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Bradley AR, Echalier A, Fairhead M, Strain-Damerell C, Brennan P, Bullock AN, Burgess-Brown NA, Carpenter EP, Gileadi O, Marsden BD, Lee WH, Yue W, Bountra C, von Delft F. The SGC beyond structural genomics: redefining the role of 3D structures by coupling genomic stratification with fragment-based discovery. Essays Biochem 2017; 61:495-503. [PMID: 29118096 PMCID: PMC5869235 DOI: 10.1042/ebc20170051] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022]
Abstract
The ongoing explosion in genomics data has long since outpaced the capacity of conventional biochemical methodology to verify the large number of hypotheses that emerge from the analysis of such data. In contrast, it is still a gold-standard for early phenotypic validation towards small-molecule drug discovery to use probe molecules (or tool compounds), notwithstanding the difficulty and cost of generating them. Rational structure-based approaches to ligand discovery have long promised the efficiencies needed to close this divergence; in practice, however, this promise remains largely unfulfilled, for a host of well-rehearsed reasons and despite the huge technical advances spearheaded by the structural genomics initiatives of the noughties. Therefore the current, fourth funding phase of the Structural Genomics Consortium (SGC), building on its extensive experience in structural biology of novel targets and design of protein inhibitors, seeks to redefine what it means to do structural biology for drug discovery. We developed the concept of a Target Enabling Package (TEP) that provides, through reagents, assays and data, the missing link between genetic disease linkage and the development of usefully potent compounds. There are multiple prongs to the ambition: rigorously assessing targets' genetic disease linkages through crowdsourcing to a network of collaborating experts; establishing a systematic approach to generate the protocols and data that comprise each target's TEP; developing new, X-ray-based fragment technologies for generating high quality chemical matter quickly and cheaply; and exploiting a stringently open access model to build multidisciplinary partnerships throughout academia and industry. By learning how to scale these approaches, the SGC aims to make structures finally serve genomics, as originally intended, and demonstrate how 3D structures systematically allow new modes of druggability to be discovered for whole classes of targets.
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Affiliation(s)
- Anthony R Bradley
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Department of Chemistry, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K
| | - Aude Echalier
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Department of Molecular and Cell Biology, Henry Wellcome Building, Lancaster Road, Leicester LE1 7RH, U.K
| | - Michael Fairhead
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Claire Strain-Damerell
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Paul Brennan
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, U.K
| | - Alex N Bullock
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Nicola A Burgess-Brown
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Elisabeth P Carpenter
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Opher Gileadi
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Brian D Marsden
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, U.K
| | - Wen Hwa Lee
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Wyatt Yue
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Chas Bountra
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Frank von Delft
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
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152
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Current perspectives in fragment-based lead discovery (FBLD). Essays Biochem 2017; 61:453-464. [PMID: 29118093 PMCID: PMC5869234 DOI: 10.1042/ebc20170028] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 02/07/2023]
Abstract
It is over 20 years since the first fragment-based discovery projects were disclosed. The methods are now mature for most ‘conventional’ targets in drug discovery such as enzymes (kinases and proteases) but there has also been growing success on more challenging targets, such as disruption of protein–protein interactions. The main application is to identify tractable chemical startpoints that non-covalently modulate the activity of a biological molecule. In this essay, we overview current practice in the methods and discuss how they have had an impact in lead discovery – generating a large number of fragment-derived compounds that are in clinical trials and two medicines treating patients. In addition, we discuss some of the more recent applications of the methods in chemical biology – providing chemical tools to investigate biological molecules, mechanisms and systems.
