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Vaccinomics-aided Next-generation Novel Multi-epitope-based Vaccine Engineering Against Multidrug Resistant Shigella Sonnei: Immunoinformatics and Chemoinformatics Approaches

Sara Aiman, Abbas Ahmad, Asifullah Khan, Yasir Ali, Abdul Malik, Musaed Alkholief, Suhail Akhtar, Raham Sher Khan, Chunhua Li ,Fazal Jalil, Yasir Ali 


Shigella sonnei is a gram-negative bacterium and is the primary cause of shigellosis in advanced countries. An exceptional rise in the prevalence of the disease has been reported in Asia, the Middle East, and Latin America. To date, no preventive vaccine is available against S. sonnei infections. This pathogen has shown resistances towards both first- and second-line antibiotics. Therefore, an effective broad spectrum vaccine development against shigellosis is indispensable. In the present study, vaccinomics-aided immunoinformatics strategies were pursued to identify potential vaccine candidates from the S. sonnei whole proteome data. Pathogen essential proteins that are non-homologous to human and human gut microbiome proteome set, are feasible candidates for this purpose. Three antigenic outer membrane proteins were prioritized to predict lead epitopes based on reverse vaccinology approach. Multi-epitope-based chimeric vaccines was designed using lead B- and T-cell epitopes combined with suitable linker and adjuvant peptide sequences to enhance immune responses against the designed vaccine. The SS-MEVC construct was prioritized based on multiple physicochemical, immunological properties, and immune-receptors docking scores. Immune simulation analysis predicted strong immunogenic response capability of the designed vaccine construct. The Molecular dynamic simulations analysis ensured stable molecular interactions of lead vaccine construct with the host receptors. 


Shigella sonnei (S. sonnei) is a rod-shaped, non-motile, gram-negative bacterium associated with actin polymerization in the host cell [1–5]. S. sonnei causes an acute intestinal infection known as shigellosis. S. sonnei originates from the harmless enterobacteriaceae family and causes debilitating diarrhea upon ingestion. The clinical symptoms of shigellosis can range from mild watery diarrhea to serious inflammatory bacillary dysentery with severe abdominal pains, fever, and bloody and mucus-filled stool [3]. Approximately 99% of shigellosis cases have been reported in underdeveloped countries with poor sanitation and hygienic conditions. Limited access to clear drinking water has encouraged the spread of enteric disease. Insufficient healthcare and malnutrition contribute to the high mortality rate in children, the elderly, and individuals with chronic health conditions [6]. Shigellosis is contagious and can easily be transmitted from person to person. Strong evidence links domestically acquired shigellosis associated with sexual transmission among homosexual men in Western industrialized countries as well as those with advanced HIV disease [6–8]. This bacterium spreads rapidly through contaminated food, water, or close oral contact with an infected individual.

Materials and methods

Multi-epitope vaccine construct (MEVC) designing

Potential vaccine design requires an adjuvant, prioritized B- and T-cell epitopes, and linker sequences to design an efficient construct with the potential to elicit a robust immune response. Multi-epitope vaccine construct elicits a stronger immune response than the individual peptides. In this study, we used six CTL epitopes, nine HTL epitopes, and three linear B-cell epitopes with appropriate linkers to design a chimeric vaccine construct. The 50S ribosomal protein L7/L12 adjuvant was incorporated into the vaccine construct at the N-terminus to enhance its stability and induce both innate and adaptive immune responses. The rigid linker EAAAK was used to connect the adjuvant to the multi-epitope sequence. Glycine-proline-rich GPGPG linkers were used to conjugate linear B-cell and HTL epitopes. Furthermore, CTL epitopes were linked with flexible AAY linkers. These linkers provide stability, prevent self-folding in the vaccine construct, enhance immunogenicity, and improve defense mechanism against specific pathogens [36].


Subtractive proteomics analysis

In this study, we utilized a subtractive proteomic approach to identify pathogen-specific vaccine proteins and design a multi-epitope subunit vaccine. The whole proteome of S. sonnei was acquired from the UniProt database (UniProt ID: UP000002529) with a total of 4,068 proteins. CD-HIT resource was used to remove redundant protein sequences with a sequence similarity index of 80%. Non-paralogous pathogen proteins were further screened against the human proteome using BLASTp analysis to remove human homologous proteins. A total of 2633 human non-homologous and non-paralogous proteins from S. sonnei were acquired for downstream analyses (S1 File).


