1
|
Aci-Sèche S, Bourg S, Bonnet P, Rebehmed J, de Brevern AG, Diharce J. A perspective on the sharing of docking data. Data Brief 2023; 49:109386. [PMID: 37492229 PMCID: PMC10365938 DOI: 10.1016/j.dib.2023.109386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 05/17/2023] [Accepted: 07/03/2023] [Indexed: 07/27/2023] Open
Abstract
Computational approaches are nowadays largely applied in drug discovery projects. Among these, molecular docking is the most used for hit identification against a drug target protein. However, many scientists in the field shed light on the lack of availability and reproducibility of the data obtained from such studies to the whole community. Consequently, sustaining and developing the efforts toward a large and fully transparent sharing of those data could be beneficial for all researchers in drug discovery. The purpose of this article is first to propose guidelines and recommendations on the appropriate way to conduct virtual screening experiments and second to depict the current state of sharing molecular docking data. In conclusion, we have explored and proposed several prospects to enhance data sharing from docking experiment that could be developed in the foreseeable future.
Collapse
Affiliation(s)
- Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 2, 45067, France
| | - Stéphane Bourg
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 2, 45067, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d'Orléans 7311, Université d'Orléans BP 6759, Orléans Cedex 2, 45067, France
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese, American University, Beirut, Lebanon
| | - Alexandre G. de Brevern
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB Bioinformatics team, 75014 Paris, France
| | - Julien Diharce
- Université Paris Cité and Université des Antilles and Université de la Réunion, INSERM, Biologie Intégrée du Globule Rouge, UMR_S 1134, DSIMB Bioinformatics team, 75014 Paris, France
| |
Collapse
|
2
|
Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
Collapse
Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
| |
Collapse
|
3
|
Avula S, Peng X, Lang X, Tortorella M, Josselin B, Bach S, Bourg S, Bonnet P, Buron F, Ruchaud S, Routier S, Neagoie C. Design and biological evaluation of substituted 5,7-dihydro-6 H-indolo[2,3- c]quinolin-6-one as novel selective Haspin inhibitors. J Enzyme Inhib Med Chem 2022; 37:1632-1650. [PMID: 35670091 PMCID: PMC9186362 DOI: 10.1080/14756366.2022.2082419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
A library of substituted indolo[2,3-c]quinolone-6-ones was developed as simplified Lamellarin isosters. Synthesis was achieved from indole after a four-step pathway sequence involving iodination, a Suzuki-Miyaura cross-coupling reaction, and a reduction/lactamization sequence. The inhibitory activity of the 22 novel derivatives was assessed on Haspin kinase. Two of them possessed an IC50 of 1 and 2 nM with selectivity towards a panel of 10 other kinases including the parent kinases DYRK1A and CLK1. The most selective compound exerted additionally a very interesting cell effect on the osteosarcoma U-2 OS cell line.
