1
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Balıkçı E, Marques ASMC, Bauer LG, Seupel R, Bennett J, Raux B, Buchan K, Simelis K, Singh U, Rogers C, Ward J, Cheng C, Szommer T, Schützenhofer K, Elkins JM, Sloman DL, Ahel I, Fedorov O, Brennan PE, Huber KVM. Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. J Med Chem 2024; 67:7245-7259. [PMID: 38635563 PMCID: PMC11089510 DOI: 10.1021/acs.jmedchem.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure-activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.
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Affiliation(s)
- Esra Balıkçı
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Anne-Sophie M. C. Marques
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Ludwig G. Bauer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Raina Seupel
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James Bennett
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Brigitt Raux
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Karly Buchan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Klemensas Simelis
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Usha Singh
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Catherine Rogers
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jennifer Ward
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Carol Cheng
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Tamas Szommer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kira Schützenhofer
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Jonathan M. Elkins
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - David L. Sloman
- Departments
of Discovery Chemistry, Merck & Co.
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Oleg Fedorov
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Paul E. Brennan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Nuffield Department of
Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kilian V. M. Huber
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
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2
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Ung DC, Pietrancosta N, Badillo EB, Raux B, Tapken D, Zlatanovic A, Doridant A, Pode-Shakked B, Raas-Rothschild A, Elpeleg O, Abu-Libdeh B, Hamed N, Papon MA, Marouillat S, Thépault RA, Stevanin G, Elegheert J, Letellier M, Hollmann M, Lambolez B, Tricoire L, Toutain A, Hepp R, Laumonnier F. GRID1/GluD1 homozygous variants linked to intellectual disability and spastic paraplegia impair mGlu1/5 receptor signaling and excitatory synapses. Mol Psychiatry 2024:10.1038/s41380-024-02469-w. [PMID: 38418578 DOI: 10.1038/s41380-024-02469-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 03/01/2024]
Abstract
The ionotropic glutamate delta receptor GluD1, encoded by the GRID1 gene, is involved in synapse formation, function, and plasticity. GluD1 does not bind glutamate, but instead cerebellin and D-serine, which allow the formation of trans-synaptic bridges, and trigger transmembrane signaling. Despite wide expression in the nervous system, pathogenic GRID1 variants have not been characterized in humans so far. We report homozygous missense GRID1 variants in five individuals from two unrelated consanguineous families presenting with intellectual disability and spastic paraplegia, without (p.Thr752Met) or with (p.Arg161His) diagnosis of glaucoma, a threefold phenotypic association whose genetic bases had not been elucidated previously. Molecular modeling and electrophysiological recordings indicated that Arg161His and Thr752Met mutations alter the hinge between GluD1 cerebellin and D-serine binding domains and the function of this latter domain, respectively. Expression, trafficking, physical interaction with metabotropic glutamate receptor mGlu1, and cerebellin binding of GluD1 mutants were not conspicuously altered. Conversely, upon expression in neurons of dissociated or organotypic slice cultures, we found that both GluD1 mutants hampered metabotropic glutamate receptor mGlu1/5 signaling via Ca2+ and the ERK pathway and impaired dendrite morphology and excitatory synapse density. These results show that the clinical phenotypes are distinct entities segregating in the families as an autosomal recessive trait, and caused by pathophysiological effects of GluD1 mutants involving metabotropic glutamate receptor signaling and neuronal connectivity. Our findings unravel the importance of GluD1 receptor signaling in sensory, cognitive and motor functions of the human nervous system.
