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Hashempour A, Khodadad N, Akbarinia S, Ghasabi F, Ghasemi Y, Nazar MMKA, Falahi S. Reverse vaccinology approaches to design a potent multiepitope vaccine against the HIV whole genome: immunoinformatic, bioinformatics, and molecular dynamics approaches. BMC Infect Dis 2024; 24:873. [PMID: 39198721 PMCID: PMC11360854 DOI: 10.1186/s12879-024-09775-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 08/20/2024] [Indexed: 09/01/2024] Open
Abstract
Substantial advances have been made in the development of promising HIV vaccines to eliminate HIV-1 infection. For the first time, one hundred of the most submitted HIV subtypes and CRFs were retrieved from the LANL database, and the consensus sequences of the eleven HIV proteins were obtained to design vaccines for human and mouse hosts. By using various servers and filters, highly qualified B-cell epitopes, as well as HTL and CD8 + epitopes that were common between mouse and human alleles and were also located in the conserved domains of HIV proteins, were considered in the vaccine constructs. With 90% coverage worldwide, the human vaccine model covers a diverse allelic population, making it widely available. Codon optimization and in silico cloning in prokaryotic and eukaryotic vectors guarantee high expression of the vaccine models in human and E. coli hosts. Molecular dynamics confirmed the stable interaction of the vaccine constructs with TLR3, TLR4, and TLR9, leading to a substantial immunogenic response to the designed vaccine. Vaccine models effectively target the humoral and cellular immune systems in humans and mice; however, experimental validation is needed to confirm these findings in silico.
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Affiliation(s)
- Ava Hashempour
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nastaran Khodadad
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Shokufeh Akbarinia
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzane Ghasabi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Shahab Falahi
- HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran.
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Mahmoodi S, Amirzakaria JZ, Ghasemian A. A novel multi-epitope peptide vaccine targeting immunogenic antigens of Ebola and monkeypox viruses with potential of immune responses provocation in silico. Biotechnol Appl Biochem 2024. [PMID: 39128888 DOI: 10.1002/bab.2646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 07/10/2024] [Indexed: 08/13/2024]
Abstract
The emergence or reemergence of monkeypox (Mpox) and Ebola virus (EBOV) agents causing zoonotic diseases remains a huge threat to human health. Our study aimed at designing a multi-epitope vaccine (MEV) candidate to target both the Mpox and EBOV agents using immunoinformatics tools. Viral protein sequences were retrieved, and potential nonallergenic, nontoxic, and antigenic epitopes were obtained. Next, cytotoxic and helper T-cell (CTL and HTL, respectively) and B-cell (BCL) epitopes were predicted, and those potential epitopes were fused utilizing proper linkers. The in silico cloning and expression processes were implemented using Escherichia coli K12. The immune responses were prognosticated using the C-ImmSim server. The MEV construct (29.53 kDa) included four BCL, two CTL, and four HTL epitopes and adjuvant. The MEV traits were pertinent in terms of antigenicity, non-allergenicity, nontoxicity, physicochemical characters, and stability. The MEV candidate was also highly expressed in E. coli K12. The strong affinity of MEV-TLR3 was confirmed using molecular docking and molecular dynamics simulation analyses. Immune simulation analyses unraveled durable activation and responses of cellular and humoral arms alongside innate immune responses. The designed MEV candidate demonstrated appropriate traits and was promising in the prediction of immune responses against both Mpox and EBOV agents. Further experimental assessments of the MEV are required to verify its efficacy.
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Affiliation(s)
- Shirin Mahmoodi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Javad Zamani Amirzakaria
- Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
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3
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Ryan N, Pratiwi SE, Mardhia M, Ysrafil Y, Liana DF, Mahyarudin M. Immunoinformatics approach for design novel multi-epitope prophylactic and therapeutic vaccine based on capsid proteins L1 and L2 and oncoproteins E6 and E7 of human papillomavirus 16 and human papillomavirus 18 against cervical cancer. Osong Public Health Res Perspect 2024; 15:307-328. [PMID: 39039819 PMCID: PMC11391375 DOI: 10.24171/j.phrp.2024.0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 05/13/2024] [Indexed: 07/24/2024] Open
Abstract
BACKGROUND This study aimed to identify the optimal protein construction for designing a multi-epitope vaccine with both prophylactic and therapeutic effects against cervical cancer, utilizing an immunoinformatics approach. The construction process involved using capsid epitopes L1 and L2, as well as oncoproteins E5, E6, and E7 from human papillomavirus (HPV) types 16 and 18. METHODS An experimental in silico analysis with an immunoinformatics approach was used to develop 2 multi-epitope vaccine constructs (A and B). Further analysis was then conducted to compare the constructs and select the one with the highest potential against cervical cancer. RESULTS This study produced 2 antigenic, non-allergenic, and nontoxic multi-epitope vaccine constructs (A and B), which exhibited the ideal physicochemical properties for a vaccine. Further analysis revealed that construct B effectively induced both cellular and humoral immune responses. CONCLUSION The multi-epitope vaccine construct B for HPV 16 and 18, designed for both prophylactic and therapeutic purposes, met the development criteria for a cervical cancer vaccine. However, these findings need to be validated through in vitro and in vivo experiments.
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Affiliation(s)
- Nicholas Ryan
- Medical Study Program, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Sari Eka Pratiwi
- Department of Biology and Pathobiology, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Mardhia Mardhia
- Department of Microbiology, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Ysrafil Ysrafil
- Department of Pharmacotherapy, Faculty of Medicine, Universitas Palangka Raya, Palangka Raya, Indonesia
| | - Delima Fajar Liana
- Department of Microbiology, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Mahyarudin Mahyarudin
- Department of Microbiology, Faculty of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
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Biswas R, Swetha RG, Basu S, Roy A, Ramaiah S, Anbarasu A. Designing multi-epitope vaccine against human cytomegalovirus integrating pan-genome and reverse vaccinology pipelines. Biologicals 2024; 87:101782. [PMID: 39003966 DOI: 10.1016/j.biologicals.2024.101782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/13/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024] Open
Abstract
Human cytomegalovirus (HCMV) is accountable for high morbidity in neonates and immunosuppressed individuals. Due to the high genetic variability of HCMV, current prophylactic measures are insufficient. In this study, we employed a pan-genome and reverse vaccinology approach to screen the target for efficient vaccine candidates. Four proteins, envelope glycoprotein M, UL41A, US23, and US28, were shortlisted based on cellular localization, high solubility, antigenicity, and immunogenicity. A total of 29 B-cell and 44 T-cell highly immunogenic and antigenic epitopes with high global population coverage were finalized using immunoinformatics tools and algorithms. Further, the epitopes that were overlapping among the finalized B-cell and T-cell epitopes were linked with suitable linkers to form various combinations of multi-epitopic vaccine constructs. Among 16 vaccine constructs, Vc12 was selected based on physicochemical and structural properties. The docking and molecular simulations of VC12 were performed, which showed its high binding affinity (-23.35 kcal/mol) towards TLR4 due to intermolecular hydrogen bonds, salt bridges, and hydrophobic interactions, and there were only minimal fluctuations. Furthermore, Vc12 eliciting a good response was checked for its expression in Escherichia coli through in silico cloning and codon optimization, suggesting it to be a potent vaccine candidate.
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Affiliation(s)
- Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Rayapadi G Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biosciences, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, 761008, Odisha, India
| | - Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biosciences, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India.
