University of Dundee

Biological Chemistry and Drug Discovery 2008

Agrawal, A., Gurusamy, K., Powis, S., Gray, D. W., Fuller, B. and Davidson, B. R. (2008) A Meta-Analysis of the Impact of the Two-Layer Method of Preservation on Human Pancreatic Islet Transplantation. Cell Transplantation. 17, 1315-1322

Aguero, F., Al-Lazikani, B., Aslett, M., Berriman, M., Buckner, F. S., Campbell, R. K., Carmona, S., Carruthers, I. M., Chan, A. W., Chen, F., Crowther, G. J., Doyle, M. A., Hertz-Fowler, C., Hopkins, A. L., McAllister, G., Nwaka, S., Overington, J. P., Pain, A., Paolini, G. V., Pieper, U., Ralph, S. A., Riechers, A., Roos, D. S., Sali, A., Shanmugam, D., Suzuki, T., Van Voorhis, W. C. and Verlinde, C. L. (2008) Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov. 7, 900-907
doi; 10.1038/nrd2684
PMID;3184002  PMC18927591

Alphey, M. S., Konig, J. and Fairlamb, A. H. (2008) Structural and mechanistic insights into type II trypanosomatid tryparedoxin-dependent peroxidases. Biochem J. 414, 375-381
doi; 10.1042/BJ20080889
PMID;2552391  PMC18522537

Andersen, O. A., Nathubhai, A., Dixon, M. J., Eggleston, I. M. and van Aalten, D. M. (2008) Structure-based dissection of the natural product cyclopentapeptide chitinase inhibitor argifin. Chem Biol. 15, 295-301
doi; 10.1016/j.chembiol.2008.02.015
PMID;3764403  PMC18355729

Barton, G. J. (2008) Sequence alignment for molecular replacement. Acta Crystallogr D Biol Crystallogr. 64, 25-32
doi; 10.1107/S0907444907046343
PMID;2394811  PMC18094464

Bayascas, J. R., Wullschleger, S., Sakamoto, K., Garcia-Martinez, J. M., Clacher, C., Komander, D., van Aalten, D. M., Boini, K. M., Lang, F., Lipina, C., Logie, L., Sutherland, C., Chudek, J. A., van Diepen, J. A., Voshol, P. J., Lucocq, J. M. and Alessi, D. R. (2008) Mutation of the PDK1 PH domain inhibits protein kinase B/Akt, leading to small size and insulin resistance. Mol Cell Biol. 28, 3258-3272
doi; 10.1128/MCB.02032-07
PMID;2423167  PMC18347057

Brenk, R., Schipani, A., James, D., Krasowski, A., Gilbert, I. H., Frearson, J. and Wyatt, P. G. (2008) Lessons learnt from assembling screening libraries for drug discovery for neglected diseases. ChemMedChem. 3, 435-444
doi; 10.1002/cmdc.200700139
PMID;2628535  PMC18064617

Cameron, S., Fyffe, S. A., Goldie, S. and Hunter, W. N. (2008) Crystal structures of Toxoplasma gondii pterin-4a-carbinolamine dehydratase and comparisons with mammalian and parasite orthologues. Mol Biochem Parasitol. 158, 131-138
doi; 10.1016/j.molbiopara.2007.12.002

Cardon, Z. G., Gray, D. W. and Lewis, L. A. (2008) The green algal underground: Evolutionary secrets of desert cells. Bioscience. 58, 114-122
doi;  10.1641/B580206

Cavazzuti, A., Paglietti, G., Hunter, W. N., Gamarro, F., Piras, S., Loriga, M., Allecca, S., Corona, P., McLuskey, K., Tulloch, L., Gibellini, F., Ferrari, S. and Costi, M. P. (2008) Discovery of potent pteridine reductase inhibitors to guide antiparasite drug development. Proc Natl Acad Sci U S A. 105, 1448-1453
doi; 10.1073/pnas.0704384105
PMID;2234164  PMC18245389

Clarke, A. J., Hurtado-Guerrero, R., Pathak, S., Schuttelkopf, A. W., Borodkin, V., Shepherd, S. M., Ibrahim, A. F. and van Aalten, D. M. (2008) Structural insights into mechanism and specificity of O-GlcNAc transferase. EMBO J. 27, 2780-2788
doi; 10.1038/emboj.2008.186
PMID;2556091  PMC18818698

Cole, C., Barber, J. D. and Barton, G. J. (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 36, W197-201
doi; 10.1093/nar/gkn238
PMID;2447793  PMC18463136