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153
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Yeh TL, Leissing TM, Abboud MI, Thinnes CC, Atasoylu O, Holt-Martyn JP, Zhang D, Tumber A, Lippl K, Lohans CT, Leung IKH, Morcrette H, Clifton IJ, Claridge TDW, Kawamura A, Flashman E, Lu X, Ratcliffe PJ, Chowdhury R, Pugh CW, Schofield CJ. Molecular and cellular mechanisms of HIF prolyl hydroxylase inhibitors in clinical trials. Chem Sci 2017; 8:7651-7668. [PMID: 29435217 PMCID: PMC5802278 DOI: 10.1039/c7sc02103h] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023] Open
Abstract
Inhibition of the human 2-oxoglutarate (2OG) dependent hypoxia inducible factor (HIF) prolyl hydroxylases (human PHD1-3) causes upregulation of HIF, thus promoting erythropoiesis and is therefore of therapeutic interest. We describe cellular, biophysical, and biochemical studies comparing four PHD inhibitors currently in clinical trials for anaemia treatment, that describe their mechanisms of action, potency against isolated enzymes and in cells, and selectivities versus representatives of other human 2OG oxygenase subfamilies. The 'clinical' PHD inhibitors are potent inhibitors of PHD catalyzed hydroxylation of the HIF-α oxygen dependent degradation domains (ODDs), and selective against most, but not all, representatives of other human 2OG dependent dioxygenase subfamilies. Crystallographic and NMR studies provide insights into the different active site binding modes of the inhibitors. Cell-based results reveal the inhibitors have similar effects on the upregulation of HIF target genes, but differ in the kinetics of their effects and in extent of inhibition of hydroxylation of the N- and C-terminal ODDs; the latter differences correlate with the biophysical observations.
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Affiliation(s)
- Tzu-Lan Yeh
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Thomas M Leissing
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Martine I Abboud
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Cyrille C Thinnes
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Onur Atasoylu
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - James P Holt-Martyn
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Dong Zhang
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Anthony Tumber
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
| | - Kerstin Lippl
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher T Lohans
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Ivanhoe K H Leung
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Helen Morcrette
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Ian J Clifton
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Timothy D W Claridge
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Akane Kawamura
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
- Radcliffe Department of Medicine , Division of Cardiovascular Medicine , BHF Centre of Research Excellence , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - Emily Flashman
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Xin Lu
- Ludwig Institute for Cancer Research , Nuffield Department of Clinical Medicine , University of Oxford , Oxford OX3 7DQ , UK
| | - Peter J Ratcliffe
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
- The Francis Crick Institute , 1 Midland Road , London NW1 1AT , UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
| | - Christopher W Pugh
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , NDMRB Roosevelt Drive , Oxford OX3 7FZ , UK
| | - Christopher J Schofield
- Chemistry Research Laboratory , Department of Chemistry , University of Oxford , Oxford OX1 3TA , UK .
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154
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Schapira M, Tyers M, Torrent M, Arrowsmith CH. WD40 repeat domain proteins: a novel target class? Nat Rev Drug Discov 2017; 16:773-786. [PMID: 29026209 PMCID: PMC5975957 DOI: 10.1038/nrd.2017.179] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Antagonism of protein-protein interactions (PPIs) with small molecules is becoming more feasible as a therapeutic approach. Successful PPI inhibitors tend to target proteins containing deep peptide-binding grooves or pockets rather than the more common large, flat protein interaction surfaces. Here, we review one of the most abundant PPI domains in the human proteome, the WD40 repeat (WDR) domain, which has a central peptide-binding pocket and is a member of the β-propeller domain-containing protein family. Recently, two WDR domain-containing proteins, WDR5 and EED, as well as other β-propeller domains have been successfully targeted by potent, specific, cell-active, drug-like chemical probes. Could WDR domains be a novel target class for drug discovery? Although the research is at an early stage and therefore not clinically validated, cautious optimism is justified, as WDR domain-containing proteins are involved in multiple disease-associated pathways. The druggability and structural diversity of WDR domain binding pockets suggest that understanding how to target this prevalent domain class will open up areas of disease biology that have so far resisted drug discovery efforts.
