Muller I.,Chesterford Research Park
Acta Crystallographica Section D: Structural Biology | Year: 2017
With continuous technical improvements at synchrotron facilities, data-collection rates have increased dramatically. This makes it possible to collect diffraction data for hundreds of protein-ligand complexes within a day, provided that a suitable crystal system is at hand. However, developing a suitable crystal system can prove challenging, exceeding the timescale of data collection by several orders of magnitude. Firstly, a useful crystallization construct of the protein of interest needs to be chosen and its expression and purification optimized, before screening for suitable crystallization and soaking conditions can start. This article reviews recent publications analysing large data sets of crystallization trials, with the aim of identifying factors that do or do not make a good crystallization construct, and gives guidance in the design of an expression construct. It provides an overview of common protein-expression systems, addresses how ligand binding can be both help and hindrance for protein purification, and describes ligand co-crystallization and soaking, with an emphasis on troubleshooting.This article aims to guide efforts in protein-ligand complex crystal structure generation, with special consideration of protein construct design, and summarizes different approaches to co-crystallization and crystal soaking. Common problems and pitfalls are highlighted. © 2017 Müller.
Sheppard D.W.,Chesterford Research Park |
Lipkin M.J.,Chesterford Research Park |
Harris C.J.,Lydith High Street |
Catana C.,Galapagos |
Current Pharmaceutical Design | Year: 2014
Compilation of an appropriate set of compounds is essential for the success of a small molecule screen. When very little is known about the target and when no or few ligands have been identified, the screening file is often made as diverse as possible. When structural information on the target or target family is available or ligands of the target are known, it is more efficient to apply a ligand- or target-focused bias, so as to predominantly screen compounds that can be expected to modulate the target. One way to achieve this is to select subsets of existing collections; another is to specifically design and synthesize libraries focused on a particular target, target family or mechanism of action. Despite the number of success stories, designing such libraries is still challenging and requires specialized knowledge, especially in emerging target areas such as protein-protein interactions (PPI), epigenetics and the ubiquitin proteasome pathway. BioFocus has successfully produced so-called SoftFocus® libraries for many years, evolving their targets from kinases to GPCRs and ion channels to difficult targets in the epigenetics and PPI fields. This article outlines several of the principles applied to SoftFocus library design, showcasing successes achieved by BioFocus' clients. In addition, screening results for a comprehensive set of BioFocus' kinase libraries against 20 kinase targets are used to demonstrate the power of the SoftFocus approach in delivering both selective and less-selective compounds and libraries against these targets. © 2014 Bentham Science Publishers.
Sloane D.A.,Yorkshire Cancer Research |
Trikic M.Z.,Yorkshire Cancer Research |
Chu M.L.H.,Stanford University |
Lamers M.B.A.C.,Chesterford Research Park |
And 5 more authors.
ACS Chemical Biology | Year: 2010
The Aurora kinases regulate multiple aspects of mitotic progression, and their overexpression in diverse tumor types makes them appealing oncology targets. An intensive research effort over the past decade has led to the discovery of chemically distinct families of small molecule Aurora kinase inhibitors, many of which have demonstrated therapeutic potential in model systems. These agents are also important tools to help dissect signaling pathways that are orchestrated by Aurora kinases, and the antiproliferative target of pan-Aurora inhibitors such as VX-680 has been validated using chemical genetic techniques. In many cases the nonspecific nature of Aurora inhibitors toward unrelated kinases is well established, potentially broadening the spectrum of cancers to which these compounds might be applied. However, unambiguously demonstrating the molecular target(s) for clinical kinase inhibitors is an important challenge, one that is absolutely critical for deciphering the molecular basis of compound specificity, resistance, and efficacy. In this paper, we have investigated amino acid requirements for Aurora A sensitivity to the benzazepine-based Aurora inhibitor MLN8054 and the close analogue MLN8237, a second-generation compound that is in phase II clinical trials. A crystallographic analysis facilitated the design and biochemical investigation of a panel of resistant Aurora A mutants, a subset of which were then selected as candidate drug-resistance targets for further evaluation. Using inducible human cell lines, we show that cells expressing near-physiological levels of a functional but partially drug-resistant Aurora A T217D mutant survive in the presence of MLN8054 or MLN8237, authenticating Aurora A as a critical antiproliferative target of these compounds. © 2010 American Chemical Society.
Harris C.J.,Lydith |
Hill R.D.,Chesterford Research Park |
Sheppard D.W.,Chesterford Research Park |
Slater M.J.,Cresset Group |
Combinatorial Chemistry and High Throughput Screening | Year: 2011
Target-focused compound libraries are collections of compounds which are designed to interact with an individual protein target or, frequently, a family of related targets (such as kinases, voltage-gated ion channels, serine/cysteine proteases). They are used for screening against therapeutic targets in order to find hit compounds that might be further developed into drugs. The design of such libraries generally utilizes structural information about the target or family of interest. In the absence of such structural information, a chemogenomic model that incorporates sequence and mutagenesis data to predict the properties of the binding site can be employed. A third option, usually pursued when no structural data are available, utilizes knowledge of the ligands of the target from which focused libraries can be developed via scaffold hopping. Consequently, the methods used for the design of target-focused libraries vary according to the quantity and quality of structural or ligand data that is available for each target family. This article describes examples of each of these design approaches and illustrates them with case studies, which highlight some of the issues and successes observed when screening target-focused libraries. © 2011 Bentham Science Publishers Ltd.
