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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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Naskar S, Harsukhbhai Chandpa H, Agarwal S, Meena J. Super epitope dengue vaccine instigated serotype independent immune protection in-silico. Vaccine 2024; 42:3857-3873. [PMID: 38616437 DOI: 10.1016/j.vaccine.2024.04.009] [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: 02/23/2024] [Revised: 03/21/2024] [Accepted: 04/04/2024] [Indexed: 06/14/2024]
Abstract
Dengue becomes the most common life-threatening infectious arbovirus disease globally, with prevalence in the tropical and subtropical areas. The major clinical features include dengue haemorrhagic fever (DHF) and dengue shock syndrome (DSS), a condition of hypovolemic shock. Four different serotypes of the dengue virus, known as dengue virus serotype (DENV)- 1, 2, 3 and 4 can infect humans. Only one vaccine is available in the market, named Dengvaxia by Sanofi Pasteur, but there is no desired outcome of this treatment due the antibody dependent enhancement (ADE) of the multiple dengue serotypes. As of now, there is no cure against dengue disease. Our goal in this work was to create a subunit vaccine based on several epitopes that would be effective against every serotype of the dengue virus. Here, computational methods like- immunoinformatics and bioinformatics were implemented to find out possible dominant epitopes. A total of 21 epitopes were chosen using various in-silico techniques from the expected 133 major histocompatibility complex (MHC)- I and major histocompatibility complex (MHC)- II epitopes, along with 95 B-cell epitopes which were greatly conserved. Immune stimulant, non-allergenic and non-toxic immunodominant epitopes (super epitopes) with a suitable adjuvant (Heparin-Binding Hemagglutinin Adhesin, HBHA) were used to construct the vaccine. Following the physicochemical analysis, vaccine construct was docked with Toll-like receptors (TLRs) to predict the immune stimulation. Consequently, the optimal docked complex that demonstrated the least amount of ligand-receptor complex deformability was used to conduct the molecular dynamics analysis. By following the codon optimization, the final vaccine molecule was administered into an expressing vector to perform in-silico cloning. The robust immune responses were generated in the in-silico immune simulation analysis. Hence, this study provides a hope to control the dengue infections. For validation of the immune outcomes, in-vitro as well as in-vivo investigations are essential.
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Affiliation(s)
- Shovan Naskar
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Hitesh Harsukhbhai Chandpa
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Shalini Agarwal
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Jairam Meena
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India.
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Salauddin M, Kayesh MEH, Ahammed MS, Saha S, Hossain MG. Development of membrane protein-based vaccine against lumpy skin disease virus (LSDV) using immunoinformatic tools. Vet Med Sci 2024; 10:e1438. [PMID: 38555573 PMCID: PMC10981917 DOI: 10.1002/vms3.1438] [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: 10/18/2023] [Revised: 02/09/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024] Open
Abstract
INTRODUCTION Lumpy skin disease, an economically significant bovine illness, is now found in previously unheard-of geographic regions. Vaccination is one of the most important ways to stop its further spread. AIM Therefore, in this study, we applied advanced immunoinformatics approaches to design and develop an effective lumpy skin disease virus (LSDV) vaccine. METHODS The membrane glycoprotein was selected for prediction of the different B- and T-cell epitopes by using the immune epitope database. The selected B- and T-cell epitopes were combined with the appropriate linkers and adjuvant resulted in a vaccine chimera construct. Bioinformatics tools were used to predict, refine and validate the 2D, 3D structures and for molecular docking with toll-like receptor 4 using different servers. The constructed vaccine candidate was further processed on the basis of antigenicity, allergenicity, solubility, different physiochemical properties and molecular docking scores. RESULTS The in silico immune simulation induced significant response for immune cells. In silico cloning and codon optimization were performed to express the vaccine candidate in Escherichia coli. This study highlights a good signal for the design of a peptide-based LSDV vaccine. CONCLUSION Thus, the present findings may indicate that the engineered multi-epitope vaccine is structurally stable and can induce a strong immune response, which should help in developing an effective vaccine towards controlling LSDV infection.
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Affiliation(s)
- Md. Salauddin
- Department of Microbiology and Public HealthKhulna Agricultural UniversityKhulnaBangladesh
| | | | - Md. Suruj Ahammed
- Department of ChemistryBangladesh University of Engineering and TechnologyDhakaBangladesh
| | - Sukumar Saha
- Department of Microbiology and HygieneBangladesh Agricultural UniversityMymensinghBangladesh
| | - Md. Golzar Hossain
- Department of Microbiology and HygieneBangladesh Agricultural UniversityMymensinghBangladesh
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4
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Ponne S, Kumar R, Vanmathi SM, Brilhante RSN, Kumar CR. Reverse engineering protection: A comprehensive survey of reverse vaccinology-based vaccines targeting viral pathogens. Vaccine 2024; 42:2503-2518. [PMID: 38523003 DOI: 10.1016/j.vaccine.2024.02.087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/30/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Vaccines have significantly reduced the impact of numerous deadly viral infections. However, there is an increasing need to expedite vaccine development in light of the recurrent pandemics and epidemics. Also, identifying vaccines against certain viruses is challenging due to various factors, notably the inability to culture certain viruses in cell cultures and the wide-ranging diversity of MHC profiles in humans. Fortunately, reverse vaccinology (RV) efficiently overcomes these limitations and has simplified the identification of epitopes from antigenic proteins across the entire proteome, streamlining the vaccine development process. Furthermore, it enables the creation of multiepitope vaccines that can effectively account for the variations in MHC profiles within the human population. The RV approach offers numerous advantages in developing precise and effective vaccines against viral pathogens, including extensive proteome coverage, accurate epitope identification, cross-protection capabilities, and MHC compatibility. With the introduction of RV, there is a growing emphasis among researchers on creating multiepitope-based vaccines aiming to stimulate the host's immune responses against multiple serotypes, as opposed to single-component monovalent alternatives. Regardless of how promising the RV-based vaccine candidates may appear, they must undergo experimental validation to probe their protection efficacy for real-world applications. The time, effort, and resources allocated to the laborious epitope identification process can now be redirected toward validating vaccine candidates identified through the RV approach. However, to overcome failures in the RV-based approach, efforts must be made to incorporate immunological principles and consider targeting the epitope regions involved in disease pathogenesis, immune responses, and neutralizing antibody maturation. Integrating multi-omics and incorporating artificial intelligence and machine learning-based tools and techniques in RV would increase the chances of developing an effective vaccine. This review thoroughly explains the RV approach, ideal RV-based vaccine construct components, RV-based vaccines designed to combat viral pathogens, its challenges, and future perspectives.
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Affiliation(s)
- Saravanaraman Ponne
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (Deemed to be University), Kirumampakkam, Puducherry 607402, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm 106 91, Sweden
| | - S M Vanmathi
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India
| | - Raimunda Sâmia Nogueira Brilhante
- Medical Mycology Specialized Center, Department of Pathology and Legal Medicine, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Chinnadurai Raj Kumar
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pondicherry 607402, India.
