PENGEMBANGAN VAKSIN MULTI-EPITOPE PROTEIN ORF1AB, ORF3A, DAN SPIKE (S) VIRUS SARS-COV 2 BERDASARKAN PREVALENSI HUMAN LEUKOCYTE ANTIGEN (HLA) DI INDONESIA DENGAN PENDEKATAN IMMUNOINFORMATIK

• Main Author: Oryza, Kristian
• Format: Final Project
• Language: Indonesia
• Subjects: Ilmu hayati ; Biologi
• Online Access: https://digilib.itb.ac.id/gdl/view/57147
• Institution: Institut Teknologi Bandung

SARS-CoV 2 is the virus that causes the COVID-19 pandemic that attacks the respiratory tract with symptoms similar to pneumonia. SARS-CoV 2 has RNA genetic material that encodes four structural proteins, 16 non-structural proteins, and six accessory proteins. Currently, most developed vaccines target the formation of an immune response against structural proteins, especially the Spike (S) protein. However, the fast mutation rate makes SARS-CoV 2 undergo changes in pathogenesis and distribution patterns and the different factors in the prevalence of Human Leukocyte Antigen (HLA) affecting the effectiveness of the vaccine. Therefore, it is necessary to have a vaccine that can induce a multi-target immune response against other proteins at the same time, especially the T cell immune response, according to the prevalence of the HLA population in Indonesia. This study aimed to carry out an immunoinformatic approach to find conserved epitopes that potentially target proteins and construct the multiepitope vaccine construction. The study was conducted by comparing the similarity using ClustalW between the sequences of SARS-CoV 2 Indonesian isolates and the reference sequence. Then the candidate epitope CTL and HTL were determined using NetCTLpan 1.1 and NetMHCIIpan 4.0, respectively. Selected epitopes were combined into a protein construct with the linker GPGPG and EAAAK with synthetic adjuvant of human beta-defensin protein – 2. The 3D modelling of the vaccine construction was performed with trRosetta, and molecular docking analysis was performed using Haddock 2.4 and CABS-dock for epitope against MHC. Based on study results, the reference sequence had a similarity index of 99%, which represented 1117 SARS-CoV 2 isolates in Indonesia. There were six candidates CTL epitope and ten candidate HTL epitope from the three target proteins that were immunogenic, nontoxic, non-allergenic, conserved (>99%), and had comprehensive HLA coverage (>3 HLA). Molecular docking to the candidate epitope showed that the binding affinity fluctuated with an average of -10.65 kcal mol-1 and -12.2 kcal mol-1 which was comparable to the control ligand -10.8 kcal mol-1 and -9.7 kcal mol-1 for MHC I and MHC II, respectively. The structure of the construction vaccine does not have a transmembrane helix, MolProbity Score 97th, Z-score ProSA -6.54, and good local model quality (negative value). Molecular docking of vaccine construction with CCR2 receptor isoform B has a binding affinity of -11.4 kcal mol-1 which is more significant than orthosteric ligand (-9.8 kcal mol-1). Analysis of the interaction between the vaccine model and CCR2 B did not reveal any hotspot residues, but 16 hydrogen bonds were formed involving the N-terminal residue of CCR2. Overall, the construction of multiepitope vaccines can be a candidate for SARS-CoV 2 vaccine against T cell immune responses.