In silico design of a multi-epitope vaccine targeting human immunodeficiency virus−tuberculosis co-infection: A reverse vaccinology approach to synergistic pathogenesis

Nabil Athoillah; Muhammad Irsyad Amien; Saski Yasmin Alfina; Ichlasul Mahdi Fardhani; Irsyad  Lutfi Elfahmi; Putri Ayu Ardiani; Mukhammad Arif Hadi Khoiruddin; Mohammad Alifi Agfareza; Mitsla Chusnica Aulia As’ar; Angga Mardro Raharjo; Atika Purnama Sari

Authors

Nabil Athoillah University of Jember, Jember, Indonesia
Muhammad Irsyad Amien University of Jember, Jember, Indonesia
Saski Yasmin Alfina University of Jember, Jember, Indonesia
Ichlasul Mahdi Fardhani University of Jember, Jember, Indonesia
Irsyad Lutfi Elfahmi University of Jember, Jember, Indonesia
Putri Ayu Ardiani University of Jember, Jember, Indonesia
Mukhammad Arif Hadi Khoiruddin University of Jember, Jember, Indonesia
Mohammad Alifi Agfareza University of Gadjah Mada, Yogyakarta, Indonesia
Mitsla Chusnica Aulia As’ar University of Papua, Sorong, Indonesia
Angga Mardro Raharjo Faculty of Medicine, University of Jember, Jember, Indonesia
Atika Purnama Sari Faculty of Medicine, University of Jember, Jember, Indonesia

Keywords:

Co-infection, human immunodeficiency virus, immunoinformatics, multi-epitope vaccine, tuberculosis

Abstract

Background: The synergism between Mycobacterium tuberculosis (Mtb) and human immunodeficiency virus (HIV) represents a global health crisis, where co-infection significantly accelerates immune failure and exacerbates mortality rates.

Objective: This study aimed to design in silico a novel multi-epitope vaccine predicted to stimulate robust, long-lasting, and concurrent immune protection against Mtb and HIV.

Methods: This reverse vaccinology study followed a multi-level immunoinformatic approach. We predicted cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and linear B-cell (LBL) epitopes. Each was tested for its ability to induce an immune response without evoking allergic or toxic reactions. Select epitopes were combined into a multi-epitope vaccine construct bearing adjuvants and linkers. It was analyzed for physicochemical characteristics, solubility, structural modeling, molecular docking with Toll-Like Receptor 4 (TLR 4), and stability. Immune simulations, codon optimization, and in silico cloning helped assess immunogenicity and establish expression potential.

Results: Proteomics prioritized 23 epitopes—11 CTL, 5 HTL, and 7 LBL. Each demonstrated high antigenicity, non-allergenicity, and non-toxicity. The final vaccine construct exhibited superior stability in normal mode analysis and strong binding affinity for TLR4, as evidenced by low-energy docking scores. Immune simulations predicted a robust secondary immune response, characterized by significant increases in antibody titers, B-cell memory, and the release of Th1-polarized cytokines: IFN-gamma and Interleukin-2. The global HLA population coverage was estimated at 99.3%, indicating broad-spectrum protective potential.

Conclusion: The multi-epitope vaccine designed here exhibited high predicted stability, safety, and robust in silico immunogenic potential. Overall, this construct is a promising candidate for a unified preventive strategy against HIV−TB co-infection, warranting further experimental validation in pre-clinical settings.

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