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Ali Z, Cardoza JV, Basak S, Narsaria U, Bhattacharjee S, G UM, Isaac SP, Franca TCC, LaPlante SR, George SS. A Multi-epitope Vaccine Candidate Against Bolivian Hemorrhagic fever Caused by Machupo Virus. Appl Biochem Biotechnol 2024; 196:2137-2160. [PMID: 37479961 DOI: 10.1007/s12010-023-04604-9] [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] [Accepted: 06/19/2023] [Indexed: 07/23/2023]
Abstract
Bolivian hemorrhagic fever (BHF) caused by Machupo virus (MACV) is a New World arenavirus having a reported mortality rate of 25-35%. The BHF starts with fever, followed by headache, and nausea which rapidly progresses to severe hemorrhagic phase within 7 days of disease onset. One of the key promoters for MACV viral entry into the cell followed by viral propagation is performed by the viral glycoprotein (GPC). GPC is post-transcriptionally cleaved into GP1, GP2 and a signal peptide. These proteins all take part in the viral infection in host body. Therefore, GPC protein is an ideal target for developing therapeutics against MACV infection. In this study, GPC protein was considered to design a multi-epitope, multivalent vaccine containing antigenic and immunogenic CTL and HTL epitopes. Different structural validations and physicochemical properties were analysed to validate the vaccine. Docking and molecular dynamics simulations were conducted to understand the interactions of the vaccine with various immune receptors. Finally, the vaccine was codon optimised in silico and along with which immune simulation studies was performed in order to evaluate the vaccine's effectiveness in triggering an efficacious immune response against MACV.
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Affiliation(s)
- Zeeshan Ali
- Krupanidhi College of Physiotherapy, Bangalore, Karnataka, 560035, India
| | | | | | | | | | | | - Samuel Paul Isaac
- Krupanidhi College of Physiotherapy, Bangalore, Karnataka, 560035, India
| | - Tanos C C Franca
- Military Institute of Engineering, Rio de Janerio, Brazil
- INRS - Centre Armand-Frappier Santé Biotechnologie, Université de Québec, Laval, Québec, H7V 1B7, Canada
- University of Hradec Kralove, Hradec Kralove, Czech Republic
| | - Steven R LaPlante
- INRS - Centre Armand-Frappier Santé Biotechnologie, Université de Québec, Laval, Québec, H7V 1B7, Canada
| | - Sudhan S George
- Krupanidhi College of Physiotherapy, Bangalore, Karnataka, 560035, India.
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Akter R, Tasneem F, Das S, Soma MA, Georgakopoulos-Soares I, Juthi RT, Sazed SA. Approaches of dengue control: vaccine strategies and future aspects. Front Immunol 2024; 15:1362780. [PMID: 38487527 PMCID: PMC10937410 DOI: 10.3389/fimmu.2024.1362780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/08/2024] [Indexed: 03/17/2024] Open
Abstract
Dengue, caused by the dengue virus (DENV), affects millions of people worldwide every year. This virus has two distinct life cycles, one in the human and another in the mosquito, and both cycles are crucial to be controlled. To control the vector of DENV, the mosquito Aedes aegypti, scientists employed many techniques, which were later proved ineffective and harmful in many ways. Consequently, the attention shifted to the development of a vaccine; researchers have targeted the E protein, a surface protein of the virus and the NS1 protein, an extracellular protein. There are several types of vaccines developed so far, such as live attenuated vaccines, recombinant subunit vaccines, inactivated virus vaccines, viral vectored vaccines, DNA vaccines, and mRNA vaccines. Along with these, scientists are exploring new strategies of developing improved version of the vaccine by employing recombinant DNA plasmid against NS1 and also aiming to prevent the infection by blocking the DENV life cycle inside the mosquitoes. Here, we discussed the aspects of research in the field of vaccines until now and identified some prospects for future vaccine developments.
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Affiliation(s)
- Runa Akter
- Department of Pharmacy, Independent University Bangladesh, Dhaka, Bangladesh
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Faria Tasneem
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Shuvo Das
- Department of Clinical Pharmacy and Pharmacology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | | | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Rifat Tasnim Juthi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Saiful Arefeen Sazed
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
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Murtaza A, Hoa NT, Dieu-Huong D, Afzal H, Tariq MH, Cheng LT, Chung YC. Advancing PEDV Vaccination: Comparison between Inactivated and Flagellin N-Terminus-Adjuvanted Subunit Vaccines. Vaccines (Basel) 2024; 12:139. [PMID: 38400123 PMCID: PMC10892538 DOI: 10.3390/vaccines12020139] [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: 12/02/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Vaccinations can serve as an important preventive measure against the porcine epidemic diarrhea (PED) virus that currently threatens the swine industry. This study focuses on the development of a fusion protein vaccine, FliC99-mCOE, which combines the N-terminus of flagellin (FliC99) with a modified core neutralizing epitope (mCOE) of PEDV. In silico immunoinformatic analysis confirmed the construct's non-toxic, non-allergenic, and highly antigenic nature. Molecular docking and molecular dynamics (MD) simulations demonstrated FliC99-mCOE's strong binding to the TLR-5 immunological receptor. Repeated exposure simulations and immunological simulations suggested enhanced cell-mediated immunity. Both FliC99-mCOE and an inactivated PEDV vaccine were produced and tested in mice. The results from cell proliferation, ELISA, and neutralization assays indicated that FliC99-mCOE effectively stimulated cellular immunity and neutralized PEDV. We conclude that the FliC99-mCOE fusion protein may serve as a promising vaccine candidate against PEDV.
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Affiliation(s)
- Asad Murtaza
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Nguyen-Thanh Hoa
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Do Dieu-Huong
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Haroon Afzal
- International Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan (N.-T.H.); (D.D.-H.); (H.A.)
| | - Muhammad Hamza Tariq
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates;
| | - Li-Ting Cheng
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Yao-Chi Chung
- Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
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Aarthy M, Pandiyan GN, Paramasivan R, Kumar A, Gupta B. Identification and prioritisation of potential vaccine candidates using subtractive proteomics and designing of a multi-epitope vaccine against Wuchereria bancrofti. Sci Rep 2024; 14:1970. [PMID: 38263422 PMCID: PMC10806236 DOI: 10.1038/s41598-024-52457-x] [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: 06/26/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
This study employed subtractive proteomics and immunoinformatics to analyze the Wuchereria bancrofti proteome and identify potential therapeutic targets, with a focus on designing a vaccine against the parasite species. A comprehensive bioinformatics analysis of the parasite's proteome identified 51 probable therapeutic targets, among which "Kunitz/bovine pancreatic trypsin inhibitor domain-containing protein" was identified as the most promising vaccine candidate. The candidate protein was used to design a multi-epitope vaccine, incorporating B-cell and T-cell epitopes identified through various tools. The vaccine construct underwent extensive analysis of its antigenic, physical, and chemical features, including the determination of secondary and tertiary structures. Docking and molecular dynamics simulations were performed with HLA alleles, Toll-like receptor 4 (TLR4), and TLR3 to assess its potential to elicit the human immune response. Immune simulation analysis confirmed the predicted vaccine's strong binding affinity with immunoglobulins, indicating its potential efficacy in generating an immune response. However, experimental validation and testing of this multi-epitope vaccine construct would be needed to assess its potential against W. bancrofti and even for a broader range of lymphatic filarial infections given the similarities between W. bancrofti and Brugia.
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Affiliation(s)
- Murali Aarthy
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - G Navaneetha Pandiyan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - R Paramasivan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre (VCRC), Puducherry, India
- Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Tandhalam, Chennai, Tamil Nadu, 602105, India
| | - Bhavna Gupta
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India.
