1
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Godoy AS, Nakamura AM, Douangamath A, Song Y, Noske GD, Gawriljuk VO, Fernandes RS, Pereira H, Oliveira K, Fearon D, Dias A, Krojer T, Fairhead M, Powell A, Dunnet L, Brandao-Neto J, Skyner R, Chalk R, Bajusz D, Bege M, Borbás A, Keserű GM, von Delft F, Oliva G. Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res 2023; 51:5255-5270. [PMID: 37115000 PMCID: PMC10250223 DOI: 10.1093/nar/gkad314] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors.
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Affiliation(s)
- Andre Schutzer Godoy
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Aline Minalli Nakamura
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Yun Song
- Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
| | - Gabriela Dias Noske
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Victor Oliveira Gawriljuk
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Rafaela Sachetto Fernandes
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Humberto D Muniz Pereira
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Ketllyn Irene Zagato Oliveira
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
| | - Daren Fearon
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Alexandre Dias
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Tobias Krojer
- BioMAX, MAX IV Laboratory, Fotongatan 2, Lund 224 84, Sweden
| | - Michael Fairhead
- Centre for Medicines Discovery, Oxford University, Oxford OX1 3QU, UK
| | - Alisa Powell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Louise Dunnet
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Jose Brandao-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Rachael Skyner
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Rod Chalk
- Centre for Medicines Discovery, Oxford University, Oxford OX1 3QU, UK
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Miklós Bege
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Molecular Recognition and Interaction Research Group, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Anikó Borbás
- Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- National Laboratory of Virology, University of Pécs, Ifjúság útja 20, H-7624 Pécs, Hungary
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- Centre for Medicines Discovery, Oxford University, Oxford OX1 3QU, UK
- Department of Biochemistry, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Glaucius Oliva
- Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil
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2
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Weiss MS, Wollenhaupt J, Correy GJ, Fraser JS, Heine A, Klebe G, Krojer T, Thunissen M, Pearce NM. Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data. Protein Sci 2022; 31:e4391. [PMID: 36040268 PMCID: PMC9424839 DOI: 10.1002/pro.4391] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/17/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022]
Abstract
In their recent commentary in Protein Science, Jaskolski et al. analyzed three randomly picked diffraction data sets from fragment-screening group depositions from the PDB and, based on that, they claimed that such data are principally problematic. We demonstrate here that if such data are treated properly, none of the proclaimed criticisms persist.
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Affiliation(s)
- Manfred S. Weiss
- Macromolecular CrystallographyHelmholtz‐Zentrum BerlinBerlinGermany
| | - Jan Wollenhaupt
- Macromolecular CrystallographyHelmholtz‐Zentrum BerlinBerlinGermany
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic SciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic SciencesUniversity of California San FranciscoSan FranciscoCaliforniaUSA
| | - Andreas Heine
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarburgGermany
| | - Gerhard Klebe
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarburgGermany
| | | | | | - Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical SciencesVU AmsterdamAmsterdamThe Netherlands
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3
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Mackinnon SR, Bezerra GA, Krojer T, Szommer T, von Delft F, Brennan PE, Yue WW. Novel Starting Points for Human Glycolate Oxidase Inhibitors, Revealed by Crystallography-Based Fragment Screening. Front Chem 2022; 10:844598. [PMID: 35601556 PMCID: PMC9114433 DOI: 10.3389/fchem.2022.844598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Primary hyperoxaluria type I (PH1) is caused by AGXT gene mutations that decrease the functional activity of alanine:glyoxylate aminotransferase. A build-up of the enzyme’s substrate, glyoxylate, results in excessive deposition of calcium oxalate crystals in the renal tract, leading to debilitating renal failure. Oxidation of glycolate by glycolate oxidase (or hydroxy acid oxidase 1, HAO1) is a major cellular source of glyoxylate, and siRNA studies have shown phenotypic rescue of PH1 by the knockdown of HAO1, representing a promising inhibitor target. Here, we report the discovery and optimization of six low-molecular-weight fragments, identified by crystallography-based fragment screening, that bind to two different sites on the HAO1 structure: at the active site and an allosteric pocket above the active site. The active site fragments expand known scaffolds for substrate-mimetic inhibitors to include more chemically attractive molecules. The allosteric fragments represent the first report of non-orthosteric inhibition of any hydroxy acid oxidase and hold significant promise for improving inhibitor selectivity. The fragment hits were verified to bind and inhibit HAO1 in solution by fluorescence-based activity assay and surface plasmon resonance. Further optimization cycle by crystallography and biophysical assays have generated two hit compounds of micromolar (44 and 158 µM) potency that do not compete with the substrate and provide attractive starting points for the development of potent and selective HAO1 inhibitors.
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Affiliation(s)
- Sabrina R. Mackinnon
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gustavo A. Bezerra
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tobias Krojer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Tamas Szommer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Frank von Delft
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Paul E. Brennan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
- *Correspondence: Paul E. Brennan, ; Wyatt W. Yue,
| | - Wyatt W. Yue
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- *Correspondence: Paul E. Brennan, ; Wyatt W. Yue,
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Pearce NM, Skyner R, Krojer T. Experiences From Developing Software for Large X-Ray Crystallography-Driven Protein-Ligand Studies. Front Mol Biosci 2022; 9:861491. [PMID: 35480897 PMCID: PMC9035521 DOI: 10.3389/fmolb.2022.861491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
The throughput of macromolecular X-ray crystallography experiments has surged over the last decade. This remarkable gain in efficiency has been facilitated by increases in the availability of high-intensity X-ray beams, (ultra)fast detectors and high degrees of automation. These developments have in turn spurred the development of several dedicated centers for crystal-based fragment screening which enable the preparation and collection of hundreds of single-crystal diffraction datasets per day. Crystal structures of target proteins in complex with small-molecule ligands are of immense importance for structure-based drug design (SBDD) and their rapid turnover is a prerequisite for accelerated development cycles. While the experimental part of the process is well defined and has by now been established at several synchrotron sites, it is noticeable that software and algorithmic aspects have received far less attention, as well as the implications of new methodologies on established paradigms for structure determination, analysis, and visualization. We will review three key areas of development of large-scale protein-ligand studies. First, we will look into new software developments for batch data processing, followed by a discussion of the methodological changes in the analysis, modeling, refinement and deposition of structures for SBDD, and the changes in mindset that these new methods require, both on the side of depositors and users of macromolecular models. Finally, we will highlight key new developments for the presentation and analysis of the collections of structures that these experiments produce, and provide an outlook for future developments.
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Affiliation(s)
- Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, Netherlands
- *Correspondence: Nicholas M. Pearce,
| | - Rachael Skyner
- OMass Therapeutics, The Oxford Science Park, Oxford, United Kingdom
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5
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Kozielski F, Sele C, Talibov VO, Lou J, Dong D, Wang Q, Shi X, Nyblom M, Rogstam A, Krojer T, Fisher Z, Knecht W. Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16. RSC Chem Biol 2022; 3:44-55. [PMID: 35128408 PMCID: PMC8729259 DOI: 10.1039/d1cb00135c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022] Open
Abstract
Since the emergence of SARS-CoV-2 in 2019, Covid-19 has developed into a serious threat to our health, social and economic systems. Although vaccines have been developed in a tour-de-force and are now increasingly available, repurposing of existing drugs has been less successful. There is a clear need to develop new drugs against SARS-CoV-2 that can also be used against future coronavirus infections. Non-structural protein 10 (nsp10) is a conserved stimulator of two enzymes crucial for viral replication, nsp14 and nsp16, exhibiting exoribonuclease and methyltransferase activities. Interfering with RNA proofreading or RNA cap formation represents intervention strategies to inhibit replication. We applied fragment-based screening using nano differential scanning fluorometry and X-ray crystallography to identify ligands targeting SARS-CoV-2 nsp10. We identified four fragments located in two distinct sites: one can be modelled to where it would be located in the nsp14-nsp10 complex interface and the other in the nsp16-nsp10 complex interface. Microscale thermophoresis (MST) experiments were used to quantify fragment affinities for nsp10. Additionally, we showed by MST that the interaction by nsp14 and 10 is weak and thereby that complex formation could be disrupted by small molecules. The fragments will serve as starting points for the development of more potent analogues using fragment growing techniques and structure-based drug design.
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Affiliation(s)
- Frank Kozielski
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Céleste Sele
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | | | - Jiaqi Lou
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Danni Dong
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Qian Wang
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Xinyue Shi
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Maria Nyblom
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | - Annika Rogstam
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
| | - Tobias Krojer
- BioMAX beamline, MAX IV Laboratory Fotongatan 2 22484 Lund Sweden
| | - Zoë Fisher
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
- European Spallation Source ERIC P.O. Box 176 22100 Lund Sweden +46 721792250
| | - Wolfgang Knecht
- Department of Biology & Lund Protein Production Platform, Lund University Sölvegatan 35 22362 Lund Sweden +46 46 2227785
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Piticchio SG, Martínez-Cartró M, Scaffidi S, Rachman M, Rodriguez-Arevalo S, Sanchez-Arfelis A, Escolano C, Picaud S, Krojer T, Filippakopoulos P, von Delft F, Galdeano C, Barril X. Discovery of Novel BRD4 Ligand Scaffolds by Automated Navigation of the Fragment Chemical Space. J Med Chem 2021; 64:17887-17900. [PMID: 34898210 DOI: 10.1021/acs.jmedchem.1c01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Fragment-based drug discovery (FBDD) is a very effective hit identification method. However, the evolution of fragment hits into suitable leads remains challenging and largely artisanal. Fragment evolution is often scaffold-centric, meaning that its outcome depends crucially on the chemical structure of the starting fragment. Considering that fragment screening libraries cover only a small proportion of the corresponding chemical space, hits should be seen as probes highlighting privileged areas of the chemical space rather than actual starting points. We have developed an automated computational pipeline to mine the chemical space around any specific fragment hit, rapidly finding analogues that share a common interaction motif but are structurally novel and diverse. On a prospective application on the bromodomain-containing protein 4 (BRD4), starting from a known fragment, the platform yields active molecules with nonobvious scaffold changes. The procedure is fast and inexpensive and has the potential to uncover many hidden opportunities in FBDD.
