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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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2
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Sternicki LM, Poulsen SA. Native Mass Spectrometry: Insights and Opportunities for Targeted Protein Degradation. Anal Chem 2023; 95:18655-18666. [PMID: 38090751 DOI: 10.1021/acs.analchem.3c03853] [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: 12/27/2023]
Abstract
Native mass spectrometry (nMS) is one of the most powerful biophysical methods for the direct observation of noncovalent protein interactions with both small molecules and other proteins. With the advent of targeted protein degradation (TPD), nMS is now emerging as a compelling approach to characterize the multiple fundamental interactions that underpin the TPD mechanism. Specifically, nMS enables the simultaneous observation of the multiple binary and ternary complexes [i.e., all combinations of E3 ligase, target protein of interest, and small molecule proximity-inducing reagents (such as PROteolysis TArgeting Chimeras (PROTACs) and molecular glues)], formed as part of the TPD equilibrium; this is not possible with any other biophysical method. In this paper we overview the proof-of-concept applications of nMS within the field of TPD and demonstrate how it is providing researchers with critical insight into the systems under study. We also provide an outlook on the scope and future opportunities offered by nMS as a core and agnostic biophysical tool for advancing research developments in TPD.
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Affiliation(s)
- Louise M Sternicki
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
| | - Sally-Ann Poulsen
- Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
- School of Environment and Science, Griffith University, Nathan, Brisbane, Queensland 4111, Australia
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3
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Characterization of a Salmonella transcription factor-DNA complex and identification of the inducer by native mass spectrometry. J Mol Biol 2022; 434:167480. [PMID: 35176290 PMCID: PMC8977229 DOI: 10.1016/j.jmb.2022.167480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022]
Abstract
FraR, a transcriptional repressor, was postulated to regulate the metabolism of the Amadori compound fructose-asparagine (F-Asn) in the foodborne pathogen Salmonella enterica. Here, the DNA- and inducer-binding affinities and stoichiometries of FraR were determined and cross-validated by electrophoretic mobility-shift assays (EMSAs) and online buffer exchange coupled to native mass spectrometry (OBE-nMS). We demonstrate the utility of OBE-nMS to characterize protein and protein-DNA complexes that are not amenable to offline exchange into volatile buffers. OBE-nMS complemented EMSAs by revealing that FraR binds to the operator DNA as a dimer and by establishing 6-phosphofructose-aspartate as the inducer that weakens DNA binding by FraR. These results provide insights into how FraR regulates the expression of F-Asn-catabolizing enzymes and add to our understanding of the intricate bacterial circuitry that dictates utilization of diverse nutrients.
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site‐Specific DNA‐Antibody Bioconjugation by Using Benzoylacrylic‐Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Daniel R. Whiten
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Peter Ravn
- AstraZeneca R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE) Milstein Building, Granta Park Cambridge CB21 6GH UK
- Current address: Department of Biotherapeutic Discovery H. Lundbeck A/S Ottiliavej 9, 2500 Valby Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- UK Dementia Research Institute University of Cambridge Cambridge CB2 0XY UK
| | - Gonçalo J. L. Bernardes
- Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
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5
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Konč J, Brown L, Whiten DR, Zuo Y, Ravn P, Klenerman D, Bernardes GJL. A Platform for Site-Specific DNA-Antibody Bioconjugation by Using Benzoylacrylic-Labelled Oligonucleotides. Angew Chem Int Ed Engl 2021; 60:25905-25913. [PMID: 34555238 PMCID: PMC9297960 DOI: 10.1002/anie.202109713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Indexed: 12/27/2022]
Abstract
Many bioconjugation strategies for DNA oligonucleotides and antibodies suffer limitations, such as site-specificity, stoichiometry and hydrolytic instability of the conjugates, which makes them unsuitable for biological applications. Here, we report a new platform for the preparation of DNA-antibody bioconjugates with a simple benzoylacrylic acid pentafluorophenyl ester reagent. Benzoylacrylic-labelled oligonucleotides prepared with this reagent can be site-specifically conjugated to a range of proteins and antibodies through accessible cysteine residues. The homogeneity of the prepared DNA-antibody bioconjugates was confirmed by a new LC-MS protocol and the bioconjugate probes were used in fluorescence or super-resolution microscopy cell imaging experiments. This work demonstrates the versatility and robustness of our bioconjugation protocol that gives site-specific, well-defined and plasma-stable DNA-antibody bioconjugates for biological applications.
