University of Dundee

Biological Chemistry and Drug Discovery 2013

Adung'a, V. O., Gadelha, C. and Field, M. C. (2013) Proteomic analysis of clathrin interactions in trypanosomes reveals dynamic evolution of endocytosis. Traffic. 14, 440-457
doi; 10.1111/tra.12040
PMC23305527

Ali, J. A., Creek, D. J., Burgess, K., Allison, H. C., Field, M. C., Maser, P. and De Koning, H. P. (2013) Pyrimidine salvage in Trypanosoma brucei bloodstream forms and the trypanocidal action of halogenated pyrimidines. Mol Pharmacol. 83, 439-453
doi; 10.1124/mol.112.082321
PMC23188714

Ali, M. and Field, M. C. (2013) Cell density-dependent ectopic expression in bloodstream form Trypanosoma brucei. Experimental parasitology. 134, 249-255
doi; 10.1016/j.exppara.2013.03.017
PMID;3659828  PMC23538029

Allen, S., Richardson, J. M., Mehlert, A. and Ferguson, M. A. (2013) Structure of a complex phosphoglycan epitope from gp72 of Trypanosoma cruzi. The Journal of biological chemistry. 288, 11093-11105
doi; 10.1074/jbc.M113.452763
PMID;3630849  PMC23436655

Alphey, M. S., Pirrie, L., Torrie, L. S., Boulkeroua, W. A., Gardiner, M., Sarkar, A., Maringer, M., Oehlmann, W., Brenk, R., Scherman, M. S., McNeil, M., Rejzek, M., Field, R. A., Singh, M., Gray, D., Westwood, N. J. and Naismith, J. H. (2013) Allosteric competitive inhibitors of the glucose-1-phosphate thymidylyltransferase (RmlA) from Pseudomonas aeruginosa. ACS chemical biology. 8, 387-396
doi; 10.1021/cb300426u
PMC23138692

Alsford, S., Field, M. C. and Horn, D. (2013) Receptor-mediated endocytosis for drug delivery in African trypanosomes: fulfilling Paul Ehrlich's vision of chemotherapy. Trends in parasitology. 29, 207-212
doi; 10.1016/j.pt.2013.03.004
PMC23601931

Aristotelous, T., Ahn, S., Shukla, A. K., Gawron, S., Sassano, M. F., Kahsai, A. W., Wingler, L. M., Zhu, X., Tripathi-Shukla, P., Huang, X. P., Riley, J., Besnard, J., Read, K. D., Roth, B. L., Gilbert, I. H., Hopkins, A. L., Lefkowitz, R. J. and Navratilova, I. (2013) Discovery of beta2 Adrenergic Receptor Ligands Using Biosensor Fragment Screening of Tagged Wild-Type Receptor. ACS Med Chem Lett. 4, 1005-1010
doi; 10.1021/ml400312j
PMID;3892729  PMC24454993

Ciulli, A. (2013) Biophysical screening for the discovery of small-molecule ligands. Methods in molecular biology. 1008, 357-388
doi; 10.1007/978-1-62703-398-5_13
PMC23729259

Cukier, C. D., Hope, A. G., Elamin, A. A., Moynie, L., Schnell, R., Schach, S., Kneuper, H., Singh, M., Naismith, J. H., Lindqvist, Y., Gray, D. W. and Schneider, G. (2013) Discovery of an Allosteric Inhibitor Binding Site in 3-Oxo-acyl-ACP Reductase from Pseudomonas aeruginosa. ACS chemical biology. 8, 2518-2527
doi; 10.1021/cb4005063
PMID;3833349  PMC24015914

Dawson, A., Trumper, P., Chrysostomou, G. and Hunter, W. N. (2013) Structure of diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase from Acinetobacter baumannii. Acta crystallographica. Section F, Structural biology and crystallization communications. 69, 611-617
doi; 10.1107/S174430911301292X
PMID;3668577  PMC23722836

De Rycker, M., Hallyburton, I., Thomas, J., Campbell, L., Wyllie, S., Joshi, D., Cameron, S., Gilbert, I. H., Wyatt, P. G., Frearson, J. A., Fairlamb, A. H. and Gray, D. W. (2013) Comparison of a high-throughput high-content intracellular Leishmania donovani assay with an axenic amastigote assay. Antimicrob Agents Chemother. 57, 2913-2922
doi; 10.1128/AAC.02398-12
PMID;3697379  PMC23571538