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Affiliation(s)
- Serena G Piticchio
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Míriam Martínez-Cartró
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Salvatore Scaffidi
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Moira Rachman
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sergio Rodriguez-Arevalo
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Ainoa Sanchez-Arfelis
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Carmen Escolano
- Laboratory of Medicinal Chemistry (Associated Unit to CSIC), Department of Pharmacology, Toxicology and Medicinal Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Sarah Picaud
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, Nuffield Department of Medicine, Oxford University, Old Road Campus Research Building, Roosevelt Drive, OX3 7DQ Oxford, United Kingdom.,Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom.,Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, United Kingdom.,Centre for Medicines Discovery, University of Oxford, Oxford OX1 3QU, United Kingdom.,Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Carles Galdeano
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain
| | - Xavier Barril
- Departament de Farmacia i Tecnología Farmacèutica, i Fisicoquímica, Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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Jansen J, Reimer KC, Nagai JS, Varghese FS, Overheul GJ, de Beer M, Roverts R, Daviran D, Fermin LA, Willemsen B, Beukenboom M, Djudjaj S, von Stillfried S, van Eijk LE, Mastik M, Bulthuis M, Dunnen WD, van Goor H, Hillebrands JL, Triana SH, Alexandrov T, Timm MC, van den Berge BT, van den Broek M, Nlandu Q, Heijnert J, Bindels EM, Hoogenboezem RM, Mooren F, Kuppe C, Miesen P, Grünberg K, Ijzermans T, Steenbergen EJ, Czogalla J, Schreuder MF, Sommerdijk N, Akiva A, Boor P, Puelles VG, Floege J, Huber TB, van Rij RP, Costa IG, Schneider RK, Smeets B, Kramann R, Achdout H, Aimon A, Bar-David E, Barr H, Ben-Shmuel A, Bennett J, Boby ML, Borden B, Bowman GR, Brun J, BVNBS S, Calmiano M, Carbery A, Cattermole E, Chernychenko E, Choder JD, Clyde A, Coffland JE, Cohen G, Cole J, Contini A, Cox L, Cvitkovic M, Dias A, Donckers K, Dotson DL, Douangamath A, Duberstein S, Dudgeon T, Dunnett L, Eastman PK, Erez N, Eyermann CJ, Fairhead M, Fate G, Fearon D, Federov O, Ferla M, Fernandes RS, Ferrins L, Foster R, Foster H, Gabizon R, Garcia-Sastre A, Gawriljuk VO, Gehrtz P, Gileadi C, Giroud C, Glass WG, Glen R, Itai glinert, Godoy AS, Gorichko M, Gorrie-Stone T, Griffen EJ, Hart SH, Heer J, Henry M, Hill M, Horrell S, Hurley MF, Israely T, Jajack A, Jnoff E, Jochmans D, John T, De Jonghe S, Kantsadi AL, Kenny PW, Kiappes J, Koekemoer L, Kovar B, Krojer T, Lee AA, Lefker BA, Levy H, London N, Lukacik P, Macdonald HB, Maclean B, Malla TR, Matviiuk T, McCorkindale W, McGovern BL, Melamed S, Michurin O, Mikolajek H, Milne BF, Morris A, Morris GM, Morwitzer MJ, Moustakas D, Nakamura AM, Neto JB, Neyts J, Nguyen L, Noske GD, Oleinikovas V, Oliva G, Overheul GJ, Owen D, Psenak V, Pai R, Pan J, Paran N, Perry B, Pingle M, Pinjari J, Politi B, Powell A, Puni R, Rangel VL, Reddi RN, Reid SP, Resnick E, Ripka EG, Robinson MC, Robinson RP, Rodriguez-Guerra J, Rosales R, Rufa D, Schofield C, Shafeev M, Shaikh A, Shi J, Shurrush K, Sing S, Sittner A, Skyner R, Smalley A, Smilova MD, Solmesky LJ, Spencer J, Strain-Damarell C, Swamy V, Tamir H, Tennant R, Thompson W, Thompson A, Thompson W, Tomasia S, Tumber A, Vakonakis I, van Rij RP, van Geel L, Varghese FS, Vaschetto M, Vitner EB, Voelz V, Volkamer A, von Delft F, von Delft A, Walsh M, Ward W, Weatherall C, Weiss S, White KM, Wild CF, Wittmann M, Wright N, Yahalom-Ronen Y, Zaidmann D, Zidane H, Zitzmann N. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids. Cell Stem Cell 2021; 29:217-231.e8. [PMID: 35032430 PMCID: PMC8709832 DOI: 10.1016/j.stem.2021.12.010] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 09/03/2021] [Accepted: 12/16/2021] [Indexed: 12/20/2022]
Abstract
Kidney failure is frequently observed during and after COVID-19, but it remains elusive whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects kidney cells and is associated with increased tubule-interstitial kidney fibrosis in patient autopsy samples. To study direct effects of the virus on the kidney independent of systemic effects of COVID-19, we infected human-induced pluripotent stem-cell-derived kidney organoids with SARS-CoV-2. Single-cell RNA sequencing indicated injury and dedifferentiation of infected cells with activation of profibrotic signaling pathways. Importantly, SARS-CoV-2 infection also led to increased collagen 1 protein expression in organoids. A SARS-CoV-2 protease inhibitor was able to ameliorate the infection of kidney cells by SARS-CoV-2. Our results suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury with subsequent fibrosis. These data could explain both acute kidney injury in COVID-19 patients and the development of chronic kidney disease in long COVID. COVID-19 patients present tubulo-interstitial kidney fibrosis compared with controls SARS-CoV-2 infection stimulates profibrotic signaling in human kidney organoids SARS-CoV-2 infection can be inhibited by a protease blocker in human kidney organoids
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Krojer T. Updates from FragMAX, a crystallographic fragment screening platform at MAX IV Laboratory. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321085172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Gonzalez A, Aurelius O, Bjelčić M, Eguiraun M, Gorgisyan I, Jagudin E, Kanchugal S, Krojer T, Milas M, Nan J, Ursby T. The BioMAX beamline for macromolecular crystallography at MAX IV. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321085226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Wollenhaupt J, Barthel T, Metz A, Lima GMA, Wallacher D, Jagudin E, Krojer T, Feiler CG, Heine A, Mueller U, Klebe G, Weiss MS. Efficiently from library to hit – crystallographic fragment screening in Berlin via structurally diverse compound libraries. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321091261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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11
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Douangamath A, Powell A, Fearon D, Collins PM, Talon R, Krojer T, Skyner R, Brandao-Neto J, Dunnett L, Dias A, Aimon A, Pearce NM, Wild C, Gorrie-Stone T, von Delft F. Achieving Efficient Fragment Screening at XChem Facility at Diamond Light Source. J Vis Exp 2021. [PMID: 34125095 DOI: 10.3791/62414] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In fragment-based drug discovery, hundreds or often thousands of compounds smaller than ~300 Da are tested against the protein of interest to identify chemical entities that can be developed into potent drug candidates. Since the compounds are small, interactions are weak, and the screening method must therefore be highly sensitive; moreover, structural information tends to be crucial for elaborating these hits into lead-like compounds. Therefore, protein crystallography has always been a gold-standard technique, yet historically too challenging to find widespread use as a primary screen. Initial XChem experiments were demonstrated in 2014 and then trialed with academic and industrial collaborators to validate the process. Since then, a large research effort and significant beamtime have streamlined sample preparation, developed a fragment library with rapid follow-up possibilities, automated and improved the capability of I04-1 beamline for unattended data collection, and implemented new tools for data management, analysis and hit identification. XChem is now a facility for large-scale crystallographic fragment screening, supporting the entire crystals-to-deposition process, and accessible to academic and industrial users worldwide. The peer-reviewed academic user program has been actively developed since 2016, to accommodate projects from as broad a scientific scope as possible, including well-validated as well as exploratory projects. Academic access is allocated through biannual calls for peer-reviewed proposals, and proprietary work is arranged by Diamond's Industrial Liaison group. This workflow has already been routinely applied to over a hundred targets from diverse therapeutic areas, and effectively identifies weak binders (1%-30% hit rate), which both serve as high-quality starting points for compound design and provide extensive structural information on binding sites. The resilience of the process was demonstrated by continued screening of SARS-CoV-2 targets during the COVID-19 pandemic, including a 3-week turn-around for the main protease.
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Affiliation(s)
- Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Ailsa Powell
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Daren Fearon
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Patrick M Collins
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Romain Talon
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus; Structural Genomics Consortium, University of Oxford
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford; Centre for Medicines Discovery, University of Oxford
| | - Rachael Skyner
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Jose Brandao-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Louise Dunnett
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Alexandre Dias
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus
| | - Anthony Aimon
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus; Structural Genomics Consortium, University of Oxford
| | - Nicholas M Pearce
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Structural Genomics Consortium, University of Oxford
| | - Conor Wild
- Structural Genomics Consortium, University of Oxford; Oxford Protein Informatics Group, Department of Statistics, Oxford University
| | | | - Frank von Delft
- Diamond Light Source Ltd, Harwell Science and Innovation Campus; Research Complex at Harwell, Harwell Science and Innovation Campus; Structural Genomics Consortium, University of Oxford; Centre for Medicines Discovery, University of Oxford; Department of Biochemistry, University of Johannesburg;
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12
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Mackinnon S, Krojer T, Foster WR, Diaz-Saez L, Tang M, Huber KVM, von Delft F, Lai K, Brennan PE, Arruda Bezerra G, Yue WW. Fragment Screening Reveals Starting Points for Rational Design of Galactokinase 1 Inhibitors to Treat Classic Galactosemia. ACS Chem Biol 2021; 16:586-595. [PMID: 33724769 PMCID: PMC8056384 DOI: 10.1021/acschembio.0c00498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 02/18/2021] [Indexed: 11/28/2022]
Abstract
Classic galactosemia is caused by loss-of-function mutations in galactose-1-phosphate uridylyltransferase (GALT) that lead to toxic accumulation of its substrate, galactose-1-phosphate. One proposed therapy is to inhibit the biosynthesis of galactose-1-phosphate, catalyzed by galactokinase 1 (GALK1). Existing inhibitors of human GALK1 (hGALK1) are primarily ATP-competitive with limited clinical utility to date. Here, we determined crystal structures of hGALK1 bound with reported ATP-competitive inhibitors of the spiro-benzoxazole series, to reveal their binding mode in the active site. Spurred by the need for additional chemotypes of hGALK1 inhibitors, desirably targeting a nonorthosteric site, we also performed crystallography-based screening by soaking hundreds of hGALK1 crystals, already containing active site ligands, with fragments from a custom library. Two fragments were found to bind close to the ATP binding site, and a further eight were found in a hotspot distal from the active site, highlighting the strength of this method in identifying previously uncharacterized allosteric sites. To generate inhibitors of improved potency and selectivity targeting the newly identified binding hotspot, new compounds were designed by merging overlapping fragments. This yielded two micromolar inhibitors of hGALK1 that were not competitive with respect to either substrate (ATP or galactose) and demonstrated good selectivity over hGALK1 homologues, galactokinase 2 and mevalonate kinase. Our findings are therefore the first to demonstrate inhibition of hGALK1 from an allosteric site, with potential for further development of potent and selective inhibitors to provide novel therapeutics for classic galactosemia.