Collapse
Affiliation(s)
- Sreenivas Avula
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science, Guangzhou, China
| | - Xudan Peng
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science, Guangzhou, China
| | - Xingfen Lang
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science, Guangzhou, China
| | - Micky Tortorella
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science, Guangzhou, China.,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Science, Hong Kong SAR, China
| | - Béatrice Josselin
- Sorbonne Université/CNRS UMR8227, Roscoff cedex, France.,Sorbonne Université/CNRS FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Roscoff cedex, France
| | - Stéphane Bach
- Sorbonne Université/CNRS UMR8227, Roscoff cedex, France.,Sorbonne Université/CNRS FR2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Roscoff cedex, France
| | - Stephane Bourg
- Institut de Chimie Organique et Analytique, Université d'Orléans, UMR CNRS 7311, Orleans, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique, Université d'Orléans, UMR CNRS 7311, Orleans, France
| | - Frédéric Buron
- Institut de Chimie Organique et Analytique, Université d'Orléans, UMR CNRS 7311, Orleans, France
| | | | - Sylvain Routier
- Institut de Chimie Organique et Analytique, Université d'Orléans, UMR CNRS 7311, Orleans, France
| | - Cleopatra Neagoie
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science, Guangzhou, China.,Centre for Regenerative Medicine and Health, Hong Kong Institute of Science and Innovation, Chinese Academy of Science, Hong Kong SAR, China
| |
Collapse
|
4
|
Buron F, Rodrigues N, Saurat T, Hiebel MA, Bourg S, Bonnet P, Nehmé R, Morin P, Percina N, Corret J, Vallée B, le Guevel R, Jourdan ML, Bénédetti H, Routier S. Design, Synthesis and SAR in 2,4,7-Trisubstituted Pyrido[3,2- d]Pyrimidine Series as Novel PI3K/mTOR Inhibitors. Molecules 2021; 26:molecules26175349. [PMID: 34500781 PMCID: PMC8434050 DOI: 10.3390/molecules26175349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/25/2021] [Accepted: 08/28/2021] [Indexed: 11/22/2022] Open
Abstract
This work describes the synthesis, enzymatic activities on PI3K and mTOR, in silico docking and cellular activities of various uncommon 2,4,7 trisubstituted pyrido[3,2-d]pyrimidines. The series synthesized offers a chemical diversity in C-7 whereas C-2 (3-hydroxyphenyl) and C-4 groups (morpholine) remain unchanged, in order to provide a better understanding of the molecular determinants of PI3K selectivity or dual activity on PI3K and mTOR. Some C-7 substituents were shown to improve the efficiency on kinases compared to the 2,4-di-substituted pyrimidopyrimidine derivatives used as references. Six novel derivatives possess IC50 values on PI3Kα between 3 and 10 nM. The compounds with the best efficiencies on PI3K and mTOR induced micromolar cytotoxicity on cancer cell lines possessing an overactivated PI3K pathway.
Collapse
Affiliation(s)
- Frédéric Buron
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Nuno Rodrigues
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Thibault Saurat
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
- Centre de Biophysique Moléculaire, CNRS Orléans, Rue Charles Sadron, 45071 Orléans, France; (J.C.); (B.V.)
| | - Marie Aude Hiebel
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Stéphane Bourg
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Reine Nehmé
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Philippe Morin
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Nathalie Percina
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
| | - Justine Corret
- Centre de Biophysique Moléculaire, CNRS Orléans, Rue Charles Sadron, 45071 Orléans, France; (J.C.); (B.V.)
| | - Béatrice Vallée
- Centre de Biophysique Moléculaire, CNRS Orléans, Rue Charles Sadron, 45071 Orléans, France; (J.C.); (B.V.)
| | - Remy le Guevel
- Campus de Villejean, ImPACcell, Structure Fédérative de Recherche BIOSIT, Université de Rennes 1, Bat 8, 2 Avenue du Pr. Leon Bernard, CS34317, 35043 Rennes, France;
| | - Marie-Lise Jourdan
- Nutrition Croissance et Métabolisme, N2C, INSERM U1069, CHU Tours, Faculté de Médecine, 10 boulevard Tonnellé, 37032 Tours, France;
| | - Hélène Bénédetti
- Centre de Biophysique Moléculaire, CNRS Orléans, Rue Charles Sadron, 45071 Orléans, France; (J.C.); (B.V.)
- Correspondence: (H.B.); (S.R.); Tel.: +33-(0)2-38-49-48-53 (S.R.)
| | - Sylvain Routier
- Institut de Chimie Organique et Analytique, Université d’Orléans, UMR CNRS 7311, rue de Chartres, BP 6759, 45067 Orléans, France; (F.B.); (N.R.); (T.S.); (M.A.H.); (S.B.); (P.B.); (R.N.); (P.M.); (N.P.)
