ArticleComputers in biology and medicine2021
Targeting multiple conformations of SARS-CoV2 Papain-Like Protease for drug repositioning: An in-silico study.
Article in Computers in biology and medicine, 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, 29 citations in OpenAlex.
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- Spiro heterocycles bearing piperidine moiety as potential scaffold for antileishmanial activity: synthesis, biological evaluation, andJournal of enzyme inhibition and medicinal chemistry · 2023Article
- Entropy driven cooperativity effect in multi-site drug optimization targeting SARS-CoV-2 papain-like protease.Cellular and molecular life sciences : CMLS · 2023Article
- Structural Analysis, Multi-Conformation Virtual Screening and Molecular Simulation to Identify Potential Inhibitors Targeting pS273R Proteases of African Swine Fever Virus.Molecules (Basel, Switzerland) · 2023Article
- New pyrazolylpyrazoline derivatives as dual acting antimalarial-antileishamanial agents: synthesis, biological evaluation and molecular modelling simulations.Journal of enzyme inhibition and medicinal chemistry · 2022Article
- Structure-guided approach on the role of substitution on amide-linked bipyrazoles and its effect on their anti-inflammatory activity.Journal of enzyme inhibition and medicinal chemistry · 2022Article
- Reactivity and binding mode of disulfiram, its metabolites, and derivatives in SARS-CoV-2 PLJournal of molecular modeling · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Phytocompounds as potential inhibitors of SARS-CoV-2 Mpro and PLpro through computational studies.Saudi journal of biological sciences · 2022Article
- Identification of bioactive molecules fromJournal of King Saud University. Science · 2022Article
- Article
- Identification of Hypericin as a Candidate Repurposed Therapeutic Agent for COVID-19 and Its Potential Anti-SARS-CoV-2 Activity.Frontiers in microbiology · 2022Article
- DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.Computers in biology and medicine · 2021Article
- Article
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Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Papain-Like Protease (PLpro) is a key protein for SARS-CoV-2 viral replication which is the cause of the emerging COVID-19 pandemic. Targeting PLpro can suppress viral replication and provide treatment options for COVID-19. Due to the dynamic nature of its binding site loop, PLpro multiple conformations were generated through a long-range 1 micro-second molecular dynamics (MD) simulation. Clustering the MD trajectory enabled us to extract representative structures for the conformational space generated. Adding to the MD representative structures, X-ray structures were involved in an ensemble docking approach to screen the FDA approved drugs for a drug repositioning endeavor. Guided by our recent benchmarking study of SARS-CoV-2 PLpro, FRED docking software was selected for such a virtual screening task. The results highlighted potential consensus binders to many of the MD clusters as well as the newly introduced X-ray structure of PLpro complexed with a small molecule. For instance, three drugs Benserazide, Dobutamine and Masoprocol showed a superior consensus enrichment against the PLpro conformations. Further MD simulations for these drugs complexed with PLpro suggested the superior stability and binding of dobutamine and masoprocol inside the binding site compared to Benserazide. Generally, this approach can facilitate identifying drugs for repositioning via targeting multiple conformations of a crucial target for the rapidly emerging COVID-19 pandemic.
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