Crane, C. M., Hirsch, A. K., Alphey, M. S., Sgraja, T., Lauw, S., Illarionova, V., Rohdich, F., Eisenreich, W., Hunter, W. N., Bacher, A. and Diederich, F. (2008) Synthesis and characterization of cytidine derivatives that inhibit the kinase IspE of the non-mevalonate pathway for isoprenoid biosynthesis. ChemMedChem. 3, 91-101
doi; 10.1002/cmdc.200700208

Crossman, A. T., Urbaniak, M. D. and Ferguson, M. A. (2008) Synthesis of 1-D-6-O-[2-(N-hydroxyaminocarbonyl)amino-2-deoxy-alpha-D-glucopyranosyl]-myo-inos itol 1-(n-octadecyl phosphate): a potential metalloenzyme inhibitor of glycosylphosphatidylinositol biosynthesis. Carbohydr Res. 343, 1478-1481
doi; 10.1016/j.carres.2008.03.028

Dawson, A., Fyfe, P. K. and Hunter, W. N. (2008) Specificity and reactivity in menaquinone biosynthesis: the structure of Escherichia coli MenD (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase). J Mol Biol. 384, 1353-1368
doi; 10.1016/j.jmb.2008.10.048
PMID;3656419  PMC18983854

Fang, J., Akwabi-Ameyaw, A., Britton, J. E., Katamreddy, S. R., Navas, F., Miller, A. B., Williams, S. P., Gray, D. W., Orband-Miller, L. A., Shearin, J. and Heyer, D. (2008) Synthesis of 3-alkyl naphthalenes as novel estrogen receptor ligands. Bioorganic & Medicinal Chemistry Letters. 18, 5075-5077
doi; DOI 10.1016/j.bmcl.2008.07.121

Ferguson, M. A. (2008) GPIs on a chip. Nat Chem Biol. 4, 223-224
doi; 10.1038/nchembio0408-223

Ferguson, M. A., Vaidya, V. S. and Bonventre, J. V. (2008) Biomarkers of nephrotoxic acute kidney injury. Toxicology. 245, 182-193
doi; 10.1016/j.tox.2007.12.024

Fyfe, P. K., Oza, S. L., Fairlamb, A. H. and Hunter, W. N. (2008) Leishmania trypanothione synthetase-amidase structure reveals a basis for regulation of conflicting synthetic and hydrolytic activities. J Biol Chem. 283, 17672-17680
doi; 10.1074/jbc.M801850200
PMID;2427367  PMC18420578

Gallo, M. B., Marques, A. S., Vieira, P. C., da Silva, M. F., Fernandes, J. B., Silva, M., Guido, R. V., Oliva, G., Thiemann, O. H., Albuquerque, S. and Fairlamb, A. H. (2008) Enzymatic inhibitory activity and trypanocidal effects of extracts and compounds from Siphoneugena densiflora O. Berg and Vitex polygama Cham. Z Naturforsch C. 63, 371-382
doi; PMID;3428908  PMC18669023

Gibellini, F., Hunter, W. N. and Smith, T. K. (2008) Biochemical characterization of the initial steps of the Kennedy pathway in Trypanosoma brucei: the ethanolamine and choline kinases. Biochem J. 415, 135-144
doi; 10.1042/BJ20080435
PMID;2552378  PMC18489261

Gray, D. W. (2008) Transient increases in methylbutenol emission following partial defoliation of Pinus ponderosa. Atmospheric Environment. 42, 4797-4802
doi; DOI 10.1016/j.atmosenv.2008.01.048

Hirsch, A. K., Alphey, M. S., Lauw, S., Seet, M., Barandun, L., Eisenreich, W., Rohdich, F., Hunter, W. N., Bacher, A. and Diederich, F. (2008) Inhibitors of the kinase IspE: structure-activity relationships and co-crystal structure analysis. Org Biomol Chem. 6, 2719-2730
doi; 10.1039/b804375b

Hopkins, A. L. (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol. 4, 682-690
doi; 10.1038/nchembio.118

Hurtado-Guerrero, R., Dorfmueller, H. C. and van Aalten, D. M. (2008) Molecular mechanisms of O-GlcNAcylation. Curr Opin Struct Biol. 18, 551-557
doi; 10.1016/

Hurtado-Guerrero, R., Raimi, O. G., Min, J., Zeng, H., Vallius, L., Shepherd, S., Ibrahim, A. F., Wu, H., Plotnikov, A. N. and van Aalten, D. M. (2008) Structural and kinetic differences between human and Aspergillus fumigatus D-glucosamine-6-phosphate N-acetyltransferase. Biochem J. 415, 217-223
doi; 10.1042/BJ20081000