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Aiman S, Farooq QUA, Han Z, Aslam M, Zhang J, Khan A, Ahmad A, Li C, Ali Y. Core-genome-mediated promising alternative drug and multi-epitope vaccine targets prioritization against infectious Clostridium difficile. PLoS One 2024; 19:e0293731. [PMID: 38241420 PMCID: PMC10798517 DOI: 10.1371/journal.pone.0293731] [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: 08/01/2023] [Accepted: 10/18/2023] [Indexed: 01/21/2024] Open
Abstract
Prevention of Clostridium difficile infection is challenging worldwide owing to its high morbidity and mortality rates. C. difficile is currently being classified as an urgent threat by the CDC. Devising a new therapeutic strategy become indispensable against C. difficile infection due to its high rates of reinfection and increasing antimicrobial resistance. The current study is based on core proteome data of C. difficile to identify promising vaccine and drug candidates. Immunoinformatics and vaccinomics approaches were employed to construct multi-epitope-based chimeric vaccine constructs from top-ranked T- and B-cell epitopes. The efficacy of the designed vaccine was assessed by immunological analysis, immune receptor binding potential and immune simulation analyses. Additionally, subtractive proteomics and druggability analyses prioritized several promising and alternative drug targets against C. difficile. These include FMN-dependent nitroreductase which was prioritized for pharmacophore-based virtual screening of druggable molecule databases to predict potent inhibitors. A MolPort-001-785-965 druggable molecule was found to exhibit significant binding affinity with the conserved residues of FMN-dependent nitroreductase. The experimental validation of the therapeutic targets prioritized in the current study may worthy to identify new strategies to combat the drug-resistant C. difficile infection.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Qurrat ul Ain Farooq
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Muneeba Aslam
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Jilong Zhang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, KP, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Yasir Ali
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, Hong Kong
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Zhang S, Nan F, Jiang S, Zhou X, Niu D, Li J, Wang H, Zhang X, Zhang X, Wang B. CRM197-conjugated peptides vaccine of HCMV pp65 and gH induce maturation of DC and effective viral-specific T cell responses. Virulence 2023; 14:2169488. [PMID: 36723437 PMCID: PMC9897769 DOI: 10.1080/21505594.2023.2169488] [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] [Indexed: 02/02/2023] Open
Abstract
Human cytomegalovirus (HCMV) infection is prevalent worldwide, and there is currently no licenced HCMV vaccine to control it. Therefore, developing an effective HCMV vaccine is a significant priority. Because of their excellent immunogenicity, the crucial components of HCMV, phosphoprotein 65 (pp65) and glycoproteins H (gH) are potential target proteins for HCMV vaccine design. In this study, we predicted and screened the dominant antigenic epitopes of B and T cells from pp65 and gH conjugated with the carrier protein cross-reacting material 197 (CRM197) to form three peptide-CRM197 vaccines (pp65-CRM197, gH-CRM197, and pp65-CRM197+gH-CRM197). Furthermore, the immunogenicity of the peptide-CRM197 vaccines and their effects on dendritic cells (DCs) were explored. The results showed that three peptide-CRM197 vaccines could induce maturation of DCs through the p38 MAPK signalling pathway and promote the release of proinflammatory factors, such as TNF-α and interleukin (IL) -6. Meanwhile, the peptide-CRM197 vaccines could effectively activate T cell and humoral immunity, which were far better than the inactivated HCMV vaccine. In conclusion, we constructed three peptide-CRM197 vaccines, which could induce multiple immune effects, providing a novel approach for HCMV vaccine design.
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Affiliation(s)
- Shuyun Zhang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China,CONTACT Bin Wang Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine Qingdao University, Qingdao, China
| | - Fulong Nan
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China,CONTACT Bin Wang Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine Qingdao University, Qingdao, China
| | - Shasha Jiang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xiaoqiong Zhou
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Delei Niu
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Jun Li
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Hui Wang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xueming Zhang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xianjuan Zhang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Bin Wang
- Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China,CONTACT Bin Wang Department of Pathogenic Biology, Department of Special Medicine, School of Basic Medicine Qingdao University, Qingdao, China
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11
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Oladipo EK, Ojo TO, Olufemi SE, Irewolede BA, Adediran DA, Abiala AG, Hezekiah OS, Idowu AF, Oladeji YG, Ikuomola MO, Olayinka AT, Akanbi GO, Idowu UA, Olubodun OA, Odunlami FD, Ogunniran JA, Akinro OP, Adegoke HM, Folakanmi EO, Usman TA, Oladokun EF, Oluwasanya GJ, Awobiyi HO, Oluwasegun JA, Akintibubo SA, Jimah EM. Proteome based analysis of circulating SARS-CoV-2 variants: approach to a universal vaccine candidate. Genes Genomics 2023; 45:1489-1508. [PMID: 37548884 DOI: 10.1007/s13258-023-01426-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 07/09/2023] [Indexed: 08/08/2023]
Abstract
The discovery of the first infectious variant in Wuhan, China, in December 2019, has posed concerns over global health due to the spread of COVID-19 and subsequent variants. While the majority of patients experience flu-like symptoms such as cold and fever, a small percentage, particularly those with compromised immune systems, progress from mild illness to fatality. COVID-19 is caused by a RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our approach involved utilizing immunoinformatic to identify vaccine candidates with multiple epitopes and ligand-binding regions in reported SARS-CoV-2 variants. Through analysis of the spike glycoprotein, we identified dominant epitopes for T-cells and B-cells, resulting in a vaccine construct containing two helper T-cell epitopes, six cytotoxic T-cell epitopes, and four linear B-cell epitopes. Prior to conjugation with adjuvants and linkers, all epitopes were evaluated for antigenicity, toxicity, and allergenicity. Additionally, we assessed the vaccine Toll-Like Receptors complex (2, 3, and 4). The vaccine construct demonstrated antigenicity, non-toxicity, and non-allergenicity, thereby enabling the host to generate antibodies with favorable physicochemical characteristics. Furthermore, the 3D structure of the B-cell construct exhibited a ProSA-web z-score plot with a value of -1.71, indicating the reliability of the designed structure. The Ramachandran plot analysis revealed that 99.6% of the amino acid residues in the vaccine subunit were located in the high favored observation region, further establishing its strong candidacy as a vaccination option.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Informatics, Adeleke University, Ede, Osun State, Nigeria.
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria.
| | - Taiwo Ooreoluwa Ojo
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Seun Elijah Olufemi
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Daniel Adewole Adediran
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Asegunloluwa Grace Abiala
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Oluwaseun Samuel Hezekiah
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Akindele Felix Idowu
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Yinmi Gabriel Oladeji
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Microbiology, Obafemi Awolowo University, Ile Ife, Osun State, Nigeria
| | - Mary Omotoyinbo Ikuomola
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Adenike Titilayo Olayinka
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Gideon Oluwamayowa Akanbi
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Usman Abiodun Idowu
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Odunola Abimbola Olubodun
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Folusho Daniel Odunlami
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - James Akinwumi Ogunniran
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Omodamola Paulina Akinro
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Hadijat Motunrayo Adegoke
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Computational Biophysical Chemistry Laboratory, Department of Pure and Applied Chemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Elizabeth Oluwatoyin Folakanmi
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Elizabeth Folakemi Oladokun
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | | | - Jerry Ayobami Oluwasegun
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Samuel Adebowale Akintibubo
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Pure and Applied Biology, Microbiology Unit, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
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12
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Bano N, Kumar A. Immunoinformatics study to explore dengue (DENV-1) proteome to design multi-epitope vaccine construct by using CD4+ epitopes. J Genet Eng Biotechnol 2023; 21:128. [PMID: 37987878 PMCID: PMC10663418 DOI: 10.1186/s43141-023-00592-9] [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: 04/24/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND Immunoinformatics is an emerging interdisciplinary field which integrates immunology, bioinformatics, and computational biology to study the immune system. In this study, we apply immunoinformatics approaches to explore the dengue proteome in order to design a multi-epitope vaccine construct. METHODS We used existing databases and algorithms to predict potential epitopes on dengue proteins and used a bioinformatics approach to identify the most promising epitopes. We then used molecular modelling to develop a multi-epitope construct which could be used as a potential vaccine. The results of this study demonstrate that immunoinformatics is a powerful tool for exploring and designing potential vaccines for infectious diseases like dengue. RESULTS Here, we found four CD4+ epitopes NLKYSVIVTVHTGDQ, ANPIVTDKEKPVNIE, LDPVVYDAKFEKQL, and VGAIALDFKPGTSGS that were used to design vaccine construct. The vaccine construct docked with TLR5. RMSD values suggest that docked complex of TLR5 and vaccine construct have putative stable interaction to induce immunogenic effects on host. CONCLUSIONS Furthermore, our study provides a proof of concept for the use of immunoinformatics approaches in DENV vaccine design. This vaccine can be effective in treating patients infected with DENV virus.
