Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes.
Nucleic Acids Res. 2014 Oct 16;
Authors: Pires DE, Blundell TL, Ascher DB
Drug resistance is a major challenge for the treatment of many diseases and a significant concern throughout the drug development process. The ability to understand and predict the effects of mutations on protein-ligand affinities and their roles in the emergence of resistance would significantly aid treatment and drug design strategies. In order to study and understand the impacts of missense mutations on the interaction of ligands with the proteome, we have developed Platinum (http://structure.bioc.cam.ac.uk/platinum). This manually curated, literature-derived database, comprising over 1000 mutations, associates for the first time experimental information on changes in affinity with three-dimensional structures of protein-ligand complexes. To minimize differences arising from experimental techniques and to directly compare binding affinities, Platinum considers only changes measured by the same group and with the same amino-acid sequence used for structure determination, providing a direct link between protein structure, how a ligand binds and how mutations alter the affinity of the ligand of the protein. We believe Platinum will be an invaluable resource for understanding the effects of mutations that give rise to drug resistance, a major problem emerging in pandemics including those caused by the influenza virus, in infectious diseases such as tuberculosis, in cancer and in many other life-threatening illnesses.
PMID: 25324307 [PubMed - as supplied by publisher]
Polyphony: superposition independent methods for ensemble-based drug discovery.
BMC Bioinformatics. 2014 Sep 30;15(1):324
Authors: Pitt WR, Montalvão RW, Blundell TL
BACKGROUND: Structure-based drug design is an iterative process, following cycles of structural biology, computer-aided design, synthetic chemistry and bioassay. In favorable circumstances, this process can lead to the structures of hundreds of protein-ligand crystal structures. In addition, molecular dynamics simulations are increasingly being used to further explore the conformational landscape of these complexes. Currently, methods capable of the analysis of ensembles of crystal structures and MD trajectories are limited and usually rely upon least squares superposition of coordinates.
RESULTS: Novel methodologies are described for the analysis of multiple structures of the same or related proteins. Statistical approaches that rely upon residue equivalence, but not superposition, are developed. Tasks that can be performed include the identification of hinge regions, allosteric conformational changes and transient binding sites. The approaches are tested on crystal structures of CDK2 and other CMGC protein kinases and a simulation of p38alpha. Known interaction - conformational change relationships are highlighted but also new ones are revealed. A transient but druggable allosteric pocket in CDK2 is predicted to occur under the CMGC insert. Furthermore, an evolutionarily-conserved conformational link from the location of this pocket, via the alphaEF-alphaF loop, to phosphorylation sites on the activation loop is discovered.
CONCLUSIONS: New methodologies are described and validated for the superimposition independent conformational analysis of large collections of structures or simulation snapshots of the same protein. The methodologies are encoded in a Python package called Polyphony, which is released as open source to accompany this paper [http://wrpitt.bitbucket.org/polyphony/].
PMID: 25265915 [PubMed - as supplied by publisher]
Design and Structural Analysis of Aromatic Inhibitors of Type II Dehydroquinase from Mycobacterium tuberculosis.
ChemMedChem. 2014 Sep 18;
Authors: Howard NI, Dias MV, Peyrot F, Chen L, Schmidt MF, Blundell TL, Abell C
3-Dehydroquinase, the third enzyme in the shikimate pathway, is a potential target for drugs against tuberculosis. Whilst a number of potent inhibitors of the Mycobacterium tuberculosis enzyme based on a 3-dehydroquinate core have been identified, they generally show little or no in vivo activity, and were synthetically complex to prepare. This report describes studies to develop tractable and drug-like aromatic analogues of the most potent inhibitors. A range of carbon-carbon linked biaryl analogues were prepared to investigate the effect of hydrogen bond acceptor and donor patterns on inhibition. These exhibited inhibitory activity in the high-micromolar range. The addition of flexible linkers in the compounds led to the identification of more potent 3-nitrobenzylgallate- and 5-aminoisophthalate-based analogues.
PMID: 25234229 [PubMed - as supplied by publisher]
DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W314-9
Authors: Pires DE, Ascher DB, Blundell TL
Cancer genome and other sequencing initiatives are generating extensive data on non-synonymous single nucleotide polymorphisms (nsSNPs) in human and other genomes. In order to understand the impacts of nsSNPs on the structure and function of the proteome, as well as to guide protein engineering, accurate in silicomethodologies are required to study and predict their effects on protein stability. Despite the diversity of available computational methods in the literature, none has proven accurate and dependable on its own under all scenarios where mutation analysis is required. Here we present DUET, a web server for an integrated computational approach to study missense mutations in proteins. DUET consolidates two complementary approaches (mCSM and SDM) in a consensus prediction, obtained by combining the results of the separate methods in an optimized predictor using Support Vector Machines (SVM). We demonstrate that the proposed method improves overall accuracy of the predictions in comparison with either method individually and performs as well as or better than similar methods. The DUET web server is freely and openly available at http://structure.bioc.cam.ac.uk/duet.
PMID: 24829462 [PubMed - indexed for MEDLINE]
Respiratory flexibility in response to inhibition of cytochrome C oxidase in Mycobacterium tuberculosis.
Antimicrob Agents Chemother. 2014 Aug 25;
Authors: Arora K, Ochoa-Montaño B, Tsang PS, Blundell TL, Dawes SS, Mizrahi V, Bayliss T, Mackenzie CJ, Cleghorn LA, Ray PC, Wyatt PG, Uh E, Lee J, Barry CE, Boshoff HI
We report here on a series of five chemically diverse scaffolds that have activity in vitro on both replicating and hypoxic non-replicating bacilli by targeting the respiratory bc1 complex in Mycobacterium tuberculosis, in a strain-dependent manner. Deletion of the cytochrome bd oxidase generated a hyper-susceptible mutant in which resistance was acquired by mutation in qcrB. These results highlight the promiscuity of the bc1 complex and highlight the risk of targeting energy metabolism with new drugs.
PMID: 25155596 [PubMed - as supplied by publisher]
Mycobacterium tuberculosis dihydrofolate reductase reveals two conformational states and a possible low affinity mechanism to antifolate drugs.
Structure. 2014 Jan 7;22(1):94-103
Authors: Dias MV, Tyrakis P, Domingues RR, Paes Leme AF, Blundell TL
Inhibition of the biosynthesis of tetrahydrofolate (THF) has long been a focus in the treatment of both cancer and infectious diseases. Dihydrofolate reductase (DHFR), which catalyzes the last step, is one of the most thoroughly explored targets of this pathway, but there are no DHFR inhibitors used for tuberculosis treatment. Here, we report a structural, site-directed mutagenesis and calorimetric analysis of Mycobacterium tuberculosis DHFR (MtDHFR) in complex with classical DHFR inhibitors. Our study provides insights into the weak inhibition of MtDHFR by trimethoprim and other antifolate drugs, such as pyrimethamine and cycloguanil. The construction of the mutant Y100F, together with calorimetric studies, gives insights into low affinity of MtDHFR for classical DHFR inhibitors. Finally, the structures of MtDHFR in complex with pyrimethamine and cycloguanil define important interactions in the active site and provide clues to the more effective design of antibiotics targeted against MtDHFR.
PMID: 24210757 [PubMed - indexed for MEDLINE]