Jefferson, E. R., Walsh, T. P. and Barton, G. J. (2008) A comparison of SCOP and CATH with respect to domain-domain interactions. Proteins. 70, 54-62
doi; 10.1002/prot.21496

Lamb, D., Schuttelkopf, A. W., van Aalten, D. M. and Brighty, D. W. (2008) Highly specific inhibition of leukaemia virus membrane fusion by interaction of peptide antagonists with a conserved region of the coiled coil of envelope. Retrovirology. 5, 70
doi; 10.1186/1742-4690-5-70
PMID;2533354  PMC18680566

Lucas-Lopez, C., Allingham, J. S., Lebl, T., Lawson, C. P., Brenk, R., Sellers, J. R., Rayment, I. and Westwood, N. J. (2008) The small molecule tool (S)-(-)-blebbistatin: novel insights of relevance to myosin inhibitor design. Org Biomol Chem. 6, 2076-2084
doi; 10.1039/b801223g
PMID;3758137  PMC18528569

Manning, J. R., Jefferson, E. R. and Barton, G. J. (2008) The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics. 9, 51
doi; 10.1186/1471-2105-9-51
PMID;2267696  PMC18221517

Manthri, S., Guther, M. L., Izquierdo, L., Acosta-Serrano, A. and Ferguson, M. A. (2008) Deletion of the TbALG3 gene demonstrates site-specific N-glycosylation and N-glycan processing in Trypanosoma brucei. Glycobiology. 18, 367-383
doi; 10.1093/glycob/cwn014

Overton, I. M., Padovani, G., Girolami, M. A. and Barton, G. J. (2008) ParCrys: a Parzen window density estimation approach to protein crystallization propensity prediction. Bioinformatics. 24, 901-907
doi; 10.1093/bioinformatics/btn055

Overton, I. M., van Niekerk, C. A., Carter, L. G., Dawson, A., Martin, D. M., Cameron, S., McMahon, S. A., White, M. F., Hunter, W. N., Naismith, J. H. and Barton, G. J. (2008) TarO: a target optimisation system for structural biology. Nucleic Acids Res. 36, W190-196
doi; 10.1093/nar/gkn141
PMID;2447720  PMC18385152

Oza, S. L., Chen, S., Wyllie, S., Coward, J. K. and Fairlamb, A. H. (2008) ATP-dependent ligases in trypanothione biosynthesis--kinetics of catalysis and inhibition by phosphinic acid pseudopeptides. FEBS J. 275, 5408-5421
doi; 10.1111/j.1742-4658.2008.06670.x
PMID;2702004  PMC18959765

Pathak, S., Dorfmueller, H. C., Borodkin, V. S. and van Aalten, D. M. (2008) Chemical dissection of the link between streptozotocin, O-GlcNAc, and pancreatic cell death. Chem Biol. 15, 799-807
doi; 10.1016/j.chembiol.2008.06.010
PMID;2568864  PMC18721751

Sellarajah, S., Boussard, C., Lekishvili, T., Brown, D. R. and Gilbert, I. H. (2008) Synthesis and testing of peptides for anti-prion activity. Eur J Med Chem. 43, 2418-2427
doi; 10.1016/j.ejmech.2008.01.041

Sgraja, T., Alphey, M. S., Ghilagaber, S., Marquez, R., Robertson, M. N., Hemmings, J. L., Lauw, S., Rohdich, F., Bacher, A., Eisenreich, W., Illarionova, V. and Hunter, W. N. (2008) Characterization of Aquifex aeolicus 4-diphosphocytidyl-2C-methyl-d-erythritol kinase - ligand recognition in a template for antimicrobial drug discovery. FEBS J. 275, 2779-2794
doi; 10.1111/j.1742-4658.2008.06418.x
PMID;2655357  PMC18422643

Sienkiewicz, N., Jaroslawski, S., Wyllie, S. and Fairlamb, A. H. (2008) Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 69, 520-533
doi; 10.1111/j.1365-2958.2008.06305.x
PMID;2610392  PMC18557814

Signorell, A., Rauch, M., Jelk, J., Ferguson, M. A. and Butikofer, P. (2008) Phosphatidylethanolamine in Trypanosoma brucei is organized in two separate pools and is synthesized exclusively by the Kennedy pathway. J Biol Chem. 283, 23636-23644
doi; 10.1074/jbc.M803600200
PMID;3259767  PMC18587155

