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McCarthy WJ, Thomas SE, Olaleye T, Boland JA, Floto RA, Williams G, Blundell TL, Coyne AG, Abell C. A Fragment-Based Competitive 19F LB-NMR Platform For Hotspot-Directed Ligand Profiling. Angew Chem Int Ed Engl 2024; 63:e202406846. [PMID: 38896426 DOI: 10.1002/anie.202406846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 06/19/2024] [Accepted: 06/19/2024] [Indexed: 06/21/2024]
Abstract
Ligand binding hotspots are regions of protein surfaces that form particularly favourable interactions with small molecule pharmacophores. Targeting interactions with these hotspots maximises the efficiency of ligand binding. Existing methods are capable of identifying hotspots but often lack assays to quantify ligand binding and direct elaboration at these sites. Herein, we describe a fragment-based competitive 19F Ligand Based NMR (LB-NMR) screening platform that enables routine, quantitative ligand profiling focused at ligand-binding hotspots. As a proof of concept, the method was applied to 4'-phosphopantetheine adenylyltransferase (PPAT) from Mycobacterium abscessus (Mabs). X-ray crystallographic characterisation of the hits from a 960-member fragment screen identified three ligand-binding hotspots across the PPAT active site. From the fragment hits a collection of 19F reporter candidates were designed and synthesised. By rigorous prioritisation and use of optimisation workflows, a single 19F reporter molecule was generated for each hotspot. Profiling the binding of a set of structurally characterised ligands by competitive 19F LB-NMR with this suite of 19F reporters recapitulated the binding affinity and site ID assignments made by ITC and X-ray crystallography. This quantitative mapping of ligand binding events at hotspot level resolution establishes the utility of the fragment-based competitive 19F LB-NMR screening platform for hotspot-directed ligand profiling.
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Affiliation(s)
- William J McCarthy
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
- Present Address: Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, UK, NW1 1AT
| | - Sherine E Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1GA
- Present Address: Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1PD
| | - Tayo Olaleye
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Jennifer A Boland
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - R Andres Floto
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, UK, CB2 0QH
- VPD Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK, CB2 0BB
| | - Glyn Williams
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK, CB2 1GA
- VPD Heart Lung Research Institute, Department of Medicine, University of Cambridge, Cambridge, UK, CB2 0BB
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK, CB2 1EW
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2
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Aschenbrenner JC, de Godoy AS, Fairhead M, Tomlinson CWE, Winokan M, Balcomb BH, Capkin E, Chandran AV, Golding M, Koekemoer L, Lithgo RM, Marples PG, Ni X, Thompson W, Wild C, Xavier MAE, Fearon D, von Delft F. Identifying novel chemical matter against the Chikungunya virus nsP3 macrodomain through crystallographic fragment screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.609196. [PMID: 39229067 PMCID: PMC11370605 DOI: 10.1101/2024.08.23.609196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Chikungunya virus (CHIKV) causes severe fever, rash and debilitating joint pain that can last for months1,2or even years. Millions of people have been infected with CHIKV, mostly in low and middle-income countries, and the virus continues to spread into new areas due to the geographical expansion of its mosquito hosts. Its genome encodes a macrodomain, which functions as an ADP-ribosyl hydrolase, removing ADPr from viral and host-cell proteins interfering with the innate immune response. Mutational studies have shown that the CHIKV nsP3 macrodomain is necessary for viral replication, making it a potential target for the development of antiviral therapeutics. We, therefore, performed a high-throughput crystallographic fragment screen against the CHIKV nsP3 macrodomain, yielding 109 fragment hits covering the ADPr-binding site and two adjacent subsites that are absent in the homologous macrodomain of SARS-CoV-2 but may be present in other alphaviruses, such as Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV). Finally, a subset of overlapping fragments was used to manually design three fragment merges covering the adenine and oxyanion subsites. The rich dataset of chemical matter and structural information discovered from this fragment screen is publicly available and can be used as a starting point for developing a CHIKV nsP3 macrodomain inhibitor.
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Affiliation(s)
- Jasmin C Aschenbrenner
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | | | - Michael Fairhead
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Charles W E Tomlinson
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Max Winokan
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Blake H Balcomb
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Eda Capkin
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Anu V Chandran
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Mathew Golding
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Lizbe Koekemoer
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Ryan M Lithgo
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Peter G Marples
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Xiaomin Ni
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Warren Thompson
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Conor Wild
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Mary-Ann E Xavier
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Daren Fearon
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
| | - Frank von Delft
- Diamond Light Source, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science & Innovation Campus, Didcot, United Kingdom
- Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
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3
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Sternicki LM, Poulsen SA. Fragment-based drug discovery campaigns guided by native mass spectrometry. RSC Med Chem 2024; 15:2270-2285. [PMID: 39026646 PMCID: PMC11253872 DOI: 10.1039/d4md00273c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 05/19/2024] [Indexed: 07/20/2024] Open
Abstract
Native mass spectrometry (nMS) is well established as a biophysical technique for characterising biomolecules and their interactions with endogenous or investigational small molecule ligands. The high sensitivity mass measurements make nMS particularly well suited for applications in fragment-based drug discovery (FBDD) screening campaigns where the detection of weakly binding ligands to a target biomolecule is crucial. We first reviewed the contributions of nMS to guiding FBDD hit identification in 2013, providing a comprehensive perspective on the early adoption of nMS for fragment screening. Here we update this initial progress with a focus on contributions of nMS that have guided FBDD for the period 2014 until end of 2023. We highlight the development of nMS adoption in FBDD in the context of other biophysical fragment screening techniques. We also discuss the roadmap for increased adoption of nMS for fragment screening beyond soluble proteins, including for guiding the discovery of fragments supporting advances in PROTAC discovery, RNA-binding small molecules and covalent therapeutic drug discovery.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University Nathan Brisbane Queensland 4111 Australia
- ARC Centre for Fragment-Based Design Australia
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4
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Meeks KR, Bogner AN, Tanner JJ. Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1). Protein Sci 2024; 33:e5072. [PMID: 39133178 PMCID: PMC11193152 DOI: 10.1002/pro.5072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 08/13/2024]
Abstract
Δ1-pyrroline-5-carboxylate reductase isoform 1 (PYCR1) is the last enzyme of proline biosynthesis and catalyzes the NAD(P)H-dependent reduction of Δ1-pyrroline-5-carboxylate to L-proline. High PYCR1 gene expression is observed in many cancers and linked to poor patient outcomes and tumor aggressiveness. The knockdown of the PYCR1 gene or the inhibition of PYCR1 enzyme has been shown to inhibit tumorigenesis in cancer cells and animal models of cancer, motivating inhibitor discovery. We screened a library of 71 low molecular weight compounds (average MW of 131 Da) against PYCR1 using an enzyme activity assay. Hit compounds were validated with X-ray crystallography and kinetic assays to determine affinity parameters. The library was counter-screened against human Δ1-pyrroline-5-carboxylate reductase isoform 3 and proline dehydrogenase (PRODH) to assess specificity/promiscuity. Twelve PYCR1 and one PRODH inhibitor crystal structures were determined. Three compounds inhibit PYCR1 with competitive inhibition parameter of 100 μM or lower. Among these, (S)-tetrahydro-2H-pyran-2-carboxylic acid (70 μM) has higher affinity than the current best tool compound N-formyl-l-proline, is 30 times more specific for PYCR1 over human Δ1-pyrroline-5-carboxylate reductase isoform 3, and negligibly inhibits PRODH. Structure-affinity relationships suggest that hydrogen bonding of the heteroatom of this compound is important for binding to PYCR1. The structures of PYCR1 and PRODH complexed with 1-hydroxyethane-1-sulfonate demonstrate that the sulfonate group is a suitable replacement for the carboxylate anchor. This result suggests that the exploration of carboxylic acid isosteres may be a promising strategy for discovering new classes of PYCR1 and PRODH inhibitors. The structure of PYCR1 complexed with l-pipecolate and NADH supports the hypothesis that PYCR1 has an alternative function in lysine metabolism.
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Affiliation(s)
- Kaylen R. Meeks
- Department of BiochemistryUniversity of MissouriColumbiaMissouriUSA
| | - Alexandra N. Bogner
- Department of BiochemistryUniversity of MissouriColumbiaMissouriUSA
- Present address:
Lilly Biotechnology CenterEli Lilly and CompanySan DiegoCaliforniaUSA
| | - John J. Tanner
- Department of BiochemistryUniversity of MissouriColumbiaMissouriUSA
- Department of ChemistryUniversity of MissouriColumbiaMissouriUSA
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5
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McCarthy WJ, van der Zouwen AJ, Bush JT, Rittinger K. Covalent fragment-based drug discovery for target tractability. Curr Opin Struct Biol 2024; 86:102809. [PMID: 38554479 DOI: 10.1016/j.sbi.2024.102809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 04/01/2024]
Abstract
An important consideration in drug discovery is the prioritization of tractable protein targets that are not only amenable to binding small molecules, but also alter disease biology in response to small molecule binding. Covalent fragment-based drug discovery has emerged as a powerful approach to aid in the identification of such protein targets. The application of irreversible binding mechanisms enables the identification of fragment hits for challenging-to-target proteins, allows proteome-wide screening in a cellular context, and makes it possible to determine functional effects with modestly potent ligands without the requirement for extensive compound optimization. Here, we provide an overview of recent approaches to covalent fragment-based screening and discuss how these have been applied to establish the tractability of unexplored binding sites on protein targets.
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Affiliation(s)
- William J McCarthy
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Antonie J van der Zouwen
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jacob T Bush
- Crick-GSK Biomedical LinkLabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK. https://twitter.com/Jake_T_Bush
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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Ni X, Godoy AS, Marples PG, Fairhead M, Balcomb BH, Ferla MP, Tomlinson CWE, Wang S, Giroud C, Aschenbrenner JC, Lithgo RM, Winokan M, Chandran AV, Thompson W, Xavier MA, Williams EP, Walsh M, Fearon D, Koekemoer L, von Delft F. Crystallographic fragment screening delivers diverse chemical scaffolds for Zika virus NS2B-NS3 protease inhibitor development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591502. [PMID: 38746305 PMCID: PMC11092485 DOI: 10.1101/2024.04.29.591502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Zika virus (ZIKV) infections cause microcephaly in new-borns and Guillain-Barre syndrome in adults raising a significant global public health concern, yet no vaccines or antiviral drugs have been developed to prevent or treat ZIKV infections. The viral protease NS3 and its co-factor NS2B are essential for the cleavage of the Zika polyprotein precursor into individual structural and non-structural proteins and is therefore an attractive drug target. Generation of a robust crystal system of co-expressed NS2B-NS3 protease has enabled us to perform a crystallographic fragment screening campaign with 1076 fragments. 48 binders with diverse chemical scaffolds were identified in the active site of the protease, with another 6 fragment hits observed in a potential allosteric binding site. Our work provides potential starting points for the development of potent NS2B-NS3 protease inhibitors. Furthermore, we have structurally characterized a potential allosteric binding pocket, identifying opportunities for allosteric inhibitor development.
