Cited by 122vaccines and immunoinformatics approachesImmunotherapy and Immune ResponsesArtificial Immune Systems Applications

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Current progress of immunoinformatics approach harnessed for cellular- and antibody-dependent vaccine design

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Kazi, Ada, Chuah, Candy, Majeed, Abu Bakar Abdul, Leow, Chiuan Herng, Lim, Boon Huat, Leow, Chiuan Yee·2018·Pathogens and Global Health

DOI 10.1080/20477724.2018.1446773PMC PMC6056828

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Abstract

Immunoinformatics plays a pivotal role in vaccine design, immunodiagnostic development, and antibody production. In the past, antibody design and vaccine development depended exclusively on immunological experiments which are relatively expensive and time-consuming. However, recent advances in the field of immunological bioinformatics have provided feasible tools which can be used to lessen the time and cost required for vaccine and antibody development. This approach allows the selection of immunogenic regions from the pathogen genomes. The ideal regions could be developed as potential vaccine candidates to trigger protective immune responses in the hosts. At present, epitope-based vaccines are attractive concepts which have been successfully trailed to develop vaccines which target rapidly mutating pathogens. In this article, we provide an overview of the current progress of immunoinformatics and their applications in the vaccine design, immune system modeling and therapeutics.

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“The current progress and developments in the field of immunoinformatics have made it possible to develop vaccine in cost-effective and timely manner (Kazi et al., 2018).”
Background
Just Keep Rolling?—An Encompassing Review towards Accelerated Vaccine Product Life Cycles
(2023) · doi:10.3390/vaccines11081287 · Cited by 11
In Silico Vaccine Design and Expression of the Multi-Component Protein Candidate against the Toxoplasma gondii Parasite from MIC13, GRA1, and SAG1 Antigens
Hosseininejad, Z., Daryani, A., Fasihi‐Ramandi, M., Asgarian‐Omran, H., Valadan, R., Nayeri, T., Dodangeh, S., & Sarvi, S. (2023) · Iranian Journal of Parasitology · doi:10.18502/ijpa.v18i3.13753 · Cited by 9
“In addition, designed vaccines are more efficient and safer than traditional vaccines (32).”
Background
A novel chimeric vaccine containing multiple epitopes for simulating robust immune activation against Klebsiella pneumoniae
Hakimian, M., Doosti, A., & Sharifzadeh, A. (2024) · BMC Immunology · doi:10.1186/s12865-024-00617-z · Cited by 8
“The primary benefit of this technology is its ability to detect many candidate vaccinations without spreading bacterial illnesses across a wet laboratory [22].”
Background
Identification and application of a neutralizing epitope within alpha-hemolysin using human serum antibodies elicited by vaccination
Wei, J., Cheng, X., Zhang, Y., Gao, C., Wang, Y., Peng, Q., Luo, P., Yang, L., Zou, Q., Zeng, H., et al. (2021) · Molecular Immunology · doi:10.1016/j.molimm.2021.03.028 · Cited by 8
Reverse vaccinology-based prediction of a multi-epitope SARS-CoV-2 vaccine and its tailoring to new coronavirus variants
Ezzemani, W., Kettani, A., Sappati, S., Kondaka, K., Ossmani, H. E., Tsukiyama–Kohara, K., Altawalah, H., Saı̈le, R., Kohara, M., Benjelloun, S., et al. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2075468 · Cited by 8
“Then, the immune simulation studies were conducted to understand the ability of our vaccine construct to elicit a cellular or hormonal immune response (Kazi et al., 2018).”
Background
Anticipation of Antigenic Sites for the Goal of Vaccine Designing Against Nipah Virus: An Immunoinformatics Inquisitive Quest
Sharma, S. K., Srivastava, S., Kumar, A., & Srivastava, V. P. (2021) · International Journal of Peptide Research and Therapeutics · doi:10.1007/s10989-021-10219-7 · Cited by 8
“The ever-expanding human population, widening interaction between humans and animals, dynamic environmental conditions, and poor sanitation are the main reasons for the outbreaks of zoonotic diseases (Kazi et al. 2018).”