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Affiliation(s)
- Sabrina
R. Mackinnon
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Tobias Krojer
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - William R. Foster
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Laura Diaz-Saez
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Manshu Tang
- Department
of Pediatrics, University of Utah, Salt Lake City, Utah 84108-6500, United States
| | - Kilian V. M. Huber
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Frank von Delft
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Diamond
Light Source, Harwell Science and Innovation
Campus, Didcot, Oxfordshire, United Kingdom, OX11 0DE
| | - Kent Lai
- Department
of Pediatrics, University of Utah, Salt Lake City, Utah 84108-6500, United States
| | - Paul E. Brennan
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
- Target
Discovery Institute, University of Oxford, Oxford, United Kingdom, OX3 7FZ
| | - Gustavo Arruda Bezerra
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
| | - Wyatt W. Yue
- Structural
Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, OX3 7DQ
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13
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Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Carvalho Martins L, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, Aimon A, Bennett JM, Brandao Neto J, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs MR, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rack JGM, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, O'Brien P, Jura N, Ashworth A, Irwin JJ, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Sci Adv 2021; 7:eabf8711. [PMID: 33853786 PMCID: PMC8046379 DOI: 10.1126/sciadv.abf8711] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/24/2021] [Indexed: 05/19/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate-ribosylation signaling. This enzyme is a promising antiviral target because catalytic mutations render viruses nonpathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of 2533 diverse fragments resulted in 214 unique macrodomain-binders. An additional 60 molecules were selected from docking more than 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several fragment hits were confirmed by solution binding using three biophysical techniques (differential scanning fluorimetry, homogeneous time-resolved fluorescence, and isothermal titration calorimetry). The 234 fragment structures explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA
| | - Iris D Young
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Luan Carvalho Martins
- Biochemistry Department, Institute for Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Dominique H Smith
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ursula Schulze-Gahmen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Tristan W Owens
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Ishan Deshpande
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Gregory E Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Aye C Thwin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Justin T Biel
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jessica K Peters
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michelle Moritz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nadia Herrera
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Huong T Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, San Francisco, CA 94158, USA
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - James M Bennett
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
| | - Jose Brandao Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
| | - Matteo P Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Martin R Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Tyler J Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Tobias Krojer
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - George Meigs
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ailsa J Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | | | - Victor L Rangel
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, São Paulo, Brazil
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Rachael E Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexei S Soares
- Photon Sciences, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Jennifer L Wierman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Natalia Jura
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, San Francisco, CA 94158, USA
| | - John J Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Biochemistry, University of California Merced, Merced, CA 95343, USA
| | - Jason E Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
- Institute for Neurodegenerative Disease, University of California San Francisco, San Francisco, CA 94158, USA
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA UK
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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14
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Ferreira IM, Quesñay JEN, Bastos AC, Rodrigues CT, Vollmar M, Krojer T, Strain-Damerell C, Burgess-Brown NA, von Delft F, Yue WW, Dias SM, Ambrosio AL. Structure and activation mechanism of the human liver-type glutaminase GLS2. Biochimie 2021; 185:96-104. [PMID: 33746066 PMCID: PMC8130709 DOI: 10.1016/j.biochi.2021.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/23/2021] [Accepted: 03/14/2021] [Indexed: 11/24/2022]
Abstract
Cancer cells exhibit an altered metabolic phenotype, consuming higher levels of the amino acid glutamine. This metabolic reprogramming depends on increased mitochondrial glutaminase activity to convert glutamine to glutamate, an essential precursor for bioenergetic and biosynthetic processes in cells. Mammals encode the kidney-type (GLS) and liver-type (GLS2) glutaminase isozymes. GLS is overexpressed in cancer and associated with enhanced malignancy. On the other hand, GLS2 is either a tumor suppressor or an oncogene, depending on the tumor type. The GLS structure and activation mechanism are well known, while the structural determinants for GLS2 activation remain elusive. Here, we describe the structure of the human glutaminase domain of GLS2, followed by the functional characterization of the residues critical for its activity. Increasing concentrations of GLS2 lead to tetramer stabilization, a process enhanced by phosphate. In GLS2, the so-called “lid loop” is in a rigid open conformation, which may be related to its higher affinity for phosphate and lower affinity for glutamine; hence, it has lower glutaminase activity than GLS. The lower affinity of GLS2 for glutamine is also related to its less electropositive catalytic site than GLS, as indicated by a Thr225Lys substitution within the catalytic site decreasing the GLS2 glutamine concentration corresponding to half-maximal velocity (K0.5). Finally, we show that the Lys253Ala substitution (corresponding to the Lys320Ala in the GLS “activation” loop, formerly known as the “gating” loop) renders a highly active protein in stable tetrameric form. We conclude that the “activation” loop, a known target for GLS inhibition, may also be a drug target for GLS2. A positive cooperative mechanism of activation is demonstrated for the liver-type glutaminase. The novel crystal structure for the glutaminase domain of human GLS2 is presented. Site-directed mutagenesis suggest the activation loop as a hotspot for inhibitor design.
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Affiliation(s)
- Igor M Ferreira
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Sao Paulo, Zip Code, 13083-970, Brazil
| | - José Edwin N Quesñay
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Sao Paulo, Zip Code, 13083-970, Brazil; Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, SP, Zip Code, 13563-120, Brazil
| | - Alliny Cs Bastos
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Sao Paulo, Zip Code, 13083-970, Brazil; Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Camila T Rodrigues
- Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, SP, Zip Code, 13563-120, Brazil
| | - Melanie Vollmar
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Claire Strain-Damerell
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK; Diamond Light Source Ltd., The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA, UK
| | - Nicola A Burgess-Brown
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK; Diamond Light Source Ltd., The Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA, UK; Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Wyatt W Yue
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.
| | - Sandra Mg Dias
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Sao Paulo, Zip Code, 13083-970, Brazil.
| | - Andre Lb Ambrosio
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Sao Paulo, Zip Code, 13083-970, Brazil; Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, SP, Zip Code, 13563-120, Brazil.
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15
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Wright ND, Collins P, Koekemoer L, Krojer T, Talon R, Nelson E, Ye M, Nowak R, Newman J, Ng JT, Mitrovich N, Wiggers H, von Delft F. The low-cost Shifter microscope stage transforms the speed and robustness of protein crystal harvesting. Acta Crystallogr D Struct Biol 2021; 77:62-74. [PMID: 33404526 PMCID: PMC7787106 DOI: 10.1107/s2059798320014114] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 10/22/2020] [Indexed: 12/05/2022] Open
Abstract
Despite the tremendous success of X-ray cryo-crystallography in recent decades, the transfer of crystals from the drops in which they are grown to diffractometer sample mounts remains a manual process in almost all laboratories. Here, the Shifter, a motorized, interactive microscope stage that transforms the entire crystal-mounting workflow from a rate-limiting manual activity to a controllable, high-throughput semi-automated process, is described. By combining the visual acuity and fine motor skills of humans with targeted hardware and software automation, it was possible to transform the speed and robustness of crystal mounting. Control software, triggered by the operator, manoeuvres crystallization plates beneath a clear protective cover, allowing the complete removal of film seals and thereby eliminating the tedium of repetitive seal cutting. The software, either upon request or working from an imported list, controls motors to position crystal drops under a hole in the cover for human mounting at a microscope. The software automatically captures experimental annotations for uploading to the user's data repository, removing the need for manual documentation. The Shifter facilitates mounting rates of 100-240 crystals per hour in a more controlled process than manual mounting, which greatly extends the lifetime of the drops and thus allows a dramatic increase in the number of crystals retrievable from any given drop without loss of X-ray diffraction quality. In 2015, the first in a series of three Shifter devices was deployed as part of the XChem fragment-screening facility at Diamond Light Source, where they have since facilitated the mounting of over 120 000 crystals. The Shifter was engineered to have a simple design, providing a device that could be readily commercialized and widely adopted owing to its low cost. The versatile hardware design allows use beyond fragment screening and protein crystallography.
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Affiliation(s)
- Nathan David Wright
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Patrick Collins
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Lizbé Koekemoer
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Romain Talon
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
| | - Elliot Nelson
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Mingda Ye
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Radosław Nowak
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Joseph Newman
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Jia Tsing Ng
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Nick Mitrovich
- Oxford Lab Technologies Ltd, Kemp House, 160 City Road, London EC1V 2N, United Kingdom
| | - Helton Wiggers
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- I04-1, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom
- Faculty of Science, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
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16
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Khan Tareque R, Hassell-Hart S, Krojer T, Bradley A, Velupillai S, Talon R, Fairhead M, Day IJ, Bala K, Felix R, Kemmitt PD, Brennan P, von Delft F, Díaz Sáez L, Huber K, Spencer J. Deliberately Losing Control of C-H Activation Processes in the Design of Small-Molecule-Fragment Arrays Targeting Peroxisomal Metabolism. ChemMedChem 2020; 15:2513-2520. [PMID: 32812371 DOI: 10.1002/cmdc.202000543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 12/16/2022]
Abstract
Combined photochemical arylation, "nuisance effect" (SN Ar) reaction sequences have been employed in the design of small arrays for immediate deployment in medium-throughput X-ray protein-ligand structure determination. Reactions were deliberately allowed to run "out of control" in terms of selectivity; for example the ortho-arylation of 2-phenylpyridine gave five products resulting from mono- and bisarylations combined with SN Ar processes. As a result, a number of crystallographic hits against NUDT7, a key peroxisomal CoA ester hydrolase, have been identified.
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Affiliation(s)
- Raysa Khan Tareque
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Storm Hassell-Hart
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Tobias Krojer
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Anthony Bradley
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Romain Talon
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Michael Fairhead
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iain J Day
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Kamlesh Bala
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
| | - Robert Felix
- Bio-Techne (Tocris Bioscience), The Watkins Building, Atlantic Road Avonmouth, Bristol, BS11 9QD, UK
| | - Paul D Kemmitt
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB10 1XL, UK
| | - Paul Brennan
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Frank von Delft
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot, Oxford, OX11 0DE, UK
- Department of Biochemistry, University of Johannesburg, Johannesburg, Auckland Park, 2006, South Africa
| | - Laura Díaz Sáez
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Kilian Huber
- Structural Genomics Consortium (SGC), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - John Spencer
- Chemistry Deparment, University of Sussex, Falmer, East Sussex, BN1 9QJ, UK
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17
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Krojer T, Fraser JS, von Delft F. Discovery of allosteric binding sites by crystallographic fragment screening. Curr Opin Struct Biol 2020; 65:209-216. [PMID: 33171388 PMCID: PMC10979522 DOI: 10.1016/j.sbi.2020.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 02/02/2023]
Abstract
Understanding allosteric regulation of proteins is fundamental to our study of protein structure and function. Moreover, allosteric binding pockets have become a major target of drug discovery efforts in recent years. However, even though the function of almost every protein can be influenced by allostery, it remains a challenge to discover, rationalise and validate putative allosteric binding pockets. This review examines how the discovery and analysis of putative allosteric binding sites have been influenced by the availability of centralised facilities for crystallographic fragment screening, along with newly developed computational methods for modelling low occupancy features. We discuss the experimental parameters required for success, and how new methods could influence the field in the future. Finally, we reflect on the general problem of how to translate these findings into actual ligand development programs.
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Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK; Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK; Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa.