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Affiliation(s)
- Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Mount Sinai Hospital, The Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Maricel Torrent
- Discovery Research, AbbVie, Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, 101 College St., Toronto, ON M5G 1L7, Canada
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155
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Harding RJ, Ferreira de Freitas R, Collins P, Franzoni I, Ravichandran M, Ouyang H, Juarez-Ornelas KA, Lautens M, Schapira M, von Delft F, Santhakumar V, Arrowsmith CH. Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin. J Med Chem 2017; 60:9090-9096. [DOI: 10.1021/acs.jmedchem.7b00933] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rachel J. Harding
- Structural
Genomics Consortium, University of Toronto, MaRS South Tower, Suite 700, 101
College Street, Toronto, Ontario M5G 1L7, Canada
| | - Renato Ferreira de Freitas
- Structural
Genomics Consortium, University of Toronto, MaRS South Tower, Suite 700, 101
College Street, Toronto, Ontario M5G 1L7, Canada
| | - Patrick Collins
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K
| | - Ivan Franzoni
- Department
of Chemistry, Davenport Chemical Laboratories, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mani Ravichandran
- Structural
Genomics Consortium, University of Toronto, MaRS South Tower, Suite 700, 101
College Street, Toronto, Ontario M5G 1L7, Canada
| | - Hui Ouyang
- GrandPharma, Wuhan City Plaza, 23rd Floor, 160
Qiaokou Road, Wuhan, Hubei 430032, China
| | - Kevin A. Juarez-Ornelas
- Department
of Chemistry, Davenport Chemical Laboratories, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mark Lautens
- Department
of Chemistry, Davenport Chemical Laboratories, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Matthieu Schapira
- Structural
Genomics Consortium, University of Toronto, MaRS South Tower, Suite 700, 101
College Street, Toronto, Ontario M5G 1L7, Canada
- Department
of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, U.K
- Structural
Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, U.K
| | - Vjayaratnam Santhakumar
- Structural
Genomics Consortium, University of Toronto, MaRS South Tower, Suite 700, 101
College Street, Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H. Arrowsmith
- Structural
Genomics Consortium, University of Toronto, MaRS South Tower, Suite 700, 101
College Street, Toronto, Ontario M5G 1L7, Canada
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156
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Foley DJ, Craven PGE, Collins PM, Doveston RG, Aimon A, Talon R, Churcher I, von Delft F, Marsden SP, Nelson A. Synthesis and Demonstration of the Biological Relevance of sp 3 -rich Scaffolds Distantly Related to Natural Product Frameworks. Chemistry 2017; 23:15227-15232. [PMID: 28983993 PMCID: PMC5703167 DOI: 10.1002/chem.201704169] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 12/18/2022]
Abstract
The productive exploration of chemical space is an enduring challenge in chemical biology and medicinal chemistry. Natural products are biologically relevant, and their frameworks have facilitated chemical tool and drug discovery. A "top-down" synthetic approach is described that enabled a range of complex bridged intermediates to be converted with high step efficiency into 26 diverse sp3 -rich scaffolds. The scaffolds have local natural product-like features, but are only distantly related to specific natural product frameworks. To assess biological relevance, a set of 52 fragments was prepared, and screened by high-throughput crystallography against three targets from two protein families (ATAD2, BRD1 and JMJD2D). In each case, 3D fragment hits were identified that would serve as distinctive starting points for ligand discovery. This demonstrates that frameworks that are distantly related to natural products can facilitate discovery of new biologically relevant regions within chemical space.
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Affiliation(s)
- Daniel J. Foley
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Philip G. E. Craven
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Patrick M. Collins
- Diamond Light Source LtdHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Richard G. Doveston
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Anthony Aimon
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Romain Talon
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of Oxford, Roosevelt DriveOxfordOX3 7DQUK
| | - Ian Churcher
- GlaxoSmithKline Medicines Research CentreStevenageSG1 2NYUK,BenevolentBio, ChurchwayLondonNW1 1LWUK
| | - Frank von Delft
- Diamond Light Source LtdHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of Oxford, Roosevelt DriveOxfordOX3 7DQUK
| | | | - Adam Nelson
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
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157
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Helliwell JR. New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences. Biosci Rep 2017; 37:BSR20170204. [PMID: 28572170 PMCID: PMC6434086 DOI: 10.1042/bsr20170204] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 'small molecule' crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography's role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.