Background
Integrated structural proteomics and machine learning-guided mapping of a highly protective precision vaccine against mycoplasma pulmonis
Khan, A., Zahid, M., Farrukh, F., Abdelsalam, S. S., Mohammad, A., Al‐Zoubi, R. M., Shkoor, M., Hssain, A. A., Wei, D., & Agouni, A. (2024) · International Immunopharmacology · doi:10.1016/j.intimp.2024.112833 · Cited by 7
Design a multi-epitope vaccine candidate against Acinetobacter baumannii using advanced computational methods
Heidarinia, H., Tajbakhsh, E., Bahrami, Y., & Rostamian, M. (2025) · AMB Express · doi:10.1186/s13568-025-01913-6 · Cited by 10
“To address this challenge, bioinformatics methods using epitope prediction algorithms have been developed, which have significantly reduced the cost and time of epitope identification (Kazi et al. 2018).”
Epitope mapping of Acinetobacter baumannii outer membrane protein W (OmpW) and laboratory study of an OmpW-derivative peptide
Heidarinia, H., Tajbakhsh, E., Rostamian, M., & Momtaz, H. (2023) · Heliyon · doi:10.1016/j.heliyon.2023.e18614 · Cited by 7
EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
Ferreira, C. D. S., Martins, Y., Souza, R. C., & de Vasconcelos, A. T. R. (2021) · PeerJ · doi:10.7717/peerj.12548 · Cited by 7
“This approach regards the wide availability of the SARS-CoV-2 NGS (Next-Generation Sequencing) information associated with human leukocyte antigen (HLA) profile (Kazi et al., 2018; Oli et al., 2020; Sharma et al., 2020) to identify T cell epitopes.”
Method
Exploring Highly Antigenic Protein of Campylobacter jejuni for Designing Epitope Based Vaccine: Immunoinformatics Approach
Gupta, N., Khan, F., & Kumar, A. (2018) · International Journal of Peptide Research and Therapeutics · doi:10.1007/s10989-018-9764-z · Cited by 7
“It allows the selection of antigenic regions from the pathogenic genomes and the most antigenic regions could be developed as potential vaccine candidates to trigger protective immune responses (Ada et al. 2018).”
Background
A novel immunoinformatic approach for design and evaluation of heptavalent multiepitope foot-and-mouth disease virus vaccine
Zaher, M. R., El-Husseiny, M. H., Hagag, N. M., Elamir, A. M., Zowalaty, M. E. E., & Tammam, R. H. (2025) · BMC Veterinary Research · doi:10.1186/s12917-025-04509-1 · Cited by 7
“Immunoinformatics and computational biology have raised the bar in the vaccine production industry through enabling a safer and more innovative way to design viral vaccines [60, 61].”
Evaluation and Designing of Epitopic-Peptide Vaccine Against Bunyamwera orthobunyavirus Using M-Polyprotein Target Sequences
Ghosh, P., Bhattacharya, M., Patra, P., Sharma, G., Patra, B. C., Lee, S., Sharma, A. R., & Chakraborty, C. (2021) · International Journal of Peptide Research and Therapeutics · doi:10.1007/s10989-021-10322-9 · Cited by 6
Screening of potential antigens from whole proteome and development of multi-epitope vaccine against Rhizopus delemar using immunoinformatics approaches
Pritam, M., Singh, G., Kumar, R., & Singh, S. P. (2022) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2022.2028676 · Cited by 6
“…Dengue, Fascioliasis, etc. because of convenience, low cost, reduced labor and/or risk of failure of the vaccine in the wet laboratory (Ali et al., 2017; Behbahani et al., 2021; Kaba et al., 2018; Kazi et al., 2018; Rahmani et al., 2019; Singh et al., 2020; Yazdani et al., 2020; Zeb et al., 2021).”
Background
In silico analysis and expression of a new chimeric antigen as a vaccine candidate against cutaneous leishmaniasis.
Motamedpour, L., Dalimi, A., Pirestani, M., & Ghaffarifar, F. (2020) · PubMed Central · doi:10.22038/ijbms.2020.45394.10561 · Cited by 6
In silico analyses and design of a chimeric protein containing epitopes of SpaC, PknG, NanH, and SodC proteins for the control of caseous lymphadenitis
Silva, M. T. D. O., de Pinho, R. B., Bezerra, F. S. B., Scholl, N. R., Moron, L. D., Alves, M. S. D., Woloski, R., Kremer, F. S., & Borsuk, S. (2021) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-021-11619-x · Cited by 6
“1 3 to cultivate the microorganism of interest (Kazi et al. 2018).”
