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Zhu L, Cui X, Yan Z, Tao Y, Shi L, Zhang X, Yao Y, Shi L. Design and evaluation of a multi-epitope DNA vaccine against HPV16. Hum Vaccin Immunother 2024; 20:2352908. [PMID: 38780076 PMCID: PMC11123455 DOI: 10.1080/21645515.2024.2352908] [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: 02/29/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024] Open
Abstract
Cervical cancer, among the deadliest cancers affecting women globally, primarily arises from persistent infection with high-risk human papillomavirus (HPV). To effectively combat persistent infection and prevent the progression of precancerous lesions into malignancy, a therapeutic HPV vaccine is under development. This study utilized an immunoinformatics approach to predict epitopes of cytotoxic T lymphocytes (CTLs) and helper T lymphocytes (HTLs) using the E6 and E7 oncoproteins of the HPV16 strain as target antigens. Subsequently, through meticulous selection of T-cell epitopes and other necessary elements, a multi-epitope vaccine was constructed, exhibiting good immunogenic, physicochemical, and structural characteristics. Furthermore, in silico simulations showed that the vaccine not only interacted well with toll-like receptors (TLR2/TLR3/TLR4), but also induced a strong innate and adaptive immune response characterized by elevated Th1-type cytokines, such as interferon-gamma (IFN-γ) and interleukin-2 (IL2). Additionally, our study investigated the effects of different immunization intervals on immune responses, aiming to optimize a time-efficient immunization program. In animal model experiments, the vaccine exhibited robust immunogenic, therapeutic, and prophylactic effects. Administered thrice, it consistently induced the expansion of specific CD4 and CD8 T cells, resulting in substantial cytokines release and increased proliferation of memory T cell subsets in splenic cells. Overall, our findings support the potential of this multi-epitope vaccine in combating HPV16 infection and signify its candidacy for future HPV vaccine development.
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Affiliation(s)
- Lanfang Zhu
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xiangjie Cui
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Zhiling Yan
- Department of Gynaecologic Oncology, The No. 3 Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yufen Tao
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Lei Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Xinwen Zhang
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Yufeng Yao
- Yunnan Key Laboratory of Vaccine Research & Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
| | - Li Shi
- Department of Immunogenetics, Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Kunming, China
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2
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Tan C, xiao Y, Liu T, Chen S, Zhou J, Zhang S, Hu Y, Wu A, Li C. Development of multi-epitope mRNA vaccine against Clostridioides difficile using reverse vaccinology and immunoinformatics approaches. Synth Syst Biotechnol 2024; 9:667-683. [PMID: 38817826 PMCID: PMC11137598 DOI: 10.1016/j.synbio.2024.05.008] [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: 01/08/2024] [Revised: 04/28/2024] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Clostridioides difficile (C. difficile), as the major pathogen of diarrhea in healthcare settings, has become increasingly prevalent within community populations, resulting in significant morbidity and mortality. However, the therapeutic options for Clostridioides difficile infection (CDI) remain limited, and as of now, no authorized vaccine is available to combat this disease. Therefore, the development of a novel vaccine against C. difficile is of paramount importance. In our study, the complete proteome sequences of 118 strains of C. difficile were downloaded and analyzed. We found four antigenic proteins that were highly conserved and can be used for epitope identification. We designed two vaccines, WLcd1 and WLcd2, that contain the ideal T-cell and B-cell epitopes, adjuvants, and the pan HLA DR-binding epitope (PADRE) sequences. The biophysical and chemical assessments of these vaccine candidates indicated that they were suitable for immunogenic applications. Molecular docking analyses revealed that WLcd1 bonded with higher affinity to Toll-like receptors (TLRs) than WLcd2. Furthermore, molecular dynamics (MD) simulations, performed using Gmx_MMPBSA v1.56, confirmed the binding stability of WLcd1 with TLR2 and TLR4. The preliminary findings suggested that this multi-epitope vaccine could be a promising candidate for protection against CDI; however, experimental studies are necessary to confirm these predictions.
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Affiliation(s)
- Caixia Tan
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yuanyuan xiao
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Ting Liu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Siyao Chen
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Juan Zhou
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Sisi Zhang
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Yiran Hu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital, Central South University, Changsha, Hunan Province, 410008, China
- National Clinical Research Center for Geriatric Disorders (XiangYa Hospital), Changsha, Hunan Province, 410008, China
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3
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Nguyen TL, Kim H. Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis. Synth Syst Biotechnol 2024; 9:391-405. [PMID: 38585591 PMCID: PMC10997871 DOI: 10.1016/j.synbio.2024.03.010] [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: 01/31/2024] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 04/09/2024] Open
Abstract
Mycobacterium tuberculosis (MTB) is the causative agent of tuberculosis (TB), a prevalent airborne infectious disease. Despite the availability of the Bacille Calmette-Guerin vaccine, its global efficacy remains modest, and tuberculosis persists as a significant global public health threat. Addressing this challenge and advancing towards the End MTB Strategy, we developed a multiepitope vaccine (MEV) based on immunoinformatics and computational approaches. Immunoinformatics screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex (MHC) allele binding, immunogenicity, antigenicity, allergenicity, toxicity, and cytokine inducibility. Selected epitopes were integrated into an MEV construct with adjuvant and linkers, forming a fully immunogenic vaccine candidate. Comprehensive analyses encompassed the evaluation of immunological and physicochemical properties, determination of tertiary structure, molecular docking with Toll-Like Receptors (TLR), molecular dynamics (MD) simulations for all atoms, and immune simulations. Our MEV comprises 534 amino acids, featuring 6 cytotoxic T lymphocyte, 8 helper T lymphocyte, and 7 linear B lymphocyte epitopes, demonstrating high antigenicity and stability. Notably, molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to TLR2. In addition, the immune simulation indicated the capacity to effectively induce elevated levels of antibodies and cytokines, emphasizing the vaccine's robust immunogenic response. This study presents a promising MEV against TB, exhibiting favorable immunological and physicochemical attributes. The findings provide theoretical support for TB vaccine development. Our study aligns with the global initiative of the End MTB Strategy, emphasizing its potential impact on addressing persistent challenges in TB control.
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Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- eGnome, Inc., Seoul, 05836, Republic of Korea
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4
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Nguyen TL, Kim H. Integrating immunoinformatics and computational epitope prediction for a vaccine candidate against respiratory syncytial virus. Infect Dis Model 2024; 9:763-774. [PMID: 38708060 PMCID: PMC11068479 DOI: 10.1016/j.idm.2024.04.005] [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: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024] Open
Abstract
Respiratory syncytial virus (RSV) poses a significant global health threat, especially affecting infants and the elderly. Addressing this, the present study proposes an innovative approach to vaccine design, utilizing immunoinformatics and computational strategies. We analyzed RSV's structural proteins across both subtypes A and B, identifying potential helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes. Criteria such as antigenicity, allergenicity, toxicity, and cytokine-inducing potential were rigorously examined. Additionally, we evaluated the conservancy of these epitopes and their population coverage across various RSV strains. The comprehensive analysis identified six major histocompatibility complex class I (MHC-I) binding, five MHC-II binding, and three B-cell epitopes. These were integrated with suitable linkers and adjuvants to form the vaccine. Further, molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors (TLR4 and TLR5), with a notable preference for TLR4. Immune simulation analysis underscored the vaccine's potential to elicit a strong immune response. This study presents a promising RSV vaccine candidate and offers theoretical support, marking a significant advancement in vaccine development efforts. However, the promising in silico findings need to be further validated through additional in vivo studies.
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Affiliation(s)
- Truc Ly Nguyen
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- eGnome, Inc., Seoul, 05836, Republic of Korea
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5
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Mursaleen S, Sarfraz A, Shehroz M, Zaman A, Rahman FU, Moura AA, Sheheryar S, Aziz S, Ullah R, Iqbal Z, Nishan U, Shah M, Sun W. Genome-level therapeutic targets identification and chimeric Vaccine designing against the Blastomyces dermatitidis. Heliyon 2024; 10:e36153. [PMID: 39224264 PMCID: PMC11367477 DOI: 10.1016/j.heliyon.2024.e36153] [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: 08/05/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024] Open
Abstract
Blastomyces dermatitidis is a thermally dimorphic fungus that can cause serious and sometimes fatal infections, including blastomycosis. After spore inhalation, a pulmonary infection develops, which can be asymptomatic and have lethal effects, such as acute respiratory distress syndrome. Its most common extra-pulmonary sites are the central nervous system, bones, skin, and genito-urinary systems. Currently, no vaccine has been approved by the FDA to prevent this infection. In the study, a peptide-based vaccine was developed against blastomycosis by using subtractive proteomics and reverse vaccinology approaches. It focuses on mining the whole genome of B. dermatitidis, identifying potential therapeutic targets, and pinpointing potential epitopes for both B- and T-cells that are immunogenic, non-allergenic, non-toxic, and highly antigenic. Multi-epitope constructs were generated by incorporating appropriate linker sequences. A linker (EAAAK) was also added to incorporate an adjuvant sequence to increase immunological potential. The addition of adjuvants and linkers ultimately resulted in the formation of a vaccine construct in which the number of amino acids was 243 and the molecular weight was 26.18 kDa. The designed antigenic and non-allergenic vaccine constructs showed suitable physicochemical properties. The vaccine's structures were predicted, and further analysis verified their interactions with the human TLR-4 receptor through protein-protein docking. Additionally, MD simulation showed a potent interaction between prioritized vaccine-receptor complexes. Immune simulation predicted that the final vaccine injections resulted in significant immune responses for the T- and B-cell immune responses. Moreover, in silico cloning ensured a high expression possibility of the lead vaccine in the E. coli (K12) vector. This study offers an initiative for the development of effective vaccines against B. dermatitidis; however, it is necessary to validate the designed vaccine's immunogenicity experimentally.
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Affiliation(s)
- Sawvara Mursaleen
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree-47150, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Faiz U Rahman
- Department of Zoology, Shangla Campus, University of Swat, Khyber Pakhtunkhwa, Pakistan
| | - Arlindo A. Moura
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | - Sheheryar Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | - Shahid Aziz
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza 60451-970, Brazil
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University Riyadh Saudi Arabia, Kingdom of Saudi Arabia
| | - Zafar Iqbal
- Department of Surgery, College of Medicine, King Saud University P.O. Box 7805, Riyadh, 11472, Kingdom of Saudi Arabia
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan-66000, Pakistan
| | - Wenwen Sun
- Department of Intensive Care Unit, Changzhou Maternity and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, 213004, China
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6
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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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7
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Cieri N, Hookeri N, Stromhaug K, Li L, Keating J, Díaz-Fernández P, Gómez-García de Soria V, Stevens J, Kfuri-Rubens R, Shao Y, Kooshesh KA, Powell K, Ji H, Hernandez GM, Abelin J, Klaeger S, Forman C, Clauser KR, Sarkizova S, Braun DA, Penter L, Kim HT, Lane WJ, Oliveira G, Kean LS, Li S, Livak KJ, Carr SA, Keskin DB, Muñoz-Calleja C, Ho VT, Ritz J, Soiffer RJ, Neuberg D, Stewart C, Getz G, Wu CJ. Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation. Nat Biotechnol 2024:10.1038/s41587-024-02348-3. [PMID: 39169264 DOI: 10.1038/s41587-024-02348-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/02/2024] [Indexed: 08/23/2024]
Abstract
T cell alloreactivity against minor histocompatibility antigens (mHAgs)-polymorphic peptides resulting from donor-recipient (D-R) disparity at sites of genetic polymorphisms-is at the core of the therapeutic effect of allogeneic hematopoietic cell transplantation (allo-HCT). Despite the crucial role of mHAgs in graft-versus-leukemia (GvL) and graft-versus-host disease (GvHD) reactions, it remains challenging to consistently link patient-specific mHAg repertoires to clinical outcomes. Here we devise an analytic framework to systematically identify mHAgs, including their detection on HLA class I ligandomes and functional verification of their immunogenicity. The method relies on the integration of polymorphism detection by whole-exome sequencing of germline DNA from D-R pairs with organ-specific transcriptional- and proteome-level expression. Application of this pipeline to 220 HLA-matched allo-HCT D-R pairs demonstrated that total and organ-specific mHAg load could independently predict the occurrence of acute GvHD and chronic pulmonary GvHD, respectively, and defined promising GvL targets, confirmed in a validation cohort of 58 D-R pairs, for the prevention or treatment of post-transplant disease recurrence.
