DEVELOPMENT OF COVID-19 MRNA MULTI-EPITOPE VACCINE USING SARS-COV-2 SPIKE AND NUCLEOCAPSID PROTEINS THROUGH REVERSE VACCINOLOGY APPROACH

• Main Author: Mirahma Febri Kurnianti, Al
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/78437
• Institution: Institut Teknologi Bandung

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a causative agent of the coronavirus disease (COVID-19) that caused a worldwide pandemic. The pandemic caused millions of deaths and caused disturbances in the economic and social interactions of the public. Although the WHO declared that the pandemic is no longer listed as a Public Health Emergency Internal Concern (PHEIC), vaccination is still required to prevent future infection of the SARS-CoV-2 new variants. This study was conducted to design the mRNA multi-epitope vaccine from spike and nucleocapsid proteins of SARS-CoV-2 through a reverse vaccinology approach and conducted sub-cloning between vector backbone pcDNA3.1(+)-UTR and insert Spike gene to evaluate if the designed backbone can be used as the backbone of mRNA multi-epitope vaccine candidate construction. A total of 20,567 nucleotide sequences of the whole genome SARS-CoV-2 was obtained from the GISAID database. Translated sequence of spike and nucleocapsid proteins used to predict linear B lymphocyte (LBL) epitope, cytotoxic T lymphocyte (CTL) epitope, and helper T lymphocyte (HTL) epitope. Predicted epitopes were selected based on antigenicity, immunogenicity, ability to induce IFN-?, allergenicity, toxicity, conservancy, physicochemical characteristics, and coverage of worldwide and Indonesian populations. The selected epitopes were used in molecular docking analysis with MHC classes I and II and were also used to construct the multi-epitope vaccine. Validated tertiary (3D) structure of the chosen vaccine candidate construction used in molecular docking with TLR4. Based on prediction and selection, this study obtained four LBL epitopes, three CTL epitopes, and five HTL epitopes. Selected CTL and HTL epitopes performed with good affinity with the MHC molecules. All epitopes were combined using linkers, and the PADRE sequence was added at the N and C-terminals of the construct. The construct is 257 amino acids long and the majority of the structure is coil (61,87%). The validation of 3D structure based on ERRAT score, Verify 3D, Ramachandran plot, and z-score obtained 76,92, 85,99%, 91,9%, and -6,01, respectively. Furthermore, molecular docking analysis shows that the interaction between the vaccine candidate and TLR4 occurred spontaneously with a binding affinity -19,3 kcal/mol. Sub-cloning was successfully conducted with bands of ~3,8 kb as insert and ~5,7 kb as vector; thus, the designed pcDNA3.1(+)-UTR can be used as the backbone of mRNA multi-epitope vaccine candidate construction. From this study obtained a construct of an mRNA vaccine candidate that hopefully induces protective immunity against future infection of the SARS-CoV-2 new variants.