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Ali L, Rauf S, Khan A, Rasool S, Raza RZ, Alshabrmi FM, Khan T, Suleman M, Waheed Y, Mohammad A, Agouni A. In silico design of multi-epitope vaccines against the hantaviruses by integrated structural vaccinology and molecular modeling approaches. PLoS One 2024; 19:e0305417. [PMID: 39042625 PMCID: PMC11265663 DOI: 10.1371/journal.pone.0305417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/29/2024] [Indexed: 07/25/2024] Open
Abstract
Hantaviruses are single-stranded RNA viruses belonging to the family Bunyaviridae that causes hantavirus cardiopulmonary syndrome (HCPS) and hemorrhagic fever with renal syndrome (HFRS) worldwide. Currently, there is no effective vaccination or therapy available for the treatment of hantavirus, hence there is a dire need for research to formulate therapeutics for the disease. Computational vaccine designing is currently a highly accurate, time and cost-effective approach for designing effective vaccines against different diseases. In the current study, we shortlisted highly antigenic proteins i.e., envelope, and nucleoprotein from the proteome of hantavirus and subjected to the selection of highly antigenic epitopes to design of next-generation multi-epitope vaccine constructs. A highly antigenic and stable adjuvant was attached to the immune epitopes (T-cell, B-cell, and HTL) to design Env-Vac, NP-Vac, and Com-Vac constructs, which exhibit stronger antigenic, non-allergenic, and favorable physiochemical properties. Moreover, the 3D structures were predicted and docking analysis revealed robust interactions with the human Toll-like receptor 3 (TLR3) to initiate the immune cascade. The total free energy calculated for Env-Vac, NP-Vac, and Com-Vac was -50.02 kcal/mol, -24.13 kcal/mol, and -62.30 kcal/mol, respectively. In silico cloning, results demonstrated a CAI value for the Env-Vac, NP-Vac, and Com-Vac of 0.957, 0.954, and 0.956, respectively, while their corresponding GC contents were 65.1%, 64.0%, and 63.6%. In addition, the immune simulation results from three doses of shots released significant levels of IgG, IgM, interleukins, and cytokines, as well as antigen clearance over time, after receiving the vaccine and two booster doses. Our vaccines against Hantavirus were found to be highly immunogenic, inducing a robust immune response that demands experimental validation for clinical usage.
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Affiliation(s)
- Liaqat Ali
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Sobiah Rauf
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Abbas Khan
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Samreen Rasool
- Department of Biochemistry, Government College University, Lahore, Pakistan
| | - Rabail Zehra Raza
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Fahad M. Alshabrmi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Taimoor Khan
- Department of Radiation Oncology, University of California, San Francisco, United States of America
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Charbagh, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Yasir Waheed
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Abdelali Agouni
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
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Prosper P, Rodríguez Puertas R, Guérin DMA, Branda MM. Computational method for designing vaccines applied to virus-like particles (VLPs) as epitope carriers. Vaccine 2024; 42:3916-3929. [PMID: 38782665 DOI: 10.1016/j.vaccine.2024.05.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 04/06/2024] [Accepted: 05/04/2024] [Indexed: 05/25/2024]
Abstract
Nonenveloped virus-like particles (VLPs) are self-assembled oligomeric structures composed of one or more proteins that originate from diverse viruses. Because these VLPs have similar antigenicity to the parental virus, they are successfully used as vaccines against cognate virus infection. Furthermore, after foreign antigenic sequences are inserted in their protein components (chimVLPs), some VLPs are also amenable to producing vaccines against pathogens other than the virus it originates from (these VLPs are named platform or epitope carrier). Designing chimVLP vaccines is challenging because the immunogenic response must be oriented against a given antigen without altering stimulant properties inherent to the VLP. An important step in this process is choosing the location of the sequence modifications because this must be performed without compromising the assembly and stability of the original VLP. Currently, many immunogenic data and computational tools can help guide the design of chimVLPs, thus reducing experimental costs and work. In this study, we analyze the structure of a novel VLP that originate from an insect virus and describe the putative regions of its three structural proteins amenable to insertion. For this purpose, we employed molecular dynamics (MD) simulations to assess chimVLP stability by comparing mutated and wild-type (WT) VLP protein trajectories. We applied this procedure to design a chimVLP that can serve as a prophylactic vaccine against the SARS-CoV-2 virus. The methodology described in this work is generally applicable for VLP-based vaccine development.
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Affiliation(s)
- Pascalita Prosper
- Instituto de Física Aplicada - INFAP, Universidad Nacional de San Luis/CONICET, Argentina, Av. Ejército de los Andes 950, 5700 San Luis, San Luis, Argentina
| | - Rafael Rodríguez Puertas
- Universidad del País Vasco (UPV/EHU), Dept. Farmacología, Facultad de Medicina, B° Sarriena S/N, 48940 Leioa, Vizcaya, Spain; Neurodegenerative Diseases, BioCruces Bizkaia Health Research Institute, Barakaldo, Spain
| | - Diego M A Guérin
- Universidad del País Vasco (UPV/EHU) and Instituto Biofisika (CSIC, UPV/EHU), B° Sarriena S/N, 48940 Leioa, Vizcaya, Spain
| | - María Marta Branda
- Instituto de Física Aplicada - INFAP, Universidad Nacional de San Luis/CONICET, Argentina, Av. Ejército de los Andes 950, 5700 San Luis, San Luis, Argentina.
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Sharif E, Nezafat N, Ahmadi FM, Mohit E. In Silico Design of CT26 Polytope and its Surface Display by ClearColi™-Derived Outer Membrane Vesicles as a Cancer Vaccine Candidate Against Colon Carcinoma. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04971-x. [PMID: 38958886 DOI: 10.1007/s12010-024-04971-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2024] [Indexed: 07/04/2024]
Abstract
Simultaneous targeting of several mutations can be useful in colorectal cancer (CRC) due to its heterogeneity and presence of somatic mutations. As CT26 mutations and expression profiles resemble those of human CRC, we focused on designing a polyepitope vaccine based on CT26 neoepitopes. Due to its low immunogenicity, outer membrane vesicles (rOMV) as an antigen delivery system and adjuvant was applied. Herein, based on previous experimental and our in silico studies four CT26 neoepitopes with the ability to bind MHC-I and MHC-II, TCR, and induce IFN-α production were selected. To increase their immunogenicity, the gp70 and PADRE epitopes were added. The order of the neoepitopes was determined through 3D structure analysis using ProSA, Verify 3D, ERRAT, and Ramachandran servers. The stable peptide-protein docking between the selected epitopes and MHC alleles strengthen our prediction. The CT26 polytope vaccine sequence was fused to the C-terminal of cytolysin A (ClyA) anchor protein and rOMVs were isolated from endotoxin-free ClearColi™ strain. The results of the C-ImmSim server showed that the ClyA-CT26 polytope vaccine could induce T and B cells immunity.The ClyA-CT26 polytope was characterized as a soluble, stable, immunogen, and non-allergen vaccine and optimized for expression in ClearColi™ 24 h after induction with 1 mM IPTG at 25 °C. Western blot analysis confirmed the expression of ClyA-CT26 polytope by ClearColi™ and also on ClearColi™-derived rOMVs. In conclusion, we found that ClearColi™-derived rOMVs with CT26 polytope can deliver CRC neoantigens and induce antitumor immunity, but in vivo immunological studies are needed to confirm vaccine efficacy.