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7
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Godoy AS, Mesquita NCMR, Noske GD, Gawriljuk VO, Lithgo RM, Balcomb BH, Aschenbrenner JC, Tomlinson CWE, Winokan M, Scheen J, Marples PG, Chandran AV, Ni X, Thompson W, Fairhead M, Fearon D, Koekemoer L, Xavier MAE, Walsh M, Oliva G, von Delft F. High-throughput crystallographic fragment screening of Zika virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591279. [PMID: 38746241 PMCID: PMC11092484 DOI: 10.1101/2024.04.27.591279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The Zika virus (ZIKV), discovered in Africa in 1947, swiftly spread across continents, causing significant concern due to its recent association with microcephaly in newborns and Guillain-Barré syndrome in adults. Despite a decrease in prevalence, the potential for a resurgence remains, necessitating urgent therapeutic interventions. Like other flaviviruses, ZIKV presents promising drug targets within its replication machinery, notably the NS3 helicase (NS3Hel) protein, which plays critical roles in viral replication. However, a lack of structural information impedes the development of specific inhibitors targeting NS3Hel. Here we applied high-throughput crystallographic fragment screening on ZIKV NS3Hel, which yielded structures that reveal 3D binding poses of 46 fragments at multiple sites of the protein, including 11 unique fragments in the RNA-cleft site. These fragment structures provide templates for direct design of hit compounds and should thus assist the development of novel direct-acting antivirals against ZIKV and related flaviviruses, thus opening a promising avenue for combating future outbreaks.
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Affiliation(s)
- Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
- ASAP Discovery Consortium: asapdiscovery.org
| | - Nathalya C M R Mesquita
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Gabriela Dias Noske
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Victor Oliveira Gawriljuk
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Ryan M Lithgo
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Blake H Balcomb
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Jasmin Cara Aschenbrenner
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Charles W E Tomlinson
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Max Winokan
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Jenke Scheen
- Open Molecular Sciences Foundation, Davis, CA 95618, USA
- ASAP Discovery Consortium: asapdiscovery.org
| | - Peter George Marples
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Anu V Chandran
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Xiaomin Ni
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Warren Thompson
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Michael Fairhead
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Daren Fearon
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Mary-Ann Elvina Xavier
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Martin Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Frank von Delft
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
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Lithgo RM, Tomlinson CWE, Fairhead M, Winokan M, Thompson W, Wild C, Aschenbrenner JC, Balcomb BH, Marples PG, Chandran AV, Golding M, Koekemoer L, Williams EP, Wang S, Ni X, MacLean E, Giroud C, Godoy AS, Xavier MA, Walsh M, Fearon D, von Delft F. Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591684. [PMID: 38746446 PMCID: PMC11092469 DOI: 10.1101/2024.04.29.591684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Enteroviruses are the causative agents of paediatric hand-foot-and-mouth disease, and a target for pandemic preparedness due to the risk of higher order complications in a large-scale outbreak. The 2A protease of these viruses is responsible for the self-cleavage of the poly protein, allowing for correct folding and assembly of capsid proteins in the final stages of viral replication. These 2A proteases are highly conserved between Enterovirus species, such as Enterovirus A71 and Coxsackievirus A16 . Inhibition of the 2A protease deranges capsid folding and assembly, preventing formation of mature virions in host cells and making the protease a valuable target for antiviral activity. Herein, we describe a crystallographic fragment screening campaign that identified 75 fragments which bind to the 2A protease including 38 unique compounds shown to bind within the active site. These fragments reveal a path for the development of non-peptidomimetic inhibitors of the 2A protease with broad-spectrum anti-enteroviral activity.
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9
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Jalencas X, Berg H, Espeland LO, Sreeramulu S, Kinnen F, Richter C, Georgiou C, Yadrykhinsky V, Specker E, Jaudzems K, Miletić T, Harmel R, Gribbon P, Schwalbe H, Brenk R, Jirgensons A, Zaliani A, Mestres J. Design, quality and validation of the EU-OPENSCREEN fragment library poised to a high-throughput screening collection. RSC Med Chem 2024; 15:1176-1188. [PMID: 38665834 PMCID: PMC11042166 DOI: 10.1039/d3md00724c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 04/28/2024] Open
Abstract
The EU-OPENSCREEN (EU-OS) European Research Infrastructure Consortium (ERIC) is a multinational, not-for-profit initiative that integrates high-capacity screening platforms and chemistry groups across Europe to facilitate research in chemical biology and early drug discovery. Over the years, the EU-OS has assembled a high-throughput screening compound collection, the European Chemical Biology Library (ECBL), that contains approximately 100 000 commercially available small molecules and a growing number of thousands of academic compounds crowdsourced through our network of European and non-European chemists. As an extension of the ECBL, here we describe the computational design, quality control and use case screenings of the European Fragment Screening Library (EFSL) composed of 1056 mini and small chemical fragments selected from a substructure analysis of the ECBL. Access to the EFSL is open to researchers from both academia and industry. Using EFSL, eight fragment screening campaigns using different structural and biophysical methods have successfully identified fragment hits in the last two years. As one of the highlighted projects for antibiotics, we describe the screening by Bio-Layer Interferometry (BLI) of the EFSL, the identification of a 35 μM fragment hit targeting the beta-ketoacyl-ACP synthase 2 (FabF), its binding confirmation to the protein by X-ray crystallography (PDB 8PJ0), its subsequent rapid exploration of its surrounding chemical space through hit-picking of ECBL compounds that contain the fragment hit as a core substructure, and the final binding confirmation of two follow-up hits by X-ray crystallography (PDB 8R0I and 8R1V).
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Affiliation(s)
- Xavier Jalencas
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88 08003 Barcelona Spain
| | - Hannes Berg
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Ludvik Olai Espeland
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
- Department of Chemistry, University of Bergen Allégaten 41 5007 Bergen Norway
| | - Sridhar Sreeramulu
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Franziska Kinnen
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Christian Richter
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
| | - Charis Georgiou
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
| | | | - Edgar Specker
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Kristaps Jaudzems
- Latvian Institute of Organic Synthesis Aizkraules 21 Riga LV-1006 Latvia
| | - Tanja Miletić
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Robert Harmel
- EU-OPENSCREEN ERIC Robert-Rössle Straße 10 13125 Berlin Germany
| | - Phil Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) Schnackenburgallee 114 22525 Hamburg Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) Theodor Stern Kai 7 60590 Frankfurt Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute for Organic Chemistry Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Chemical Biology, Goethe University Max-von-Laue-Str. 7 60438 Frankfurt/M Germany
- Instruct-ERIC Oxford House, Parkway Court, John Smith Drive Oxford OX4 2JY UK
| | - Ruth Brenk
- Department of Biomedicine, University of Bergen Jonas Lies Vei 91 5020 Bergen Norway
- Computational Biology Unit, University of Bergen Thormøhlensgate 55 5008 Bergen Norway
| | - Aigars Jirgensons
- Latvian Institute of Organic Synthesis Aizkraules 21 Riga LV-1006 Latvia
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) Schnackenburgallee 114 22525 Hamburg Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD) Theodor Stern Kai 7 60590 Frankfurt Germany
| | - Jordi Mestres
- Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute Parc de Recerca Biomèdica (PRBB), Doctor Aiguader 88 08003 Barcelona Spain
- Institut de Quimica Computacional i Catalisi, Facultat de Ciencies, Universitat de Girona Maria Aurelia Capmany 69 17003 Girona Catalonia Spain
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10
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Favaro A, Sturlese M. A Novel NMR-Based Protocol to Screen Ultralow Molecular Weight Fragments. J Med Chem 2024; 67:3874-3884. [PMID: 38426508 DOI: 10.1021/acs.jmedchem.3c02222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Fragment-based lead discovery has emerged as one of the most efficient screening strategies for finding hit molecules in drug discovery. Recently, a novel strategy based on a class of fragments characterized by an ultralow molecular weight (ULMW) has been proposed. These fragments bind to the target with a very low affinity, requiring reliable biophysical methods for detection. The most notable application of ULMW used a set of 81 fragments, named MiniFrags, and screened them by X-ray crystallography. We extended the utilization of this novel class of fragments to another gold standard technique for fragment-based screening: nuclear magnetic resonance (NMR). Here, we present a novel NMR protocol to detect and analyze such weak interactions in a challenging real-world scenario: a flexible target with a flat, water-exposed binding site. We identified a subset of 69 highly water-soluble MiniFrags that were screened against the antiapoptotic protein human Bfl-1.
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Affiliation(s)
- Annagiulia Favaro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, 35131 Padova, Italy
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11
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Keeley A, Kopranovic A, Di Lorenzo V, Ábrányi-Balogh P, Jänsch N, Lai LN, Petri L, Orgován Z, Pölöske D, Orlova A, Németh A, Desczyk C, Imre T, Bajusz D, Moriggl R, Meyer-Almes FJ, Keserü GM. Electrophilic MiniFrags Revealed Unprecedented Binding Sites for Covalent HDAC8 Inhibitors. J Med Chem 2024; 67:572-585. [PMID: 38113354 PMCID: PMC10788917 DOI: 10.1021/acs.jmedchem.3c01779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/06/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023]
Abstract
Screening of ultra-low-molecular weight ligands (MiniFrags) successfully identified viable chemical starting points for a variety of drug targets. Here we report the electrophilic analogues of MiniFrags that allow the mapping of potential binding sites for covalent inhibitors by biochemical screening and mass spectrometry. Small electrophilic heterocycles and their N-quaternized analogues were first characterized in the glutathione assay to analyze their electrophilic reactivity. Next, the library was used for systematic mapping of potential covalent binding sites available in human histone deacetylase 8 (HDAC8). The covalent labeling of HDAC8 cysteines has been proven by tandem mass spectrometry measurements, and the observations were explained by mutating HDAC8 cysteines. As a result, screening of electrophilic MiniFrags identified three potential binding sites suitable for the development of allosteric covalent HDAC8 inhibitors. One of the hit fragments was merged with a known HDAC8 inhibitor fragment using different linkers, and the linker length was optimized to result in a lead-like covalent inhibitor.
