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Alawam AS, Alwethaynani MS. Construction of an aerolysin-based multi-epitope vaccine against Aeromonas hydrophila: an in silico machine learning and artificial intelligence-supported approach. Front Immunol 2024; 15:1369890. [PMID: 38495891 PMCID: PMC10940347 DOI: 10.3389/fimmu.2024.1369890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024] Open
Abstract
Aeromonas hydrophila, a gram-negative coccobacillus bacterium, can cause various infections in humans, including septic arthritis, diarrhea (traveler's diarrhea), gastroenteritis, skin and wound infections, meningitis, fulminating septicemia, enterocolitis, peritonitis, and endocarditis. It frequently occurs in aquatic environments and readily contacts humans, leading to high infection rates. This bacterium has exhibited resistance to numerous commercial antibiotics, and no vaccine has yet been developed. Aiming to combat the alarmingly high infection rate, this study utilizes in silico techniques to design a multi-epitope vaccine (MEV) candidate against this bacterium based on its aerolysin toxin, which is the most toxic and highly conserved virulence factor among the Aeromonas species. After retrieval, aerolysin was processed for B-cell and T-cell epitope mapping. Once filtered for toxicity, antigenicity, allergenicity, and solubility, the chosen epitopes were combined with an adjuvant and specific linkers to create a vaccine construct. These linkers and the adjuvant enhance the MEV's ability to elicit robust immune responses. Analyses of the predicted and improved vaccine structure revealed that 75.5%, 19.8%, and 1.3% of its amino acids occupy the most favored, additional allowed, and generously allowed regions, respectively, while its ERRAT score reached nearly 70%. Docking simulations showed the MEV exhibiting the highest interaction and binding energies (-1,023.4 kcal/mol, -923.2 kcal/mol, and -988.3 kcal/mol) with TLR-4, MHC-I, and MHC-II receptors. Further molecular dynamics simulations demonstrated the docked complexes' remarkable stability and maximum interactions, i.e., uniform RMSD, fluctuated RMSF, and lowest binding net energy. In silico models also predict the vaccine will stimulate a variety of immunological pathways following administration. These analyses suggest the vaccine's efficacy in inducing robust immune responses against A. hydrophila. With high solubility and no predicted allergic responses or toxicity, it appears safe for administration in both healthy and A. hydrophila-infected individuals.
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Affiliation(s)
- Abdullah S. Alawam
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Maher S. Alwethaynani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Saudi Arabia
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Almanaa TN. Design of a novel multi-epitopes vaccine against Escherichia fergusonii: a pan-proteome based in- silico approach. Front Immunol 2023; 14:1332378. [PMID: 38143752 PMCID: PMC10739491 DOI: 10.3389/fimmu.2023.1332378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Escherichia fergusonii a gram-negative rod-shaped bacterium in the Enterobacteriaceae family, infect humans, causing serious illnesses such as urinary tract infection, cystitis, biliary tract infection, pneumonia, meningitis, hemolytic uremic syndrome, and death. Initially treatable with penicillin, antibiotic misuse led to evolving resistance, including resistance to colistin, a last-resort drug. With no licensed vaccine, the study aimed to design a multi-epitope vaccine against E. fergusonii. The study started with the retrieval of the complete proteome of all known strains and proceeded to filter the surface exposed virulent proteins. Seventeen virulent proteins (4 extracellular, 4 outer membranes, 9 periplasmic) with desirable physicochemical properties were identified from the complete proteome of known strains. Further, these proteins were processed for B-cell and T-cell epitope mapping. Obtained epitopes were evaluated for antigenicity, allergenicity, solubility, MHC-binding, and toxicity and the filtered epitopes were fused by specific linkers and an adjuvant into a vaccine construct. Structure of the vaccine candidate was predicted and refined resulting in 78.1% amino acids in allowed regions and VERIFY3D score of 81%. Vaccine construct was docked with TLR-4, MHC-I, and MHC-II, showing binding energies of -1040.8 kcal/mol, -871.4 kcal/mol, and -1154.6 kcal/mol and maximum interactions. Further, molecular dynamic simulation of the docked complexes was carried out resulting in a significant stable nature of the docked complexes (high B-factor and deformability values, lower Eigen and high variance values) in terms of intermolecular binding conformation and interactions. The vaccine was also reported to stimulate a variety of immunological pathways after administration. In short, the designed vaccine revealed promising predictions about its immune protective potential against E. fergusonii infections however experimental validation is needed to validate the results.
