In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529)

Authors

DOI:

https://doi.org/10.33448/rsd-v11i10.33126

Keywords:

Covid-19; Molecular docking; Natural molecules.

Abstract

COVID-19 is a highly contagious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becoming a major threat worldwide due to its fast-spreading nature and more aggressive variants, such as the case of Omicron. The main interaction structure of the virus with the host cell is the spike region of the Spike protein called RBD, a structure that has had several mutations, making the search for drugs difficult. Based on this scenario, the present work aimed to evaluate the profile of interactions between molecules of natural origin against the RBD region of the Spike (S) protein of SARS-CoV-2, Ômicron variant. In the first methodological step, there was a molecular modeling of the RBD structure of a sequence obtained in Brazil and tests for its characterization and structural validation. Then, molecular docking was performed between 6 phytochemical ligands: Curcumin, Carvacrol (±)-Limonene, Glycyrrhizin, Allicin and Quercetin-3-Arabinoside in the specific region modeled RBD, after obtaining the best results, the complexes formed were evaluated by RMSD and RMSF. In the homology of the RBD region, a structure with low structural errors was obtained. In the interactions of each phytochemical, the molecules glycyrrhizin and quercetin showed higher molecular affinity, binding to the active site found in RBD. Molecular dynamics confirmed the interaction of ligands and the stability of the complexes during the simulations. Quercetin and glycyrrhizin showed a potential molecule binding to the RBD region of protein S, from the genome of the unprecedented omicron variant of SARS-CoV-2 sequenced in Brazil.

Author Biographies

Helyson Lucas Bezerra Braz, Universidade Federal do Ceará

Graduado em Química pela Universidade Estadual do Ceará (UECE), Mestre e Doutorando em Ciências Morfofuncionais pela Faculdade de Medicina da Universidade Federal do Ceará (UFC).

Fernanda Martins de Souza, Universidade Federal do Ceará

Farmacêutica pela Universidade Federal do Ceará (UFC). Mestranda em Ciências Morfofuncionais na Universidade Federal do Ceará. 

João Junior Faustino Soares, Universidade Federal do Ceará

Mestrando em Ciências Morfofuncionais. Pós-Graduação em Citologia Clínica pelo Centro de Consultoria Educacional e FACEAT Faculdade Centro de Estudos Avançados e Tecnologia, Recife-PE. Graduado em Biomedicina pela Faculdade Santa Maria, Cajazeiras-PB. Graduado em Farmácia pela Faculdade Santa Maria, Cajazeiras-PB.

Renata de Sousa Alves, Universidade Federal do Ceará

Possui graduação em Farmácia - Habilitação em Análises Clínicas pela Universidade Federal do Ceará (2003), Mestrado (2005) e Doutorado (2008) em Farmacologia pela Universidade Federal do Ceará. Tem experiência na área de Farmácia, com ênfase em Análises Clínicas e Farmacologia, atuando principalmente nos seguintes temas: Função renal, Disfunção endotelial, Venenos e Toxinas animais

Roberta Jeane Bezerra Jorge, Universidade Federal do Ceará

Graduada em Enfermagem pela Universidade de Fortaleza. Especialista em Enfermagem Clínica: aspectos farmacológicos e patológicos o cuidar pela Universidade Estadual do Ceará. Mestre em Farmacologia pela Universidade Federal do Ceará. Doutora em Farmacologia pela Universidade Federal do Ceará com período sanduíche na área de proteômica de venenos no Instituto de Biomedicina de Valencia- Espanha. Atua principalmente nos seguintes temas: Farmacologia renal; Farmacologia de venenos e toxinas animais e seus potenciais terapêuticos e Produtos naturais antiofidicos.

Gilberto Santos Cerqueira, Universidade Federal do Ceará

Possui Licenciatura em Ciências Biológicas, Especialista em Hematologia clínica (UFC) e Análises Clínicas (FIJ), Título de Proficiência em Anatomia Macroscópica Humana pela Sociedade Brasileira de Anatomia - SBA. Possui experiência na área de Ensino, Formação de Professores e Tecnologia Educacionais. Professor na Faculdade de Medicina na Universidade Federal do Ceará. 

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Published

05/08/2022

How to Cite

BRAZ, H. L. B. .; SOUZA, F. M. de .; SOARES, J. J. F. .; ALVES, R. de S.; JORGE, R. J. B.; CERQUEIRA, G. S. In silico study of phytochemicals in the Receptor-Binding Domain (RBD) region of the SARS-CoV-2 spike protein (Omicron variant, B.1.1.529). Research, Society and Development, [S. l.], v. 11, n. 10, p. e404111033126, 2022. DOI: 10.33448/rsd-v11i10.33126. Disponível em: https://rsdjournal.org/index.php/rsd/article/view/33126. Acesso em: 27 nov. 2022.

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Section

Health Sciences