Computational Screening Using a Combination of Ligand-Based Machine Learning and Molecular Docking Methods for the Repurposing of Antivirals Targeting the SARS-CoV-2 Main Protease.

COVID-19 Drug repurposing Ligand-based virtual screening Molecular docking Mpro

Journal

Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences
ISSN: 2008-2231
Titre abrégé: Daru
Pays: Switzerland
ID NLM: 101125969

Informations de publication

Date de publication:
31 Oct 2023
Historique:
received: 21 02 2023
accepted: 20 09 2023
medline: 1 11 2023
pubmed: 1 11 2023
entrez: 1 11 2023
Statut: aheadofprint

Résumé

COVID-19 is an infectious disease caused by SARS-CoV-2, a close relative of SARS-CoV. Several studies have searched for COVID-19 therapies. The topics of these works ranged from vaccine discovery to natural products targeting the SARS-CoV-2 main protease (M This study aims to repurpose 10692 drugs in DrugBank by using ligand-based virtual screening (LBVS) machine learning (ML) with Konstanz Information Miner (KNIME) to seek potential therapeutics based on M This study identified 3,166 compound candidates inhibiting M Results demonstrated the efficiency of LBVS combined with MD. This combined strategy provided positive evidence showing that the top screened drugs, including CCX-140, which had the lowest MD score, can be reasonably advanced to the in vitro phase. This combined method may accelerate the discovery of therapies for novel or orphan diseases from existing drugs.

Sections du résumé

BACKGROUND BACKGROUND
COVID-19 is an infectious disease caused by SARS-CoV-2, a close relative of SARS-CoV. Several studies have searched for COVID-19 therapies. The topics of these works ranged from vaccine discovery to natural products targeting the SARS-CoV-2 main protease (M
METHOD METHODS
This study aims to repurpose 10692 drugs in DrugBank by using ligand-based virtual screening (LBVS) machine learning (ML) with Konstanz Information Miner (KNIME) to seek potential therapeutics based on M
RESULTS RESULTS
This study identified 3,166 compound candidates inhibiting M
CONCLUSION CONCLUSIONS
Results demonstrated the efficiency of LBVS combined with MD. This combined strategy provided positive evidence showing that the top screened drugs, including CCX-140, which had the lowest MD score, can be reasonably advanced to the in vitro phase. This combined method may accelerate the discovery of therapies for novel or orphan diseases from existing drugs.

Identifiants

DOI: 10.1007/s40199-023-00484-w PMID: 37907683
pubmed: 37907683
doi: 10.1007/s40199-023-00484-w
pii: 10.1007/s40199-023-00484-w
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© 2023. The Author(s), under exclusive licence to Tehran University of Medical Sciences.

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Auteurs

Gusti Putu Wahyunanda Crista Yuda (GPWC)

Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia.

Naufa Hanif (N)

Master Student of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, 06100, Turkey.

Adam Hermawan (A)

Laboratory of Macromolecular Engineering, Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia. adam_apt@ugm.ac.id.
Laboratory of Advanced Pharmaceutical Sciences. APSLC Building, Faculty of Pharmacy, Universitas Gadjah Mada Sekip Utara II, 55281, Yogyakarta, Indonesia. adam_apt@ugm.ac.id.
ORCID: 0000-0001-5851-3691

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