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Affiliation(s)
- Taghreed N. Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Sharma P, Sharma P, Ahmad S, Kumar A. Chikungunya Virus Vaccine Development: Through Computational Proteome Exploration for Finding of HLA and cTAP Binding Novel Epitopes as Vaccine Candidates. Int J Pept Res Ther 2022; 28:50. [PMID: 35069056 PMCID: PMC8762984 DOI: 10.1007/s10989-021-10347-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2021] [Indexed: 12/19/2022]
Abstract
Chikungunya virus is a major arbovirus of great public health concern in the whole world, but no vaccine is yet available, still advance therapeutic treatment and effective vaccines are in progress. The present multistep screening and structural binding analysis with CHIKV proteome exploration can be crucial in the development phase of CHIKV epitope based vaccine. The approach employed in two phases (i) Sequence based screening of peptides through propred and IEDB Server (ii) Structure based study through autodocking and NAMD VMD simulation analysis. Among all 29 extracted peptides, only two peptides 2LLANTTFPC10 of protein E3 and 98VNSVAIPLL106 of protein nsP3 were observed most prominent over all consider parameters such as peptide conserve nature, supertype population coverage, TAP binding, docking and simulation study. During docking interaction study, the best peptide and allele docked complexes such as 2LLANTTFPC10–B*0702 allele and 98VNSVAIPLL106–A*0301 allele exhibited best binding energy of − 3.13 kcal/mol and − 3.19 kcal/mol, respectively, with stable bonding patterns and their motion during NAMD simulation which confirm conserve peptide and allele stable interaction. The current study also exhibited the good docking interaction of both peptides 2LLANTTFPC10 and 98VNSVAIPLL106 with c TAP1 protein (1jj7 -PDB ID) cavity which confirm as a channel passageway to peptide transport through the cytoplasm to lumen of ER during antigen processing and presentation. Overall, this multistep screening and crosscheck structural binding analysis with an exploration of the complete proteome of CHIKV can be a novel step in the development of CHIKV epitope based vaccine as well as diagnostic development with aspect of time, cost and side effects.
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Affiliation(s)
- Priti Sharma
- D. S. Degree College, Aligarh, Dr. B. R. Ambedkar Univeristy, Agra, 282004 India
| | - Pawan Sharma
- Institute of Engineering and Technology, Mangalayatan University, Aligarh, 202145 India
| | - Sheeba Ahmad
- D. S. Degree College, Aligarh, Dr. B. R. Ambedkar Univeristy, Agra, 282004 India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University, G.T. Road, Kanpur, 209217 India
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Khan F, Kumar A. An integrative docking and simulation-based approach towards the development of epitope-based vaccine against enterotoxigenic Escherichia coli. ACTA ACUST UNITED AC 2021; 10:11. [PMID: 33619446 PMCID: PMC7890383 DOI: 10.1007/s13721-021-00287-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/16/2020] [Accepted: 01/25/2021] [Indexed: 11/28/2022]
Abstract
Enterotoxigenic E.coli is causing diarrheal illness in children as well as adults with the majority of the cases occurring in developing countries. To reduce the number of cases occurring worldwide, the development of an effectual vaccine against these bacteria can be the only prevention. This conjectural work was performed using modern bioinformatics tools for investigation of proteome of ETEC strain E24377A. Different computational vaccinology approaches were deployed to assess several parameters including antigenicity, allergenicity, stability, localization, molecular weight and toxicity of the predicted epitopes required for good vaccine candidate to elicit immune response against diarrhea. We estimated two known control antigens, epitope 141STLPETTVV149 of Hepatitis B virus and epitope 265ILRGSVAHK273 of H1N1 Nucleoprotein in an attempt to corroborate our research work. Furthermore molecular docking was performed to evaluate the interaction between HLA allele and peptide, the peptide QYGGGNSAL and peptide LPYFELRWL were considered to be the most promiscuous T cell epitopes with the highest binding energy value of −2.09 kcal/mol and −1.84 kcal/mol, respectively. In addition, dynamic simulation revealed good stability of the vaccine construct as well as population coverage analysis exhibits the highest population coverage in the regions of East Asia, India, Northeast Asia, South Asia and North America. Therefore, these two epitopes can be further synthesized for wet lab analysis and could be considered as a promising vaccine against diarrhea.