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Affiliation(s)
- Nishat Bano
- Department of Biotechnology, Faculty of Engineering and Technology Rama University, G.T. Road, Kanpur, 209217, India
| | - Ajay Kumar
- Department of Biotechnology, Faculty of Engineering and Technology Rama University, G.T. Road, Kanpur, 209217, India.
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13
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Shah M, Jaan S, Shehroz M, Sarfraz A, Asad K, Wara TU, Zaman A, Ullah R, Ali EA, Nishan U, Ojha SC. Deciphering the Immunogenicity of Monkeypox Proteins for Designing the Potential mRNA Vaccine. ACS OMEGA 2023; 8:43341-43355. [PMID: 38024731 PMCID: PMC10652822 DOI: 10.1021/acsomega.3c07866] [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: 10/09/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
The Monkeypox virus (MPXV), an orthopox virus, is responsible for monkeypox in humans, a zoonotic disease similar to smallpox. This infection first appeared in the 1970s in humans and then in 2003, after which it kept on spreading all around the world. To date, various antivirals have been used to cure this disease, but now, MPXV has developed resistance against these, thus increasing the need for an alternative cure for this deadly disease. In this study, we devised a reverse vaccinology approach against MPXV using a messenger RNA (mRNA) vaccine by pinning down the antigenic proteins of this virus. By using bioinformatic tools, we predicted prospective immunogenic B and T lymphocyte epitopes. Based on cytokine inducibility score, nonallergenicity, nontoxicity, antigenicity, and conservancy, the final epitopes were selected. Our analysis revealed the stable structure of the mRNA vaccine and its efficient expression in host cells. Furthermore, strong interactions were demonstrated with toll-like receptors 2 (TLR2) and 4 (TLR4) according to the molecular dynamic simulation studies. The in silico immune simulation analyses revealed an overall increase in the immune responses following repeated exposure to the designed vaccine. Based on our findings, the vaccine candidate designed in this study has the potential to be tested as a promising novel mRNA therapeutic vaccine against MPXV infection.
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Affiliation(s)
- Mohibullah Shah
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Samavia Jaan
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
- School
of Biochemistry and Biotechnology, University
of the Punjab, Lahore 54590, Pakistan
| | - Muhammad Shehroz
- Department
of Bioinformatics, Kohsar University Murree, Murree 47150 Pakistan
| | - Asifa Sarfraz
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Khamna Asad
- School
of Biochemistry and Biotechnology, University
of the Punjab, Lahore 54590, Pakistan
| | - Tehreem Ul Wara
- Department
of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Aqal Zaman
- Department
of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Riaz Ullah
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University Riyadh 11451, Saudi Arabia
| | - Essam A. Ali
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Umar Nishan
- Department
of Chemistry, Kohat University of Science
& Technology, Kohat 26000, Pakistan
| | - Suvash Chandra Ojha
- Department
of Infectious Diseases, The Affiliated Hospital
of Southwest Medical University, 646000 Luzhou, China
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14
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Moten D, Batsalova T, Apostolova D, Mladenova T, Dzhambazov B, Teneva I. In Silico Design of a New Epitope-Based Vaccine against Grass Group 1 Allergens. Adv Respir Med 2023; 91:486-503. [PMID: 37987298 PMCID: PMC10660545 DOI: 10.3390/arm91060036] [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: 08/31/2023] [Revised: 10/09/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023]
Abstract
Allergic diseases are a global public health problem that affects up to 30% of the population in industrialized societies. More than 40% of allergic patients suffer from grass pollen allergy. Grass pollen allergens of group 1 and group 5 are the major allergens, since they induce allergic reactions in patients at high rates. In this study, we used immunoinformatic approaches to design an effective epitope-based vaccine against the grass group 1 allergens. After the alignment of all known pollen T-cell and B-cell epitopes from pollen allergens available in the public databases, the epitope GTKSEVEDVIPEGWKADTSY was identified as the most suitable for further analyses. The target sequence was subjected to immunoinformatics analyses to predict antigenic T-cell and B-cell epitopes. Population coverage analysis was performed for CD8+ and CD4+ T-cell epitopes. The selected T-cell epitopes (VEDVIPEGW and TKSEVEDVIPEGWKA) covered 78.87% and 98.20% of the global population and 84.57% and 99.86% of the population of Europe. Selected CD8+, CD4+ T-cell and B-cell epitopes have been validated by molecular docking analysis. CD8+ and CD4+ T-cell epitopes showed a very strong binding affinity to major histocompatibility complex (MHC) class I (MHC I) molecules and MHC class II (MHC II) molecules with global energy scores of -72.1 kcal/mol and -89.59 kcal/mol, respectively. The human IgE-Fc (PDB ID 4J4P) showed a lower affinity with B-cell epitope (ΔG = -34.4 kcal/mol), while the Phl p 2-specific human IgE Fab (PDB ID 2VXQ) had the lowest binding with the B-cell epitope (ΔG = -29.9 kcal/mol). Our immunoinformatics results demonstrated that the peptide GTKSEVEDVIPEGWKADTSY could stimulate the immune system and we performed ex vivo tests showed that the investigated epitope activates T cells isolated from patients with grass pollen allergy, but it is not recognized by IgE antibodies specific for grass pollen allergens. This confirms the importance of such studies to establish universal epitopes to serve as a basis for developing an effective vaccine against a particular group of allergens. Further in vivo studies are needed to validate the effectiveness of such a vaccine against grass pollen allergens.