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Affiliation(s)
- Aaron
B. Keeley
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Aleksandra Kopranovic
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Vincenzo Di Lorenzo
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Niklas Jänsch
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Linh N. Lai
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - László Petri
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Zoltán Orgován
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Daniel Pölöske
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Anna Orlova
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - András
György Németh
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Charlotte Desczyk
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - Tímea Imre
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- MS
Metabolomics
Research Group, Research Centre for Natural
Sciences, Magyar tudósok
krt 2, H-1117 Budapest, Hungary
| | - Dávid Bajusz
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
| | - Richard Moriggl
- Institute
of Animal Breeding and Genetics, University
of Veterinary Medicine, 1210 Vienna, Austria
| | - Franz-Josef Meyer-Almes
- Department
of Chemical Engineering and Biotechnology, University of Applied Sciences Darmstadt, Haardtring 100, 64295 Darmstadt, Germany
| | - György M. Keserü
- Medicinal
Chemistry Research Group, Research Centre
for Natural Sciences, Magyar tudósok krt 2, H-1117 Budapest, Hungary
- Department
of Organic Chemistry and Technology, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
- National
Laboratory for Drug Research and Development, H-1117 Budapest, Hungary
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12
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Stegmann DP, Steuber J, Fritz G, Wojdyla JA, Sharpe ME. Fast fragment and compound screening pipeline at the Swiss Light Source. Methods Enzymol 2023; 690:235-284. [PMID: 37858531 DOI: 10.1016/bs.mie.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Crystallography-based fragment screening is a highly effective technique employed in structure-based drug discovery to expand the range of lead development opportunities. It allows screening and sorting of weakly binding, low molecular mass fragments, which can be developed into larger high-affinity lead compounds. Technical improvements at synchrotron beamlines, design of innovative libraries mapping chemical space efficiently, effective soaking methods and enhanced data analysis have enabled the implementation of high-throughput fragment screening pipelines at multiple synchrotron facilities. This widened access to CBFS beyond the pharma industry has allowed academic users to rapidly screen large quantities of fragment-soaked protein crystals. The positive outcome of a CBFS campaign is a set of structures that present the three-dimensional arrangement of fragment-protein complexes in detail, thereby providing information on the location and the mode of interaction of bound fragments. Through this review, we provide users with a comprehensive guide that sets clear expectations before embarking on a crystallography-based fragment screening campaign. We present a list of essential pre-requirements that must be assessed, including the suitability of your current crystal system for a fragment screening campaign. Furthermore, we extensively discuss the available methodological options, addressing their limitations and providing strategies to overcome them. Additionally, we provide a brief perspective on how to proceed once hits are obtained. Notably, we emphasize the solutions we have implemented for instrumentation and software development within our Fast Fragment and Compound Screening pipeline. We also highlight third-party software options that can be utilized for rapid refinement and hit assessment.
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Affiliation(s)
| | - Julia Steuber
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Stuttgart, Germany
| | - Günter Fritz
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Stuttgart, Germany.
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13
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Salvini CLA, Darlot B, Davison J, Martin MP, Tudhope SJ, Turberville S, Kawamura A, Noble MEM, Wedge SR, Crawford JJ, Waring MJ. Fragment expansion with NUDELs - poised DNA-encoded libraries. Chem Sci 2023; 14:8288-8294. [PMID: 37564419 PMCID: PMC10411621 DOI: 10.1039/d3sc01171b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Optimisation of the affinity of lead compounds is a critical challenge in the identification of drug candidates and chemical probes and is a process that takes many years. Fragment-based drug discovery has become established as one of the methods of choice for drug discovery starting with small, low affinity compounds. Due to their low affinity, the evolution of fragments to desirable levels of affinity is often a key challenge. The accepted best method for increasing the potency of fragments is by iterative fragment growing, which can be very time consuming and complex. Here, we introduce a paradigm for fragment hit optimisation using poised DNA-encoded chemical libraries (DELs). The synthesis of a poised DEL, a partially constructed library that retains a reactive handle, allows the coupling of any active fragment for a specific target protein, allowing rapid discovery of potent ligands. This is illustrated for bromodomain-containing protein 4 (BRD4), in which a weakly binding fragment was coupled to a 42-member poised DEL via Suzuki-Miyaura cross coupling resulting in the identification of an inhibitor with 51 nM affinity in a single step, representing an increase in potency of several orders of magnitude from an original fragment. The potency of the compound was shown to arise from the synergistic combination of substructures, which would have been very difficult to discover by any other method and was rationalised by X-ray crystallography. The compound showed attractive lead-like properties suitable for further optimisation and demonstrated BRD4-dependent cellular pharmacology. This work demonstrates the power of poised DELs to rapidly optimise fragments, representing an attractive generic approach to drug discovery.
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Affiliation(s)
- Catherine L A Salvini
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Benoit Darlot
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Jack Davison
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
| | - Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Susan J Tudhope
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Shannon Turberville
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Akane Kawamura
- Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
- Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - Stephen R Wedge
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Translational and Clinical Research Institute, Newcastle University Paul O'Gorman Building NE2 4HH UK
| | - James J Crawford
- Genentech Inc. 1 DNA Way South San Francisco California 94080 USA
| | - Michael J Waring
- Cancer Research Horizons Therapeutic Innovation Newcastle Drug Discovery Group, Chemistry, School of Natural and Environmental Sciences, Newcastle University Bedson Building NE1 7RU UK
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14
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Bryan DR, Kulp JL, Mahapatra MK, Bryan RL, Viswanathan U, Carlisle MN, Kim S, Schutte WD, Clarke KV, Doan TT, Kulp JL. BMaps: A Web Application for Fragment-Based Drug Design and Compound Binding Evaluation. J Chem Inf Model 2023; 63:4229-4236. [PMID: 37406353 DOI: 10.1021/acs.jcim.3c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Fragment-based drug design uses data about where, and how strongly, small chemical fragments bind to proteins, to assemble new drug molecules. Over the past decade, we have been successfully using fragment data, derived from thermodynamically rigorous Monte Carlo fragment-protein binding simulations, in dozens of preclinical drug programs. However, this approach has not been available to the broader research community because of the cost and complexity of doing simulations and using design tools. We have developed a web application, called BMaps, to make fragment-based drug design widely available with greatly simplified user interfaces. BMaps provides access to a large repository (>550) of proteins with 100s of precomputed fragment maps, druggable hot spots, and high-quality water maps. Users can also employ their own structures or those from the Protein Data Bank and AlphaFold DB. Multigigabyte data sets are searched to find fragments in bondable orientations, ranked by a binding-free energy metric. The designers use this to select modifications that improve affinity and other properties. BMaps is unique in combining conventional tools such as docking and energy minimization with fragment-based design, in a very easy to use and automated web application. The service is available at https://www.boltzmannmaps.com.
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Affiliation(s)
- Daniel R Bryan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - John L Kulp
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States
| | - Manoj K Mahapatra
- Kanak Manjari Institute of Pharmaceutical Sciences, Rourkela 769015, Odisha, India
| | - Richard L Bryan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Usha Viswanathan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Micah N Carlisle
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Surim Kim
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Zymergen, Inc., 430 E. 29th Street, Suite 625, New York, New York 10016, United States
| | - William D Schutte
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Kevaughn V Clarke
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Tony T Doan
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - John L Kulp
- Conifer Point Pharmaceuticals, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
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15
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Martin MP, Endicott JA, Noble MEM, Tatum NJ. Crystallographic fragment screening in academic cancer drug discovery. Methods Enzymol 2023; 690:211-234. [PMID: 37858530 DOI: 10.1016/bs.mie.2023.06.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Fragment-based drug discovery (FBDD) has brought several drugs to the clinic, notably to target proteins once considered to be challenging, or even undruggable. Screening in FBDD relies upon observing and/or measuring weak (millimolar-scale) binding events using biophysical techniques or crystallographic fragment screening. This latter structural approach provides no information about binding affinity but can reveal binding mode and atomic detail on protein-fragment interactions to accelerate hit-to-lead development. In recent years, high-throughput platforms have been developed at synchrotron facilities to screen thousands of fragment-soaked crystals. However, using accessible manual techniques it is possible to run informative, smaller-scale screens within an academic lab setting. This chapter describes general protocols for home laboratory-scale fragment screening, from fragment soaking through to structure solution and, where appropriate, signposts to background, protocols or alternatives elsewhere.
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Affiliation(s)
- Mathew P Martin
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Jane A Endicott
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Martin E M Noble
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom
| | - Natalie J Tatum
- Cancer Research Horizons Therapeutic Innovation, Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Translation and Clinical Research Institute, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, United Kingdom.
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16
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Wang ZZ, Shi XX, Huang GY, Hao GF, Yang GF. Fragment-based drug discovery supports drugging 'undruggable' protein-protein interactions. Trends Biochem Sci 2023; 48:539-552. [PMID: 36841635 DOI: 10.1016/j.tibs.2023.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/05/2023] [Accepted: 01/31/2023] [Indexed: 02/26/2023]
Abstract
Protein-protein interactions (PPIs) have important roles in various cellular processes, but are commonly described as 'undruggable' therapeutic targets due to their large, flat, featureless interfaces. Fragment-based drug discovery (FBDD) has achieved great success in modulating PPIs, with more than ten compounds in clinical trials. Here, we highlight the progress of FBDD in modulating PPIs for therapeutic development. Targeting hot spots that have essential roles in both fragment binding and PPIs provides a shortcut for the development of PPI modulators via FBDD. We highlight successful cases of cracking the 'undruggable' problems of PPIs using fragment-based approaches. We also introduce new technologies and future trends. Thus, we hope that this review will provide useful guidance for drug discovery targeting PPIs.