Duc, C., Sherstnev, A., Cole, C., Barton, G. J. and Simpson, G. G. (2013) Transcription Termination and Chimeric RNA Formation Controlled by Arabidopsis thaliana FPA. PLoS genetics. 9, e1003867
doi; 10.1371/journal.pgen.1003867
PMID;3814327  PMC24204292

Duce, S. L., D'Alessandro, M., Du, Y., Jagpal, B., Gilbert, F. J., Crichton, L., Barker, S., Collinson, J. M. and Miedzybrodzka, Z. (2013) 3D MRI analysis of the lower legs of treated idiopathic congenital talipes equinovarus (clubfoot). PloS one. 8, e54100
doi; 10.1371/journal.pone.0054100
PMID;3559654  PMC23382871

Fang, W., Du, T., Raimi, O. G., Hurtado-Guerrero, R., Urbaniak, M. D., Ibrahim, A. F., Ferguson, M. A., Jin, C. and van Aalten, D. M. (2013) Genetic and structural validation of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase as an antifungal target. Molecular microbiology. 89, 479-493
doi; 10.1111/mmi.12290
PMC23750903

Ferguson, F. M., Fedorov, O., Chaikuad, A., Philpott, M., Muniz, J. R., Felletar, I., von Delft, F., Heightman, T., Knapp, S., Abell, C. and Ciulli, A. (2013) Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain. J Med Chem. 56, 10183-10187
doi; 10.1021/jm401582c
PMID;3905694  PMC24304323

Field, H. I., Coulson, R. M. and Field, M. C. (2013) An automated graphics tool for comparative genomics: the Coulson plot generator. BMC bioinformatics. 14, 141
doi; 10.1186/1471-2105-14-141
PMID;3668160  PMC23621955

Field, M. C., Koreny, L. and Rout, M. P. (2013) Enriching the pore: Splendid complexity from humble origins. Trafficdoi; 10.1111/tra.12141
PMC24279500

Fleming, J. R., Morgan, R. E., Fyfe, P. K., Kelly, S. M. and Hunter, W. N. (2013) The architecture of Trypanosoma brucei tubulin-binding cofactor B and implications for function. The FEBS journal. 280, 3270-3280
doi; 10.1111/febs.12308
PMID;3806363  PMC23627368

Gabernet-Castello, C., O'Reilly, A. J., Dacks, J. B. and Field, M. C. (2013) Evolution of Tre-2/Bub2/Cdc16 (TBC) Rab GTPase-activating proteins. Mol Biol Cell
24, 1574-1583
doi; 10.1091/mbc.E12-07-0557
PMID;3655817  PMC23485563

Gilbert, I. H. (2013) Drug discovery for neglected diseases: molecular target-based and phenotypic approaches. J Med Chem. 56, 7719-7726
doi; 10.1021/jm400362b
PMID;3954685  PMC24015767

Glover, L., Alsford, S. and Horn, D. (2013) DNA break site at fragile subtelomeres determines probability and mechanism of antigenic variation in African trypanosomes. PLoS pathogens. 9, e1003260
doi; 10.1371/journal.ppat.1003260
PMID;3610638  PMC23555264

Glover, L., Hutchinson, S., Alsford, S., McCulloch, R., Field, M. C. and Horn, D. (2013) Antigenic variation in African trypanosomes: the importance of chromosomal and nuclear context in VSG expression control. Cellular microbiology. 15, 1984-1993
doi; 10.1111/cmi.12215
PMC24047558

Gould, M. K., Bachmaier, S., Ali, J. A., Alsford, S., Tagoe, D. N., Munday, J. C., Schnaufer, A. C., Horn, D., Boshart, M. and de Koning, H. P. (2013) Cyclic AMP effectors in African trypanosomes revealed by genome-scale RNA interference library screening for resistance to the phosphodiesterase inhibitor CpdA. Antimicrobial agents and chemotherapy. 57, 4882-4893
doi; 10.1128/AAC.00508-13
PMID;3811416  PMC23877697