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Affiliation(s)
- Elham Sharif
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, No. 2660, Vali-e-Asr Ave, Tehran, 1991953381, Iran
| | - Navid Nezafat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Elham Mohit
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, No. 2660, Vali-e-Asr Ave, Tehran, 1991953381, Iran.
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Kumar A, Dutt M, Dehury B, Martinez GS, Singh KP, Kelvin DJ. Formulation of next-generation polyvalent vaccine candidates against three important poxviruses by targeting DNA-dependent RNA polymerase using an integrated immunoinformatics and molecular modeling approach. J Infect Public Health 2024; 17:102470. [PMID: 38865776 DOI: 10.1016/j.jiph.2024.102470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/27/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Poxviruses comprise a group of large double-stranded DNA viruses and are known to cause diseases in humans, livestock animals, and other animal species. The Mpox virus (MPXV; formerly Monkeypox), variola virus (VARV), and volepox virus (VPXV) are among the prevalent poxviruses of the Orthopoxviridae genera. The ongoing Mpox infectious disease pandemic caused by the Mpox virus has had a major impact on public health across the globe. To date, only limited repurposed antivirals and vaccines are available for the effective treatment of Mpox and other poxviruses that cause contagious diseases. METHODS The present study was conducted with the primary goal of formulating multi-epitope vaccines against three evolutionary closed poxviruses i.e., MPXV, VARV, and VPXV using an integrated immunoinformatics and molecular modeling approach. DNA-dependent RNA polymerase (DdRp), a potential vaccine target of poxviruses, has been used to determine immunodominant B and T-cell epitopes followed by interactions analysis with Toll-like receptor 2 at the atomic level. RESULTS Three multi-epitope vaccine constructs, namely DdRp_MPXV (V1), DdRp_VARV (V2), and DdRp_VPXV (V3) were designed. These vaccine constructs were found to be antigenic, non-allergenic, non-toxic, and soluble with desired physicochemical properties. Protein-protein docking and interaction profiling analysis depicts a strong binding pattern between the targeted immune receptor TLR2 and the structural models of the designed vaccine constructs, and manifested a number of biochemical bonds (hydrogen bonds, salt bridges, and non-bonded contacts). State-of-the-art all-atoms molecular dynamics simulations revealed highly stable interactions of vaccine constructs with TLR2 at the atomic level throughout the simulations on 300 nanoseconds. Additionally, the outcome of the immune simulation analysis suggested that designed vaccines have the potential to induce protective immunity against targeted poxviruses. CONCLUSIONS Taken together, formulated next-generation polyvalent vaccines were found to have good efficacy against closely related poxviruses (MPXV, VARV, and VPXV) as demonstrated by our extensive immunoinformatics and molecular modeling evaluations; however, further experimental investigations are still needed.
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Affiliation(s)
- Anuj Kumar
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Mansi Dutt
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Budheswar Dehury
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Krishna Pal Singh
- Mahatma Jyotiba Phule Rohilkhand University, Bareilly, Uttar Pradesh, India
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada.
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Roy A, Swetha RG, Basu S, Biswas R, Ramaiah S, Anbarasu A. Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1. 3 Biotech 2024; 14:176. [PMID: 38855144 PMCID: PMC11153438 DOI: 10.1007/s13205-024-04022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Herpes simplex virus type-1 (HSV-1), the etiological agent of sporadic encephalitis and recurring oral (sometimes genital) infections in humans, affects millions each year. The evolving viral genome reduces susceptibility to existing antivirals and, thus, necessitates new therapeutic strategies. Immunoinformatics strategies have shown promise in designing novel vaccine candidates in the absence of a clinically licensed vaccine to prevent HSV-1. However, to encourage clinical translation, the HSV-1 pan-genome was integrated with the reverse-vaccinology pipeline for rigorous screening of universal vaccine candidates. Viral targets were screened from 104 available complete genomes. Among 364 proteins, envelope glycoprotein D being an outer membrane protein with a high antigenicity score (> 0.4) and solubility (> 0.6) was selected for epitope screening. A total of 17 T-cell and 4 B-cell epitopes with highly antigenic, immunogenic, non-toxic properties and high global population coverage were identified. Furthermore, 8 vaccine constructs were designed using different combinations of epitopes and suitable linkers. VC-8 was identified as the most potential vaccine candidate regarding chemical and structural stability. Molecular docking revealed high interactive affinity (low binding energy: - 56.25 kcal/mol) of VC-8 with the target elicited by firm intermolecular H-bonds, salt-bridges, and hydrophobic interactions, which was validated with simulations. Compatibility of the vaccine candidate to be expressed in pET-29(a) + plasmid was established by in silico cloning studies. Immune simulations confirmed the potential of VC-8 to trigger robust B-cell, T-cell, cytokine, and antibody-mediated responses, thereby suggesting a promising candidate for the future of HSV-1 prevention. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04022-6.
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Affiliation(s)
- Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Rayapadi G. Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, Odisha 761008 India
| | - Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
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Alawadi ZI, Alsultan A, Alsallami D, Alnomasy SF, Alqasmi M, Almufarriji FM, Alotaibi BS, Mazhari BBZ, Alenazy R. Designing a multiepitope mRNA-based vaccine against enterotoxigenic Escherichia coli infection in calves: Immunoinformatics and molecular modeling approach. Open Vet J 2024; 14:1417-1425. [PMID: 39055761 PMCID: PMC11268904 DOI: 10.5455/ovj.2024.v14.i6.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/21/2024] [Indexed: 07/27/2024] Open
Abstract
Background Escherichia coli is one of the serious pathogens causing various infections in the animal field, such as neonatal calf diarrhea, which is responsible for mortality associated with diarrhea during the first days of life. Aim Current work is aimed at designing an effective and safe multiepitope vaccine candidate against E. coli infection in calves based on the fimbrial protein K99 of Enterotoxigenic E. coli (ETEC) and Immuno-informatics. Methods A conserved sequence of K99 protein was generated, and then highly antigenic, nonallergic, and overlapped epitopes were used to construct a multiepitope vaccine. Five THL, six MHC II, and four beta cell epitopes were targeted to create the candidate. The candidate vaccine was produced utilizing 15 epitopes and three types of linkers, two types of untranslated region (UTR) human hemoglobin subunit beta (HBB), UTR beta-globin (Rabb), and RpfE protein as an immunomodulation adjuvant. Results Immuno-informatics analysis of the constructed protein showed that the protein was antigenic (antigenic score of 0.8841), stable, nonallergen, and soluble. Furthermore, the Immuno-informatics and physiochemical analysis of the constructed protein showed a stable, nonallergic, soluble, hydrophilic, and acidic PI (isoelectric point). of 9.34. Docking of the candidate vaccine with the toll-like receptor TLR3 was performed, and results showed a strong interaction between the immune receptor and the vaccine. Finally, the expression efficiency of the construct in E. coli was estimated via computational cloning of the vaccine sequence into Pet28a. Conclusion Results of immunoinformatics and in silico approaches reveal that the designed vaccine is antigenic, stable, and able to bind to the immune cell receptors. Our results interpret the proposed multiepitope mRNA vaccine as a good preventive option against E. coli infection in calves.
