotype O9a O-antigen polysaccharide (O-PS) is a model for glycan biosynthesis and export by the ATP-binding cassette transporter-dependent pathway. The polymannose O9a O-PS is synthesized as a polyprenol-linked glycan by mannosyltransferase enzymes located at the cytoplasmic membrane. The chain length of the O9a O-PS is tightly regulated by the WbdD enzyme. WbdD first phosphorylates the terminal non-reducing mannose of the O-PS and then methylates the phosphate, stopping polymerization. The 2.2?angstrom resolution structure of WbdD reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C-terminal coiled-coil domain reminiscent of eukaryotic DMPK (Myotonic Dystrophy Protein Kinase) family kinases such as Rho-associated protein kinase (ROCK). WbdD phosphorylates 2-a-d-mannosyl-d-mannose (2a-MB), a short mimic of the O9a polymer. Mutagenesis identifies those residues important in catalysis and substrate recognition and the in vivo phenotypes of these mutants are used to dissect the termination reaction. We have determined the structures of co-complexes of WbdD with two known eukaryotic protein kinase inhibitors. Although these are potent inhibitors in vitro, they do not show any in vivo activity. The structures reveal new insight into O-PS chain-length regulation in this important model system.

2012-11-01T00:00:00Z Hagelueken, Gregor Huang, Hexian Clarke, Bradley R. Lebl, Tomas Whitfield, Chris Naismith, James H. The Escherichia coli serotype O9a O-antigen polysaccharide (O-PS) is a model for glycan biosynthesis and export by the ATP-binding cassette transporter-dependent pathway. The polymannose O9a O-PS is synthesized as a polyprenol-linked glycan by mannosyltransferase enzymes located at the cytoplasmic membrane. The chain length of the O9a O-PS is tightly regulated by the WbdD enzyme. WbdD first phosphorylates the terminal non-reducing mannose of the O-PS and then methylates the phosphate, stopping polymerization. The 2.2?angstrom resolution structure of WbdD reveals a bacterial methyltransferase domain joined to a eukaryotic kinase domain. The kinase domain is again fused to an extended C-terminal coiled-coil domain reminiscent of eukaryotic DMPK (Myotonic Dystrophy Protein Kinase) family kinases such as Rho-associated protein kinase (ROCK). WbdD phosphorylates 2-a-d-mannosyl-d-mannose (2a-MB), a short mimic of the O9a polymer. Mutagenesis identifies those residues important in catalysis and substrate recognition and the in vivo phenotypes of these mutants are used to dissect the termination reaction. We have determined the structures of co-complexes of WbdD with two known eukaryotic protein kinase inhibitors. Although these are potent inhibitors in vitro, they do not show any in vivo activity. The structures reveal new insight into O-PS chain-length regulation in this important model system. Ballester, Pedro Mangold, Martina Howard, Nigel Marchese Robinson, Richard Abell, Chris Blumberger, Jochen Mitchell, John B. O. http://hdl.handle.net/10023/3282 2012-12-12T13:31:34Z 2012-12-07T00:00:00Z

Abstract: One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated Ki ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification.

2012-12-07T00:00:00Z Ballester, Pedro Mangold, Martina Howard, Nigel Marchese Robinson, Richard Abell, Chris Blumberger, Jochen Mitchell, John B. O. One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated Ki ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification. Wang, Yi Kirsch, Peer Lebl, Tomas Slawin, Alexandra M. Z. O'Hagan, David http://hdl.handle.net/10023/3261 2013-05-12T04:36:38Z 2012-08-10T00:00:00Z

Abstract: Cyclododecane adopts a square-like structure with corner and edge CH2 groups. In this study erythro- and threo-1,2-difluorocyclododecanes were prepared to explore whether the two vicinal C-F bonds, with different relative configurations, preferably locate at corner/edge or edge/edge locations. Conformational analysis comparing the diastereoisomers was explored by using a combination of F-19{H-1} NMR spectroscopy, computational studies and, in the case of the threo isomer, X-ray structural analysis. In the lowest energy conformers for both diastereoisomers the vicinal C-F bonds are located corner/edge, rather than edge/edge. These structures avoid placing a C-F bond endo into the ring, and appear to benefit from C-CHF-C angle widening, which relaxes 1,4-H, H transannular interactions.

2012-08-10T00:00:00Z Wang, Yi Kirsch, Peer Lebl, Tomas Slawin, Alexandra M. Z. O'Hagan, David Cyclododecane adopts a square-like structure with corner and edge CH2 groups. In this study erythro- and threo-1,2-difluorocyclododecanes were prepared to explore whether the two vicinal C-F bonds, with different relative configurations, preferably locate at corner/edge or edge/edge locations. Conformational analysis comparing the diastereoisomers was explored by using a combination of F-19{H-1} NMR spectroscopy, computational studies and, in the case of the threo isomer, X-ray structural analysis. In the lowest energy conformers for both diastereoisomers the vicinal C-F bonds are located corner/edge, rather than edge/edge. These structures avoid placing a C-F bond endo into the ring, and appear to benefit from C-CHF-C angle widening, which relaxes 1,4-H, H transannular interactions. Martin, Anthony Chartoire, Anthony Raymond Georges Slawin, Alexandra Martha Zoya Nolan, Steven Patrick http://hdl.handle.net/10023/3257 2013-05-12T04:36:45Z 2012-09-27T00:00:00Z

Abstract: The use of [Pd(NHC)(cinnamyl)Cl] precatalysts in the direct arylation of heterocycles has been investigated. Among four different precatalysts, [Pd(SIPr)(cinnamyl)Cl] proved to be the most efficient promoter of the reaction. The C–H functionalization of sulfuror nitrogen-containing heterocycles has been achieved at low catalyst loadings. These catalyst charges range from 0.1 to 0.01 mol % palladium.

2012-09-27T00:00:00Z Martin, Anthony Chartoire, Anthony Raymond Georges Slawin, Alexandra Martha Zoya Nolan, Steven Patrick The use of [Pd(NHC)(cinnamyl)Cl] precatalysts in the direct arylation of heterocycles has been investigated. Among four different precatalysts, [Pd(SIPr)(cinnamyl)Cl] proved to be the most efficient promoter of the reaction. The C–H functionalization of sulfuror nitrogen-containing heterocycles has been achieved at low catalyst loadings. These catalyst charges range from 0.1 to 0.01 mol % palladium. Hageluken, Gregor Ward, Richard James Naismith, Jim Schiemann, Olav http://hdl.handle.net/10023/3160 2013-05-12T04:06:51Z 2012-04-01T00:00:00Z

Abstract: MtsslWizard is a computer program, which operates as a plugin for the PyMOL molecular graphics system. MtsslWizard estimates distances between spin labels on proteins quickly with user configurable options through a simple graphical interface. The program searches for ensembles of possible MTSSL conformations that do not clash with a static model of the protein. Options include restricting the search procedure to published rotamer libraries of MTSSL or scoring for contacts with protein. Once conformations are assigned, distance distributions between two or more sites are calculated, displayed and can be exported to other software. The program's use is evaluated in a number of challenging test cases and its performance discussed. The strength of the program is its accuracy and simplicity.

2012-04-01T00:00:00Z Hageluken, Gregor Ward, Richard James Naismith, Jim Schiemann, Olav MtsslWizard is a computer program, which operates as a plugin for the PyMOL molecular graphics system. MtsslWizard estimates distances between spin labels on proteins quickly with user configurable options through a simple graphical interface. The program searches for ensembles of possible MTSSL conformations that do not clash with a static model of the protein. Options include restricting the search procedure to published rotamer libraries of MTSSL or scoring for contacts with protein. Once conformations are assigned, distance distributions between two or more sites are calculated, displayed and can be exported to other software. The program's use is evaluated in a number of challenging test cases and its performance discussed. The strength of the program is its accuracy and simplicity. Raeisaenen, Minna T. Slater (nee Phillips), Anna G. Champness, Neil R. Buck, Manfred http://hdl.handle.net/10023/3073 2013-05-12T04:09:17Z 2012-01-01T00:00:00Z

Abstract: 1,7-Diadamantanethioperylene-3,4:9,10-tetracarboxylic diimide, (Ad-S)(2)-PTCDI, adsorbed on Au (111) from solution was investigated by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). (Ad-S)(2)-PTCDI forms a well-ordered monolayer whose structure is described by a (2 root 63 x root 19) R19.1 degrees chiral unit cell containing four molecules. Codeposition of (Ad-S)(2)-PTCDI with 1,3,5-triazine-2,4,6-triamine (melamine) yields a honeycomb network whose (7 root 3 x 7 root 3)R30 degrees unit cell is identical to the unsubstituted PTCDI/melamine analogue. The effect of the adamantyl thioether moieties on the adsorption of guest molecules is investigated using adamantane thiol and C-60. While the thioether units do not affect the packing of adamantane thiol molecules a pronounced influence is seen in the case of fullerene. Pore modification involving different combinations of enantiomers of (Ad-S)(2)-PTCDI give rise to distinctly different arrangements of C-60 molecules. The diversity of patterns is further increased by the presence of unsubstituted PTCDI molecules. Description: This work was supported by the UK Engineering Physical Sciences Research Council (EPRSC) and the EU.

2012-01-01T00:00:00Z Raeisaenen, Minna T. Slater (nee Phillips), Anna G. Champness, Neil R. Buck, Manfred 1,7-Diadamantanethioperylene-3,4:9,10-tetracarboxylic diimide, (Ad-S)(2)-PTCDI, adsorbed on Au (111) from solution was investigated by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). (Ad-S)(2)-PTCDI forms a well-ordered monolayer whose structure is described by a (2 root 63 x root 19) R19.1 degrees chiral unit cell containing four molecules. Codeposition of (Ad-S)(2)-PTCDI with 1,3,5-triazine-2,4,6-triamine (melamine) yields a honeycomb network whose (7 root 3 x 7 root 3)R30 degrees unit cell is identical to the unsubstituted PTCDI/melamine analogue. The effect of the adamantyl thioether moieties on the adsorption of guest molecules is investigated using adamantane thiol and C-60. While the thioether units do not affect the packing of adamantane thiol molecules a pronounced influence is seen in the case of fullerene. Pore modification involving different combinations of enantiomers of (Ad-S)(2)-PTCDI give rise to distinctly different arrangements of C-60 molecules. The diversity of patterns is further increased by the presence of unsubstituted PTCDI molecules. Zhou, Linna Ishizaki, Hironori Spitzer, Michaela Taylor, Kerrie Temperley, Nicholas Johnson, Stephen Brear, Paul Gautier, Philippe Zeng, Zhiqiang Mitchell, Amy Narayan, Vikram McNeil, Ewan Melton, David Smith, Terry K Tyers, Mike Westwood, Nicholas James Patton, Elizabeth http://hdl.handle.net/10023/3043 2013-05-12T04:33:59Z 2012-07-27T00:00:00Z

Abstract: Understanding how drugs work in vivo is critical for drug design and for maximizing the potential of currently available drugs. 5-nitrofurans are a class of pro-drugs widely used to treat bacterial and trypanosome infections, but despite relative specificity 5-nitrofurans often cause serious toxic side-effects in people. Here, we use yeast, zebrafish and human in vitro systems to assess the biological activity of 5-nitrofurans, and identify a conserved interaction between aldehyde dehydrogenase (ALDH) 2 and 5-nitrofurans across these species. In addition, we show that the activity of nifurtimox, a 5-nitrofuran anti-trypanosome pro-drug, is dependent on zebrafish Aldh2 and that nifurtimox is a substrate for human ALDH2. This study reveals a conserved and biologically relevant ALDH2-5-nitrofuran interaction that may have important implications for managing the toxicity of 5nitrofuran treatment.

2012-07-27T00:00:00Z Zhou, Linna Ishizaki, Hironori Spitzer, Michaela Taylor, Kerrie Temperley, Nicholas Johnson, Stephen Brear, Paul Gautier, Philippe Zeng, Zhiqiang Mitchell, Amy Narayan, Vikram McNeil, Ewan Melton, David Smith, Terry K Tyers, Mike Westwood, Nicholas James Patton, Elizabeth Understanding how drugs work in vivo is critical for drug design and for maximizing the potential of currently available drugs. 5-nitrofurans are a class of pro-drugs widely used to treat bacterial and trypanosome infections, but despite relative specificity 5-nitrofurans often cause serious toxic side-effects in people. Here, we use yeast, zebrafish and human in vitro systems to assess the biological activity of 5-nitrofurans, and identify a conserved interaction between aldehyde dehydrogenase (ALDH) 2 and 5-nitrofurans across these species. In addition, we show that the activity of nifurtimox, a 5-nitrofuran anti-trypanosome pro-drug, is dependent on zebrafish Aldh2 and that nifurtimox is a substrate for human ALDH2. This study reveals a conserved and biologically relevant ALDH2-5-nitrofuran interaction that may have important implications for managing the toxicity of 5nitrofuran treatment. Patrick, Scott R. Boogaerts, Ine I. F. Gaillard, Sylvain Slawin, Alexandra M. Z. Nolan, Steven P. http://hdl.handle.net/10023/3035 2013-05-19T00:34:17Z 2011-07-01T00:00:00Z

Abstract: The role of silver additives is examined in the context of gold-mediated functionalisation of aromatic C-H bonds. Doubt is cast on the commonly cited route of halide abstraction from gold and evidence of substrate activation is given.

2011-07-01T00:00:00Z Patrick, Scott R. Boogaerts, Ine I. F. Gaillard, Sylvain Slawin, Alexandra M. Z. Nolan, Steven P. The role of silver additives is examined in the context of gold-mediated functionalisation of aromatic C-H bonds. Doubt is cast on the commonly cited route of halide abstraction from gold and evidence of substrate activation is given. Tsiouri, Mantha Skorda, Konstantina Papadimitriou, Christos Li, Yang Woollins, J. Derek Plakatouras, John C. http://hdl.handle.net/10023/3034 2013-05-12T03:35:21Z 2010-01-01T00:00:00Z

Abstract: The novel lanthanide(III) complexes [Ln(NO3)(2)L](NO3)center dot 3MeOH (Ln = La 1, Pr 2) and [Ln(NO3)(3)L](NO3)center dot 2MeOH (Ln = Gd 3, Yb 4), where L = (NE,N'E)-2,2'-(ethane-1,2-diylbis(oxy))bis(N-(pyridin-2-ylmethylene)ethanamine), have been obtained by direct reaction of the Schiff base ligand and the corresponding hydrated lanthanide(III) nitrates in methanol. All complexes were characterized spectroscopically and thermogravimetrically. Complex 4 was also characterized with crystallographic studies: orthorhombic P2(1)2(1)2(1), a = 10.6683(14), b = 13.4752(15), c = 19.3320(26) angstrom. In the molecular structure of 4, Yb(III) is surrounded by all donor atoms of the Schiff base (four nitrogen and two oxygen atoms) and four oxygen atoms belonging to two bidentate chelating nitrato ligands.