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Affiliation(s)
- Dzhemal Moten
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Tsvetelina Batsalova
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Desislava Apostolova
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Tsvetelina Mladenova
- Department of Botany and Biological Education, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria;
| | - Balik Dzhambazov
- Department of Developmental Biology, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria; (D.M.); (T.B.); (D.A.); (B.D.)
| | - Ivanka Teneva
- Department of Botany and Biological Education, Faculty of Biology, Paisii Hilendarski University of Plovdiv, 24 Tsar Assen Str., 4000 Plovdiv, Bulgaria;
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15
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Ishaq Z, Zaheer T, Waseem M, Shahwar Awan H, Ullah N, AlAsmari AF, AlAsmari F, Ali A. Immunoinformatics aided designing of a next generation poly-epitope vaccine against uropathogenic Escherichia coli to combat urinary tract infections. J Biomol Struct Dyn 2023:1-21. [PMID: 37811774 DOI: 10.1080/07391102.2023.2266018] [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: 03/18/2023] [Accepted: 09/27/2023] [Indexed: 10/10/2023]
Abstract
Urinary tract infections (UTIs) are the second most prevalent bacterial infections and uropathogenic Escherichia coli (UPEC) stands among the primary causative agents of UTIs. The usage of antibiotics is the routine therapy being used in various countries to treat UTIs but becoming ineffective because of increasing antibiotic resistance among UPEC strains. Thus, there must be the development of some alternative treatment strategies such as vaccine development against UPEC. In the following study, pan-genomics along with reverse vaccinology approaches is used under the framework of bioinformatics for the identification of core putative vaccine candidates, employing 307 UPEC genomes (complete and draft), available publicly. A total of nine T-cell epitopes (derived from B-cells) of both MHC classes (I and II), were prioritized among three potential protein candidates. These epitopes were then docked together by using linkers (GPGPG and AAY) and an adjuvant (Cholera Toxin B) to form a poly-valent vaccine construct. The chimeric vaccine construct was undergone by molecular modelling, further refinement and energy minimization. We predicted positive results of the vaccine construct in immune simulations with significantly high levels of immune cells. The protein-protein docking analysis of vaccine construct with toll-like receptors predicted efficient binding, which was further validated by molecular dynamics simulation of vaccine construct with TLR-2 and TLR-4 at 120 ns, resulting in stable complexes' conformation throughout the simulation run. Overall, the vaccine construct demonstrated positive antigenic response. In future, this chimeric vaccine construct or the identified epitopes could be experimentally validated for the development of UPEC vaccines against UTIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zaara Ishaq
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tahreem Zaheer
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Department of Biology, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Maaz Waseem
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Hayeqa Shahwar Awan
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- Shifa International Hospitals Ltd, Islamabad, Pakistan
| | - Nimat Ullah
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- NYU Langone Health, New York, United States
| | - Abdullah F AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fawaz AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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16
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Khan MAS, Miah MI, Rahman SR. A comprehensive immunoinformatic analysis of chitin deacetylase's and MP88 for designing multi-epitope vaccines against Cryptococcus neoformans. J Biomol Struct Dyn 2023:1-16. [PMID: 37723882 DOI: 10.1080/07391102.2023.2258410] [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: 03/07/2023] [Accepted: 09/06/2023] [Indexed: 09/20/2023]
Abstract
Cryptococcus neoformans causes life-threatening pneumonia and meningitis and is regarded as one of the leading killers of immunocompromised individuals. There is currently no vaccine against this pathogen. Recently, WHO placed it at the top among the critical priority groups in the fungal priority pathogens to accelerate the development of effective treatments. Numerous studies suggested the potential of subunit vaccines to overcome the challenges associated with live and inactivated whole-cell vaccines. Therefore, this study exploited integrated reverse vaccinology and immunoinformatic approach to construct and characterize multi-epitope vaccines targeting chitin deacetylases (Cda1, Cda2, Cda3) and MP88 of C. neoformans. 4 CTL, 8 HTL and 6 B cell epitopes were fused with different adjuvants and appropriate linkers to design two multi-epitope vaccines (VC1 and VC2). Both chimeric constructs were predicted to be highly antigenic, non-allergenic, non-toxic, soluble and had satisfactory physicochemical properties. Molecular docking and binding free energy calculation revealed strong binding interactions between vaccine constructs and human TLRs (TLR-2 and TLR-4). Classical MD Simulation and Normal mode analysis verified the stability of the vaccine-TLR complex in the biological environment. Codon adaptation, cloning and in silico expression suggested the efficient expression of recombinant vaccine proteins in E. coli. Both candidates also generated robust immune profiles comprising innate, adaptive and humoral immune responses. Taken together, experimental validations of our findings through extensive in vitro and in vivo testing might provide an effective vaccine for prophylactic control of C. neoformans.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Md Ibrahim Miah
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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17
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Guo X, Pan X, Sun Q, Hu Y, Shi J. Design of a novel multiepitope vaccine against Chlamydia pneumoniae using the extracellular protein as a target. Sci Rep 2023; 13:15070. [PMID: 37700027 PMCID: PMC10497608 DOI: 10.1038/s41598-023-42222-x] [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: 05/11/2023] [Accepted: 09/06/2023] [Indexed: 09/14/2023] Open
Abstract
Chlamydia pneumoniae (C. pneumoniae) infection in humans is universal and causes various respiratory infectious diseases, making a safe and effective preventive vaccine essential. In this study, a multi-epitope vaccine with CTLA-4 extracellular structure was constructed by an immunoinformatics approach. Since MOMP protein is the major extracellular protein in C. pneumoniae and has good immunogenicity and high conservation, we selected the MOMP protein of C. pneumoniae as the antigen target, predicted the T and B cell epitopes of the MOMP protein and then connected the CTLA-4 extracellular structure with the predicted dominant epitopes by various linkers to construct a multi-epitope vaccine. The biochemical characterization of the multi-epitope vaccine showed its immunogenicity and anti-allergic properties. The tertiary structure of this vaccine, along with molecular docking, molecular dynamics simulation, and principal component analysis, showed that the multi-epitope vaccine structure interacted with B7 (B7-1, B7-2) and toll-like receptors (TLR-2, TLR-4). Ultimately, the vaccine was cloned and effectively expressed in silico on an insect baculovirus expression vector (pFastBac1). These analyses showed that the designed vaccine could potentially target antigen-presenting cells and was immune to C. pneumoniae, which provided novel strategies for developing the vaccine.
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Affiliation(s)
- Xiaomei Guo
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan, China
- Kunming Medical University, Kunming, Yunnan, China
| | - Xiaohong Pan
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan, China
| | - Qiangming Sun
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan, China.
- National Kunming High-Level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan, China.
- Kunming Medical University, Kunming, Yunnan, China.
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-Borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 935 Jiaoling Road, Kunming, 650118, Yunnan, China.
- National Kunming High-Level Biosafety Primate Research Center, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
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18
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Al-Kubati AAG, Kandeel M, Hussen J, Hemida MG, Al-Mubarak AIA. Immunoinformatic prediction of the pathogenicity of bovine viral diarrhea virus genotypes: implications for viral virulence determinants, designing novel diagnostic assays and vaccines development. Front Vet Sci 2023; 10:1130147. [PMID: 37483297 PMCID: PMC10359904 DOI: 10.3389/fvets.2023.1130147] [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: 12/22/2022] [Accepted: 05/31/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction Bovine viral diarrhea virus (BVDV) significantly impacts the bovine industries, both dairy and beef sectors. BVDV can infect various domestic and wild animals, most notably cattle. The dynamic variations among BVDV serotypes due to the continuous genetic diversity, especially in BVDV1 (BVDV1), reduce the effectiveness of the currently available vaccines and reduce the specificity/sensitivity of the diagnostic assays. The development of novel, safe, and effective vaccines against BVDV requires deep knowledge of the antigenicity and virulence of the virus. Previous studies on the antigenicity and the virulence of BVDV serotypes have been mainly focused on one or a few BVDV proteins. While however, little is known about the orchestration of all BVDV in the context of viral virulence and immunogenicity. The main aim of the current study was to do a comparative computational evaluation of the immunogenicity, and virulence for all the encoded proteins of both BVDV1 and BVDV2 and their sub-genotypes. Methods To achieve this goal, 11,737 protein sequences were retrieved from Virus Pathogen Resource. The analysis involved a total of 4,583 sequences after the removal of short sequences and those with unknown collection time. We used the MP3 tool to map the pathogenic proteins across different BVDV strains. The potential protective and the epitope motifs were predicted using the VaxiJen and EMBOSS antigen tools, respectively. Results and discussion The virulence prediction revealed that the NS4B proteins of both BVDV1 and BVDV2 likely have essential roles in BVDV virulence. Similarly, both the capsid (C) and the NS4-A proteins of BVDV1 and the Npro and P7 proteins of BVDV2 are likely important virulent factors. There was a clear trend of increasing predicted virulence with the progression of time in the case of BVDV1 proteins, but that was not the case for the BVDV2 proteins. Most of the proteins of the two BVDV serotypes possess antigens predicted immunogens except Npro, P7, and NS4B. However, the predicted antigenicity of the BVDV1 was significantly higher than that of BVDV2. Meanwhile, the predicted immunogenicity of the immunodominant-E2 protein has been decreasing over time. Based on our predicted antigenicity and pathogenicity studies of the two BVDV serotypes, the sub-genotypes (1a, 1f, 1k, 2a, and 2b) may represent ideal candidates for the development of future vaccines against BVDV infection in cattle. In summary, we identified some common differences between the two BVDV genotypes (BVDV1 and BVDV2) and their sub-genotypes regarding their protein antigenicity and pathogenicity. The data presented here will increase our understanding of the molecular pathogenesis of BVDV infection in cattle. It will also pave the way for developing some novel diagnostic assays and novel vaccines against BVDV in the near future.