Graf, F. E., Ludin, P., Wenzler, T., Kaiser, M., Brun, R., Pyana, P. P., Buscher, P., de Koning, H. P., Horn, D. and Maser, P. (2013) Aquaporin 2 mutations in Trypanosoma brucei gambiense field isolates correlate with decreased susceptibility to pentamidine and melarsoprol. PLoS neglected tropical diseases. 7, e2475
doi; 10.1371/journal.pntd.0002475
PMID;3794916  PMC24130910

Hampton, S. E., Schipani, A., Bosch-Navarrete, C., Recio, E., Kaiser, M., Kahnberg, P., Gonzalez-Pacanowska, D., Johansson, N. G. and Gilbert, I. H. (2013) Investigation of acyclic uridine amide and 5'-amido nucleoside analogues as potential inhibitors of the Plasmodium falciparum dUTPase. Bioorg Med Chem. 21, 5876-5885
doi; 10.1016/j.bmc.2013.07.004
PMID;3776224  PMC23916149

Horn, D. and Duraisingh, M. T. (2013) Antiparasitic Chemotherapy: From Genomes to Mechanisms. Annual review of pharmacology and toxicologydoi; 10.1146/annurev-pharmtox-011613-135915
PMC24050701

Jackson, A. P., Allison, H. C., Barry, J. D., Field, M. C., Hertz-Fowler, C. and Berriman, M. (2013) A cell-surface phylome for African trypanosomes. PLoS neglected tropical diseases. 7, e2121
doi; 10.1371/journal.pntd.0002121
PMID;3605285  PMC23556014

Kerkhoven, E. J., Achcar, F., Alibu, V. P., Burchmore, R. J., Gilbert, I. H., Trybilo, M., Driessen, N. N., Gilbert, D., Breitling, R., Bakker, B. M. and Barrett, M. P. (2013) Handling uncertainty in dynamic models: the pentose phosphate pathway in Trypanosoma brucei. PLoS Comput Biol. 9, e1003371
doi; 10.1371/journal.pcbi.1003371
PMID;3854711  PMC24339766

Koumandou, V. L., Boehm, C., Horder, K. A. and Field, M. C. (2013) Evidence for recycling of invariant surface transmembrane domain proteins in African trypanosomes. Eukaryotic cell. 12, 330-342
doi; 10.1128/EC.00273-12
PMID;3571300  PMC23264644

Koumandou, V. L., Wickstead, B., Ginger, M. L., van der Giezen, M., Dacks, J. B. and Field, M. C. (2013) Molecular paleontology and complexity in the last eukaryotic common ancestor. Critical reviews in biochemistry and molecular biology. 48, 373-396
doi; 10.3109/10409238.2013.821444
PMID;3791482  PMC23895660

Kramer, S., Bannerman-Chukualim, B., Ellis, L., Boulden, E. A., Kelly, S., Field, M. C. and Carrington, M. (2013) Differential localization of the two T. brucei poly(A) binding proteins to the nucleus and RNP granules suggests binding to distinct mRNA pools. PloS one. 8, e54004
doi; 10.1371/journal.pone.0054004
PMID;3559699  PMC23382864

Lyons, R., Iwase, A., Gansewig, T., Sherstnev, A., Duc, C., Barton, G. J., Hanada, K., Higuchi-Takeuchi, M., Matsui, M., Sugimoto, K., Kazan, K., Simpson, G. G. and Shirasu, K. (2013) The RNA-binding protein FPA regulates flg22-triggered defense responses and transcription factor activity by alternative polyadenylation. Scientific reports. 3, 2866
doi; 10.1038/srep02866
PMID;3793224  PMC24104185

MacKenzie, K. F., Clark, K., Naqvi, S., McGuire, V. A., Noehren, G., Kristariyanto, Y., van den Bosch, M., Mudaliar, M., McCarthy, P. C., Pattison, M. J., Pedrioli, P. G., Barton, G. J., Toth, R., Prescott, A. and Arthur, J. S. (2013) PGE(2) induces macrophage IL-10 production and a regulatory-like phenotype via a protein kinase A-SIK-CRTC3 pathway. Journal of immunology. 190, 565-577
doi; 10.4049/jimmunol.1202462
PMID;3620524  PMC23241891

