Design of multi-epitope-based therapeutic vaccine candidates from HBc and HBx proteins of hepatitis B virus using reverse vaccinology and immunoinformatics approaches
Patricia Gita Naully, Marselina Irasonia Tan, Husna Nugrahapraja, Aluicia Anita Artarini, Reza Aditama, Ernawati Arifin Giri-Rachman
Abstract
The major problem in cases of chronic hepatitis B (CHB) is the failure of the patient’s immune response to eliminate the covalently closed circular DNA (cccDNA) minichromosome of hepatitis B virus (HBV). Epigenetic regulation involving the HBV core protein (HBc) and HBV X protein (HBx) influences the transcription and stability of the cccDNA minichromosome. The HBc and/or HBx-based therapeutic vaccines that have been developed cannot accommodate differences between HBV genotypes.
Introduction
Although the prophylactic vaccine for hepatitis B virus (HBV) is available, around 254 million people globally remain chronically infected. Indonesia and two other countries represented 50% of the global burden [1]. According to the Hepatitis Global 2024 report, one million people have died because of chronic hepatitis B virus infection (CHB). CHB has the potential to cause a high mortality because it can progress to cirrhosis and liver cancer [2]. The main problem of CHB is the persistent presence of HBV covalently closed circular DNA (cccDNA) minichromosome in hepatocytes, whose stability, conformation, and transcription can be affected by epigenetic regulation [3–6].
Materials and method
Construction of the consensus amino acid sequence of all HBV genotypes
All HBV protein sequences were downloaded from the NCBI Entrez Protein databases on May 5, 2024 (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi). HBc and HBx sequences for 10 HBV genotypes were searched using the Basic Local Alignment Search Tool (BLAST) with the query of HBV genotype A2 (Accession Number: KY003230). The following BLAST parameters were used: E-value < 0.05; bitscore > 50; %identity > 30; %positive > 30, and %query coverage > 50 [35]. BLAST results were manually curated to exclude partial, truncated, and recombinant HBc and HBx sequences.
Results
Consensus amino acid sequence construction and epitope prediction
The NCBI Entrez Protein database contains 19,350 HBV protein sequences. After selection using BLAST, there were 13,610 HBc sequences and 12,333 HBx sequences. Data were collected from 10 HBV genotypes across various countries in Africa, America, Australia, Asia, and Europe, spanning the years 1963 to 2023. Consensus sequences were successfully obtained using the MSA technique (Fig 1). The results showed that out of 185 amino acids in HBc and 154 amino acids in HBx, 11 amino acids in HBc and 26 amino acids in HBx have a conservation level below 85%. Consequently, there are 7 conserved regions in both HBc and HBx proteins (Table 1).
Discussion
This study effectively designed multi-epitope HBc and HBx-based therapeutic vaccine candidates using the RV approach. RV refers to various computational analyses used to predict epitopes from large, continuously expanding, and easily accessible genomic or proteomic datasets [79]. To predict epitopes accurately and minimize variation between viral genotypes, consensus sequence derived from extensive datasets are required. The consensus sequences generated in this study showed several differences compared to those reported by Saeed et al. [80].
Acknowledgments
Thanks to Biomods for the discussion on molecular dynamics simulations. All figures were combined using the BioRender illustration tool.
Citation: Naully PG, Tan MI, Nugrahapraja H, Artarini AA, Aditama R, Giri-Rachman EA (2024) Design of multi-epitope-based therapeutic vaccine candidates from HBc and HBx proteins of hepatitis B virus using reverse vaccinology and immunoinformatics approaches. PLoS ONE 19(12): e0313269. https://doi.org/10.1371/journal.pone.0313269
Editor: Sheikh Arslan Sehgal, Cholistan University of Veterinary and Animal Sciences, PAKISTAN
Received: August 16, 2024; Accepted: October 21, 2024; Published: December 6, 2024
Copyright: © 2024 Naully et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the manuscript and its Supporting information files.
Funding: This study was funded by the Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia under the Basic Research Scheme [036/E5/PG.02.00.PL/2024] awarded to EAG-R.
Competing interests: The authors have declared that no competing interests exist.