2010-01-01T00:00:00Z Tsiouri, Mantha Skorda, Konstantina Papadimitriou, Christos Li, Yang Woollins, J. Derek Plakatouras, John C. The novel lanthanide(III) complexes [Ln(NO3)(2)L](NO3)center dot 3MeOH (Ln = La 1, Pr 2) and [Ln(NO3)(3)L](NO3)center dot 2MeOH (Ln = Gd 3, Yb 4), where L = (NE,N'E)-2,2'-(ethane-1,2-diylbis(oxy))bis(N-(pyridin-2-ylmethylene)ethanamine), have been obtained by direct reaction of the Schiff base ligand and the corresponding hydrated lanthanide(III) nitrates in methanol. All complexes were characterized spectroscopically and thermogravimetrically. Complex 4 was also characterized with crystallographic studies: orthorhombic P2(1)2(1)2(1), a = 10.6683(14), b = 13.4752(15), c = 19.3320(26) angstrom. In the molecular structure of 4, Yb(III) is surrounded by all donor atoms of the Schiff base (four nitrogen and two oxygen atoms) and four oxygen atoms belonging to two bidentate chelating nitrato ligands. Li, Yang Hua, Guo-Xiong Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/3020 2013-05-12T03:35:10Z 2009-02-23T00:00:00Z

Abstract: The X-ray structures of 12 primary selenoamides are reported. Metric parameters are provided, together with an illustration of the range of hydrogen bonding motifs. Description: The authors are grateful to the University of St Andrews and the Engineering and Physical Science Research Council (EPSRC, U.K.) for financial support.

2009-02-23T00:00:00Z Li, Yang Hua, Guo-Xiong Slawin, Alexandra M. Z. Woollins, J. Derek The X-ray structures of 12 primary selenoamides are reported. Metric parameters are provided, together with an illustration of the range of hydrogen bonding motifs. Perez-Nueno, Violeta I. Venkatraman, Vishwesh Mavridis, Lazaros Ritchie, David W. http://hdl.handle.net/10023/3009 2012-12-12T13:15:39Z 2011-01-01T00:00:00Z

Abstract: Polypharmacology is becoming an increasingly important aspect in drug design. Pharmaceutical companies are discovering more and more cases in which multiple drugs bind to a given target (promiscuous targets) and in which a given drug binds to more than one target (promiscuous ligands). These phenomena are clearly of great importance when considering drug side-effects. In the last 4 years, more than 30 drugs have been tested against more than 40 novel secondary targets based on promiscuity predictions. Current methods for predicting promiscuity typically aim to relate protein receptors according to their primary sequences, the similarity of their ligands, and more recently, the similarity of their ligand binding pockets. Here, we present a spherical harmonic (SH) surface shape-based approach to predict rapidly promiscuous ligands and targets by comparing sets of SH ligand and protein shapes, respectively. We present details of our approach applied to a wide range of PDB complexes comprising ligands in a selected subset of the MDL Drug Data Report (MDDR) database which are distributed over 249 diverse pharmacological targets. The shape similarity of each ligand to each target’s ligand set is quantified and used to predict promiscuity. We also analyse the correlation between binding pocket and ligand shapes. We compare our promiscuity predictions with experimental activity values extracted from the BindingDB database.

2011-01-01T00:00:00Z Perez-Nueno, Violeta I. Venkatraman, Vishwesh Mavridis, Lazaros Ritchie, David W. Polypharmacology is becoming an increasingly important aspect in drug design. Pharmaceutical companies are discovering more and more cases in which multiple drugs bind to a given target (promiscuous targets) and in which a given drug binds to more than one target (promiscuous ligands). These phenomena are clearly of great importance when considering drug side-effects. In the last 4 years, more than 30 drugs have been tested against more than 40 novel secondary targets based on promiscuity predictions. Current methods for predicting promiscuity typically aim to relate protein receptors according to their primary sequences, the similarity of their ligands, and more recently, the similarity of their ligand binding pockets. Here, we present a spherical harmonic (SH) surface shape-based approach to predict rapidly promiscuous ligands and targets by comparing sets of SH ligand and protein shapes, respectively. We present details of our approach applied to a wide range of PDB complexes comprising ligands in a selected subset of the MDL Drug Data Report (MDDR) database which are distributed over 249 diverse pharmacological targets. The shape similarity of each ligand to each target’s ligand set is quantified and used to predict promiscuity. We also analyse the correlation between binding pocket and ligand shapes. We compare our promiscuity predictions with experimental activity values extracted from the BindingDB database. Randorn, Chamnan Irvine, John T. S. Robertson, Peter http://hdl.handle.net/10023/3004 2013-05-12T02:34:46Z 2008-01-01T00:00:00Z

Abstract: Visible-light-activated yellow amorphous TiO2 (yam-TiO2) was synthesised by a simple and organic-free precipitation method. TiN, an alternative precursor for TiO2 preparation, was dissolved in hydrogen peroxide under acidic condition ( pH similar to 1) adjusted by nitric acid. The yellow precipitate was obtained after adjusting pH of the resultant red brown solution to 2 with NH4OH. The BET surface area of this sample was 261 m(2)/g. The visible light photoactivity was evaluated on the basis of the photobleaching of methylene blue (MB) in an aqueous solution by using a 250 W metal halide bulb equipped with UV cutoff filter (lambda > 420 nm) under aerobic conditions. Yam-TiO2 exhibits an interesting property of being both surface adsorbent and photoactive under visible light. It was assigned to the eta(2)-peroxide, an active intermediate form of the addition of H2O2 into crystallined TiO2 photocatalyst. It can be concluded that an active intermediate form of titanium peroxo species in photocatalytic process can be synthesised and used as a visible-light-driven photocatalyst. Copyright (C) 2008 Chamnan Randorn et al.

2008-01-01T00:00:00Z Randorn, Chamnan Irvine, John T. S. Robertson, Peter Visible-light-activated yellow amorphous TiO2 (yam-TiO2) was synthesised by a simple and organic-free precipitation method. TiN, an alternative precursor for TiO2 preparation, was dissolved in hydrogen peroxide under acidic condition ( pH similar to 1) adjusted by nitric acid. The yellow precipitate was obtained after adjusting pH of the resultant red brown solution to 2 with NH4OH. The BET surface area of this sample was 261 m(2)/g. The visible light photoactivity was evaluated on the basis of the photobleaching of methylene blue (MB) in an aqueous solution by using a 250 W metal halide bulb equipped with UV cutoff filter (lambda > 420 nm) under aerobic conditions. Yam-TiO2 exhibits an interesting property of being both surface adsorbent and photoactive under visible light. It was assigned to the eta(2)-peroxide, an active intermediate form of the addition of H2O2 into crystallined TiO2 photocatalyst. It can be concluded that an active intermediate form of titanium peroxo species in photocatalytic process can be synthesised and used as a visible-light-driven photocatalyst. Copyright (C) 2008 Chamnan Randorn et al. She, Zhe Di Falco, Andrea Hähner, Georg Buck, Manfred http://hdl.handle.net/10023/2933 2013-05-12T04:12:33Z 2012-02-06T00:00:00Z

Abstract: Self-assembled monolayers (SAMs) of 4'-methylbiphenyl-4-thiol (MBP0) adsorbed on polycrystalline gold substrates served as templates to control electrochemical deposition of Cu structures from acidic solution, and enabled the subsequent lift-off of the metal structures by attachment to epoxy glue. By exploiting the negative-resist behaviour of MBP0, the SAM was patterned by means of electron-beam lithography. For high deposition contrast a two-step procedure was employed involving a nucleation phase around −0.7 V versus Cu2+/Cu and a growth phase at around −0.35 V versus Cu2+/Cu. Structures with features down to 100 nm were deposited and transferred with high fidelity. By using substrates with different surface morphologies, AFM measurements revealed that the roughness of the substrate is a crucial factor but not the only one determining the roughness of the copper surface that is exposed after lift-off.

2012-02-06T00:00:00Z She, Zhe Di Falco, Andrea Hähner, Georg Buck, Manfred Self-assembled monolayers (SAMs) of 4'-methylbiphenyl-4-thiol (MBP0) adsorbed on polycrystalline gold substrates served as templates to control electrochemical deposition of Cu structures from acidic solution, and enabled the subsequent lift-off of the metal structures by attachment to epoxy glue. By exploiting the negative-resist behaviour of MBP0, the SAM was patterned by means of electron-beam lithography. For high deposition contrast a two-step procedure was employed involving a nucleation phase around −0.7 V versus Cu2+/Cu and a growth phase at around −0.35 V versus Cu2+/Cu. Structures with features down to 100 nm were deposited and transferred with high fidelity. By using substrates with different surface morphologies, AFM measurements revealed that the roughness of the substrate is a crucial factor but not the only one determining the roughness of the copper surface that is exposed after lift-off. Holliday, Gemma L. Almonacid, Daniel E. Bartlett, Gail J. O'Boyle, Noel M. Torrance, James W. Murray-Rust, Peter Mitchell, John Blayney Owen Thornton, Janet M. http://hdl.handle.net/10023/2890 2013-05-12T03:33:07Z 2007-01-01T00:00:00Z

Abstract: MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACIE/.

2007-01-01T00:00:00Z Holliday, Gemma L. Almonacid, Daniel E. Bartlett, Gail J. O'Boyle, Noel M. Torrance, James W. Murray-Rust, Peter Mitchell, John Blayney Owen Thornton, Janet M. MACiE (Mechanism, Annotation and Classification in Enzymes) is a database of enzyme reaction mechanisms, and is publicly available as a web-based data resource. This paper presents the first release of a web-based search tool to explore enzyme reaction mechanisms in MACiE. We also present Version 2 of MACiE, which doubles the dataset available (from Version 1). MACiE can be accessed from http://www.ebi.ac.uk/thornton-srv/databases/MACIE/. Nath, Neetika Mitchell, John B. O. http://hdl.handle.net/10023/2883 2013-05-12T04:34:38Z 2012-04-24T00:00:00Z

Abstract: Background: We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism in descriptors, and also three approaches that encode only the overall chemical reaction. Both cross-validation and also an external test set are used. Results: The three descriptor sets encoding overall chemical transformation perform better than the two descriptions of mechanism. SVM and RF models perform comparably well; kNN is less successful. Oxidoreductases and hydrolases are relatively well predicted by all types of descriptor; isomerases are well predicted by overall reaction descriptors but not by mechanistic ones. Conclusions: Our results suggest that pairs of similar enzyme reactions tend to proceed by different mechanisms. Oxidoreductases, hydrolases, and to some extent isomerases and ligases, have clear chemical signatures, making them easier to predict than transferases and lyases. We find evidence that isomerases as a class are notably mechanistically diverse and that their one shared property, of substrate and product being isomers, can arise in various unrelated ways. The performance of the different machine learning algorithms is in line with many cheminformatics applications, with SVM and RF being roughly equally effective. kNN is less successful, given the role that non-local information plays in successful classification. We note also that, despite a lack of clarity in the literature, EC number prediction is not a single problem; the challenge of predicting protein function from available sequence data is quite different from assigning an EC classification from a cheminformatics representation of a reaction.

2012-04-24T00:00:00Z Nath, Neetika Mitchell, John B. O. Background: We investigate the relationships between the EC (Enzyme Commission) class, the associated chemical reaction, and the reaction mechanism by building predictive models using Support Vector Machine (SVM), Random Forest (RF) and k-Nearest Neighbours (kNN). We consider two ways of encoding the reaction mechanism in descriptors, and also three approaches that encode only the overall chemical reaction. Both cross-validation and also an external test set are used. Results: The three descriptor sets encoding overall chemical transformation perform better than the two descriptions of mechanism. SVM and RF models perform comparably well; kNN is less successful. Oxidoreductases and hydrolases are relatively well predicted by all types of descriptor; isomerases are well predicted by overall reaction descriptors but not by mechanistic ones. Conclusions: Our results suggest that pairs of similar enzyme reactions tend to proceed by different mechanisms. Oxidoreductases, hydrolases, and to some extent isomerases and ligases, have clear chemical signatures, making them easier to predict than transferases and lyases. We find evidence that isomerases as a class are notably mechanistically diverse and that their one shared property, of substrate and product being isomers, can arise in various unrelated ways. The performance of the different machine learning algorithms is in line with many cheminformatics applications, with SVM and RF being roughly equally effective. kNN is less successful, given the role that non-local information plays in successful classification. We note also that, despite a lack of clarity in the literature, EC number prediction is not a single problem; the challenge of predicting protein function from available sequence data is quite different from assigning an EC classification from a cheminformatics representation of a reaction. Tran, An X. Dong, Changjiang Whitfield, Chris http://hdl.handle.net/10023/2880 2012-12-12T13:28:15Z 2010-10-22T00:00:00Z

Abstract: LptC is a conserved bitopic inner membrane protein from Escherichia coli involved in the export of lipopolysaccharide from its site of synthesis in the cytoplasmic membrane to the outer membrane. LptC forms a complex with the ATP-binding cassette transporter, LptBFG, which is thought to facilitate the extraction of lipopolysaccharide from the inner membrane and release it into a translocation pathway that includes the putative periplasmic chaperone LptA. Cysteine modification experiments established that the catalytic domain of LptC is oriented toward the periplasm. The structure of the periplasmic domain is described at a resolution of 2.2-angstrom from x-ray crystallographic data. The periplasmic domain of LptC consists of a twisted boat structure with two beta-sheets in apposition to each other. The beta-sheets contain seven and eight antiparallel beta-strands, respectively. This structure bears a high degree of resemblance to the crystal structure of LptA. Like LptA, LptC binds lipopolysaccharide in vitro. In vitro, LptA can displace lipopolysaccharide from LptC (but not vice versa), consistent with their locations and their proposed placement in a unidirectional export pathway. Description: This work is supported by a Wellcome Trust Career Development Fellowship to C.D.