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158
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Thomas SE, Mendes V, Kim SY, Malhotra S, Ochoa-Montaño B, Blaszczyk M, Blundell TL. Structural Biology and the Design of New Therapeutics: From HIV and Cancer to Mycobacterial Infections: A Paper Dedicated to John Kendrew. J Mol Biol 2017; 429:2677-2693. [PMID: 28648615 DOI: 10.1016/j.jmb.2017.06.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
Abstract
Interest in applications of protein crystallography to medicine was evident, as the first high-resolution structures emerged in the 50s and 60s. In Cambridge, Max Perutz and John Kendrew sought to understand mutations in sickle cell and other genetic diseases related to hemoglobin, while in Oxford, the group of Dorothy Hodgkin became interested in long-lasting zinc-insulin crystals for treatment of diabetes and later considered insulin redesign, as synthetic insulins became possible. The use of protein crystallography in structure-guided drug discovery emerged as enzyme structures allowed the identification of potential inhibitor-binding sites and optimization of interactions of hits using the structure of the target protein. Early examples of this approach were the use of the structure of renin to design antihypertensives and the structure of HIV protease in design of AIDS antivirals. More recently, use of structure-guided design with fragment-based drug discovery, which reduces the size of screening libraries by decreasing complexity, has improved ligand efficiency in drug design and has been used to progress three oncology drugs through clinical trials to FDA approval. We exemplify current developments in structure-guided target identification and fragment-based lead discovery with efforts to develop new antimicrobials for mycobacterial infections.
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Affiliation(s)
- Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - So Yeon Kim
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Bernardo Ochoa-Montaño
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Michal Blaszczyk
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA UK.
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159
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Mylona A, Carr S, Aller P, Moraes I, Treisman R, Evans G, Foadi J. A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software. CRYSTALS 2017; 7:242. [PMID: 29456874 PMCID: PMC5813789 DOI: 10.3390/cryst7080242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences.
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Affiliation(s)
- Anastasia Mylona
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stephen Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford OX11 0FA, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Pierre Aller
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Isabel Moraes
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Richard Treisman
- Signalling and Transcription Laboratory, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - James Foadi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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160
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Affiliation(s)
- Xavier Barril
- a Facultat de Farmacia and Institut de Biomedicina (IBUB) , Universitat de Barcelona , Barcelona , Spain.,b Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona , Spain
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161
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Blundell TL. Protein crystallography and drug discovery: recollections of knowledge exchange between academia and industry. IUCRJ 2017; 4:308-321. [PMID: 28875019 PMCID: PMC5571795 DOI: 10.1107/s2052252517009241] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 06/20/2017] [Indexed: 05/19/2023]
Abstract
The development of structure-guided drug discovery is a story of knowledge exchange where new ideas originate from all parts of the research ecosystem. Dorothy Crowfoot Hodgkin obtained insulin from Boots Pure Drug Company in the 1930s and insulin crystallization was optimized in the company Novo in the 1950s, allowing the structure to be determined at Oxford University. The structure of renin was developed in academia, on this occasion in London, in response to a need to develop antihypertensives in pharma. The idea of a dimeric aspartic protease came from an international academic team and was discovered in HIV; it eventually led to new HIV antivirals being developed in industry. Structure-guided fragment-based discovery was developed in large pharma and biotechs, but has been exploited in academia for the development of new inhibitors targeting protein-protein interactions and also antimicrobials to combat mycobacterial infections such as tuberculosis. These observations provide a strong argument against the so-called 'linear model', where ideas flow only in one direction from academic institutions to industry. Structure-guided drug discovery is a story of applications of protein crystallography and knowledge exhange between academia and industry that has led to new drug approvals for cancer and other common medical conditions by the Food and Drug Administration in the USA, as well as hope for the treatment of rare genetic diseases and infectious diseases that are a particular challenge in the developing world.
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Affiliation(s)
- Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, England
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