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Affiliation(s)
- Dévina C Ung
- UMR 1253, iBrain, Université de Tours, Inserm, 37032, Tours, France
| | - Nicolas Pietrancosta
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
- Laboratoire des biomolécules, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
| | | | - Brigitt Raux
- Univ. Bordeaux, CNRS, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Daniel Tapken
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Andjela Zlatanovic
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
| | - Adrien Doridant
- Univ. Bordeaux, CNRS, IINS, UMR 5297, F-33000, Bordeaux, France
| | - Ben Pode-Shakked
- The Institute for Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, 5262000, Israel
- Talpiot Medical Leadership Program, Sheba Medical Center, Tel-Hashomer, 5262000, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Annick Raas-Rothschild
- The Institute for Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, 5262000, Israel
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Bassam Abu-Libdeh
- Department of Pediatrics, Makassed Hospital and Faculty of Medicine, Al-Quds University, East Jerusalem, Jerusalem, Palestine
| | - Nasrin Hamed
- Faculty of Medicine, Tel-Aviv University, Tel-Aviv, 69978, Israel
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, 5262000, Israel
| | | | | | | | - Giovanni Stevanin
- Univ. Bordeaux, INCIA, UMR 5287 CNRS EPHE, F-33000, Bordeaux, France
| | | | | | - Michael Hollmann
- Department of Biochemistry I - Receptor Biochemistry, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, D-44780, Bochum, Germany
| | - Bertrand Lambolez
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
| | - Ludovic Tricoire
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France
| | - Annick Toutain
- UMR 1253, iBrain, Université de Tours, Inserm, 37032, Tours, France.
- Unité fonctionnelle de Génétique Médicale, Centre Hospitalier Universitaire, 37044, Tours, France.
| | - Régine Hepp
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine - Institut de Biologie Paris Seine, 75005, Paris, France.
| | - Frédéric Laumonnier
- UMR 1253, iBrain, Université de Tours, Inserm, 37032, Tours, France.
- Service de Génétique, Centre Hospitalier Universitaire, 37044, Tours, France.
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3
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Raux B, Buchan KA, Bennett J, Christott T, Dowling MS, Farnie G, Fedorov O, Gamble V, Gileadi C, Giroud C, Huber KVM, Korczynska M, Limberakis C, Narayanan A, Owen DR, Sáez LD, Stock IA, Londregan AT. Discovery of PFI-6, a small-molecule chemical probe for the YEATS domain of MLLT1 and MLLT3. Bioorg Med Chem Lett 2024; 98:129546. [PMID: 37944866 DOI: 10.1016/j.bmcl.2023.129546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/19/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Epigenetic proteins containing YEATS domains (YD) are an emerging target class in drug discovery. Described herein are the discovery and characterization efforts associated with PFI-6, a new chemical probe for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). For hit identification, fragment-like mimetics of endogenous YD ligands (crotonylated histone-containing proteins), were synthesized via parallel medicinal chemistry (PMC) and screened for MLLT1 binding. Subsequent SAR studies led to iterative MLLT1/3 binding and selectivity improvements, culminating in the discovery of PFI-6. PFI-6 demonstrates good affinity and selectivity for MLLT1/3 vs. other human YD proteins (YEATS2/4) and engages MLLT3 in cells. Small-molecule X-ray co-crystal structures of two molecules, including PFI-6, bound to the YD of MLLT1/3 are also described. PFI-6 may be a useful tool molecule to better understand the biological effects associated with modulation of MLLT1/3.
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Affiliation(s)
- Brigitt Raux
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Karly A Buchan
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - James Bennett
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Thomas Christott
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Gillian Farnie
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Oleg Fedorov
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Vicki Gamble
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Carina Gileadi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Charline Giroud
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Kilian V M Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | | | - Chris Limberakis
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Arjun Narayanan
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Dafydd R Owen
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Laura Díaz Sáez
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Ingrid A Stock
- Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Allyn T Londregan
- Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA.