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18
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Schuller M, Correy GJ, Gahbauer S, Fearon D, Wu T, Díaz RE, Young ID, Martins LC, Smith DH, Schulze-Gahmen U, Owens TW, Deshpande I, Merz GE, Thwin AC, Biel JT, Peters JK, Moritz M, Herrera N, Kratochvil HT, Aimon A, Bennett JM, Neto JB, Cohen AE, Dias A, Douangamath A, Dunnett L, Fedorov O, Ferla MP, Fuchs M, Gorrie-Stone TJ, Holton JM, Johnson MG, Krojer T, Meigs G, Powell AJ, Rangel VL, Russi S, Skyner RE, Smith CA, Soares AS, Wierman JL, Zhu K, Jura N, Ashworth A, Irwin J, Thompson MC, Gestwicki JE, von Delft F, Shoichet BK, Fraser JS, Ahel I. Fragment Binding to the Nsp3 Macrodomain of SARS-CoV-2 Identified Through Crystallographic Screening and Computational Docking. bioRxiv 2020:2020.11.24.393405. [PMID: 33269349 PMCID: PMC7709169 DOI: 10.1101/2020.11.24.393405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The SARS-CoV-2 macrodomain (Mac1) within the non-structural protein 3 (Nsp3) counteracts host-mediated antiviral ADP-ribosylation signalling. This enzyme is a promising antiviral target because catalytic mutations render viruses non-pathogenic. Here, we report a massive crystallographic screening and computational docking effort, identifying new chemical matter primarily targeting the active site of the macrodomain. Crystallographic screening of diverse fragment libraries resulted in 214 unique macrodomain-binding fragments, out of 2,683 screened. An additional 60 molecules were selected from docking over 20 million fragments, of which 20 were crystallographically confirmed. X-ray data collection to ultra-high resolution and at physiological temperature enabled assessment of the conformational heterogeneity around the active site. Several crystallographic and docking fragment hits were validated for solution binding using three biophysical techniques (DSF, HTRF, ITC). Overall, the 234 fragment structures presented explore a wide range of chemotypes and provide starting points for development of potent SARS-CoV-2 macrodomain inhibitors.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Taiasean Wu
- Institute for Neurodegenerative Disease, University of California San Francisco, CA, USA
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, CA, USA
| | - Roberto Efraín Díaz
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
- Tetrad Graduate Program, University of California San Francisco, CA, USA
| | - Iris D. Young
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Luan Carvalho Martins
- Biochemistry Department, Institute for Biological Sciences, Federal University of Minas Gerais. Belo Horizonte, Brazil
| | - Dominique H. Smith
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA, USA
| | - Ursula Schulze-Gahmen
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Tristan W. Owens
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Ishan Deshpande
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Gregory E. Merz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Aye C. Thwin
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Justin T. Biel
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Jessica K. Peters
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Michelle Moritz
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Nadia Herrera
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Huong T. Kratochvil
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - QCRG Structural Biology Consortium
- Quantitative Biosciences Institute (QBI) Coronavirus Research Group Structural Biology Consortium, University of California San Francisco, CA, USA
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James M. Bennett
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
| | - Jose Brandao Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
| | - Matteo P. Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Martin Fuchs
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Tyler J. Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Tobias Krojer
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - George Meigs
- Department of Biochemistry and Biophysics, University of California San Francisco, CA, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ailsa J. Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | | | - Victor L Rangel
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- School of Pharmaceutical Sciences of Ribeirao Preto, University of Sao Paulo, São Paulo, Brazil
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Rachael E. Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Clyde A. Smith
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | | | - Jennifer L. Wierman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Natalia Jura
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, CA, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA, USA
| | - John Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA, USA
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
- Institute for Neurodegenerative Disease, University of California San Francisco, CA, USA
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Centre for Medicines Discovery, University of Oxford, South Parks Road, Headington, OX3 7DQ, UK
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco San Francisco, CA, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, USA
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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19
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Douangamath A, Fearon D, Gehrtz P, Krojer T, Lukacik P, Owen CD, Resnick E, Strain-Damerell C, Aimon A, Ábrányi-Balogh P, Brandão-Neto J, Carbery A, Davison G, Dias A, Downes TD, Dunnett L, Fairhead M, Firth JD, Jones SP, Keeley A, Keserü GM, Klein HF, Martin MP, Noble MEM, O'Brien P, Powell A, Reddi RN, Skyner R, Snee M, Waring MJ, Wild C, London N, von Delft F, Walsh MA. Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease. Nat Commun 2020; 11:5047. [PMID: 33028810 PMCID: PMC7542442 DOI: 10.1038/s41467-020-18709-w] [Citation(s) in RCA: 292] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments were progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.
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Affiliation(s)
- Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Paul Gehrtz
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Petra Lukacik
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - C David Owen
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Efrat Resnick
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Claire Strain-Damerell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Anna Carbery
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Gemma Davison
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Alexandre Dias
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Thomas D Downes
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael Fairhead
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - James D Firth
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - S Paul Jones
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Aaron Keeley
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - György M Keserü
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, H-1117, Budapest, Hungary
| | - Hanna F Klein
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Mathew P Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Martin E M Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Paul O'Gorman Building, Medical School, Framlington Place, Newcastle University, Newcastle upon Tyne, NE2 4AD, UK
| | - Peter O'Brien
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Ailsa Powell
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Rambabu N Reddi
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Matthew Snee
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Michael J Waring
- Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer, Chemistry, School of Natural and Environmental Sciences, Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Conor Wild
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Nir London
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.
- Department of Biochemistry, University of Johannesburg, Auckland Park, 2006, South Africa.
| | - Martin A Walsh
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK.
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
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20
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Kidd SL, Fowler E, Reinhardt T, Compton T, Mateu N, Newman H, Bellini D, Talon R, McLoughlin J, Krojer T, Aimon A, Bradley A, Fairhead M, Brear P, Díaz-Sáez L, McAuley K, Sore HF, Madin A, O'Donovan DH, Huber KVM, Hyvönen M, von Delft F, Dowson CG, Spring DR. Demonstration of the utility of DOS-derived fragment libraries for rapid hit derivatisation in a multidirectional fashion. Chem Sci 2020; 11:10792-10801. [PMID: 34094333 PMCID: PMC8162264 DOI: 10.1039/d0sc01232g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/14/2020] [Indexed: 12/26/2022] Open
Abstract
Organic synthesis underpins the evolution of weak fragment hits into potent lead compounds. Deficiencies within current screening collections often result in the requirement of significant synthetic investment to enable multidirectional fragment growth, limiting the efficiency of the hit evolution process. Diversity-oriented synthesis (DOS)-derived fragment libraries are constructed in an efficient and modular fashion and thus are well-suited to address this challenge. To demonstrate the effective nature of such libraries within fragment-based drug discovery, we herein describe the screening of a 40-member DOS library against three functionally distinct biological targets using X-Ray crystallography. Firstly, we demonstrate the importance for diversity in aiding hit identification with four fragment binders resulting from these efforts. Moreover, we also exemplify the ability to readily access a library of analogues from cheap commercially available materials, which ultimately enabled the exploration of a minimum of four synthetic vectors from each molecule. In total, 10-14 analogues of each hit were rapidly accessed in three to six synthetic steps. Thus, we showcase how DOS-derived fragment libraries enable efficient hit derivatisation and can be utilised to remove the synthetic limitations encountered in early stage fragment-based drug discovery.
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Affiliation(s)
- Sarah L Kidd
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Elaine Fowler
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Till Reinhardt
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Thomas Compton
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Natalia Mateu
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Hector Newman
- School of Life Sciences, University of Warwick Coventry UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
| | - Dom Bellini
- School of Life Sciences, University of Warwick Coventry UK
| | - Romain Talon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
| | - Joseph McLoughlin
- Department of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Tobias Krojer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford UK
| | - Anthony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
| | - Anthony Bradley
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
| | - Michael Fairhead
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
| | - Paul Brear
- Department of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Laura Díaz-Sáez
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford UK
| | - Katherine McAuley
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
| | - Hannah F Sore
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Andrew Madin
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | | | - Kilian V M Huber
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot OX11 0QX UK
- Structural Genomics Consortium (SGC), University of Oxford Oxford OX3 7DQ UK
- Department of Biochemistry, University of Johannesburg Auckland Park 2006 South Africa
| | | | - David R Spring
- Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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21
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Hassell-Hart S, Runcie A, Krojer T, Doyle J, Lineham E, Ocasio CA, Neto BAD, Fedorov O, Marsh G, Maple H, Felix R, Banks R, Ciulli A, Picaud S, Filippakopoulos P, von Delft F, Brennan P, Stewart HJS, Chevassut TJ, Walker M, Austin C, Morley S, Spencer J. Synthesis and Biological Investigation of (+)-JD1, an Organometallic BET Bromodomain Inhibitor. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00750] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Storm Hassell-Hart
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
| | - Andrew Runcie
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH Scotland, U.K
| | - Tobias Krojer
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | - Jordan Doyle
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
| | - Ella Lineham
- Biochemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QQ, U.K
| | - Cory A. Ocasio
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
| | - Brenno A. D. Neto
- Laboratory of Medicinal and Technological Chemistry, University of Brasília, Chemistry Institute (IQ-UnB), Campus Universitário Darcy
Ribeiro, Brasília, Q3 Distrito Federal 70904-970, Brazil
| | - Oleg Fedorov
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | - Graham Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Hannah Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Robert Felix
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Rebecca Banks
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road,
Avonmouth, Bristol BS11 9QD, U.K
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH Scotland, U.K
| | - Sarah Picaud
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | | | - Frank von Delft
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K
| | - Paul Brennan
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, U.K
| | - Helen J. S. Stewart
- Brighton and Sussex Medical School, University of Sussex, Brighton BN1 9PS, U.K
| | | | - Martin Walker
- Eurofins Integrated Discovery UK Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, U.K
| | - Carol Austin
- Eurofins Integrated Discovery UK Ltd., Fyfield Business & Research Park, Fyfield Road, Ongar, Essex CM5 0GS, U.K
| | - Simon Morley
- Biochemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QQ, U.K
| | - John Spencer
- Chemistry Department, School of Life Sciences, University of Sussex, Brighton BN1 9QJ, U.K
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22
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Pfeffer I, Brewitz L, Krojer T, Jensen SA, Kochan GT, Kershaw NJ, Hewitson KS, McNeill LA, Kramer H, Münzel M, Hopkinson RJ, Oppermann U, Handford PA, McDonough MA, Schofield CJ. Aspartate/asparagine-β-hydroxylase crystal structures reveal an unexpected epidermal growth factor-like domain substrate disulfide pattern. Nat Commun 2019; 10:4910. [PMID: 31659163 PMCID: PMC6817910 DOI: 10.1038/s41467-019-12711-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/26/2019] [Indexed: 01/18/2023] Open
Abstract
AspH is an endoplasmic reticulum (ER) membrane-anchored 2-oxoglutarate oxygenase whose C-terminal oxygenase and tetratricopeptide repeat (TPR) domains present in the ER lumen. AspH catalyses hydroxylation of asparaginyl- and aspartyl-residues in epidermal growth factor-like domains (EGFDs). Here we report crystal structures of human AspH, with and without substrate, that reveal substantial conformational changes of the oxygenase and TPR domains during substrate binding. Fe(II)-binding by AspH is unusual, employing only two Fe(II)-binding ligands (His679/His725). Most EGFD structures adopt an established fold with a conserved Cys1–3, 2–4, 5–6 disulfide bonding pattern; an unexpected Cys3–4 disulfide bonding pattern is observed in AspH-EGFD substrate complexes, the catalytic relevance of which is supported by studies involving stable cyclic peptide substrate analogues and by effects of Ca(II) ions on activity. The results have implications for EGFD disulfide pattern processing in the ER and will enable medicinal chemistry efforts targeting human 2OG oxygenases. AspH catalyses hydroxylation of asparagine and aspartate residues in epidermal growth factor-like domains (EGFDs). Here, the authors present crystal structures of AspH with and without substrates and show that AspH uses EFGD substrates with a non-canonical disulfide pattern.
