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Wilders H, Biggs G, Rowe SM, Cawood EE, Riziotis IG, Rendina AR, Grant EK, Pettinger J, Fallon DJ, Skehel M, House D, Tomkinson NCO, Bush JT. Expedited SARS-CoV-2 Main Protease Inhibitor Discovery through Modular 'Direct-to-Biology' Screening. Angew Chem Int Ed Engl 2024:e202418314. [PMID: 39630105 DOI: 10.1002/anie.202418314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 11/15/2024] [Indexed: 12/12/2024]
Abstract
Reactive fragment (RF) screening has emerged as an efficient method for ligand discovery across the proteome, irrespective of a target's perceived tractability. To date, however, the efficiency of subsequent optimisation campaigns has largely been low-throughput, constrained by the need for synthesis and purification of target compounds. We report an efficient platform for 'direct-to-biology' (D2B) screening of cysteine-targeting chloroacetamide RFs, wherein synthesis is performed in 384-well plates allowing direct assessment in downstream biological assays without purification. Here, the developed platform was used to optimise inhibitors of SARS-CoV-2 main protease (MPro), an established drug target for the treatment of COVID-19. An initial RF hit was developed into a series of potent inhibitors, and further exploration using D2B screening enabled a 'switch' to a reversible inhibitor series. This example of ligand discovery for MPro illustrates the acceleration that D2B chemistry can offer for optimising RFs towards covalent inhibitor candidates, as well as providing future impetus to explore the evolution of RFs into non-covalent ligands.
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Affiliation(s)
- Harry Wilders
- Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Crick-GSK Biomedical Linklabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - George Biggs
- Crick-GSK Biomedical Linklabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Sam M Rowe
- Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Emma E Cawood
- Crick-GSK Biomedical Linklabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Ioannis G Riziotis
- Crick-GSK Biomedical Linklabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Alan R Rendina
- Screening, Profiling and Mechanistic Biology, GSK, 1250 South Collegeville Road, Collegevill, PA, 19426, US
| | - Emma K Grant
- Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Jonathan Pettinger
- Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Crick-GSK Biomedical Linklabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - David J Fallon
- Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David House
- Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Crick-GSK Biomedical Linklabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Nicholas C O Tomkinson
- Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Jacob T Bush
- Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Crick-GSK Biomedical Linklabs, GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK
- Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
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Paterson LC, Humphreys PG, Kelly HA, Kerr WJ. Collaborative GSK-University of Strathclyde doctoral research and training programmes: Transforming approaches to industry-academia engagement. Drug Discov Today 2024; 29:104162. [PMID: 39245346 DOI: 10.1016/j.drudis.2024.104162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/23/2024] [Accepted: 09/05/2024] [Indexed: 09/10/2024]
Abstract
A global biopharma company, GSK, and the University of Strathclyde have developed an expansive and transformative research and training partnership originating in chemistry-aligned disciplines, with subsequent extensive expansion across further areas of the company. This has opened unique approaches for the delivery of collaborative research innovations while also enhancing the professional development and learning of GSK personnel, in addition to other embedded researchers and collaborating scientists, on a pathway towards more rapid and efficient discovery of new medicines.
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Affiliation(s)
- Laura C Paterson
- University of Strathclyde, Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, UK
| | | | - Henry A Kelly
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK.
| | - William J Kerr
- University of Strathclyde, Pure and Applied Chemistry, 295 Cathedral Street, Glasgow G1 1XL, UK.
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3
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Bon C, Goretzki B, Flamme M, Shelton C, Davis H, Lima F, Garcia F, Brittain S, Brocklehurst CE. Oxadiazolines as Photoreleasable Labels for Drug Target Identification. J Am Chem Soc 2024; 146:26759-26765. [PMID: 39288302 DOI: 10.1021/jacs.4c06936] [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: 09/19/2024]
Abstract
Photoaffinity labeling is a widely used technique for studying ligand-protein and protein-protein interactions. Traditional photoaffinity labels utilize nonspecific C-H bond insertion reactions mediated by a highly reactive intermediate. Despite being the most widely used photoaffinity labels, diazirines exhibit limited compatibility with downstream organic reactions and suffer from storage stability concerns. This study introduces oxadiazolines as innovative and complementary photoactivatable labels for addition to the toolbox and demonstrates their application in vitro and through in cellulo labeling experiments. Oxadiazolines can be easily synthesized from ketone moieties and cleaved with 302-330 nm light to cleanly liberate a diazo reactive moiety that can covalently modify nucleophilic amino acid residues. Notably, oxadiazolines are compatible with various organic reaction conditions and functional groups, allowing for the exploration of a large chemical space. Several known inhibitors featuring the oxadiazoline functionality were prepared without affecting their binding affinity. Furthermore, we confirmed the ability of oxadiazolines to form covalent bonds with proteins upon UV-irradiation, both in vitro and in cellulo, yielding comparable results to those of the matched diazirine compounds.