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Affiliation(s)
- Nicoletta Cieri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Nidhi Hookeri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kari Stromhaug
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Liang Li
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Julia Keating
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paula Díaz-Fernández
- Department of Immunology, Instituto de Investigación Sanitaria Princesa (IIS-IP), Hospital Universitario de La Princesa, Madrid, Spain
| | - Valle Gómez-García de Soria
- Department of Hematology, Instituto de Investigación Sanitaria Princesa (IIS-IP), Hospital Universitario de La Princesa, Madrid, Spain
| | - Jonathan Stevens
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Raphael Kfuri-Rubens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Yiren Shao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Kaila Powell
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Helen Ji
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gabrielle M Hernandez
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Jennifer Abelin
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Susan Klaeger
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Proteomic and Genomic Technologies, Genentech Inc, South San Francisco, CA, USA
| | - Cleo Forman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Siranush Sarkizova
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - David A Braun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Hematology, Oncology, and Tumorimmunology, Campus Virchow Klinikum, Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Haesook T Kim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William J Lane
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Leslie S Kean
- Harvard Medical School, Boston, MA, USA
- Division Hematology/Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA
| | - Shuqiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth J Livak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Derin B Keskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Computer Science, Metropolitan College, Boston University, Boston, MA, USA
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Cecilia Muñoz-Calleja
- Department of Immunology, Instituto de Investigación Sanitaria Princesa (IIS-IP), Hospital Universitario de La Princesa, Madrid, Spain
- Department of Medicine, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Vincent T Ho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jerome Ritz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Donna Neuberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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8
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Arshad NF, Nordin FJ, Foong LC, In LLA, Teo MYM. Engineering receptor-binding domain and heptad repeat domains towards the development of multi-epitopes oral vaccines against SARS-CoV-2 variants. PLoS One 2024; 19:e0306111. [PMID: 39146295 PMCID: PMC11326571 DOI: 10.1371/journal.pone.0306111] [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: 08/29/2023] [Accepted: 06/11/2024] [Indexed: 08/17/2024] Open
Abstract
The inability of existing vaccines to cope with the mutation rate has highlighted the need for effective preventative strategies for COVID-19. Through the secretion of immunoglobulin A, mucosal delivery of vaccines can effectively stimulate mucosal immunity for better protection against SARS-CoV-2 infection. In this study, various immunoinformatic tools were used to design a multi-epitope oral vaccine against SARS-CoV-2 based on its receptor-binding domain (RBD) and heptad repeat (HR) domains. T and B lymphocyte epitopes were initially predicted from the RBD and HR domains of SARS-CoV-2, and potential antigenic, immunogenic, non-allergenic, and non-toxic epitopes were identified. Epitopes that are highly conserved and have no significant similarity to human proteome were selected. The epitopes were joined with appropriate linkers, and an adjuvant was added to enhance the vaccine efficacy. The vaccine 3D structure constructs were docked with toll-like receptor 4 (TLR-4) and TLR1-TLR2, and the binding affinity was calculated. The designed multi-epitope vaccine construct (MEVC) consisted of 33 antigenic T and B lymphocyte epitopes. The results of molecular dockings and free binding energies confirmed that the MEVC effectively binds to TLR molecules, and the complexes were stable. The results suggested that the designed MEVC is a potentially safe and effective oral vaccine against SARS-CoV-2. This in silico study presents a novel approach for creating an oral multi-epitope vaccine against the rapidly evolving SARS-CoV-2 variants. These findings offer valuable insights for developing an effective strategy to combat COVID-19. Further preclinical and clinical studies are required to confirm the efficacy of the MEVC vaccine.
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Affiliation(s)
- Nur Farhanah Arshad
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Fariza Juliana Nordin
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Lian Chee Foong
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med X Clinical Stem Cell Research Center, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Michelle Yee Mun Teo
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
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9
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Rastogi A, Gautam S, Kumar M. Bioinformatic elucidation of conserved epitopes to design a potential vaccine candidate against existing and emerging SARS-CoV-2 variants of concern. Heliyon 2024; 10:e35129. [PMID: 39157328 PMCID: PMC11328099 DOI: 10.1016/j.heliyon.2024.e35129] [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: 09/27/2023] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 08/20/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 poses a significant adverse effects on health and economy globally. Due to mutations in genome, COVID-19 vaccine efficacy decreases. We used immuno-informatics to design a Multi epitope vaccine (MEV) candidate for SARS-CoV-2 variants of concern (VOCs). Hence, we predicted binders/epitopes MHC-I, CD8+, MHC-II, CD4+, and CTLs from spike, membrane and envelope proteins of VOCs. In addition, we assessed the conservation of these binders and epitopes across different VOCs. Subsequently, we designed MEV by combining the predicted CTL and CD4+ epitopes from spike protein, peptide linkers, and an adjuvant. Further, we evaluated the binding of MEV candidate against immune receptors namely HLA class I histocompatibility antigen, HLA class II histocompatibility antigen, and TLR4, achieving binding scores of -1265.3, -1330.7, and -1337.9. Molecular dynamics and normal mode analysis revealed stable docking complexes. Moreover, immune simulation suggested MEV candidate elicits both innate and adaptive immune response. We anticipate that this conserved MEV candidate will provide protection from VOCs and emerging strains.
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Affiliation(s)
- Amber Rastogi
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh, 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sakshi Gautam
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh, 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manoj Kumar
- Virology Unit and Bioinformatics Centre, Institute of Microbial Technology, Council of Scientific and Industrial Research (CSIR), Sector 39A, Chandigarh, 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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Kant R, Khan MS, Chopra M, Saluja D. Artificial intelligence-driven reverse vaccinology for Neisseria gonorrhoeae vaccine: Prioritizing epitope-based candidates. Front Mol Biosci 2024; 11:1442158. [PMID: 39193221 PMCID: PMC11347834 DOI: 10.3389/fmolb.2024.1442158] [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: 06/01/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
Neisseria gonorrhoeae is the causative agent of the sexually transmitted disease gonorrhea. The increasing prevalence of this disease worldwide, the rise of antibiotic-resistant strains, and the difficulties in treatment necessitate the development of a vaccine, highlighting the significance of preventative measures to control and eradicate the infection. Currently, there is no widely available vaccine, partly due to the bacterium's ability to evade natural immunity and the limited research investment in gonorrhea compared to other diseases. To identify distinct vaccine candidates, we chose to focus on the uncharacterized, hypothetical proteins (HPs) as our initial approach. Using the in silico method, we first carried out a comprehensive assessment of hypothetical proteins of Neisseria gonorrhoeae, encompassing assessments of physicochemical properties, cellular localization, secretary pathways, transmembrane regions, antigenicity, toxicity, and prediction of B-cell and T-cell epitopes, among other analyses. Detailed analysis of all HPs resulted in the functional annotation of twenty proteins with a great degree of confidence. Further, using the immuno-informatics approach, the prediction pipeline identified one CD8+ restricted T-cell epitope, seven linear B-cell epitopes, and seven conformational B-cell epitopes as putative epitope-based peptide vaccine candidates which certainly require further validation in laboratory settings. The study accentuates the promise of functional annotation and immuno-informatics in the systematic design of epitope-based peptide vaccines targeting Neisseria gonorrhoeae.
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Affiliation(s)
- Ravi Kant
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence (IoE), University of Delhi, Delhi, India
| | - Mohd. Shoaib Khan
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Madhu Chopra
- Laboratory of Molecular Modeling and Anticancer Drug Development, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Daman Saluja
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
- Delhi School of Public Health, Institute of Eminence (IoE), University of Delhi, Delhi, India
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11
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Zhou Z, Zhu F, Ma S, Tan C, Yang H, Zhang P, Xu Y, Qin R, Luo Y, Chen J, Pan P. Design of Cryptococcus neoformans multi-epitope vaccine based on immunoinformatics method. Med Mycol 2024; 62:myae080. [PMID: 39122658 DOI: 10.1093/mmy/myae080] [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: 03/23/2024] [Revised: 07/01/2024] [Accepted: 08/08/2024] [Indexed: 08/12/2024] Open
Abstract
Cryptococcus neoformans is a widely distributed opportunistic pathogenic fungus. While C. neoformans commonly infects immunocompromised individuals, it can also affect those who are immunocompetent. Transmission of C. neoformans primarily occurs through the respiratory tract, leading to the development of meningitis. The mortality rate of Cryptococcal meningitis is high, and treatment options are limited. Cryptococcus neoformans infections pose a significant public health threat and currently lack targeted and effective response strategies. This study aimed to screen T lymphocyte (cytotoxic T lymphocyte and helper T lymphocyte) and B lymphocyte epitopes derived from four C. neoformans antigens and develop two multi-epitope vaccines by combining them with various adjuvants. Molecular docking results demonstrated that the vaccines bind stably to Toll-like receptor 4 ( and induce innate immunity. The credibility of the molecular docking results was validated through subsequent molecular dynamics simulations. Furthermore, the results of immune simulation analyses underscored the multi-epitope vaccine's capability to effectively induce robust humoral and cellular immune responses within the host organism. These two vaccines have demonstrated theoretical efficacy against C. neoformans infection as indicated by computer analysis. Nevertheless, additional experimental validation is essential to substantiate the protective efficacy of the vaccines.
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Affiliation(s)
- Ziyou Zhou
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Fei Zhu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Shiyang Ma
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Caixia Tan
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
- Department of Infection Control Center of Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hang Yang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Peipei Zhang
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yizhong Xu
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Rongliu Qin
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Yuying Luo
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Jie Chen
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Pinhua Pan
- Department of Respiratory Medicine, National Key Clinical Specialty, Branch of National Clinical Research Center for Respiratory Disease, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- Clinical Research Center for Respiratory Diseases in Hunan Province, Changsha, Hunan 410008, China
- Hunan Engineering Research Center for Intelligent Diagnosis and Treatment of Respiratory Disease, Changsha, Hunan 410025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China
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12
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Aiman S, Ali Y, Malik A, Alkholief M, Ahmad A, Akhtar S, Ali S, Khan A, Li C, Shams S. Immunoinformatic-guided novel mRNA vaccine designing to elicit immunogenic responses against the endemic Monkeypox virus. J Biomol Struct Dyn 2024; 42:6292-6306. [PMID: 37424185 DOI: 10.1080/07391102.2023.2233627] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/01/2023] [Indexed: 07/11/2023]
Abstract
Monkeypox virus (MPXV) is an orthopoxvirus, causing zoonotic infections in humans with smallpox-like symptoms. The WHO reported MPXV cases in May 2022 and the outbreak caused significant morbidity threats to immunocompromised individuals and children. Currently, no clinically validated therapies are available against MPXV infections. The present study is based on immunoinformatics approaches to design mRNA-based novel vaccine models against MPXV. Three proteins were prioritized based on high antigenicity, low allergenicity, and toxicity values to predict T- and B-cell epitopes. Lead T- and B-cell epitopes were used to design vaccine constructs, linked with epitope-specific linkers and adjuvant to enhance immune responses. Additional sequences, including Kozak sequence, MITD sequence, tPA sequence, Goblin 5', 3' UTRs, and a poly(A) tail were added to design stable and highly immunogenic mRNA vaccine construct. High-quality structures were predicted by molecular modeling and 3D-structural validation of the vaccine construct. Population coverage and epitope-conservancy speculated broader protection of designed vaccine model against multiple MPXV infectious strains. MPXV-V4 was eventually prioritized based on its physicochemical and immunological parameters and docking scores. Molecular dynamics and immune simulations analyses predicted significant structural stability and binding affinity of the top-ranked vaccine model with immune receptors to elicit cellular and humoral immunogenic responses against the MPXV. The pursuance of experimental and clinical follow-up of these prioritized constructs may lay the groundwork to develop safe and effective vaccine against MPXV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yasir Ali
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Abdul Malik
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Musaed Alkholief
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Suhail Akhtar
- A.T. Still University of Health Sciences, Kirksville, MO, USA
| | - Sajid Ali
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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13
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Oladipo EK, Oyelakin OD, Aiyelabegan AO, Olajide EO, Olatayo VO, Owolabi KP, Shittu YB, Olugbodi RO, Ajala HA, Rukayat RA, Olayiwola DO, Irewolede BA, Jimah EM, Oloke JK, Ojo TO, Ajani OF, Iwalokun BA, Kolawole OM, Ariyo OE, Adediran DA, Olufemi SE, Onyeaka H. Exploring computational approaches to design mRNA Vaccine against vaccinia and Mpox viruses. Immun Inflamm Dis 2024; 12:e1360. [PMID: 39150224 PMCID: PMC11328121 DOI: 10.1002/iid3.1360] [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: 08/02/2023] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Messenger RNA (mRNA) vaccines emerged as a powerful tool in the fight against infections. Unlike traditional vaccines, this unique type of vaccine elicits robust and persistent innate and humoral immune response with a unique host cell-mediated pathogen gene expression and antigen presentation. METHODS This offers a novel approach to combat poxviridae infections. From the genome of vaccinia and Mpox viruses, three key genes (E8L, E7R, and H3L) responsible for virus attachment and virulence were selected and employed for designing the candidate mRNA vaccine against vaccinia and Mpox viral infection. Various bioinformatics tools were employed to generate (B cell, CTL, and HTL) epitopes, of which 28 antigenic and immunogenic epitopes were selected and are linked to form the mRNA vaccine construct. Additional components, including a 5' cap, 5' UTR, adjuvant, 3' UTR, and poly(A) tail, were incorporated to enhance stability and effectiveness. Safety measures such as testing for human homology and in silico immune simulations were implemented to avoid autoimmunity and to mimics the immune response of human host to the designed mRNA vaccine, respectively. The mRNA vaccine's binding affinity was evaluated by docking it with TLR-2, TLR-3, TLR-4, and TLR-9 receptors which are subsequently followed by molecular dynamics simulations for the highest binding one to predict the stability of the binding complex. RESULTS With a 73% population coverage, the mRNA vaccine looks promising, boasting a molecular weight of 198 kDa and a molecular formula of C8901H13609N2431O2611S48 and it is said to be antigenic, nontoxic and nonallergic, making it safe and effective in preventing infections with Mpox and vaccinia viruses, in comparison with other insilico-designed vaccine for vaccinia and Mpox viruses. CONCLUSIONS However, further validation through in vivo and in vitro techniques is underway to fully assess its potential.