Background
Application of Reverse Vaccinology and Immunoinformatic Strategies for the Identification of Vaccine Candidates Against Shigella flexneri
Leow, C. Y., Chuah, C., Majeed, A. B. A., Norazmi, M. N., & Leow, C. Y. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1900-1_2 · Cited by 6
A multi-epitope vaccine targeting a key virulence factor ClfA: An In-silico approach to combat Staphylococcus aureus infections
Nirob, M. N. H., Sultana, I., Arian, T. A., Islam, M. S., Moniruzzzaman, M., Nosi, S. J., Halder, S. K., Shil, A., & Himel, M. K. (2025) · PLoS ONE · doi:10.1371/journal.pone.0334885 · Cited by 5
“Immunoinformatic research has made significant strides in recent memory, resulting in useful programs and platforms that are helping speed up and lower the expense of developing traditional vaccines [106].”
In Silico Analysis of the ROP29 Protein as a Vaccine Candidate Against Toxoplasma gondii
KarimiPourSaryazdi, A., Ghaffarifar, F., Dalimi, A., Foroutan, M., Horton, J. D., & Sadraei, J. (2024) · Journal of Parasitology Research · doi:10.1155/2024/1918202 · Cited by 5
In Silico–Based Investigation of the Immunogenicity and Biochemical Attributes of Toxoplasma gondii Apical Membrane Antigen 1 (TgAMA1)
Foroutan, M., Ghaffari, A. D., Ghaffarifar, F., KarimiPourSaryazdi, A., Birgani, A. A., Majidiani, H., Cortes, H. C. E., & Elsheikha, H. M. (2025) · Journal of Parasitology Research · doi:10.1155/japr/3514414 · Cited by 4
Mass spectrometry-based immunopeptidomics and computational vaccinology strategies for the identification of universal Shigella immunogenic candidates
Shabani, N. R. M., Ismail, C. M. K. H., Anthony, A. A., Leow, C. Y., Chuah, C., Majeed, A. B. A., Norazmi, M. N., He, Y., Singh, K. K. B., & Leow, C. Y. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105900 · Cited by 4
Completing the pieces of a puzzle: in-depth probing of Toxoplasma gondii rhoptry protein 4 as a promising target for vaccination using an in-silico approach
Foroutan, M., & Shadravan, M. M. (2024) · Clinical and Experimental Vaccine Research · doi:10.7774/cevr.2024.13.4.359 · Cited by 4
Molecular dynamics simulation based prediction of T-cell epitopes for the production of effector molecules for liver cancer immunotherapy
Zafar, S., Bai, Y.-H., Muhammad, S. A., Guo, J.-L., Khurram, H., Zafar, S., Muqaddas, I., Shaikh, R. S., & Bai, B. (2025) · PLoS ONE · doi:10.1371/journal.pone.0309049 · Cited by 4
In Silico Analysis and Characterization of the Immunogenicity of Toxoplasma gondii Rhoptry Protein 18
Foroutan, M., KarimiPourSaryazdi, A., Ghaffari, A. D., Majidiani, H., Birgani, A. A., Karimzadeh‐Soureshjani, E., Soltani, S., & Elsheikha, H. M. (2025) · Bioinformatics and Biology Insights · doi:10.1177/11779322251315924 · Cited by 5
“41,77,91 The prediction of epitopes primarily relies on several protein structural features.”
Integration: Gospel for immune bioinformatician on epitope-based therapy
Sun, B., Zhang, J., Li, Z., Xie, M., Luo, C., Wang, Y., Chen, L., Wang, Y., Jiang, D., & Yang, K. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1075419 · Cited by 4
“This is probably because of the inherent defects in computer algorithms based on epitope databases for ﬁ tting functions (8, 11).”
