Análise in silico da ligação do sítio polibásico de SARS-CoV-2 a serina proteases relacionadas a Furina através de docagem e dinâmica molecular, indicando contatos possivelmente relevantes

Abstract

In December 2019, a new virus from the Coronaviridae family, called SARS-CoV-2, was identified. This virus, responsible for a severe acute respiratory syndrome, caused the COVID-19 pandemic and millions of deaths worldwide. One of the adaptations of this virus that allows it to infect humans is the insertion of a polybasic cleavage site, forming the PRRARS sequence, in its spike protein. This polybasic site is recognized and cleaved by the Furina enzyme, separating the S1 and S2 subunits of the protein. After cleavage by Furina, the spike assumes an active conformation that can potentiate the viral infection through virus-cell fusion, and, mainly, through cell-cell fusion in a process that causes syncytia. In this study, we investigated in silico the interactions that can occur between the loop that contains the polybasic site and the enzyme Furina, studying the interactions that may be relevant to the fit and their behavior during molecular dynamics simulations. The Furina enzyme is part of a family of proprotein convertase subtilisin/kexin, the PCSKs, and therefore, PCSK enzymes 1 to 9 were also investigated to verify whether they could, in the same way, be acting in the activation of the viral protein. For this, we modeled a peptide covering the sequence of the polybasic cleavage site and it was docked over the active site of the enzymes. Then, we performed molecular dynamics simulations to study and characterize the interactions between the peptide and the binding pocket of each enzyme. Thus, we verified that the Furina enzyme performs salt bridge interactions between P1 arginine and two aspartates from its S1 binding pocket, ASP258 and ASP306, and also hydrogen interactions between P1 and PRO256. In addition, we found a link between P3 arginine and aspartate ASP191 from Furina S2 binding pocket. For the other PCSKs, we observed a weak affinity between PCSK1 and PCSK5 to the peptide, requiring further studies to prove whether these enzymes could cleave the site. PCSK2, on the other hand, presented interactions very similar to those presented by Furina, being able to perform interactions through two aspartates and a proline from the S1 binding pocket to the P1 residue, and a binding of an aspartate close to the S2 subsite with P3. Thus, we propose that PCSK2 may possibly be participating in the cleavage and activation of the spike, enhancing infection by the SARS-CoV-2 virus.