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Affiliation(s)
- Elijah K Oladipo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Laboratory of Molecular Biology, Immunology and Bioinformatics, Department of Microbiology, Adeleke University, Ede, Osun State, Nigeria
| | - Olanrewaju D Oyelakin
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Abdulsamad O Aiyelabegan
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Elizabeth O Olajide
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Molecular Biology and Biotechnology Department, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Victoria O Olatayo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Kaothar P Owolabi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Yewande B Shittu
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Rhoda O Olugbodi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Hezekiah A Ajala
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Raji A Rukayat
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Deborah O Olayiwola
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife A Irewolede
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Esther M Jimah
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Julius K Oloke
- Department of Natural Sciences, Precious Cornerstone University, Ibadan, Oyo State, Nigeria
| | - Taiwo O Ojo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Olumide F Ajani
- African Centre for Disease Control HQ, Addis Ababa, Ethiopia
| | - Bamidele A Iwalokun
- Molecular Biology and Biotechnology Department, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Olatunji M Kolawole
- Department of Microbiology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olumuyiwa E Ariyo
- Department of Medicine, Infectious Disease and Tropical Medicine Unit, Federal Teaching Hospital, Ido Ekiti, Ekiti State, Nigeria
| | - Daniel A Adediran
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Seun E Olufemi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
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14
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Moqbel Hassan Alzubaydi N, Oun Ali Z, Al-Asadi S, Al-Kahachi R. Design and characterization of a multi-epitope vaccine targeting Chlamydia abortus using immunoinformatics approach. J Biomol Struct Dyn 2024; 42:6660-6677. [PMID: 37774751 DOI: 10.1080/07391102.2023.2240891] [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: 03/01/2023] [Accepted: 07/06/2023] [Indexed: 10/01/2023]
Abstract
Chlamydiosis is a widespread ailment affecting humans, livestock, and wildlife, caused by C. abortus, a member of the Chlamydia genus. This disease leads to reproductive disorders in bovines and poses a zoonotic risk, resulting in adverse outcomes such as abortion, stillbirths, weak offspring, endometritis, repeat breeding, and perinatal mortality. However, current chlamydiosis vaccines have limitations in terms of safety, efficacy, and stability, necessitating the development of effective and safe alternatives. In this study, our objective was to design a multi-epitope vaccine (MEV) targeting all strains of C. abortus using bioinformatics and immunoinformatics approaches. We identified highly antigenic and non-allergic proteins (yidC, yajC, secY, CAB503, and CAB746) using VaxiJen and AlgPred tools. Physicochemical analyses and secondary structure predictions confirmed protein stability through ProtParam and SOPMA methods. Furthermore, we employed IEDB-AR, NETMHCpan, and ToxinPred2 tools to predict cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), and B-cell epitopes, resulting in the identification of conserved epitopes for further analysis. The MEV construct, consisting of 545 amino acids, incorporated the adjuvant Beta defensin-3, along with 9 CTL epitopes and 21 HTL epitopes linked by EAAAK, KK, and AAY linkers. We assessed the safety and immunogenicity of the vaccine through comprehensive evaluations of antigenicity, toxicity, allergenicity, and physicochemical properties. Structural stability and quality were examined using 3D modeling via the ab initio approach with the Robetta platform. Molecular docking analysis explored the compatibility of the MEV with Toll-like receptor 9 (TLR9) using ClusPro, while molecular dynamics simulation with the DESMOND Maestro software predicted the stability and flexibility of the docked complex. Despite promising in silico findings, further wet lab investigations are crucial to validate the safety and efficacy of the MEV. Successful development and validation of this MEV hold significant potential in combatting chlamydiosis in both animal and human populations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Zainab Oun Ali
- Department of Radiology Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | - Sura Al-Asadi
- Department of Laboratory Techniques, College of Health and Medical Techniques, Middle Technical University, Baghdad, Iraq
| | - Rusul Al-Kahachi
- Department of Scholarships and Cultural Relationship, Republic of Iraq Ministry of Higher Education and Scientific Research, Baghdad, Iraq
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15
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Morgan RN, Ismail NSM, Alshahrani MY, Aboshanab KM. Multi-epitope peptide vaccines targeting dengue virus serotype 2 created via immunoinformatic analysis. Sci Rep 2024; 14:17645. [PMID: 39085250 PMCID: PMC11291903 DOI: 10.1038/s41598-024-67553-1] [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: 04/16/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024] Open
Abstract
The Middle East has witnessed a greater spread of infectious Dengue viruses, with serotype 2 (DENV-2) being the most prevalent form. Through this work, multi-epitope peptide vaccines against DENV-2 that target E and nonstructural (NS1) proteins were generated through an immunoinformatic approach. MHC class I and II and LBL epitopes among NS1 and envelope E proteins sequences were predicted and their antigenicity, toxicity, and allergenicity were investigated. Studies of the population coverage denoted the high prevalence of NS1 and envelope-E epitopes among different countries where DENV-2 endemic. Further, both the CTL and HTL epitopes retrieved from NS1 epitopes exhibited high conservancies' percentages with other DENV serotypes (1, 3, and 4). Three vaccine constructs were created and the expected immune responses for the constructs were estimated using C-IMMSIM and HADDOCK (against TLR 2,3,4,5, and 7). Molecular dynamics simulation for vaccine construct 2 with TLR4 denoted high binding affinity and stability of the construct with the receptor which might foretell favorable in vivo interaction and immune responses.
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Affiliation(s)
- Radwa N Morgan
- Drug Radiation Research Department, National Centre for Radiation Research and Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Nasser S M Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, 9088, Abha, Saudi Arabia
| | - Khaled M Aboshanab
- Microbiology and Immunology Department, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Abbassia, POB: 11566, Cairo, 11566, Egypt.
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16
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Das T, Datta S, Sen A. Revolutionizing Nipah virus vaccinology: insights into subunit vaccine development strategies and immunological advances. In Silico Pharmacol 2024; 12:69. [PMID: 39070666 PMCID: PMC11282045 DOI: 10.1007/s40203-024-00246-9] [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: 01/16/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
The Nipah virus (NiV), a zoonotic virus in the Henipavirus genus of the Paramyxoviridae family, emerged in Malaysia in 1998 and later spread globally. Diseased patients may have a 40- 70% chance of fatality depending on the severity and early medication. The recent outbreak of NiV was reported in Kerala (India) by a new strain of MCL-19-H-1134 isolate. Currently, no vaccines are available, highlighting the critical need for a conclusive remedy. Our study aims to develop a subunit vaccine against the NiV by analyzing its proteome. NiV genome and proteome sequences were obtained from the NCBI database. A phylogenetic tree was constructed based on genome alignment. T-cell, helper T-cell, and B-cell epitopes were predicted from the protein sequences using NetCTL-1.2, NetMHCIIPan-4.1, and IEDB servers, respectively. High-affinity epitopes for human receptors were selected to construct a multi-epitope vaccine (MEV). These epitopes' antigenicity, toxicity, and allergenicity were evaluated using VaxiJen, AllergenFP-v.1.0, and AllergenFP algorithms. Molecular interactions with specific receptors were analyzed using PyRx and ClusPro. Amino acid interactions were visualized and analyzed using PyMOL and LigPlot. Immuno-simulation was conducted using C-ImmSim to assess the immune response elicited by the MEV. Finally, the vaccine cDNA was inserted into the pET28a(+) expression vector using SnapGene tool for in silico cloning in an E. coli host. The potential for an imminent outbreak cannot be overlooked. A subunit vaccine is more cost-effective and time-efficient. With additional in vitro and in vivo validation, this vaccine could become a superior preventive measure against NiV disease. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00246-9.
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Affiliation(s)
- Tapas Das
- Department of Botany, University of North Bengal, Siliguri, India
| | - Sutapa Datta
- Department of Botany, University of North Bengal, Siliguri, India
| | - Arnab Sen
- Department of Botany, University of North Bengal, Siliguri, India
- Bioinformatics Facility Centre, University of North Bengal, Siliguri, India
- Biswa Bangla Genome Centre, University of North Bengal, Siliguri, India
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Roy SK, Biswas MS, Foyzur Raman M, Hasan R, Rahmann Z, Uddin PK MM. A computational approach to developing a multi-epitope vaccine for combating Pseudomonas aeruginosa-induced pneumonia and sepsis. Brief Bioinform 2024; 25:bbae401. [PMID: 39133098 PMCID: PMC11318047 DOI: 10.1093/bib/bbae401] [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: 05/22/2024] [Revised: 07/16/2024] [Accepted: 07/30/2024] [Indexed: 08/13/2024] Open
Abstract
Pseudomonas aeruginosa is a complex nosocomial infectious agent responsible for numerous illnesses, with its growing resistance variations complicating treatment development. Studies have emphasized the importance of virulence factors OprE and OprF in pathogenesis, highlighting their potential as vaccine candidates. In this study, B-cell, MHC-I, and MHC-II epitopes were identified, and molecular linkers were active to join these epitopes with an appropriate adjuvant to construct a vaccine. Computational tools were employed to forecast the tertiary framework, characteristics, and also to confirm the vaccine's composition. The potency was weighed through population coverage analysis and immune simulation. This project aims to create a multi-epitope vaccine to reduce P. aeruginosa-related illness and mortality using immunoinformatics resources. The ultimate complex has been determined to be stable, soluble, antigenic, and non-allergenic upon inspection of its physicochemical and immunological properties. Additionally, the protein exhibited acidic and hydrophilic characteristics. The Ramachandran plot, ProSA-web, ERRAT, and Verify3D were employed to ensure the final model's authenticity once the protein's three-dimensional structure had been established and refined. The vaccine model showed a significant binding score and stability when interacting with MHC receptors. Population coverage analysis indicated a global coverage rate of 83.40%, with the USA having the highest coverage rate, exceeding 90%. Moreover, the vaccine sequence underwent codon optimization before being cloned into the Escherichia coli plasmid vector pET-28a (+) at the EcoRI and EcoRV restriction sites. Our research has developed a vaccine against P. aeruginosa that has strong binding affinity and worldwide coverage, offering an acceptable way to mitigate nosocomial infections.
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Affiliation(s)
- Suronjit Kumar Roy
- Department of Biochemistry and Biotechnology, Khwaja Yunus Ali University, Sirajganj 6751, Bangladesh
| | - Mohammad Shahangir Biswas
- Department of Biochemistry and Biotechnology, Khwaja Yunus Ali University, Sirajganj 6751, Bangladesh
- Department of Public Health, Daffodil International University, Dhaka 1216, Bangladesh
| | - Md Foyzur Raman
- Department of Biochemistry and Biotechnology, Khwaja Yunus Ali University, Sirajganj 6751, Bangladesh
| | - Rubait Hasan
- Department of Biochemistry and Biotechnology, Khwaja Yunus Ali University, Sirajganj 6751, Bangladesh
| | - Zahidur Rahmann
- Institute of Biological Science, Rajshahi University, Motihar, Rajshahi 6205, Bangladesh
| | - Md Moyen Uddin PK
- Riceland Healthcare, 538 Broadway Ave, Winnie, TX 77665, United States
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Oladipo EK, Akinleye TM, Adeyemo SF, Akinboade MW, Siyanbola KF, Adetunji VA, Arowosegbe OA, Olatunji VK, Adaramola EO, Afolabi HO, Ajani CD, Siyanbola TP, Folakanmi EO, Irewolede BA, Okesanya OJ, Ajani OF, Ariyo OE, Jimah EM, Iwalokun BA, Kolawole OM, Oloke JK, Onyeaka H. mRNA vaccine design for Epstein-Barr virus: an immunoinformatic approach. In Silico Pharmacol 2024; 12:68. [PMID: 39070665 PMCID: PMC11269547 DOI: 10.1007/s40203-024-00244-x] [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: 12/06/2023] [Accepted: 07/14/2024] [Indexed: 07/30/2024] Open
Abstract
Epstein-Barr Virus (EBV), structurally similar to other herpes viruses, possess significant global health challenges as it causes infectious mononucleosis and is also associated with various cancers. Due to this widespread impact, an effective messenger RNA (mRNA) vaccine is paramount to help curb its spread, further underscoring the need for its development. This study, following an immunoinformatic approach, aimed to design a comprehensive mRNA vaccine against the EBV by selecting antigenic proteins, predicting Linear B-cell epitopes, cytotoxic T-cell lymphocyte (CTL) and helper T-cell lymphocyte (HTL) epitopes, and assessing vaccine characteristics. Seventy-nine EBV isolates from diverse geographical regions were examined. Additionally, the vaccine construct's physicochemical properties, transmembrane domains, solubility, and secondary structures were analysed. Molecular docking was conducted with Toll-Like Receptor 5 (TLR-5). Population coverage was assessed for selected major histocompatibility complex (MHC) alleles, and immune response was simulated. The result of this study highlighted a vaccine construct with high antigenicity, non-toxicity, and non-allergenicity and possessed favourable physicochemical properties. The vaccine's 3D structure is native-like and strongly binds with TLR-5, indicating a solid affinity with TLR-5. The selected MHC alleles provided broad universal population coverage of 89.1%, and the immune simulations suggested a robust and wide-ranging immunogenic response, activating critical immune cells, antibodies, and cytokines. These findings provide a solid foundation for further development and testing of the EBV candidate vaccine, offering potential solutions for combating EBV infections.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Laboratory of Molecular Biology, Immunology and Bioinformatics, Department of Microbiology, Adeleke University, Ede, Osun State Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomosho, Oyo State Nigeria
| | - Temitope Michael Akinleye
- Genomics Unit, Helix Biogen Institute, Ogbomosho, Oyo State Nigeria
- Department of Anatomy and Advanced Research Center for Tumor Immunology, Inje University College of Medicine, 75 Bokji-ro, Busanjin-gu, Busan, 47392 Republic of Korea
| | | | | | | | | | | | | | | | | | | | | | | | | | - Olalekan John Okesanya
- Faculty of Medicine, Department of Public Health and Maritime Transport, Laboratory of Hygiene and Epidemiology, University of Thessaly, Papakyriazi 22, Larissa, 41222 Greece
| | - Olumide Faith Ajani
- African Centre for Disease Control and Prevention (African CDC), Addis Ababa, Ethiopia
| | - Olumuyiwa Elijah Ariyo
- Department of Medicine, Infectious Diseases and Tropical Medicine Unit, Federal Teaching Hospital, Ido-Ekiti, Ekiti State Nigeria
| | | | - Bamidele Abiodun Iwalokun
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research, Lagos, Nigeria
| | | | - Julius Kola Oloke
- Department of Natural Science, Precious Cornerstone, Ibadan, 200132 Nigeria
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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Mikaeel S, Doosti A, Sharifzadeh A. Putative new combination vaccine candidates identified by reverse vaccinology and genomic approaches to control enteric pathogens. BMC Immunol 2024; 25:46. [PMID: 39034396 PMCID: PMC11265179 DOI: 10.1186/s12865-024-00626-y] [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: 12/12/2023] [Accepted: 06/07/2024] [Indexed: 07/23/2024] Open
Abstract
OBJECTIVES The pathogenic microorganisms that cause intestinal diseases can significantly jeopardize people's health. Currently, there are no authorized treatments or vaccinations available to combat the germs responsible for intestinal disease. METHODS Using immunoinformatics, we developed a potent multi-epitope Combination (combo) vaccine versus Salmonella and enterohemorrhagic E. coli. The B and T cell epitopes were identified by performing a conservancy assessment, population coverage analysis, physicochemical attributes assessment, and secondary and tertiary structure assessment of the chosen antigenic polypeptide. The selection process for vaccine development included using several bioinformatics tools and approaches to finally choose two linear B-cell epitopes, five CTL epitopes, and two HTL epitopes. RESULTS The vaccine had strong immunogenicity, cytokine production, immunological properties, non-toxicity, non-allergenicity, stability, and potential efficacy against infections. Disulfide bonding, codon modification, and computational cloning were also used to enhance the stability and efficacy of expression in the host E. coli. The vaccine's structure has a strong affinity for the TLR4 ligand and is very durable, as shown by molecular docking and molecular modeling. The results of the immunological simulation demonstrated that both B and T cells had a heightened response to the vaccination component. CONCLUSIONS The comprehensive in silico analysis reveals that the proposed vaccine will likely elicit a robust immune response against pathogenic bacteria that cause intestinal diseases. Therefore, it is a promising option for further experimental testing.