In-silico design and evaluation of a novel mRNA vaccine against human bocavirus 1: A neglected viral pathogen
Rubab, A., Sarfraz, A., Khan, M. U., Fawy, K. F., & Shah, M. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.111344 · Cited by 3
Evaluation of Launaea Angustifolia Extract Treatment on Rat Blood Serum Enzymes and Histology of Liver and Kidney
Ammari, A. A., Alhimaidi, A. R., Amran, R. A., Ghadi, M. G. A., & Rady, A. M. (2023) · Indian Journal of Animal Research · doi:10.18805/ijar.bf-1614 · Cited by 3
Immunoinformatics aided designing of a next generation poly-epitope vaccine against uropathogenic Escherichia coli to combat urinary tract infections
Ishaq, Z., Zaheer, T., Waseem, M., Awan, H. S., Ullah, N., Alasmari, A. F., Alasmari, F. F., & Ali, A. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2266018 · Cited by 3
“While we acknowledge the potential of immunoinfor-matics-based vaccine designs, it’s crucial to understand and address the inherent limitations in this approach (Kazi et al., 2018).”
A Novel Chimeric Antigen as a Vaccine Candidate against Leishmania major: In silico Analysis
Ahmadpour, N. B., Dalimi, A., Pirestani, M., & Sadraei, J. (2021) · Iranian Journal of Parasitology · doi:10.18502/ijpa.v16i2.6267 · Cited by 3
“Meantime, ABCpred server (6, 11) was used.”
Background
Design of a novel multi-epitope vaccine candidate against endometrial cancer using immunoinformatics and bioinformatics approaches
Li, X., Wen, H., Xiao, X., Ren, Z., Tan, C., & Fu, C. M. (2023) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2023.2263213 · Cited by 3
“The development of immunoinformatics and bioinformatics approaches has significantly accelerated the process of epitope identification and screening by reducing the time and cost required for vaccine design (Kazi et al., 2018).”
Toxoplasma gondii ( GRA10 ): A Closer Glance Into Immunogenic and Biochemical Characteristics Using In Silico Approach
Mohammadi, M. K., & Ghaffari, A. D. (2025) · Parasite Immunology · doi:10.1111/pim.70004 · Cited by 5
“Users can predict B cell epitopes considering various chemical and physical characteristics such as polarity, accessibility, hydro-philicity, exposed surface, turns and mobility/flexibility [38, 39].”
Identification of Potent Vaccine Candidates Against Campylobacter jejuni Using Immunoinformatics Approach
Gupta, N., & Kumar, A. (2019) · International Journal of Peptide Research and Therapeutics · doi:10.1007/s10989-019-09933-0 · Cited by 3
“It permits the choice of antigenic locales from the pathogenic genomes and the most antigenic areas could be created as potential immunization possibility to trigger defensive immune responses (Ada et al. 2018).”
Background
Immunoselective progression of a multi-epitope-based subunit vaccine candidate to convey protection against the parasite Onchocerca lupi
Rahman, M. N., Ahmed, S., Hasan, M., Shuvo, M. S. A., Islam, M. A., Hasan, R., Roy, S., Hossain, H., & Mia, M. M. (2023) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2023.101209 · Cited by 3
Design and validation of a multi-epitope vaccine candidate against Acinetobacter baumannii using advanced computational methodsPreprint
Heidarinia, H., Tajbakhsh, E., Rostamian, M., & Momtaz, H. (2023) · Research Square · doi:10.21203/rs.3.rs-3182215/v1 · Cited by 3
Conserved Domains in Variable Surface Lipoproteins A-G of Mycoplasma hyorhinis May Serve as Probable Multi-Epitope Candidate Vaccine: Computational Reverse Vaccinology Approach
Zubair, M., Wang, J., Yu, Y., Rasheed, M. A., Faisal, M. S., Dawood, A. S., Ashraf, M. A., Shao, G., Feng, Z., & Xiong, Q. (2023) · Veterinary Sciences · doi:10.3390/vetsci10090557 · Cited by 2
Chimeric vaccine design against the conserved TonB-dependent receptor-like β-barrel domain from the outer membrane tbpA and hpuB proteins of Kingella kingae ATCC 23330
Mashraqi, M. M., Alzamami, A., Alturki, N. A., Almasaudi, H. H., Ahmed, I., Alshamrani, S., & Basharat, Z. (2023) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1258834 · Cited by 2
“Immunoinformatics approaches can accelerate the vaccine design process and reduce the cost by predicting epitopes that are likely to be effective (Kazi et al., 2018).”
