ArticleJournal of biomolecular structure & dynamics2021
Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CL
Article in Journal of biomolecular structure & dynamics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers, 1 of them a synthesis that pooled it.
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Who cites it
72 citing papers in PubMed, 1 synthesis or guideline pooled it, 124 citations in OpenAlex.
- Computational drug discovery and repurposing for the treatment of COVID-19: A systematic review.Bioorganic chemistry · 2021Pooled it
- Identification of Novel Drug Molecules Against NS3-Like Helicase Enzyme of Alongshan Virus.Molecular biotechnology · 2025Article
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- An automated positive selection screen in yeast provides support for boron-containing compounds as inhibitors of SARS-CoV-2 main protease.Microbiology spectrum · 2024Article
- Breaking the Chain: Protease Inhibitors as Game Changers in Respiratory Viruses Management.International journal of molecular sciences · 2024Review
- Network pharmacology, molecular docking, and dynamics analyses to predict the antiviral activity of ginger constituents against coronavirus infection.Scientific reports · 2024Article
- A comprehensive review on recent nanosystems for enhancing antifungal activity of fenticonazole nitrate from different routes of administration.Drug delivery · 2023Review
- A Multifaceted Computational Approach to Understanding the MERS-CoV Main Protease and Brown Algae Compounds' Interaction.Marine drugs · 2023Article
- Antimicrobial activities of metabolites isolated from endophytic Aspergillus flavus of Sarcophyton ehrenbergi supported by in-silico study and NMR spectroscopy.Fungal biology and biotechnology · 2023Article
- Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease.Molecular diversity · 2023Article
- An In Silico Molecular Modelling-Based Prediction of Potential Keap1 Inhibitors fromMolecules (Basel, Switzerland) · 2023Article
- Article
- Integrating virtual screening, pharmacoinformatics profiling, and molecular dynamics: identification of promising inhibitors targeting 3CLpro of SARS-CoV-2.Frontiers in molecular biosciences · 2023Article
- Fenticonazole nitrate loaded trans-novasomes for effective management of tinea corporis: design characterization,Drug delivery · 2022Article
- Molecular and Structural Analysis of Specific Mutations from Saudi Isolates of SARS-CoV-2 RNA-Dependent RNA Polymerase and their Implications on Protein Structure and Drug-Protein Binding.Molecules (Basel, Switzerland) · 2022Article
- A new glimpse on the active site of SARS-CoV-2 3CLpro, coupled with drug repurposing study.Molecular diversity · 2022Article
- The effect of various compounds on the COVID mechanisms, from chemical to molecular aspects.Biophysical chemistry · 2022Review
- Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- Search for Novel Potent Inhibitors of the SARS-CoV-2 Papain-like Enzyme: A Computational Biochemistry Approach.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Computational Investigations of Traditional Chinese Medicinal Compounds against the Omicron Variant of SARS-CoV-2 to Rescue the Host Immune System.Pharmaceuticals (Basel, Switzerland) · 2022Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 5 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The SARS-CoV-2 was confirmed to cause the global pandemic of coronavirus disease 2019 (COVID-19). The 3-chymotrypsin-like protease (3CLpro), an essential enzyme for viral replication, is a valid target to combat SARS-CoV and MERS-CoV. In this work, we present a structure-based study to identify potential covalent inhibitors containing a variety of chemical warheads. The targeted Asinex Focused Covalent (AFCL) library was screened based on different reaction types and potential covalent inhibitors were identified. In addition, we screened FDA-approved protease inhibitors to find candidates to be repurposed against SARS-CoV-2 3CLpro. A number of compounds with significant covalent docking scores were identified. These compounds were able to establish a covalent bond (C-S) with the reactive thiol group of Cys145 and to form favorable interactions with residues lining the substrate-binding site. Moreover, paritaprevir and simeprevir from FDA-approved protease inhibitors were identified as potential inhibitors of SARS-CoV-2 3CLpro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CLpro were characterized by molecular dynamics (MD) simulations. The identified compounds are potential inhibitors worthy of further development as COVID-19 drugs. Importantly, the identified FDA-approved anti-hepatitis-C virus (HCV) drugs paritaprevir and simeprevir could be ready for clinical trials to treat infected patients and help curb COVID-19. Communicated by Ramaswamy H. Sarma.
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