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Affiliation(s)
- Zhi-Zheng Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Xing-Xing Shi
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Guang-Yi Huang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China; National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, PR China.
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, Central China Normal University, Wuhan, 430079, PR China.
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17
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Whitehouse RL, Alwan WS, Ilyichova OV, Taylor AJ, Chandrashekaran IR, Mohanty B, Doak BC, Scanlon MJ. Fragment screening libraries for the identification of protein hot spots and their minimal binding pharmacophores. RSC Med Chem 2023; 14:135-143. [PMID: 36760747 PMCID: PMC9890547 DOI: 10.1039/d2md00253a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Fragment-based drug design relies heavily on structural information for the elaboration and optimisation of hits. The ability to identify neighbouring binding hot spots, energetically favourable interactions and conserved binding motifs in protein structures through X-ray crystallography can inform the evolution of fragments into lead-like compounds through structure-based design. The composition of fragment libraries can be designed and curated to fit this purpose and herein, we describe and compare screening libraries containing compounds comprising between 2 and 18 heavy atoms. We evaluate the properties of the compounds in these libraries and assess their ability to probe protein surfaces for binding hot spots.
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Affiliation(s)
- Rebecca L Whitehouse
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Wesam S Alwan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Olga V Ilyichova
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Australian Synchrotron, ANSTO Clayton VIC 3168 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Ashley J Taylor
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Indu R Chandrashekaran
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Bradley C Doak
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
| | - Martin J Scanlon
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- ARC Training Centre for Fragment Based Design, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
- Monash Fragment Platform, Monash Institute of Pharmaceutical Sciences, Monash University Parkville VIC 3052 Australia
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18
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Chen PY, Han LT. Study on the molecular mechanism of anti-liver cancer effect of Evodiae fructus by network pharmacology and QSAR model. Front Chem 2023; 10:1060500. [PMID: 36700075 PMCID: PMC9868320 DOI: 10.3389/fchem.2022.1060500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction: Evodiae Fructus (EF) is the dried, near ripe fruit of Euodia rutaecarpa (Juss.) Benth in Rutaceae. Numerous studies have demonstrated its anti-liver cancer properties. However, the molecular mechanism of Evodiae fructus against liver cancer and its structure-activity connection still require clarification. Methods: We utilized network pharmacology and a QSAR (2- and 3-dimensional) model to study the anti-liver cancer effect of Evodiae fructus. First, by using network pharmacology to screen the active substances and targets of Evodiae fructus, we investigated the signaling pathways involved in the anti-liver cancer actions of Evodiae fructus. The 2D-QSAR pharmacophore model was then used to predict the pIC50 values of compounds. The hiphop method was used to create an ideal 3D-QSAR pharmacophore model for the prediction of Evodiae fructus compounds. Finally, molecular docking was used to validate the rationality of the pharmacophore, and molecular dynamics was used to disclose the stability of the compounds by assessing the trajectories in 10 ns using RMSD, RMSF, Rg, and hydrogen bonding metrics. Results: In total, 27 compounds were acquired from the TCMSP and TCM-ID databases, and 45 intersection targets were compiled using Venn diagrams. Network integration analysis was used in this study to identify SRC as a primary target. Key pathways were discovered by KEGG pathway analysis, including PD-L1 expression and PD-1 checkpoint pathway, EGFR tyrosine kinase inhibitor resistance, and ErbB signaling pathway. Using a 2D-QSAR pharmacophore model and the MLR approach to predict chemical activity, ten highly active compounds were found. Two hydrophobic features and one hydrogen bond acceptor feature in the 3D-QSAR pharmacophore model were validated by training set chemicals. The results of molecular docking revealed that 10 active compounds had better docking scores with SRC and were linked to residues via hydrogen and hydrophobic bonds. Molecular dynamics was used to show the structural stability of obacunone, beta-sitosterol, and sitosterol. Conclusion:Pharmacophore 01 has high selectivity and the ability to distinguish active and inactive compounds, which is the optimal model for this study. Obacunone has the optimal binding ability with SRC. The pharmacophore model proposed in this study provides theoretical support for further screening effective anti-cancer Chinese herbal compounds and optimizing the compound structure.
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Affiliation(s)
- Peng-Yu Chen
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China
| | - Lin-Tao Han
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, China,Key Laboratory of Traditional Chinese Medicine Resources and Prescription, Ministry of Education, Wuhan, China,*Correspondence: Lin-Tao Han,
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19
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Yu W, Weber DJ, MacKerell AD. Computer-Aided Drug Design: An Update. Methods Mol Biol 2023; 2601:123-152. [PMID: 36445582 PMCID: PMC9838881 DOI: 10.1007/978-1-0716-2855-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Computer-aided drug design (CADD) approaches are playing an increasingly important role in understanding the fundamentals of ligand-receptor interactions and helping medicinal chemists design therapeutics. About 5 years ago, we presented a chapter devoted to an overview of CADD methods and covered typical CADD protocols including structure-based drug design (SBDD) and ligand-based drug design (LBDD) approaches that were frequently used in the antibiotic drug design process. Advances in computational hardware and algorithms and emerging CADD methods are enhancing the accuracy and ability of CADD in drug design and development. In this chapter, an update to our previous chapter is provided with a focus on new CADD approaches from our laboratory and other peers that can be employed to facilitate the development of antibiotic therapeutics.
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Affiliation(s)
- Wenbo Yu
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA.
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland, Baltimore, MD, USA.
| | - David J Weber
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
- Institute for Bioscience and Biotechnology Research (IBBR), Rockville, MD, USA.
- Center for Biomolecular Therapeutics (CBT), School of Medicine, University of Maryland, Baltimore, MD, USA.
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20
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Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
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Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
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21
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Davison G, Martin MP, Turberville S, Dormen S, Heath R, Heptinstall AB, Lawson M, Miller DC, Ng YM, Sanderson JN, Hope I, Wood DJ, Cano C, Endicott JA, Hardcastle IR, Noble MEM, Waring MJ. Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions. J Med Chem 2022; 65:15416-15432. [PMID: 36367089 PMCID: PMC9706561 DOI: 10.1021/acs.jmedchem.2c01357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Indexed: 11/13/2022]
Abstract
The development of ligands for biological targets is critically dependent on the identification of sites on proteins that bind molecules with high affinity. A set of compounds, called FragLites, can identify such sites, along with the interactions required to gain affinity, by X-ray crystallography. We demonstrate the utility of FragLites in mapping the binding sites of bromodomain proteins BRD4 and ATAD2 and demonstrate that FragLite mapping is comparable to a full fragment screen in identifying ligand binding sites and key interactions. We extend the FragLite set with analogous compounds derived from amino acids (termed PepLites) that mimic the interactions of peptides. The output of the FragLite maps is shown to enable the development of ligands with leadlike potency. This work establishes the use of FragLite and PepLite screening at an early stage in ligand discovery allowing the rapid assessment of tractability of protein targets and informing downstream hit-finding.
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Affiliation(s)
- Gemma Davison
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Mathew P. Martin
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Shannon Turberville
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Selma Dormen
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Richard Heath
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Amy B. Heptinstall
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Marie Lawson
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Duncan C. Miller
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Yi Min Ng
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - James N. Sanderson
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Ian Hope
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Daniel J. Wood
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Céline Cano
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Jane A. Endicott
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Ian R. Hardcastle
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Martin E. M. Noble
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Michael J. Waring
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
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22
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Bon M, Bilsland A, Bower J, McAulay K. Fragment-based drug discovery-the importance of high-quality molecule libraries. Mol Oncol 2022; 16:3761-3777. [PMID: 35749608 PMCID: PMC9627785 DOI: 10.1002/1878-0261.13277] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/16/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is now established as a complementary approach to high-throughput screening (HTS). Contrary to HTS, where large libraries of drug-like molecules are screened, FBDD screens involve smaller and less complex molecules which, despite a low affinity to protein targets, display more 'atom-efficient' binding interactions than larger molecules. Fragment hits can, therefore, serve as a more efficient start point for subsequent optimisation, particularly for hard-to-drug targets. Since the number of possible molecules increases exponentially with molecular size, small fragment libraries allow for a proportionately greater coverage of their respective 'chemical space' compared with larger HTS libraries comprising larger molecules. However, good library design is essential to ensure optimal chemical and pharmacophore diversity, molecular complexity, and physicochemical characteristics. In this review, we describe our views on fragment library design, and on what constitutes a good fragment from a medicinal and computational chemistry perspective. We highlight emerging chemical and computational technologies in FBDD and discuss strategies for optimising fragment hits. The impact of novel FBDD approaches is already being felt, with the recent approval of the covalent KRASG12C inhibitor sotorasib highlighting the utility of FBDD against targets that were long considered undruggable.
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Affiliation(s)
- Marta Bon
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Alan Bilsland
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Justin Bower
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Kirsten McAulay
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
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23
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Martin MP, Noble MEM. Exiting the tunnel of uncertainty: crystal soak to validated hit. Acta Crystallogr D Struct Biol 2022; 78:1294-1302. [PMID: 36322414 PMCID: PMC9629488 DOI: 10.1107/s2059798322009986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/12/2022] [Indexed: 11/28/2022] Open
Abstract
Crystallographic fragment screens provide an efficient and effective way to identify small-molecule ligands of a crystallized protein. Due to their low molecular weight, such hits tend to have low, often unquantifiable, affinity for their target, complicating the twin challenges of validating the hits as authentic solution-phase ligands of the target and identifying the `best' hit(s) for further elaboration. In this article, approaches that address these challenges are assessed. Using retrospective analysis of a recent ATAD2 hit-identification campaign, alongside other examples of successful fragment-screening campaigns, it is suggested that hit validation and prioritization are best achieved by a `triangulation' approach in which the results of multiple available biochemical and biophysical techniques are correlated to develop qualitative structure-activity relationships (SARs). Such qualitative SARs may indeed be the only means by which to navigate a project through the tunnel of uncertainty that prevails before on-scale biophysical, biochemical and/or biological measurements become possible.