2010-10-22T00:00:00Z Tran, An X. Dong, Changjiang Whitfield, Chris LptC is a conserved bitopic inner membrane protein from Escherichia coli involved in the export of lipopolysaccharide from its site of synthesis in the cytoplasmic membrane to the outer membrane. LptC forms a complex with the ATP-binding cassette transporter, LptBFG, which is thought to facilitate the extraction of lipopolysaccharide from the inner membrane and release it into a translocation pathway that includes the putative periplasmic chaperone LptA. Cysteine modification experiments established that the catalytic domain of LptC is oriented toward the periplasm. The structure of the periplasmic domain is described at a resolution of 2.2-angstrom from x-ray crystallographic data. The periplasmic domain of LptC consists of a twisted boat structure with two beta-sheets in apposition to each other. The beta-sheets contain seven and eight antiparallel beta-strands, respectively. This structure bears a high degree of resemblance to the crystal structure of LptA. Like LptA, LptC binds lipopolysaccharide in vitro. In vitro, LptA can displace lipopolysaccharide from LptC (but not vice versa), consistent with their locations and their proposed placement in a unidirectional export pathway. Konstantinou-Kirtay, Chrysi Mitchell, John Blayney Owen Lumley, James A. http://hdl.handle.net/10023/2867 2013-05-12T03:33:07Z 2007-01-26T00:00:00Z

Abstract: Background: The need for fast and accurate scoring functions has been driven by the increased use of in silico virtual screening twinned with high-throughput screening as a method to rapidly identify potential candidates in the early stages of drug development. We examine the ability of some the most common scoring functions (GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus) to discriminate correctly and efficiently between active and non-active compounds among a library of similar to 3,600 diverse decoy compounds in a virtual screening experiment against heat shock protein 90 (Hsp90). Results: Firstly, we investigated two ranking methodologies, GOLD(rank) and BestScore(rank). GOLD(rank) is based on ranks generated using GOLD. The various scoring functions, GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus, are applied to the pose ranked number one by GOLD for that ligand. BestScore(rank) uses multiple poses for each ligand and independently chooses the best ranked pose of the ligand according to each different scoring function. Secondly, we considered the effect of introducing the Thr184 hydrogen bond tether to guide the docking process towards a particular solution, and its effect on enrichment. Thirdly, we considered normalisation to account for the known bias of scoring functions to select larger molecules. All the scoring functions gave fairly similar enrichments, with the exception of PMF which was consistently the poorest performer. In most cases, GOLD was marginally the best performing individual function; the Consensus score usually performed similarly to the best single scoring function. Our best results were obtained using the Thr184 tether in combination with the BestScore(rank) protocol and normalisation for molecular weight. For that particular combination, DOCK was the best individual function; DOCK recovered 90% of the actives in the top 10% of the ranked list; Consensus similarly recovered 89% of the actives in its top 10%. Conclusion: Overall, we demonstrate the validity of virtual screening as a method for identifying new leads from a pool of ligands with similar physicochemical properties and we believe that the outcome of this study provides useful insight into the setting up of a suitable docking and scoring protocol, resulting in enrichment of 'target active' compounds. Description: This work was funded by the EPSRC, InsightFaraday (now part of the Chemistry Innovation Knowledge Transfer Network), Arrow Therapeutics Ltd and Unilever plc.

2007-01-26T00:00:00Z Konstantinou-Kirtay, Chrysi Mitchell, John Blayney Owen Lumley, James A. Background: The need for fast and accurate scoring functions has been driven by the increased use of in silico virtual screening twinned with high-throughput screening as a method to rapidly identify potential candidates in the early stages of drug development. We examine the ability of some the most common scoring functions (GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus) to discriminate correctly and efficiently between active and non-active compounds among a library of similar to 3,600 diverse decoy compounds in a virtual screening experiment against heat shock protein 90 (Hsp90). Results: Firstly, we investigated two ranking methodologies, GOLD(rank) and BestScore(rank). GOLD(rank) is based on ranks generated using GOLD. The various scoring functions, GOLD, ChemScore, DOCK, PMF, BLEEP and Consensus, are applied to the pose ranked number one by GOLD for that ligand. BestScore(rank) uses multiple poses for each ligand and independently chooses the best ranked pose of the ligand according to each different scoring function. Secondly, we considered the effect of introducing the Thr184 hydrogen bond tether to guide the docking process towards a particular solution, and its effect on enrichment. Thirdly, we considered normalisation to account for the known bias of scoring functions to select larger molecules. All the scoring functions gave fairly similar enrichments, with the exception of PMF which was consistently the poorest performer. In most cases, GOLD was marginally the best performing individual function; the Consensus score usually performed similarly to the best single scoring function. Our best results were obtained using the Thr184 tether in combination with the BestScore(rank) protocol and normalisation for molecular weight. For that particular combination, DOCK was the best individual function; DOCK recovered 90% of the actives in the top 10% of the ranked list; Consensus similarly recovered 89% of the actives in its top 10%. Conclusion: Overall, we demonstrate the validity of virtual screening as a method for identifying new leads from a pool of ligands with similar physicochemical properties and we believe that the outcome of this study provides useful insight into the setting up of a suitable docking and scoring protocol, resulting in enrichment of 'target active' compounds. Almonacid, Daniel E. Yera, Emmanuel R. Mitchell, John Blayney Owen Babbitt, Patricia C. http://hdl.handle.net/10023/2866 2013-05-19T00:33:10Z 2010-03-12T00:00:00Z

Abstract: Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation. Description: The authors thank the National Institutes of Health (NIH R01 GM60595 to PCB) and the Scottish Universities Life Sciences Alliance (SULSA to JBOM) for funding.

2010-03-12T00:00:00Z Almonacid, Daniel E. Yera, Emmanuel R. Mitchell, John Blayney Owen Babbitt, Patricia C. Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine definitions of EC sub-subclasses for improved discrimination in their classification of enzyme reactions. The results also indicate that mechanistic convergence of reaction steps is widespread, suggesting that quantitative measurement of mechanistic similarity can inform approaches for functional annotation. Cannon, EO Nigsch, F Mitchell, John Blayney Owen http://hdl.handle.net/10023/2865 2013-05-12T02:31:51Z 2008-02-18T00:00:00Z

Abstract: Background We have introduced a new Hybrid descriptor composed of the MACCS key descriptor encoding topological information and Ballester and Richards' Ultrafast Shape Recognition (USR) descriptor. The latter one is calculated from the moments of the distribution of the interatomic distances, and in this work we also included higher moments than in the original implementation. Results The performance of this Hybrid descriptor is assessed using Random Forest and a dataset of 116,476 molecules. Our dataset includes 5,245 molecules in ten classes from the 2005 World Anti-Doping Agency (WADA) dataset and 111,231 molecules from the National Cancer Institute (NCI) database. In a 10-fold Monte Carlo cross-validation this dataset was partitioned into three distinct parts for training, optimisation of an internal threshold that we introduced, and validation of the resulting model. The standard errors obtained were used to assess statistical significance of observed improvements in performance of our new descriptor. Conclusion The Hybrid descriptor was compared to the MACCS key descriptor, USR with the first three (USR), four (UF4) and five (UF5) moments, and a combination of MACCS with USR (three moments). The MACCS key descriptor was not combined with UF5, due to similar performance of UF5 and UF4. Superior performance in terms of all figures of merit was found for the MACCS/UF4 Hybrid descriptor with respect to all other descriptors examined. These figures of merit include recall in the top 1% and top 5% of the ranked validation sets, precision, F-measure, area under the Receiver Operating Characteristic curve and Matthews Correlation Coefficient. Description: The authors thank the EPSRC and Unilever plc for funding.

2008-02-18T00:00:00Z Cannon, EO Nigsch, F Mitchell, John Blayney Owen Background We have introduced a new Hybrid descriptor composed of the MACCS key descriptor encoding topological information and Ballester and Richards' Ultrafast Shape Recognition (USR) descriptor. The latter one is calculated from the moments of the distribution of the interatomic distances, and in this work we also included higher moments than in the original implementation. Results The performance of this Hybrid descriptor is assessed using Random Forest and a dataset of 116,476 molecules. Our dataset includes 5,245 molecules in ten classes from the 2005 World Anti-Doping Agency (WADA) dataset and 111,231 molecules from the National Cancer Institute (NCI) database. In a 10-fold Monte Carlo cross-validation this dataset was partitioned into three distinct parts for training, optimisation of an internal threshold that we introduced, and validation of the resulting model. The standard errors obtained were used to assess statistical significance of observed improvements in performance of our new descriptor. Conclusion The Hybrid descriptor was compared to the MACCS key descriptor, USR with the first three (USR), four (UF4) and five (UF5) moments, and a combination of MACCS with USR (three moments). The MACCS key descriptor was not combined with UF5, due to similar performance of UF5 and UF4. Superior performance in terms of all figures of merit was found for the MACCS/UF4 Hybrid descriptor with respect to all other descriptors examined. These figures of merit include recall in the top 1% and top 5% of the ranked validation sets, precision, F-measure, area under the Receiver Operating Characteristic curve and Matthews Correlation Coefficient. O'Boyle, NM Palmer, DS Nigsch, F Mitchell, John Blayney Owen http://hdl.handle.net/10023/2864 2013-05-12T02:31:49Z 2008-10-29T00:00:00Z

Abstract: Background We present a novel feature selection algorithm, Winnowing Artificial Ant Colony (WAAC), that performs simultaneous feature selection and model parameter optimisation for the development of predictive quantitative structure-property relationship (QSPR) models. The WAAC algorithm is an extension of the modified ant colony algorithm of Shen et al. (J Chem Inf Model 2005, 45: 1024–1029). We test the ability of the algorithm to develop a predictive partial least squares model for the Karthikeyan dataset (J Chem Inf Model 2005, 45: 581–590) of melting point values. We also test its ability to perform feature selection on a support vector machine model for the same dataset. Results Starting from an initial set of 203 descriptors, the WAAC algorithm selected a PLS model with 68 descriptors which has an RMSE on an external test set of 46.6°C and R2 of 0.51. The number of components chosen for the model was 49, which was close to optimal for this feature selection. The selected SVM model has 28 descriptors (cost of 5, ε of 0.21) and an RMSE of 45.1°C and R2 of 0.54. This model outperforms a kNN model (RMSE of 48.3°C, R2 of 0.47) for the same data and has similar performance to a Random Forest model (RMSE of 44.5°C, R2 of 0.55). However it is much less prone to bias at the extremes of the range of melting points as shown by the slope of the line through the residuals: -0.43 for WAAC/SVM, -0.53 for Random Forest. Conclusion With a careful choice of objective function, the WAAC algorithm can be used to optimise machine learning and regression models that suffer from overfitting. Where model parameters also need to be tuned, as is the case with support vector machine and partial least squares models, it can optimise these simultaneously. The moving probabilities used by the algorithm are easily interpreted in terms of the best and current models of the ants, and the winnowing procedure promotes the removal of irrelevant descriptors. Description: The authors thank the BBSRC (NMOB and JBOM – grant BB/C51320X/1), Pfizer (DSP and JBOM – through the Pfizer Institute for Pharmaceutical Materials Science), and Unilever for funding FN and JBOM and for supporting the Centre for Molecular Science Informatics.

2008-10-29T00:00:00Z O'Boyle, NM Palmer, DS Nigsch, F Mitchell, John Blayney Owen Background We present a novel feature selection algorithm, Winnowing Artificial Ant Colony (WAAC), that performs simultaneous feature selection and model parameter optimisation for the development of predictive quantitative structure-property relationship (QSPR) models. The WAAC algorithm is an extension of the modified ant colony algorithm of Shen et al. (J Chem Inf Model 2005, 45: 1024–1029). We test the ability of the algorithm to develop a predictive partial least squares model for the Karthikeyan dataset (J Chem Inf Model 2005, 45: 581–590) of melting point values. We also test its ability to perform feature selection on a support vector machine model for the same dataset. Results Starting from an initial set of 203 descriptors, the WAAC algorithm selected a PLS model with 68 descriptors which has an RMSE on an external test set of 46.6°C and R2 of 0.51. The number of components chosen for the model was 49, which was close to optimal for this feature selection. The selected SVM model has 28 descriptors (cost of 5, ε of 0.21) and an RMSE of 45.1°C and R2 of 0.54. This model outperforms a kNN model (RMSE of 48.3°C, R2 of 0.47) for the same data and has similar performance to a Random Forest model (RMSE of 44.5°C, R2 of 0.55). However it is much less prone to bias at the extremes of the range of melting points as shown by the slope of the line through the residuals: -0.43 for WAAC/SVM, -0.53 for Random Forest. Conclusion With a careful choice of objective function, the WAAC algorithm can be used to optimise machine learning and regression models that suffer from overfitting. Where model parameters also need to be tuned, as is the case with support vector machine and partial least squares models, it can optimise these simultaneously. The moving probabilities used by the algorithm are easily interpreted in terms of the best and current models of the ants, and the winnowing procedure promotes the removal of irrelevant descriptors. Holliday, G L Mitchell, John Blayney Owen Murray-Rust, P http://hdl.handle.net/10023/2863 2012-12-12T12:53:53Z 2004-10-26T00:00:00Z

Abstract: Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions. It should be noted that readers of this paper will benefit from having an SVG (Scalable Vector Graphics) viewer plugin. Description: The authors thank the EPSRC for financial support of this project and Unilever for their support of the Centre for Molecular Science Informatics.

2004-10-26T00:00:00Z Holliday, G L Mitchell, John Blayney Owen Murray-Rust, P Reactions with many steps can be represented by a single XML-based table of the atoms, bonds and electrons. For each step the complete Chemical Markup Language 1 representation of all components is obtained and a snapshot representing the end point of the step is generated. These snapshots can then be combined to give an animated description of the complete reaction, both in "2D" chemical structure diagrams and in three dimensions. Here we demonstrate the method's power with enzymatic reactions. It should be noted that readers of this paper will benefit from having an SVG (Scalable Vector Graphics) viewer plugin. Murray-Rust, P Mitchell, John Blayney Owen Rzepa, H S http://hdl.handle.net/10023/2862 2013-05-12T03:33:13Z 2005-06-07T00:00:00Z

Abstract: Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols.

2005-06-07T00:00:00Z Murray-Rust, P Mitchell, John Blayney Owen Rzepa, H S Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be re-distributed without permission. This has led to a failure to adopt modern informatics and software techniques and therefore paucity of chemistry in bioinformatics. New technology, however, offers the hope of making chemical data (compounds and properties) free during the authoring process. We argue that the technology is already available; we require a collective agreement to enhance publication protocols. Murray-Rust, P Mitchell, John Blayney Owen Rzepa, H S http://hdl.handle.net/10023/2861 2013-05-12T03:33:12Z 2005-07-18T00:00:00Z

Abstract: The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective.

2005-07-18T00:00:00Z Murray-Rust, P Mitchell, John Blayney Owen Rzepa, H S The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective. Lain, Sonia Hollick, Jonathan J. Campbell, Johanna Staples, Oliver D. Higgins, Maureen Aoubala, Mustapha McCarthy, Anna Appleyard, Virginia Murray, Karen E. Baker, Lee Thompson, Alastair Mathers, Joanne Holland, Stephen J. Stark, Michael J. R. Pass, Georgia Woods, Julie Lane, David P. Westwood, Nicholas J. http://hdl.handle.net/10023/2845 2013-05-19T04:31:03Z 2008-05-06T00:00:00Z

Abstract: We have carried out a cell-based screen aimed at discovering small molecules that activate p53 and have the potential to decrease tumor growth. Here, we describe one of our hit compounds, tenovin-1, along with a more water-soluble analog, tenovin-6. Via a yeast genetic screen, biochemical assays, and target validation studies in mammalian cells, we show that tenovins act through inhibition of the protein-deacetylating activities of SirT1 and SirT2, two important members of the sirtuin family. Tenovins are active on mammalian cells at one-digit micromolar concentrations and decrease tumor growth in vivo as single agents. This underscores the utility of these compounds as biological tools for the study of sirtuin function as well as their potential therapeutic interest.