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Affiliation(s)
- Juraj Konč
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Libby Brown
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Daniel R Whiten
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Yukun Zuo
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Peter Ravn
- AstraZeneca, R&D BioPharmaceuticals Unit
- Antibody Discovery & Protein Engineering (ADPE), Milstein Building, Granta Park, Cambridge, CB21 6GH, UK.,Current address: Department of Biotherapeutic Discovery, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,UK Dementia Research Institute, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Gonçalo J L Bernardes
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
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Villemagne B, Machelart A, Tran NC, Flipo M, Moune M, Leroux F, Piveteau C, Wohlkönig A, Wintjens R, Li X, Gref R, Brodin P, Deprez B, Baulard AR, Willand N. Fragment-Based Optimized EthR Inhibitors with in Vivo Ethionamide Boosting Activity. ACS Infect Dis 2020; 6:366-378. [PMID: 32011115 DOI: 10.1021/acsinfecdis.9b00277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Killing more than one million people each year, tuberculosis remains the leading cause of death from a single infectious agent. The growing threat of multidrug-resistant strains of Mycobacterium tuberculosis stresses the need for alternative therapies. EthR, a mycobacterial transcriptional regulator, is involved in the control of the bioactivation of the second-line drug ethionamide. We have previously reported the discovery of in vitro nanomolar boosters of ethionamide through fragment-based approaches. In this study, we have further explored the structure-activity and structure-property relationships in this chemical family. By combining structure-based drug design and in vitro evaluation of the compounds, we identified a new oxadiazole compound as the first fragment-based ethionamide booster which proved to be active in vivo, in an acute model of tuberculosis infection.
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Affiliation(s)
- Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Arnaud Machelart
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ngoc Chau Tran
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alexandre Wohlkönig
- Structural Biology Brussels and Molecular and Cellular Interactions, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie bioorganique et Macromoléculaire (CP206/04), Institut de Pharmacie, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Xue Li
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Ruxandra Gref
- Institut des Sciences Moléculaires d’Orsay, UMR CNRS 8214, Université Paris-Sud, Université Paris Saclay, 91400 Orsay, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL−Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
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7
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Prevet H, Moune M, Tanina A, Kemmer C, Herledan A, Frita R, Wohlkönig A, Bourotte M, Villemagne B, Leroux F, Gitzinger M, Baulard AR, Déprez B, Wintjens R, Willand N, Flipo M. A fragment-based approach towards the discovery of N-substituted tropinones as inhibitors of Mycobacterium tuberculosis transcriptional regulator EthR2. Eur J Med Chem 2019; 167:426-438. [PMID: 30784877 DOI: 10.1016/j.ejmech.2019.02.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/04/2019] [Accepted: 02/07/2019] [Indexed: 01/27/2023]
Abstract
Tuberculosis (TB) caused by the pathogen Mycobacterium tuberculosis, represents one of the most challenging threat to public health worldwide, and with the increasing resistance to approved TB drugs, it is needed to develop new strategies to address this issue. Ethionamide is one of the most widely used drugs for the treatment of multidrug-resistant TB. It is a prodrug that requires activation by mycobacterial monooxygenases to inhibit the enoyl-ACP reductase InhA, which is involved in mycolic acid biosynthesis. Very recently, we identified that inhibition of a transcriptional repressor, termed EthR2, derepresses a new bioactivation pathway that results in the boosting of ethionamide activation. Herein, we describe the identification of potent EthR2 inhibitors using fragment-based screening and structure-based optimization. A target-based screening of a fragment library using thermal shift assay followed by X-ray crystallography identified 5 hits. Rapid optimization of the tropinone chemical series led to compounds with improved in vitro potency.
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Affiliation(s)
- Hugues Prevet
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Martin Moune
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, U1019-UMR8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Abdalkarim Tanina
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | | | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Rosangela Frita
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, U1019-UMR8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Alexandre Wohlkönig
- Structural Biology Brussels, Vlaams Instituut voor Biotechnology (VIB), B-1050, Brussels, Belgium
| | | | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Marc Gitzinger
- Bioversys AG, Hochbergerstrasse 60C, 4057, Basel, Switzerland
| | - Alain R Baulard
- Institut Pasteur de Lille, Univ. Lille, CNRS, Inserm, CHU Lille, U1019-UMR8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - René Wintjens
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
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8
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Mass Spectrometry- and Computational Structural Biology-Based Investigation of Proteins and Peptides. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:265-287. [PMID: 31347053 DOI: 10.1007/978-3-030-15950-4_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent developments of mass spectrometry (MS) allow us to identify, estimate, and characterize proteins and protein complexes. At the same time, structural biology helps to determine the protein structure and its structure-function relationship. Together, they aid to understand the protein structure, property, function, protein-complex assembly, protein-protein interaction, and dynamics. The present chapter is organized with illustrative results to demonstrate how experimental mass spectrometry can be combined with computational structural biology for detailed studies of protein's structures. We have used tumor differentiation factor protein/peptide as ligand and Hsp70/Hsp90 as receptor protein as examples to study ligand-protein interaction. To investigate possible protein conformation, we will describe two proteins-lysozyme and myoglobin. As an application of MS-based assignment of disulfide bridges, the case of the spider venom polypeptide Phα1β will also be discussed.