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Affiliation(s)
- Mathew P. Martin
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Martin E. M. Noble
- Cancer Research UK Drug Discovery Unit, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
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24
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Lucas SCC, Börjesson U, Bostock MJ, Cuff J, Edfeldt F, Embrey KJ, Eriksson PO, Gohlke A, Gunnarson A, Lainchbury M, Milbradt AG, Moore R, Rawlins PB, Sinclair I, Stubbs C, Storer RI. Fragment screening at AstraZeneca: developing the next generation biophysics fragment set. RSC Med Chem 2022; 13:1052-1057. [PMID: 36324499 PMCID: PMC9491351 DOI: 10.1039/d2md00154c] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/29/2022] [Indexed: 05/18/2024] Open
Abstract
Fragment based drug discovery is a critical part of the lead generation toolbox and relies heavily on a readily available, high quality fragment library. Over years of use, the AstraZeneca fragment set had become partially depleted and instances of compound deterioration had been found. It was recognised that a redevelopment was required. This provided an opportunity to evolve our screening sets strategy, whilst ensuring that the quality of the fragment set met the robust requirements of fragment screening campaigns. In this communication we share the strategy employed, in particular highlighting two aspects of our approach that we believe others in the community would benefit from, namely that; (i) fragments were selected with input from Medicinal Chemists at an early stage, and (ii) the library was arranged in a layered format to ensure maximum flexibility on a per target basis.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Ulf Börjesson
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | - Mark J Bostock
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - John Cuff
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca Alderley Park UK
| | - Fredrik Edfeldt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | - Kevin J Embrey
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Per-Olof Eriksson
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | - Andrea Gohlke
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Anders Gunnarson
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Gothenburg Sweden
| | | | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Rachel Moore
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Alderley Park UK
| | - Philip B Rawlins
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - Ian Sinclair
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca Alderley Park UK
| | - Christopher Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca Cambridge UK
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca Cambridge UK
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25
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Kognole AA, Hazel A, MacKerell AD. SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules. J Chem Theory Comput 2022; 18:5672-5691. [PMID: 35913731 PMCID: PMC9474704 DOI: 10.1021/acs.jctc.2c00381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA molecules can act as potential drug targets in different diseases, as their dysregulated expression or misfolding can alter various cellular processes. Noncoding RNAs account for ∼70% of the human genome, and these molecules can have complex tertiary structures that present a great opportunity for targeting by small molecules. In the present study, the site identification by ligand competitive saturation (SILCS) computational approach is extended to target RNA, termed SILCS-RNA. Extensions to the method include an enhanced oscillating excess chemical potential protocol for the grand canonical Monte Carlo calculations and individual simulations of the neutral and charged solutes from which the SILCS functional group affinity maps (FragMaps) are calculated for subsequent binding site identification and docking calculations. The method is developed and evaluated against seven RNA targets and their reported small molecule ligands. SILCS-RNA provides a detailed characterization of the functional group affinity pattern in the small molecule binding sites, recapitulating the types of functional groups present in the ligands. The developed method is also shown to be useful for identification of new potential binding sites and identifying ligand moieties that contribute to binding, granular information that can facilitate ligand design. However, limitations in the method are evident including the ability to map the regions of binding sites occupied by ligand phosphate moieties and to fully account for the wide range of conformational heterogeneity in RNA associated with binding of different small molecules, emphasizing inherent challenges associated with applying computer-aided drug design methods to RNA. While limitations are present, the current study indicates how the SILCS-RNA approach may enhance drug discovery efforts targeting RNAs with small molecules.
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Affiliation(s)
- Abhishek A Kognole
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, Baltimore, Maryland 21201, United States
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26
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Osipov EM, Munawar AH, Beelen S, Fearon D, Douangamath A, Wild C, Weeks SD, Van Aerschot A, von Delft F, Strelkov SV. Discovery of novel druggable pockets on polyomavirus VP1 through crystallographic fragment-based screening to develop capsid assembly inhibitors. RSC Chem Biol 2022; 3:1013-1027. [PMID: 35974998 PMCID: PMC9347357 DOI: 10.1039/d2cb00052k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/24/2022] [Indexed: 11/21/2022] Open
Abstract
Polyomaviruses are a family of ubiquitous double-stranded DNA viruses many of which are human pathogens. These include BK polyomavirus which causes severe urinary tract infection in immunocompromised patients and Merkel cell polyomavirus associated with aggressive cancers. The small genome of polyomaviruses lacks conventional drug targets, and no specific drugs are available at present. Here we focus on the main structural protein VP1 of BK polyomavirus which is responsible for icosahedral capsid formation. To provide a foundation towards rational drug design, we crystallized truncated VP1 pentamers and subjected them to a high-throughput screening for binding drug-like fragments through a direct X-ray analysis. To enable a highly performant screening, rigorous optimization of the crystallographic pipeline and processing with the latest generation PanDDA2 software were necessary. As a result, a total of 144 binding hits were established. Importantly, the hits are well clustered in six surface pockets. Three pockets are located on the outside of the pentamer and map on the regions where the 'invading' C-terminal arm of another pentamer is attached upon capsid assembly. Another set of three pockets is situated within the wide pore along the five-fold axis of the VP1 pentamer. These pockets are situated at the interaction interface with the minor capsid protein VP2 which is indispensable for normal functioning of the virus. Here we systematically analyse the three outside pockets which are highly conserved across various polyomaviruses, while point mutations in these pockets are detrimental for viral replication. We show that one of the pockets can accommodate antipsychotic drug trifluoperazine. For each pocket, we derive pharmacophore features which enable the design of small molecules preventing the interaction between VP1 pentamers and therefore inhibiting capsid assembly. Our data lay a foundation towards a rational development of first-in-class drugs targeting polyomavirus capsid.
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Affiliation(s)
| | - Ali H Munawar
- Biocrystallography, KU Leuven Herestraat 49 Leuven Belgium
- Orthogon Therapeutics LLC 45 Dan Road Suite 126 Canton MA 02021 USA
- Pledge Tx B.V. Gaston Geenslaan 1 Leuven Belgium
| | - Steven Beelen
- Biocrystallography, KU Leuven Herestraat 49 Leuven Belgium
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot 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 UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
| | - Conor Wild
- Centre for Medicines Discovery, University of Oxford South Parks Road Headington OX3 7DQ UK
- Department of Statistics, University of Oxford 29 St Giles' Oxford OX1 3LB UK
| | - Stephen D Weeks
- Biocrystallography, KU Leuven Herestraat 49 Leuven Belgium
- Pledge Tx B.V. Gaston Geenslaan 1 Leuven Belgium
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven Herestraat 49 Leuven Belgium
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus Didcot UK
- Research Complex at Harwell, Harwell Science and Innovation Campus Didcot OX11 0FA UK
- 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
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27
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Liu J, Yuan S, Yao Y, Wang J, Scalabrino G, Jiang S, Sheridan H. Network Pharmacology and Molecular Docking Elucidate the Underlying Pharmacological Mechanisms of the Herb Houttuynia cordata in Treating Pneumonia Caused by SARS-CoV-2. Viruses 2022; 14:v14071588. [PMID: 35891565 PMCID: PMC9324059 DOI: 10.3390/v14071588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Used in Asian countries, including China, Japan, and Thailand, Houttuynia cordata Thumb (H. cordata; Saururaceae, HC) is a traditional herbal medicine that possesses favorable antiviral properties. As a potent folk therapy used to treat pulmonary infections, further research is required to fully elucidate the mechanisms of its pharmacological activities and explore its therapeutic potential for treating pneumonia caused by SARS-CoV-2. This study explores the pharmacological mechanism of HC on pneumonia using a network pharmacological approach combined with reprocessing expression profiling by high-throughput sequencing to demonstrate the therapeutic mechanisms of HC for treating pneumonia at a systemic level. The integration of these analyses suggested that target factors are involved in four signaling pathways, including PI3K-Akt, Jak-STAT, MAPK, and NF-kB. Molecular docking and molecular dynamics simulation were applied to verify these results, indicating a stable combination between four metabolites (Afzelin, Apigenin, Kaempferol, Quercetin) and six targets (DPP4, ELANE, HSP90AA1, IL6, MAPK1, SERPINE1). These natural metabolites have also been reported to bind with ACE2 and 3CLpro of SARS-CoV-2, respectively. The data suggest that HC exerts collective therapeutic effects against pneumonia caused by SARS-CoV-2 and provides a theoretical basis for further study of the active drug-like ingredients and mechanism of HC in treating pneumonia.
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Affiliation(s)
- Junying Liu
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02PN40 Dublin, Ireland; (J.L.); (J.W.); (G.S.)
| | - Shouli Yuan
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100080, China;
| | - Yao Yao
- Biocomputing and Developmental Systems, Lero—The Science Foundation Ireland Research Centre for Software, Department of Computer Science & Information Systems, The University of Limerick, V94T9PX Limerick, Ireland;
| | - Jinfan Wang
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02PN40 Dublin, Ireland; (J.L.); (J.W.); (G.S.)
| | - Gaia Scalabrino
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02PN40 Dublin, Ireland; (J.L.); (J.W.); (G.S.)
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai 200032, China
- Correspondence: (S.J.); (H.S.)
| | - Helen Sheridan
- NatPro Center, School of Pharmacy and Pharmaceutical Sciences, Trinity College Dublin, D02PN40 Dublin, Ireland; (J.L.); (J.W.); (G.S.)
- Correspondence: (S.J.); (H.S.)
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28
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Kell SR, Wang Z, Ji H. Fragment hopping protocol for the design of small-molecule protein-protein interaction inhibitors. Bioorg Med Chem 2022; 69:116879. [PMID: 35749838 DOI: 10.1016/j.bmc.2022.116879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/29/2022] [Accepted: 06/08/2022] [Indexed: 11/02/2022]
Abstract
Fragment-based ligand discovery (FBLD) is one of the most successful approaches to designing small-molecule protein-protein interaction (PPI) inhibitors. The incorporation of computational tools to FBLD allows the exploration of chemical space in a time- and cost-efficient manner. Herein, a computational protocol for the development of small-molecule PPI inhibitors using fragment hopping, a fragment-based de novo design approach, is described and a case study is presented to illustrate the efficiency of this protocol. Fragment hopping facilitates the design of PPI inhibitors from scratch solely based on key binding features in the PPI complex structure. This approach is an open system that enables the inclusion of different state-of-the-art programs and softwares to improve its performances.
