ArticleChemistry, an Asian journal2021
Atomistic De-novo Inhibitor Generation-Guided Drug Repurposing for SARS-CoV-2 Spike Protein with Free-Energy Validation by Well-Tempered Metadynamics.
Article in Chemistry, an Asian journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Mechanism of the Early Catalytic Events in the Collagenolysis by Matrix Metalloproteinase-1.Chemphyschem : a European journal of chemical physics and physical chemistry · 2023Article
- Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies.Chemical science · 2022Article
- Structures of the SARS-CoV-2 spike glycoprotein and applications for novel drug development.Frontiers in pharmacology · 2022Review
- Distant residues modulate conformational opening in SARS-CoV-2 spike protein.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Atomistic De-novo Inhibitor Generation-Guided Drug Repurposing for SARS-CoV-2 Spike Protein with Free-Energy Validation by Well-Tempered Metadynamics.Chemistry, an Asian journal · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Computational drug design is increasingly becoming important with new and unforeseen diseases like COVID-19. In this study, we present a new computational de novo drug design and repurposing method and applied it to find plausible drug candidates for the receptor binding domain (RBD) of SARS-CoV-2 (COVID-19). Our study comprises three steps: atom-by-atom generation of new molecules around a receptor, structural similarity mapping to existing approved and investigational drugs, and validation of their binding strengths to the viral spike proteins based on rigorous all-atom, explicit-water well-tempered metadynamics free energy calculations. By choosing the receptor binding domain of the viral spike protein, we showed that some of our new molecules and some of the repurposable drugs have stronger binding to RBD than hACE2. To validate our approach, we also calculated the free energy of hACE2 and RBD, and found it to be in an excellent agreement with experiments. These pool of drugs will allow strategic repurposing against COVID-19 for a particular prevailing conditions.
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Registered trials
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