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Affiliation(s)
- Inga Pfeffer
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Sacha A Jensen
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Grazyna T Kochan
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Nadia J Kershaw
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsty S Hewitson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Luke A McNeill
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Holger Kramer
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford, OX1 3QX, UK
| | - Martin Münzel
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK.,NDORMS, Botnar Research Centre, University of Oxford, Old Road, Oxford, OX3 7LD, UK
| | - Penny A Handford
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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23
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Resnick E, Bradley A, Gan J, Douangamath A, Krojer T, Sethi R, Geurink PP, Aimon A, Amitai G, Bellini D, Bennett J, Fairhead M, Fedorov O, Gabizon R, Gan J, Guo J, Plotnikov A, Reznik N, Ruda GF, Díaz-Sáez L, Straub VM, Szommer T, Velupillai S, Zaidman D, Zhang Y, Coker AR, Dowson CG, Barr HM, Wang C, Huber KVM, Brennan PE, Ovaa H, von Delft F, London N. Rapid Covalent-Probe Discovery by Electrophile-Fragment Screening. J Am Chem Soc 2019; 141:8951-8968. [PMID: 31060360 PMCID: PMC6556873 DOI: 10.1021/jacs.9b02822] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covalent probes can display unmatched potency, selectivity, and duration of action; however, their discovery is challenging. In principle, fragments that can irreversibly bind their target can overcome the low affinity that limits reversible fragment screening, but such electrophilic fragments were considered nonselective and were rarely screened. We hypothesized that mild electrophiles might overcome the selectivity challenge and constructed a library of 993 mildly electrophilic fragments. We characterized this library by a new high-throughput thiol-reactivity assay and screened them against 10 cysteine-containing proteins. Highly reactive and promiscuous fragments were rare and could be easily eliminated. In contrast, we found hits for most targets. Combining our approach with high-throughput crystallography allowed rapid progression to potent and selective probes for two enzymes, the deubiquitinase OTUB2 and the pyrophosphatase NUDT7. No inhibitors were previously known for either. This study highlights the potential of electrophile-fragment screening as a practical and efficient tool for covalent-ligand discovery.
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Affiliation(s)
| | - Anthony Bradley
- 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
| | | | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus , Didcot OX11 0QX , U.K
| | | | - Ritika Sethi
- Structural Biology Research Center , VIB , Brussels , Belgium.,Structural Biology Brussels , Vrije Universiteit Brussel , Brussels , Belgium
| | - Paul P Geurink
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Anthony Aimon
- 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
| | | | - Dom Bellini
- School of Life Sciences , University of Warwick , Coventry , U.K
| | | | | | | | | | - Jin Gan
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Jingxu Guo
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | | | | | | | | | | | - Alun R Coker
- Division of Medicine , University College London , Gower Street , London WC1E 6BT , U.K
| | | | | | | | | | - Paul E Brennan
- School of Life Sciences , University of Warwick , Coventry , U.K.,Alzheimer's Research UK Oxford Drug Discovery Institute , University of Oxford , NDMRB, Roosevelt Drive , Oxford OX3 7FZ , U.K
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology , Leiden University Medical Center , Einthovenweg 20 , 2333 ZC Leiden , The Netherlands
| | - Frank von Delft
- 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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24
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Pfeiffer M, Johansson C, Krojer T, Kavanagh KL, Oppermann U, Nidetzky B. A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase. ACS Catal 2019; 9:2962-2968. [PMID: 30984471 PMCID: PMC6454399 DOI: 10.1021/acscatal.9b00064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/22/2019] [Indexed: 01/25/2023]
Abstract
![]()
Biosynthesis
of 6-deoxy sugars, including l-fucose, involves
a mechanistically complex, enzymatic 4,6-dehydration of hexose nucleotide
precursors as the first committed step. Here, we determined pre- and
postcatalytic complex structures of the human GDP-mannose 4,6-dehydratase
at atomic resolution. These structures together with results of molecular
dynamics simulation and biochemical characterization of wildtype and
mutant enzymes reveal elusive mechanistic details of water elimination
from GDP-mannose C5″ and C6″, coupled to NADP-mediated
hydride transfer from C4″ to C6″. We show that concerted
acid–base catalysis from only two active-site groups, Tyr179 and Glu157, promotes a syn 1,4-elimination
from an enol (not an enolate) intermediate. We also show that the
overall multistep catalytic reaction involves the fewest position
changes of enzyme and substrate groups and that it proceeds under
conserved exploitation of the basic (minimal) catalytic machinery
of short-chain dehydrogenase/reductases.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
| | - Catrine Johansson
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Kathryn L Kavanagh
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
- Botnar Research Centre, University of Oxford, Oxford OX3 7LD, United Kingdom
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, 79085 Freiburg, Germany
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, 8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology, 8010 Graz, Austria
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25
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Pearce NM, Bradley AR, Krojer T, Marsden BD, Deane CM, von Delft F. Partial-occupancy binders identified by the Pan-Dataset Density Analysis method offer new chemical opportunities and reveal cryptic binding sites. Struct Dyn 2017; 4:032104. [PMID: 28345007 PMCID: PMC5336473 DOI: 10.1063/1.4974176] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
Crystallographic fragment screening uses low molecular weight compounds to probe the protein surface and although individual protein-fragment interactions are high quality, fragments commonly bind at low occupancy, historically making identification difficult. However, our new Pan-Dataset Density Analysis method readily identifies binders missed by conventional analysis: for fragment screening data of lysine-specific demethylase 4D (KDM4D), the hit rate increased from 0.9% to 10.6%. Previously unidentified fragments reveal multiple binding sites and demonstrate: the versatility of crystallographic fragment screening; that surprisingly large conformational changes are possible in crystals; and that low crystallographic occupancy does not by itself reflect a protein-ligand complex's significance.
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Affiliation(s)
| | - Anthony R Bradley
- Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, United Kingdom
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, United Kingdom
| | | | - Charlotte M Deane
- Department of Statistics, University of Oxford , 24-29 St Giles, Oxford OX1 3LB, United Kingdom
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26
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Collins PM, Ng JT, Talon R, Nekrosiute K, Krojer T, Douangamath A, Brandao-Neto J, Wright N, Pearce NM, von Delft F. Gentle, fast and effective crystal soaking by acoustic dispensing. Acta Crystallogr D Struct Biol 2017; 73:246-255. [PMID: 28291760 PMCID: PMC5349437 DOI: 10.1107/s205979831700331x] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/28/2017] [Indexed: 01/25/2023]
Abstract
A high-throughput method is described for crystal soaking using acoustic droplet ejection, and its effectiveness is demonstrated. The steady expansion in the capacity of modern beamlines for high-throughput data collection, enabled by increasing X-ray brightness, capacity of robotics and detector speeds, has pushed the bottleneck upstream towards sample preparation. Even in ligand-binding studies using crystal soaking, the experiment best able to exploit beamline capacity, a primary limitation is the need for gentle and nontrivial soaking regimens such as stepwise concentration increases, even for robust and well characterized crystals. Here, the use of acoustic droplet ejection for the soaking of protein crystals with small molecules is described, and it is shown that it is both gentle on crystals and allows very high throughput, with 1000 unique soaks easily performed in under 10 min. In addition to having very low compound consumption (tens of nanolitres per sample), the positional precision of acoustic droplet ejection enables the targeted placement of the compound/solvent away from crystals and towards drop edges, allowing gradual diffusion of solvent across the drop. This ensures both an improvement in the reproducibility of X-ray diffraction and increased solvent tolerance of the crystals, thus enabling higher effective compound-soaking concentrations. The technique is detailed here with examples from the protein target JMJD2D, a histone lysine demethylase with roles in cancer and the focus of active structure-based drug-design efforts.
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Affiliation(s)
- Patrick M Collins
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Jia Tsing Ng
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, England
| | - Romain Talon
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, England
| | - Karolina Nekrosiute
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tobias Krojer
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, England
| | - Alice Douangamath
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Jose Brandao-Neto
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Nathan Wright
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, England
| | - Nicholas M Pearce
- Structural Genomics Consortium (SGC), University of Oxford, Oxford OX3 7DQ, England
| | - Frank von Delft
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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27
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Pearce NM, Krojer T, von Delft F. Proper modelling of ligand binding requires an ensemble of bound and unbound states. Acta Crystallogr D Struct Biol 2017; 73:256-266. [PMID: 28291761 PMCID: PMC5349438 DOI: 10.1107/s2059798317003412] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/01/2017] [Indexed: 12/01/2022] Open
Abstract
Although noncovalent binding by small molecules cannot be assumed a priori to be stoichiometric in the crystal lattice, occupancy refinement of ligands is often avoided by convention. Occupancies tend to be set to unity, requiring the occupancy error to be modelled by the B factors, and residual weak density around the ligand is necessarily attributed to `disorder'. Where occupancy refinement is performed, the complementary, superposed unbound state is rarely modelled. Here, it is shown that superior accuracy is achieved by modelling the ligand as partially occupied and superposed on a ligand-free `ground-state' model. Explicit incorporation of this model of the crystal, obtained from a reference data set, allows constrained occupancy refinement with minimal fear of overfitting. Better representation of the crystal also leads to more meaningful refined atomic parameters such as the B factor, allowing more insight into dynamics in the crystal. An outline of an approach for algorithmically generating ensemble models of crystals is presented, assuming that data sets representing the ground state are available. The applicability of various electron-density metrics to the validation of the resulting models is assessed, and it is concluded that ensemble models consistently score better than the corresponding single-state models. Furthermore, it appears that ignoring the superposed ground state becomes the dominant source of model error, locally, once the overall model is accurate enough; modelling the local ground state properly is then more meaningful than correcting all remaining model errors globally, especially for low-occupancy ligands. Implications for the simultaneous refinement of B factors and occupancies, and for future evaluation of the limits of the approach, in particular its behaviour at lower data resolution, are discussed.
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Affiliation(s)
- Nicholas M. Pearce
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Aukland Park, Johannesburg 2006, South Africa
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28
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Krojer T, Talon R, Pearce N, Collins P, Douangamath A, Brandao-Neto J, Dias A, Marsden B, von Delft F. The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination. Acta Crystallogr D Struct Biol 2017; 73:267-278. [PMID: 28291762 PMCID: PMC5349439 DOI: 10.1107/s2059798316020234] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/20/2016] [Indexed: 11/11/2022] Open
Abstract
XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.
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Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Romain Talon
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Nicholas Pearce
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Patrick Collins
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Alice Douangamath
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Jose Brandao-Neto
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Alexandre Dias
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
| | - Brian Marsden
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford OX3 7FY, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
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29
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Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop. Structure 2016; 24:502-508. [PMID: 27050687 DOI: 10.1016/j.str.2016.02.017] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 02/24/2016] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
Abstract
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.