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Affiliation(s)
- Saeed Mikaeel
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Abbas Doosti
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Ali Sharifzadeh
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Department of Microbiology, Faculty of Veterinary Medicine, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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20
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Kafle A, Ojha SC. Advancing vaccine development against Opisthorchis viverrini: A synergistic integration of omics technologies and advanced computational tools. Front Pharmacol 2024; 15:1410453. [PMID: 39076588 PMCID: PMC11284087 DOI: 10.3389/fphar.2024.1410453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/31/2024] Open
Abstract
The liver fluke O. viverrini (Opisthorchis viverrini), a neglected tropical disease (NTD), endemic to the Great Mekong Subregion (GMS), mainly afflicts the northeastern region of Thailand. It is a leading cause of cholangiocarcinoma (CCA) in humans. Presently, the treatment modalities for opisthorchiasis incorporate the use of the antihelminthic drug praziquantel, the rapid occurrence of reinfection, and the looming threat of drug resistance highlight the urgent need for vaccine development. Recent advances in "omics" technologies have proven to be a powerful tool for such studies. Utilizing candidate proteins identified through proteomics and refined via immunoproteomics, reverse vaccinology (RV) offers promising prospects for designing vaccines targeting essential antibody responses to eliminate parasite. Machine learning-based computational tools can predict epitopes of candidate protein/antigens exhibiting high binding affinities for B cells, MHC classes I and II, indicating strong potential for triggering both humoral and cell-mediated immune responses. Subsequently, these vaccine designs can undergo population-specific testing and docking/dynamics studies to assess efficacy and synergistic immunogenicity. Hence, refining proteomics data through immunoinformatics and employing computational tools to generate antigen-specific targets for trials offers a targeted and efficient approach to vaccine development that applies to all domains of parasite infections. In this review, we delve into the strategic antigen selection process using omics modalities for the O. viverrini parasite and propose an innovative framework for vaccine design. We harness omics technologies to revolutionize vaccine development, promising accelerated discoveries and streamlined preclinical and clinical evaluations.
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Affiliation(s)
- Alok Kafle
- Department of Tropical Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- WHO Collaborating Centre for Research and Control of Opisthorchiasis, Khon Kaen University, Khon Kaen, Thailand
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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21
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Andrade TEG, Peña MS, Fiorotti J, de Souza Bin R, Caetano AR, Connelley T, de Miranda Santos IKF. The DRB3 gene of the bovine major histocompatibility complex: discovery, diversity and distribution of alleles in commercial breeds of cattle and applications for development of vaccines. J Dairy Sci 2024:S0022-0302(24)00989-5. [PMID: 39004123 DOI: 10.3168/jds.2023-24628] [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: 12/28/2023] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
The bovine Major Histocompatibility Complex (MHC), also known as the Bovine Leucocyte Antigen (BoLA) complex, is the genomic region that encodes the most important molecules for antigen presentation to initiate immune responses. The first evidence of MHC in bovines pointed to a locus containing 2 antigens, one detected by cytotoxic antiserum (MHC class I) and another studied by mixed lymphocyte culture tests (MHC class II). The most studied gene in the BoLA region is the highly polymorphic BoLA-DRB3, which encodes a β chain with a peptide groove domain involved in antigen presentation for T cells that will develop and co-stimulate cellular and humoral effector responses. BoLA-DRB3 alleles have been associated with outcomes in infectious diseases such as mastitis, trypanosomiasis, and tick loads, and with production traits. To catalog these alleles, 2 nomenclature methods were proposed, and the current use of both systems makes it difficult to list, comprehend and apply these data effectively. In this review we have organized the knowledge available in all of the reports on the frequencies of BoLA-DRB3 alleles. It covers information from studies made in at least 26 countries on more than 30 breeds; studies are lacking in countries that are important producers of cattle livestock. We highlight practical applications of BoLA studies for identification of markers associated with resistance to infectious and parasitic diseases, increased production traits and T cell epitope mapping, in addition to genetic diversity and conservation studies of commercial and creole and locally adapted breeds. Finally, we provide support for the need of studies to discover new BoLA alleles and uncover unknown roles of this locus in production traits.
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Affiliation(s)
| | | | - Jéssica Fiorotti
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Renan de Souza Bin
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Timothy Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
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22
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Sethi G, Varghese RP, Lakra AK, Nayak SS, Krishna R, Hwang JH. Immunoinformatics and structural aided approach to develop multi-epitope based subunit vaccine against Mycobacterium tuberculosis. Sci Rep 2024; 14:15923. [PMID: 38987613 PMCID: PMC11237054 DOI: 10.1038/s41598-024-66858-5] [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: 03/16/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
Tuberculosis is a highly contagious disease caused by Mycobacterium tuberculosis (Mtb), which is one of the prominent reasons for the death of millions worldwide. The bacterium has a substantially higher mortality rate than other bacterial diseases, and the rapid rise of drug-resistant strains only makes the situation more concerning. Currently, the only licensed vaccine BCG (Bacillus Calmette-Guérin) is ineffective in preventing adult pulmonary tuberculosis prophylaxis and latent tuberculosis re-activation. Therefore, there is a pressing need to find novel and safe vaccines that provide robust immune defense and have various applications. Vaccines that combine epitopes from multiple candidate proteins have been shown to boost immunity against Mtb infection. This study applies an immunoinformatic strategy to generate an adequate multi-epitope immunization against Mtb employing five antigenic proteins. Potential B-cell, cytotoxic T lymphocyte, and helper T lymphocyte epitopes were speculated from the intended proteins and coupled with 50 s ribosomal L7/L12 adjuvant, and the vaccine was constructed. The vaccine's physicochemical profile demonstrates antigenic, soluble, and non-allergic. In the meantime, docking, molecular dynamics simulations, and essential dynamics analysis revealed that the multi-epitope vaccine structure interacted strongly with Toll-like receptors (TLR2 and TLR3). MM-PBSA analysis was performed to ascertain the system's intermolecular binding free energies accurately. The immune simulation was applied to the vaccine to forecast its immunogenic profile. Finally, in silico cloning was used to validate the vaccine's efficacy. The immunoinformatics analysis suggests the multi-epitope vaccine could induce specific immune responses, making it a potential candidate against Mtb. However, validation through the in-vivo study of the developed vaccine is essential to assess its efficacy and immunogenicity profile, which will assure active protection against Mtb.
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Affiliation(s)
- Guneswar Sethi
- Department of Predictive Toxicology, Korea Institute of Toxicology (KIT), Daejeon, Republic of Korea
- Animal Model Research Group, Korea Institute of Toxicology, 30 Baehak 1-gil, Jeonguep, Jeollabuk-do, 56212, Republic of Korea
| | | | - Avinash Kant Lakra
- Translational Health Science and Technology Institute, Faridabad, Haryana, 121001, India
| | | | - Ramadas Krishna
- Department of Bioinformatics, Pondicherry University, Puducherry, 605014, India.
| | - Jeong Ho Hwang
- Animal Model Research Group, Korea Institute of Toxicology, 30 Baehak 1-gil, Jeonguep, Jeollabuk-do, 56212, Republic of Korea.
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Shah M, Sitara F, Sarfraz A, Shehroz M, Wara TU, Perveen A, Ullah N, Zaman A, Nishan U, Ahmed S, Ullah R, Ali EA, Ojha SC. Development of a subunit vaccine against the cholangiocarcinoma causing Opisthorchis viverrini: a computational approach. Front Immunol 2024; 15:1281544. [PMID: 39050853 PMCID: PMC11266093 DOI: 10.3389/fimmu.2024.1281544] [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: 08/22/2023] [Accepted: 06/26/2024] [Indexed: 07/27/2024] Open
Abstract
Opisthorchis viverrini is the etiological agent of the disease opisthorchiasis and related cholangiocarcinoma (CCA). It infects fish-eating mammals and more than 10 million people in Southeast Asia suffered from opisthorchiasis with a high fatality rate. The only effective drug against this parasite is Praziquantel, which has significant side effects. Due to the lack of appropriate treatment options and the high death rate, there is a dire need to develop novel therapies against this pathogen. In this study, we designed a multi-epitope chimeric vaccine design against O. viverrini by using immunoinformatics approaches. Non-allergenic and immunogenic MHC-1, MHC-2, and B cell epitopes of three candidate proteins thioredoxin peroxidase (Ov-TPx-1), cathepsin F1 (Ov-CF-1) and calreticulin (Ov-CALR) of O. viverrini, were predicted to construct a potent multiepitope vaccine. The coverage of the HLA-alleles of these selected epitopes was determined globally. Four vaccine constructs made by different adjuvants and linkers were evaluated in the context of their physicochemical properties, antigenicity, and allergenicity. Protein-protein docking and MD simulation found that vaccines 3 was more stable and had a higher binding affinity for TLR2 and TLR4 immune receptors. In-silico restriction cloning of vaccine model led to the formation of plasmid constructs for expression in a suitable host. Finally, the immune simulation showed strong immunological reactions to the engineered vaccine. These findings suggest that the final vaccine construct has the potential to be validated by in vivo and in vitro experiments to confirm its efficacy against the CCA causing O. viverrini.
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Affiliation(s)
- Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Farva Sitara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree, Pakistan
| | - Tehreem Ul Wara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Asia Perveen
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Najeeb Ullah
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Sarfraz Ahmed
- Wellman Center for Photomedicine, Harvard Medical School, Massachusetts General Hospital, Boston, MA, United States
| | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University Riyadh, Riyadh, Saudi Arabia
| | - Essam A. Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Ezzemani W, Ouladlahsen A, Altawalah H, Saile R, Sarih M, Kettani A, Ezzikouri S. Identification of novel T-cell epitopes on monkeypox virus and development of multi-epitopes vaccine using immunoinformatics approaches. J Biomol Struct Dyn 2024; 42:5349-5364. [PMID: 37354141 DOI: 10.1080/07391102.2023.2226733] [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: 10/25/2022] [Accepted: 06/10/2023] [Indexed: 06/26/2023]
Abstract
Monkeypox virus (MPV) is closely related to the smallpox virus, and previous data from Africa suggest that the smallpox vaccine (VARV) is at least 85% effective in preventing MPV. No multi-epitope vaccine has yet been developed to prevent MPV infection. In this work, we used in silico structural biology and advanced immunoinformatic strategies to design a multi-epitope subunit vaccine against MPV infection. The designed vaccine sequence is adjuvanted with CpG-ODN and includes HTL/CTL epitopes for similar proteins between vaccinia virus (VACV) that induced T-cell production in vaccinated volunteers and the first draft sequence of the MPV genome associated with the suspected outbreak in several countries, May 2022. In addition, the specific binding of the modified vaccine and the immune Toll-like receptor 9 (TLR9) was estimated by molecular interaction studies. Strong interaction in the binding groove as well as good docking scores confirmed the stringency of the modified vaccine. The stability of the interaction was confirmed by a classical molecular dynamics simulation and normal mode analysis. Then, the immune simulation also indicated the ability of this vaccine to induce an effective immune response against MPV. Codon optimization and in silico cloning of the vaccine into the pET-28a (+) vector also showed its expression potential in the E. coli K12 system. The promising data obtained from the various in silico studies indicate that this vaccine is effective against MPV. However, additional in vitro and in vivo studies are still needed to confirm its efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ahd Ouladlahsen
- Faculté de médecine et de pharmacie, Université Hassan II, Casablanca, Morocco
- Service des maladies infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - M'hammed Sarih
- Service de Parasitologie et des Maladies Vectorielles, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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25
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Mancebo FJ, Nuévalos M, Lalchandani J, Martín Galiano AJ, Fernández-Ruiz M, Aguado JM, García-Ríos E, Pérez-Romero P. Cytomegalovirus UL44 protein induces a potent T-cell immune response in mice. Antiviral Res 2024; 227:105914. [PMID: 38759930 DOI: 10.1016/j.antiviral.2024.105914] [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: 02/21/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Due to the severity of CMV infection in immunocompromised individuals the development of a vaccine has been declared a priority. However, despite the efforts made there is no yet a vaccine available for clinical use. We designed an approach to identify new CMV antigens able to inducing a broad immune response that could be used in future vaccine formulations. We have used serum samples from 28 kidney transplant recipients, with a previously acquired CMV-specific immune response to identify viral proteins that were recognized by the antibodies present in the patient serum samples by Western blot. A band of approximately 45 kDa, identified as UL44, was detected by most serum samples. UL44 immunogenicity was tested in BALB/c mice that received three doses of the UL44-pcDNA DNA vaccine. UL44 elicited both, a strong antibody response and CMV-specific cellular response. Using bioinformatic analysis we demonstrated that UL44 is a highly conserved protein and contains epitopes that are able to activate CD8 lymphocytes of the most common HLA alleles in the world population. We constructed a UL44 ORF deletion mutant virus that produced no viral progeny, suggesting that UL44 is an essential viral protein. In addition, other authors have demonstrated that UL44 is one of the most abundant viral proteins after infection and have suggested an essential role of UL44 in viral replication. Altogether, our data suggests that UL44 is a potent antigen, and favored by its abundance, it may be a good candidate to include in a vaccine formulation.
