The Discovery of a Putative Allosteric Site in the SARS-CoV-2 Spike Protein Using an Integrated Structural/Dynamic Approach

Abstract

SARS-CoV-2 has caused the largest pandemic of the twenty-first century , threatening the life and economy of all countries in the world. The identification of novel therapies and vaccines that can mitigate or control this global health threat is among the most important challenges facing biomedical sciences. To construct a long-term strategy to fight both SARS-CoV-2 and other possible future threats from coronaviruses, it is critical to understand the molecular mechanisms underlying the virus action. The viral entry and associated infectivity stems from the formation of the SARS-CoV-2 spike protein complex with angiotensin-converting enzyme 2 (ACE2). The detection of putative allosteric sites on the viral spike protein molecule can be used to elucidate the molecular pathways that can be targeted with allosteric drugs to weaken the spike-ACE2 interaction and, thus, reduce viral infectivity. In this study, we present the results of the application of different computational methods aimed at detecting allosteric sites on the SARS-CoV-2 spike protein. The adopted tools consisted of the protein contact networks (PCNs), SEPAS (Affinity by Flexibility), and perturbation response scanning (PRS) based on elastic network modes. All of these methods were applied to the ACE2 complex with both the SARS-CoV2 and SARS-CoV spike proteins. All of the adopted analyses converged toward a specific region (allosteric modulation region [AMR]), present in both complexes and predicted to act as an allosteric site modulating the binding of the spike protein with ACE2. Preliminary results on hepcidin (a molecule with strong structural and sequence with AMR) indicated an inhibitory effect on the binding affinity of the spike protein toward the ACE2 protein.

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

“…Long-duration modeling can also be applied to in silico screening of molecules that could inhibit the S RBD-ACE2 interaction 8,9,33 . These may be antibodies, peptides or small molecules that either bind directly to the interaction surface or act allosterically to stabilize S RBD in a conformation with low ACE2 binding affinity.…”

“…Our findings reveal that free S RBD has assumed an optimized ACE2 binding-ready conformation, incurring little entropic penalty for binding, an evolutionary adaptation that contributes to its high affinity for the receptor 6 . We further identified high probability molecular binding interactions that inform both vaccine design and therapeutic development, which may include recombinant ACE2-based spike decoys 7 and/or allosteric S RBD-ACE2 binding inhibitors 8,9 to prevent or arrest infection and thus disease.…”

Studying the Effects of ACE2 Mutations on the Stability, Dynamics, and Dissociation Process of SARS-CoV-2 S1/hACE2 Complexes

“…This region of S1 is close to recently discovered allosteric modulator region of the S1 protein. 74 Residues at positions 225, 452, and 485 of ACE2 protein are highly coupled with the distal residues of the S1 protein dynamically. Therefore, the mentioned positions of ACE2 play a critical role in information transfer between ACE2 and S1 subunits of the complex.…”

COVID-19 and iron dysregulation: distant sequence similarity between hepcidin and the novel coronavirus spike glycoprotein

“…Of more importance right now would be the theoretical and/or actual elucidation of the structure of the spike protein TM-CT junction region and a comparison with the available hepcidin structures (the Pfam hepcidin entry, PF06446, currently references six PDB structures). Of note, a recent in silico study has reported on a predicted structural similarity and compatibility between hepcidin and an allosteric site in the SARS-CoV-2 spike protein [32].…”