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Affiliation(s)
- Paul D Adams
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley Laboratory, Department of Bioengineering, UC Berkeley, Berkeley, CA 94720-8235, USA
| | | | - Cary Bauer
- Bruker AXS, Inc., Madison, WI 53711, USA
| | | | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Talapady N Bhat
- Biosystems and Biomaterials Division, NIST, Gaithersburg, MD 20899, USA
| | | | - Evan Bolton
- National Center for Biotechnology Information, U.S. National Library of Medicine, Bethesda, MD 20894, USA
| | | | - David Brown
- School of Biosciences, University of Kent, Canterbury CT2 7NH, UK; Charles River Ltd., Structural Biology and Biophysics, Cambridge CB10 1XL, UK
| | - Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kirk L Clark
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Tom Darden
- OpenEye Scientific, Cambridge, MA 02142, USA
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Victoria A Feher
- Drug Design Data Resource and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Colin R Groom
- Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, UK.
| | | | - Jorg Hendle
- Structural Biology, Lilly Biotechnology Center, San Diego, CA 92121, USA
| | | | - Andrzej Joachimiak
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gerard J Kleywegt
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Joseph Marcotrigiano
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Alan E Mark
- School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
| | - John L Markley
- BioMagResBank, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706-1544, USA
| | - Matthew Miller
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA
| | - Gaetano T Montelione
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Atsushi Nakagawa
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Haruki Nakamura
- Protein Data Bank Japan, Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | | | - Marc Nicklaus
- Computer-Aided Drug Design Group, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | | | | | | | - Susan Pieniazek
- Bristol-Myers Squibb Research and Development, Pennington, NJ 08534, USA
| | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Steven Sheriff
- Bristol-Myers Squibb Research and Development, Princeton, NJ 08543, USA
| | - Oliver Smart
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - John Spurlino
- Janssen Pharmaceuticals, Inc., Spring House, PA 19002, USA
| | - Terry Stouch
- Science For Solutions, LLC, West Windsor, NJ 08550, USA
| | - Radka Svobodova
- CEITEC-Central European Institute of Technology and National Centre for Biomolecular Research, Masaryk University Brno, 625 00 Brno, Czech Republic
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | | | - Dale Tronrud
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Sameer Velankar
- Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Suzanna C Ward
- Cambridge Crystallographic Data Centre, Cambridge CB2 1EZ, UK
| | | | - John D Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Huanwang Yang
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jasmine Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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30
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Lobley CMC, Sandy J, Sanchez-Weatherby J, Mazzorana M, Krojer T, Nowak RP, Sorensen TL. A generic protocol for protein crystal dehydration using the HC1b humidity controller. Acta Crystallogr D Struct Biol 2016; 72:629-40. [PMID: 27139626 PMCID: PMC4854313 DOI: 10.1107/s2059798316003065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/21/2016] [Indexed: 11/11/2022]
Abstract
Dehydration may change the crystal lattice and affect the mosaicity, resolution and quality of X-ray diffraction data. A dehydrating environment can be generated around a crystal in several ways with various degrees of precision and complexity. This study uses a high-precision crystal humidifier/dehumidifier to provide an airstream of known relative humidity in which the crystals are mounted: a precise yet hassle-free approach to altering crystal hydration. A protocol is introduced to assess the impact of crystal dehydration systematically applied to nine experimental crystal systems. In one case, that of glucose isomerase, dehydration triggering a change of space group from I222 to P21212 was observed. This observation is supported by an extended study of the behaviour of the glucose isomerase crystal structure during crystal dehydration.
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Affiliation(s)
- Carina M C Lobley
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - James Sandy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | | | - Marco Mazzorana
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7DQ, England
| | - Radosław P Nowak
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7DQ, England
| | - Thomas L Sorensen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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31
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Pike ACW, Garman EF, Krojer T, von Delft F, Carpenter EP. An overview of heavy-atom derivatization of protein crystals. Acta Crystallogr D Struct Biol 2016; 72:303-18. [PMID: 26960118 PMCID: PMC4784662 DOI: 10.1107/s2059798316000401] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 01/08/2016] [Indexed: 11/11/2022] Open
Abstract
Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative.
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Affiliation(s)
- Ashley C. W. Pike
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Elspeth F. Garman
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England
- Department of Biochemistry, University of Johannesburg, Aukland Park 2006, South Africa
| | - Elisabeth P. Carpenter
- Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX11 9HP, England
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32
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Cox OB, Krojer T, Collins P, Monteiro O, Talon R, Bradley A, Fedorov O, Amin J, Marsden BD, Spencer J, von Delft F, Brennan PE. A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem Sci 2016; 7:2322-2330. [PMID: 29910922 PMCID: PMC5977933 DOI: 10.1039/c5sc03115j] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/21/2015] [Indexed: 01/08/2023] Open
Abstract
Research into the chemical biology of bromodomains has been driven by the development of acetyl-lysine mimetics. The ligands are typically anchored by binding to a highly conserved asparagine residue. Atypical bromodomains, for which the asparagine is mutated, have thus far proven elusive targets, including PHIP(2) whose parent protein, PHIP, has been linked to disease progression in diabetes and cancers. The PHIP(2) binding site contains a threonine in place of asparagine, and solution screening have yielded no convincing hits. We have overcome this hurdle by combining the sensitivity of X-ray crystallography, used as the primary fragment screen, with a strategy for rapid follow-up synthesis using a chemically-poised fragment library, which allows hits to be readily modified by parallel chemistry both peripherally and in the core. Our approach yielded the first reported hit compounds of PHIP(2) with measurable IC50 values by an AlphaScreen competition assay. The follow-up libraries of four poised fragment hits improved potency into the sub-mM range while showing good ligand efficiency and detailed structural data.
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Affiliation(s)
- Oakley B Cox
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , Oxford OX3 7FZ , UK .
- Diamond Light Source (DLS) , Harwell Science and Innovation Campus , Didcot , OX11 0DE , UK .
| | - Tobias Krojer
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
| | - Patrick Collins
- Diamond Light Source (DLS) , Harwell Science and Innovation Campus , Didcot , OX11 0DE , UK .
| | - Octovia Monteiro
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , Oxford OX3 7FZ , UK .
| | - Romain Talon
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
| | - Anthony Bradley
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
| | - Oleg Fedorov
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , Oxford OX3 7FZ , UK .
| | - Jahangir Amin
- Department of Chemistry , School of Life Sciences , University of Sussex , Brighton , BN1 9QJ , UK
| | - Brian D Marsden
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
- Kennedy Institute of Rheumatology , Nuffield Department of Orthopaedics , Rheumatology and Musculoskeletal Sciences , University of Oxford , Roosevelt Drive, Headington , Oxford OX3 7FY , UK
| | - John Spencer
- Department of Chemistry , School of Life Sciences , University of Sussex , Brighton , BN1 9QJ , UK
| | - Frank von Delft
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
- Diamond Light Source (DLS) , Harwell Science and Innovation Campus , Didcot , OX11 0DE , UK .
- Department of Biochemistry , University of Johannesburg , Aukland Park 2006 , South Africa
| | - Paul E Brennan
- Structural Genomics Consortium (SGC) , University of Oxford , Oxford OX3 7DQ , UK
- Target Discovery Institute (TDI) , Nuffield Department of Medicine , University of Oxford , Oxford OX3 7FZ , UK .
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33
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Bavetsias V, Lanigan RM, Ruda GF, Atrash B, McLaughlin MG, Tumber A, Mok NY, Le Bihan YV, Dempster S, Boxall K, Jeganathan F, Hatch SB, Savitsky P, Velupillai S, Krojer T, England K, Sejberg J, Thai C, Donovan A, Pal A, Scozzafava G, Bennett J, Kawamura A, Johansson C, Szykowska A, Gileadi C, Burgess-Brown N, von Delft F, Oppermann U, Walters Z, Shipley J, Raynaud FI, Westaway SM, Prinjha RK, Fedorov O, Burke R, Schofield C, Westwood IM, Bountra C, Müller S, van Montfort RL, Brennan PE, Blagg J. 8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors. J Med Chem 2016; 59:1388-409. [PMID: 26741168 PMCID: PMC4770324 DOI: 10.1021/acs.jmedchem.5b01635] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Indexed: 11/29/2022]
Abstract
We report the discovery of N-substituted 4-(pyridin-2-yl)thiazole-2-amine derivatives and their subsequent optimization, guided by structure-based design, to give 8-(1H-pyrazol-3-yl)pyrido[3,4-d]pyrimidin-4(3H)-ones, a series of potent JmjC histone N-methyl lysine demethylase (KDM) inhibitors which bind to Fe(II) in the active site. Substitution from C4 of the pyrazole moiety allows access to the histone peptide substrate binding site; incorporation of a conformationally constrained 4-phenylpiperidine linker gives derivatives such as 54j and 54k which demonstrate equipotent activity versus the KDM4 (JMJD2) and KDM5 (JARID1) subfamily demethylases, selectivity over representative exemplars of the KDM2, KDM3, and KDM6 subfamilies, cellular permeability in the Caco-2 assay, and, for 54k, inhibition of H3K9Me3 and H3K4Me3 demethylation in a cell-based assay.
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Affiliation(s)
- Vassilios Bavetsias
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Rachel M. Lanigan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Gian Filippo Ruda
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Butrus Atrash
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Mark G. McLaughlin
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Anthony Tumber
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - N. Yi Mok
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Yann-Vaï Le Bihan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Sally Dempster
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Katherine
J. Boxall
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Fiona Jeganathan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Stephanie B. Hatch
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Pavel Savitsky
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Srikannathasan Velupillai
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Tobias Krojer
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Katherine
S. England
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jimmy Sejberg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Ching Thai
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Adam Donovan
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Akos Pal
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Giuseppe Scozzafava
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James
M. Bennett
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Catrine Johansson
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Aleksandra Szykowska
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Carina Gileadi
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Nicola
A. Burgess-Brown
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Frank von Delft
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, U.K.
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Udo Oppermann
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Botnar Research
Centre, NIHR Oxford Biomedical Research
Unit, Oxford OX3 7LD, U.K.
| | - Zoe Walters
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Janet Shipley
- Divisions of Molecular Pathology and Cancer
Therapeutics, The Institute of Cancer Research, London SM2 5NG, U.K.
| | - Florence I. Raynaud
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Susan M. Westaway
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Rab K. Prinjha
- Epinova Discovery Performance Unit, Medicines
Research Centre, GlaxoSmithKline R&D, Stevenage SG1 2NY, U.K.
| | - Oleg Fedorov
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | | | - Isaac M. Westwood
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Chas Bountra
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
| | - Susanne Müller
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Rob L.
M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
| | - Paul E. Brennan
- Structural Genomics
Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, U.K.
- Target Discovery Institute (TDI), Nuffield Department
of Medicine, University of Oxford, NDMRB Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Julian Blagg
- Cancer
Research UK Cancer Therapeutics Unit, The
Institute of Cancer Research, 15 Cotswold Road, London SM2 5NG, U.K.
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34
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Korczynska M, Le DD, Younger N, Gregori-Puigjané E, Tumber A, Krojer T, Velupillai S, Gileadi C, Nowak RP, Iwasa E, Pollock SB, Ortiz Torres I, Oppermann U, Shoichet BK, Fujimori DG. Docking and Linking of Fragments To Discover Jumonji Histone Demethylase Inhibitors. J Med Chem 2015; 59:1580-98. [PMID: 26699912 DOI: 10.1021/acs.jmedchem.5b01527] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Development of tool molecules that inhibit Jumonji demethylases allows for the investigation of cancer-associated transcription. While scaffolds such as 2,4-pyridinedicarboxylic acid (2,4-PDCA) are potent inhibitors, they exhibit limited selectivity. To discover new inhibitors for the KDM4 demethylases, enzymes overexpressed in several cancers, we docked a library of 600,000 fragments into the high-resolution structure of KDM4A. Among the most interesting chemotypes were the 5-aminosalicylates, which docked in two distinct but overlapping orientations. Docking poses informed the design of covalently linked fragment compounds, which were further derivatized. This combined approach improved affinity by ∼ 3 log-orders to yield compound 35 (Ki = 43 nM). Several hybrid inhibitors were selective for KDM4C over the related enzymes FIH, KDM2A, and KDM6B while lacking selectivity against the KDM3 and KDM5 subfamilies. Cocrystal structures corroborated the docking predictions. This study extends the use of structure-based docking from fragment discovery to fragment linking optimization, yielding novel KDM4 inhibitors.
