ABSTRACT
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has killed over 5 million people and is causing a devastating social and economic impact all over the world. The rise of new variants represents a difficult challenge due to the loss of vaccine and natural immunity, and increased transmissibility. These variants contain mutations in the spike glycoprotein, which mediates fusion between the viral and host cell membranes, via its receptor binding domain (RBD) that binds to angiotensin-converting enzyme 2 (ACE2). To understand the effect of RBD mutations, a lot of attention has been given to the RBD-ACE2 interaction. However, this type of analysis is limited since it ignores the conformational dynamics of the RBD itself. Observing that some variants mutations occur in residues that are not in direct contact with ACE2, we hypothesized that they could affect RBD conformational dynamics. To test this, we performed long atomistic molecular dynamics simulations to investigate the structural dynamics of wt RBD, and that of three variants (alpha, beta and delta). Our results show that in solution, wt RBD presents two distinct conformations: an 'open' conformation where it is free to bind ACE2;and a 'closed' conformation, where the RBM ridge blocks the binding surface. The alpha and beta variants significantly impact the open/closed equilibrium, shifting it towards the open conformation by roughly 20%. This shift likely increases ACE2 binding affinity. In the delta variant RBD simulations, the closed conformation was never observed. Instead, the system alternated between the before mentioned open conformation and an alternative 'reversed' one, with a significantly changed orientation of the RBMridge flanking the RBD. These results support the hypothesis that variants impact RBD conformational dynamics in a direction that simultaneously promotes efficient binding to ACE2 and antibody escape.
ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic, which escalated into a global pandemic in early 2020, accounting for more than 400 million infections and more than 6 million confirmed deaths worldwide (as of 2022/03/10). The SARS-CoV-2 mechanism of transmission and infection involves the binding of the virus to the angiotensin-converting enzyme 2 (ACE2) host receptor through the receptor-binding domain (RBD) of the spike (S) protein. The RBD is a privileged target of our immune system and antiviral therapies. Throughout last year multiple vaccines and new therapeutics against SARS-CoV-2 have been developed. However, their effectiveness is challenged by the continuous evolution of SARS-CoV-2, accompanying the origin and spread of new variants of concern (VOC): Alpha, Beta, Gamma, Delta, and recently, Omicron. Among the reported mutations in the VOC S proteins, several are specific to the RBD, which are associated with higher transmissibility or the ability to escape the immune response of previously infected patients. (Previously published in: Greaney, A.J. et al. (2021) Cell Host Microbe 29,44- 57). In late 2021, the newly SARS-CoV-2 Omicron VOC raised considerable global concern due to the presence of more than 30 mutations in the S protein, 15 of which occur in the RBD (Previously published in: Mannar D et al. (2022) Science 375,760-764). Here we investigated the impact of the VOC RBD mutations on its interaction with ACE2, with a major focus on the Omicron RBD, by performing microsecond molecular dynamics (MD) simulations of this complex. Our analysis of the binding and structural dynamics of these mutations provided a detailed characterization of the binding mode between the VOC RBDs and the receptor. This allowed us to understand the role of key residues in the VOC RBD-ACE2 interface and the effect of specific substitutions on the binding affinity via the establishment of new inter-protein contacts.