ArticleJournal of King Saud University. Science2021
Combined docking methods and molecular dynamics to identify effective antiviral 2, 5-diaminobenzophenonederivatives against SARS-CoV-2.
Article in Journal of King Saud University. Science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 49 citations in OpenAlex.
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- Revealing Propolis Potential Activity on Inhibiting Estrogen Receptor and Heat Shock Protein 90 Overexpressed in Breast Cancer by Bioinformatics Approaches.Bioinformatics and biology insights · 2024Article
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- Galactoside-Based Molecule Enhanced Antimicrobial Activity through Acyl Moiety Incorporation: Synthesis and In Silico Exploration for Therapeutic Target.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Therapeutic Promises of Plant Metabolites against Monkeypox Virus: An In Silico Study.Advances in virology · 2023Article
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- Benchmarked molecular docking integrated molecular dynamics stability analysis for prediction of SARS-CoV-2 papain-like protease inhibition by olive secoiridoids.Journal of King Saud University. Science · 2023Article
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- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Targeting omicron and other reported SARS-CoV-2 lineages by potent inhibitors of main protease 3CL Mpro: Molecular simulation analysis.The Journal of infection · 2022Article
- Design of novel benzimidazole derivatives as potential α-amylase inhibitors using QSAR, pharmacokinetics, molecular docking, and molecular dynamics simulation studies.Journal of molecular modeling · 2022Article
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Authors and funding
6 authors at 4 institutions in 4 countries.
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No grant is acknowledged in the PubMed record.
Abstract
The aim of this work is to contribute to the research in finding lead compounds for clinical use, to identify new drugs that target the SARS-CoV-2 virus main protease (Mpro). In this study, we used molecular docking strategies to analyze 2.5-diaminobenzophenone compounds against Malaria and to compare results with the Nelfinavir as a FDA-approved HIV-1 protease inhibitor recommended for the treatment of COVID-19. These efforts identified the potential compounds against SAR-COV-2 Mpro with the docking scores ranges from -6.1 to -7.75 kcal/mol, which exhibited better interactions than the Nelfinavir. Among thirty-six studied, compounds 20c, 24c, 30c, 34c, 35c and 36c showed the highest affinity and involved in forming hydrophobic interactions with Glu166, Thr24, Thr25, and Thr26 residues and forming H-bonding interactions with Gln189, Cys145, and His41residues. Pharmacokinetic properties and toxicity (ADMET) were also determined for identified compounds. This study result in the identification of two compounds 35 and 36 having high binding affinity, good pharmacokinetics properties and lowest toxicity. The structural stability and dynamics of lead compounds within the active site of 3CLpro was also examined using molecular dynamics (MD) simulation. Essential dynamics demonstrated that the two complexes remain stable during the entire duration of simulation. We have shown that these two lead molecules would have the potential to act as promising drug-candidates and would be of interest as starting point for designing compounds against the SARS-CoV-2.
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