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Affiliation(s)
- Zainab Isam Alawadi
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Al- Diwaniyah, Iraq
| | - Amjed Alsultan
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Al- Diwaniyah, Iraq
| | - Dhama Alsallami
- Department of Physiology, Pharmacology and Biochemistry, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Sultan F. Alnomasy
- Medical Laboratories Department, College of Applied Medical Sciences in Al- Quwayiyah, Shaqra University, Shaqra, Saudi Arabia
| | - Mohammed Alqasmi
- Department of Medical Laboratory, College of Applied Medical Sciences-Shaqra, Shaqra University, Shaqra, Saudi Arabia
| | - Fawaz M. Almufarriji
- Medical Laboratories Department, College of Applied Medical Sciences in Al- Quwayiyah, Shaqra University, Shaqra, Saudi Arabia
| | - Bader S. Alotaibi
- Medical Laboratories Department, College of Applied Medical Sciences in Al- Quwayiyah, Shaqra University, Shaqra, Saudi Arabia
| | - Bi Bi Zainab Mazhari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakakah, Saudi Arabia
| | - Rawaf Alenazy
- Department of Medical Laboratory, College of Applied Medical Sciences-Shaqra, Shaqra University, Shaqra, Saudi Arabia
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Moin AT, Rani NA, Patil RB, Robin TB, Ullah MA, Rahim Z, Rahman MF, Zubair T, Hossain M, Mollah AKMM, Absar N, Hossain M, Manchur MA, Islam NN. In-silico formulation of a next-generation polyvalent vaccine against multiple strains of monkeypox virus and other related poxviruses. PLoS One 2024; 19:e0300778. [PMID: 38758816 PMCID: PMC11101047 DOI: 10.1371/journal.pone.0300778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/05/2024] [Indexed: 05/19/2024] Open
Abstract
Mpox (formerly known as monkeypox) virus and some related poxviruses including smallpox virus pose a significant threat to public health, and effective prevention and treatment strategies are needed. This study utilized a reverse vaccinology approach to retrieve conserved epitopes for monkeypox virus and construct a vaccine that could provide cross-protection against related viruses with similar antigenic properties. The selected virulent proteins of monkeypox virus, MPXVgp165, and Virion core protein P4a, were subjected to epitope mapping for vaccine construction. Two vaccines were constructed using selected T cell epitopes and B cell epitopes with PADRE and human beta-defensins adjuvants conjugated in the vaccine sequence. Both constructs were found to be highly antigenic, non-allergenic, nontoxic, and soluble, suggesting their potential to generate an adequate immune response and be safe for humans. Vaccine construct 1 was selected for molecular dynamic simulation studies. The simulation studies revealed that the TLR8-vaccine complex was more stable than the TLR3-vaccine complex. The lower RMSD and RMSF values of the TLR8 bound vaccine compared to the TLR3 bound vaccine suggested better stability and consistency of hydrogen bonds. The Rg values of the vaccine chain bound to TLR8 indicated overall stability, whereas the vaccine chain bound to TLR3 showed deviations throughout the simulation. These results suggest that the constructed vaccine could be a potential preventive measure against monkeypox and related viruses however, further experimental validation is required to confirm these findings.
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Affiliation(s)
- Abu Tayab Moin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Maharashtra, India
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md. Asad Ullah
- Faculty of Biological Sciences, Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Zahidur Rahim
- Department of Zoology, Jahangirnagar University, Dhaka, Bangladesh
| | - Md. Foyzur Rahman
- Department of Pharmacy, Dhaka International University, Dhaka, Bangladesh
| | | | - Mohabbat Hossain
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | | | - Nurul Absar
- Faculty of Basic Medical and Pharmaceutical Sciences, Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Khulshi, Chittagong, Bangladesh
| | - Mahboob Hossain
- Department of Mathematics and Natural Sciences, Microbiology Program, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Mohammed Abul Manchur
- Faculty of Biological Sciences, Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nazneen Naher Islam
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
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12
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Kumar A, Misra G, Mohandas S, Yadav PD. Multi-epitope vaccine design using in silico analysis of glycoprotein and nucleocapsid of NIPAH virus. PLoS One 2024; 19:e0300507. [PMID: 38728300 PMCID: PMC11086869 DOI: 10.1371/journal.pone.0300507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/29/2024] [Indexed: 05/12/2024] Open
Abstract
According to the 2018 WHO R&D Blueprint, Nipah virus (NiV) is a priority disease, and the development of a vaccine against NiV is strongly encouraged. According to criteria used to categorize zoonotic diseases, NiV is a stage III disease that can spread to people and cause unpredictable outbreaks. Since 2001, the NiV virus has caused annual outbreaks in Bangladesh, while in India it has caused occasional outbreaks. According to estimates, the mortality rate for infected individuals ranges from 70 to 91%. Using immunoinformatic approaches to anticipate the epitopes of the MHC-I, MHC-II, and B-cells, they were predicted using the NiV glycoprotein and nucleocapsid protein. The selected epitopes were used to develop a multi-epitope vaccine construct connected with linkers and adjuvants in order to improve immune responses to the vaccine construct. The 3D structure of the engineered vaccine was anticipated, optimized, and confirmed using a variety of computer simulation techniques so that its stability could be assessed. According to the immunological simulation tests, it was found that the vaccination elicits a targeted immune response against the NiV. Docking with TLR-3, 7, and 8 revealed that vaccine candidates had high binding affinities and low binding energies. Finally, molecular dynamic analysis confirms the stability of the new vaccine. Codon optimization and in silico cloning showed that the proposed vaccine was expressed to a high degree in Escherichia coli. The study will help in identifying a potential epitope for a vaccine candidate against NiV. The developed multi-epitope vaccine construct has a lot of potential, but they still need to be verified by in vitro & in vivo studies.
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Affiliation(s)
- Anoop Kumar
- Molecular Diagnostic Laboratory, National Institute of Biologicals, Noida, Uttar Pradesh, India
| | - Gauri Misra
- Molecular Diagnostic Laboratory, National Institute of Biologicals, Noida, Uttar Pradesh, India
| | - Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
| | - Pragya D. Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
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13
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Guo Z, Ren H, Chang Q, Liu R, Zhou X, Xue K, Sun T, Luo J, Wang F, Ge J. Lactobacilli-derived adjuvants combined with immunoinformatics-driven multi-epitope antigens based approach protects against Clostridium perfringens in a mouse model. Int J Biol Macromol 2024; 267:131475. [PMID: 38608984 DOI: 10.1016/j.ijbiomac.2024.131475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 03/28/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Clostridium perfringens is ubiquitously distributed and capable of secreting toxins, posing a significant threat to animal health. Infections caused by Clostridium perfringens, such as Necrotic Enteritis (NE), result in substantial economic losses to the livestock industry annually. However, there is no effective commercial vaccine available. Hence, we set out to propose an effective approach for multi-epitope subunit vaccine construction utilizing biomolecules. We utilized immunoinformatics to design a novel multi-epitope antigen against C. perfringens (CPMEA). Furthermore, we innovated novel bacterium-like particles (BLPs) through thermal acid treatment of various Lactobacillus strains and selected BLP23017 among them. Then, we detailed the structure of CPMEA and BLPs and utilized them to prepare a multi-epitope vaccine. Here, we showed that our vaccine provided full protection against C. perfringens infection after a single dose in a mouse model. Additionally, BLP23017 notably augmented the secretion of secretory immunoglobulin A (sIgA) and enhanced antibody production. We conclude that our vaccine possess safety and high efficacy, making it an excellent candidate for preventing C. perfringens infection. Moreover, we demonstrate our approach to vaccine construction and the preparation of BLP23017 with distinct advantages may contribute to the prevention of a wider array of diseases and the novel vaccine development.
