A SARS-COV-2 SELF-AMPLIFYING MRNA VACCINE DESIGN FOR INDONESIA POPULATION USING REVERSE VACCINOLOGY APPROACH

• Main Author: Claudia, Brigitta
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/57149
• Institution: Institut Teknologi Bandung

Massive vaccine distribution is considered as one of crucial step to prevent the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) as the causative agent of COVID-19. Nevertheless, due to the fact that none of the vaccine is originally self-produced at this time in this country, the vaccine supply significantly depends on its availability in the manufacturer’s country. Therefore, independent production of COVID-19 vaccine is required to accelerate the generation of specific protective immunity among Indonesian effectively. This study was conducted to design the multiepitope self-amplifying mRNA vaccine which consist of selected B-cell and T-cell epitope from surface glycoprotein (S protein) and nucleophosphoprotein (N protein) of SARS-CoV-2 sample obtained from Southeast Asia. It all started from the prediction of B-cell and T-cell epitope from the consensus sequence of each protein target constructed by 838 samples. Commonly distributed HLA class I and II alleles in the Indonesia population were used to determine peptide sequences that can possibly trigger the high specificity T-cell response for this population. Epitopes which considered highly antigenic, highly conserved, non-allergen, non-toxic, hydrophilic, and showed ? 25% population coverage were selected to construct the multiepitope vaccine by adding associated linkers and human ?-defensin 2 (hBD-2) or CTB (cholera toxin B) as adjuvant. The best vaccine candidate was chosen based on the analysis of tertiary structure validation, aggregation test, and molecular docking of each vaccine with TLR-4, TLR-8, HLA-A*24:02 dan HLA-DRB1*04:05. Interacting binding residue and molecular dynamics simulation then conducted to the docking complex of the best vaccine and each receptor to confirm their interactions. Selected multiepitope vaccine was added by the nsp gene encoding the RdRp that allows the RNA replication in the host cell before inserting them to the restriction site of pcDNA3.1(+) as the vector plasmid. Based on the epitope prediction and selection, this study obtained seven B-cell epitopes and four T-cell epitopes (performed good affinity both with Cytotoxic and Helper T-cell). Tertiary structure validation and molecular docking towards various immune receptor determined one best multiepitope construction that has 269 aa in length, contains hBD-2 adjuvant and PADRE carrier peptide, dominates by coil structure, majority of residues are predicted to be accessible by solvent with low risk of aggregation, and shows high population coverage (99,26%). It was predicted to bind properly with all mentioned immune receptor since the docking complex showed good affinity of binding, involved the active reside of receptor in the interaction, and performed quite stable complex in the molecular dynamic simulation. This study finally proposed a plasmid with pcDNA3.1(+) as the backbone encoding the SARS-CoV-2 multiepitope self-amplifying mRNA that hopefully induce protective immunity for Indonesian effectively. Further in vitro and in vivo experiment are suggested to be done to validate the proposed results of this study.