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Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants
Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil; Hospital de Clínicas, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil.
Luleå University of Technology, Department of Engineering Sciences and Mathematics, Energy Science. Arrhenius Laboratory, Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden; State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China; Centre of Advanced Research in Bionanoconjugates and Biopolymers, Petru Poni Institute of Macromolecular Chemistry, Iasi, Romania.ORCID iD: 0000-0001-9783-4535
Departamento de Ciências Biomoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States.
2021 (English)In: Frontiers in Medical Technology, E-ISSN 2673-3129, Vol. 3, article id 694347Article in journal (Refereed) Published
Abstract [en]

The COVID-19 pandemic has spread worldwide. However, as soon as the first vaccines—the only scientifically verified and efficient therapeutic option thus far—were released, mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged, raising doubts about their efficiency. This study aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor-binding domain (RBD) and angiotensin-converting enzyme II (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state, in which the virus can interact with the cellular receptor, ACE2, rather than due to alterations in the complexation RBD-ACE2, since the difference observed in the free energy values was small (although more attractive in general). Conversely, the South African/Beta variant (B.1.351), compared with the SARS-CoV-2 wild type (wt), is much more stable in the opened state with one or two RBDs in the up position than in the closed state with three RBDs in the down position favoring the infection. Such results contribute to understanding the natural history of disease and indicate possible strategies for developing new therapeutic molecules and adjusting the vaccine doses for higher B-cell antibody production.

Place, publisher, year, edition, pages
Frontiers Media S.A., 2021. Vol. 3, article id 694347
Keywords [en]
SARS-CoV-2, mutations, conformational states, coronavirus, electrostatic interactions, epitopes, binding affinity, protein–protein interactions
National Category
Infectious Medicine
Research subject
Energy Engineering
Identifiers
URN: urn:nbn:se:ltu:diva-89224DOI: 10.3389/fmedt.2021.694347ISI: 001009692100001PubMedID: 35047936Scopus ID: 2-s2.0-85119909294OAI: oai:DiVA.org:ltu-89224DiVA, id: diva2:1637488
Funder
Swedish National Infrastructure for Computing (SNIC)Swedish Research Council
Note

Godkänd;2022;Nivå 0;2022-03-14 (joosat);

Funder: Fundação de Amparo à Pesquisa do Estado de São Paulo (Fapesp 2020/07158-2 (FLBdS)); Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq 305393/2020-0 (FLBdS), PIBIC/CNPq 2020-1732 (CCG)); Ministry of Research, and Innovation of Romania (CNCS-UEFISCDI, PN-III-P4-ID-PCCF-2016-0050, within PNCDI III)

Available from: 2022-02-14 Created: 2022-02-14 Last updated: 2024-03-07Bibliographically approved

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