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Affiliation(s)
- Francisco J Mancebo
- National Center for Microbiology, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Marcos Nuévalos
- National Center for Microbiology, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | - Jaanam Lalchandani
- National Center for Microbiology, Instituto de Salud Carlos III. Majadahonda, Madrid, Spain
| | | | - Mario Fernández-Ruiz
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre', Instituto de Investigación Biomédica Hospital "12 de Octubre' (imas12) Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - José María Aguado
- Unit of Infectious Diseases, Hospital Universitario "12 de Octubre', Instituto de Investigación Biomédica Hospital "12 de Octubre' (imas12) Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Estéfani García-Ríos
- Instituto de Agroquímica y Tecnología de Alimentos (IATA), Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain.
| | - Pilar Pérez-Romero
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
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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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Sharma AD, Grewal RK, Gorle S, Cuspoca AF, Kaushik V, Rajjak Shaikh A, Cavallo L, Chawla M. T cell epitope based vaccine design while targeting outer capsid proteins of rotavirus strains infecting neonates: an immunoinformatics approach. J Biomol Struct Dyn 2024; 42:4937-4955. [PMID: 37382214 DOI: 10.1080/07391102.2023.2226721] [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: 03/23/2023] [Accepted: 06/05/2023] [Indexed: 06/30/2023]
Abstract
Gastrointestinal diarrhea is majorly caused by the rotavirus (RV) in the children who generally are under the age group of 5 years. WHO estimates that ∼95% of the children contract RV infection, by this age. The disease is highly contagious; notably in many cases, it is proven fatal with high mortality rates especially in the developing countries. In India alone, an estimated 145,000 yearly deaths occurs due to RV related gastrointestinal diarrhea. WHO pre-qualified vaccines that are available for RV are all live attenuated vaccines with modest efficacy range between 40 and 60%. Further, the risk of intussusceptions has been reported in some children on RV vaccination. Thus, in a quest to develop alternative candidate to overcome challenges associated with these oral vaccines, we chose immunoinformatics approach to design a multi-epitope vaccine (MEV) while targeting the outer capsid viral proteinsVP4 and VP7 of the neonatal strains of rotavirus. Interestingly, ten epitopes, that is, six CD8+T-cells and four CD4+T-cell epitopes were identified which were predicted to be antigenic, non-allergic, non-toxic and stable. These epitopes were then linked to adjuvants, linkers, and PADRE sequences to create a multi-epitope vaccine for RV. The in silico designed RV-MEV and human TLR5 complex displayed stable interactions during molecular dynamics simulations. Further, the immune simulation studies of RV-MEV corroborated that the vaccine candidate emerges as a promising immunogen. Future investigations while performing in vitro and in vivo analyses with designed RV-MEV construct are highly desirable to warrant the potential of this vaccine candidate in protective immunity against different strains of RVs infecting neonates.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arijit Das Sharma
- School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Ravneet Kaur Grewal
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Suresh Gorle
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Andrés Felipe Cuspoca
- Grupo de Investigación Epidemiología Clínica de Colombia (GRECO), Universidad Pedagógica y Tecnológica de Colombia, Tunja, Colombia
- Centro de Atención e Investigación Médica - CAIMED, Chía, Colombia
| | - Vikas Kaushik
- School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, Haryana, India
| | - Luigi Cavallo
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohit Chawla
- Physical Sciences and Engineering Division, Kaust Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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28
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Cavalcanti-Dantas VDM, Fernandes B, Dantas PHLF, Uchoa GR, Mendes AF, Araújo Júnior WOD, Castellano LRC, Fernandes AIV, Goulart LR, Oliveira RADS, Assis PACD, Souza JRD, Morais CNLD. Differential epitope prediction across diverse circulating variants of SARS-COV-2 in Brazil. Comput Biol Chem 2024; 112:108139. [PMID: 38972100 DOI: 10.1016/j.compbiolchem.2024.108139] [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: 10/18/2023] [Revised: 06/09/2024] [Accepted: 06/22/2024] [Indexed: 07/09/2024]
Abstract
COVID-19, caused by the SARS-COV-2 virus, induces numerous immunological reactions linked to the severity of the clinical condition of those infected. The surface Spike protein (S protein) present in Sars-CoV-2 is responsible for the infection of host cells. This protein presents a high rate of mutations, which can increase virus transmissibility, infectivity, and immune evasion. Therefore, we propose to evaluate, using immunoinformatic techniques, the predicted epitopes for the S protein of seven variants of Sars-CoV-2. MHC class I and II epitopes were predicted and further assessed for their immunogenicity, interferon-gamma (IFN-γ) inducing capacity, and antigenicity. For B cells, linear and structural epitopes were predicted. For class I MHC epitopes, 40 epitopes were found for the clades of Wuhan, Clade 2, Clade 3, and 20AEU.1, Gamma, and Delta, in addition to 38 epitopes for Alpha and 44 for Omicron. For MHC II, there were differentially predicted epitopes for all variants and eight equally predicted epitopes. These were evaluated for differences in the MHC II alleles to which they would bind. Regarding B cell epitopes, 16 were found in the Wuhan variant, 14 in 22AEU.1 and in Clade 3, 15 in Clade 2, 11 in Alpha and Delta, 13 in Gamma, and 9 in Omicron. When compared, there was a reduction in the number of predicted epitopes concerning the Spike protein, mainly in the Delta and Omicron variants. These findings corroborate the need for updates seen today in bivalent mRNA vaccines against COVID-19 to promote a targeted immune response to the main circulating variant, Omicron, leading to more robust protection against this virus and avoiding cases of reinfection. When analyzing the specific epitopes for the RBD region of the spike protein, the Omicron variant did not present a B lymphocyte epitope from position 390, whereas the epitope at position 493 for MHC was predicted only for the Alpha, Gamma, and Omicron variants.
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Affiliation(s)
| | | | | | | | | | | | | | - Ana Isabel Vieira Fernandes
- Health Promotion Department of the Medical Sciences Center and Division for Infectious and Parasitic Diseases, Lauro Wanderley University Hospital, Federal University of Paraiba, Brazil
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Kaur B, Karnwal A, Bansal A, Malik T. An Immunoinformatic-Based In Silico Identification on the Creation of a Multiepitope-Based Vaccination Against the Nipah Virus. BIOMED RESEARCH INTERNATIONAL 2024; 2024:4066641. [PMID: 38962403 PMCID: PMC11221950 DOI: 10.1155/2024/4066641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/30/2024] [Accepted: 06/01/2024] [Indexed: 07/05/2024]
Abstract
The zoonotic viruses pose significant threats to public health. Nipah virus (NiV) is an emerging virus transmitted from bats to humans. The NiV causes severe encephalitis and acute respiratory distress syndrome, leading to high mortality rates, with fatality rates ranging from 40% to 75%. The first emergence of the disease was found in Malaysia in 1998-1999 and later in Bangladesh, Cambodia, Timor-Leste, Indonesia, Singapore, Papua New Guinea, Vietnam, Thailand, India, and other South and Southeast Asian nations. Currently, no specific vaccines or antiviral drugs are available. The potential advantages of epitope-based vaccines include their ability to elicit specific immune responses while minimizing potential side effects. The epitopes have been identified from the conserved region of viral proteins obtained from the UniProt database. The selection of conserved epitopes involves analyzing the genetic sequences of various viral strains. The present study identified two B cell epitopes, seven cytotoxic T lymphocyte (CTL) epitopes, and seven helper T lymphocyte (HTL) epitope interactions from the NiV proteomic inventory. The antigenic and physiological properties of retrieved protein were analyzed using online servers ToxinPred, VaxiJen v2.0, and AllerTOP. The final vaccine candidate has a total combined coverage range of 80.53%. The tertiary structure of the constructed vaccine was optimized, and its stability was confirmed with the help of molecular simulation. Molecular docking was performed to check the binding affinity and binding energy of the constructed vaccine with TLR-3 and TLR-5. Codon optimization was performed in the constructed vaccine within the Escherichia coli K12 strain, to eliminate the danger of codon bias. However, these findings must require further validation to assess their effectiveness and safety. The development of vaccines and therapeutic approaches for virus infection is an ongoing area of research, and it may take time before effective interventions are available for clinical use.
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Affiliation(s)
- Beant Kaur
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Arun Karnwal
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Anu Bansal
- School of Bioengineering and BiosciencesLovely Professional University, Phagwara, Punjab 144411, India
| | - Tabarak Malik
- Department of Biomedical SciencesInstitute of HealthJimma University, Jimma, Ethiopia
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30
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Rasool D, Jan SA, Khan SU, Nahid N, Ashfaq UA, Umar A, Qasim M, Noor F, Rehman A, Shahzadi K, Alshammari A, Alharbi M, Nisar MA. Subtractive proteomics-based vaccine targets annotation and reverse vaccinology approaches to identify multiepitope vaccine against Plesiomonas shigelloides. Heliyon 2024; 10:e31304. [PMID: 38845922 PMCID: PMC11153098 DOI: 10.1016/j.heliyon.2024.e31304] [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: 03/30/2023] [Revised: 05/09/2024] [Accepted: 05/14/2024] [Indexed: 06/09/2024] Open
Abstract
Plesiomonas shigelloides, an aquatic bacterium belonging to the Enterobacteriaceae family, is a frequent cause of gastroenteritis with diarrhea and gastrointestinal severe disease. Despite decades of research, discovering a licensed and globally accessible vaccine is still years away. Developing a putative vaccine that can combat the Plesiomonas shigelloides infection by boosting population immunity against P. shigelloides is direly needed. In the framework of the current study, the entire proteome of P. shigelloides was explored using subtractive genomics integrated with the immunoinformatics approach for designing an effective vaccine construct against P. shigelloides. The overall stability of the vaccine construct was evaluated using molecular docking, which demonstrated that MEV showed higher binding affinities with toll-like receptors (TLR4: 51.5 ± 10.3, TLR2: 60.5 ± 9.2) and MHC receptors(MHCI: 79.7 ± 11.2 kcal/mol, MHCII: 70.4 ± 23.7). Further, the therapeutic efficacy of the vaccine construct for generating an efficient immune response was evaluated by computational immunological simulation. Finally, computer-based cloning and improvement in codon composition without altering amino acid sequence led to the development of a proposed vaccine. In a nutshell, the findings of this study add to the existing knowledge about the pathogenesis of this infection. The schemed MEV can be a possible prophylactic agent for individuals infected with P. shigelloides. Nevertheless, further authentication is required to guarantee its safeness and immunogenic potential.
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Affiliation(s)
- Danish Rasool
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 44000, Pakistan
| | - Sohail Ahmad Jan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, 44000, Pakistan
| | | | - Nazia Nahid
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Ahitsham Umar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Abdur Rehman
- Center of Bioinformatics, College of Life Sciences, Northwest A & F Uiversity, yangling, 712100, Shaanxi, China
| | - Kiran Shahzadi
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh, 11451, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Post Box 2455, Riyadh, 11451, Saudi Arabia
| | - Muhammad Atif Nisar
- College of Science and Engineering, Flinders University, Adelaide, 5042, Australia
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Bean DJ, Monroe J, Liang YM, Borberg E, Senussi Y, Swank Z, Chalise S, Walt D, Weinberg J, Sagar M. Heterotypic immunity from prior SARS-CoV-2 infection but not COVID-19 vaccination associates with lower endemic coronavirus incidence. Sci Transl Med 2024; 16:eado7588. [PMID: 38865483 DOI: 10.1126/scitranslmed.ado7588] [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: 02/19/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Immune responses from prior severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and COVID-19 vaccination mitigate disease severity, but they do not fully prevent subsequent infections, especially from genetically divergent strains. We examined the incidence of and immune differences against human endemic coronaviruses (eCoVs) as a proxy for response against future genetically heterologous coronaviruses (CoVs). We assessed differences in symptomatic eCoV and non-CoV respiratory disease incidence among those with known prior SARS-CoV-2 infection or previous COVID-19 vaccination but no documented SARS-CoV-2 infection or neither exposure. Retrospective cohort analyses suggest that prior SARS-CoV-2 infection, but not previous COVID-19 vaccination alone, associates with a lower incidence of subsequent symptomatic eCoV infection. There was no difference in non-CoV incidence, implying that the observed difference was eCoV specific. In a second cohort where both cellular and humoral immunity were measured, those with prior SARS-CoV-2 spike protein exposure had lower eCoV-directed neutralizing antibodies, suggesting that neutralization is not responsible for the observed decreased eCoV disease. The three groups had similar cellular responses against the eCoV spike protein and nucleocapsid antigens. However, CD8+ T cell responses to the nonstructural eCoV proteins nsp12 and nsp13 were higher in individuals with previous SARS-CoV-2 infection as compared with the other groups. This association between prior SARS-CoV-2 infection and decreased incidence of eCoV disease may therefore be due to a boost in CD8+ T cell responses against eCoV nsp12 and nsp13, suggesting that incorporation of nonstructural viral antigens in a future pan-CoV vaccine may improve vaccine efficacy.
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Affiliation(s)
- David J Bean
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Janet Monroe
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Yan Mei Liang
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Ella Borberg
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Yasmeen Senussi
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Zoe Swank
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Sujata Chalise
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - David Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Manish Sagar
- Department of Virology, Immunology and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
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32
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Braz JDM, Batista MVDA. Immunoinformatics-Based Design of Multi-epitope DNA and mRNA Vaccines Against Zika Virus. Bioinform Biol Insights 2024; 18:11779322241257037. [PMID: 38827811 PMCID: PMC11143849 DOI: 10.1177/11779322241257037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
In this study, we used an immunoinformatics approach to predict antigenic epitopes of Zika virus (ZIKV) proteins to assist in designing a vaccine antigen against ZIKV. We performed the prediction of CD8+ T-lymphocyte and antigenic B-cell epitopes of ZIKV proteins. The binding interactions of T-cell epitopes with major histocompatibility complex class I (MHC-I) proteins were assessed. We selected the antigenic, conserved, nontoxic, and immunogenic epitopes, which indicated significant interactions with the human leucocyte antigen (HLA-A and HLA-B) alleles and worldwide population coverage of 76.35%. The predicted epitopes were joined with the help of linkers and an adjuvant. The vaccine antigen was then analyzed through molecular docking with TLR3 and TLR8, and it was in silico cloned in the pVAX1 vector to be used as a DNA vaccine and designed as a mRNA vaccine.