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Affiliation(s)
- Zhiyuan Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Hongkun Ren
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Qingru Chang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Runhang Liu
- State Key Laboratory for Animal Disease control and prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyao Zhou
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Kun Xue
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Tong Sun
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Jilong Luo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China
| | - Fang Wang
- State Key Laboratory for Animal Disease control and prevention, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin 150030, China; Heilongjiang Provincial Key Laboratory of Zoonosis, Harbin 150030, China.
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14
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Ghaffar SA, Tahir H, Muhammad S, Shahid M, Naqqash T, Faisal M, Albekairi TH, Alshammari A, Albekairi NA, Manzoor I. Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches. Front Immunol 2024; 15:1380732. [PMID: 38690283 PMCID: PMC11058264 DOI: 10.3389/fimmu.2024.1380732] [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: 02/02/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Haemophilus parainfluenzae is a Gram-negative opportunist pathogen within the mucus of the nose and mouth without significant symptoms and has an ability to cause various infections ranging from ear, eye, and sinus to pneumonia. A concerning development is the increasing resistance of H. parainfluenzae to beta-lactam antibiotics, with the potential to cause dental infections or abscesses. The principal objective of this investigation is to utilize bioinformatics and immuno-informatic methodologies in the development of a candidate multi-epitope Vaccine. The investigation focuses on identifying potential epitopes for both B cells (B lymphocytes) and T cells (helper T lymphocytes and cytotoxic T lymphocytes) based on high non-toxic and non-allergenic characteristics. The selection process involves identifying human leukocyte antigen alleles demonstrating strong associations with recognized antigenic and overlapping epitopes. Notably, the chosen alleles aim to provide coverage for 90% of the global population. Multi-epitope constructs were designed by using suitable linker sequences. To enhance the immunological potential, an adjuvant sequence was incorporated using the EAAAK linker. The final vaccine construct, comprising 344 amino acids, was achieved after the addition of adjuvants and linkers. This multi-epitope Vaccine demonstrates notable antigenicity and possesses favorable physiochemical characteristics. The three-dimensional conformation underwent modeling and refinement, validated through in-silico methods. Additionally, a protein-protein molecular docking analysis was conducted to predict effective binding poses between the multi-epitope Vaccine and the Toll-like receptor 4 protein. The Molecular Dynamics (MD) investigation of the docked TLR4-vaccine complex demonstrated consistent stability over the simulation period, primarily attributed to electrostatic energy. The docked complex displayed minimal deformation and enhanced rigidity in the motion of residues during the dynamic simulation. Furthermore, codon translational optimization and computational cloning was performed to ensure the reliability and proper expression of the multi-Epitope Vaccine. It is crucial to emphasize that despite these computational validations, experimental research in the laboratory is imperative to demonstrate the immunogenicity and protective efficacy of the developed vaccine. This would involve practical assessments to ascertain the real-world effectiveness of the multi-epitope Vaccine.
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Affiliation(s)
- Sana Abdul Ghaffar
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Haneen Tahir
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sher Muhammad
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Tahir Naqqash
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Thamer H. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Irfan Manzoor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- Department of Biology, Indiana University, Bloomington, IN, United States
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15
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Ponne S, Kumar R, Vanmathi SM, Brilhante RSN, Kumar CR. Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens. Vaccine 2024; 42:2503-2518. [PMID: 38523003 DOI: 10.1016/j.vaccine.2024.02.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Vaccines have significantly reduced the impact of numerous deadly viral infections. However, there is an increasing need to expedite vaccine development in light of the recurrent pandemics and epidemics. Also, identifying vaccines against certain viruses is challenging due to various factors, notably the inability to culture certain viruses in cell cultures and the wide-ranging diversity of MHC profiles in humans. Fortunately, reverse vaccinology (RV) efficiently overcomes these limitations and has simplified the identification of epitopes from antigenic proteins across the entire proteome, streamlining the vaccine development process. Furthermore, it enables the creation of multiepitope vaccines that can effectively account for the variations in MHC profiles within the human population. The RV approach offers numerous advantages in developing precise and effective vaccines against viral pathogens, including extensive proteome coverage, accurate epitope identification, cross-protection capabilities, and MHC compatibility. With the introduction of RV, there is a growing emphasis among researchers on creating multiepitope-based vaccines aiming to stimulate the host's immune responses against multiple serotypes, as opposed to single-component monovalent alternatives. Regardless of how promising the RV-based vaccine candidates may appear, they must undergo experimental validation to probe their protection efficacy for real-world applications. The time, effort, and resources allocated to the laborious epitope identification process can now be redirected toward validating vaccine candidates identified through the RV approach. However, to overcome failures in the RV-based approach, efforts must be made to incorporate immunological principles and consider targeting the epitope regions involved in disease pathogenesis, immune responses, and neutralizing antibody maturation. Integrating multi-omics and incorporating artificial intelligence and machine learning-based tools and techniques in RV would increase the chances of developing an effective vaccine. This review thoroughly explains the RV approach, ideal RV-based vaccine construct components, RV-based vaccines designed to combat viral pathogens, its challenges, and future perspectives.
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Affiliation(s)
- Saravanaraman Ponne
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (Deemed to be University), Kirumampakkam, Puducherry 607402, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 106 91, Sweden
| | - S M Vanmathi
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India
| | - Raimunda Sâmia Nogueira Brilhante
- Medical Mycology Specialized Center, Department of Pathology and Legal Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Chinnadurai Raj Kumar
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India.
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de Araújo LP, de Melo Santos NC, Corsetti PP, de Almeida LA. Immunoinformatic Approach for Rational Identification of Immunogenic Peptides Against Host Entry and/or Exit Mpox Proteins and Potential Multiepitope Vaccine Construction. J Infect Dis 2024; 229:S285-S292. [PMID: 37804521 DOI: 10.1093/infdis/jiad443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/27/2023] [Accepted: 10/03/2023] [Indexed: 10/09/2023] Open
Abstract
COVID-19 has intensified humanity's concern about the emergence of new pandemics. Since 2018, epidemic outbreaks of the mpox virus have become worrisome. In June 2022, the World Health Organization declared the disease a global health emergency, with 14 500 cases reported by the Centers for Disease Control and Prevention in 60 countries. Therefore, the development of a vaccine based on the current virus genome is paramount in combating new cases. In view of this, we hypothesized the obtainment of rational immunogenic peptides predicted from proteins responsible for entry of the mpox virus into the host (A17L, A26L/A30L, A33R, H2R, L1R), exit (A27L, A35R, A36R, C19L), and both (B5R). To achieve this, we aligned the genome sequencing data of mpox virus isolated from an infected individual in the United States in June 2022 (ON674051.1) with the reference genome dated 2001 (NC_003310.1) for conservation analysis. The Immune Epitope Database server was used for the identification and characterization of the epitopes of each protein related to major histocompatibility complex I or II interaction and recognition by B-cell receptors, resulting in 138 epitopes for A17L, 233 for A28L, 48 for A33R, 77 for H2R, 77 for L1R, 270 for A27L, 72 for A35R, A36R, 148 for C19L, and 276 for B5R. These epitopes were tested in silico for antigenicity, physicochemical properties, and allergenicity, resulting in 51, 40, 10, 34, 38, 57, 25, 7, 47, and 53 epitopes, respectively. Additionally, to select an epitope with the highest promiscuity of binding to major histocompatibility complexes and B-cell receptor simultaneously, all epitopes of each protein were aligned, and the most repetitive and antigenic regions were identified. By classifying the results, we obtained 23 epitopes from the entry proteins, 16 from the exit proteins, and 7 from both. Subsequently, 1 epitope from each protein was selected, and all 3 were fused to construct a chimeric protein that has potential as a multiepitope vaccine. The constructed vaccine was then analyzed for its physicochemical, antigenic, and allergenic properties. Protein modeling, molecular dynamics, and molecular docking were performed on Toll-like receptors 2, 4, and 8, followed by in silico immune simulation of the vaccine. Finally, the results indicate an effective, stable, and safe vaccine that can be further tested, especially in vitro and in vivo, to validate the findings demonstrated in silico.