2008-05-06T00:00:00Z Lain, Sonia Hollick, Jonathan J. Campbell, Johanna Staples, Oliver D. Higgins, Maureen Aoubala, Mustapha McCarthy, Anna Appleyard, Virginia Murray, Karen E. Baker, Lee Thompson, Alastair Mathers, Joanne Holland, Stephen J. Stark, Michael J. R. Pass, Georgia Woods, Julie Lane, David P. Westwood, Nicholas J. We have carried out a cell-based screen aimed at discovering small molecules that activate p53 and have the potential to decrease tumor growth. Here, we describe one of our hit compounds, tenovin-1, along with a more water-soluble analog, tenovin-6. Via a yeast genetic screen, biochemical assays, and target validation studies in mammalian cells, we show that tenovins act through inhibition of the protein-deacetylating activities of SirT1 and SirT2, two important members of the sirtuin family. Tenovins are active on mammalian cells at one-digit micromolar concentrations and decrease tumor growth in vivo as single agents. This underscores the utility of these compounds as biological tools for the study of sirtuin function as well as their potential therapeutic interest. Lowe, Robert Mussa, Hamse Y. Nigsch, Florian Glen, Robert C. Mitchell, John B. O. http://hdl.handle.net/10023/2463 2013-05-12T04:12:46Z 2012-01-26T00:00:00Z

Abstract: The mechanism of phospholipidosis is still not well understood. Numerous different mechanisms have been proposed, varying from direct inhibition of the breakdown of phospholipids to the binding of a drug compound to the phospholipid, preventing breakdown. We have used a probabilistic method, the Parzen-Rosenblatt Window approach, to build a model from the ChEMBL dataset which can predict from a compound's structure both its primary pharmaceutical target and other targets with which it forms off-target, usually weaker, interactions. Using a small dataset of 182 phospholipidosis-inducing and non-inducing compounds, we predict their off-target activity against targets which could relate to phospholipidosis as a side-effect of a drug. We link these targets to specific mechanisms of inducing this lysosomal build-up of phospholipids in cells. Thus, we show that the induction of phospholipidosis is likely to occur by separate mechanisms when triggered by different cationic amphiphilic drugs. We find that both inhibition of phospholipase activity and enhanced cholesterol biosynthesis are likely to be important mechanisms. Furthermore, we provide evidence suggesting four specific protein targets. Sphingomyelin phosphodiesterase, phospholipase A2 and lysosomal phospholipase A1 are shown to be likely targets for the induction of phospholipidosis by inhibition of phospholipase activity, while lanosterol synthase is predicted to be associated with phospholipidosis being induced by enhanced cholesterol biosynthesis. This analysis provides the impetus for further experimental tests of these hypotheses.

2012-01-26T00:00:00Z Lowe, Robert Mussa, Hamse Y. Nigsch, Florian Glen, Robert C. Mitchell, John B. O. The mechanism of phospholipidosis is still not well understood. Numerous different mechanisms have been proposed, varying from direct inhibition of the breakdown of phospholipids to the binding of a drug compound to the phospholipid, preventing breakdown. We have used a probabilistic method, the Parzen-Rosenblatt Window approach, to build a model from the ChEMBL dataset which can predict from a compound's structure both its primary pharmaceutical target and other targets with which it forms off-target, usually weaker, interactions. Using a small dataset of 182 phospholipidosis-inducing and non-inducing compounds, we predict their off-target activity against targets which could relate to phospholipidosis as a side-effect of a drug. We link these targets to specific mechanisms of inducing this lysosomal build-up of phospholipids in cells. Thus, we show that the induction of phospholipidosis is likely to occur by separate mechanisms when triggered by different cationic amphiphilic drugs. We find that both inhibition of phospholipase activity and enhanced cholesterol biosynthesis are likely to be important mechanisms. Furthermore, we provide evidence suggesting four specific protein targets. Sphingomyelin phosphodiesterase, phospholipase A2 and lysosomal phospholipase A1 are shown to be likely targets for the induction of phospholipidosis by inhibition of phospholipase activity, while lanosterol synthase is predicted to be associated with phospholipidosis being induced by enhanced cholesterol biosynthesis. This analysis provides the impetus for further experimental tests of these hypotheses. Liu, Huanting Naismith, James Henderson http://hdl.handle.net/10023/2456 2013-05-12T03:04:02Z 2008-12-04T00:00:00Z

Abstract: Background: Mutagenesis plays an essential role in molecular biology and biochemistry. It has also been used in enzymology and protein science to generate proteins which are more tractable for biophysical techniques. The ability to quickly and specifically mutate a residue(s) in protein is important for mechanistic and functional studies. Although many site-directed mutagenesis methods have been developed, a simple, quick and multi-applicable method is still desirable. Results: We have developed a site-directed plasmid mutagenesis protocol that preserved the simple one step procedure of the QuikChange (TM) site-directed mutagenesis but enhanced its efficiency and extended its capability for multi-site mutagenesis. This modified protocol used a new primer design that promoted primer-template annealing by eliminating primer dimerization and also permitted the newly synthesized DNA to be used as the template in subsequent amplification cycles. These two factors we believe are the main reasons for the enhanced amplification efficiency and for its applications in multi-site mutagenesis. Conclusion: Our modified protocol significantly increased the efficiency of single mutation and also allowed facile large single insertions, deletions/truncations and multiple mutations in a single experiment, an option incompatible with the standard QuikChange (TM). Furthermore the new protocol required significantly less parental DNA which facilitated the DpnI digestion after the PCR amplification and enhanced the overall efficiency and reliability. Using our protocol, we generated single site, multiple single-site mutations and a combined insertion/deletion mutations. The results demonstrated that this new protocol imposed no additional reagent costs (beyond basic QuikChange T) but increased the overall success rates.

2008-12-04T00:00:00Z Liu, Huanting Naismith, James Henderson Background: Mutagenesis plays an essential role in molecular biology and biochemistry. It has also been used in enzymology and protein science to generate proteins which are more tractable for biophysical techniques. The ability to quickly and specifically mutate a residue(s) in protein is important for mechanistic and functional studies. Although many site-directed mutagenesis methods have been developed, a simple, quick and multi-applicable method is still desirable. Results: We have developed a site-directed plasmid mutagenesis protocol that preserved the simple one step procedure of the QuikChange (TM) site-directed mutagenesis but enhanced its efficiency and extended its capability for multi-site mutagenesis. This modified protocol used a new primer design that promoted primer-template annealing by eliminating primer dimerization and also permitted the newly synthesized DNA to be used as the template in subsequent amplification cycles. These two factors we believe are the main reasons for the enhanced amplification efficiency and for its applications in multi-site mutagenesis. Conclusion: Our modified protocol significantly increased the efficiency of single mutation and also allowed facile large single insertions, deletions/truncations and multiple mutations in a single experiment, an option incompatible with the standard QuikChange (TM). Furthermore the new protocol required significantly less parental DNA which facilitated the DpnI digestion after the PCR amplification and enhanced the overall efficiency and reliability. Using our protocol, we generated single site, multiple single-site mutations and a combined insertion/deletion mutations. The results demonstrated that this new protocol imposed no additional reagent costs (beyond basic QuikChange T) but increased the overall success rates. Lou, Hubing Chen, Min Black, Susan S. Bushell, Simon R. Ceccarelli, Matteo Mach, Tivadar Beis, Konstantinos Low, Alison S. Bamford, Victoria A. Booth, Ian R. Bayley, Hagan Naismith, James H. http://hdl.handle.net/10023/2448 2013-05-12T04:11:59Z 2011-10-28T00:00:00Z

Abstract: Antibiotic-resistant bacteria, particularly Gram negative species, present significant health care challenges. The permeation of antibiotics through the outer membrane is largely effected by the porin superfamily, changes in which contribute to antibiotic resistance. A series of antibiotic resistant E. coli isolates were obtained from a patient during serial treatment with various antibiotics. The sequence of OmpC changed at three positions during treatment giving rise to a total of four OmpC variants (denoted OmpC20, OmpC26, OmpC28 and OmpC33, in which OmpC20 was derived from the first clinical isolate). We demonstrate that expression of the OmpC K12 porin in the clinical isolates lowers the MIC, consistent with modified porin function contributing to drug resistance. By a range of assays we have established that the three mutations that occur between OmpC20 and OmpC33 modify transport of both small molecules and antibiotics across the outer membrane. This results in the modulation of resistance to antibiotics, particularly cefotaxime. Small ion unitary conductance measurements of the isolated porins do not show significant differences between isolates. Thus, resistance does not appear to arise from major changes in pore size. Crystal structures of all four OmpC clinical mutants and molecular dynamics simulations also show that the pore size is essentially unchanged. Molecular dynamics simulations suggest that perturbation of the transverse electrostatic field at the constriction zone reduces cefotaxime passage through the pore, consistent with laboratory and clinical data. This subtle modification of the transverse electric field is a very different source of resistance than occlusion of the pore or wholesale destruction of the transverse field and points to a new mechanism by which porins may modulate antibiotic passage through the outer membrane.

2011-10-28T00:00:00Z Lou, Hubing Chen, Min Black, Susan S. Bushell, Simon R. Ceccarelli, Matteo Mach, Tivadar Beis, Konstantinos Low, Alison S. Bamford, Victoria A. Booth, Ian R. Bayley, Hagan Naismith, James H. Antibiotic-resistant bacteria, particularly Gram negative species, present significant health care challenges. The permeation of antibiotics through the outer membrane is largely effected by the porin superfamily, changes in which contribute to antibiotic resistance. A series of antibiotic resistant E. coli isolates were obtained from a patient during serial treatment with various antibiotics. The sequence of OmpC changed at three positions during treatment giving rise to a total of four OmpC variants (denoted OmpC20, OmpC26, OmpC28 and OmpC33, in which OmpC20 was derived from the first clinical isolate). We demonstrate that expression of the OmpC K12 porin in the clinical isolates lowers the MIC, consistent with modified porin function contributing to drug resistance. By a range of assays we have established that the three mutations that occur between OmpC20 and OmpC33 modify transport of both small molecules and antibiotics across the outer membrane. This results in the modulation of resistance to antibiotics, particularly cefotaxime. Small ion unitary conductance measurements of the isolated porins do not show significant differences between isolates. Thus, resistance does not appear to arise from major changes in pore size. Crystal structures of all four OmpC clinical mutants and molecular dynamics simulations also show that the pore size is essentially unchanged. Molecular dynamics simulations suggest that perturbation of the transverse electrostatic field at the constriction zone reduces cefotaxime passage through the pore, consistent with laboratory and clinical data. This subtle modification of the transverse electric field is a very different source of resistance than occlusion of the pore or wholesale destruction of the transverse field and points to a new mechanism by which porins may modulate antibiotic passage through the outer membrane. Paytubi, Sonia McMahon, Stephen Graham, Shirley Liu, Huanting Botting, Catherine Helen Makarova, Kira S. Kroonin, Eugene V. Naismith, Jim White, Malcolm F http://hdl.handle.net/10023/2108 2013-05-19T04:31:14Z 2012-02-14T00:00:00Z

Abstract: Single-stranded DNA binding proteins (SSBs) based on the OB-fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination and repair. We demonstrate that the thermoproteales, a clade of hyperthermophilic crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term "ThermoDBP", exemplified by protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the thermoproteales – a highly unusual example where a “ubiquitous” protein has been lost in evolution.

2012-02-14T00:00:00Z Paytubi, Sonia McMahon, Stephen Graham, Shirley Liu, Huanting Botting, Catherine Helen Makarova, Kira S. Kroonin, Eugene V. Naismith, Jim White, Malcolm F Single-stranded DNA binding proteins (SSBs) based on the OB-fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination and repair. We demonstrate that the thermoproteales, a clade of hyperthermophilic crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term "ThermoDBP", exemplified by protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the thermoproteales – a highly unusual example where a “ubiquitous” protein has been lost in evolution. Waddell, Paul G. Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1980 2013-05-12T03:35:22Z 2010-08-16T00:00:00Z

Abstract: The X-ray structures of (5) cis-PtBr2(P(OMe)(3))(2), (6) cis-PtBr2(P(OMe)(2)Ph)(2), (7) cis-PtBr2(P(OMe)Ph-2)(2), (8) cis-PtBr2(PPh3)(2), (9) cis-PtI2(P(OMe)(3))(2), (10) cis-PtI2(P(OMe)(2)Ph)(2), (11) cis-PtI2(P(OMe)Ph-2)(2) and (12) cis-PtI2(PPh3)(2) are reported and compared with the previously reported chloride analogues. The magnitude of the J{Pt-P} varies linearly with the Pt-P bond length (l(Pt-P) = 2.421 - J/24255) for these 12 complexes.