Manna, P. T., Kelly, S. and Field, M. C. (2013) Adaptin evolution in kinetoplastids and emergence of the variant surface glycoprotein coat in African trypanosomatids. Molecular phylogenetics and evolution. 67, 123-128
doi; 10.1016/j.ympev.2013.01.002
PMID;3650584  PMC23337175

McElroy, S. P., Nomura, T., Torrie, L. S., Warbrick, E., Gartner, U., Wood, G. and McLean, W. H. (2013) A lack of premature termination codon read-through efficacy of PTC124 (Ataluren) in a diverse array of reporter assays. PLoS biology. 11, e1001593
doi; 10.1371/journal.pbio.1001593
PMID;3692445  PMC23824517

Mok, N. Y., Maxe, S. and Brenk, R. (2013) Locating Sweet Spots for Screening Hits and Evaluating Pan-Assay Interference Filters from the Performance Analysis of Two Lead-like Libraries. Journal of chemical information and modelingdoi; 10.1021/ci300382f
PMID;3739413  PMC23451880

Morley, A. D., Pugliese, A., Birchall, K., Bower, J., Brennan, P., Brown, N., Chapman, T., Drysdale, M., Gilbert, I. H., Hoelder, S., Jordan, A., Ley, S. V., Merritt, A., Miller, D., Swarbrick, M. E. and Wyatt, P. G. (2013) Fragment-based hit identification: thinking in 3D. Drug Discov Today. 18, 1221-1227
doi; 10.1016/j.drudis.2013.07.011
PMC23906694

Moynie, L., Schnell, R., McMahon, S. A., Sandalova, T., Boulkerou, W. A., Schmidberger, J. W., Alphey, M., Cukier, C., Duthie, F., Kopec, J., Liu, H., Jacewicz, A., Hunter, W. N., Naismith, J. H. and Schneider, G. (2013) The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery. Acta crystallographica. Section F, Structural biology and crystallization communications. 69, 25-34
doi; 10.1107/S1744309112044739
PMID;3539698  PMC23295481

Murugesan, D., Kaiser, M., White, K. L., Norval, S., Riley, J., Wyatt, P. G., Charman, S. A., Read, K. D., Yeates, C. and Gilbert, I. H. (2013) Structure-activity relationship studies of pyrrolone antimalarial agents. ChemMedChem. 8, 1537-1544
doi; 10.1002/cmdc.201300177
PMID;3963473  PMC23918316

Murugesan, D., Mital, A., Kaiser, M., Shackleford, D. M., Morizzi, J., Katneni, K., Campbell, M., Hudson, A., Charman, S. A., Yeates, C. and Gilbert, I. H. (2013) Discovery and structure-activity relationships of pyrrolone antimalarials. J Med Chem. 56, 2975-2990
doi; 10.1021/jm400009c
PMID;3624797  PMC23517371

Nguyen, S., Jones, D. C., Wyllie, S., Fairlamb, A. H. and Phillips, M. A. (2013) Allosteric activation of trypanosomatid deoxyhypusine synthase by a catalytically dead paralog. The Journal of biological chemistry. 288, 15256-15267
doi; 10.1074/jbc.M113.461137
PMID;3663545  PMC23525104

Ong, H. B., Sienkiewicz, N., Wyllie, S., Patterson, S. and Fairlamb, A. H. (2013) Trypanosoma brucei (UMP synthase null mutants) are avirulent in mice, but recover virulence upon prolonged culture in vitro while retaining pyrimidine auxotrophy. Molecular microbiology. 90, 443-455
doi; 10.1111/mmi.12376
PMC23980694

Patterson, S., Wyllie, S., Stojanovski, L., Perry, M. R., Simeons, F. R., Norval, S., Osuna-Cabello, M., De Rycker, M., Read, K. D. and Fairlamb, A. H. (2013) The R enantiomer of the antitubercular drug PA-824 as a potential oral treatment for visceral Leishmaniasis. Antimicrobial agents and chemotherapy. 57, 4699-4706
doi; 10.1128/AAC.00722-13
PMID;3811480  PMC23856774