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4
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Londregan AT, Aitmakhanova K, Bennett J, Byrnes LJ, Canterbury DP, Cheng X, Christott T, Clemens J, Coffey SB, Dias JM, Dowling MS, Farnie G, Fedorov O, Fennell KF, Gamble V, Gileadi C, Giroud C, Harris MR, Hollingshead BD, Huber K, Korczynska M, Lapham K, Loria PM, Narayanan A, Owen DR, Raux B, Sahasrabudhe PV, Ruggeri RB, Sáez LD, Stock IA, Thuma BA, Tsai A, Varghese AE. Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4. J Med Chem 2023; 66:460-472. [PMID: 36562986 DOI: 10.1021/acs.jmedchem.2c01421] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of small-molecule YEATS4 binders have been discovered as part of an ongoing research effort to generate high-quality probe molecules for emerging and/or challenging epigenetic targets. Analogues such as 4d and 4e demonstrate excellent potency and selectivity for YEATS4 binding versus YEATS1,2,3 and exhibit good physical properties and in vitro safety profiles. A new X-ray crystal structure confirms direct binding of this chemical series to YEATS4 at the lysine acetylation recognition site of the YEATS domain. Multiple analogues engage YEATS4 with nanomolar potency in a whole-cell nanoluciferase bioluminescent resonance energy transfer assay. Rodent pharmacokinetic studies demonstrate the competency of several analogues as in vivo-capable binders.
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Affiliation(s)
- Allyn T Londregan
- Pfizer Medicine Design, Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | | | - James Bennett
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Laura J Byrnes
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Daniel P Canterbury
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Xiayun Cheng
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Thomas Christott
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Jennifer Clemens
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Steven B Coffey
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - João M Dias
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Gillian Farnie
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Kimberly F Fennell
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Vicki Gamble
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Carina Gileadi
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Charline Giroud
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Michael R Harris
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Brett D Hollingshead
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kilian Huber
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Magdalena Korczynska
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Kimberly Lapham
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Paula M Loria
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Arjun Narayanan
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Dafydd R Owen
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts 02139, United States
| | - Brigitt Raux
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Parag V Sahasrabudhe
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Roger B Ruggeri
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Laura Díaz Sáez
- Centre for Medicines Discovery, NDM, University of Oxford, Oxford OX3 7DQ, U.K
| | - Ingrid A Stock
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Benjamin A Thuma
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Andy Tsai
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
| | - Alison E Varghese
- Pfizer Worldwide Research and Development, Groton, Connecticut 06340, United States
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5
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Hoffer L, Voitovich YV, Raux B, Carrasco K, Muller C, Fedorov AY, Derviaux C, Amouric A, Betzi S, Horvath D, Varnek A, Collette Y, Combes S, Roche P, Morelli X. Integrated Strategy for Lead Optimization Based on Fragment Growing: The Diversity-Oriented-Target-Focused-Synthesis Approach. J Med Chem 2018; 61:5719-5732. [PMID: 29883107 DOI: 10.1021/acs.jmedchem.8b00653] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Over the past few decades, hit identification has been greatly facilitated by advances in high-throughput and fragment-based screenings. One major hurdle remaining in drug discovery is process automation of hit-to-lead (H2L) optimization. Here, we report a time- and cost-efficient integrated strategy for H2L optimization as well as a partially automated design of potent chemical probes consisting of a focused-chemical-library design and virtual screening coupled with robotic diversity-oriented de novo synthesis and automated in vitro evaluation. The virtual library is generated by combining an activated fragment, corresponding to the substructure binding to the target, with a collection of functionalized building blocks using in silico encoded chemical reactions carefully chosen from a list of one-step organic transformations relevant in medicinal chemistry. The proof of concept was demonstrated using the optimization of bromodomain inhibitors as a test case, leading to the validation of several compounds with improved affinity by several orders of magnitude.