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Affiliation(s)
- Corentin Bon
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Benedikt Goretzki
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Marie Flamme
- Chemical and Analytical Development, Novartis Development, Novartis Pharma AG, Basel 4056, Switzerland
| | - Claude Shelton
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Cambridge, Massachusetts 02139, United States
| | - Holly Davis
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Fabio Lima
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
| | - Francisco Garcia
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Cambridge, Massachusetts 02139, United States
| | - Scott Brittain
- Discovery Sciences, Novartis Biomedical Research, Novartis Pharma AG, Cambridge, Massachusetts 02139, United States
| | - Cara E Brocklehurst
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4056, Switzerland
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4
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Lucas SCC, Blackwell JH, Hewitt SH, Semple H, Whitehurst BC, Xu H. Covalent hits and where to find them. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100142. [PMID: 38278484 DOI: 10.1016/j.slasd.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 01/28/2024]
Abstract
Covalent hits for drug discovery campaigns are neither fantastic beasts nor mythical creatures, they can be routinely identified through electrophile-first screening campaigns using a suite of different techniques. These include biophysical and biochemical methods, cellular approaches, and DNA-encoded libraries. Employing best practice, however, is critical to success. The purpose of this review is to look at state of the art covalent hit identification, how to identify hits from a covalent library and how to select compounds for medicinal chemistry programmes.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK.
| | | | - Sarah H Hewitt
- Mechanistic and Structural Biology, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, AstraZeneca R&D, Cambridge, UK
| | | | - Hua Xu
- Mechanistic and structural Biology, Discovery Sciences, AstraZeneca R&D, Waltham, USA
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5
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Feral A, Martin AR, Desfoux A, Amblard M, Vezenkov LL. Covalent-reversible peptide-based protease inhibitors. Design, synthesis, and clinical success stories. Amino Acids 2023; 55:1775-1800. [PMID: 37330416 DOI: 10.1007/s00726-023-03286-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated human peptidases are implicated in a large variety of diseases such as cancer, hypertension, and neurodegeneration. Viral proteases for their part are crucial for the pathogens' maturation and assembly. Several decades of research were devoted to exploring these precious therapeutic targets, often addressing them with synthetic substrate-based inhibitors to elucidate their biological roles and develop medications. The rational design of peptide-based inhibitors offered a rapid pathway to obtain a variety of research tools and drug candidates. Non-covalent modifiers were historically the first choice for protease inhibition due to their reversible enzyme binding mode and thus presumably safer profile. However, in recent years, covalent-irreversible inhibitors are having a resurgence with dramatic increase of their related publications, preclinical and clinical trials, and FDA-approved drugs. Depending on the context, covalent modifiers could provide more effective and selective drug candidates, hence requiring lower doses, thereby limiting off-target effects. Additionally, such molecules seem more suitable to tackle the crucial issue of cancer and viral drug resistances. At the frontier of reversible and irreversible based inhibitors, a new drug class, the covalent-reversible peptide-based inhibitors, has emerged with the FDA approval of Bortezomib in 2003, shortly followed by 4 other listings to date. The highlight in the field is the breathtakingly fast development of the first oral COVID-19 medication, Nirmatrelvir. Covalent-reversible inhibitors can hipothetically provide the safety of the reversible modifiers combined with the high potency and specificity of their irreversible counterparts. Herein, we will present the main groups of covalent-reversible peptide-based inhibitors, focusing on their design, synthesis, and successful drug development programs.
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Affiliation(s)
- Anthony Feral
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
| | | | | | - Muriel Amblard
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
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6
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Csorba N, Ábrányi-Balogh P, Keserű GM. Covalent fragment approaches targeting non-cysteine residues. Trends Pharmacol Sci 2023; 44:802-816. [PMID: 37770315 DOI: 10.1016/j.tips.2023.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.
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Affiliation(s)
- Noémi Csorba
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary.
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