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Affiliation(s)
- Anwar A. G. Al-Kubati
- Department of Veterinary Medicine, Faculty of Agriculture and Veterinary Medicine, Thamar University, Thamar, Yemen
| | - Mahmoud Kandeel
- Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
- Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Jamal Hussen
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, New York, NY, United States
| | - Maged Gomaa Hemida
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
| | - Abdullah I. A. Al-Mubarak
- Department of Microbiology, College of Veterinary Medicine, King Faisal University, Al-Hofuf, Saudi Arabia
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, New York, NY, United States
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19
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Dhanushkumar T, Kamaraj B, Vasudevan K, Gopikrishnan M, Dasegowda KR, Rambabu M, George Priya Doss C. Structural immunoinformatics approach for rational design of a multi-epitope vaccine against triple negative breast cancer. Int J Biol Macromol 2023:125209. [PMID: 37271264 DOI: 10.1016/j.ijbiomac.2023.125209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/22/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
TNBC is a highly malignant breast cancer known for its aggressive behavior affecting young female adults. The standard treatment for TNBC includes surgery, chemotherapy, and radiotherapy, which often have significant side effects. Therefore, novel preventive methods are required to combat TNBC effectively. In this study, we utilized immunoinformatics to construct an in-silico vaccine against TNBC using the TRIM25 molecule via the reverse vaccinology method. Four vaccines were designed by generating T and B-cell epitopes linked with four different linkers. The modeled vaccine was docked and the results showed that vaccine-3 exhibited the highest affinity with the immune receptors. The molecular dynamics results revealed that the binding affinity and stability of Vaccine-3 were greater than those of Vaccine 2 complexes. This study has great potential preventive measures for TNBC, and further research is warranted to evaluate its efficacy in preclinical settings. This study presents an innovative preventive strategy for triple-negative breast cancer (TNBC) through immunoinformatics and reverse vaccinology to develop an in-silico vaccine. Leveraging these innovative techniques offers a novel avenue for combating the complex challenges associated with TNBC. This approach demonstrates considerable potential as a significant breakthrough in preventive measures for this particularly aggressive and malignant form of breast cancer.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Balu Kamaraj
- Department of Dental Education, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - Mohanraj Gopikrishnan
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India
| | - K R Dasegowda
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Majji Rambabu
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
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Fahira A, Amin RS, Arshad U, Khan MI, Shah Syed AA, Alshammari A, Yang Q, Wang Z, Ali L, Shi Y. Chimeric vaccine design against the epidemic Langya Henipavirus using immunoinformatics and validation via immune simulation approaches. Heliyon 2023; 9:e17376. [PMID: 37484358 PMCID: PMC10361368 DOI: 10.1016/j.heliyon.2023.e17376] [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: 03/14/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023] Open
Abstract
In July 2022, a new virus called Langya virus (LayV) was discovered in China in patients who had a fever. This virus is a type of Henipavirus (HNV) and is considered a potential threat as it could spread from animals to humans. It causes respiratory disease with symptoms including fever, coughing, and fatigue and is closely linked to two other henipaviruses that are known to infect humans, namely Hendra and Nipah viruses. These viruses may cause fatal respiratory illnesses. Investigators believe that the LayV is spread by shrews, and may have infected humans directly or via an intermediary species. Thus, the use of vaccines or immunizations against LayV is an alternate strategy for disease prevention. In this study, we employed various immunoinformatics methods to predict B cell, HTL and T cell epitopes from the LayV proteome in order to find the most promising candidate for a LayV vaccine. The most potent epitopes that are immunogenic and non-allergenic were joined with each other through suitable linkers. Human β-defensin 2 was employed as an adjuvant to increase the immunogenicity of the vaccine construct. The final sequence of a multi-epitope vaccine construct was modelled for docking with TLRs. Concisely, our results suggest that the docked complexes of vaccine-TLRs seemed to be stable. Additionally, in silico cloning was done using E. coli as the host in order to validate the expression of our designed vaccine construct. The GC content of 54.39% and CAI value of 0.94 revealed that the vaccine component expresses efficiently in the host. This study presents the novel vaccine construct for LayV which will be essential for further experimental validations to confirm the immunogenicity and safety of the proposed vaccine structure, and eventually to treat HNV-related diseases.
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Affiliation(s)
- Aamir Fahira
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Centre for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, Shandong Province, China
| | | | - Uzma Arshad
- Gujranwala Medical College, Gujranwala, Punjab, Pakistan
| | - Muhammad Idrees Khan
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ali Alamdar Shah Syed
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Centre for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Qiangzhen Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Centre for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Centre for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, Shandong Province, China
| | - Liaqat Ali
- Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, USA
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Centre for Brain Science, Shanghai Jiao Tong University, Shanghai, China
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, Shandong Province, China
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21
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Kakakhel S, Ahmad A, Mahdi WA, Alshehri S, Aiman S, Begum S, Shams S, Kamal M, Imran M, Shakeel F, Khan A. Annotation of Potential Vaccine Targets and Designing of mRNA-Based Multi-Epitope Vaccine against Lumpy Skin Disease Virus via Reverse Vaccinology and Agent-Based Modeling. Bioengineering (Basel) 2023; 10:bioengineering10040430. [PMID: 37106617 PMCID: PMC10135540 DOI: 10.3390/bioengineering10040430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/15/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023] Open
Abstract
Lumpy skin disease is a fatal emerging disease of cattle, which has started to gain extensive attention due to its rapid incursions across the globe. The disease epidemic causes economic loss and cattle morbidity. Currently, there are no specific treatments and safe vaccines against the lumpy skin disease virus (LSDV) to halt the spread of the disease. The current study uses genome-scan vaccinomics analyses to prioritize promiscuous vaccine candidate proteins of the LSDV. These proteins were subjected to top-ranked B- and T-cell epitope prediction based on their antigenicity, allergenicity, and toxicity values. The shortlisted epitopes were connected using appropriate linkers and adjuvant sequences to design multi-epitope vaccine constructs. Three vaccine constructs were prioritized based on their immunological and physicochemical properties. The model constructs were back-translated to nucleotide sequences and codons were optimized. The Kozak sequence with a start codon along with MITD, tPA, Goblin 5′, 3′ UTRs, and a poly(A) tail sequences were added to design a stable and highly immunogenic mRNA vaccine. Molecular docking followed by MD simulation analysis predicted significant binding affinity and stability of LSDV-V2 construct within bovine immune receptors and predicted it to be the top-ranked candidate to stimulate the humeral and cellular immunogenic responses. Furthermore, in silico restriction cloning predicted feasible gene expression of the LSDV-V2 construct in a bacterial expression vector. It could prove worthwhile to validate the predicted vaccine models experimentally and clinically against LSDV.