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Affiliation(s)
- Juciene de Matos Braz
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | - Marcus Vinicius de Aragão Batista
- Laboratory of Molecular Genetics and Biotechnology (GMBio), Department of Biology, Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
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Das NC, Gorai S, Gupta PSS, Panda SK, Rana MK, Mukherjee S. Immune targeting of filarial glutaredoxin through a multi-epitope peptide-based vaccine: A reverse vaccinology approach. Int Immunopharmacol 2024; 133:112120. [PMID: 38657497 DOI: 10.1016/j.intimp.2024.112120] [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: 01/14/2024] [Revised: 04/07/2024] [Accepted: 04/17/2024] [Indexed: 04/26/2024]
Abstract
Despite the efforts of global programme to eliminate lymphatic filariasis (GPELF), the threat of lymphatic filariasis (LF) still looms over humanity in terms of long-term disabilities, and morbidities across the globe. In light of this situation, investigators have chosen to focus on the development of immunotherapeutics targeting the physiologically important filarial-specific proteins. Glutaredoxin (16.43 kDa) plays a pivotal role in filarial redox biology, serving as a vital contributor. In the context of the intra-host survival of filarial parasites, this antioxidant helps in mitigating the oxidative stress imposed by the host immune system. Given its significant contribution, the development of a vaccine targeting glutaredoxin holds promise as a new avenue for achieving a filaria-free world. Herein, multi-epitope-based vaccine was designed using advanced immunoinformatics approach. Initially, 4B-cell epitopes and 6 T-cell epitopes (4 MHC I and 2 MHC II) were identified from the 146 amino acid long sequence of glutaredoxin of the human filarid, Wuchereria bancrofti. Subsequent clustering of these epitopes with linker peptides finalized the vaccine structure. To boost TLR-mediated innate immunity, TLR-specific adjuvants were incorporated into the designed vaccine. After that, experimental analyses confirm the designed vaccine, Vac4 as anefficient ligand of human TLR5 to elicit protective innate immunity against filarial glutaredoxin. Immune simulation further demonstrated abundant levels of IgG and IgM as crucial contributors in triggering vaccine-induced adaptive responses in the recipients. Hence, to facilitate the validation of immunogenicity of the designed vaccine, Vac4 was cloned in silico in pET28a(+) expression vector for recombinant production. Taken together, our findings suggest that vaccine-mediated targeting of filarial glutaredoxin could be a future option for intervening LF on a global scale.
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Affiliation(s)
- Nabarun Chandra Das
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India
| | - Sampa Gorai
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India
| | - Parth Sarthi Sen Gupta
- School of Biosciences & Bioengineering, D. Y. Patil International University, Akurdi, Pune 411044, India
| | - Saroj Kumar Panda
- Department of Chemistry, Indian Institute of Science Education and Research, Berhampur, India
| | - Malay Kumar Rana
- Department of Chemistry, Indian Institute of Science Education and Research, Berhampur, India
| | - Suprabhat Mukherjee
- Integrative Biochemistry & Immunology Laboratory, Department of Animal Science, Kazi Nazrul University, Asansol 713 340, West Bengal, India.
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34
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Rani NA, Robin TB, Prome AA, Ahmed N, Moin AT, Patil RB, Sikder MNA, Bappy MNI, Afrin D, Hossain FMA, Islam T, Zinnah KMA. Development of multi epitope subunit vaccines against emerging carp viruses Cyprinid herpesvirus 1 and 3 using immunoinformatics approach. Sci Rep 2024; 14:11783. [PMID: 38782944 PMCID: PMC11116410 DOI: 10.1038/s41598-024-61074-7] [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: 07/02/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Cyprinid herpesvirus is a causative agent of a destructive disease in common and koi carp (Cyprinus carpio), which leads to substantial global financial losses in aquaculture industries. Among the strains of C. herpesvirus, C. herpesvirus 1 (CyHV-1) and C. herpesvirus 3 (CyHV-3) are known as highly pathogenic to carp fishes in Europe, Asia, and Africa. To date, no effective vaccine has been developed to combat these viruses. This study aimed to develop unique multi-epitope subunit vaccines targeting the CyHV-1 and CyHV-3 using a reverse vaccinology approach. The study began with a comprehensive literature review to identify the most critical proteins, which were then subjected to in silico analyses to predict highly antigenic epitopes. These analyses involved assessing antigenicity, transmembrane topology screening, allergenecity, toxicity, and molecular docking approaches. We constructed two multi-epitope-based vaccines incorporating a suitable adjuvant and appropriate linkers. It revealed that both the vaccines are non-toxic and immunogenic. The tertiary structures of the vaccine proteins were generated, refined, and validated to ensure their suitability. The binding affinity between the vaccine constructs and TLR3 and TLR5 receptors were assessed by molecular docking studies. Molecular dynamics simulations indicated that vaccine construct V1 exhibited greater stability with both TLR3 and TLR5 based on RMSD analysis. Hydrogen bond analysis revealed a stronger binding affinity between the vaccine constructs and TLR5 compared to TLR3. Furthermore, MM-PBSA analysis suggested that both vaccine constructs exhibited a better affinity for TLR5. Considering all aspects, the results suggest that in silico development of CyHV vaccines incorporating multiple epitopes holds promise for management of diseases caused by CyHV-1 and CyHV-3. However, further in vivo trials are highly recommended to validate the efficacies of these vaccines.
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Affiliation(s)
- Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Anindita Ash Prome
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Nadim Ahmed
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Abu Tayab Moin
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Rajesh B Patil
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy, Sinhgad Technical Education Society's, Off Sinhgad Road, Vadgaon (Bk), Pune, Maharashtra, 411041, India
| | - Mohammad Nurul Azim Sikder
- Institute of Marine Sciences, Faculty of Marine Sciences and Fisheries, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Md Nazmul Islam Bappy
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Dilruba Afrin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh
| | - Ferdaus Mohd Altaf Hossain
- Faculty of Veterinary, Animal and Biomedical Science, Sylhet Agricultural University, Sylhet, Bangladesh
- Department of Dairy Science, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706, Bangladesh.
| | - Kazi Md Ali Zinnah
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
- Department of Animal and Fish Biotechnology, Sylhet Agricultural University, Sylhet, 3100, Bangladesh.
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Naveed M, Hassan A, Aziz T, Ali U, Khan AA, Alharbi M, Alshammari A. Integrating 16S rRNA profiling and in-silico analysis for an epitope-based vaccine strategy against Achromobacter xylosoxidans infection. Int Immunopharmacol 2024; 135:112287. [PMID: 38776850 DOI: 10.1016/j.intimp.2024.112287] [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: 04/14/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Achromobacter xylosoxidans is an aerobic, catalase-positive, non-pigment-forming, Gram-negative, and motile bacterium. It potentially causes a wide range of human infections in cystic fibrosis and non-cystic fibrosis patients. However, developing a safe preventive or therapeutic solution against A. xylosoxidans remains challenging. This study aimed to construct an epitope-based vaccine candidate using immunoinformatic techniques. A. xylosoxidans was isolated from an auto workshop in Lahore, and its identification was confirmed through 16S rRNA amplification and bioinformatic analysis. Two protein targets with GenBank accession numbers AKP90890.1 and AKP90355.1 were selected for the vaccine construct. Both proteins exhibited antigenicity, with scores of 0.757 and 0.580, respectively and the epitopes were selected based on the IC50 value using the ANN 4.0 and NN-align 2.3 epitope prediction method for MHC I and MHC II epitopes respectively and predicted epitopes were analyzed for antigenicity, allergenicity and pathogenicity. The vaccine construct demonstrated structural stability, thermostability, solubility, and hydrophilicity. The vaccine produced 250 B-memory cells per mm3 and approximately 16,000 IgM + IgG counts, indicating an effective immune response against A. xylosoxidans. Moreover, the vaccine candidate interacted stably with toll-like receptor 5, a pattern recognition receptor, with a confidence score of 0.98. These results highlight the potency of the designed vaccine candidate, suggesting its potential to withstand rigorous in vitro and in vivo clinical trials. This epitope-based vaccine could serve as the first preventive immunotherapy against A. xylosoxidans infections, addressing this bacterium's health and financial burdens. The findings demonstrate the value of employing immunoinformatic tools in vaccine development, paving the way for more precise and tailored approaches to combating microbial threats.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan.
| | - Ali Hassan
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Tariq Aziz
- Department of Agriculture University of Ioannina Arta 47100 Greece.
| | - Urooj Ali
- Department of Biotechnology, Quaid-I-Azam University, Islamabad Pakistan
| | - Ayaz Ali Khan
- Department of Biotechnology, University of Malakand Chakdara Dir Lower 18800 Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Bhattacharya K, Chanu NR, Jha SK, Khanal P, Paudel KR. In silico design and evaluation of a multiepitope vaccine targeting the nucleoprotein of Puumala orthohantavirus. Proteins 2024. [PMID: 38742930 DOI: 10.1002/prot.26703] [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: 03/14/2024] [Revised: 04/19/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
The Puumala orthohantavirus is present in the body of the bank vole (Myodes glareolus). Humans infected with this virus may develop hemorrhagic fever accompanying renal syndrome. In addition, the infection may further lead to the failure of an immune system completely. The present study aimed to propose a possible vaccine by employing bioinformatics techniques to identify B and T-cell antigens. The best multi-epitope of potential immunogenicity was generated by combining epitopes. Additionally, the linkers EAAAK, AAY, and GPGPG were utilized in order to link the epitopes successfully. Further, C-ImmSim was used to perform in silico immunological simulations upon the vaccine. For the purpose of conducting expression tests in Escherichia coli, the chimeric protein construct was cloned using Snapgene into the pET-9c vector. The designed vaccine showed adequate results, evidenced by the global population coverage and favorable immune response. The developed vaccine was found to be highly effective and to have excellent population coverage in a number of computer-based assessments. This work is fully dependent on the development of nucleoprotein-based vaccines, which would constitute a significant step forward if our findings were used in developing a global vaccination to combat the Puumala virus.
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Affiliation(s)
- Kunal Bhattacharya
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, India
- Royal School of Pharmacy, The Assam Royal Global University, Guwahati, Assam, India
| | - Nongmaithem Randhoni Chanu
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, India
- Faculty of Pharmaceutical Science, Assam Downtown University, Guwahati, Assam, India
| | - Saurav Kumar Jha
- Department of Biological Sciences and Bioengineering (BSBE), Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Pukar Khanal
- Department of Pharmacology and Toxicology, KLE College of Pharmacy, Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, New South Wales, Australia
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da Silva OLT, da Silva MK, Rodrigues-Neto JF, Santos Lima JPM, Manzoni V, Akash S, Fulco UL, Bourhia M, Dawoud TM, Nafidi HA, Sitotaw B, Akter S, Oliveira JIN. Advancing molecular modeling and reverse vaccinology in broad-spectrum yellow fever virus vaccine development. Sci Rep 2024; 14:10842. [PMID: 38735993 PMCID: PMC11089047 DOI: 10.1038/s41598-024-60680-9] [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: 10/31/2023] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
Yellow fever outbreaks are prevalent, particularly in endemic regions. Given the lack of an established treatment for this disease, significant attention has been directed toward managing this arbovirus. In response, we developed a multiepitope vaccine designed to elicit an immune response, utilizing advanced immunoinformatic and molecular modeling techniques. To achieve this, we predicted B- and T-cell epitopes using the sequences from all structural (E, prM, and C) and nonstructural proteins of 196 YFV strains. Through comprehensive analysis, we identified 10 cytotoxic T-lymphocyte (CTL) and 5T-helper (Th) epitopes that exhibited overlap with B-lymphocyte epitopes. These epitopes were further evaluated for their affinity to a wide range of human leukocyte antigen system alleles and were rigorously tested for antigenicity, immunogenicity, allergenicity, toxicity, and conservation. These epitopes were linked to an adjuvant ( β -defensin) and to each other using ligands, resulting in a vaccine sequence with appropriate physicochemical properties. The 3D structure of this sequence was created, improved, and quality checked; then it was anchored to the Toll-like receptor. Molecular Dynamics and Quantum Mechanics/Molecular Mechanics simulations were employed to enhance the accuracy of docking calculations, with the QM portion of the simulations carried out utilizing the density functional theory formalism. Moreover, the inoculation model was able to provide an optimal codon sequence that was inserted into the pET-28a( +) vector for in silico cloning and could even stimulate highly relevant humoral and cellular immunological responses. Overall, these results suggest that the designed multi-epitope vaccine can serve as prophylaxis against the yellow fever virus.
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Affiliation(s)
- Ohana Leticia Tavares da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil
| | - Maria Karolaynne da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil
| | - Joao Firmino Rodrigues-Neto
- Multicampi School of Medical Sciences, Federal University of Rio Grande do Norte, Caicó, RN, 59300-000, Brazil
| | - Joao Paulo Matos Santos Lima
- Department of Biochemistry, Bioscience Center, Federal University of Rio Grande do Norte, Natal, RN, 59064-741, Brazil
| | - Vinicius Manzoni
- Physics Institute, Federal University of Alagoas, Maceio, AL, 57072-970, Brazil
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Sukrabad, Dhaka, 1207, Bangladesh
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, 70000, Laayoune, Morocco
| | - Turki M Dawoud
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, 2325, Quebec City, QC, G1V 0A6, Canada
| | - Baye Sitotaw
- Department of Biology, Bahir Dar University, P.O. Box 79, Bahir Dar, Ethiopia.
| | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, 1205, Bangladesh
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande Do Norte, Natal, RN, 59064-741, Brazil.
