Computational Studies of SARS-CoV-2 3CLpro: Insights from MD Simulations.

Alessandro Grottesi,Carmine Talarico,Andrea R Beccari,Carmen Cerchia,Andrew Emerson,Francesco Frigerio,Erik Lindahl,Neva Bešker,Candida Manelfi

doi:10.3390/ijms21155346

Abstract

Given the enormous social and health impact of the pandemic triggered by severe acute respiratory syndrome 2 (SARS-CoV-2), the scientific community made a huge effort to provide an immediate response to the challenges posed by Coronavirus disease 2019 (COVID-19). One of the most important proteins of the virus is an enzyme, called 3CLpro or main protease, already identified as an important pharmacological target also in SARS and Middle East respiratory syndrome virus (MERS) viruses. This protein triggers the production of a whole series of enzymes necessary for the virus to carry out its replicating and infectious activities. Therefore, it is crucial to gain a deeper understanding of 3CLpro structure and function in order to effectively target this enzyme. All-atoms molecular dynamics (MD) simulations were performed to examine the different conformational behaviors of the monomeric and dimeric form of SARS-CoV-2 3CLpro apo structure, as revealed by microsecond time scale MD simulations. Our results also shed light on the conformational dynamics of the loop regions at the entry of the catalytic site. Studying, at atomic level, the characteristics of the active site and obtaining information on how the protein can interact with its substrates will allow the design of molecules able to block the enzymatic function crucial for the virus.

Highlights

A novel coronavirus has been identified as the pathogen responsible for the outbreak of a severe, rapidly developing pneumonia (Coronavirus disease 2019, COVID-19), which has broken out in Wuhan, China, in 2019
The computational study presented here reports the analysis of 2 μs trajectories of the monomeric and the dimeric form of the SARS-CoV-2 3CLpro
It is worth noting that the starting structure of dimeric 3CLpro of our simulation was taken from the holo 3CLpro where the ligand was removed

Summary

Introduction

A novel coronavirus (severe acute respiratory syndrome coronavirus 2, SARS-CoV-2) has been identified as the pathogen responsible for the outbreak of a severe, rapidly developing pneumonia (Coronavirus disease 2019, COVID-19), which has broken out in Wuhan, China, in 2019. SARS-CoV-2 is a single-stranded, positive-sense RNA virus belonging to the family of beta-coronavirus. The first ORFs (ORF1a/b) directly translate two polyproteins: pp1a and pp1ab. These polyproteins are processed by virally encoded chymotrypsin-like protease (3CLpro) or main protease (Mpro) and one or two papain-like protease (PLpro) into 16 non-structural proteins (nsps). The spike protein S forms the outer layer of the coronavirus, giving the characteristic crown-like aspect, and initiates host cell invasion via binding to the angiotensin-converting enzyme 2 (ACE2). This process requires S protein priming by host cell serine protease TMPRSS2 [3]. Because there is no human homolog of 3CLpro, and given the critical role 3CLpro plays in the replication of the virus [4], it represents a valid target for the design of antiviral therapies [5,6]

Methods

Results

Conclusion