Glycosylation as a key for enhancing drug recognition into spike glycoprotein of SARS-CoV-2
Author(s)
Georcki Ropón‐Palacios
Jhon Pérez-Silva
Gustavo E. Olivos-Ramírez
Manuel Enrique Chenet Zuta
Víctor Villanueva
Sheyla Carmen-Sifuentes
Kewin Otazu
Yaritza L. Ramirez-Díaz
Ihosvany Camps
Date Issued
8 de diciembre de 2021
Type
Preprint
Abstract
The emergence of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and its spread since 2019 represents the major public health problem worldwide nowadays, generating a high number of infections and deaths. That’s why, in addition to vaccination campaigns, the design of a drug to help in the treatment of severe cases of COVID-19 is being investigated. In relation to SARS-CoV-2, one of its most studied proteins is the spike protein (S protein), which mediates host-cell entry and is heavily glycosylated. Regarding the latter, several investigations have been carried out, since it plays an important role in the evasion of the host's immune system and contributes to protein folding and the thermostability of the viral particle. For that reason, our objective was to evaluate the impact of glycosylations on the drug recognition on two domains of the S protein, the receptor-binding domain (RBD) and the N-terminal domain (NTD) through molecular dynamics simulations and computational biophysics analysis. Our results show that glycosylations in the S protein induce structural stability and changes in rigidity/flexibility related to the number of glycosylations in the structure. These structural changes are important for its biological activity as well as the correct interaction of ligands in the RBD and NTD regions. Additionally, we evidenced a roto-translation phenomenon in the interaction of the ligand with RBD in the absence of glycosylation, which disappears due to the influence of glycosylation and the convergence of metastable states in RBM. Similarly, glycosylations in NTD promote an induced-fit phenomenon, which is not observed in the absence of glycosylations; this process is decisive for the activity of the ligand at the cryptic site. Altogether, these results provide an explanation of glycosylation relevance in biophysical properties and drug recognition to S protein of SARS-CoV-2 which must be considered in the rational drug development and virtual screening targeting S protein.
Subjects