Perry, M. R., Wyllie, S., Raab, A., Feldmann, J. and Fairlamb, A. H. (2013) Chronic exposure to arsenic in drinking water can lead to resistance to antimonial drugs in a mouse model of visceral leishmaniasis. Proceedings of the National Academy of Sciences of the United States of America. 110, 19932-19937
doi; 10.1073/pnas.1311535110
PMC24167266

Pizarro, J. C., Hills, T., Senisterra, G., Wernimont, A. K., Mackenzie, C., Norcross, N. R., Ferguson, M. A., Wyatt, P. G., Gilbert, I. H. and Hui, R. (2013) Exploring the Trypanosoma brucei Hsp83 potential as a target for structure guided drug design. PLoS neglected tropical diseases. 7, e2492
doi; 10.1371/journal.pntd.0002492
PMID;3798429  PMC24147171

Pizarro, J. C., Hills, T., Senisterra, G., Wernimont, A. K., Mackenzie, C., Norcross, N. R., Ferguson, M. A. J., Wyatt, P. G., Gilbert, I. H. and Hui, R. (2013) Exploring the Trypanosoma brucei Hsp83 Potential as a Target for Structure Guided Drug Design. Plos Neglected Tropical Diseases. 7doi; 10.1371/journal.pntd.0002492
PMCWOS:000330376500031

Rao, V. A., Shepherd, S. M., Owen, R. and Hunter, W. N. (2013) Structure of Pseudomonas aeruginosa inosine 5'-monophosphate dehydrogenase. Acta crystallographica. Section F, Structural biology and crystallization communications. 69, 243-247
doi; 10.1107/S1744309113002352
PMID;3606566  PMC23519796

Rimsa, V., Eadsforth, T. C. and Hunter, W. N. (2013) Structure of the SCAN domain of human paternally expressed gene 3 protein. PloS one. 8, e69538
doi; 10.1371/journal.pone.0069538
PMID;3720700  PMC23936039

Rimsa, V., Eadsforth, T. C. and Hunter, W. N. (2013) Two high-resolution structures of the human E3 ubiquitin ligase Siah1. Acta crystallographica. Section F, Structural biology and crystallization communications. 69, 1339-1343
doi; 10.1107/S1744309113031448
PMC24316825

Rudd, S. G., Glover, L., Jozwiakowski, S. K., Horn, D. and Doherty, A. J. (2013) PPL2 Translesion Polymerase Is Essential for the Completion of Chromosomal DNA Replication in the African Trypanosome. Molecular cell. 52, 554-565
doi; 10.1016/j.molcel.2013.10.034
PMC24267450

Saunders, S. P., Goh, C. S., Brown, S. J., Palmer, C. N., Porter, R. M., Cole, C., Campbell, L. E., Gierlinski, M., Barton, G. J., Schneider, G., Balmain, A., Prescott, A. R., Weidinger, S., Baurecht, H., Kabesch, M., Gieger, C., Lee, Y. A., Tavendale, R., Mukhopadhyay, S., Turner, S. W., Madhok, V. B., Sullivan, F. M., Relton, C., Burn, J., Meggitt, S., Smith, C. H., Allen, M. A., Barker, J. N., Reynolds, N. J., Cordell, H. J., Irvine, A. D., McLean, W. H., Sandilands, A. and Fallon, P. G. (2013) Tmem79/Matt is the matted mouse gene and is a predisposing gene for atopic dermatitis in human subjects. The Journal of allergy and clinical immunology. 132, 1121-1129
doi; 10.1016/j.jaci.2013.08.046
PMID;3834151  PMC24084074

Sharkey, T. D., Gray, D. W., Pell, H. K., Breneman, S. R. and Topper, L. (2013) Isoprene Synthase Genes Form a Monophyletic Clade of Acyclic Terpene Synthases in the Tps-B Terpene Synthase Family. Evolution. 67, 1026-1040
doi; Doi 10.1111/Evo.12013
 

Silvestre, H. L., Blundell, T. L., Abell, C. and Ciulli, A. (2013) Integrated biophysical approach to fragment screening and validation for fragment-based lead discovery. Proc Natl Acad Sci U S A. 110, 12984-12989
doi; 10.1073/pnas.1304045110
PMID;3740835  PMC23872845