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Affiliation(s)
| | | | - Patrícia Paiva Corsetti
- Departamento de Microbiologia e Imunologia, Universidade Federal de Alfenas, Alfenas, Brazil
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Izadi M, Mirzaei F, Bagherzadeh MA, Ghiabi S, Khalifeh A. Discovering conserved epitopes of Monkeypox: Novel immunoinformatic and machine learning approaches. Heliyon 2024; 10:e24972. [PMID: 38318007 PMCID: PMC10839993 DOI: 10.1016/j.heliyon.2024.e24972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 02/07/2024] Open
Abstract
The Monkeypox virus, an Orthopoxvirus with zoonotic origins, has been responsible for a growing number of human infections reminiscent of smallpox since May 2022, as reported by the World Health Organization. As of now, there are no established medical treatments for managing Monkeypox infections. In this study, we used machine learning to select conserved epitopes. Proteins were determined using Reverse Vaccinology and Gene Ontology subcellular localization, and their epitopes were predicted. NextClade was used to calculate the number of mutations in each amino acid position using 2433 Monkeypox sequences. The Unsupervised Nearest Neighbor machine learning algorithm and ideal matrix [0 0] were used to calculate the conservancy score of epitopes. Six proteins were determined for epitope prediction. Finally, 47 MHC-I epitopes, 5 MHC-II epitopes, and 10 Linear B cell epitopes were discovered. Our method can select epitopes for vaccine design to prevent viruses with accelerated evolution and high mutation rate.
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Affiliation(s)
- Mohammad Izadi
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Mirzaei
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Shamim Ghiabi
- Department of Medical Chemistry, Faculty of Pharmacy, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alireza Khalifeh
- Department of Pathology, Faculty of Dentistry, Shiraz Branch, Islamic Azad of University, Shiraz, Iran
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Dhanushkumar T, Selvam PK, M E S, Vasudevan K, C GPD, Zayed H, Kamaraj B. Rational design of a multivalent vaccine targeting arthropod-borne viruses using reverse vaccinology strategies. Int J Biol Macromol 2024; 258:128753. [PMID: 38104690 DOI: 10.1016/j.ijbiomac.2023.128753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 11/17/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Viruses transmitted by arthropods, such as Dengue, Zika, and Chikungunya, represent substantial worldwide health threats, particularly in countries like India. The lack of approved vaccines and effective antiviral therapies calls for developing innovative strategies to tackle these arboviruses. In this study, we employed immunoinformatics methodologies, incorporating reverse vaccinology, to design a multivalent vaccine targeting the predominant arboviruses. Epitopes of B and T cells were recognized within the non-structural proteins of Dengue, Zika, and Chikungunya viruses. The predicted epitopes were enhanced with adjuvants β-defensin and RS-09 to boost the vaccine's immunogenicity. Sixteen distinct vaccine candidates were constructed, each incorporating epitopes from all three viruses. FUVAC-11 emerged as the most promising vaccine candidate through molecular docking and molecular dynamics simulations, demonstrating favorable binding interactions and stability. Its effectiveness was further evaluated using computational immunological studies confirming strong immune responses. The in silico cloning performed using the pET-28a(+) plasmid facilitates the future experimental implementation of this vaccine candidate, paving the way for potential advancements in combating these significant arboviral threats. However, further in vitro and in vivo studies are warranted to confirm the results obtained in this computational study, which highlights the effectiveness of immunoinformatics and reverse vaccinology in creating vaccines against major Arboviruses, offering a promising model for developing vaccines for other vector-borne diseases and enhancing global health security.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Prasanna Kumar Selvam
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Santhosh M E
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
| | - Hatem Zayed
- Department of Biomedical Sciences College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Balu Kamaraj
- Department of Dental Education, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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Albutti A. An integrated multi-pronged reverse vaccinology and biophysical approaches for identification of potential vaccine candidates against Nipah virus. Saudi Pharm J 2023; 31:101826. [PMID: 38028215 PMCID: PMC10651679 DOI: 10.1016/j.jsps.2023.101826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Nipah virus, a paramyxovirus linked to Hendra virus that first appeared in Malaysia and is the etiological agent of viral lethal encephalitis, has emerged as a strong threat to the health community in recent decades. Viral infections are seriously affecting global health. Since there are now no efficient therapeutic options, it will take considerable effort to develop appropriate therapeutic management for the Nipah virus. The main purpose of this study was to design a messenger RNA-based multi-epitope vaccine construct against Nipah virus. This purpose was achieved through multiple immunogenic epitopes prediction using Nipah virus antigenic protein using the immune epitope database and analysis resource (IEDB) followed by the vaccine construction and processing. As in multi-epitopes vaccine construction we selected immunogenic potential fragments of viral proteins, therefore in host immune stimulation we observed proper immune responses toward a multi-epitopes vaccine. In this study, the Nipah virus V protein was used to identify immunodominant epitopes utilizing several reverse vaccinology, immunoinformatics and biophysical methods. The potential antigenic predicted epitopes were further analyzed for immunoinformatics analysis and only selected probable antigenic and non-toxic epitopes were used in designing a multi-epitope mRNA based in silico vaccine against the target pathogen. In vaccine designing a total number of 03B cell epitopes, 09 Cytotoxic T lymphocytes (CTLs) and 01 Helper T lymphocytes (HTL) were prioritized as a good vaccine candidate. In the vaccine construction phase, the selected epitopes were linked together using EAAAK, GPGPG, KK, and AAY linkers, and B-defensin (adjuvant), and MITD sequences were also added to the vaccine construct to increase the potency. After vaccine construction, the physiochemical properties of the vaccine construct were evaluated which predicted that the vaccine construct comprises 320 amino acids with 34.29 kDa (kDa) molecular weight. The instability index was 36.55 proving its stability with the aliphatic index of 82.88. Furthermore, 9.0 theoretical pI and -0.317, GRAVY (Grand Average of Hydropathy) values were predicted in physicochemical properties analysis. A solubility check was applied against the vaccine construct depicting that the vaccine construct is soluble with its calculated value of 0.6. Additionally, after prediction the 3D structure was modeled and refined for docking analysis, the refined 3D structure of the vaccine candidate was further checked for binding affinity with immune cell receptors through docking analysis, in the docking analysis we observed that the vaccine construct has a good binding affinity with immune cells receptor and can induce a proper immune response in host cells. As we predicted effective binding of the designed vaccine construct, hence it can further facilitate the development of vaccine formulation against the Nipah virus. Additionally, molecular dynamic simulation was done using the AMBER v20 package for analysis of the dynamic behaviour of the docked complexes and we observed proper binding stability of the vaccine with target receptor. In C-immune simulation, different humoral and cellular antibody titer was observed in response to the vaccine. Overall using bioinformatics, immunoinformatics, and biophysical approaches we observed that this mRNA base epitopes vaccine construct could facilitate the proof of concept for the formation of the experimental base vaccine against the Nipah virus, as the in silico predictions indicated that the vaccine is highly promising in terms of developing protective immunity. However experimental validation is required to disclose the real immune-protective efficacy of the vaccine.