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Affiliation(s)
| | | | | | | | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, U.K.,Nuffield Department of Clinical Medicine, Target Discovery Institute (TDI), University of Oxford , Oxford OX3 7BN, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, U.K
| | | | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, U.K
| | - Radosław P Nowak
- Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, U.K
| | | | | | | | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford , Oxford OX3 7DQ, U.K.,Botnar Research Center, University of Oxford , Oxford OX3 7LD, U.K
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35
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Froese DS, Michaeli A, McCorvie TJ, Krojer T, Sasi M, Melaev E, Goldblum A, Zatsepin M, Lossos A, Álvarez R, Escribá PV, Minassian BA, von Delft F, Kakhlon O, Yue WW. Structural basis of glycogen branching enzyme deficiency and pharmacologic rescue by rational peptide design. Hum Mol Genet 2015. [PMID: 26199317 PMCID: PMC4581599 DOI: 10.1093/hmg/ddv280] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Glycogen branching enzyme 1 (GBE1) plays an essential role in glycogen biosynthesis by generating α-1,6-glucosidic branches from α-1,4-linked glucose chains, to increase solubility of the glycogen polymer. Mutations in the GBE1 gene lead to the heterogeneous early-onset glycogen storage disorder type IV (GSDIV) or the late-onset adult polyglucosan body disease (APBD). To better understand this essential enzyme, we crystallized human GBE1 in the apo form, and in complex with a tetra- or hepta-saccharide. The GBE1 structure reveals a conserved amylase core that houses the active centre for the branching reaction and harbours almost all GSDIV and APBD mutations. A non-catalytic binding cleft, proximal to the site of the common APBD mutation p.Y329S, was found to bind the tetra- and hepta-saccharides and may represent a higher-affinity site employed to anchor the complex glycogen substrate for the branching reaction. Expression of recombinant GBE1-p.Y329S resulted in drastically reduced protein yield and solubility compared with wild type, suggesting this disease allele causes protein misfolding and may be amenable to small molecule stabilization. To explore this, we generated a structural model of GBE1-p.Y329S and designed peptides ab initio to stabilize the mutation. As proof-of-principle, we evaluated treatment of one tetra-peptide, Leu-Thr-Lys-Glu, in APBD patient cells. We demonstrate intracellular transport of this peptide, its binding and stabilization of GBE1-p.Y329S, and 2-fold increased mutant enzymatic activity compared with untreated patient cells. Together, our data provide the rationale and starting point for the screening of small molecule chaperones, which could become novel therapies for this disease.
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Affiliation(s)
- D Sean Froese
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | | | - Thomas J McCorvie
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Tobias Krojer
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Meitav Sasi
- Department of Neurology, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Esther Melaev
- Department of Neurology, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Amiram Goldblum
- Pepticom LTD, Jerusalem, Israel, Institute for Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Alexander Lossos
- Department of Neurology, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel
| | - Rafael Álvarez
- Department of Biology, University of the Balearic Islands, Palma de Mallorca E-07122, Spain and
| | - Pablo V Escribá
- Department of Biology, University of the Balearic Islands, Palma de Mallorca E-07122, Spain and
| | - Berge A Minassian
- Program in Genetics and Genomic Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Frank von Delft
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK
| | - Or Kakhlon
- Department of Neurology, Hadassah-Hebrew University Medical Center, Ein Kerem, Jerusalem, Israel,
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, OX3 7DQ, UK,
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England KS, Tumber A, Krojer T, Scozzafava G, Ng SS, Daniel M, Szykowska A, Che K, von Delft F, Burgess-Brown NA, Kawamura A, Schofield CJ, Brennan PE. Optimisation of a triazolopyridine based histone demethylase inhibitor yields a potent and selective KDM2A (FBXL11) inhibitor. Medchemcomm 2014; 5:1879-1886. [PMID: 26682034 PMCID: PMC4678576 DOI: 10.1039/c4md00291a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A potent inhibitor of the JmjC histone lysine demethylase KDM2A (compound 35, pIC50 7.2) with excellent selectivity over representatives from other KDM subfamilies has been developed; the discovery that a triazolopyridine compound binds to the active site of JmjC KDMs was followed by optimisation of the triazole substituent for KDM2A inhibition and selectivity.
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Affiliation(s)
- Katherine S. England
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Giuseppe Scozzafava
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Stanley S. Ng
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Michelle Daniel
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Aleksandra Szykowska
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - KaHing Che
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK
| | - Nicola A. Burgess-Brown
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | | | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford, OX3 7FZ, UK
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37
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Horita S, Scotti J, McDonough M, Sekirnik R, Chowdhury R, Krojer T, Thalhammer A, Aik W, Oppermann U, Schofield C. Crystal structures of 2OG oxygenases involved in ribosomal protein hydroxylation. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314096958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Post-translational modifications play diverse biological functions. Hydroxylation of collagen proteins has long been a recognised post-translational modification in eukaryotes. In the case of collagen, hydroxylation of prolyl residues, by 2-oxoglutarate and iron dependent enzymes (2OG oxygenases), in collagen proteins allows for the stabilisation of the collagen triple helix structure through conformational restraint and through the addition of a hydrogen bond donor. Additionally, hydroxylation of lysine side chains of collagen is required for cross-linking collagen (and possibly other proteins) in the extra-cellular matrix. Post-translational prolyl hydroxylation also plays a pivotal role in transcriptional regulation of the hypoxic response, as catalyzed by the hypoxia inducible factor / HIF prolyl hydroxylases (PHDs or EGLN enzymes). Recently, ribosomal protein hydroxylation catalyzed by 2OG- and Fe(II)-dependent oxygenases has been found to be a highly conserved post-translational modification in eukaryotes and prokaryotes (Ge et al and Loenarz et al). We present several crystal structures of 2OG oxygenases involved in ribosomal protein hydroxylation.
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Lobley C, Sanchez-Weatherby J, Sandy J, Mazzorana M, Krojer T, Sorensen T. When protein crystal dehydration helps. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314096624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
A typical protein crystal contains 30-60% solvent. For a naked crystal, this solvent is distributed between solvent shells, where water and solvent molecules make specific interactions with the crystalline protein, and solvent channels filled with disordered solvent molecules. This internal solvent map of the crystal can be modified by placing the crystal in a dehydrating environment. This may in turn induce changes to the crystal lattice and affect mosaicity, resolution and quality of diffraction data. A dehydrating environment can be generated around a crystal in several ways with various degrees of precision and complexity. In this study we have used the HC1 device (Maatel) to mount crystals an air stream of known relative humidity – a precise yet hassle-free approach to altering crystal hydration. We set out to analyse a range of different crystals to establish usable protocols that will allow one to explore to crystal hydration space, either by preparing samples before synchrotron beamtime or by undertaking the experiments during beamtime. Our results, considered in the light of the literature surrounding crystal dehydration, provide guidance for when dehydration can help diffraction.
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Korczynska M, Le D, Gregori-Puigjané E, Younger N, Krojer T, Tumber A, Oppermann U, Galonić Fujimori D, Shoichet B. Virtual Screening of Histone Lysine Demethylase(JMJD2) identifies new inhibitors. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314091797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The JmjC domain-containing proteins are hydroxylases that confer posttranslational modifications on histone tails, by removing methylation marks on methylated lysine residues. This serves to either promote or repress gene transcription. The JMJD2A-D family members include the enzyme Jumonji domain 2C (JMJD2C), which specifically demethylates di- and trimethylated histone H3 at Lys 9 or Lys 36.[1] Dysregulation of JMJD2C has been implicated in prostate, colonic, and breast cancer as the demethylase can modify the expression levels of oncogenes.[2] The goal of the present study was to identify potent and selective small-molecule inhibitors of JMJD2C, to be used as chemical biology tools to further investigate the role of JMJD2C in cell proliferation and survival. Using high-resolution crystal structures of the JMJD2 subfamily members as templates, we have performed a small molecule virtual docking screen. From the ~3 million molecules that were docked, this experiment identified 21 compounds as possible leads. These compounds were tested against JMJD2C in enzymatic assays and here we report an overall hit rate of 76%, with 8 compounds demonstrating an IC50 of 176μM to 1.18μM. A molecule containing a salicylate core was selected as a candidate for optimization and thus far we have completed several rounds of iterative target-specific compound docking, hybrid molecule design, compound synthesis and in vitro characterization. Notably, our method demonstrated a substantial increase in potency when we linked two docked fragments together and further derivatized this new scaffold, through which we have successfully derived a 65nM inhibitor of JMJD2C. A compound representing the inhibitor scaffold has been co-crystallized with JMJD2A to a resolution of 2.4 Å. In the crystal structure each asymmetric unit contains two JMJD2A monomers, each bound to a single inhibitor molecule. This complex-structure superposes well with the docked pose for the hybrid series of compounds. We are now focusing our efforts on identifying an inhibitor that is selective for the JMJD2 family over other JmjC domain-containing proteins.
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Douangamath A, Brandao-Neto J, Williams M, Fearn R, Krojer T, Aller P, Henderson K, Longhi E, Allianelli L, Von Delft F. I04-1, a future 'fragment screening' beamline facility at Diamond Light Source. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314092092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
I04-1 is one of the six macromolecular crystallography (MX) beamlines at Diamond Light Source (DLS), the third generation synchrotron light source in the UK. It was built and delivered in 2010 as a stable and reliable fixed-wavelength MX station. It is currently preparing to release its user programme for exploiting fragment screening using X-ray crystallography in structural medicinal chemistry projects. For this purpose, the beamline has been going through several upgrades in order to achieve unattended high-throughput ligand crystallography. The new developments are aiming at improving the flux, stability and reliability of the beamline and its auto-alignment. In parallel, a peripheral laboratory is being set up to provide a facility for medium throughput compound soaking. Jointly with the Structural Genomics Consortium (SGC), a semi-automatic crystal soaking and harvesting scheme, which will provide hundreds of MX samples per day, is being tested at DLS. The beamline can currently process 400 crystals per day. However, the recent upgrades and automation should further improve that throughput. In this presentation, we will summarise the current specifications of the beamline and its new features, the development of a peripheral laboratory for compounds soaking and underline the remaining work.
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Canning P, Cooper CD, Krojer T, Murray JW, Pike AC, Chaikuad A, Keates T, Thangaratnarajah C, Hojzan V, Ayinampudi V, Marsden BD, Gileadi O, Knapp S, von Delft F, Bullock AN. Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases. J Biol Chem 2013. [DOI: 10.1074/jbc.a112.437996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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42
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Froese DS, Vollmar M, Puranik S, Cannone G, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Oppermann U, Yue WW. Structure of malonyl CoA decarboxylase provides insight in catalysis and disease mutations. Acta Crystallogr A 2013. [DOI: 10.1107/s0108767313096980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hopkinson RJ, Tumber A, Yapp C, Chowdhury R, Aik W, Che KH, Li XS, Kristensen JBL, King ONF, Chan MC, Yeoh KK, Choi H, Walport LJ, Thinnes CC, Bush JT, Lejeune C, Rydzik AM, Rose NR, Bagg EA, McDonough MA, Krojer T, Yue WW, Ng SS, Olsen L, Brennan PE, Oppermann U, Muller-Knapp S, Klose RJ, Ratcliffe PJ, Schofield CJ, Kawamura A. 5-Carboxy-8-hydroxyquinoline is a Broad Spectrum 2-Oxoglutarate Oxygenase Inhibitor which Causes Iron Translocation. Chem Sci 2013; 4:3110-3117. [PMID: 26682036 PMCID: PMC4678600 DOI: 10.1039/c3sc51122g] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
2-Oxoglutarate and iron dependent oxygenases are therapeutic targets for human diseases. Using a representative 2OG oxygenase panel, we compare the inhibitory activities of 5-carboxy-8-hydroxyquinoline (IOX1) and 4-carboxy-8-hydroxyquinoline (4C8HQ) with that of two other commonly used 2OG oxygenase inhibitors, N-oxalylglycine (NOG) and 2,4-pyridinedicarboxylic acid (2,4-PDCA). The results reveal that IOX1 has a broad spectrum of activity, as demonstrated by the inhibition of transcription factor hydroxylases, representatives of all 2OG dependent histone demethylase subfamilies, nucleic acid demethylases and γ-butyrobetaine hydroxylase. Cellular assays show that, unlike NOG and 2,4-PDCA, IOX1 is active against both cytosolic and nuclear 2OG oxygenases without ester derivatisation. Unexpectedly, crystallographic studies on these oxygenases demonstrate that IOX1, but not 4C8HQ, can cause translocation of the active site metal, revealing a rare example of protein ligand-induced metal movement.