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Affiliation(s)
- Fariya Khan
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University Uttar Pradesh, Kanpur, 209217 India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University Uttar Pradesh, Kanpur, 209217 India
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Khan F, Kumar A. Vaccine Design and Immunoinformatics. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Hossan MI, Chowdhury AS, Hossain MU, Khan MA, Mahmood TB, Mizan S. Immunoinformatics aided-design of novel multi-epitope based peptide vaccine against Hendra henipavirus through proteome exploration. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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Srivastava S, Sharma SK, Srivastava V, Kumar A. Proteomic Exploration of Listeria monocytogenes for the Purpose of Vaccine Designing Using a Reverse Vaccinology Approach. Int J Pept Res Ther 2020; 27:779-799. [PMID: 33144851 PMCID: PMC7595573 DOI: 10.1007/s10989-020-10128-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2020] [Indexed: 12/14/2022]
Abstract
Listeriosis is a major foodborne infection provoked by a bacterium known as Listeria monocytogenes. It is one of the predominant causes of death in pregnant women, infants, and immunocompromised persons. Despite such fatal effects, until now there is no proper medication or drug available for such a serious foodborne infection. One of the most promising ways to deal with this challenge is vaccination. This present study aims at the prediction of B cell epitopes for subunit vaccine designing against Listeria monocytogenes using a reverse vaccinology approach. Among screened out 299 epitopes of strain F2365 of Listeria monocytogenes, based on the VaxiJen score, the top 20 epitopes were selected. 3D modeling of epitopes and alleles was generated by PEPstrMOD and Swiss Model respectively. Molecular docking reveals 4 epitopes viz., MKFLFPLKL, CEETFGIRL, FLKIDPPIL, and VRHHGGGHK based on binding energy. All 4 epitopes were investigated for non-toxicity, binding affinity, and population coverage. After vigorous investigation, epitope FLKIDPPIL was anticipated as the best vaccine contender. The stability of the FLKIDPPIL-HLA DRB1 _0101 complex was proved by performing the simulation. Here, predicted peptide through the Insilico approach may become a potential remedy against listeriosis, after the wet-lab approach and clinical trials.
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Affiliation(s)
- Shivani Srivastava
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University Uttar Pradesh, Kanpur, 209217 India
| | - Suraj Kumar Sharma
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University Uttar Pradesh, Kanpur, 209217 India
| | - Vivek Srivastava
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University Uttar Pradesh, Kanpur, 209217 India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology, Rama University Uttar Pradesh, Kanpur, 209217 India
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Gupta SR, Gupta E, Ohri A, Shrivastava SK, Kachhwaha S, Sharma V, Mishra RK, Niraj RRK. Comparative Proteome Analysis of Mycobacterium Tuberculosis Strains - H37Ra, H37Rv, CCDC5180, and CAS/NITR204: A Step Forward to Identify Novel Drug Targets. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180817999200531165148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background:
Mycobacterium tuberculosis is a causative agent of tuberculosis. It is a
non-motile, acid-fast, obligatory aerobic bacterium. Finding novel drug targets in Mycobacterium
tuberculosis has become extremely important as the bacterium is evolving into a more dangerous
multi-drug resistant pathogen. The predominant strains in India belong to the Central-Asian, East-
African Indian, and Beijing clad. For the same reason, the whole proteomes of a non-virulent strain
(H37Ra), a virulent (H37Rv) and two clinical strains, a Central-Asian clad (CAS/NITR204) and a
Beijing clad (CCDC5180) have been selected for comparative study. Selecting a phylogenetically
close and majorly studied non-virulent strain is helpful in removing the common and undesired proteins
from the study.