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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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Sarvmeili J, Baghban Kohnehrouz B, Gholizadeh A, Shanehbandi D, Ofoghi H. Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer. Sci Rep 2024; 14:10297. [PMID: 38704475 PMCID: PMC11069592 DOI: 10.1038/s41598-024-61025-2] [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: 11/13/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The ideal vaccines for combating diseases that may emerge in the future require more than simply inactivating a few pathogenic strains. This study aims to provide a peptide-based multi-epitope vaccine effective against various severe acute respiratory syndrome coronavirus 2 strains. To design the vaccine, a library of peptides from the spike, nucleocapsid, membrane, and envelope structural proteins of various strains was prepared. Then, the final vaccine structure was optimized using the fully protected epitopes and the fynomer scaffold. Using bioinformatics tools, the antigenicity, allergenicity, toxicity, physicochemical properties, population coverage, and secondary and three-dimensional structures of the vaccine candidate were evaluated. The bioinformatic analyses confirmed the high quality of the vaccine. According to further investigations, this structure is similar to native protein and there is a stable and strong interaction between vaccine and receptors. Based on molecular dynamics simulation, structural compactness and stability in binding were also observed. In addition, the immune simulation showed that the vaccine can stimulate immune responses similar to real conditions. Finally, codon optimization and in silico cloning confirmed efficient expression in Escherichia coli. In conclusion, the fynomer-based vaccine can be considered as a new style in designing and updating vaccines to protect against coronavirus disease.
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Affiliation(s)
- Javad Sarvmeili
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 51666, Iran
| | | | - Ashraf Gholizadeh
- Department of Animal Biology, University of Tabriz, Tabriz, 51666, Iran
| | - Dariush Shanehbandi
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 51666, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, 33131, Iran
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Mortazavi B, Molaei A, Fard NA. Multi-epitopevaccines, from design to expression; an in silico approach. Hum Immunol 2024; 85:110804. [PMID: 38658216 DOI: 10.1016/j.humimm.2024.110804] [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: 03/01/2024] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Abstract
The development of vaccines against a wide range of infectious diseases and pathogens often relies on multi-epitope strategies that can effectively stimulate both humoral and cellular immunity. Immunoinformatics tools play a pivotal role in designing such vaccines, enhancing immune response potential, and minimizing the risk of failure. This review presents a comprehensive overview of practical tools for epitope prediction and the associated immune responses. These immunoinformatics tools facilitate the selection of epitopes based on parameters such as antigenicity, absence of toxic and allergenic sequences, secondary and tertiary structures, sequence conservation, and population coverage. The chosen epitopes can be tailored for B-cells or T-cells, both of which require further assessments covered in this study. We offer a range of suitable linkers that effectively separate cytotoxic T lymphocyte and helper T lymphocyte epitopes while preserving their functionality. Additionally, we identify various adjuvants for specific purposes. We delve into the evaluation of MHC-epitope interactions, MHC clusters, and the simulation of final constructs through molecular docking techniques. We provide diverse linkers and adjuvants optimized for epitope functions to bolster immune responses through epitope attachment. By leveraging these comprehensive tools, the development of multi-epitope vaccines holds the promise of robust immunity and a significant reduction in experimental costs.
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Affiliation(s)
- Behnam Mortazavi
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ali Molaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Najaf Allahyari Fard
- Department of systems Biotechnology, Faculty of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Ahmad S, Demneh FM, Rehman B, Almanaa TN, Akhtar N, Pazoki-Toroudi H, Shojaeian A, Ghatrehsamani M, Sanami S. In silico design of a novel multi-epitope vaccine against HCV infection through immunoinformatics approaches. Int J Biol Macromol 2024; 267:131517. [PMID: 38621559 DOI: 10.1016/j.ijbiomac.2024.131517] [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: 11/11/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/17/2024]
Abstract
Infection with the hepatitis C virus (HCV) is one of the causes of liver cancer, which is the world's sixth most prevalent and third most lethal cancer. The current treatments do not prevent reinfection; because they are expensive, their usage is limited to developed nations. Therefore, a prophylactic vaccine is essential to control this virus. Hence, in this study, an immunoinformatics method was applied to design a multi-epitope vaccine against HCV. The best B- and T-cell epitopes from conserved regions of the E2 protein of seven HCV genotypes were joined with the appropriate linkers to design a multi-epitope vaccine. In addition, cholera enterotoxin subunit B (CtxB) was included as an adjuvant in the vaccine construct. This study is the first to present this epitopes-adjuvant combination. The vaccine had acceptable physicochemical characteristics. The vaccine's 3D structure was predicted and validated. The vaccine's binding stability with Toll-like receptor 2 (TLR2) and TLR4 was confirmed using molecular docking and molecular dynamics (MD) simulation. The immune simulation revealed the vaccine's efficacy by increasing the population of B and T cells in response to vaccination. In silico expression in Escherichia coli (E. coli) was also successful.
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Affiliation(s)
- Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, P.O. Box 36, Lebanon; Department of Natural Sciences, Lebanese American University, Beirut, P.O. Box 36, Lebanon
| | - Fatemeh Mobini Demneh
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Bushra Rehman
- Institute of Biotechnology and Microbiology, Bacha khan University, Charsadda, Pakistan
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, India
| | - Hamidreza Pazoki-Toroudi
- Department of Physiology & Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Shojaeian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mahdi Ghatrehsamani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Samira Sanami
- Abnormal Uterine Bleeding Research Center, Semnan University of Medical Sciences, Semnan, Iran.
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Mooney AH, Draper SL, Burn OK, Anderson RJ, Compton BJ, Tang C, Farrand KJ, Di Lucia P, Ravà M, Fumagalli V, Giustini L, Bono E, Godfrey DI, Heath WR, Yuan W, Chisari FV, Guidotti LG, Iannacone M, Sidney J, Sette A, Gulab SA, Painter GF, Hermans IF. Preclinical evaluation of therapeutic vaccines for chronic hepatitis B that stimulate antiviral activities of T cells and NKT cells. JHEP Rep 2024; 6:101038. [PMID: 38694959 PMCID: PMC11061331 DOI: 10.1016/j.jhepr.2024.101038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 05/04/2024] Open
Abstract
Background & Aims Liver diseases resulting from chronic HBV infection are a significant cause of morbidity and mortality. Vaccines that elicit T-cell responses capable of controlling the virus represent a treatment strategy with potential for long-term effects. Here, we evaluated vaccines that induce the activity of type I natural killer T (NKT) cells to limit viral replication and license stimulation of conventional antiviral T-cells. Methods Vaccines were prepared by conjugating peptide epitopes to an NKT-cell agonist to promote co-delivery to antigen-presenting cells, encouraging NKT-cell licensing and stimulation of T cells. Activity of the conjugate vaccines was assessed in transgenic mice expressing the complete HBV genome, administered intravenously to maximise access to NKT cell-rich tissues. Results The vaccines induced only limited antiviral activity in unmanipulated transgenic hosts, likely attributable to NKT-cell activation as T-cell tolerance to viral antigens is strong. However, in a model of chronic hepatitis B involving transfer of naive HBcAg-specific CD8+ T cells into the transgenic mice, which typically results in specific T-cell dysfunction without virus control, vaccines containing the targeted HBcAg epitope induced prolonged antiviral activity because of qualitatively improved T-cell stimulation. In a step towards a clinical product, vaccines were prepared using synthetic long peptides covering clusters of known HLA-binding epitopes and shown to be immunogenic in HLA transgenic mice. Predictions based on HLA distribution suggest a product containing three selected SLP-based vaccines could give >90 % worldwide coverage, with an average of 3.38 epitopes targeted per individual. Conclusions The novel vaccines described show promise for further clinical development as a treatment for chronic hepatitis B. Impact and Implications Although there are effective prophylactic vaccines for HBV infection, it is estimated that 350-400 million people worldwide have chronic hepatitis B, putting these individuals at significant risk of life-threatening liver diseases. Therapeutic vaccination aimed at activating or boosting HBV-specific T-cell responses holds potential as a strategy for treating chronic infection, but has so far met with limited success. Here, we show that a glycolipid-peptide conjugate vaccine designed to coordinate activity of type I NKT cells alongside conventional antiviral T cells has antiviral activity in a mouse model of chronic infection. It is anticipated that a product based on a combination of three such conjugates, each prepared using long peptides covering clusters of known HLA-binding epitopes, could be developed further as a treatment for chronic hepatitis B with broad global HLA coverage.
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Affiliation(s)
- Anna H. Mooney
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Sarah L. Draper
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Olivia K. Burn
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Regan J. Anderson
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Benjamin J. Compton
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Chingwen Tang
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Pietro Di Lucia
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Micol Ravà
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Valeria Fumagalli
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Leonardo Giustini
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Bono
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dale I. Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Parkville, Australia
| | - William R. Heath
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia
| | - Weiming Yuan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francis V. Chisari
- Department of Immunology & Microbial Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Luca G. Guidotti
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Matteo Iannacone
- Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shivali A. Gulab
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
- Avalia Immunotherapies Limited, Wellington, New Zealand
| | - Gavin F. Painter
- Ferrier Research Institute, Victoria University of Wellington, Wellington, New Zealand
| | - Ian F. Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand
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Yaseen AR, Suleman M, Jabeen A, Nezami L, Qadri AS, Arif A, Arshad I, Iqbal K, Yaqoob T, Khan Z. Design and computational evaluation of a novel multi-epitope hybrid vaccine against monkeypox virus: Potential targets and immunogenicity assessment for pandemic preparedness. Biologicals 2024; 86:101770. [PMID: 38749079 DOI: 10.1016/j.biologicals.2024.101770] [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: 02/22/2024] [Revised: 04/15/2024] [Accepted: 05/06/2024] [Indexed: 06/11/2024] Open
Abstract
Monkeypox is a type of DNA-enveloped virus that belongs to the orthopoxvirus family, closely related to the smallpox virus. It can cause an infectious disease in humans known as monkeypox disease. Although there are multiple drugs and vaccines designed to combat orthopoxvirus infections, with a primary focus on smallpox, the recent spread of the monkeypox virus to over 50 countries have ignited a mounting global concern. This unchecked viral proliferation has raised apprehensions about the potential for a pandemic corresponding to the catastrophic impact of COVID-19. This investigation explored the structural proteins of monkeypox virus as potential candidates for designing a novel hybrid multi-epitope vaccine. The epitopes obtained from the selected proteins were screened to ensure their non-allergenicity, non-toxicity, and antigenicity to trigger T and B-cell responses. The interaction of the vaccine with toll-like receptor-3 (TLR-3) and major histocompatibility complexes (MHCs) was assessed using Cluspro 2.0. To establish the reliability of the docked complexes, a comprehensive evaluation was conducted using Immune and MD Simulations and Normal Mode Analysis. However, to validate the computational results of this study, additional in-vitro and in-vivo research is essential.
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Affiliation(s)
- Allah Rakha Yaseen
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Muhammad Suleman
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Aqsa Jabeen
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Laiba Nezami
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan.
| | - Abdul Salam Qadri
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan; Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, 54000, Pakistan.
| | - Ayesha Arif
- Centre for Applied Molecular biology (CAMB), University of the Punjab, Lahore, 54590, Pakistan.
| | - Iram Arshad
- Institute of Biochemistry and Biotechnology, University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan.
| | - Khadija Iqbal
- Institute of Biochemistry and Biotechnology, University of Veterinary & Animal Sciences, Lahore, 54000, Pakistan.
| | - Tasuduq Yaqoob
- School of Biological Sciences, Faculty of Life Sciences, University of the Punjab, Lahore, 54590, Pakistan.
| | - Zoha Khan
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, 54590, Pakistan.
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Martínez D, Fang L, Meza-Torres C, Garavito G, López-Lluch G, Egea E. Toward Consensus Epitopes B and T of Tropomyosin Involved in Cross-Reactivity across Diverse Allergens: An In Silico Study. Biomedicines 2024; 12:884. [PMID: 38672238 PMCID: PMC11048304 DOI: 10.3390/biomedicines12040884] [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: 12/03/2023] [Revised: 01/08/2024] [Accepted: 01/12/2024] [Indexed: 04/28/2024] Open
Abstract
Tropomyosin (TM) is a pan-allergen with cross-reactivity to arthropods, insects, and nematodes in tropical regions. While IgE epitopes of TM contribute to sensitization, T-cell (MHC-II) epitopes polarize the Th2 immune response. This study aimed to identify linear B and T consensus epitopes among house dust mites, cockroaches, Ascaris lumbricoides, shrimp, and mosquitoes, exploring the molecular basis of cross-reactivity in allergic diseases. Amino acid sequences of Der p 10, Der f 10, Blo t 10, Lit v 1, Pen a 1, Pen m 1, rAsc l 3, Per a 7, Bla g 7, and Aed a 10 were collected from Allergen Nomenclature and UniProt. B epitopes were predicted using AlgPred 2.0 and BepiPred 3.0. T epitopes were predicted with NetMHCIIpan 4.1 against 10 HLA-II alleles. Consensus epitopes were obtained through analysis and Epitope Cluster Analysis in the Immune Epitope Database. We found 7 B-cell epitopes and 28 linear T-cell epitopes binding to MHC II. A unique peptide (residues 160-174) exhibited overlap between linear B-cell and T-cell epitopes, highly conserved across tropomyosin sequences. These findings shed light on IgE cross-reactivity among the tested species. The described immuno-informatics pipeline and epitopes can inform in vitro research and guide synthetic multi-epitope proteins' design for potential allergology immunotherapies. Further in silico studies are warranted to confirm epitope accuracy and guide future experimental protocols.
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Affiliation(s)
- Dalgys Martínez
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Institute for Immunological Research, University of Cartagena, Cartagena 130014, Colombia
| | - Luis Fang
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
| | - Catherine Meza-Torres
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Department of Physiology, Anatomy, and Cellular Biology, Andalusian Centre for Development Biology (CABD-CSIC-JA), Pablo de Olavide University, 41013 Seville, Spain;
| | - Gloria Garavito
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Health Sciences Division, Universidad Simón Bolívar, Barranquilla 080002, Colombia
| | - Guillermo López-Lluch
- Department of Physiology, Anatomy, and Cellular Biology, Andalusian Centre for Development Biology (CABD-CSIC-JA), Pablo de Olavide University, 41013 Seville, Spain;
| | - Eduardo Egea
- Department of Medicine, Health Sciences Division, Universidad del Norte, Barranquilla 081007, Colombia; (D.M.); (L.F.); (C.M.-T.); (G.G.)
