ArticleMolecules (Basel, Switzerland)2021
Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design.
Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 19 citations in OpenAlex.
- Molecular Dynamics Simulations and Current Trends in Designing New Antivirals Targeting Proteases: A Review from 2018 to 2025.Current drug targets · 2026Review
- Structural Basis for TGF-β Mimetic Peptide-Induced Signaling Activation Through Molecular Dynamics Simulations.International journal of molecular sciences · 2025Article
- SARS-CoV-2 Mpro Dihedral Angles Reveal Allosteric Signaling.Proteins · 2025Article
- Potential Broad-Spectrum Antiviral Agents: A Key Arsenal Against Newly Emerging and Reemerging Respiratory RNA Viruses.International journal of molecular sciences · 2025Review
- Article
- Computational Insights into Acrylamide Fragment Inhibition of SARS-CoV-2 Main Protease.Current issues in molecular biology · 2024Article
- Breaking the Chain: Protease Inhibitors as Game Changers in Respiratory Viruses Management.International journal of molecular sciences · 2024Review
- SARS-CoV-2 3CLPro Dihedral Angles Reveal Allosteric Signaling.bioRxiv : the preprint server for biology · 2024Article
- A Tale of Two Proteases: MPharmaceuticals (Basel, Switzerland) · 2023Review
- Computational Analysis of SAM Analogs as Methyltransferase Inhibitors of nsp16/nsp10 Complex from SARS-CoV-2.International journal of molecular sciences · 2022Article
- In Silico Study towards Repositioning of FDA-Approved Drug Candidates for Anticoronaviral Therapy: Molecular Docking, Molecular Dynamics and Binding Free Energy Calculations.Molecules (Basel, Switzerland) · 2022Article
- Signal peptide peptidase: a potential therapeutic target for parasitic and viral infections.Expert opinion on therapeutic targets · 2022Review
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15 authors at 4 institutions in 1 country.
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Abstract
SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the replication of SARS-CoV-2 by inhibiting Mpro. However, the mechanism of action has still not been studied very clearly. In this work, the interaction mechanism of four HIV protease inhibitors Darunavir (DRV), Lopinavir (LPV), Nelfinavir (NFV), and Ritonavire (RTV) targeting SARS-CoV-2 Mpro was explored by applying docking, molecular dynamics (MD) simulations, and MM-GBSA methods using the broad-spectrum antiviral drug Ribavirin (RBV) as the negative and nonspecific control. Our results revealed that LPV, RTV, and NFV have higher binding affinities with Mpro, and they all interact with catalytic residues His41 and the other two key amino acids Met49 and Met165. Pharmacophore model analysis further revealed that the aromatic ring, hydrogen bond donor, and hydrophobic group are the essential infrastructure of Mpro inhibitors. Overall, this study applied computational simulation methods to study the interaction mechanism of HIV-1 protease inhibitors with SARS-CoV-2 Mpro, and the findings provide useful insights for the development of novel anti-SARS-CoV-2 agents for the treatment of COVID-19.
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