Stokes, M. J., Guther, M. L., Turnock, D. C., Prescott, A. R., Martin, K. L., Alphey, M. S. and Ferguson, M. A. (2008) The synthesis of UDP-N-acetylglucosamine is essential for bloodstream form trypanosoma brucei in vitro and in vivo and UDP-N-acetylglucosamine starvation reveals a hierarchy in parasite protein glycosylation. J Biol Chem. 283, 16147-16161
doi; 10.1074/jbc.M709581200
PMID;2414269  PMC18381290

Sundaramoorthy, R., Fyfe, P. K. and Hunter, W. N. (2008) Structure of Staphylococcus aureus EsxA suggests a contribution to virulence by action as a transport chaperone and/or adaptor protein. J Mol Biol. 383, 603-614
doi; 10.1016/j.jmb.2008.08.047
PMID;3465917  PMC18773907

Towler, M. C., Fogarty, S., Hawley, S. A., Pan, D. A., Martin, D. M., Morrice, N. A., McCarthy, A., Galardo, M. N., Meroni, S. B., Cigorraga, S. B., Ashworth, A., Sakamoto, K. and Hardie, D. G. (2008) A novel short splice variant of the tumour suppressor LKB1 is required for spermiogenesis. Biochem J. 416, 1-14
doi; 10.1042/BJ20081447

Urbaniak, M. D., Crossman, A. and Ferguson, M. A. (2008) Probing Trypanosoma brucei glycosylphosphatidylinositol biosynthesis using novel precursor-analogues. Chem Biol Drug Des. 72, 127-132
doi; 10.1111/j.1747-0285.2008.00688.x

Urbaniak, M. D., Yashunsky, D. V., Crossman, A., Nikolaev, A. V. and Ferguson, M. A. (2008) Probing enzymes late in the trypanosomal glycosylphosphatidylinositol biosynthetic pathway with synthetic glycosylphosphatidylinositol analogues. ACS Chem Biol. 3, 625-634
doi; 10.1021/cb800143w

Vaidya, V. S., Ferguson, M. A. and Bonventre, J. V. (2008) Biomarkers of acute kidney injury. Annu Rev Pharmacol Toxicol. 48, 463-493
doi; 10.1146/annurev.pharmtox.48.113006.094615
PMID;2742480  PMC17937594

Vaidya, V. S., Waikar, S. S., Ferguson, M. A., Collings, F. B., Sunderland, K., Gioules, C., Bradwin, G., Matsouaka, R., Betensky, R. A., Curhan, G. C. and Bonventre, J. V. (2008) Urinary biomarkers for sensitive and specific detection of acute kidney injury in humans. Clin Transl Sci. 1, 200-208
doi; 10.1111/j.1752-8062.2008.00053.x
PMID;2638059  PMC19212447

van Aalten, D. M. and Strynadka, N. C. (2008) Putting glycobiology on a structural footing. Curr Opin Struct Biol. 18, 525-526
doi; 10.1016/

Villa, F., Deak, M., Alessi, D. R. and van Aalten, D. M. (2008) Structure of the OSR1 kinase, a hypertension drug target. Proteins. 73, 1082-1087
doi; 10.1002/prot.22238

Walsh, T. P., Webber, C., Searle, S., Sturrock, S. S. and Barton, G. J. (2008) SCANPS: a web server for iterative protein sequence database searching by dynamic programing, with display in a hierarchical SCOP browser. Nucleic Acids Res. 36, W25-29
doi; 10.1093/nar/gkn320
PMID;2447745  PMC18503088

Wyatt, P. G., Woodhead, A. J., Berdini, V., Boulstridge, J. A., Carr, M. G., Cross, D. M., Davis, D. J., Devine, L. A., Early, T. R., Feltell, R. E., Lewis, E. J., McMenamin, R. L., Navarro, E. F., O'Brien, M. A., O'Reilly, M., Reule, M., Saxty, G., Seavers, L. C., Smith, D. M., Squires, M. S., Trewartha, G., Walker, M. T. and Woolford, A. J. (2008) Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H-pyrazole-3-carboxamide (AT7519), a novel cyclin dependent kinase inhibitor using fragment-based X-ray crystallography and structure based drug design. J Med Chem. 51, 4986-4999
doi; 10.1021/jm800382h

Wyllie, S., Vickers, T. J. and Fairlamb, A. H. (2008) Roles of trypanothione S-transferase and tryparedoxin peroxidase in resistance to antimonials. Antimicrob Agents Chemother. 52, 1359-1365
doi; 10.1128/AAC.01563-07
PMID;2292513  PMC18250189

Yamada, Y., Wang, H. Y., Fukuzawa, M., Barton, G. J. and Williams, J. G. (2008) A new family of transcription factors. Development. 135, 3093-3101
doi; 10.1242/dev.026377
PMID;3586674  PMC18701541