In Silico Screening of Prospective MHC Class I and II Restricted T-Cell Based Epitopes of the Spike Protein of SARS-CoV-2 for Designing of a Peptide Vaccine for COVID-19

Abstract

Multiple vaccines were developed and administered to immunize people worldwide against SARS-CoV-2 infection. However, changes in platelet count following the course of vaccination have been reported by many studies, suggesting vaccine-induced thrombocytopenia. In this context, designing an effective targeted subunit vaccine with high specificity and efficiency for people with low platelet counts has become a challenge for researchers. Using the in silico-based approaches and methods, the present study explored the antigenic epitopes of the spike protein of SARS-CoV-2 involved in initial binding of the virus with the angiotensin converting enzyme-2 receptor (ACE-2) on the respiratory epithelial cells. The top ten major histocompatibility complex-I (MHC-I) and MHC-II restricted epitopes were found to have 95.26% and 99.99% HLA-class-I population coverage, respectively. Among the top ten promiscuous MHC-I restricted epitopes, ’FTISVTTEI’ had the highest global HLA population coverage of 53.24%, with an antigenic score of 0.85 and a docking score of −162.4 Kcal/mol. The epitope ‘KLNDLCFTNV’ had the best antigenic score of 2.69 and an HLA population coverage of 43.4% globally. The study predicted and documented the most suitable epitopes with the widest global HLA coverage for synthesis of an efficient peptide-based vaccine against the deadly COVID-19.

Immunoinformatics design of a novel multiepitope vaccine candidate against non-typhoidal salmonellosis caused bySalmonellaKentucky using outer membrane proteins A, C, and F

“…This study leverages the immunogenic properties of OMPs, along with the fliC protein, to design an innovative multiepitope vaccine (MEV). The computational approach to designing chimeric membrane proteins aims to optimize the advantages of these molecular gateways and signaling networks [65, 66, 67].…”

SARS-CoV-2 Spike protein peptides displayed in the Pyrococcus furiosus RAD system preserve epitopes antigenicity, immunogenicity, and virus-neutralizing activity of antibodies

“…Sequences that cover RAD-SCoV-30 and RAD-SCoV-31 ( 424 KLPDDFTGCVIAWNSNNLDSK 445 and 431 GCVIAWNSNNLDSKVGGNYNY 452 , respectively) were previously demonstrated to be recognized by antibodies (hNAbs) 22 and to induce neutralizing antibodies 18 , 21 . RAD-SCoV-42 ( 508 YRVVVLSFELLHAPATVCGPK 529 ) is recognized by the antigen presenting cells MHC-I molecules 18 , 23 and the peptide covering the sequence of the RAD-SCoV-07 ( 442 DDSKVGGNYNYLY 452 ), and part of RAD-SCoV-30 and RAD-SCoV-31 ( 424 KLPDDFTGCVIAWNSNNLDSK 445 and 431 GCVIAWNSNNLDSKVGGNYNY 452 , respectively) can induce antibodies capable of neutralizing the virus 18 , 21 , 22 (Table 1 ). RAD-SCoV-13 and RAD-SCoV-15 contain immunodominant epitopes that induced antibodies that are capable of inhibiting SARS-CoV-2 pseudoviruses 24 , 25 .…”

SARS-CoV-2 Spike protein peptides displayed in the Pyrococcus furiosus RAD system preserve epitopes antigenicity, immunogenicity, and virus-neutralizing activity of antibodies

“…Peptides that cover most part of RAD-SCoV-18 (sequence 340 LYNSASFSTFKCYGVSPTKLN 361 ) have been described to induce CD8 + T-cells in previous studies 18,20,21 were previously demonstrated to be recognized by antibodies (hNAbs) 22 and to induce neutralizing antibodies 18,21 . RAD-SCoV-42 ( 508 YRVVVLSFELLHAPATVCGPK 529 ) is recognized by the antigen presenting cells MHC-I molecules 18,23 and the peptide covering the sequence of the RAD-SCoV-07 ( 442 DDSKVGGNYNYLY 452 ), and part of RAD-SCoV-30 and RAD-SCoV-31 ( 424 KLPDDFTGCVIAWNSNNLDSK 445 and 431 GCVIAWNSNNLDSKVG-GNYNY 452 , respectively) can induce antibodies capable of neutralizing the virus 18,21,22 (Table 1). RAD-SCoV-13 and RAD-SCoV-15 contain immunodominant epitopes that induced antibodies that are capable of inhibiting SARS-CoV-2 pseudoviruses 24,25 .…”

“…( 508 YRVVVLSFELLHAPATVCGPK 529 ) was shown to be recognized by the antigen presenting cells MHC-I molecules [18,23] and the peptide covering the sequence of the RAD-SCoV-07 ( 442 DDSKVGGNYNYLY 452 ) and RAD-ScoV-32 ( 438 SNNL DSKVGGNYNYLYRLFRK 459 ) also induced antibodies capable to neutralize the viral infection. [22] Amino acids sequences contained in RAD-SCoV-03…”