2010-08-16T00:00:00Z Waddell, Paul G. Slawin, Alexandra M. Z. Woollins, J. Derek The X-ray structures of (5) cis-PtBr2(P(OMe)(3))(2), (6) cis-PtBr2(P(OMe)(2)Ph)(2), (7) cis-PtBr2(P(OMe)Ph-2)(2), (8) cis-PtBr2(PPh3)(2), (9) cis-PtI2(P(OMe)(3))(2), (10) cis-PtI2(P(OMe)(2)Ph)(2), (11) cis-PtI2(P(OMe)Ph-2)(2) and (12) cis-PtI2(PPh3)(2) are reported and compared with the previously reported chloride analogues. The magnitude of the J{Pt-P} varies linearly with the Pt-P bond length (l(Pt-P) = 2.421 - J/24255) for these 12 complexes. Knight, Fergus Ross Fuller, Amy Buehl, Michael Slawin, Alexandra Martha Zoya Woollins, J Derek http://hdl.handle.net/10023/1918 2013-05-12T03:04:20Z 2010-08-16T00:00:00Z

Abstract: A range of structurally diverse compounds 1-15 {Nap[SPh]2•Br4 (Nap = naphthalene-1,8-diyl); Nap[SePh][EPh]•Br4 (E = Se, S); Nap[SePh]2•I2; Nap[SePh][EPh]•3/2I2 (E = Se, S); Nap[TePh][G]•X2 (G = SePh, SPh, Br, I; X = Br, I); and [Nap(PPh2OH)(SPh)]+Br3-} formed from the reactions between peri-substituted naphthalene chalcogen donors D1-D8 {Nap[ER][E0R] (ER/E0R = SPh, SePh, TePh); Nap[TePh][X] (X = Br, I); and Nap[PPh2][SPh]} and dibromine and diiodine were characterized by X-ray crystallography and where possible by multinuclear NMR, IR, and MS. X-ray data for 1-15 were analyzed by naphthalene ring torsions, peri-atom displacement, splay angle magnitude, peri-distance, aromatic ring orientations, and quasi-linear three-body arrangements. The hypervalent linear moieties are considered in the context of the charge-transfer model and the 3c-4e model introduced by Pimentel and Rundle. In general, the conformation of the final products obeyed the rule based on charge-transfer that “seesaw” (X-ER2-X, 10-E-4) adducts arise when the halogen (X) is more electronegative than the chalcogen (E), and if the converse is true then, CT “spoke” (X-X-ER2, 8-E-3) adducts are formed. Upon treatment with dibromine, selenium donor compounds D2 {Nap[SePh]2} and D3 {Nap[SePh][SPh]} afford unusual tribromide salts of bromoselenyl cations containing a hypervalent X-E---E` 3c-4e type interaction. Upon treatment with diiodine, D2 and D3 form “Z-shaped”, “extended spoke” adducts containing an uncommon 2:3 donor/chalcogen ratio and incorporating chains of I2 held together by rare I---I interactions. As expected, “seesaw” 10-E-4 adducts are formed following the reaction of Te donors D4-D7 {Nap[TePh][X] (X = Br, I); Nap[TePh][EPh] (E = Se, S)} with the dihalogens. Naphthalene distortion in general is comparable between respective donor compounds and products 1-15. Ionic species 2 and 3 display a noticeable reduction in molecular distortion explained by the relief of steric strain via weak peri-interactions and the onset of 3c-4e bonding.

2010-08-16T00:00:00Z Knight, Fergus Ross Fuller, Amy Buehl, Michael Slawin, Alexandra Martha Zoya Woollins, J Derek A range of structurally diverse compounds 1-15 {Nap[SPh]2•Br4 (Nap = naphthalene-1,8-diyl); Nap[SePh][EPh]•Br4 (E = Se, S); Nap[SePh]2•I2; Nap[SePh][EPh]•3/2I2 (E = Se, S); Nap[TePh][G]•X2 (G = SePh, SPh, Br, I; X = Br, I); and [Nap(PPh2OH)(SPh)]+Br3-} formed from the reactions between peri-substituted naphthalene chalcogen donors D1-D8 {Nap[ER][E0R] (ER/E0R = SPh, SePh, TePh); Nap[TePh][X] (X = Br, I); and Nap[PPh2][SPh]} and dibromine and diiodine were characterized by X-ray crystallography and where possible by multinuclear NMR, IR, and MS. X-ray data for 1-15 were analyzed by naphthalene ring torsions, peri-atom displacement, splay angle magnitude, peri-distance, aromatic ring orientations, and quasi-linear three-body arrangements. The hypervalent linear moieties are considered in the context of the charge-transfer model and the 3c-4e model introduced by Pimentel and Rundle. In general, the conformation of the final products obeyed the rule based on charge-transfer that “seesaw” (X-ER2-X, 10-E-4) adducts arise when the halogen (X) is more electronegative than the chalcogen (E), and if the converse is true then, CT “spoke” (X-X-ER2, 8-E-3) adducts are formed. Upon treatment with dibromine, selenium donor compounds D2 {Nap[SePh]2} and D3 {Nap[SePh][SPh]} afford unusual tribromide salts of bromoselenyl cations containing a hypervalent X-E---E` 3c-4e type interaction. Upon treatment with diiodine, D2 and D3 form “Z-shaped”, “extended spoke” adducts containing an uncommon 2:3 donor/chalcogen ratio and incorporating chains of I2 held together by rare I---I interactions. As expected, “seesaw” 10-E-4 adducts are formed following the reaction of Te donors D4-D7 {Nap[TePh][X] (X = Br, I); Nap[TePh][EPh] (E = Se, S)} with the dihalogens. Naphthalene distortion in general is comparable between respective donor compounds and products 1-15. Ionic species 2 and 3 display a noticeable reduction in molecular distortion explained by the relief of steric strain via weak peri-interactions and the onset of 3c-4e bonding. Overton, Ian M. Graham, Shirley Gould, Katherine A. Hinds, Jason Botting, Catherine H. Shirran, Sally Barton, Geoffrey J. Coote, Peter J. http://hdl.handle.net/10023/1911 2013-05-12T04:05:20Z 2011-05-12T00:00:00Z

Abstract: Background: Staphylococcus aureus is a major human pathogen and strains resistant to existing treatments continue to emerge. Development of novel treatments is therefore important. Antimicrobial peptides represent a source of potential novel antibiotics to combat resistant bacteria such as Methicillin-Resistant Staphylococcus aureus (MRSA). A promising antimicrobial peptide is ranalexin, which has potent activity against Gram-positive bacteria, and particularly S. aureus. Understanding mode of action is a key component of drug discovery and network biology approaches enable a global, integrated view of microbial physiology, including mechanisms of antibiotic killing. We developed a systems-wide functional association network approach to integrate proteome and transcriptome profiles, enabling study of drug resistance and mode of action. Results: The functional association network was constructed by Bayesian logistic regression, providing a framework for identification of antimicrobial peptide (ranalexin) response modules from S. aureus MRSA-252 transcriptome and proteome profiling. These signatures of ranalexin treatment revealed multiple killing mechanisms, including cell wall activity. Cell wall effects were supported by gene disruption and osmotic fragility experiments. Furthermore, twenty-two novel virulence factors were inferred, while the VraRS two-component system and PhoU-mediated persister formation were implicated in MRSA tolerance to cationic antimicrobial peptides. Conclusions: This work demonstrates a powerful integrative approach to study drug resistance and mode of action. Our findings are informative to the development of novel therapeutic strategies against Staphylococcus aureus and particularly MRSA.

2011-05-12T00:00:00Z Overton, Ian M. Graham, Shirley Gould, Katherine A. Hinds, Jason Botting, Catherine H. Shirran, Sally Barton, Geoffrey J. Coote, Peter J. Background: Staphylococcus aureus is a major human pathogen and strains resistant to existing treatments continue to emerge. Development of novel treatments is therefore important. Antimicrobial peptides represent a source of potential novel antibiotics to combat resistant bacteria such as Methicillin-Resistant Staphylococcus aureus (MRSA). A promising antimicrobial peptide is ranalexin, which has potent activity against Gram-positive bacteria, and particularly S. aureus. Understanding mode of action is a key component of drug discovery and network biology approaches enable a global, integrated view of microbial physiology, including mechanisms of antibiotic killing. We developed a systems-wide functional association network approach to integrate proteome and transcriptome profiles, enabling study of drug resistance and mode of action. Results: The functional association network was constructed by Bayesian logistic regression, providing a framework for identification of antimicrobial peptide (ranalexin) response modules from S. aureus MRSA-252 transcriptome and proteome profiling. These signatures of ranalexin treatment revealed multiple killing mechanisms, including cell wall activity. Cell wall effects were supported by gene disruption and osmotic fragility experiments. Furthermore, twenty-two novel virulence factors were inferred, while the VraRS two-component system and PhoU-mediated persister formation were implicated in MRSA tolerance to cationic antimicrobial peptides. Conclusions: This work demonstrates a powerful integrative approach to study drug resistance and mode of action. Our findings are informative to the development of novel therapeutic strategies against Staphylococcus aureus and particularly MRSA. Sieffert, Nicolas Buehl, Michael http://hdl.handle.net/10023/1847 2013-05-19T04:31:11Z 2010-06-16T00:00:00Z

Abstract: We report a comprehensive density functional theory (DFT) study of the mechanism of the methanol dehydrogenation reaction catalyzed by [RuH2(H2)(PPh3)3]. Using the B97-D dispersion-corrected functional, four pathways have been fully characterized, which differ in the way the critical beta-hydrogen transfer step is brought about (e.g., by prior dissociation of one PPh3 ligand). All these pathways are found to be competitive (Delta G double dagger = 27.0-32.1 kcal/mol at 150 degrees C) and strongly interlocked. The reaction can thus follow multiple reaction channels, a feature which is expected to be at the origin of the good kinetics of this system. Our results also point to the active role of PPh3 ligands, which undergo significant conformational changes as the reaction occurs, and provide insights into the role of the base, which acts as a "co-catalyst" by facilitating proton transfers within active species. Activation barriers decrease on going from methanol to ethanol and 2-propanol substrates, in accord with experiment.

2010-06-16T00:00:00Z Sieffert, Nicolas Buehl, Michael We report a comprehensive density functional theory (DFT) study of the mechanism of the methanol dehydrogenation reaction catalyzed by [RuH2(H2)(PPh3)3]. Using the B97-D dispersion-corrected functional, four pathways have been fully characterized, which differ in the way the critical beta-hydrogen transfer step is brought about (e.g., by prior dissociation of one PPh3 ligand). All these pathways are found to be competitive (Delta G double dagger = 27.0-32.1 kcal/mol at 150 degrees C) and strongly interlocked. The reaction can thus follow multiple reaction channels, a feature which is expected to be at the origin of the good kinetics of this system. Our results also point to the active role of PPh3 ligands, which undergo significant conformational changes as the reaction occurs, and provide insights into the role of the base, which acts as a "co-catalyst" by facilitating proton transfers within active species. Activation barriers decrease on going from methanol to ethanol and 2-propanol substrates, in accord with experiment. Bjornsson, Ragnar Buehl, Michael http://hdl.handle.net/10023/1816 2013-05-12T04:02:11Z 2010-06-01T00:00:00Z

Abstract: Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C6H6)(CO)(3), MnO3F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omega PBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters.

2010-06-01T00:00:00Z Bjornsson, Ragnar Buehl, Michael Electric field gradients (EFGs) were computed for the first-row transition metal nuclei in Cr(C6H6)(CO)(3), MnO3F, Mn(CO)(5)H, MnCp(CO)(3), Co(CO)(4)H, Co(CO)(3)(NO) and VCp(CO)(4), for which experimental gas-phase data (in form of nuclear quadrupole coupling constants) are available from microwave spectroscopy. A variety of exchange-correlation functionals were assessed, among which range-separated hybrids (such as CAM-B3LYP or LC-omega PBE) perform best, followed by global hybrids (such as B3LYP and PBE0) and gradient-corrected functionals (such as BP86). While large basis sets are required on the metal atom for converged EFGs, smaller basis sets can be employed on the ligands. In most cases, EFGs show little sensitivity toward the geometrical parameters. Bushell, Simon R. Lou, Hubing Wallat, Gregor D. Beis, Konstantinos Whitfield, Chris Naismith, James H. http://hdl.handle.net/10023/1800 2013-05-12T04:03:01Z 2010-12-01T00:00:00Z

Abstract: External polysaccharide capsules provide a physical barrier that is employed by many species of bacteria for the purposes of host evasion and persistence. Wzi is a 53 kDa outer membrane beta-barrel protein that is thought to play a role in the attachment of group 1 capsular polysaccharides to the cell surface. The purification and crystallization of an Escherichia coli homologue of Wzi is reported and diffraction data from native and selenomethionine-incorporated protein crystals are presented. Crystals of C-terminally His(6)-tagged Wzi diffracted to 2.8 A resolution. Data processing showed that the crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 128.8, b = 152.8, c = 94.4 A, alpha = beta = gamma = 90 degrees. A His-tagged selenomethionine-containing variant of Wzi has also been crystallized in the same space group and diffraction data have been recorded to 3.8 A resolution. Data processing shows that the variant crystal has similar unit-cell parameters to the native crystal. Description: Supported by a grant from The Wellcome Trust (081862/Z/06/Z)

2010-12-01T00:00:00Z Bushell, Simon R. Lou, Hubing Wallat, Gregor D. Beis, Konstantinos Whitfield, Chris Naismith, James H. External polysaccharide capsules provide a physical barrier that is employed by many species of bacteria for the purposes of host evasion and persistence. Wzi is a 53 kDa outer membrane beta-barrel protein that is thought to play a role in the attachment of group 1 capsular polysaccharides to the cell surface. The purification and crystallization of an Escherichia coli homologue of Wzi is reported and diffraction data from native and selenomethionine-incorporated protein crystals are presented. Crystals of C-terminally His(6)-tagged Wzi diffracted to 2.8 A resolution. Data processing showed that the crystals belonged to the orthorhombic space group C222, with unit-cell parameters a = 128.8, b = 152.8, c = 94.4 A, alpha = beta = gamma = 90 degrees. A His-tagged selenomethionine-containing variant of Wzi has also been crystallized in the same space group and diffraction data have been recorded to 3.8 A resolution. Data processing shows that the variant crystal has similar unit-cell parameters to the native crystal. Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek http://hdl.handle.net/10023/1783 2013-05-12T03:35:11Z 2010-03-01T00:00:00Z

Abstract: The title compound, [PdCl2(C8H11O2P)(2)], has a comparable structure to those of related palladium dichloride complexes containing trimethyl phosphinite and methyl diphenyl phosphinite. The Pd atom is located on a crystallographic twofold rotation axis: thus, there is just one half-molecule in the asymmetric unit. The structure is isomorphous with the platinum analogue cis-[PtCl2{P(OMe)(2)Ph}(2)].

2010-03-01T00:00:00Z Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek The title compound, [PdCl2(C8H11O2P)(2)], has a comparable structure to those of related palladium dichloride complexes containing trimethyl phosphinite and methyl diphenyl phosphinite. The Pd atom is located on a crystallographic twofold rotation axis: thus, there is just one half-molecule in the asymmetric unit. The structure is isomorphous with the platinum analogue cis-[PtCl2{P(OMe)(2)Ph}(2)]. Li, Yang Hua, Guoxiong Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1782 2013-05-12T03:35:08Z 2009-10-01T00:00:00Z

Abstract: In the crystal of the title compound, C10H14N2O, double supramolecular layers of PhCH2CH2CH2NHC(O)NH2 are formed parallel to the bc plane by intermolecular N-H center dot center dot center dot O hydrogen bonding, with R-2(2)(8) and R-2(1)(6) motifs in the b- and c-axis directions, respectively. The mean plane of the C-ar-C-C group makes a dihedral angle of 84.8 (2)degrees with the benzene ring.

