A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments.

Animals Databases, Chemical Humans Internet Molecular Docking Simulation Software
ADME-Tox docking molecular mechanics structure refinement virtual screening web server

Journal

International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791

Informations de publication

Date de publication:
19 Sep 2019
Historique:
received: 16 07 2019
revised: 03 09 2019
accepted: 17 09 2019
entrez: 25 9 2019
pubmed: 25 9 2019
medline: 6 2 2020
Statut: epublish

Résumé

Chemical biology and drug discovery are complex and costly processes. In silico screening approaches play a key role in the identification and optimization of original bioactive molecules and increase the performance of modern chemical biology and drug discovery endeavors. Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening (via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]). The online tools FAF-Drugs4, MTiOpenScreen, and AMMOS2 are implemented in the freely accessible RPBS (Ressource Parisienne en Bioinformatique Structurale) platform. The proposed protocol allows users to screen thousands of small molecules and to download the top 1500 docked molecules that can be further processed online. Users can then decide to purchase a small list of compounds for in vitro validation. To demonstrate the potential of this online-based protocol, we performed virtual screening experiments of 4574 approved drugs against three cancer targets. The results were analyzed in the light of published drugs that have already been repositioned on these targets. We show that our protocol is able to identify active drugs within the top-ranked compounds. The web-based protocol is user-friendly and can successfully guide the identification of new promising molecules for chemical biology and drug discovery purposes.

Identifiants

DOI: 10.3390/ijms20184648 PMID: 31546814 PMC: PMC6769597
pubmed: 31546814
pii: ijms20184648
doi: 10.3390/ijms20184648
pmc: PMC6769597
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : Institut National de la Santé et de la Recherche Médicale
ID : Inserm
Organisme : Université Paris Descartes
ID : Université Paris Descartes
Organisme : the National Science Fund of Bulgaria
ID : DN 17/6
Organisme : Agence Nationale de la Recherche
ID : ToxME
Organisme : CampusFrance
ID : Rila

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Auteurs

Nathalie Lagarde (N)

Laboratoire GBCM, EA7528, Conservatoire National des Arts et Métiers, 2 Rue Conté, Hésam Université, 75003 Paris, France. nathalie.lagarde@lecnam.net.

Elodie Goldwaser (E)

Inserm U1268 MCTR, CNRS UMR 8038 CiTCoM - Univ. de Paris, Faculté de Pharmacie de Paris, 4 av de l'Observatoire, CEDEX 06, 75270 Paris, France. elodie.goldwaser@inserm.fr.

Tania Pencheva (T)

Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad G. Bonchev Str., 1113 Sofia, Bulgaria. tania.pencheva@biomed.bas.bg.

Dessislava Jereva (D)

Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad G. Bonchev Str., 1113 Sofia, Bulgaria. dessi@biomed.bas.bg.

Ilza Pajeva (I)

Department of QSAR and Molecular Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad G. Bonchev Str., 1113 Sofia, Bulgaria. pajeva@biomed.bas.bg.

Julien Rey (J)

Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, F-75013 Paris, France. julien.rey@univ-paris-diderot.fr.

Pierre Tuffery (P)

Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, F-75013 Paris, France. pierre.tuffery@univ-paris-diderot.fr.

Bruno O Villoutreix (BO)

University of Lille, Inserm, Institut Pasteur de Lille, U1177, F-59000 Lille, France. bruno.villoutreix@inserm.fr.

Maria A Miteva (MA)

Inserm U1268 MCTR, CNRS UMR 8038 CiTCoM - Univ. de Paris, Faculté de Pharmacie de Paris, 4 av de l'Observatoire, CEDEX 06, 75270 Paris, France. maria.mitev@inserm.fr.

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