Background
Comprehensive bioinformatics assessments of the ROP34 of Toxoplasma gondii to approach vaccine candidates
Mohammadhasani, F., Ghaffari, A. D., & Asadi, M. (2024) · Discover Applied Sciences · doi:10.1007/s42452-024-06189-2 · Cited by 1
“Bcepred anticipated continuous B-cell epitopes by considering factors like polarity, hydrophilicity, flexibility, accessibility, turns, and antigenic propensity, achieving accuracies ranging from 58.7% [45, 46].”
Influential
Forecast of cytotoxic T lymphocyte epitope using sequence weighting and artificial neural network based on EasyPred modeler
Singh, S. P., Singh, G., & Mishra, B. N. (2025) · Exploration of Immunology · doi:10.37349/ei.2025.1003215 · Cited by 1
In silico Analysis of Toxoplasma gondii Surface and Secretory Proteins for the Design of a Novel Chimeric Vaccine
Nayeri, T., Asl, A. D., Ghaffarifar, F., & Moridnia, A. (2025) · The Open Microbiology Journal · doi:10.2174/0118742858411659251007070159 · Cited by 1
Immunoinformatics-guided design of a conserved multi-epitope vaccine candidate against pathogenic human coronaviruses
Lim, C. P., Bingöl, E. N., de Oliveira, J. J., Chuah, C., Khan, M. A., Douradinha, B. G., Leow, C. Y., & Leow, C. Y. (2026) · Naunyn-Schmiedeberg s Archives of Pharmacology · doi:10.1007/s00210-026-05714-x · Cited by 1
“Advances in immunoinformatics have allowed the development and improvement of in silico tools, which aids in reverse vaccinology for the design of vaccine candidates against diverse pathogens (Lim et al. 2022; Kazi et al. 2018; Lim et al. 2024; Douradinha 2024).”
Developing COVID-19 Vaccines by Innovative Bioinformatics Approaches
Jakhar, R., Sehrawat, N., & Gakhar, S. K. (2021) · EAI/Springer Innovations in Communication and Computing · doi:10.1007/978-3-030-68936-0_9 · Cited by 1
Trichinellosis: A Hidden Threat in Meat Consumption
(2023) · International Journal of Agriculture and Biosciences · doi:10.47278/book.zoon/2023.72 · Cited by 1

Authors: Kazi, A., Chuah, C., Majeed, A. B. A., Leow, C. H., Lim, B. H., & Leow, C. Y.
Affiliations: Universiti Sains Malaysia (MY)
Universiti Teknologi MARA System (MY)
,
ORCID: Kazi, Ada
Chuah, Candy
Majeed, Abu Bakar Abdul
Leow, Chiuan Herng
Lim, Boon Huat
Leow, Chiuan Yee
Venue: Pathogens and Global Health
Publisher: Informa UK Limited
Published: 2018-03-12
Volume: 112
Issue: 3
Pages: 123-131
ISSN: 2047-7724 (ISSN-L)
2047-7732
DOI: 10.1080/20477724.2018.1446773
PMC: PMC6056828
OpenAlex: W2789811841
Cited by: 122
References: 80
Citations by year: 2026: 6 · 2025: 19 · 2024: 12 · 2023: 17 · 2022: 9 · 2021: 28 · 2020: 22 · 2019: 6 · 2018: 3
FWCI: 5.25
Type: journal article
Language: en
Update notices: correction (2018-04-27)
Open access: green
www.ncbi.nlm.nih.gov
Locations: Pathogens and Global Health (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Higher Institutions Centre of Excellence Program (311/CIPPM/4401005)
Fundamental Research Grant Scheme (203/CIPPM/6171199)
The Malaysian Ministry of Higher Education of the Higher Institutions Centre of Excellence Program (311/CIPPM/4401005)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
Physical Sciences › Computer Science › Artificial Intelligence › Artificial Immune Systems Applications
Keywords: immunoinformatics, vaccine design, antibody design, epitope-based vaccine, immune system modeling, B-cell epitopes
MeSH terms: Animals, Epitopes, Humans, Immunity, Cellular, Vaccines, Computational Biology, Drug Discovery, Immunity, Humoral

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