2009-10-01T00:00:00Z Li, Yang Hua, Guoxiong Slawin, Alexandra M. Z. Woollins, J. Derek In the crystal of the title compound, C10H14N2O, double supramolecular layers of PhCH2CH2CH2NHC(O)NH2 are formed parallel to the bc plane by intermolecular N-H center dot center dot center dot O hydrogen bonding, with R-2(2)(8) and R-2(1)(6) motifs in the b- and c-axis directions, respectively. The mean plane of the C-ar-C-C group makes a dihedral angle of 84.8 (2)degrees with the benzene ring. Li, Yang Hua, Guoxiong Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1781 2013-05-12T03:35:06Z 2009-11-01T00:00:00Z

Abstract: In the title compound, NCCH2C6H4CH2CN, the bond lengths and angles are within normal ranges. The benzene ring makes dihedral angles of 4.94 (8) and 77.04 (8)degrees with the C-C-C-N mean planes. Weak non-conventional C-H center dot center dot center dot N hydrogen bonds are effective in the stabilization of the crystal structure. The weak C-H center dot center dot center dot N contacts form antiparallel chains running in the a + c direction, and ring systems with two N-atom acceptors and four H-atom donors.

2009-11-01T00:00:00Z Li, Yang Hua, Guoxiong Slawin, Alexandra M. Z. Woollins, J. Derek In the title compound, NCCH2C6H4CH2CN, the bond lengths and angles are within normal ranges. The benzene ring makes dihedral angles of 4.94 (8) and 77.04 (8)degrees with the C-C-C-N mean planes. Weak non-conventional C-H center dot center dot center dot N hydrogen bonds are effective in the stabilization of the crystal structure. The weak C-H center dot center dot center dot N contacts form antiparallel chains running in the a + c direction, and ring systems with two N-atom acceptors and four H-atom donors. Li, Yang Hua, Guoxiong Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1780 2013-05-12T03:35:05Z 2009-11-01T00:00:00Z

Abstract: The asymmetric unit of the title compound, C12H12O5P2, contains four independent molecules, generating two dimers via pairs of intermolecular O-H center dot center dot center dot O hydrogen bonds, forming R-2(2) (8) rings. The two aryl rings of each molecule form dihedral angles of 108.6 (1), 103.2 (1), 12.5 (2) and 8.1 (2)degrees in the four molecules.

2009-11-01T00:00:00Z Li, Yang Hua, Guoxiong Slawin, Alexandra M. Z. Woollins, J. Derek The asymmetric unit of the title compound, C12H12O5P2, contains four independent molecules, generating two dimers via pairs of intermolecular O-H center dot center dot center dot O hydrogen bonds, forming R-2(2) (8) rings. The two aryl rings of each molecule form dihedral angles of 108.6 (1), 103.2 (1), 12.5 (2) and 8.1 (2)degrees in the four molecules. Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek http://hdl.handle.net/10023/1779 2013-05-12T03:35:05Z 2009-11-01T00:00:00Z

Abstract: The title compound, [PtCl2(C9H21O3P)(2)], was obtained from a solution of PtCl2(COD) ( COD = 1,5-cyclooctadiene) and triisopropylphosphite in dichloromethane. The complex features a Pt(II) atom coordinated by two Cl and two P atoms, yielding a slightly distorted cis square-planar geometry.

2009-11-01T00:00:00Z Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek The title compound, [PtCl2(C9H21O3P)(2)], was obtained from a solution of PtCl2(COD) ( COD = 1,5-cyclooctadiene) and triisopropylphosphite in dichloromethane. The complex features a Pt(II) atom coordinated by two Cl and two P atoms, yielding a slightly distorted cis square-planar geometry. Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek http://hdl.handle.net/10023/1778 2013-05-12T03:35:04Z 2009-11-01T00:00:00Z

Abstract: The title compound, [PdCl2(C3H9O3P)(2)], which is isotypic with its platinum analogue, adopts a slightly distorted cis square-planar geometry for the Pd centre.

2009-11-01T00:00:00Z Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek The title compound, [PdCl2(C3H9O3P)(2)], which is isotypic with its platinum analogue, adopts a slightly distorted cis square-planar geometry for the Pd centre. Li, Yang Shi, Qi Slawin, Alexandra M. Z. Woollins, J. Derek Dong, Jinxiang http://hdl.handle.net/10023/1777 2013-05-12T03:35:03Z 2009-12-01T00:00:00Z

Abstract: The title compound, [Zn(C2H8N2)(3)](SiF6), was synthesized ionothermally using choline chloride-imidazolidone as solvent and template provider. In the crystal structure, the anions and cations are located on special positions of site symmetry 3.2 and show a typical octahedral geometry. The Zn-II ion is coordinated by six N atoms from three ethylenediamine molecules. The crystal structure displays weak hydrogen bonding between [SiF6](2-) anions and the ethylenediamine NH hydrogen atoms.

2009-12-01T00:00:00Z Li, Yang Shi, Qi Slawin, Alexandra M. Z. Woollins, J. Derek Dong, Jinxiang The title compound, [Zn(C2H8N2)(3)](SiF6), was synthesized ionothermally using choline chloride-imidazolidone as solvent and template provider. In the crystal structure, the anions and cations are located on special positions of site symmetry 3.2 and show a typical octahedral geometry. The Zn-II ion is coordinated by six N atoms from three ethylenediamine molecules. The crystal structure displays weak hydrogen bonding between [SiF6](2-) anions and the ethylenediamine NH hydrogen atoms. Bhattacharyya, Pravat Woollins, John Derek http://hdl.handle.net/10023/1776 2013-05-19T00:33:52Z 2001-08-20T00:00:00Z

Abstract: [PhP(Se)(mu -Se)](2) selenates secondary and tertiary amides to the corresponding selenoamides in 30-70% yields at 130 degreesC in toluene and indolizine-3-aldehydes to selenoaldehydes in 40-59% yield at 25 degreesC. (C) 2001 Elsevier Science Ltd. All rights reserved.

2001-08-20T00:00:00Z Bhattacharyya, Pravat Woollins, John Derek [PhP(Se)(mu -Se)](2) selenates secondary and tertiary amides to the corresponding selenoamides in 30-70% yields at 130 degreesC in toluene and indolizine-3-aldehydes to selenoaldehydes in 40-59% yield at 25 degreesC. (C) 2001 Elsevier Science Ltd. All rights reserved. Hua, Guoxiong Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1775 2013-05-12T03:35:23Z 2010-10-01T00:00:00Z

Abstract: In the title compound, C14H12Br2Se2, the Se-Se bond length [2.3034 (9) angstrom] is similar to those in diphenyl diselenide [2.3066 (7) and 2.3073 (10) angstrom] and shorter than that in 1,8-diselenonaphthalene [2.0879 (8) angstrom]. The molecule adopts a classical gauche conformation.

2010-10-01T00:00:00Z Hua, Guoxiong Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek In the title compound, C14H12Br2Se2, the Se-Se bond length [2.3034 (9) angstrom] is similar to those in diphenyl diselenide [2.3066 (7) and 2.3073 (10) angstrom] and shorter than that in 1,8-diselenonaphthalene [2.0879 (8) angstrom]. The molecule adopts a classical gauche conformation. Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek http://hdl.handle.net/10023/1774 2013-05-12T03:35:17Z 2010-05-01T00:00:00Z

Abstract: The title compound, [Pd2Cl4(C8H11O2P)(2)], is binuclear and disposed about a crystallographic centre of symmetry with a Pd center dot center dot center dot Pd distance of 3.4662 (17) angstrom. It has a similar geometry to that observed in the triphenylphosphite and triphenylphosphine analogues. The Pd-P bond length is ca 0.04 angstrom shorter than those in mononuclear PdCl2(P(OMe)(2)Ph)(2), possibly due to the lower trans-influence of the bridging Cl- compared to a single-bonded Cl- atom.

2010-05-01T00:00:00Z Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek The title compound, [Pd2Cl4(C8H11O2P)(2)], is binuclear and disposed about a crystallographic centre of symmetry with a Pd center dot center dot center dot Pd distance of 3.4662 (17) angstrom. It has a similar geometry to that observed in the triphenylphosphite and triphenylphosphine analogues. The Pd-P bond length is ca 0.04 angstrom shorter than those in mononuclear PdCl2(P(OMe)(2)Ph)(2), possibly due to the lower trans-influence of the bridging Cl- compared to a single-bonded Cl- atom. Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek http://hdl.handle.net/10023/1773 2013-05-12T03:35:13Z 2010-04-01T00:00:00Z

Abstract: The title compound, [Sb(C6H5)(3)(N2S2)], contains a molecular entity that is very similar to that of the known polymorph of Sb(S2N2)Ph-3 [Kunkel et al. (1997). Z. Naturforsch. Teil B, 52, 193-198], differing only in the orientation of the phenyl rings. The bond order in the SNSN unit is S-N=S=N, consisting of one long S-N bond, an intermediate length N=S bond and a short S=N bond.

2010-04-01T00:00:00Z Slawin, Alexandra M. Z. Waddell, Paul G. Woollins, J. Derek The title compound, [Sb(C6H5)(3)(N2S2)], contains a molecular entity that is very similar to that of the known polymorph of Sb(S2N2)Ph-3 [Kunkel et al. (1997). Z. Naturforsch. Teil B, 52, 193-198], differing only in the orientation of the phenyl rings. The bond order in the SNSN unit is S-N=S=N, consisting of one long S-N bond, an intermediate length N=S bond and a short S=N bond. Hua, Guoxiong Henry, John B. Li, Yang Mount, Andrew R. Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1772 2013-05-12T03:35:13Z 2010-04-07T00:00:00Z

Abstract: Reaction of 2,4-bis(phenyl)-1,3-diselenadiphosphetane-2,4-diselenide [PhP(Se)(mu-Se)](2) (Woollins' reagent, WR) with one equivalent of 1,4-diarylbutane-1,4-diones 1a-g in refluxing toluene affords the corresponding 2,5-diarylselenophenes 2a-g in excellent yields (up to 99%). Alternatively, the 2,5-diarylselenophenes (2a and 2b) can be obtained in 70-80% yields from the reaction of arylacetylene with an equivalent of O-methyl Se-hydrogen phenylphosphonodiselenoate; the latter was derived from WR and methanol. The first X-ray structure of 2,5-diarylselenophenes is presented along with characterisation of their redox properties.

2010-04-07T00:00:00Z Hua, Guoxiong Henry, John B. Li, Yang Mount, Andrew R. Slawin, Alexandra M. Z. Woollins, J. Derek Reaction of 2,4-bis(phenyl)-1,3-diselenadiphosphetane-2,4-diselenide [PhP(Se)(mu-Se)](2) (Woollins' reagent, WR) with one equivalent of 1,4-diarylbutane-1,4-diones 1a-g in refluxing toluene affords the corresponding 2,5-diarylselenophenes 2a-g in excellent yields (up to 99%). Alternatively, the 2,5-diarylselenophenes (2a and 2b) can be obtained in 70-80% yields from the reaction of arylacetylene with an equivalent of O-methyl Se-hydrogen phenylphosphonodiselenoate; the latter was derived from WR and methanol. The first X-ray structure of 2,5-diarylselenophenes is presented along with characterisation of their redox properties. Hua, Guoxiong Zhang, Qingzhi Li, Yang Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1771 2013-05-12T02:34:13Z 2008-11-01T00:00:00Z

Abstract: The reaction of 2,4-bis(phenyl)-1,3-diselenadiphosphetane-2,4- diselenide (Woollins' Reagent, WR) with phenylalkyl-cyanamides (RR'NC N, R = PhCH2CH2, R' = CH3 and R = PhCH2CH2CH2, R' = H) in refluxing toluene led to novel heterocyclic selenazadiphospholaminediselenides 1 and 2 (43% and 42% yields), the latter being hydrolyzed to the unusual zwitterionic carbamidoyl(phenyl) phosphinodiselenoic acids 3 and 4 in excellent yields (96% and 98%).

2008-11-01T00:00:00Z Hua, Guoxiong Zhang, Qingzhi Li, Yang Slawin, Alexandra M. Z. Woollins, J. Derek The reaction of 2,4-bis(phenyl)-1,3-diselenadiphosphetane-2,4- diselenide (Woollins' Reagent, WR) with phenylalkyl-cyanamides (RR'NC N, R = PhCH2CH2, R' = CH3 and R = PhCH2CH2CH2, R' = H) in refluxing toluene led to novel heterocyclic selenazadiphospholaminediselenides 1 and 2 (43% and 42% yields), the latter being hydrolyzed to the unusual zwitterionic carbamidoyl(phenyl) phosphinodiselenoic acids 3 and 4 in excellent yields (96% and 98%). Fuller, Amy Scott-Hayward, Lindesay Alexandra Sarah Li, Yang Buehl, Michael Slawin, Alexandra Martha Zoya Woollins, J Derek http://hdl.handle.net/10023/1769 2013-05-19T00:33:31Z 2010-04-28T00:00:00Z

Abstract: The first fully automated small-molecule robotic X-ray diffractometer is described. After demonstrating the utility of the instrument using multiple samples of ammonium bitartrate, we investigated the conformational chirality of diphenyl dichalcogenide (E2Ph2, where E = S, Se, or Te). Structural and computational studies suggest that the two enantiomers are energetically indistinguishable. Therefore, it was unsurprising that we found (in 35 suitable data collections) the proportion 0.51:0.49 of M-S2Ph2 to P-S2Ph2 in the bulk sample. Interestingly, after 65 data collections of Te2Ph2, (46 provided suitable data sets), we found the proportion 0.72 +/- 0.13 of M-Te2Ph2, suggesting there could be a statistically significant preference for the M-enantiomer in the sample examined here. We found that Se2Ph2 underwent homochiral crystallization, with all 24 crystals being M. Our experiments may represent a salutary lesson in statistical analysis.

2010-04-28T00:00:00Z Fuller, Amy Scott-Hayward, Lindesay Alexandra Sarah Li, Yang Buehl, Michael Slawin, Alexandra Martha Zoya Woollins, J Derek The first fully automated small-molecule robotic X-ray diffractometer is described. After demonstrating the utility of the instrument using multiple samples of ammonium bitartrate, we investigated the conformational chirality of diphenyl dichalcogenide (E2Ph2, where E = S, Se, or Te). Structural and computational studies suggest that the two enantiomers are energetically indistinguishable. Therefore, it was unsurprising that we found (in 35 suitable data collections) the proportion 0.51:0.49 of M-S2Ph2 to P-S2Ph2 in the bulk sample. Interestingly, after 65 data collections of Te2Ph2, (46 provided suitable data sets), we found the proportion 0.72 +/- 0.13 of M-Te2Ph2, suggesting there could be a statistically significant preference for the M-enantiomer in the sample examined here. We found that Se2Ph2 underwent homochiral crystallization, with all 24 crystals being M. Our experiments may represent a salutary lesson in statistical analysis. Hua, Guoxiong Fuller, Amy L. Li, Yang Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1766 2013-05-12T03:35:21Z 2010-08-01T00:00:00Z

Abstract: Refluxing a toluene solution of Woollins' reagent, WR, with difunctional aromatic substrates (aryldiamines and aryldithiols) leads to a series of novel five-to seven-membered heterocycles 2a-e, 4a, 4b and 6a-c with an E-P(Se)-E' (E, E' = N, S, Se) linkage in 7-98% isolated yields. This method offers a new approach to the library of phosphorus-selenium heterocyclic compounds. All new compounds have been characterized by IR, H-1, C-13, P-31, Se-77 NMR, mass spectrometry and elemental analysis or accurate mass measurement. Four representative X-ray structures are reported.