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Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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20
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Ullah A, Rehman B, Khan S, Almanaa TN, Waheed Y, Hassan M, Naz T, Ul Haq M, Muhammad R, Sanami S, Irfan M, Ahmad S. An In Silico Multi-epitopes Vaccine Ensemble and Characterization Against Nosocomial Proteus penneri. Mol Biotechnol 2023:10.1007/s12033-023-00949-y. [PMID: 37934390 DOI: 10.1007/s12033-023-00949-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Proteus penneri (P. penneri) is a bacillus-shaped, gram-negative, facultative anaerobe bacterium that is primarily an invasive pathogen and the etiological agent of several hospital-associated infections. P. penneri strains are naturally resistant to macrolides, amoxicillin, oxacillin, penicillin G, and cephalosporins; in addition, no vaccines are available against these strains. This warrants efforts to propose a theoretical based multi-epitope vaccine construct to prevent pathogen infections. In this research, reverse vaccinology bioinformatics and immunoinformatics approaches were adopted for vaccine target identification and construction of a multi-epitope vaccine. In the first phase, a core proteome dataset of the targeted pathogen was obtained using the NCBI database and subjected to bacterial pan-genome analysis using bacterial pan-genome analysis (BPGA) to predict core protein sequences which were then used to find good vaccine target candidates. This identified two proteins, Hcp family type VI secretion system effector and superoxide dismutase family protein, as promising vaccine targets. Afterward using the IEDB database, different B-cell and T-cell epitopes were predicted. A set of four epitopes "KGSVNVQDRE, NTGKLTGTR, IIHSDSWNER, and KDGKPVPALK" were chosen for the development of a multi-epitope vaccine construct. A 183 amino acid long vaccine design was built along with "EAAAK" and "GPGPG" linkers and a cholera toxin B-subunit adjuvant. The designed vaccine model comprised immunodominant, non-toxic, non-allergenic, and physicochemical stable epitopes. The model vaccine was docked with MHC-I, MHC-II, and TLR-4 immune cell receptors using the Cluspro2.0 web server. The binding energy score of the vaccine was - 654.7 kcal/mol for MHC-I, - 738.4 kcal/mol for MHC-II, and - 695.0 kcal/mol for TLR-4. A molecular dynamic simulation was done using AMBER v20 package for dynamic behavior in nanoseconds. Additionally, MM-PBSA binding free energy analysis was done to test intermolecular binding interactions between docked molecules. The MM-GBSA net binding energy score was - 148.00 kcal/mol, - 118.00 kcal/mol, and - 127.00 kcal/mol for vaccine with TLR-4, MHC-I, and MHC-II, respectively. Overall, these in silico-based predictions indicated that the vaccine is highly promising in terms of developing protective immunity against P. penneri. However, additional experimental validation is required to unveil the real immune response to the designed vaccine.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 2500, Pakistan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Bushra Rehman
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, 44000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, 1401, Lebanon
| | - Muhammad Hassan
- Department of Pharmacy, Bacha Khan University, Charsadda, 24461, Pakistan
| | - Tahira Naz
- Department of Chemical and Life Sciences, Qurtuba University of Science and Technology, Peshawar, Pakistan
| | - Mehboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, 25000, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 2500, Pakistan
| | - Samira Sanami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32611, USA
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 2500, Pakistan.
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Beirut, Lebanon.
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Sarfraz A, Wara TU, Sheheryar, Chen K, Ansari SH, Zaman A, Nishan U, Iqbal A, Ullah R, Ali EA, Shah M, Ojha SC. Structural informatics approach for designing an epitope-based vaccine against the brain-eating Naegleria fowleri. Front Immunol 2023; 14:1284621. [PMID: 37965306 PMCID: PMC10642955 DOI: 10.3389/fimmu.2023.1284621] [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: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Primary Amoebic Meningoencephalitis (PAM), a severe lethal brain disease, is caused by a parasite, Naegleria fowleri, also known as the "brain-eating amoeba". The chances of a patient's recovery after being affected by this parasite are very low. Only 5% of people are known to survive this life-threatening infection. Despite the fact that N. fowleri causes a severe, fatal infection, there is no proper treatment available to prevent or cure it. In this context, it is necessary to formulate a potential vaccine that could be able to combat N. fowleri infection. The current study aimed at developing a multi-epitope subunit vaccine against N. fowleri by utilizing immunoinformatics techniques and reverse vaccinology approaches. The T- and B-cell epitopes were predicted by various tools. In order to choose epitopes with the ability to trigger both T- and B-cell-mediated immune responses, the epitopes were put through a screening pipeline including toxicity, antigenicity, cytokine-inductivity, and allergenicity analysis. Three vaccine constructs were designed from the generated epitopes linked with linkers and adjuvants. The modeled vaccines were docked with the immune receptors, where vaccine-1 showed the highest binding affinity. Binding affinity and stability of the docked complex were confirmed through normal mode analysis and molecular dynamic simulations. Immune simulations developed the immune profile, and in silico cloning affirmed the expression probability of the vaccine construct in Escherichia coli (E. coli) strain K12. This study demonstrates an innovative preventative strategy for the brain-eating amoeba by developing a potential vaccine through immunoinformatics and reverse vaccinology approaches. This study has great preventive potential for Primary Amoebic Meningoencephalitis, and further research is required to assess the efficacy of the designed vaccine.
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Affiliation(s)
- Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Tehreem Ul Wara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Sheheryar
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | | | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Anwar Iqbal
- Department of Chemical Sciences, University of Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Campos-Ruíz MA, Illades-Aguiar B, Del Moral-Hernández O, Romo-Castillo M, Salazar-García M, Espinoza-Rojo M, Vences-Velázquez A, Cortés-Sarabia K, Luna-Pineda VM. Immunized mice naturally process in silico-derived peptides from the nucleocapsid of SARS-CoV-2. BMC Microbiol 2023; 23:319. [PMID: 37898784 PMCID: PMC10612231 DOI: 10.1186/s12866-023-03076-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 10/18/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is an excellent immunogen that promotes the production of high-titer antibodies. N protein-derived peptides identified using a bioinformatics approach can potentially be used to develop a new generation of vaccines or diagnostic methods for detecting SARS-CoV-2 and its variants. However, further studies must demonstrate their capacity to be naturally processed by the immune system. OBJECTIVE We aimed to examine the in vivo processing and recognition of in silico-identified peptides using the serum of immunized animals with the complete protein. METHODS Recombinant N (Nrec) protein was subcutaneously administered to six Balb/c mice. Enzyme-linked immunosorbent assay (ELISA), western blotting, dot blotting, and immunoprecipitation were performed to evaluate the recognition of the complete protein and in silico-derived peptides. RESULTS The serum of immunized mice recognized ~ 62.5 ng/µL of Nrec with high specificity to linear and conformational epitopes. Dot blot analysis showed that peptides Npep2 and Npep3 were the most reactive. CONCLUSION Our data confirm the high immunogenicity of the SARS-CoV-2 N protein and provide evidence on the antigenicity of two peptides located in the N-arm/RNA-binding domain (Npep2) and oligomerization domain/C-tail (Npep3), considered the biologically active site of the N protein.
