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Interaction of Hydroxychloroquine with SARS-CoV2 Functional Proteins Using All-atoms Non-equilibrium Alchemical Simulations

Abstract

Using a combination of enhanced sampling molecular dynamics techniques and non-equilibrium alchemical transformations with full atomistic details, we have shown that hydroxychloroquine (HCQ) may act as a mild inhibitor of important functional proteins for SARS-CoV2 replication, with potency increasing in the series PLpro, 3CLpro, RdRp. By analyzing the bound state configurations, we were able to improve the potency for the 3CLpro target, designing a novel HCQ-inspired compound, named PMP329, with predicted nanomolar activity. If confirmed in vitro, our results provide a molecular rationale for the use of HCQ or of strictly related derivatives in the treatment of Covid-19

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Supplementary files

Article information


Submitted
18 May 2020
Accepted
30 Jun 2020
First published
30 Jun 2020

Chem. Commun., 2020, Accepted Manuscript
Article type
Communication

Interaction of Hydroxychloroquine with SARS-CoV2 Functional Proteins Using All-atoms Non-equilibrium Alchemical Simulations

P. Procacci, M. Macchiagodena, M. PAGLIAI, G. Guarnieri and F. Iannone, Chem. Commun., 2020, Accepted Manuscript , DOI: 10.1039/D0CC03558K

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