2010-08-01T00:00:00Z Hua, Guoxiong Fuller, Amy L. Li, Yang Slawin, Alexandra M. Z. Woollins, J. Derek Refluxing a toluene solution of Woollins' reagent, WR, with difunctional aromatic substrates (aryldiamines and aryldithiols) leads to a series of novel five-to seven-membered heterocycles 2a-e, 4a, 4b and 6a-c with an E-P(Se)-E' (E, E' = N, S, Se) linkage in 7-98% isolated yields. This method offers a new approach to the library of phosphorus-selenium heterocyclic compounds. All new compounds have been characterized by IR, H-1, C-13, P-31, Se-77 NMR, mass spectrometry and elemental analysis or accurate mass measurement. Four representative X-ray structures are reported. Matuska, Vit Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1765 2013-05-12T03:35:11Z 2010-03-15T00:00:00Z

Abstract: A series of 5-alkyl/aryl-1,3 lambda(4)delta(2),2,4,5-dithiadiazarsoles RAs(S2N2) (R = Me, Et, Pr-i, Bu-t, Ph, Mes) were prepared by a ligand exchange between [(Bu2Sn)-Bu-n(S2N2)](2) and the corresponding organodihalogenoarsines RAsX2 (X = Cl, I). All products were characterized by NMR, IR, and Raman spectroscopies and mass spectrometry. The crystal structures of the aryldithiadiazarsoles (R = Ph, Mes) were determined.

2010-03-15T00:00:00Z Matuska, Vit Slawin, Alexandra M. Z. Woollins, J. Derek A series of 5-alkyl/aryl-1,3 lambda(4)delta(2),2,4,5-dithiadiazarsoles RAs(S2N2) (R = Me, Et, Pr-i, Bu-t, Ph, Mes) were prepared by a ligand exchange between [(Bu2Sn)-Bu-n(S2N2)](2) and the corresponding organodihalogenoarsines RAsX2 (X = Cl, I). All products were characterized by NMR, IR, and Raman spectroscopies and mass spectrometry. The crystal structures of the aryldithiadiazarsoles (R = Ph, Mes) were determined. Knight, Fergus R. Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1764 2013-05-12T03:35:18Z 2010-05-27T00:00:00Z

Abstract: A series of three platinum(II) halide complexes 2-4 [Pt(X)(2)(Nap(PPh2)(SPh))] (Nap = naphthalene-1,8-diyl: X = Cl, Br, I) and a ruthenium(II) p-cymene complex 5 [Ru(eta(6)-(MeC6H4Pr)-Pr-i)(Cl){Nap(PPh2)(SPh)}]Cl-+(-) of the sterically crowded pen-substituted naphthalene phosphine 1 have been prepared. The compounds were fully characterised by multinuclear NMR. IR and MS and X-ray data for 1-5 are compared. Molecular structures are analysed by naphthalene ring torsions, pert-atom displacement, splay angle magnitude, P center dot center dot center dot S interactions, aromatic ring orientations and geometry around the metal centre. Platinum adopts a strictly square planar geometry which increases the distortion of the naphthalene skeleton in 2-4. Conversely, the classical-piano stool conformation of 5 results in a pseudo-octahedral conformation around the ruthenium atom which influences the naphthalene geometry to a much lesser extent with distortion of a similar magnitude to the free ligand 1. (c) 2010 Elsevier Ltd. All rights reserved.

2010-05-27T00:00:00Z Knight, Fergus R. Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek A series of three platinum(II) halide complexes 2-4 [Pt(X)(2)(Nap(PPh2)(SPh))] (Nap = naphthalene-1,8-diyl: X = Cl, Br, I) and a ruthenium(II) p-cymene complex 5 [Ru(eta(6)-(MeC6H4Pr)-Pr-i)(Cl){Nap(PPh2)(SPh)}]Cl-+(-) of the sterically crowded pen-substituted naphthalene phosphine 1 have been prepared. The compounds were fully characterised by multinuclear NMR. IR and MS and X-ray data for 1-5 are compared. Molecular structures are analysed by naphthalene ring torsions, pert-atom displacement, splay angle magnitude, P center dot center dot center dot S interactions, aromatic ring orientations and geometry around the metal centre. Platinum adopts a strictly square planar geometry which increases the distortion of the naphthalene skeleton in 2-4. Conversely, the classical-piano stool conformation of 5 results in a pseudo-octahedral conformation around the ruthenium atom which influences the naphthalene geometry to a much lesser extent with distortion of a similar magnitude to the free ligand 1. (c) 2010 Elsevier Ltd. All rights reserved. Knight, Fergus R. Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1763 2013-05-12T03:35:18Z 2010-05-10T00:00:00Z

Abstract: Reaction of 8-methoxy-1-naphthyllithium (2) with one equivalent of chlorodiphenylphosphine gives the novel (8-methoxynaphth-1-yl)diphenylphosphine (3) which was oxidised to the corresponding sulfide (4) and selenide (5) by reaction with sulfur and selenium, respectively. The P center dot center dot center dot O peri distance is significantly increased in 4 and 5 at 2.819(3)[2.793(3)] and 2.827(3) [2.806(3)] angstrom [values in square brackets are for the second independent molecules in each case] relative to the value in 3 of 2.678(2) angstrom. There are short E center dot center dot center dot O interactions ie O(1)center dot center dot center dot S(1) 3.165(3) [3.124(3)], 0(1)center dot center dot center dot Se(1) 3.247(3) [3.200(2)] angstrom and these may be repulsive and responsible for the increased P center dot center dot center dot O separation. The use of the naphthalene backbone in the synthesis of a potential hemilabile ligand is demonstrated by the synthesis and X-ray structure of (8-methoxynaphth-1-yl)diethoxyphosphine ruthenium p-cymene dichloride (6). (C) 2010 Elsevier Ltd. All rights reserved.

2010-05-10T00:00:00Z Knight, Fergus R. Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek Reaction of 8-methoxy-1-naphthyllithium (2) with one equivalent of chlorodiphenylphosphine gives the novel (8-methoxynaphth-1-yl)diphenylphosphine (3) which was oxidised to the corresponding sulfide (4) and selenide (5) by reaction with sulfur and selenium, respectively. The P center dot center dot center dot O peri distance is significantly increased in 4 and 5 at 2.819(3)[2.793(3)] and 2.827(3) [2.806(3)] angstrom [values in square brackets are for the second independent molecules in each case] relative to the value in 3 of 2.678(2) angstrom. There are short E center dot center dot center dot O interactions ie O(1)center dot center dot center dot S(1) 3.165(3) [3.124(3)], 0(1)center dot center dot center dot Se(1) 3.247(3) [3.200(2)] angstrom and these may be repulsive and responsible for the increased P center dot center dot center dot O separation. The use of the naphthalene backbone in the synthesis of a potential hemilabile ligand is demonstrated by the synthesis and X-ray structure of (8-methoxynaphth-1-yl)diethoxyphosphine ruthenium p-cymene dichloride (6). (C) 2010 Elsevier Ltd. All rights reserved. Knight, Fergus R. Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1762 2013-05-12T03:35:07Z 2009-01-01T00:00:00Z

Abstract: In the isomorphous binuclear Cu2X2L2 systems (L = (8-phenylthionaphth-1-yl)diphenylphosphine the Cu center dot center dot center dot Cu separation is reduced as the halide size increases.

2009-01-01T00:00:00Z Knight, Fergus R. Fuller, Amy L. Slawin, Alexandra M. Z. Woollins, J. Derek In the isomorphous binuclear Cu2X2L2 systems (L = (8-phenylthionaphth-1-yl)diphenylphosphine the Cu center dot center dot center dot Cu separation is reduced as the halide size increases. Geethalakshmi, K. R. Waller, Mark P. Thiel, Walter Buehl, Michael http://hdl.handle.net/10023/1757 2013-05-12T04:02:22Z 2009-04-02T00:00:00Z

Abstract: QM/MM models of the peroxo forms of vanadium-containing haloperoxidases (VHPOs) are critically assessed in terms of active site geometries, hydrogen bonds within the active site, isotropic and anisotropic V-51 NMR chemical shifts, and TD-DFT excitation energies. The geometric stability within the active site of the protein is comparable to the respective native forms, as indicated by low standard deviations in bond lengths across a number of local minima sampled along MID trajectories. There is a significant calculated upfield shift in delta(V-51) upon formation of the peroxo from the respective native forms for both the vanadium-containing chloroperoxidase (VCPO) and vanadium-containing bromoperoxidase (VBPO) models, which is in qualitative agreement with V-51 NMR experiments of VBPO in solution. The models show appreciable differences between the anisotropic chemical shifts of the different protonation states of the peroxo form of VHPO. The most likely candidates for the peroxo forms of the VHPO enzymes appear to be unprotonated or have a single proton on either of the equatorial oxygen ligands, based on QM/MM modeling in combination with X-ray, V-51 NMR, and UV-vis data.

2009-04-02T00:00:00Z Geethalakshmi, K. R. Waller, Mark P. Thiel, Walter Buehl, Michael QM/MM models of the peroxo forms of vanadium-containing haloperoxidases (VHPOs) are critically assessed in terms of active site geometries, hydrogen bonds within the active site, isotropic and anisotropic V-51 NMR chemical shifts, and TD-DFT excitation energies. The geometric stability within the active site of the protein is comparable to the respective native forms, as indicated by low standard deviations in bond lengths across a number of local minima sampled along MID trajectories. There is a significant calculated upfield shift in delta(V-51) upon formation of the peroxo from the respective native forms for both the vanadium-containing chloroperoxidase (VCPO) and vanadium-containing bromoperoxidase (VBPO) models, which is in qualitative agreement with V-51 NMR experiments of VBPO in solution. The models show appreciable differences between the anisotropic chemical shifts of the different protonation states of the peroxo form of VHPO. The most likely candidates for the peroxo forms of the VHPO enzymes appear to be unprotonated or have a single proton on either of the equatorial oxygen ligands, based on QM/MM modeling in combination with X-ray, V-51 NMR, and UV-vis data. Buehl, Michael Reimann, Christoph Pantazis, Dimitrios A. Bredow, Thomas Neese, Frank http://hdl.handle.net/10023/1756 2013-05-19T00:33:44Z 2008-09-01T00:00:00Z

Abstract: A set of 41 metal-ligand bond distances in 25 third-row transition-metal complexes, for which precise structural data are known in the gas phase, is used to assess optimized and zero-point averaged geometries obtained from DFT computations with various exchange-correlation functionals and basis sets. For a given functional (except LSDA) Stuttgart-type quasi-relativistic effective core potentials and an all-electron scalar relativistic approach (ZORA) tend to produce very similar geometries. In contrast to the lighter congeners, LSDA affords reasonably accurate geometries of 5d-metal complexes, as it is among the functionals with the lowest mean and standard deviations from experiment. For this set the ranking of some other popular density functionals, ordered according to decreasing standard deviation, is BLYP > VSXC > BP86 approximate to BPW91 approximate to TPSS approximate to B3LYP approximate to PBE > TPSSh > B3PW91 approximate to B3P86 approximate to PBE hybrid. In this case hybrid functionals are superior to their nonhybrid variants. In addition, we have reinvestigated the previous test sets for 3d- (Buhl M.; Kabrede, H. J. Chem. Theory Comput. 2006, 2, 1282-1290) and 4d- (Waller, M. P.; Buhl, M. J. Comput. Chem. 2007,28,1531-1537) transition-metal complexes using all-electron scalar relativistic DFT calculations in addition to the published nonrelativistic and ECP results. For this combined test set comprising first-, second-, and third-row metal complexes, B3P86 and PBE hybrid are indicated to perform best. A remarkably consistent standard deviation of around 2 pm in metal-ligand bond distances is achieved over the entire set of d-block elements.

2008-09-01T00:00:00Z Buehl, Michael Reimann, Christoph Pantazis, Dimitrios A. Bredow, Thomas Neese, Frank A set of 41 metal-ligand bond distances in 25 third-row transition-metal complexes, for which precise structural data are known in the gas phase, is used to assess optimized and zero-point averaged geometries obtained from DFT computations with various exchange-correlation functionals and basis sets. For a given functional (except LSDA) Stuttgart-type quasi-relativistic effective core potentials and an all-electron scalar relativistic approach (ZORA) tend to produce very similar geometries. In contrast to the lighter congeners, LSDA affords reasonably accurate geometries of 5d-metal complexes, as it is among the functionals with the lowest mean and standard deviations from experiment. For this set the ranking of some other popular density functionals, ordered according to decreasing standard deviation, is BLYP > VSXC > BP86 approximate to BPW91 approximate to TPSS approximate to B3LYP approximate to PBE > TPSSh > B3PW91 approximate to B3P86 approximate to PBE hybrid. In this case hybrid functionals are superior to their nonhybrid variants. In addition, we have reinvestigated the previous test sets for 3d- (Buhl M.; Kabrede, H. J. Chem. Theory Comput. 2006, 2, 1282-1290) and 4d- (Waller, M. P.; Buhl, M. J. Comput. Chem. 2007,28,1531-1537) transition-metal complexes using all-electron scalar relativistic DFT calculations in addition to the published nonrelativistic and ECP results. For this combined test set comprising first-, second-, and third-row metal complexes, B3P86 and PBE hybrid are indicated to perform best. A remarkably consistent standard deviation of around 2 pm in metal-ligand bond distances is achieved over the entire set of d-block elements. Sieffert, Nicolas Buehl, Michael http://hdl.handle.net/10023/1755 2013-05-12T04:02:19Z 2009-06-01T00:00:00Z

Abstract: The binding enthalpy of a triphenylphosphine ligand in Ru(CO)Cl (PPh3)3(CH=CHPh) is studied with "standard" (BP86 and B3LYP), dispersion-corrected (B3LYP-D and B97-D), and highly parametrized (M05 and M06 series) density functionals. An appropriate treatment of noncovalent interactions is mandatory because these turn out to account for a large fraction of the metal-ligand interaction energy. Among the tested methods, B97-D and the M06 series of functionals best reproduce the experimental binding enthalpy value of Sponsler et al. (Inorg. Chem. 2007, 46, 561).