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Affiliation(s)
- Shelby R Kell
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, United States; Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Zhen Wang
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, United States; Department of Chemistry, University of South Florida, Tampa, FL 33620, United States
| | - Haitao Ji
- Drug Discovery Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, United States; Department of Chemistry, University of South Florida, Tampa, FL 33620, United States.
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29
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Willis N, Mahy W, Sipthorp J, Zhao Y, Woodward HL, Atkinson BN, Bayle ED, Svensson F, Frew S, Jeganathan F, Monaghan A, Benvegnù S, Jolly S, Vecchia L, Ruza RR, Kjær S, Howell S, Snijders AP, Bictash M, Salinas PC, Vincent JP, Jones EY, Whiting P, Fish PV. Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit. J Med Chem 2022; 65:7212-7230. [PMID: 35536179 PMCID: PMC9150124 DOI: 10.1021/acs.jmedchem.2c00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Indexed: 12/26/2022]
Abstract
Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer's disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets.
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Affiliation(s)
- Nicky
J. Willis
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - William Mahy
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - James Sipthorp
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Yuguang Zhao
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Hannah L. Woodward
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Benjamin N. Atkinson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Elliott D. Bayle
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Fredrik Svensson
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Sarah Frew
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Fiona Jeganathan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Amy Monaghan
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Stefano Benvegnù
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Sarah Jolly
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Luca Vecchia
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Reinis R. Ruza
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Svend Kjær
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - Steven Howell
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | | | - Magda Bictash
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Patricia C. Salinas
- Department
of Cell and Developmental Biology, Laboratory for Molecular and Cellular
Biology, University College London, London WC1E 6BT, U.K.
| | - Jean-Paul Vincent
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
| | - E. Yvonne Jones
- Division
of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, The Henry Wellcome Building for Genomic Medicine,
Roosevelt Drive, Oxford OX3 7BN, U.K.
| | - Paul Whiting
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
| | - Paul V. Fish
- Alzheimer’s
Research UK UCL Drug Discovery Institute, University College London, Cruciform Building, Gower Street, London WC1E 6BT, U.K.
- The
Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, U.K.
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30
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Revillo Imbernon J, Jacquemard C, Bret G, Marcou G, Kellenberger E. Comprehensive analysis of commercial fragment libraries. RSC Med Chem 2022; 13:300-310. [PMID: 35434627 PMCID: PMC8942207 DOI: 10.1039/d1md00363a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
Screening of fragment libraries is a valuable approach to the drug discovery process. The quality of the library is one of the keys to success, and more particularly the design or choice of a library has to meet the specificities of the research program. In this study, we made an inventory of the commercial fragment libraries and we established a methodology which allows any library to be positioned in relation to the complete offer currently on the market, by addressing the following questions: does this chemical library look like another chemical library? What is the coverage of the current chemical space by this chemical library? What are the characteristic structural features of the fragments of this chemical library? We based our analysis on 2D and 3D chemical descriptors, framework class generation and the generative topographic map. We identified 59 270 scaffolds, which can be searched in a dedicated web site (https://gtmfrag.drugdesign.unistra.fr) and developed a model which accounts for fragment diversity while being easy to interpret (download at 10.5281/zenodo.5534434).
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Affiliation(s)
- Julia Revillo Imbernon
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Guillaume Bret
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Gilles Marcou
- Laboratory of Chemoinformatics, UMR7177 CNRS Université de StrasbourgStrasbourgFrance
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
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31
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Frederickson M, Selvam IR, Evangelopoulos D, McLean KJ, Katariya MM, Tunnicliffe RB, Campbell B, Kavanagh ME, Charoensutthivarakul S, Blankley RT, Levy CW, de Carvalho LPS, Leys D, Munro AW, Coyne AG, Abell C. A new strategy for hit generation: Novel in cellulo active inhibitors of CYP121A1 from Mycobacterium tuberculosis via a combined X-ray crystallographic and phenotypic screening approach (XP screen). Eur J Med Chem 2022; 230:114105. [PMID: 35065413 PMCID: PMC8856928 DOI: 10.1016/j.ejmech.2022.114105] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/06/2022] [Accepted: 01/06/2022] [Indexed: 12/27/2022]
Abstract
There is a pressing need for new drugs against tuberculosis (TB) to combat the growing resistance to current antituberculars. Herein a novel strategy is described for hit generation against promising TB targets involving X-ray crystallographic screening in combination with phenotypic screening. This combined approach (XP Screen) affords both a validation of target engagement as well as determination of in cellulo activity. The utility of this method is illustrated by way of an XP Screen against CYP121A1, a cytochrome P450 enzyme from Mycobacterium tuberculosis (Mtb) championed as a validated drug discovery target. A focused screening set was synthesized and tested by such means, with several members of the set showing promising activity against Mtb strain H37Rv. One compound was observed as an X-ray hit against CYP121A1 and showed improved activity against Mtb strain H37Rv under multiple assay conditions (pan-assay activity). Data obtained during X-ray crystallographic screening were utilized in a structure-based campaign to design a limited number of analogues (less than twenty), many of which also showed pan-assay activity against Mtb strain H37Rv. These included the benzo[b][1,4]oxazine derivative (MIC90 6.25 μM), a novel hit compound suitable as a starting point for a more involved hit to lead candidate medicinal chemistry campaign. CYP121 from M.tuberculosis has been previously shown to be a crucial target for the survival of the mycobacteria. Strategies previously employed have identified high affinity inhibitors however these have lacked activity on M.tuberculosis. The strategy reported here uses a combination of X-ray crystallography and phenotypic screening (XP Screen) to identify compounds. The XP screen approach identified a number of compounds which show good affinity (up to 3.2 μM) and MIC against M.tuberculosis (up to 6.25 μM).
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32
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Goel H, Hazel A, Yu W, Jo S, MacKerell AD. Application of Site-Identification by Ligand Competitive Saturation in Computer-Aided Drug Design. NEW J CHEM 2022; 46:919-932. [PMID: 35210743 PMCID: PMC8863107 DOI: 10.1039/d1nj04028f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Site Identification by Ligand Competitive Saturation (SILCS) is a molecular simulation approach that uses diverse small solutes in aqueous solution to obtain functional group affinity patterns of a protein or other macromolecule. This involves employing a combined Grand Canonical Monte Carlo (GCMC)-molecular dynamics (MD) method to sample the full 3D space of the protein, including deep binding pockets and interior cavities from which functional group free energy maps (FragMaps) are obtained. The information content in the maps, which include contributions from protein flexibilty and both protein and functional group desolvation contributions, can be used in many aspects of the drug discovery process. These include identification of novel ligand binding pockets, including allosteric sites, pharmacophore modeling, prediction of relative protein-ligand binding affinities for database screening and lead optimization efforts, evaluation of protein-protein interactions as well as in the formulation of biologics-based drugs including monoclonal antibodies. The present article summarizes the various tools developed in the context of the SILCS methodology and their utility in computer-aided drug design (CADD) applications, showing how the SILCS toolset can improve the drug-development process on a number of fronts with respect to both accuracy and throughput representing a new avenue of CADD applications.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States
| | - Anthony Hazel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States
| | - Sunhwan Jo
- SilcsBio LLC, 1100 Wicomico St. Suite 323, Baltimore, MD, 21230, United States
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20, Penn St. Baltimore, Maryland 21201, United States., SilcsBio LLC, 1100 Wicomico St. Suite 323, Baltimore, MD, 21230, United States.,, Tel: 410-706-7442, Fax: 410-706-5017
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33
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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] [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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34
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Chen PY, Yuan C, Hong ZC, Zhang Y, Ke XG, Yu B, Wang C, Xiao XC, Wu HZ, Yang YF. Revealing the mechanism of "Huai Hua San" in the treatment of ulcerative colitis based on network pharmacology and experimental study. JOURNAL OF ETHNOPHARMACOLOGY 2021; 281:114321. [PMID: 34118340 DOI: 10.1016/j.jep.2021.114321] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE "Huai Hua San" (HHS) is one of the first hundred ancient classic prescriptions drugs, which is commonly used to treat hemorrhoids, colitis, and other symptoms of wind heat in stool. However, the potential molecular mechanism of action of this substance remains unclear. AIMS OF THE STUDY In this study, we explored the active compounds of HHS for the treatment of ulcerative colitis (UC), predicted the potential targets of the drug, and studied its mechanism of action through network pharmacology via in vitro and in vivo experiments. MATERIALS AND METHODS First, we identified the active compounds and key targets of HHS for treating UC via network pharmacology. The key signaling pathways associated with the anti-inflammatory effect of HHS were analyzed. The anti-inflammatory effects of HHS and its active compounds were studied using the RAW264.7 inflammatory cell model in vitro. Furthermore, we used the dextran sulfate sodium (DSS) mouse model to explore the efficacy and mechanism of HHS in UC in vivo, and the expression level of key proteins were detected by Western blotting. RESULTS In all, 23 compounds and 97 targets were obtained from TCMSP database, PharmMapper database, and GeneCards database. After enrichment via Kyoto Encyclopedia of Genes and Genomes (KEGG), HIF-1 signaling pathway, PI3K/AKT signaling pathway, and VEGF signaling pathway were identified to be the top three signaling pathways associated with UC treatment. The results of molecular docking showed that the docking scores of the top 10 active compounds were higher than the threshold values. In vitro, different concentrations of HHS and the four main active compounds could effectively inhibit the release of inflammatory cytokines interleukin (IL)-6, tumor necrosis factor (TNF)-α, and IL-1 β. In vivo, HHS could alleviate UC symptoms. CONCLUSION Taken together, the treatment of UC with HHS may alleviate the inflammatory response of the colon, and HHS mainly inhibits the EGFR/PI3K/AKT/HIF-1/VEGF signaling pathways.
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Affiliation(s)
- Peng-Yu Chen
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Chong Yuan
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Zong-Chao Hong
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Ying Zhang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Xin-Ge Ke
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Bing Yu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Chen Wang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Xue-Cheng Xiao
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - He-Zhen Wu
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, 430065, China; Collaborative Innovation Center of Traditional Chinese Medicine of New Products for Geriatrics Hubei Province, Wuhan, 430065, China.
| | - Yan-Fang Yang
- Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065, China; Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan, 430065, China; Collaborative Innovation Center of Traditional Chinese Medicine of New Products for Geriatrics Hubei Province, Wuhan, 430065, China.
