Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2

Juan Aranda; Milosz Wieczór; Montserrat Terrazas; Isabelle Brun-Heath; Modesto Orozco

doi:10.1016/j.checat.2022.03.019

Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2

Chem Catal. 2022 May 19;2(5):1084-1099. doi: 10.1016/j.checat.2022.03.019. Epub 2022 Apr 19.

Authors

Juan Aranda¹, Milosz Wieczór^{1

2}, Montserrat Terrazas^{1

3}, Isabelle Brun-Heath¹, Modesto Orozco^{1

4}

Affiliations

¹ Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.
² Department of Physical Chemistry, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland.
³ Department of Inorganic and Organic Chemistry, Section of Organic Chemistry, IBUB, University of Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain.
⁴ Departament de Bioquímica i Biomedicine, Universitat de Barcelona, Universitat de Barcelona, Avinguda Diagonal 645, 08028 Barcelona, Spain.

Abstract

We combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while being poorly recognized by human RNA polymerase II (RNA Pol II). A comparison of incorporation rates between natural and antiviral nucleotides shows that remdesivir is incorporated more slowly into the nascent RNA compared with ATP, leading to an RNA duplex that is structurally very similar to an unmodified one, arguing against the hypothesis that remdesivir is a competitive inhibitor of ATP. We characterize the entire mechanism of reaction, finding that viral RdRp is highly processive and displays a higher catalytic rate of incorporation than human RNA Pol II. Overall, our study provides the first detailed explanation of the replication mechanism of RdRp.

Keywords: QM/MM; RNA-dependent RNA polymerase; SARS-CoV-2; antivirals; biocatalysis; free energy calculations; reaction mechanism; remdesivir; viral replication.