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Generate, Repurpose, Validate: A Receptor-Mediated Atom-by-Atom Drug Generation for SARS-Cov-2 Spike Protein and Similarity-Mapped Drug Repurposing for COVID-19 with Rigorous Free Energy Validation Using Well-Tempered Metadynamics

preprint
submitted on 17.05.2020 and posted on 18.05.2020 by Rituparno Chowdhury, Venkata Sai Sreyas Adury, Amal Vijay, Reman K. Singh, Arnab Mukherjee
Finding a cure for Covid-19 is of immediate and paramount importance. In this study, we propose new and repurpose drugs to prevent SARS-Cov-2 (Covid-19) viral attack on human cells. Our study comprises three steps: generation of new molecules, 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 well-tempered metadynamics free energy calculations. We show that some of our new molecules and some of the existing drugs bind more strongly than human ACE2 protein to the viral spike protein. Therefore, these drug molecules may have the potential to be repurposed as a preventive therapy for Covid-19, subject to further experimental verifications.

Funding

This work was partially supported by Department of Biotechnology, India (BT/PR34215/AI/133/22/2019). Authors acknowledge the support and the resources provided by ‘PARAM Brahma Facility’ under the National Supercomputing Mission, Government of India at the Indian Institute of Science Education and Research, Pune.

RC (fellow id SX-1411075) and VSSA (fellow id: SX-1711011) thank KVPY and AV thanks CSIR for their fellowships.

History

Email Address of Submitting Author

arnab.mukherjee@iiserpune.ac.in

Institution

Indian institute of science education and research Pune

Country

India

ORCID For Submitting Author

0000-0001-5691-6120

Declaration of Conflict of Interest

All authors have contributed equally and there is no conflict of interest.

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