Objective:
The study compares the whole proteome of non-virulent strain with the other three virulent
strains to find a unique protein responsible for virulence in virulent strains. It is expected that
the drugs developed against identified targets will be specific to the virulent strains. Additionally, to
assure minimal toxicity to the host, we also screened the human proteome.
Methods:
Comparative proteome analysis was used for target identification and in silico validation
of identified target protein Rv2466c, identification of the respective ligand of the identified target
protein and binding interaction study using Molecular docking and Molecular Dynamic Simulation
study were used in this study.
Results and Discussion:
Finally, eleven proteins were found to be unique in virulent strain only and
out of which, Rv2466c (PDB-ID: 4ZIL) was found to be an essential protein and identified as a putative
drug target protein for further study. The compound glutathione was found to be a suitable
inhibitor for Rv2466c. In this study, we used a comparative proteomics approach to identify novel
target proteins.
Conclusion:
This study is unique as we are assured that the study will move forward the research in
a new direction to cure the deadly disease (tuberculosis) caused by Mycobacterium tuberculosis.
Rv2466c was identified as a novel drug target and glutathione as a respective ligand of Rv2466c.
Discovery of the novel drug target as well as the drug will provide a solution to drug resistance as
well as the infection caused by Mycobacterium tuberculosis.
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Affiliation(s)
| | - Ekta Gupta
- Dr B. Lal Institute of Biotechnology Jaipur, Jaipur, India
| | - Avnam Ohri
- Dr B. Lal Institute of Biotechnology Jaipur, Jaipur, India
| | | | | | - Vinay Sharma
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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Nain Z, Abdulla F, Rahman MM, Karim MM, Khan MSA, Sayed SB, Mahmud S, Rahman SMR, Sheam MM, Haque Z, Adhikari UK. Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches. J Biomol Struct Dyn 2019; 38:4850-4867. [PMID: 31709929 DOI: 10.1080/07391102.2019.1692072] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Elizabethkingia anophelis is an emerging human pathogen causing neonatal meningitis, catheter-associated infections and nosocomial outbreaks with high mortality rates. Besides, they are resistant to most antibiotics used in empirical therapy. In this study, therefore, we used immunoinformatic approaches to design a prophylactic peptide vaccine against E. anophelis as an alternative preventive measure. Initially, cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-lymphocyte (LBL) epitopes were predicted from the highest antigenic protein. The CTL and HTL epitopes together had a population coverage of 99.97% around the world. Eventually, six CTL, seven HTL, and two LBL epitopes were selected and used to construct a multi-epitope vaccine. The vaccine protein was found to be highly immunogenic, non-allergenic, and non-toxic. Codon adaptation and in silico cloning were performed to ensure better expression within E. coli K12 host system. The stability of the vaccine structure was also improved by disulphide bridging. In addition, molecular docking and dynamics simulation revealed strong and stable binding affinity between the vaccine and toll-like receptor 4 (TLR4) molecule. The immune simulation showed higher levels of T-cell and B-cell activities which was in coherence with actual immune response. Repeated exposure simulation resulted in higher clonal selection and faster antigen clearance. Nevertheless, experimental validation is required to ensure the immunogenic potency and safety of this vaccine to control E. anophelis infection in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zulkar Nain
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Faruq Abdulla
- Department of Statistics, Faculty of Sciences, Islamic University, Kushtia, Bangladesh
| | - M Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mohammad Minnatul Karim
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md Shakil Ahmed Khan
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sifat Bin Sayed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Shafi Mahmud
- Department of Biotechnology and Genetic Engineering, Faculty of Life and Earth Science, Rajshahi University, Rajshahi, Bangladesh
| | - S M Raihan Rahman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md Moinuddin Sheam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Zahurul Haque
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
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Gupta E, Gupta SRR, Niraj RRK. Identification of Drug and Vaccine Target in Mycobacterium leprae: A Reverse Vaccinology Approach. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09936-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Exploring Highly Antigenic Protein of Campylobacter jejuni for Designing Epitope Based Vaccine: Immunoinformatics Approach. Int J Pept Res Ther 2018. [DOI: 10.1007/s10989-018-9764-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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