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35
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Norton D, Bonnette WG, Callahan JF, Carr MG, Griffiths-Jones CM, Heightman TD, Kerns JK, Nie H, Rich SJ, Richardson C, Rumsey W, Sanchez Y, Verdonk ML, Willems HMG, Wixted WE, Wolfe L, Woolford AJA, Wu Z, Davies TG. Fragment-Guided Discovery of Pyrazole Carboxylic Acid Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2 Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction. J Med Chem 2021; 64:15949-15972. [PMID: 34705450 DOI: 10.1021/acs.jmedchem.1c01351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NRF2-mediated cytoprotective response is central to cellular homoeostasis, and there is increasing interest in developing small-molecule activators of this pathway as therapeutics for diseases involving chronic oxidative stress. The protein KEAP1, which regulates NRF2, is a key point for pharmacological intervention, and we recently described the use of fragment-based drug discovery to develop a tool compound that directly disrupts the protein-protein interaction between NRF2 and KEAP1. We now present the identification of a second, chemically distinct series of KEAP1 inhibitors, which provided an alternative chemotype for lead optimization. Pharmacophoric information from our original fragment screen was used to identify new hit matter through database searching and to evolve this into a new lead with high target affinity and cell-based activity. We highlight how knowledge obtained from fragment-based approaches can be used to focus additional screening campaigns in order to de-risk projects through the rapid identification of novel chemical series.
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Affiliation(s)
- David Norton
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - William G Bonnette
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - James F Callahan
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Maria G Carr
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - Tom D Heightman
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | - Jeffrey K Kerns
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Hong Nie
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Sharna J Rich
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William Rumsey
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Yolanda Sanchez
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Marcel L Verdonk
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
| | | | - William E Wixted
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Lawrence Wolfe
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | | | - Zining Wu
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426-0989, United States
| | - Thomas G Davies
- Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, U.K
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36
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Martino E, Chiarugi S, Margheriti F, Garau G. Mapping, Structure and Modulation of PPI. Front Chem 2021; 9:718405. [PMID: 34692637 PMCID: PMC8529325 DOI: 10.3389/fchem.2021.718405] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Because of the key relevance of protein–protein interactions (PPI) in diseases, the modulation of protein-protein complexes is of relevant clinical significance. The successful design of binding compounds modulating PPI requires a detailed knowledge of the involved protein-protein system at molecular level, and investigation of the structural motifs that drive the association of the proteins at the recognition interface. These elements represent hot spots of the protein binding free energy, define the complex lifetime and possible modulation strategies. Here, we review the advanced technologies used to map the PPI involved in human diseases, to investigate the structure-function features of protein complexes, and to discover effective ligands that modulate the PPI for therapeutic intervention.
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Affiliation(s)
- Elisa Martino
- Laboratorio NEST, Scuola Normale Superiore, Pisa, Italy
| | - Sara Chiarugi
- Laboratorio NEST, Scuola Normale Superiore, Pisa, Italy.,BioStructures Lab, Istituto Italiano di Tecnologia (IIT@NEST), Pisa, Italy
| | | | - Gianpiero Garau
- BioStructures Lab, Istituto Italiano di Tecnologia (IIT@NEST), Pisa, Italy
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37
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Metz A, Wollenhaupt J, Glöckner S, Messini N, Huber S, Barthel T, Merabet A, Gerber HD, Heine A, Klebe G, Weiss MS. Frag4Lead: growing crystallographic fragment hits by catalog using fragment-guided template docking. Acta Crystallogr D Struct Biol 2021; 77:1168-1182. [PMID: 34473087 PMCID: PMC8411975 DOI: 10.1107/s2059798321008196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022] Open
Abstract
In recent years, crystallographic fragment screening has matured into an almost routine experiment at several modern synchrotron sites. The hits of the screening experiment, i.e. small molecules or fragments binding to the target protein, are revealed along with their 3D structural information. Therefore, they can serve as useful starting points for further structure-based hit-to-lead development. However, the progression of fragment hits to tool compounds or even leads is often hampered by a lack of chemical feasibility. As an attractive alternative, compound analogs that embed the fragment hit structurally may be obtained from commercial catalogs. Here, a workflow is reported based on filtering and assessing such potential follow-up compounds by template docking. This means that the crystallographic binding pose was integrated into the docking calculations as a central starting parameter. Subsequently, the candidates are scored on their interactions within the binding pocket. In an initial proof-of-concept study using five starting fragments known to bind to the aspartic protease endothiapepsin, 28 follow-up compounds were selected using the designed workflow and their binding was assessed by crystallography. Ten of these compounds bound to the active site and five of them showed significantly increased affinity in isothermal titration calorimetry of up to single-digit micromolar affinity. Taken together, this strategy is capable of efficiently evolving the initial fragment hits without major synthesis efforts and with full control by X-ray crystallography.
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Affiliation(s)
- Alexander Metz
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Jan Wollenhaupt
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Steffen Glöckner
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Niki Messini
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Simon Huber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Tatjana Barthel
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
| | - Ahmed Merabet
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Hans-Dieter Gerber
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Manfred S. Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Albert-Einstein-Straße 15, D-12489 Berlin, Germany
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Chen PY, Wang C, Zhang Y, Yuan C, Yu B, Ke XG, Wu HZ, Yang YF, Xiao XC. Predicting the Molecular Mechanism of “Angong Niuhuang Pills” in the Treatment of COVID-19 Based on Network Pharmacology. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211024032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Introduction Angong Niuhuang Pills (AGNH), a Chinese patent medicine recommended in the “Diagnosis and Treatment Plan for COVID-19 (8th Edition),” may be clinically effective in treating COVID-19. The active components and signal pathways of AGNH through network pharmacology have been examined, and its potential mechanisms determined. Methods We screened the components in the Traditional Chinese Medicine Systems Pharmacology (TCMSP) via Drug-like properties (DL) and Oral bioavailability (OB); PharmMapper and GeneCards databases were used to collect components and COVID-19 related targets; KEGG pathway annotation and GO bioinformatics analysis were based on KOBAS3.0 database; “herb-components-targets-pathways” (H-C-T-P) network and protein-protein interaction network (PPI) were constructed by Cytoscape 3.6.1 software and STRING 10.5 database; we utilized virtual molecular docking to predict the binding ability of the active components and key proteins. Results A total of 87 components and 40 targets were screened in AGNH. The molecular docking results showed that the docking scores of the top 3 active components and the targets were all greater than 90. Conclusion Through network pharmacology research, we found that moslosooflavone, oroxylin A, and salvigenin in AGNH can combine with ACE2 and 3CL, and then are involved in the MAPK and JAK-STAT signaling pathways. Finally, it is suggested that AGNH may have a role in the treatment of COVID-19.
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Affiliation(s)
- Peng-yu Chen
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
| | - Chen Wang
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
| | - Ying Zhang
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
| | - Chong Yuan
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
| | - Bing Yu
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
| | - Xin-ge Ke
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
| | - He-zhen Wu
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
- Hubei Geriatrics New Products Collaborative Innovation Center of Chinese Medicine, Wuhan, China
| | - Yan-fang Yang
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
- Hubei Key Laboratory of Chinese Medicine Resources and Chemistry, Wuhan, China
- Hubei Geriatrics New Products Collaborative Innovation Center of Chinese Medicine, Wuhan, China
| | - Xue-cheng Xiao
- Department of pharmacy, Hubei University of Chinese Medicine, Wu Han, China
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Nguyen D, Xie X, Jakobi S, Terwesten F, Metz A, Nguyen TXP, Palchykov VA, Heine A, Reuter K, Klebe G. Targeting a Cryptic Pocket in a Protein-Protein Contact by Disulfide-Induced Rupture of a Homodimeric Interface. ACS Chem Biol 2021; 16:1090-1098. [PMID: 34081441 DOI: 10.1021/acschembio.1c00296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Interference with protein-protein interfaces represents an attractive as well as challenging option for therapeutic intervention and drug design. The enzyme tRNA-guanine transglycosylase, a target to fight Shigellosis, is only functional as a homodimer. Although we previously produced monomeric variants by site-directed mutagenesis, we only crystallized the functional dimer, simply because upon crystallization the local protein concentration increases and favors formation of the dimer interface, which represents an optimal and highly stable packing of the protein in the solid state. Unfortunately, this prevents access to structural information about the interface geometry in its monomeric state and complicates the development of modulators that can interfere with and prevent dimer formation. Here, we report on a cysteine-containing protein variant in which, under oxidizing conditions, a disulfide linkage is formed. This reinforces a novel packing geometry of the enzyme. In this captured quasi-monomeric state, the monomer units arrange in a completely different way and, thus, expose a loop-helix motif, originally embedded into the old interface, now to the surface. The motif adopts a geometry incompatible with the original dimer formation. Via the soaking of fragments into the crystals, we identified several hits accommodating a cryptic binding site next to the loop-helix motif and modulated its structural features. Our study demonstrates the druggability of the interface by breaking up the homodimeric protein using an introduced disulfide cross-link. By rational concepts, we increased the potency of these fragments to a level where we confirmed their binding by NMR to a nondisulfide-linked TGT variant. The idea of intermediately introducing a disulfide linkage may serve as a general concept of how to transform a homodimer interface into a quasi-monomeric state and give access to essential structural and design information.
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Affiliation(s)
- Dzung Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Xiulan Xie
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Stephan Jakobi
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Felix Terwesten
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Alexander Metz
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - T. X. Phong Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Vitalii A. Palchykov
- Research Institute of Chemistry and Geology, Oles Honchar Dnipro National University, 72 Gagarina Avenue, Dnipro 49010, Ukraine
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, 35032 Marburg, Germany
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021; 60:13331-13342. [PMID: 33951246 PMCID: PMC8251789 DOI: 10.1002/anie.202100273] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Indexed: 01/01/2023]
Abstract
Tubulin plays essential roles in vital cellular activities and is the target of a wide range of proteins and ligands. Here, using a combined computational and crystallographic fragment screening approach, we addressed the question of how many binding sites exist in tubulin. We identified 27 distinct sites, of which 11 have not been described previously, and analyzed their relationship to known tubulin-protein and tubulin-ligand interactions. We further observed an intricate pocket communication network and identified 56 chemically diverse fragments that bound to 10 distinct tubulin sites. Our results offer a unique structural basis for the development of novel small molecules for use as tubulin modulators in basic research applications or as drugs. Furthermore, our method lays down a framework that may help to discover new pockets in other pharmaceutically important targets and characterize them in terms of chemical tractability and allosteric modulation.