Srikannathasan, V., English, G., Bui, N. K., Trunk, K., O'Rourke, P. E., Rao, V. A., Vollmer, W., Coulthurst, S. J. and Hunter, W. N. (2013) Structural basis for type VI secreted peptidoglycan DL-endopeptidase function, specificity and neutralization in Serratia marcescens. Acta crystallographica. Section D, Biological crystallography. 69, 2468-2482
doi; 10.1107/S0907444913022725
PMC24311588

Sullivan, L., Wall, S. J., Carrington, M. and Ferguson, M. A. (2013) Proteomic selection of immunodiagnostic antigens for human African trypanosomiasis and generation of a prototype lateral flow immunodiagnostic device. PLoS neglected tropical diseases. 7, e2087
doi; 10.1371/journal.pntd.0002087
PMID;3584999  PMC23469310

Urbaniak, M. D., Collie, I. T., Fang, W., Aristotelous, T., Eskilsson, S., Raimi, O. G., Harrison, J., Navratilova, I. H., Frearson, J. A., van Aalten, D. M. and Ferguson, M. A. (2013) A novel allosteric inhibitor of the uridine diphosphate N-acetylglucosamine pyrophosphorylase from Trypanosoma brucei. ACS chemical biology. 8, 1981-1987
doi; 10.1021/cb400411x
PMID;3780468  PMC23834437

Urbaniak, M. D., Martin, D. M. and Ferguson, M. A. (2013) Global quantitative SILAC phosphoproteomics reveals differential phosphorylation is widespread between the procyclic and bloodstream form lifecycle stages of Trypanosoma brucei. Journal of proteome research. 12, 2233-2244
doi; 10.1021/pr400086y
PMID;3646404  PMC23485197

van Dam, T. J., Townsend, M. J., Turk, M., Schlessinger, A., Sali, A., Field, M. C. and Huynen, M. A. (2013) Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proceedings of the National Academy of Sciences of the United States of America. 110, 6943-6948
doi; 10.1073/pnas.1221011110
PMID;3637775  PMC23569277

Woodland, A., Grimaldi, R., Luksch, T., Cleghorn, L. A., Ojo, K. K., Van Voorhis, W. C., Brenk, R., Frearson, J. A., Gilbert, I. H. and Wyatt, P. G. (2013) From on-target to off-target activity: identification and optimisation of Trypanosoma brucei GSK3 inhibitors and their characterisation as anti-Trypanosoma brucei drug discovery lead molecules. ChemMedChem. 8, 1127-1137
doi; 10.1002/cmdc.201300072
PMID;3728731  PMC23776181

Woodland, A., Grimaldi, R., Luksch, T., Cleghorn, L. A. T., Ojo, K. K., Van Voorhis, W. C., Brenk, R., Frearson, J. A., Gilbert, I. H. and Wyatt, P. G. (2013) From On-Target to Off-Target Activity: Identification and Optimisation of Trypanosoma brucei GSK3 Inhibitors and Their Characterisation as Anti-Trypanosoma brucei Drug Discovery Lead Molecules. Chemmedchem. 8, 1127-1137
doi; 10.1002/cmdc.201300072

Wyllie, S., Patterson, S. and Fairlamb, A. H. (2013) Assessing the essentiality of Leishmania donovani nitroreductase and its role in nitro drug activation. Antimicrob Agents Chemother. 57, 901-906
doi; 10.1128/AAC.01788-12
PMID;3553740  PMC23208716

Zoltner, M., Fyfe, P. K., Palmer, T. and Hunter, W. N. (2013) Characterization of Staphylococcus aureus EssB, an integral membrane component of the Type VII secretion system: atomic resolution crystal structure of the cytoplasmic segment. The Biochemical journal. 449, 469-477
doi; 10.1042/BJ20121209
PMID;3526858  PMC23098276

Zoltner, M., Norman, D. G., Fyfe, P. K., El Mkami, H., Palmer, T. and Hunter, W. N. (2013) The architecture of EssB, an integral membrane component of the type VII secretion system. Structure. 21, 595-603
doi; 10.1016/j.str.2013.02.007
PMID;3694306  PMC23499020