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Affiliation(s)
- Sehrish Kakakhel
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, KP, Pakistan
| | - Abbas Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan 23200, KP, Pakistan
| | - Wael A. Mahdi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sultan Alshehri
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia
| | - Sara Aiman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, KP, Pakistan
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Sara Begum
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, KP, Pakistan
| | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, KP, Pakistan
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Mohd. Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Faiyaz Shakeel
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan 23200, KP, Pakistan
- Correspondence:
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Madanagopal P, Muthusamy S, Pradhan SN, Prince PR. Construction and validation of a multi-epitope in silico vaccine model for lymphatic filariasis by targeting Brugia malayi: a reverse vaccinology approach. BULLETIN OF THE NATIONAL RESEARCH CENTRE 2023; 47:47. [PMID: 36987521 PMCID: PMC10037386 DOI: 10.1186/s42269-023-01013-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Lymphatic filariasis (LF), often referred to as elephantiasis, has been identified as one of the 17 neglected tropical diseases by the World Health Organization. Currently, there are no vaccines available to treat this infection in humans. Therefore, with the objective of devising a novel preventive measure, we exploited an immunoinformatics approach to design a multi-epitope-based subunit vaccine for LF, that can elicit a variety of immune responses within the host. In this study, different B cell, TC cell, and TH cell-binding epitopes were screened from the antigenic proteins of Brugia malayi and they were passed through several immunological filters to determine the optimal epitopes. RESULTS As a result, 15 CD8+, 3 CD4+, and 3 B cell epitopes were found to be prominent, antigenic, non-toxic, immunogenic and non-allergenic. The presence of conformational B cell epitopes and cytokine-inducing epitopes confirmed the humoral and cell-mediated immune response that would be triggered by the constructed vaccine model. Following that, the selected epitopes and TLR-4-specific adjuvant were ligated by appropriate peptide linkers to finalize the vaccine construct. Protein-protein docking of the vaccine structure with the TLR4 receptor predicted strong binding affinity and hence putatively confirms its ability to elicit an immune response. Further, the efficiency of the vaccine candidate to provide a long-lasting protective immunity was assessed by in silico immune simulation. The reverse translated vaccine sequence was also virtually cloned in the pET28a (+) plasmid after the optimization of the gene sequence. CONCLUSION So taken together, by monitoring the overall in silico assessment, we hypothesize that our engineered peptide vaccine could be a viable prophylactic approach in the development of vaccines against the threat of human lymphatic filariasis. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1186/s42269-023-01013-0.
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Affiliation(s)
| | | | | | - Prabhu Rajaiah Prince
- Department of Biotechnology, Anna University, Chennai, India
- The Hamburg Centre for Ultrafast Imaging (CUI), University of Hamburg, Hamburg, Germany
- Institute for Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Infammation, University of Hamburg, c/o DESY, 22603, Hamburg, Germany
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Ikram A, Alzahrani B, Zaheer T, Sattar S, Rasheed S, Aurangzeb M, Ishaq Y. An In Silico Deep Learning Approach to Multi-Epitope Vaccine Design: A Hepatitis E Virus Case Study. Vaccines (Basel) 2023; 11:vaccines11030710. [PMID: 36992295 DOI: 10.3390/vaccines11030710] [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: 11/08/2022] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
Hepatitis E Virus (HEV) is a major cause of acute and chronic hepatitis. The severity of HEV infection increases manyfold in pregnant women and immunocompromised patients. Despite the extensive research on HEV in the last few decades, there is no widely available vaccine yet. In the current study, immunoinformatic analyses were applied to predict a multi-epitope vaccine candidate against HEV. From the ORF2 region, 41 conserved and immunogenic epitopes were prioritized. These epitopes were further analyzed for their probable antigenic and non-allergenic combinations with several linkers. The stability of the vaccine construct was confirmed by molecular dynamic simulations. The vaccine construct is potentially antigenic and docking analysis revealed stable interactions with TLR3. These results suggest that the proposed vaccine can efficiently stimulate both cellular and humoral immune responses. However, further studies are needed to determine the immunogenicity of the vaccine construct.
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Affiliation(s)
- Aqsa Ikram
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore (UOL), Lahore 54000, Pakistan
| | - Badr Alzahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Tahreem Zaheer
- Department of Biological Physics, Eötvös Loránd University, Pázmány Péter Sétány 1/A, 1117 Budapest, Hungary
| | - Sobia Sattar
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore (UOL), Lahore 54000, Pakistan
| | - Sidra Rasheed
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore (UOL), Lahore 54000, Pakistan
| | - Muhammad Aurangzeb
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore (UOL), Lahore 54000, Pakistan
| | - Yasmeen Ishaq
- Institute of Molecular Biology and Biotechnology (IMBB), University of Lahore (UOL), Lahore 54000, Pakistan
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24
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Waqas M, Aziz S, Bushra A, Halim SA, Ali A, Ullah S, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. Employing an immunoinformatics approach revealed potent multi-epitope based subunit vaccine for lymphocytic choriomeningitis virus. J Infect Public Health 2023; 16:214-232. [PMID: 36603375 DOI: 10.1016/j.jiph.2022.12.023] [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: 07/25/2022] [Revised: 12/10/2022] [Accepted: 12/28/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Lymphocytic choriomeningitis virus (LCMV) infects many individuals worldwide and causes severe infection in the immunosuppressant recipient, spontaneous abortion, and congenital disabilities in infants. OBJECTIVES There is no specific vaccine or therapeutics available to protect against LCMV infection; thus, there is a need to design a potential vaccine to combat the virus by developing immunity in the population. Herein, we attempted to design a potent multi-epitope vaccine for LCMV using immunoinformatics methods. METHODS The whole proteome of the virus was screened and mapped to extract immunodominant B-cell and T-cell epitopes which were fused with appropriate linkers (EAAAK, GGGS, AAY, GPGPG, and AAY), PADRE sequence (13aa) and an adjuvant (50 S ribosomal protein L7/L12) to formulate a multi-epitope vaccine ensemble. Codon adaptation and in silico cloning of the constructed vaccine were carried out using bioinformatics tools. The secondary and tertiary structure of the vaccine construct was predicted and refined. The physicochemical profile of the designed vaccine was analyzed, and the multi-epitope vaccine's potential to bind Toll-like receptors (TLR2 and TLR4) was evaluated through molecular docking and molecular dynamics simulations. Computational immune simulation of the designed vaccine antigen was performed using the C-ImmSim server. RESULTS The designed multi-epitope-based vaccine (613 aa) comprised 26 immunodominant (six B-cell, nine cytotoxic T lymphocytes, and 11 helper T lymphocytes) epitopes and is predicted antigenic, non-toxic, non-allergen, soluble, and topographically accessible with a suitable physicochemical profile. The designed vaccine is expected to cover a broad worldwide population (96.35 %) and stimulate a robust adaptive immune response against the virus upon administration. In silico cloning of the constructed vaccine in PET28a (+) vector ensured its optimal expression in the Escherichia coli system. Molecular docking, molecular dynamics simulation, and binding free energy estimation collectively support the stability and energetically favourable interaction of the modeled vaccine-TLR2/4 complexes. CONCLUSION The designed multi-epitope vaccine in the present study could serve as a potential vaccine candidate to protect against LMCV infection; however, the experimental validation and safety testing of the vaccine is warranted to validate the study's outcomes.
