Molecular docking and dynamic simulation of conserved B cell epitope of SARS-CoV-2 glycoprotein Indonesian isolates: an immunoinformatic approach

Abstract

Background: An immunoinformatic approach may be useful to investigate the conserved region in the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Indonesia isolates. The aim of this study was to investigate Indonesian SARS-CoV-2 isolates based on B cell epitopes by targeting the conserved regions in the spike glycoprotein to trigger increased multi-variant virus neutralization and memory response for the development of vaccine seed candidates. Methods: SARS-CoV-2 spike glycoprotein gene sequences originating from Indonesia were compared with Wuhan (China), the United Kingdom, South Africa, India, the United States, and Brazil isolates obtained from the NCBI and GISAID databases. The recognition of antigens was carried out directly using B cells through the B cell receptor (BCR). An indirect B cell activation by Cluster of Differentiation (CD)4+ T cells and major histocompatibility complex (MHC)-II was predicted through the binding with human leukocyte antigen (HLA) based on IC50 value. In addition, vaccine allergenicity and toxicity were investigated. During the molecular complex examination, the 3D peptide structure was investigated and the lowest amount of energy formed when the vaccine candidate peptide bound to BCR and MHC-II was calculated. Results: As a result, the spike glycoprotein sequences of Indonesian SARS-CoV-2 isolates had conserved regions which were very similar to reference countries such as China, the United Kingdom, South Africa, India, the United States, and Brazil. Conclusion: It was predicted that the conserved regions could be identified as the epitope of B and T CD4+ cells that produced the peptides for vaccine candidate with antigenic, non-allergen, and non-toxic properties.

The evaluations of the inhibition of orlistat on Clostridium perfringens sialidase (NanI) activity by in vitro and in silico approaches

“…However; a higher value of RMSF demonstrates more flexible movements, whereas a low value of RMSF specifies restricted movements throughout the simulation from its average position [7] . When the resultant distance is less than four, the interaction is deemed stable [33] . When the RMSF graphs were examined, higher RMSF values were observed for NanI‐orlistat than NanI and NanI‐quercetin in certain regions and it turned out to be statistically significant.…”

“…[7] When the resultant distance is less than four, the interaction is deemed stable. [33] When the RMSF graphs were examined, higher RMSF values were observed for NanI-orlistat than NanI and NanI-quercetin in certain regions and it turned out to be statistically significant.…”

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“…The mutational and variable nature of COVID-19 renders it impossible to explain it with changes in a single gene. Hence, the management of COVID-19 patients cannot be implemented by a method, instead diverse methods, including multi-targeted agents and multi-modalities treatment ( Fahmi et al, 2021 ; Rantam et al, 2021 ). It is essential to explore novel and promising biomarkers for the early diagnosis and management of COVID-19 ( Zhong et al, 2020 ; Gattinoni et al, 2021 ).…”

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“…RMSF is caused by atoms interacting with peptide and protein residues at a specified distance. When the resultant distance is smaller than 4, the interaction complex is considered to be stable ( 23 ).…”