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Affiliation(s)
- Mario Aldair Campos-Ruíz
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Berenice Illades-Aguiar
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Oscar Del Moral-Hernández
- Laboratorio de Virología, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Mariana Romo-Castillo
- Laboratorio de Investigación en COVID-19, Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Ciudad de México, México
- Programa Investigadoras e Investigadores por México, Consejo Nacional de Humanidades, Ciencias y Tecnologías, Ciudad de México, México
| | - Marcela Salazar-García
- Laboratorio de Biología del Desarrollo y Teratogénesis Experimental, Hospital Infantil de México Federico Gómez, Ciudad de México, México
| | - Mónica Espinoza-Rojo
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Amalia Vences-Velázquez
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México
| | - Karen Cortés-Sarabia
- Laboratorio de Inmunobiología y Diagnóstico Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Guerrero, México.
| | - Victor M Luna-Pineda
- Laboratorio de Investigación en COVID-19, Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Ciudad de México, México.
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23
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Andrei G, Snoeck R. Differences in pathogenicity among the mpox virus clades: impact on drug discovery and vaccine development. Trends Pharmacol Sci 2023; 44:719-739. [PMID: 37673695 DOI: 10.1016/j.tips.2023.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/11/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023]
Abstract
Since May 2022, mpox virus (MPXV) has attracted considerable attention due to a multi-country outbreak. Marked differences in epidemiology, transmission, and pathology between the 2022 global mpox outbreak (clade IIb) and classical mpox disease, endemic in Africa (clades I and IIa) have been highlighted. MPXV genome analysis has identified the genomic changes characterizing clade IIb and the drivers of MPXV rapid evolution. Although mpox cases have largely declined, MPXV cryptic transmission and microevolution continues, which may lead to an MPXV of unpredictable pathogenicity. Vaccines and antivirals developed against variola virus, the agent that caused the extinguished plague smallpox, have been used to contain the 2022 mpox outbreak. In this review article, recent findings on MPXV origin and evolution and relevant models able to recapitulate differences in MPXV pathogenicity, which are important for drug and vaccine development, are discussed.
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Affiliation(s)
- Graciela Andrei
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
| | - Robert Snoeck
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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Farzan M, Farzan M, Mirzaei Y, Aiman S, Azadegan-Dehkordi F, Bagheri N. Immunoinformatics-based multi-epitope vaccine design for the re-emerging monkeypox virus. Int Immunopharmacol 2023; 123:110725. [PMID: 37556996 DOI: 10.1016/j.intimp.2023.110725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND On May 7, 2022, WHO reported a new monkeypox case. By May 2023 over 80,000 cases had been reported worldwide outside previously endemic nations. (This primarily affected the men who have sex with men (MSM) community in rich nations). The present research aims to develop a multi-epitope vaccine for the monkeypox virus (MPXV) using structural and cell surface proteins. METHODS The first part of the research involved retrieving protein sequences. The Immune Epitope Database (IEDB) was then used to analyze the B and T lymphocyte epitopes. After analyzing the sensitizing properties, toxicity, antigenicity, and molecular binding, appropriate linkers were utilizedto connect selected epitopes to adjuvants, and the structure of the vaccine was formulated. Algorithms from the field of immunoinformatics predicted the secondary and tertiary structures of vaccines. The physical, chemical, and structural properties were refined and validated to achieve maximum stability. Molecular docking and molecular dynamic simulations were subsequently employed to assess the vaccine's efficacy. Afterward, the ability of the vaccine to interact with toll-like receptors 3 and 4 (TLR3 and TLR4) was evaluated. Finally, the optimized sequence was then introduced into the Escherichia coli (E. coli) PET30A + vector. RESULTS An immunoinformatics evaluation suggested that such a vaccine might be safe revealed that this vaccine is safe, hydrophilic, temperature- and condition-stable, and can stimulate innate immunity by binding to TLR3 and TLR4. CONCLUSION Our findings suggest that the first step in MPXV pathogenesis is structural and cell surface epitopes. In this study, the most effective and promising epitopes were selected and designed throughprecision servers. Furthermore,through the utilization of multi-epitope structures and a combination of two established adjuvants, this research has the potential to be a landmarkin developing an antiviralvaccine against MPXV. However, additional in vitro and in vivo tests are required to confirm these results.
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Affiliation(s)
- Mahour Farzan
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mahan Farzan
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Yousef Mirzaei
- Department of Medical Biochemical Analysis, Cihan University-Erbil, Kurdistan Region, Iraq
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fatemeh Azadegan-Dehkordi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Nader Bagheri
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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25
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Alarifi AM, Alshahrani NZ, Sah R. Are Saudi Healthcare Workers Willing to Receive the Monkeypox Virus Vaccine? Evidence from a Descriptive-Baseline Survey. Trop Med Infect Dis 2023; 8:396. [PMID: 37624334 PMCID: PMC10459197 DOI: 10.3390/tropicalmed8080396] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023] Open
Abstract
Since Saudi Arabia has already confirmed multiple monkeypox (Mpox) cases, it is essential to initiate timely preventive measures, including the implementation of vaccines. In this cross-sectional study, an online survey was conducted among healthcare workers (HCWs) in Saudi Arabia to understand their willingness to receive the Mpox vaccine. A structured questionnaire was used to gather the data. The study comprised 734 samples. Our study found that among study participants, 52.7% were willing to receive the Mpox vaccine and showed that sociodemographic factors were not significantly associated with vaccine willingness. Previous vaccination history (such as influenza and COVID-19) was significantly associated with Mpox vaccine willingness. The respondents reported that the main reasons for receiving the Mpox vaccine were their trust in the Saudi Health Ministry (57.7%) and their understanding that the vaccine was a social responsibility (44.6%). Furthermore, the majority of the respondents (74.7%) reported that they were motivated by the need to protect themselves, their family and their friends. Insufficient vaccine information and fear of unknown adverse reactions were the most reported reasons for an unwillingness to receive the Mpox vaccine. In conclusion, increasing Mpox vaccine-related awareness and focusing on greater information dissemination to reduce fear and increase vaccine uptake is highly recommended.
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Affiliation(s)
- Abdullah M. Alarifi
- Department of Public Health, College of Health Sciences, Saudi Electronic University, Riyadh 13323, Saudi Arabia
| | - Najim Z. Alshahrani
- Department of Family and Community Medicine, Faculty of Medicine, University of Jeddah, Jeddah 21589, Saudi Arabia
| | - Ranjit Sah
- Department of Microbiology, Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu 44600, Nepal
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune 411018, India
- Department of Public Health Dentistry, Dr. D.Y. Patil Dental College and Hospital, Dr. D.Y. Patil Vidyapeeth, Pune 411018, India
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