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Ashraf SN, Blackwell JH, Holdgate GA, Lucas SCC, Solovyeva A, Storer RI, Whitehurst BC. Hit me with your best shot: Integrated hit discovery for the next generation of drug targets. Drug Discov Today 2024; 29:104143. [PMID: 39173704 DOI: 10.1016/j.drudis.2024.104143] [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: 05/31/2024] [Revised: 08/07/2024] [Accepted: 08/16/2024] [Indexed: 08/24/2024]
Abstract
Identification of high-quality hit chemical matter is of vital importance to the success of drug discovery campaigns. However, this goal is becoming ever harder to achieve as the targets entering the portfolios of pharmaceutical and biotechnology companies are increasingly trending towards novel and traditionally challenging to drug. This demand has fuelled the development and adoption of numerous new screening approaches, whereby the contemporary hit identification toolbox comprises a growing number of orthogonal and complementary technologies including high-throughput screening, fragment-based ligand design, affinity screening (affinity-selection mass spectrometry, differential scanning fluorimetry, DNA-encoded library screening), as well as increasingly sophisticated computational predictive approaches. Herein we describe how an integrated strategy for hit discovery, whereby multiple hit identification techniques are tactically applied, selected in the context of target suitability and resource priority, represents an optimal and often essential approach to maximise the likelihood of identifying quality starting points from which to develop the next generation of medicines.
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Affiliation(s)
- S Neha Ashraf
- Hit Discovery, Discovery Science, AstraZeneca R&D, Cambridge CB2 0AA, UK
| | - J Henry Blackwell
- Hit Discovery, Discovery Science, AstraZeneca R&D, Cambridge CB2 0AA, UK
| | | | - Simon C C Lucas
- Hit Discovery, Discovery Science, AstraZeneca R&D, Cambridge CB2 0AA, UK
| | - Alisa Solovyeva
- Hit Discovery, Discovery Science, AstraZeneca R&D, Gothenburg SE-431 83, Sweden
| | - R Ian Storer
- Hit Discovery, Discovery Science, AstraZeneca R&D, Cambridge CB2 0AA, UK.
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2
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Lucas SCC, Blackwell JH, Börjesson U, Hargreaves D, Milbradt AG, Bostock MJ, Ahmed S, Beaumont K, Cheung T, Demanze S, Gohlke A, Guerot C, Haider A, Kantae V, Kauffman GW, Kinzel O, Kupcova L, Lainchbury MD, Lamb ML, Leon L, Palisse A, Sacchetto C, Storer RI, Su N, Thomson C, Vales J, Chen Y, Hu X. Structure-Based Optimization of a Series of Covalent, Cell Active Bfl-1 Inhibitors. J Med Chem 2024; 67:16455-16479. [PMID: 39291659 DOI: 10.1021/acs.jmedchem.4c01288] [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
Bfl-1, a member of the Bcl-2 family of proteins, plays a crucial role in apoptosis regulation and has been implicated in cancer cell survival and resistance to venetoclax therapy. Due to the unique cysteine residue in the BH3 binding site, the development of covalent inhibitors targeting Bfl-1 represents a promising strategy for cancer treatment. Herein, the optimization of a covalent cellular tool from a lead-like hit using structure based design is described. Informed by a reversible X-ray fragment screen, the strategy to establish interactions with a key glutamic acid residue (Glu78) and optimize binding in a cryptic pocket led to a 1000-fold improvement in biochemical potency without increasing reactivity of the warhead. Compound (R,R,S)-26 has a kinact/KI of 4600 M-1 s-1, shows <1 μM caspase activation in a cellular assay and cellular target engagement, and has good physicochemical properties and a promising in vivo profile.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - J Henry Blackwell
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ulf Börjesson
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - David Hargreaves
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Mark J Bostock
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Samiyah Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Tony Cheung
- Oncology Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Sylvain Demanze
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andrea Gohlke
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Carine Guerot
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Afreen Haider
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Vasudev Kantae
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Gregory W Kauffman
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Olaf Kinzel
- Medicinal Chemistry, Oncology R&D, Acerta B.V., a Member of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Lea Kupcova
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Michelle L Lamb
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Leonardo Leon
- Oncology Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Adeline Palisse
- Medicinal Chemistry, Oncology R&D, Acerta B.V., a Member of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Claudia Sacchetto
- Bioscience, Oncology R&D, Acerta B.V., a Member of the AstraZeneca Group, Oss 5349, The Netherlands
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Nancy Su
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Clare Thomson
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - John Vales
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Yunhua Chen
- Pharmaron Beijing Co., Ltd., Beijing 100176, P. R. China
| | - Xiaolong Hu
- Pharmaron Beijing Co., Ltd., Beijing 100176, P. R. China
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3
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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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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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Woodhead AJ, Erlanson DA, de Esch IJP, Holvey RS, Jahnke W, Pathuri P. Fragment-to-Lead Medicinal Chemistry Publications in 2022. J Med Chem 2024; 67:2287-2304. [PMID: 38289623 DOI: 10.1021/acs.jmedchem.3c02070] [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: 02/02/2024]
Abstract
This Perspective is the eighth in an annual series that summarizes successful fragment-to-lead (F2L) case studies published each year. A tabulated summary of relevant articles published in 2022 is provided, and features such as target class, screening methods, and ligand efficiency are discussed both for the 2022 examples and for the combined examples over the years 2015-2022. In addition, trends and new developments in the field are summarized. In 2022, 18 publications described successful fragment-to-lead studies, including the development of three clinical compounds (MTRX1719, MK-8189, and BI-823911).
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Affiliation(s)
- Andrew J Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Blvd., South San Francisco, California 94080, United States
| | - 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
| | - Rhian S Holvey
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Wolfgang Jahnke
- Novartis Biomedical Research, Discovery Sciences, 4002 Basel, Switzerland
| | - Puja Pathuri
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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6
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Whitehurst BC, Bauer MR, Edfeldt F, Gunnarsson A, Margreitter C, Rawlins PB, Storer RI. Design and Evaluation of a Low Hydrogen Bond Donor Count Fragment Screening Set to Aid Hit Generation of PROTACs Intended for Oral Delivery. J Med Chem 2023. [PMID: 37224440 DOI: 10.1021/acs.jmedchem.3c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The development of orally bioavailable PROTACs presents a significant challenge due to the inflated physicochemical properties of such heterobifunctional molecules. Molecules occupying this "beyond rule of five" space often demonstrate limited oral bioavailability due to the compounding effects of elevated molecular weight and hydrogen bond donor count (among other properties), but it is possible to achieve sufficient oral bioavailability through physicochemical optimization. Herein, we disclose the design and evaluation of a low hydrogen bond donor count (≤1 HBD) fragment screening set to aid hit generation of PROTACs intended for an oral route of delivery. We demonstrate that application of this library can enhance fragment screens against PROTAC proteins of interest and ubiquitin ligases, yielding fragment hits containing ≤1 HBD suitable for optimizing toward orally bioavailable PROTACs.
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Affiliation(s)
- Benjamin C Whitehurst
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Matthias R Bauer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Fredrik Edfeldt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Anders Gunnarsson
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Christian Margreitter
- Molecular AI, Discovery Sciences, R&D, AstraZeneca, Mölndal, Gothenburg 431 50, Sweden
| | - Philip B Rawlins
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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