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Affiliation(s)
- Richard J. Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK
| | - Clarence Yapp
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - WeiShen Aik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ka Hing Che
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K
| | - Xuan Shirley Li
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Jan B. L. Kristensen
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Oliver N. F. King
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Kar Kheng Yeoh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Louise J. Walport
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Cyrille C. Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Jacob T. Bush
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Clarisse Lejeune
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Anna M. Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Nathan R. Rose
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Eleanor A. Bagg
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Michael A. McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Wyatt W. Yue
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Stanley S. Ng
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
| | - Lars Olsen
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K
- Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K
| | | | - Robert J. Klose
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K
| | - Peter J. Ratcliffe
- Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7LD, UK
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Froese DS, Forouhar F, Tran TH, Vollmar M, Kim YS, Lew S, Neely H, Seetharaman J, Shen Y, Xiao R, Acton TB, Everett JK, Cannone G, Puranik S, Savitsky P, Krojer T, Pilka ES, Kiyani W, Lee WH, Marsden BD, von Delft F, Allerston CK, Spagnolo L, Gileadi O, Montelione GT, Oppermann U, Yue WW, Tong L. Crystal structures of malonyl-coenzyme A decarboxylase provide insights into its catalytic mechanism and disease-causing mutations. Structure 2013; 21:1182-92. [PMID: 23791943 PMCID: PMC3701320 DOI: 10.1016/j.str.2013.05.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/09/2013] [Accepted: 05/09/2013] [Indexed: 01/17/2023]
Abstract
Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design. Structures of human and bacterial MCDs were determined at up to 2.3 Å resolution Distinct tetrameric and dimeric MCD oligomerizations were observed Unexpected homology to the GNAT superfamily gives insights into catalytic mechanism The structures provide the molecular basis for the disease-causing mutations in MCD
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Affiliation(s)
- D Sean Froese
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
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45
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Krojer T, Pike ACW, von Delft F. Squeezing the most from every crystal: the fine details of data collection. Acta Crystallogr D Biol Crystallogr 2013; 69:1303-13. [PMID: 23793157 PMCID: PMC3689534 DOI: 10.1107/s0907444913013280] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Accepted: 05/14/2013] [Indexed: 11/11/2022]
Abstract
Modern synchrotron beamlines offer instrumentation of unprecedented quality, which in turn encourages increasingly marginal experiments, and for these, as much as ever, the ultimate success of data collection depends on the experience, but especially the care, of the experimenter. A representative set of difficult cases has been encountered at the Structural Genomics Consortium, a worldwide structural genomics initiative of which the Oxford site currently deposits three novel human structures per month. Achieving this target relies heavily on frequent visits to the Diamond Light Source, and the variety of crystal systems still demand customized data collection, diligent checks and careful planning of each experiment. Here, an overview is presented of the techniques and procedures that have been refined over the years and that are considered synchrotron best practice.
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Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, Oxford University, Roosevelt Drive, Oxford OX3 7DQ, England
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46
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Canning P, Cooper CDO, Krojer T, Murray JW, Pike ACW, Chaikuad A, Keates T, Thangaratnarajah C, Hojzan V, Marsden BD, Gileadi O, Knapp S, von Delft F, Bullock AN. Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases. J Biol Chem 2013; 288:7803-7814. [PMID: 23349464 PMCID: PMC3597819 DOI: 10.1074/jbc.m112.437996] [Citation(s) in RCA: 192] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cullin-RING ligases are multisubunit E3 ubiquitin ligases that recruit substrate-specific adaptors to catalyze protein ubiquitylation. Cul3-based Cullin-RING ligases are uniquely associated with BTB adaptors that incorporate homodimerization, Cul3 assembly, and substrate recognition into a single multidomain protein, of which the best known are BTB-BACK-Kelch domain proteins, including KEAP1. Cul3 assembly requires a BTB protein “3-box” motif, analogous to the F-box and SOCS box motifs of other Cullin-based E3s. To define the molecular basis for this assembly and the overall architecture of the E3, we determined the crystal structures of the BTB-BACK domains of KLHL11 both alone and in complex with Cul3, along with the Kelch domain structures of KLHL2 (Mayven), KLHL7, KLHL12, and KBTBD5. We show that Cul3 interaction is dependent on a unique N-terminal extension sequence that packs against the 3-box in a hydrophobic groove centrally located between the BTB and BACK domains. Deletion of this N-terminal region results in a 30-fold loss in affinity. The presented data offer a model for the quaternary assembly of this E3 class that supports the bivalent capture of Nrf2 and reveals potential new sites for E3 inhibitor design.
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Affiliation(s)
- Peter Canning
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | | | - Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - James W Murray
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Ashley C W Pike
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Apirat Chaikuad
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Tracy Keates
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | | | - Viktorija Hojzan
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Brian D Marsden
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Frank von Delft
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Alex N Bullock
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.
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47
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Rose NR, Woon ECY, Tumber A, Walport LJ, Chowdhury R, Li XS, King ONF, Lejeune C, Ng SS, Krojer T, Chan MC, Rydzik AM, Hopkinson RJ, Che KH, Daniel M, Strain-Damerell C, Gileadi C, Kochan G, Leung IKH, Dunford J, Yeoh KK, Ratcliffe PJ, Burgess-Brown N, von Delft F, Muller S, Marsden B, Brennan PE, McDonough MA, Oppermann U, Klose RJ, Schofield CJ, Kawamura A. Plant growth regulator daminozide is a selective inhibitor of human KDM2/7 histone demethylases. J Med Chem 2012; 55:6639-43. [PMID: 22724510 DOI: 10.1021/jm300677j] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The JmjC oxygenases catalyze the N-demethylation of N(ε)-methyl lysine residues in histones and are current therapeutic targets. A set of human 2-oxoglutarate analogues were screened using a unified assay platform for JmjC demethylases and related oxygenases. Results led to the finding that daminozide (N-(dimethylamino)succinamic acid, 160 Da), a plant growth regulator, selectively inhibits the KDM2/7 JmjC subfamily. Kinetic and crystallographic studies reveal that daminozide chelates the active site metal via its hydrazide carbonyl and dimethylamino groups.
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Affiliation(s)
- Nathan R Rose
- Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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48
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Froese DS, Krojer T, Wu X, Shrestha R, Kiyani W, von Delft F, Gravel RA, Oppermann U, Yue WW. Structure of MMACHC Reveals an Arginine-Rich Pocket and a Domain-Swapped Dimer for Its B12 Processing Function. Biochemistry 2012; 51:5083-90. [DOI: 10.1021/bi300150y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Xuchu Wu
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada
| | | | | | | | - Roy A. Gravel
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada
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49
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Sawa J, Malet H, Krojer T, Canellas F, Ehrmann M, Clausen T. Molecular adaptation of the DegQ protease to exert protein quality control in the bacterial cell envelope. J Biol Chem 2011; 286:30680-30690. [PMID: 21685389 DOI: 10.1074/jbc.m111.243832] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To react to distinct stress situations and to prevent the accumulation of misfolded proteins, all cells employ a number of proteases and chaperones, which together set up an efficient protein quality control system. The functionality of proteins in the cell envelope of Escherichia coli is monitored by the HtrA proteases DegS, DegP, and DegQ. In contrast with DegP and DegS, the structure and function of DegQ has not been addressed in detail. Here, we show that substrate binding triggers the conversion of the resting DegQ hexamer into catalytically active 12- and 24-mers. Interestingly, substrate-induced oligomer reassembly and protease activation depends on the first PDZ domain but not on the second. Therefore, the regulatory mechanism originally identified in DegP should be a common feature of HtrA proteases, most of which encompass only a single PDZ domain. Using a DegQ mutant lacking the second PDZ domain, we determined the high resolution crystal structure of a dodecameric HtrA complex. The nearly identical domain orientation of protease and PDZ domains within 12- and 24-meric HtrA complexes reveals a conserved PDZ1 → L3 → LD/L1/L2 signaling cascade, in which loop L3 senses the repositioned PDZ1 domain of higher order, substrate-engaged particles and activates protease function. Furthermore, our in vitro and in vivo data imply a pH-related function of DegQ in the bacterial cell envelope.
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Affiliation(s)
- Justyna Sawa
- Institute of Molecular Pathology, A-1030 Vienna, Austria
| | - Hélène Malet
- Department of Biological Sciences, Institute of Structural Molecular Biology, Birkbeck College, London WC1E 7HX, United Kingdom
| | - Tobias Krojer
- Institute of Molecular Pathology, A-1030 Vienna, Austria
| | | | - Michael Ehrmann
- Centre for Medical Biotechnology, Faculty of Biology and Geography, University Duisburg-Essen, 45117 Essen, Germany
| | - Tim Clausen
- Institute of Molecular Pathology, A-1030 Vienna, Austria.
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50
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Krojer T, von Delft F. Assessment of radiation damage behaviour in a large collection of empirically optimized datasets highlights the importance of unmeasured complicating effects. J Synchrotron Radiat 2011; 18:387-97. [PMID: 21525647 PMCID: PMC3083914 DOI: 10.1107/s0909049511008235] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 03/03/2011] [Indexed: 05/21/2023]
Abstract
The radiation damage behaviour in 43 datasets of 34 different proteins collected over a year was examined, in order to gauge the reliability of decay metrics in practical situations, and to assess how these datasets, optimized only empirically for decay, would have benefited from the precise and automatic prediction of decay now possible with the programs RADDOSE [Murray, Garman & Ravelli (2004). J. Appl. Cryst. 37, 513-522] and BEST [Bourenkov & Popov (2010). Acta Cryst. D66, 409-419]. The results indicate that in routine practice the diffraction experiment is not yet characterized well enough to support such precise predictions, as these depend fundamentally on three interrelated variables which cannot yet be determined robustly and practically: the flux density distribution of the beam; the exact crystal volume; the sensitivity of the crystal to dose. The former two are not satisfactorily approximated from typical beamline information such as nominal beam size and transmission, or two-dimensional images of the beam and crystal; the discrepancies are particularly marked when using microfocus beams (<20 µm). Empirically monitoring decay with the dataset scaling B factor (Bourenkov & Popov, 2010) appears more robust but is complicated by anisotropic and/or low-resolution diffraction. These observations serve to delineate the challenges, scientific and logistic, that remain to be addressed if tools for managing radiation damage in practical data collection are to be conveniently robust enough to be useful in real time.
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Affiliation(s)
- Tobias Krojer
- Structural Genomics Consortium, University of Oxford, Oxford, UK
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