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Tanina A, Wohlkönig A, Soror SH, Flipo M, Villemagne B, Prevet H, Déprez B, Moune M, Perée H, Meyer F, Baulard AR, Willand N, Wintjens R. A comprehensive analysis of the protein-ligand interactions in crystal structures of Mycobacterium tuberculosis EthR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:248-258. [PMID: 30553830 DOI: 10.1016/j.bbapap.2018.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/05/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
Abstract
The Mycobacterium tuberculosis EthR is a member of the TetR family of repressors, controlling the expression of EthA, a mono-oxygenase responsible for the bioactivation of the prodrug ethionamide. This protein was established as a promising therapeutic target against tuberculosis, allowing, when inhibited by a drug-like molecule, to boost the action of ethionamide. Dozens of EthR crystal structures have been solved in complex with ligands. Herein, we disclose EthR structures in complex with 18 different small molecules and then performed in-depth analysis on the complete set of EthR structures that provides insights on EthR-ligand interactions. The 81 molecules solved in complex with EthR show a large diversity of chemical structures that were split up into several chemical clusters. Two of the most striking common points of EthR-ligand interactions are the quasi-omnipresence of a hydrogen bond bridging compounds with Asn179 and the high occurrence of π-π interactions involving Phe110. A systematic analysis of the protein-ligand contacts identified eight hot spot residues that defined the basic structural features governing the binding mode of small molecules to EthR. Implications for the design of new potent inhibitors are discussed.
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Affiliation(s)
- Abdalkarim Tanina
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Alexandre Wohlkönig
- Center for Structural Biology, Vlaams Instituut voor Biotechnology (VIB), B-1050 Brussels, Belgium
| | - Sameh H Soror
- Center of scientific excellence, Helwan Structural Biology Research, Faculty of Pharmacy, Helwan University, Ain helwan, 11792 Helwan, Cairo, Egypt
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Hugues Prevet
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Hélène Perée
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Franck Meyer
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL- Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.
| | - René Wintjens
- Unité Microbiologie, Bioorganique et Macromoléculaire (CP206/04), département R3D, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050 Brussels, Belgium.
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Prieri M, Frita R, Probst N, Sournia-Saquet A, Bourotte M, Déprez B, Baulard AR, Willand N. Efficient analoging around ethionamide to explore thioamides bioactivation pathways triggered by boosters in Mycobacterium tuberculosis. Eur J Med Chem 2018; 159:35-46. [DOI: 10.1016/j.ejmech.2018.09.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/27/2018] [Accepted: 09/14/2018] [Indexed: 11/17/2022]
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Moiani D, Ronato DA, Brosey CA, Arvai AS, Syed A, Masson JY, Petricci E, Tainer JA. Targeting Allostery with Avatars to Design Inhibitors Assessed by Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities. Methods Enzymol 2018. [PMID: 29523233 DOI: 10.1016/bs.mie.2017.11.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
For inhibitor design, as in most research, the best system is question dependent. We suggest structurally defined allostery to design specific inhibitors that target regions beyond active sites. We choose systems allowing efficient quality structures with conformational changes as optimal for structure-based design to optimize inhibitors. We maintain that evolutionarily related targets logically provide molecular avatars, where this Sanskrit term for descent includes ideas of functional relationships and of being a physical embodiment of the target's essential features without requiring high sequence identity. Appropriate biochemical and cell assays provide quantitative measurements, and for biomedical impacts, any inhibitor's activity should be validated in human cells. Specificity is effectively shown empirically by testing if mutations blocking target activity remove cellular inhibitor impact. We propose this approach to be superior to experiments testing for lack of cross-reactivity among possible related enzymes, which is a challenging negative experiment. As an exemplary avatar system for protein and DNA allosteric conformational controls, we focus here on developing separation-of-function inhibitors for meiotic recombination 11 nuclease activities. This was achieved not by targeting the active site but rather by geometrically impacting loop motifs analogously to ribosome antibiotics. These loops are neighboring the dimer interface and active site act in sculpting dsDNA and ssDNA into catalytically competent complexes. One of our design constraints is to preserve DNA substrate binding to geometrically block competing enzymes and pathways from the damaged site. We validate our allosteric approach to controlling outcomes in human cells by reversing the radiation sensitivity and genomic instability in BRCA mutant cells.
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Affiliation(s)
- Davide Moiani
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Daryl A Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada; Laval University Cancer Research Center, Québec City, QC, Canada
| | - Chris A Brosey
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Andrew S Arvai
- The Scripps Research Institute, La Jolla, CA, United States
| | - Aleem Syed
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Québec City, QC, Canada; Laval University Cancer Research Center, Québec City, QC, Canada
| | | | - John A Tainer
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States; Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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Mass spectrometry for fragment screening. Essays Biochem 2017; 61:465-473. [PMID: 28986384 DOI: 10.1042/ebc20170071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/31/2022]
Abstract
Fragment-based approaches in chemical biology and drug discovery have been widely adopted worldwide in both academia and industry. Fragment hits tend to interact weakly with their targets, necessitating the use of sensitive biophysical techniques to detect their binding. Common fragment screening techniques include differential scanning fluorimetry (DSF) and ligand-observed NMR. Validation and characterization of hits is usually performed using a combination of protein-observed NMR, isothermal titration calorimetry (ITC) and X-ray crystallography. In this context, MS is a relatively underutilized technique in fragment screening for drug discovery. MS-based techniques have the advantage of high sensitivity, low sample consumption and being label-free. This review highlights recent examples of the emerging use of MS-based techniques in fragment screening.
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