Kandziora N.,Leibniz University of Hanover |
Andexer J.N.,University of Cambridge |
Andexer J.N.,Albert Ludwigs University of Freiburg |
Moss S.J.,Chesterford Research Park |
And 4 more authors.
Chemical Science | Year: 2014
Formation of Z-configured double bonds in reduced polyketides is uncommon and their origins have not been extensively studied. To investigate the origin of the Z-configured double bond in the macrolide borrelidin, the recombinant dehydratase domains BorDH2 and BorDH3 were assayed with a synthetic analogue of the predicted tetraketide substrate. The configuration of the dehydrated products was determined to be E in both cases by comparison to synthetic standards. Detailed NMR spectroscopic analysis of the biosynthetic intermediate pre-borrelidin confirmed the E,E-configuration of the full-length polyketide synthase product. In contrast to a previously-proposed hypothesis, our results show that in this case the Z-configured double bond is not formed via dehydration from a 3 l-configured precursor, but rather as the result of a later isomerization process. © 2014 the Partner Organisations.
Doudou S.,University of Manchester |
Sharma R.,University of Manchester |
Henchman R.H.,University of Manchester |
Sheppard D.W.,University of Manchester |
And 2 more authors.
Journal of Chemical Information and Modeling | Year: 2010
The binding of a selection of competitive imidazo [1,2-b] pyridazine inhibitors of PIM-1 kinase with nanomolar activity has been analyzed using computational methods. Molecular dynamics simulations using umbrella sampling to determine a potential of mean force have been used to accurately predict the relative free energies of binding of these inhibitors, from -4.3 to -9.5 kcal mol-1, in excellent agreement with the trends observed in previous experimental assays. The relative activity of the inhibitors could not be accounted for by any single effect or interaction within the active site and could only be fully reproduced when the overall free energies were considered, including important contributions from interactions outside the hinge region and using explicit solvent in the active site. The potential of mean force for the displacement of the glycine-rich phosphate binding loop (P-loop) has also been estimated and shown to be an important feature in the binding of these ligands. © 2010 American Chemical Society.
Sheppard D.W.,Chesterford Research Park |
Macritchie J.A.,Chesterford Research Park
Drug Discovery Today: Technologies | Year: 2013
The use of gene-focussed libraries for screening against protein targets can improve timelines for drug discovery projects. This is especially true when the library is based on a novel core scaffold, avoiding the potential need to scaffold hop from early hits. Identification of an appropriate novel scaffold is therefore integral to the success of such a library. In this article we outline a new method to aid scaffold design that combines structure-based virtual screening (VS) with a second phase in which fragmentation of the output is made before the final scaffold design step. Through consideration of a refined set of bound fragments, in the context of the compounds from which they originated, appropriate vectors for appended R-groups can be assigned before validation of the final library. © 2012 Elsevier Ltd.
Hewings D.S.,University of Oxford |
Fedorov O.,University of Oxford |
Filippakopoulos P.,University of Oxford |
Martin S.,University of Oxford |
And 13 more authors.
Journal of Medicinal Chemistry | Year: 2013
The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested. © 2013 American Chemical Society.
Burli R.W.,Chesterford Research Park |
Haughan A.F.,Chesterford Research Park |
Hodges A.J.,Chesterford Research Park
Autoimmunity | Year: 2010
Until the recent advent of genetically engineered drugs, small molecules constituted the predominant method of treatment for autoimmune diseases. Both modalities have advantages and disadvantages; while protein-based therapeutics interfere very selectively with the function of their biological targets, they have to be administered subcutaneously or intravenously. Small molecules have the potential for oral administration. Due to their cell permeability, they can interact with extra- and intracellular targets, thus opening opportunities for interfering with novel biochemical pathways. We herein describe the preclinical stages of typical small-molecule research programmes and outline hurdles that may have to be overcome. A few examples of small molecules that are currently under clinical evaluation and arose from diverse discovery pathways will be discussed. © 2010 Informa UK, Ltd.
Bergner A.,Chesterford Research Park |
Bergner A.,Boehringer Ingelheim |
Parel S.P.,Chesterford Research Park |
Parel S.P.,Exquiron Biotech AG
Journal of Chemical Information and Modeling | Year: 2013
Ligand-based virtual screening and computational hit expansion methods undoubtedly facilitate the finding of novel active chemical entities, utilizing already existing knowledge of active compounds. It has been demonstrated that the parallel execution of complementary similarity search methods enhances the performance of such virtual screening campaigns. In this article, we examine the use of virtualized template (query, seed) structures as an extension to common search methods, such as fingerprint and pharmacophore graph-based similarity searches. We demonstrate that template virtualization by bioisosteric enumeration and other rule-based methods, in combination with standard similarity search techniques, represents a powerful approach for hit expansion following high-throughput screening campaigns. The reliability of the methods is demonstrated by four different test data sets representing different target classes and two hit finding case studies on the epigenetic targets G9a and LSD1. © 2013 American Chemical Society.