Immunoinformatics of the Highly Conserved Region of Severe Acute Respiratory Syndrome Coronavirus 2 Spike Glycoprotein–Cholera Toxin B Subunit as a Vaccine Antigen and Its Interaction with Ganglioside GM

Background: Before conducting challenge tests, cholera toxin B subunit (CTB) was incorporated into the highly conserved region (HCR) through a genetic fusion strategy. CTB will facilitate interaction between the HCR spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and ganglioside GM1 (GM1), facilitating antigen uptake and promoting mucosal immune responses. An immunoinformatic approach was subsequently employed to characterize the antigen. Methods: Antigen structure prediction was conducted using Iterative Threading ASSEmbly Refinement, Robetta, and 3Dpro, furthermore validated with ERRAT and PROCHECK. Antigenic potential was predicted using VaxiJen and ANTIGENpro. T-cell epitope and B-cell epitope prediction was conducted using Immune Epitope Database, antigenic.pl, Support vector machine–based tripeptide epitope predictor (SVMTriP), ABCpred. Allergenicity was assessed using AllerCatPro and AlgPred. Molecular docking was performed using AutoDock Vina. Results: The optimal structure was generated by Robetta, showing an overall quality factor of 92.434. The antigenic potential score is 0.4054, classified as a “probable antigen.” The top five residue scores for major histocompatibility complex Class I (MHC-I) epitopes ranged from 0.825045 to 0.938498, while major histocompatibility complex Class II (MHC-II) epitope scores ranged from 0.8355 to 0.8601. B-cell epitopes recommended by SVMTriP scored 1.000 and 0.975. AllerCatPro predicted the construct to be “nonallergenic.” Molecular docking of HCR spike glycoprotein of SARS-CoV-2–CTB with ganglioside GM1 yielded the best ΔG value of − 6.8 kcal/mol. Conclusions: Immunoinformatics of the HCR spike glycoprotein of SARS-CoV-2 fused with CTB suggests its potential as a safe, nonallergenic vaccine candidate with the ability to interact with the GM1 ligand and stimulate cellular adaptive immune responses. These findings highlight its potential as a SARS-CoV-2 vaccine candidate, warranting further validation through experimental studies.