- Correspondence: (H.B.); (S.R.); Tel.: +33-(0)2-38-49-48-53 (S.R.)
| |
Collapse
|
5
|
Bosc N, Muller C, Hoffer L, Lagorce D, Bourg S, Derviaux C, Gourdel ME, Rain JC, Miller TW, Villoutreix BO, Miteva MA, Bonnet P, Morelli X, Sperandio O, Roche P. Fr-PPIChem: An Academic Compound Library Dedicated to Protein-Protein Interactions. ACS Chem Biol 2020; 15:1566-1574. [PMID: 32320205 PMCID: PMC7399473 DOI: 10.1021/acschembio.0c00179] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Protein-protein interactions (PPIs) mediate nearly every cellular process and represent attractive targets for modulating disease states but are challenging to target with small molecules. Despite this, several PPI inhibitors (iPPIs) have entered clinical trials, and a growing number of PPIs have become validated drug targets. However, high-throughput screening efforts still endure low hit rates mainly because of the use of unsuitable screening libraries. Here, we describe the collective effort of a French consortium to build, select, and store in plates a unique chemical library dedicated to the inhibition of PPIs. Using two independent predictive models and two updated databases of experimentally confirmed PPI inhibitors developed by members of the consortium, we built models based on different training sets, molecular descriptors, and machine learning methods. Independent statistical models were used to select putative PPI inhibitors from large commercial compound collections showing great complementarity. Medicinal chemistry filters were applied to remove undesirable structures from this set (such as PAINS, frequent hitters, and toxic compounds) and to improve drug likeness. The remaining compounds were subjected to a clustering procedure to reduce the final size of the library while maintaining its chemical diversity. In practice, the library showed a 46-fold activity rate enhancement when compared to a non-iPPI-enriched diversity library in high-throughput screening against the CD47-SIRPα PPI. The Fr-PPIChem library is plated in 384-well plates and will be distributed on demand to the scientific community as a powerful tool for discovering new chemical probes and early hits for the development of potential therapeutic drugs.
Collapse
Affiliation(s)
- Nicolas Bosc
- Inserm U973 MTi, 25 rue Hélène Brion 75013 Paris
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR3528, 28 rue du Dr Roux 75015 Paris
| | - Christophe Muller
- IPC Drug Discovery Platform, Institut Paoli-Calmettes, 232 Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Laurent Hoffer
- CRCM, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille Univ, 13009 Marseille, France
| | - David Lagorce
- Université de Paris, INSERM US14, Plateforme Maladies Rares - Orphanet, 75014 Paris, France
| | - Stéphane Bourg
- Institut de Chimie Organique et Analytique (ICOA), Université d’Orléans, UMR CNRS 7311, BP 6759, 45067 Orléans. France
| | - Carine Derviaux
- IPC Drug Discovery Platform, Institut Paoli-Calmettes, 232 Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Marie-Edith Gourdel
- Hybrigenics Services SAS, 1 rue Pierre Fontaine, 91000 Evry Courcouronnes, France
| | - Jean-Christophe Rain
- Hybrigenics Services SAS, 1 rue Pierre Fontaine, 91000 Evry Courcouronnes, France
| | - Thomas W. Miller
- IPC Drug Discovery Platform, Institut Paoli-Calmettes, 232 Boulevard de Sainte-Marguerite, 13009, Marseille, France
| | - Bruno O. Villoutreix
- Université de Lille, INSERM, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France
| | - Maria A. Miteva
- Inserm U1268 MCTR, CNRS UMR 8038 CiTCoM – Univ. De Paris, Faculté de Pharmacie de Paris, 75006 Paris, France
| | - Pascal Bonnet
- Institut de Chimie Organique et Analytique (ICOA), Université d’Orléans, UMR CNRS 7311, BP 6759, 45067 Orléans. France
| | - Xavier Morelli
- IPC Drug Discovery Platform, Institut Paoli-Calmettes, 232 Boulevard de Sainte-Marguerite, 13009, Marseille, France
- CRCM, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille Univ, 13009 Marseille, France
| | - Olivier Sperandio
- Inserm U973 MTi, 25 rue Hélène Brion 75013 Paris
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR3528, 28 rue du Dr Roux 75015 Paris
| | - Philippe Roche
- CRCM, CNRS, INSERM, Institut Paoli-Calmettes, Aix-Marseille Univ, 13009 Marseille, France
| |
Collapse
|