2009-06-01T00:00:00Z Sieffert, Nicolas Buehl, Michael The binding enthalpy of a triphenylphosphine ligand in Ru(CO)Cl (PPh3)3(CH=CHPh) is studied with "standard" (BP86 and B3LYP), dispersion-corrected (B3LYP-D and B97-D), and highly parametrized (M05 and M06 series) density functionals. An appropriate treatment of noncovalent interactions is mandatory because these turn out to account for a large fraction of the metal-ligand interaction energy. Among the tested methods, B97-D and the M06 series of functionals best reproduce the experimental binding enthalpy value of Sponsler et al. (Inorg. Chem. 2007, 46, 561). Buehl, Michael http://hdl.handle.net/10023/1754 2013-05-12T04:02:18Z 2009-07-01T00:00:00Z

Abstract: Periodic density functional computations have been performed for solid [UO2F4(H2O)][NMe4]2·2H(2)O at the BLYP level. A model with disordered fluoro and aquo ligands in the uranyl anion is significantly lower in energy than one with a symmetrical assignment of these sites, which was favored in the original X-ray crystallography study. According to optimized energies and Car-Parrinello molecular dynamics (CPMD) simulations, the [UO2F4(H2O)]2- ion in the solid is stable with respect to loss of the coordinated water molecule. In contrast, CPMD simulations had found this ligand to be unbound in aqueous solution. The role of the counterions in stabilizing the higher coordination number in the crystal is discussed.

2009-07-01T00:00:00Z Buehl, Michael Periodic density functional computations have been performed for solid [UO2F4(H2O)][NMe4]2·2H(2)O at the BLYP level. A model with disordered fluoro and aquo ligands in the uranyl anion is significantly lower in energy than one with a symmetrical assignment of these sites, which was favored in the original X-ray crystallography study. According to optimized energies and Car-Parrinello molecular dynamics (CPMD) simulations, the [UO2F4(H2O)]2- ion in the solid is stable with respect to loss of the coordinated water molecule. In contrast, CPMD simulations had found this ligand to be unbound in aqueous solution. The role of the counterions in stabilizing the higher coordination number in the crystal is discussed. Buehl, Michael http://hdl.handle.net/10023/1753 2013-05-12T04:02:27Z 2011-03-21T00:00:00Z 2011-03-21T00:00:00Z Buehl, Michael Buehl, Michael Schreckenbach, Georg Sieffert, Nicolas Wipff, Georges http://hdl.handle.net/10023/1752 2013-05-12T04:02:17Z 2009-11-02T00:00:00Z

Abstract: The inclusion of NH4+ as counterions in Car-Parrinello molecular dynamics (CPMD) simulations of anionic uranyl(VI) complexes is proposed as a viable approach to modeling "real" aqueous solutions. For [UO2F4(H2O)](2-) in water, it is shown that the inclusion of two NH4+ ions strengthens the bond between uranyl and the water ligand by ca. 2 kcal/mol, improving the accordance with experiment. According to CPMD simulations for [UO2X5]-[NH4](3) (X = F, OH) in water, the fifth fluoride is bound much stronger than the fifth OH-. Implications for a recently proposed model for oxygen exchange in uranyl hydroxide are discussed.

2009-11-02T00:00:00Z Buehl, Michael Schreckenbach, Georg Sieffert, Nicolas Wipff, Georges The inclusion of NH4+ as counterions in Car-Parrinello molecular dynamics (CPMD) simulations of anionic uranyl(VI) complexes is proposed as a viable approach to modeling "real" aqueous solutions. For [UO2F4(H2O)](2-) in water, it is shown that the inclusion of two NH4+ ions strengthens the bond between uranyl and the water ligand by ca. 2 kcal/mol, improving the accordance with experiment. According to CPMD simulations for [UO2X5]-[NH4](3) (X = F, OH) in water, the fifth fluoride is bound much stronger than the fifth OH-. Implications for a recently proposed model for oxygen exchange in uranyl hydroxide are discussed. Buehl, Michael Schreckenbach, Georg http://hdl.handle.net/10023/1751 2013-05-12T04:02:15Z 2010-04-19T00:00:00Z

Abstract: A recently proposed pathway for the scrambling of axial (uranyl) and equatorial 0 atoms in [UO2(OH)4]2- (1) is refined using Car-Parrinello molecular dynamics (CPMD) simulations in an explicit solvent (water) and with model counterions (NH4+). According to constrained CPMD/BLYP simulations and thermodynamic integration, 1 can be deprotonated to [UO3(OH)3]3- with a T-shaped UO3 group (Delta A = 7.1 kcal/mol), which in turn can undergo a solvent-assisted proton transfer via a cis-[UO2(OH)4]2-center dot OH- complex and a total overall barrier of Delta A(double dagger) = 12.5 kcal/mol. According to computed relative energies of trans- and cis-[UO2(OH)4]2- in the gas phase and in a polarizable continuum, "pure" functionals such as BLYP underestimate this overall barrier somewhat, and estimates of Delta A(double dagger) approximate to 16 and 17 kcal/mol are obtained at the B3LYP and CCSD(T) levels, respectively, in excellent agreement with the experiment.

2010-04-19T00:00:00Z Buehl, Michael Schreckenbach, Georg A recently proposed pathway for the scrambling of axial (uranyl) and equatorial 0 atoms in [UO2(OH)4]2- (1) is refined using Car-Parrinello molecular dynamics (CPMD) simulations in an explicit solvent (water) and with model counterions (NH4+). According to constrained CPMD/BLYP simulations and thermodynamic integration, 1 can be deprotonated to [UO3(OH)3]3- with a T-shaped UO3 group (Delta A = 7.1 kcal/mol), which in turn can undergo a solvent-assisted proton transfer via a cis-[UO2(OH)4]2-center dot OH- complex and a total overall barrier of Delta A(double dagger) = 12.5 kcal/mol. According to computed relative energies of trans- and cis-[UO2(OH)4]2- in the gas phase and in a polarizable continuum, "pure" functionals such as BLYP underestimate this overall barrier somewhat, and estimates of Delta A(double dagger) approximate to 16 and 17 kcal/mol are obtained at the B3LYP and CCSD(T) levels, respectively, in excellent agreement with the experiment. Florence, Gordon John Morris, Joanne Charleen Murray, Ross George Osler, Jonathan Reddy, Vanga R. Smith, Terry K http://hdl.handle.net/10023/1685 2013-05-12T03:36:21Z 2011-02-04T00:00:00Z

Abstract: A stereocontrolled total synthesis of (+)-chamuvarinin, isolated from the root extract of Uvaria Chamae, utilizes a convergent modular strategy to construct the adjacently linked C15−C28 ether array, followed by a late-stage Julia−Kocienski olefination to append the butenolide motif. This constitutes the first total synthesis of (+)-chamuvarinin, defining the relative and absolute configuration of this unique annonaceous acetogenin. Description: Supported by grants from EPSRC (EP/F011458/1) and The Wellcome Trust (086658).

2011-02-04T00:00:00Z Florence, Gordon John Morris, Joanne Charleen Murray, Ross George Osler, Jonathan Reddy, Vanga R. Smith, Terry K A stereocontrolled total synthesis of (+)-chamuvarinin, isolated from the root extract of Uvaria Chamae, utilizes a convergent modular strategy to construct the adjacently linked C15−C28 ether array, followed by a late-stage Julia−Kocienski olefination to append the butenolide motif. This constitutes the first total synthesis of (+)-chamuvarinin, defining the relative and absolute configuration of this unique annonaceous acetogenin. Hua, Guoxiong Li, Yang Slawin, Alexandra M. Z. Woollins, J. Derek http://hdl.handle.net/10023/1682 2013-05-12T02:36:16Z 2008-01-01T00:00:00Z

Abstract: The structure of the title compound, C23H21OPSe2, consists of fused puckered five- and six-membered rings, PSeC2O and C5O, respectively, with a C2O bridgehead. The C5O ring adopts a chair conformation, whilst the C2PSeO ring has an envelope conformation.

2008-01-01T00:00:00Z Hua, Guoxiong Li, Yang Slawin, Alexandra M. Z. Woollins, J. Derek The structure of the title compound, C23H21OPSe2, consists of fused puckered five- and six-membered rings, PSeC2O and C5O, respectively, with a C2O bridgehead. The C5O ring adopts a chair conformation, whilst the C2PSeO ring has an envelope conformation. Buehl, Michael Peters, Dietmund Herges, Rainer http://hdl.handle.net/10023/1674 2013-05-12T04:02:25Z 2009-01-01T00:00:00Z

Abstract: Ni-61 chemical shifts of Ni(all-trans-cdt) L (cdt = cyclododecatriene, L = none, CO, PMe3), Ni(CO)(4), Ni(C2H4)(2)(PMe3), Ni(cod)(2) (cod = cyclooctadiene) and Ni(PX3)(4) (X = Me, F, Cl) are computed at the GIAO (gauge-including atomic orbitals), BPW91, B3LYP and BHandHLYP levels, using BP86-optimised geometries and an indirect referencing scheme. For this set of compounds, substituent effects on delta(Ni-61) are better described with hybrid functionals than with the pure BPW91 functional. On going from Ni(all-trans-cdt) to Ni(all-cis-cdt) the computations predict substantial shielding of the Ni-61 nucleus by nearly 700 ppm, as well as a sharp increase of the electric field gradient at this position. The latter result is predicted to afford an undetectably broad Ni-61 NMR line for the all-cis-cdt complex, rationalizing the apparent failure to record the NMR spectrum experimentally.

2009-01-01T00:00:00Z Buehl, Michael Peters, Dietmund Herges, Rainer Ni-61 chemical shifts of Ni(all-trans-cdt) L (cdt = cyclododecatriene, L = none, CO, PMe3), Ni(CO)(4), Ni(C2H4)(2)(PMe3), Ni(cod)(2) (cod = cyclooctadiene) and Ni(PX3)(4) (X = Me, F, Cl) are computed at the GIAO (gauge-including atomic orbitals), BPW91, B3LYP and BHandHLYP levels, using BP86-optimised geometries and an indirect referencing scheme. For this set of compounds, substituent effects on delta(Ni-61) are better described with hybrid functionals than with the pure BPW91 functional. On going from Ni(all-trans-cdt) to Ni(all-cis-cdt) the computations predict substantial shielding of the Ni-61 nucleus by nearly 700 ppm, as well as a sharp increase of the electric field gradient at this position. The latter result is predicted to afford an undetectably broad Ni-61 NMR line for the all-cis-cdt complex, rationalizing the apparent failure to record the NMR spectrum experimentally. Kowatz, Thomas Morrison, James P. Tanner, Martin E. Naismith, James H. http://hdl.handle.net/10023/1642 2013-05-12T03:04:22Z 2010-07-01T00:00:00Z

Abstract: Bacteria synthesize a wide array of unusual carbohydrate molecules, which they use in a variety of ways. The carbohydrate L-glycero-D-manno-heptose is an important component of lipopolysaccharide and is synthesized in a complex series of enzymatic steps. One step involves the epimerization at the C6 '' position converting ADP-D-glycero-D-manno-heptose into ADP-L-glycero-D-manno-heptose. The enzyme responsible is a member of the short chain dehydrogenase superfamily, known as ADP-L-glycero-D-manno-heptose 6-epimerase (AGME). The structure of the enzyme was known but the arrangement of the catalytic site with respect to the substrate is unclear. We now report the structure of AGME bound to a substrate mimic, ADP-beta-D-mannose, which has the same stereochemical configuration as the substrate. The complex identifies the key residues and allows mechanistic insight into this novel enzyme. Description: Supported by Wellcome Trust grant 081862/Z/06/Z

2010-07-01T00:00:00Z Kowatz, Thomas Morrison, James P. Tanner, Martin E. Naismith, James H. Bacteria synthesize a wide array of unusual carbohydrate molecules, which they use in a variety of ways. The carbohydrate L-glycero-D-manno-heptose is an important component of lipopolysaccharide and is synthesized in a complex series of enzymatic steps. One step involves the epimerization at the C6 '' position converting ADP-D-glycero-D-manno-heptose into ADP-L-glycero-D-manno-heptose. The enzyme responsible is a member of the short chain dehydrogenase superfamily, known as ADP-L-glycero-D-manno-heptose 6-epimerase (AGME). The structure of the enzyme was known but the arrangement of the catalytic site with respect to the substrate is unclear. We now report the structure of AGME bound to a substrate mimic, ADP-beta-D-mannose, which has the same stereochemical configuration as the substrate. The complex identifies the key residues and allows mechanistic insight into this novel enzyme. Overton, I M van Niekerk, C A Carter, L G Dawson, A Martin, D M Cameron, S McMahon, S A White, Malcolm Frederick Hunter, W N Naismith, James Henderson Barton, G J http://hdl.handle.net/10023/1028 2013-05-12T02:05:16Z 2008-07-01T00:00:00Z

Abstract: TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative. Description: This work was funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC) Structural Proteomics of Rational Targets (SPoRT) initiative, (Grant BBS/B/14434). Funding to pay the Open Access publication charges for this article was provided by BBSRC.

2008-07-01T00:00:00Z Overton, I M van Niekerk, C A Carter, L G Dawson, A Martin, D M Cameron, S McMahon, S A White, Malcolm Frederick Hunter, W N Naismith, James Henderson Barton, G J TarO (http://www.compbio.dundee.ac.uk/taro) offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques. The protein sequence is analysed by 17 algorithms and compared to 8 databases. TarO gathers putative homologues, including orthologues, and then obtains predictions of properties for these sequences including crystallisation propensity, protein disorder and post-translational modifications. Analyses are run on a high-performance computing cluster, the results integrated, stored in a database and accessed through a web-based user interface. Output is in tabulated format and in the form of an annotated multiple sequence alignment (MSA) that may be edited interactively in the program Jalview. TarO also simplifies the gathering of additional annotations via the Distributed Annotation System, both from the MSA in Jalview and through links to Dasty2. Routes to other information gateways are included, for example to relevant pages from UniProt, COG and the Conserved Domains Database. Open access to TarO is available from a guest account with private accounts for academic use available on request. Future development of TarO will include further analysis steps and integration with the Protein Information Management System (PIMS), a sister project in the BBSRC Structural Proteomics of Rational Targets initiative. Aitken, R. Alan http://hdl.handle.net/10023/670 2010-12-07T15:28:09Z 2000-01-01T00:00:00Z

Abstract: The title stabilised ylides, readily prepared in one step from acid chlorides, are converted upon FVP at 850 °C into 2-substituted benzofurans. When the acyl group is aromatic it appears unchanged as the 2- substituent in the product while for aliphatic examples degradation processes may lead to 2-alkenyl products.

2000-01-01T00:00:00Z Aitken, R. Alan The title stabilised ylides, readily prepared in one step from acid chlorides, are converted upon FVP at 850 °C into 2-substituted benzofurans. When the acyl group is aromatic it appears unchanged as the 2- substituent in the product while for aliphatic examples degradation processes may lead to 2-alkenyl products.