S. sonnei, an Escherichia coli pathovar, is a gram-negative bacterium that causes bacillary dysentery and bloody diarrhea in humans. Currently, S. sonnei is a globally emerging pathogen and the leading cause of shigellosis in high-income countries. The unusually high number of cases of multi drug-resistant (MDR) and extensively drug-resistant (XDR) S. sonnei is a public health concern, as treatment options for moderate to severe cases are extremely limited [64]. Antibiotic resistance in bacteria has reached to a dangerous level, and strains resistant to most of the commonly used antibiotics are now routinely reported in many countries worldwide [65]. Therefore, new therapeutic strategies are needed to prevent MDR and XDR shigellosis. As antibiotic resistance increases, effective vaccine development has become the best alternative against such pathogens. Subtractive proteomics have been widely used to identify potential therapeutic targets for various pathogens. Advanced immunoinformatics and vaccinomics approaches are currently gaining interest in identifying potential pathogen-specific vaccine targets and designing potent vaccines against multiple resistant pathogens [66]. Reverse vaccinology and immunoinformatics approaches are cost- and time-effective with high efficacy compared to conventional vaccine development methods. 


The present study employed an integrated subtractive proteomics and immunoinformatics approach to identify potential vaccine candidates against MDR S. sonnai. Highly antigenic B- and T-cell epitopes were prioritized to design a multi-epitope-based vaccine construct using suitable adjuvant and linker sequences to elicit the host immune system. Inmmunological and physiochemical properties ensured the antigenic, non-allergenic, non-toxic, and soluble behavior of the vaccine construct. Immune simulation predicted high cellular and humoral responses induced by the proposed vaccine with long-lasting innate immunity. Molecular docking ensured the binding affinity of the vaccine with human TLR4 receptor. MD simulations speculated the molecular stability of the vaccine in the cellular environment. In silico cloning predicted effective gene expression capability of the designed vaccine construct in E. coli expression system. Further in vitro and in vivo investigations are suggested to validate the efficacy of the proposed vaccine against S. sonnai infections.


The authors thank Dr. Chunhua Li from Beijing University of Technology, China and Dr. Asifullah from Abdul Wali Khan University Mardan, Pakistan for providing technical support and supervising this research.

Citation: Aiman S, Ahmad A, Khan A, Ali Y, Malik A, Alkholief M, et al. (2023) Vaccinomics-aided next-generation novel multi-epitope-based vaccine engineering against multidrug resistant Shigella Sonnei: Immunoinformatics and chemoinformatics approaches. PLoS ONE 18(11): e0289773.

Editor: Prashant Kumar, The University of Kansas, UNITED STATES

Received: February 22, 2023; Accepted: July 25, 2023; Published: November 22, 2023

Copyright: © 2023 Aiman 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: The authors extend their appreciation to King Saud University for funding this work through research supporting project [RSP2023R376], Riyadh, Saudi Arabia and National Natural Science Foundation of China [31971180].

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: BLAST, Basic Local Alignment Search Tool; CAI, Codon Adaptation Index; CTL, Cytotoxic T Lymphocyte; GRAVY, Grand Average of Hydropathicity; HIV, Human immunodeficiency virus; HTL, Helper T Lymphocyte; IEDB, Immune Epitope Database; JCAT, Java Codon Adaptation Tool; LDMI, Developmental and Molecular Immunology; MD, Molecular Dynamic; MEVC, Multi-epitope Vaccine Construct; MHC-I, Major Histocompatibility Complex Class I; MHC-II, Major Histocompatibility Complex Class II; NCBI, National Center for Biotechnology Information; NICHHD, National Institute of Child Health and Human Development; NMA, Normal Mode Analysis; PDB, Protein Data Bank; Rg, Radius of Gyration; RMSD, Root-Mean-Square Deviation; RMSF, Root Mean Square Fluctuation; SMM, Stabilize Matrix Method.

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