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Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - Dario Gioia
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
| | - Andrea E. Prota
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
| | - May E. Sharpe
- Swiss Light SourcePaul Scherrer Institut5232Villigen PSISwitzerland
| | - Andrea Cavalli
- Computational & Chemical BiologyIstituto Italiano di Tecnologiavia Morego, 3016163GenovaItaly
- Department of Pharmacy and BiotechnologyAlma Mater StudiorumUniversity of Bolognavia Belmeloro 640126BolognaItaly
| | - Michel O. Steinmetz
- Laboratory of Biomolecular ResearchDepartment of Biology and ChemistryPaul Scherrer Institut5232Villigen PSISwitzerland
- University of BaselBiozentrum4056BaselSwitzerland
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41
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Mühlethaler T, Gioia D, Prota AE, Sharpe ME, Cavalli A, Steinmetz MO. Comprehensive Analysis of Binding Sites in Tubulin. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tobias Mühlethaler
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Dario Gioia
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
| | - Andrea E. Prota
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - May E. Sharpe
- Swiss Light Source Paul Scherrer Institut 5232 Villigen PSI Switzerland
| | - Andrea Cavalli
- Computational & Chemical Biology Istituto Italiano di Tecnologia via Morego, 30 16163 Genova Italy
- Department of Pharmacy and Biotechnology Alma Mater Studiorum University of Bologna via Belmeloro 6 40126 Bologna Italy
| | - Michel O. Steinmetz
- Laboratory of Biomolecular Research Department of Biology and Chemistry Paul Scherrer Institut 5232 Villigen PSI Switzerland
- University of Basel Biozentrum 4056 Basel Switzerland
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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. SCIENCE ADVANCES 2021; 7:eabf8711. [PMID: 33853786 PMCID: PMC8046379 DOI: 10.1126/sciadv.abf8711] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [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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Banford S, McCorvie TJ, Pey AL, Timson DJ. Galactosemia: Towards Pharmacological Chaperones. J Pers Med 2021; 11:jpm11020106. [PMID: 33562227 PMCID: PMC7914515 DOI: 10.3390/jpm11020106] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
Galactosemia is a rare inherited metabolic disease resulting from mutations in the four genes which encode enzymes involved in the metabolism of galactose. The current therapy, the removal of galactose from the diet, is inadequate. Consequently, many patients suffer lifelong physical and cognitive disability. The phenotype varies from almost asymptomatic to life-threatening disability. The fundamental biochemical cause of the disease is a decrease in enzymatic activity due to failure of the affected protein to fold and/or function correctly. Many novel therapies have been proposed for the treatment of galactosemia. Often, these are designed to treat the symptoms and not the fundamental cause. Pharmacological chaperones (PC) (small molecules which correct the folding of misfolded proteins) represent an exciting potential therapy for galactosemia. In theory, they would restore enzyme function, thus preventing downstream pathological consequences. In practice, no PCs have been identified for potential application in galactosemia. Here, we review the biochemical basis of the disease, identify opportunities for the application of PCs and describe how these might be discovered. We will conclude by considering some of the clinical issues which will affect the future use of PCs in the treatment of galactosemia.
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Affiliation(s)
- Samantha Banford
- South Eastern Health and Social Care Trust, Downpatrick BT30 6RL, UK;
| | - Thomas J. McCorvie
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain;
| | - David J. Timson
- School of Pharmacy and Biomolecular Sciences, The University of Brighton, Brighton BN2 4GJ, UK
- Correspondence:
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Kanev GK, de Graaf C, Westerman BA, de Esch IJP, Kooistra AJ. KLIFS: an overhaul after the first 5 years of supporting kinase research. Nucleic Acids Res 2021; 49:D562-D569. [PMID: 33084889 PMCID: PMC7778968 DOI: 10.1093/nar/gkaa895] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Kinases are a prime target of drug development efforts with >60 drug approvals in the past two decades. Due to the research into this protein family, a wealth of data has been accumulated that keeps on growing. KLIFS-Kinase-Ligand Interaction Fingerprints and Structures-is a structural database focusing on how kinase inhibitors interact with their targets. The aim of KLIFS is to support (structure-based) kinase research through the systematic collection, annotation, and processing of kinase structures. Now, 5 years after releasing the initial KLIFS website, the database has undergone a complete overhaul with a new website, new logo, and new functionalities. In this article, we start by looking back at how KLIFS has been used by the research community, followed by a description of the renewed KLIFS, and conclude with showcasing the functionalities of KLIFS. Major changes include the integration of approved drugs and inhibitors in clinical trials, extension of the coverage to atypical kinases, and a RESTful API for programmatic access. KLIFS is available at the new domain https://klifs.net.
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Affiliation(s)
- Georgi K Kanev
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Bart A Westerman
- Department of Neurosurgery, Amsterdam University Medical Centers, Cancer Center Amsterdam, Brain Tumor Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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46
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Wakefield AE, Yueh C, Beglov D, Castilho MS, Kozakov D, Keserű GM, Whitty A, Vajda S. Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J Chem Inf Model 2020; 60:6612-6623. [PMID: 33291870 DOI: 10.1021/acs.jcim.0c00877] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. Each protein structure in the set binds a fragment, which is extended into larger ligands in other structures without substantial change in its binding mode. Structures of the same proteins without any bound ligand are also collected to form an unbound benchmark. We also discuss a set developed by Astex Pharmaceuticals for the validation of hot and warm spots for fragment binding. The set is based on the assumption that a fragment that occurs in diverse ligands in the same subpocket identifies a binding hot spot. Since this set includes only ligand-bound proteins, we added a set with unbound structures. All four sets were tested using FTMap, a computational analogue of fragment screening experiments to form a baseline for testing other prediction methods, and differences among the sets are discussed.
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Affiliation(s)
- Amanda E Wakefield
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Christine Yueh
- Acpharis Inc., Holliston, Massachusetts 01746, United States
| | - Dmitri Beglov
- Acpharis Inc., Holliston, Massachusetts 01746, United States
| | - Marcelo S Castilho
- Faculdade de Farmácia da Universidade Federal da Bahia, Bahia, Salvador, BA 40170-115, Brazil
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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47
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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Jahnke W, Erlanson DA, de Esch IJP, Johnson CN, Mortenson PN, Ochi Y, Urushima T. Fragment-to-Lead Medicinal Chemistry Publications in 2019. J Med Chem 2020; 63:15494-15507. [PMID: 33226222 DOI: 10.1021/acs.jmedchem.0c01608] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fragment-based drug discovery (FBDD) has grown and matured to a point where it is valuable to keep track of its extent and details of application. This Perspective summarizes successful fragment-to-lead stories published in 2019. It is the fifth in a series that started with literature published in 2015. The analysis of screening methods, optimization strategies, and molecular properties of hits and leads are presented in the hope of informing best practices for FBDD. Moreover, FBDD is constantly evolving, and the latest technologies and emerging trends are summarized. These include covalent FBDD, FBDD for the stabilization of proteins or protein-protein interactions, FBDD for enzyme activators, new screening technologies, and advances in library design and chemical synthesis.
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Affiliation(s)
- Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Boulevard, South San Francisco, California 94080, United States of America
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Christopher N Johnson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Paul N Mortenson
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Yuji Ochi
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Tatsuya Urushima
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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49
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Hanzawa H, Shimada T, Takahashi M, Takahashi H. Revisiting biomolecular NMR spectroscopy for promoting small-molecule drug discovery. JOURNAL OF BIOMOLECULAR NMR 2020; 74:501-508. [PMID: 32306215 DOI: 10.1007/s10858-020-00314-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Recently, there has been increasing interest in new modalities such as therapeutic antibodies and gene therapy at a number of pharmaceutical companies. Moreover, in small-molecule drug discovery at such companies, efforts have focused on hard-to-drug targets such as inhibiting protein-protein interactions. Biomolecular NMR spectroscopy has been used in drug discovery in a variety of ways, such as for the reliable detection of binding and providing three-dimensional structural information for structure-based drug design. The advantages of using NMR spectroscopy have been known for decades (Jahnke in J Biomol NMR 39:87-90, (2007); Gossert and Jahnke in Prog Nucl Magn Reson Spectrosc 97:82-125, (2016)). For tackling hard-to-drug targets and increasing the success in discovering drug molecules, in-depth analysis of drug-target protein interactions performed by biophysical methods will be more and more essential. Here, we review the advantages of NMR spectroscopy as a key technology of biophysical methods and also discuss issues such as using cutting-edge NMR spectrometers and increasing the demand of utilizing conformational dynamics information for promoting small-molecule drug discovery.
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Affiliation(s)
- Hiroyuki Hanzawa
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan.
| | - Takashi Shimada
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Mizuki Takahashi
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, 1-16-13 Kita-Kasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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50
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Brear P, Ball D, Stott K, D'Arcy S, Hyvönen M. Proposed Allosteric Inhibitors Bind to the ATP Site of CK2α. J Med Chem 2020; 63:12786-12798. [PMID: 33119282 DOI: 10.1021/acs.jmedchem.0c01173] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CK2α is a ubiquitous, well-studied kinase that is a target for small-molecule inhibition, for treatment of cancers. While many different classes of adenosine 5'-triphosphate (ATP)-competitive inhibitors have been described for CK2α, they tend to suffer from significant off-target activity and new approaches are needed. A series of inhibitors of CK2α has recently been described as allosteric, acting at a previously unidentified binding site. Given the similarity of these inhibitors to known ATP-competitive inhibitors, we have investigated them further. In our thorough structural and biophysical analyses, we have found no evidence that these inhibitors bind to the proposed allosteric site. Rather, we report crystal structures, competitive isothermal titration calorimetry (ITC) and NMR, hydrogen-deuterium exchange (HDX) mass spectrometry, and chemoinformatic analyses that all point to these compounds binding in the ATP pocket. Comparisons of our results and experimental approach with the data presented in the original report suggest that the primary reason for the disparity is nonspecific inhibition by aggregation.
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Affiliation(s)
- Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Darby Ball
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
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