Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations

Abstract

The novel coronavirus (nCOV-2019) outbreak has put the world on edge, causing millions of cases and hundreds of thousands of deaths all around the world, as of June 2020, let alone the societal and economic impacts of the crisis. The spike protein of nCOV-2019 resides on the virion’s surface mediating coronavirus entry into host cells by binding its receptor binding domain (RBD) to the host cell surface receptor protein, angiotensin converter enzyme (ACE2). Our goal is to provide a detailed structural mechanism of how nCOV-2019 recognizes and establishes contacts with ACE2 and its difference with an earlier severe acute respiratory syndrome coronavirus (SARS-COV) in 2002 via extensive molecular dynamics (MD) simulations. Numerous mutations have been identified in the RBD of nCOV-2019 strains isolated from humans in different parts of the world. In this study, we investigated the effect of these mutations as well as other Ala-scanning mutations on the stability of the RBD/ACE2 complex. It is found that most of the naturally occurring mutations to the RBD either slightly strengthen or have the same binding affinity to ACE2 as the wild-type nCOV-2019. This means that the virus had sufficient binding affinity to its receptor at the beginning of the crisis. This also has implications for any vaccine design endeavors since these mutations could act as antibody escape mutants. Furthermore, in silico Ala-scanning and long-timescale MD simulations highlight the crucial role of the residues at the interface of RBD and ACE2 that may be used as potential pharmacophores for any drug development endeavors. From an evolutional perspective, this study also identifies how the virus has evolved from its predecessor SARS-COV and how it could further evolve to become even more infectious.

Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike Protein Receptor-Binding Domain

“…2d). Similar to the simulations of the RBD-ACE2 complex 12 , the MD simulations of the mutants of the unbound RBD in this work do not show large perturbing effects on the average conformational state. This suggests that while these mutants may have an impact on the stability of the binding interface with ACE2, they do not greatly perturb the conformational state of the RBD in solution and may even serve to reduce the conformational sampling of the unbound RBD.…”

“…It is important to consider how mutations perturb the conformation and dynamics of the RBD, especially during an ongoing pandemic as mutations continue to accumulate 12,13 . Continued identification and evaluation of mutants is crucial in order to better understand the evolving nature of the pandemic, and to ensure that the treatments and vaccines whose primary target is the Spike protein continue to be effective.…”

Millisecond-scale molecular dynamics simulation of spike RBD structure reveals evolutionary adaption of SARS-CoV-2 to stably bind ACE2

“…While others have performed MD simulations for S RBD-ACE2 or peptides that interact with spike or ACE2 to prevent binding, [25][26][27][28] to our knowledge, MD simulations of both free and bound S RBD for the durations have not been previously reported. These millisecond scale MD simulations provide remarkably strong support for the findings described herein.…”

Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2

“…1 b) with reported substitutions to G(2) I(7) N(3400) R(2) T(2) X(20), where X denotes any amino acid. Deep mutational scanning of the RBD has shown that a mutation at S477 has a potential to affect the stability of the RBD as well as its binding to hACE2 15 , whereas the structural effect of residue S477 in context of intra-RBD interactions is lesser understood while it is reported that the residues S477 and T478 in SARS-CoV-2 are responsible for specific and efficient interactions with hACE2 and provide an edge over SARS-CoV 16 , 17 . Therefore, we investigate the structural contribution of residue S477 in the RBD in order to understand its role in hACE2 binding.…”