- Health Sciences Division, Universidad Simón Bolívar, Barranquilla 080002, Colombia
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Rizarullah, Aditama R, Giri-Rachman EA, Hertadi R. Designing a Novel Multiepitope Vaccine from the Human Papilloma Virus E1 and E2 Proteins for Indonesia with Immunoinformatics and Molecular Dynamics Approaches. ACS OMEGA 2024; 9:16547-16562. [PMID: 38617694 PMCID: PMC11007845 DOI: 10.1021/acsomega.4c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 04/16/2024]
Abstract
One of the deadliest malignant cancer in women globally is cervical cancer. Specifically, cervical cancer is the second most common type of cancer in Indonesia. The main infectious agent of cervical cancer is the human papilloma virus (HPV). Although licensed prophylactic vaccines are available, cervical cancer cases are on the rise. Therapy using multiepitope-based vaccines is a very promising therapy for cervical cancer. This study aimed to develop a multiepitope vaccine based on the E1 and E2 proteins of HPV 16, 18, 45, and 52 using in silico. In this study, we develop a novel multiepitope vaccine candidate using an immunoinformatic approach. We predicted the epitopes of the cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) and evaluated their immunogenic properties. Population coverage analysis of qualified epitopes was conducted to determine the successful use of the vaccine worldwide. The epitopes were constructed into a multiepitope vaccine by using AAY linkers between the CTL epitopes and GPGPG linkers between the HTL epitopes. The tertiary structure of the multiepitope vaccine was modeled with AlphaFold and was evaluated by Prosa-web. The results of vaccine construction were analyzed for B-cell epitope prediction, molecular docking with Toll like receptor-4 (TLR4), and molecular dynamics simulation. The results of epitope prediction obtained 4 CTL epitopes and 7 HTL epitopes that are eligible for construction of multiepitope vaccines. Prediction of the physicochemical properties of multiepitope vaccines obtained good results for recombinant protein production. The interaction showed that the interaction of the multiepitope vaccine-TLR4 complex is stable based on the binding free energy value -106.5 kcal/mol. The results of the immune response simulation show that multiepitope vaccine candidates could activate the adaptive and humoral immune systems and generate long-term B-cell memory. According to these results, the development of a multiepitope vaccine with a reverse vaccinology approach is a breakthrough to develop potential cervical cancer therapeutic vaccines.
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Affiliation(s)
- Rizarullah
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
- Department
of Biochemistry, Faculty of Medicine, Abulyatama
University, Jl. Blangbintang Lama, Aceh Besar 23372, Indonesia
| | - Reza Aditama
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Ernawati Arifin Giri-Rachman
- Genetics
and Molecular Biotechnology Research Division, School of Life Sciences
and Technology, Bandung Institute of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
| | - Rukman Hertadi
- Biochemistry
and Biomolecular Engineering Research Division, Faculty of Mathematics
and Natural Sciences, Bandung Institute
of Technology, Jl. Ganesa No. 10, Bandung 40132, Indonesia
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46
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Slieker RC, Warmerdam DO, Vermeer MH, van Doorn R, Heemskerk MHM, Scheeren FA. Reassessing human MHC-I genetic diversity in T cell studies. Sci Rep 2024; 14:7966. [PMID: 38575727 PMCID: PMC10995142 DOI: 10.1038/s41598-024-58777-2] [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: 11/01/2023] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
The Major Histocompatibility Complex class I (MHC-I) system plays a vital role in immune responses by presenting antigens to T cells. Allele specific technologies, including recombinant MHC-I technologies, have been extensively used in T cell analyses for COVID-19 patients and are currently used in the development of immunotherapies for cancer. However, the immense diversity of MHC-I alleles presents challenges. The genetic diversity serves as the foundation of personalized medicine, yet it also poses a potential risk of exacerbating healthcare disparities based on MHC-I alleles. To assess potential biases, we analysed (pre)clinical publications focusing on COVID-19 studies and T cell receptor (TCR)-based clinical trials. Our findings reveal an underrepresentation of MHC-I alleles associated with Asian, Australian, and African descent. Ensuring diverse representation is vital for advancing personalized medicine and global healthcare equity, transcending genetic diversity. Addressing this disparity is essential to unlock the full potential of T cells for enhancing diagnosis and treatment across all individuals.
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Affiliation(s)
- Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniël O Warmerdam
- Centre for Future Affordable & Sustainable Therapy Development (FAST), The Hague, The Netherlands
| | - Maarten H Vermeer
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Dermatology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mirjam H M Heemskerk
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ferenc A Scheeren
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands.
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Swain SK, Panda S, Sahu BP, Mahapatra SR, Dey J, Sarangi R, Misra N. Inferring B-cell derived T-cell receptor induced multi-epitope-based vaccine candidate against enterovirus 71: a reverse vaccinology approach. Clin Exp Vaccine Res 2024; 13:132-145. [PMID: 38752008 PMCID: PMC11091429 DOI: 10.7774/cevr.2024.13.2.132] [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: 08/26/2023] [Accepted: 03/30/2024] [Indexed: 05/18/2024] Open
Abstract
Purpose Enterovirus 71, a pathogen that causes hand-foot and mouth disease (HFMD) is currently regarded as an increasing neurotropic virus in Asia and can cause severe complications in pediatric patients with blister-like sores or rashes on the hand, feet, and mouth. Notwithstanding the significant burden of the disease, no authorized vaccine is available. Previously identified attenuated and inactivated vaccines are worthless over time owing to changes in the viral genome. Materials and Methods A novel vaccine construct using B-cell derived T-cell epitopes from the virulent polyprotein found the induction of possible immune response. In order to boost the immune system, a beta-defensin 1 preproprotein adjuvant with EAAAK linker was added at the N-terminal end of the vaccine sequence. Results The immunogenicity of the designed, refined, and verified prospective three-dimensional-structure of the multi-epitope vaccine was found to be quite high, exhibiting non-allergenic and antigenic properties. The vaccine candidates bound to toll-like receptor 3 in a molecular docking analysis, and the efficacy of the potential vaccine to generate a strong immune response was assessed through in silico immunological simulation. Conclusion Computational analysis has shown that the proposed multi-epitope vaccine is possibly safe for use in humans and can elicit an immune response.
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Affiliation(s)
- Subrat Kumar Swain
- Department of Medical Research, IMS and SUM Hospital, Siksha “O” Anusandhan Deemed to be University, Bhubaneswar, India
| | - Subhasmita Panda
- Department of Pediatrics, IMS and SUM Hospital, Siksha “O” Anusandhan Deemed to be University, Bhubaneswar, India
| | - Basanta Pravas Sahu
- School of Biological Science, The University of Hong Kong, Hong Kong
- Decipline of Biosciences and Biomedical Engineering, Indian Institute of Technology, Indore, India
| | - Soumya Ranjan Mahapatra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Jyotirmayee Dey
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Rachita Sarangi
- Department of Pediatrics, IMS and SUM Hospital, Siksha “O” Anusandhan Deemed to be University, Bhubaneswar, India
| | - Namrata Misra
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
- KIIT-Technology Business Incubator (KIIT-TBI), Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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Samudrala M, Dhaveji S, Savsani K, Dakshanamurthy S. AutoEpiCollect, a Novel Machine Learning-Based GUI Software for Vaccine Design: Application to Pan-Cancer Vaccine Design Targeting PIK3CA Neoantigens. Bioengineering (Basel) 2024; 11:322. [PMID: 38671743 PMCID: PMC11048108 DOI: 10.3390/bioengineering11040322] [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: 02/27/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Previous epitope-based cancer vaccines have focused on analyzing a limited number of mutated epitopes and clinical variables preliminarily to experimental trials. As a result, relatively few positive clinical outcomes have been observed in epitope-based cancer vaccines. Further efforts are required to diversify the selection of mutated epitopes tailored to cancers with different genetic signatures. To address this, we developed the first version of AutoEpiCollect, a user-friendly GUI software, capable of generating safe and immunogenic epitopes from missense mutations in any oncogene of interest. This software incorporates a novel, machine learning-driven epitope ranking method, leveraging a probabilistic logistic regression model that is trained on experimental T-cell assay data. Users can freely download AutoEpiCollectGUI with its user guide for installing and running the software on GitHub. We used AutoEpiCollect to design a pan-cancer vaccine targeting missense mutations found in the proto-oncogene PIK3CA, which encodes the p110ɑ catalytic subunit of the PI3K kinase protein. We selected PIK3CA as our gene target due to its widespread prevalence as an oncokinase across various cancer types and its lack of presence as a gene target in clinical trials. After entering 49 distinct point mutations into AutoEpiCollect, we acquired 361 MHC Class I epitope/HLA pairs and 219 MHC Class II epitope/HLA pairs. From the 49 input point mutations, we identified MHC Class I epitopes targeting 34 of these mutations and MHC Class II epitopes targeting 11 mutations. Furthermore, to assess the potential impact of our pan-cancer vaccine, we employed PCOptim and PCOptim-CD to streamline our epitope list and attain optimized vaccine population coverage. We achieved a world population coverage of 98.09% for MHC Class I data and 81.81% for MHC Class II data. We used three of our predicted immunogenic epitopes to further construct 3D models of peptide-HLA and peptide-HLA-TCR complexes to analyze the epitope binding potential and TCR interactions. Future studies could aim to validate AutoEpiCollect's vaccine design in murine models affected by PIK3CA-mutated or other mutated tumor cells located in various tissue types. AutoEpiCollect streamlines the preclinical vaccine development process, saving time for thorough testing of vaccinations in experimental trials.
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Affiliation(s)
- Madhav Samudrala
- College of Arts and Sciences, The University of Virginia, Charlottesville, VA 22903, USA
| | | | - Kush Savsani
- College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA 22043, USA
| | - Sivanesan Dakshanamurthy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
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Bautista E, Jung YH, Jaramillo M, Ganesh H, Varma A, Savsani K, Dakshanamurthy S. AutoPepVax, a Novel Machine-Learning-Based Program for Vaccine Design: Application to a Pan-Cancer Vaccine Targeting EGFR Missense Mutations. Pharmaceuticals (Basel) 2024; 17:419. [PMID: 38675381 PMCID: PMC11053815 DOI: 10.3390/ph17040419] [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: 03/03/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The current epitope selection methods for peptide vaccines often rely on epitope binding affinity predictions, prompting the need for the development of more sophisticated in silico methods to determine immunologically relevant epitopes. Here, we developed AutoPepVax to expedite and improve the in silico epitope selection for peptide vaccine design. AutoPepVax is a novel program that automatically identifies non-toxic and non-allergenic epitopes capable of inducing tumor-infiltrating lymphocytes by considering various epitope characteristics. AutoPepVax employs random forest classification and linear regression machine-learning-based models, which are trained with datasets derived from tumor samples. AutoPepVax, along with documentation on how to run the program, is freely available on GitHub. We used AutoPepVax to design a pan-cancer peptide vaccine targeting epidermal growth factor receptor (EGFR) missense mutations commonly found in lung adenocarcinoma (LUAD), colorectal adenocarcinoma (CRAD), glioblastoma multiforme (GBM), and head and neck squamous cell carcinoma (HNSCC). These mutations have been previously targeted in clinical trials for EGFR-specific peptide vaccines in GBM and LUAD, and they show promise but lack demonstrated clinical efficacy. Using AutoPepVax, our analysis of 96 EGFR mutations identified 368 potential MHC-I-restricted epitope-HLA pairs from 49,113 candidates and 430 potential MHC-II-restricted pairs from 168,669 candidates. Notably, 19 mutations presented viable epitopes for MHC I and II restrictions. To evaluate the potential impact of a pan-cancer vaccine composed of these epitopes, we used our program, PCOptim, to curate a minimal list of epitopes with optimal population coverage. The world population coverage of our list ranged from 81.8% to 98.5% for MHC Class II and Class I epitopes, respectively. From our list of epitopes, we constructed 3D epitope-MHC models for six MHC-I-restricted and four MHC-II-restricted epitopes, demonstrating their epitope binding potential and interaction with T-cell receptors. AutoPepVax's comprehensive approach to in silico epitope selection addresses vaccine safety, efficacy, and broad applicability. Future studies aim to validate the AutoPepVax-designed vaccines with murine tumor models that harbor the studied mutations.
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Affiliation(s)
- Enrico Bautista
- Georgetown University School of Medicine, Washington, DC 20007, USA
| | | | | | - Harrish Ganesh
- Virginia Commonwealth University, Richmond, VA 22043, USA
| | - Aryaan Varma
- The George Washington University, Washington, DC 20052, USA
| | - Kush Savsani
- Virginia Commonwealth University, Richmond, VA 22043, USA
| | - Sivanesan Dakshanamurthy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
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50
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Li M, Yu M, Yuan Y, Li D, Ye D, Zhao M, Lin Z, Shi L. Designing a conjugate vaccine targeting Klebsiella pneumoniae ST258 and ST11. Heliyon 2024; 10:e27417. [PMID: 38486755 PMCID: PMC10938132 DOI: 10.1016/j.heliyon.2024.e27417] [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: 09/22/2023] [Revised: 02/28/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a common bacterium that can cause iatrogenic infection. Recently, the rise of antibiotic resistance among K. pneumoniae strains is one key factor associated with antibiotic treatment failure. Hencefore, there is an urgent need for effective K. pneumoniae vaccines. This study aimed to design a multi-epitope vaccine (MEV) candidate against K. pneumonia by utilizing an immunoinformatics method. In this study, we obtained 15 cytotoxic T lymphocyte epitopes, 10 helper T lymphocyte epitopes, 6 linear B-cell epitopes, and 2 conformational B-cell epitopes for further research. Then, we designed a multi-epitope vaccine composed of a total of 743 amino acids, containing the epitopes linked by GPGPG flexible links and an EAAAK linker to the Cholera Toxin Subunit B coadjuvant. The observed properties of the MEV, including non-allergenicity, high antigenicity, and hydrophilicity, are noteworthy. The improvements in the tertiary structure through structural refinement and disulfide bonding, coupled with promising molecular interactions revealed by molecular dynamics simulations with TLR4, position the MEV as a strong candidate for further investigation against K. pneumoniae.
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Affiliation(s)
- Min Li
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Mingkai Yu
- School of Life Science and Technology, Southeast University, Xinjiekou Street, Xuanwu District, Nanjing, Jiangsu Province, China
| | - Yigang Yuan
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Danyang Li
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Daijiao Ye
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Min Zhao
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Zihan Lin
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Liuzhi Shi
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
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