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Affiliation(s)
- Laurent Hoffer
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Yuliia V Voitovich
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,Department of Organic Chemistry , Lobachevsky State University of Nizhni Novgorod , 23 Gagarin Avenue , 603950 Nizhni Novgorod , Russia
| | - Brigitt Raux
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Kendall Carrasco
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Christophe Muller
- IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Aleksey Y Fedorov
- Department of Organic Chemistry , Lobachevsky State University of Nizhni Novgorod , 23 Gagarin Avenue , 603950 Nizhni Novgorod , Russia
| | - Carine Derviaux
- IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Agnès Amouric
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Stéphane Betzi
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Dragos Horvath
- Laboratoire de Chemoinformatique, CNRS UMR7140 , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Alexandre Varnek
- Laboratoire de Chemoinformatique, CNRS UMR7140 , 1 rue Blaise Pascal , 67000 Strasbourg , France
| | - Yves Collette
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
| | - Sébastien Combes
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Philippe Roche
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France
| | - Xavier Morelli
- CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France
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6
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Point V, Bénarouche A, Zarrillo J, Guy A, Magnez R, Fonseca L, Raux B, Leclaire J, Buono G, Fotiadu F, Durand T, Carrière F, Vaysse C, Couëdelo L, Cavalier JF. Slowing down fat digestion and absorption by an oxadiazolone inhibitor targeting selectively gastric lipolysis. Eur J Med Chem 2016; 123:834-848. [DOI: 10.1016/j.ejmech.2016.08.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/05/2016] [Accepted: 08/06/2016] [Indexed: 01/13/2023]
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Milhas S, Raux B, Betzi S, Derviaux C, Roche P, Restouin A, Basse MJ, Rebuffet E, Lugari A, Badol M, Kashyap R, Lissitzky JC, Eydoux C, Hamon V, Gourdel ME, Combes S, Zimmermann P, Aurrand-Lions M, Roux T, Rogers C, Müller S, Knapp S, Trinquet E, Collette Y, Guillemot JC, Morelli X. Protein-Protein Interaction Inhibition (2P2I)-Oriented Chemical Library Accelerates Hit Discovery. ACS Chem Biol 2016; 11:2140-8. [PMID: 27219844 DOI: 10.1021/acschembio.6b00286] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein-protein interactions (PPIs) represent an enormous source of opportunity for therapeutic intervention. We and others have recently pinpointed key rules that will help in identifying the next generation of innovative drugs to tackle this challenging class of targets within the next decade. We used these rules to design an oriented chemical library corresponding to a set of diverse "PPI-like" modulators with cores identified as privileged structures in therapeutics. In this work, we purchased the resulting 1664 structurally diverse compounds and evaluated them on a series of representative protein-protein interfaces with distinct "druggability" potential using homogeneous time-resolved fluorescence (HTRF) technology. For certain PPI classes, analysis of the hit rates revealed up to 100 enrichment factors compared with nonoriented chemical libraries. This observation correlates with the predicted "druggability" of the targets. A specific focus on selectivity profiles, the three-dimensional (3D) molecular modes of action resolved by X-ray crystallography, and the biological activities of identified hits targeting the well-defined "druggable" bromodomains of the bromo and extraterminal (BET) family are presented as a proof-of-concept. Overall, our present study illustrates the potency of machine learning-based oriented chemical libraries to accelerate the identification of hits targeting PPIs. A generalization of this method to a larger set of compounds will accelerate the discovery of original and potent probes for this challenging class of targets.
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Affiliation(s)
- Sabine Milhas
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
- CNRS, Aix-Marseille
Université, Screening Platform AD2P, AFMB UMR7257, 13288, Marseille, France
| | - Brigitt Raux
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Stéphane Betzi
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Carine Derviaux
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Philippe Roche
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Audrey Restouin
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Marie-Jeanne Basse
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Etienne Rebuffet
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Adrien Lugari
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Marion Badol
- Cisbio Bioassays, R&D, Parc Marcel Boiteux, BP 84175, 30200 Codolet, France
| | - Rudra Kashyap
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
- Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium
| | - Jean-Claude Lissitzky
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Cécilia Eydoux
- CNRS, Aix-Marseille
Université, Screening Platform AD2P, AFMB UMR7257, 13288, Marseille, France
| | - Véronique Hamon
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | | | - Sébastien Combes
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Pascale Zimmermann
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
- Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium
| | - Michel Aurrand-Lions
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Thomas Roux
- Cisbio Bioassays, R&D, Parc Marcel Boiteux, BP 84175, 30200 Codolet, France
| | - Catherine Rogers
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7FZ, U.K
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Susanne Müller
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7FZ, U.K
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Stefan Knapp
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7FZ, U.K
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Goethe-University, Institute
for Pharmaceutical Chemistry and Buchmann
Institute for Life Science, Campus Riedberg, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Eric Trinquet
- Cisbio Bioassays, R&D, Parc Marcel Boiteux, BP 84175, 30200 Codolet, France
| | - Yves Collette
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
| | - Jean-Claude Guillemot
- CNRS, Aix-Marseille
Université, Screening Platform AD2P, AFMB UMR7257, 13288, Marseille, France
| | - Xavier Morelli
- CNRS, INSERM, Aix-Marseille Université, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, CS30059, 13273 Marseille Cedex 9, France
- CNRS, Aix-Marseille
Université, Screening Platform AD2P, AFMB UMR7257, 13288, Marseille, France
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Raux B, Voitovich Y, Derviaux C, Lugari A, Rebuffet E, Milhas S, Priet S, Roux T, Trinquet E, Guillemot JC, Knapp S, Brunel JM, Fedorov AY, Collette Y, Roche P, Betzi S, Combes S, Morelli X. Exploring Selective Inhibition of the First Bromodomain of the Human Bromodomain and Extra-terminal Domain (BET) Proteins. J Med Chem 2016; 59:1634-41. [PMID: 26735842 DOI: 10.1021/acs.jmedchem.5b01708] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A midthroughput screening follow-up program targeting the first bromodomain of the human BRD4 protein, BRD4(BD1), identified an acetylated-mimic xanthine derivative inhibitor. This compound binds with an affinity in the low micromolar range yet exerts suitable unexpected selectivity in vitro against the other members of the bromodomain and extra-terminal domain (BET) family. A structure-based program pinpointed a role of the ZA loop, paving the way for the development of potent and selective BET-BRDi probes.
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Affiliation(s)
- Brigitt Raux
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Yuliia Voitovich
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France.,Department of Organic Chemistry, Lobachevsky State University of Nizhni Novgorod , Gagarina av. 23, Nizhni Novgorod 603950, Russia
| | - Carine Derviaux
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Adrien Lugari
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Etienne Rebuffet
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Sabine Milhas
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France.,Screening Platform AD2P, CNRS, AFMB UMR 7257, Aix-Marseille Université , 13288 Marseille, France
| | - Stéphane Priet
- Screening Platform AD2P, CNRS, AFMB UMR 7257, Aix-Marseille Université , 13288 Marseille, France
| | - Thomas Roux
- Cisbio Bioassays, R&D , Parc Marcel Boiteux, BP 84175, 30200 Codolet, France
| | - Eric Trinquet
- Cisbio Bioassays, R&D , Parc Marcel Boiteux, BP 84175, 30200 Codolet, France
| | - Jean-Claude Guillemot
- Screening Platform AD2P, CNRS, AFMB UMR 7257, Aix-Marseille Université , 13288 Marseille, France
| | - Stefan Knapp
- Target Discovery Institute, University of Oxford , NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K.,Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Goethe-University , Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Science, Campus Riedberg, Max-von Laue Str. 9, 60438 Frankfurt am Main, Germany
| | - Jean-Michel Brunel
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Alexey Yu Fedorov
- Department of Organic Chemistry, Lobachevsky State University of Nizhni Novgorod , Gagarina av. 23, Nizhni Novgorod 603950, Russia
| | - Yves Collette
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Philippe Roche
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Stéphane Betzi
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Sébastien Combes
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
| | - Xavier Morelli
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherche en Cancérologie de Marseille (CRCM), UMR 7258; INSERM U1068; Institut Paoli-Calmettes; Aix-Marseille Université, UM105 , 13273 Marseille, France
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9
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Delorme V, Raux B, Puppo R, Leclaire J, Cavalier JF, Marc S, Kamarajugadda PK, Buono G, Fotiadu F, Canaan S, Carrière F. Supported inhibitor for fishing lipases in complex biological media and mass spectrometry identification. Biochimie 2014; 107 Pt A:124-34. [DOI: 10.1016/j.biochi.2014.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/16/2014] [Indexed: 12/24/2022]
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