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Affiliation(s)
- Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman; Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Peshawar 25000, Pakistan
| | - Aiman Bushra
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, 2100, Pakistan
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan 45142, Saudi Arabia; Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum, Sudan
| | - Ashraf N Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Nizwa, Sultanate of Oman.
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Waqas M, Aziz S, Liò P, Khan Y, Ali A, Iqbal A, Khan F, Almajhdi FN. Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets. Front Immunol 2023; 14:1091941. [PMID: 36776835 PMCID: PMC9908764 DOI: 10.3389/fimmu.2023.1091941] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Introduction The current monkeypox (MPX) outbreak, caused by the monkeypox virus (MPXV), has turned into a global concern, with over 59,000 infection cases and 23 deaths worldwide. Objectives Herein, we aimed to exploit robust immunoinformatics approach, targeting membrane-bound, enveloped, and extracellular proteins of MPXV to formulate a chimeric antigen. Such a strategy could similarly be applied for identifying immunodominant epitopes and designing multi-epitope vaccine ensembles in other pathogens responsible for chronic pathologies that are difficult to intervene against. Methods A reverse vaccinology pipeline was used to select 11 potential vaccine candidates, which were screened and mapped to predict immunodominant B-cell and T-cell epitopes. The finalized epitopes were merged with the aid of suitable linkers, an adjuvant (Resuscitation-promoting factor), a PADRE sequence (13 aa), and an HIV TAT sequence (11 aa) to formulate a multivalent epitope vaccine. Bioinformatics tools were employed to carry out codon adaptation and computational cloning. The tertiary structure of the chimeric vaccine construct was modeled via I-TASSER, and its interaction with Toll-like receptor 4 (TLR4) was evaluated using molecular docking and molecular dynamics simulation. C-ImmSim server was implemented to examine the immune response against the designed multi-epitope antigen. Results and discussion The designed chimeric vaccine construct included 21 immunodominant epitopes (six B-cell, eight cytotoxic T lymphocyte, and seven helper T-lymphocyte) and is predicted non-allergen, antigenic, soluble, with suitable physicochemical features, that can promote cross-protection among the MPXV strains. The selected epitopes indicated a wide global population coverage (93.62%). Most finalized epitopes have 70%-100% sequence similarity with the experimentally validated immune epitopes of the vaccinia virus, which can be helpful in the speedy progression of vaccine design. Lastly, molecular docking and molecular dynamics simulation computed stable and energetically favourable interaction between the putative antigen and TLR4. Conclusion Our results show that the multi-epitope vaccine might elicit cellular and humoral immune responses and could be a potential vaccine candidate against the MPXV infection. Further experimental testing of the proposed vaccine is warranted to validate its safety and efficacy profile.
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Affiliation(s)
- Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Pietro Liò
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Yumna Khan
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Faizullah Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Fahad Nasser Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Andongma BT, Huang Y, Chen F, Tang Q, Yang M, Chou SH, Li X, He J. In silico design of a promiscuous chimeric multi-epitope vaccine against Mycobacterium tuberculosis. Comput Struct Biotechnol J 2023; 21:991-1004. [PMID: 36733703 PMCID: PMC9883148 DOI: 10.1016/j.csbj.2023.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/15/2023] [Accepted: 01/15/2023] [Indexed: 01/18/2023] Open
Abstract
Tuberculosis (TB) is a global health threat, killing approximately 1.5 million people each year. The eradication of Mycobacterium tuberculosis, the main causative agent of TB, is increasingly challenging due to the emergence of extensive drug-resistant strains. Vaccination is considered an effective way to protect the host from pathogens, but the only clinically approved TB vaccine, Bacillus Calmette-Guérin (BCG), has limited protection in adults. Multi-epitope vaccines have been found to enhance immunity to diseases by selectively combining epitopes from several candidate proteins. This study aimed to design a multi-epitope vaccine against TB using an immuno-informatics approach. Through functional enrichment, we identified eight proteins secreted by M. tuberculosis that are either required for pathogenesis, secreted into extracellular space, or both. We then analyzed the epitopes of these proteins and selected 16 helper T lymphocyte epitopes with interferon-γ inducing activity, 15 cytotoxic T lymphocyte epitopes, and 10 linear B-cell epitopes, and conjugated them with adjuvant and Pan HLA DR-binding epitope (PADRE) using appropriate linkers. Moreover, we predicted the tertiary structure of this vaccine, its potential interaction with Toll-Like Receptor-4 (TLR4), and the immune response it might elicit. The results showed that this vaccine had a strong affinity for TLR4, which could significantly stimulate CD4+ and CD8+ cells to secrete immune factors and B lymphocytes to secrete immunoglobulins, so as to obtain good humoral and cellular immunity. Overall, this multi-epitope protein was predicted to be stable, safe, highly antigenic, and highly immunogenic, which has the potential to serve as a global vaccine against TB.
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Affiliation(s)
- Binda T. Andongma
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Yazheng Huang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Fang Chen
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qing Tang
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Min Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xinfeng Li
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China,Correspondence to: The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, Hubei 430070, PR China.
| | - Jin He
- State Key Laboratory of Agricultural Microbiology & Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China,Correspondence to: The State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, No. 1 Shizishan Street, Wuhan, Hubei 430070, PR China.
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Mishra S, Rout M, Panda S, Singh SK, Sinha R, Dehury B, Pati S. An immunoinformatic approach towards development of a potent and effective multi-epitope vaccine against monkeypox virus (MPXV). J Biomol Struct Dyn 2023; 41:11714-11727. [PMID: 36591724 DOI: 10.1080/07391102.2022.2163426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/22/2022] [Indexed: 01/03/2023]
Abstract
Monkeypox is a viral zoonotic disease, often transmitted to humans from animals. While the whole world is haggling with the COVID-19 pandemic, the emergence of the monkeypox virus (MPXV) arose as a new challenge to mankind. Till date, numerous cases related to the MPXV have been reported in several countries across the globe, but, its momentary distribution in the current time has left everyone in fright with increasing mortality and limited clinically approved treatments. Therefore, it is of immense importance to develop a potent and highly effective vaccine capable of inducing desired immunogenic responses against the highly contagious MPXV. Herein, using various immunoinformatic and computational biology tools, we made an attempt to develop a multi-epitope vaccine construct against the MPXV which is antigenic, non-allergen and non-toxic in nature and capable of exhibiting immunogenic behavior. The sequence of vaccine construct was designed using the proposed 4 MHC-I, 3 MHC-II and 4 B-cell epitopes linked with suitable adjuvant and linkers. The modeled structure of the vaccine construct was used to assess its interaction with the Toll-like Receptor 4 (TLR4) using ClusPro and HADDOCK. All-atoms molecular dynamics simulation of the MPXV vaccine construct-TLR4 complex followed by a high level of gene expression of the construct within the bacterial system affirmed its stability along with induction of immunogenic response within the host cell. Altogether, our immunoinformatic approach aid in the development of a stable chimeric vaccine construct against MPXV and needs further experimental validation for its immunological relevance and usefulness as a vaccine candidate.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sunita Panda
- Mycology Laboratory, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Susheel Kumar Singh
- Vaccine and Diagnostic Laboratory, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Rohan Sinha
- Department of Computer Science and Engineering, National Institute of Technology Patna, Patna, Bihar, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Bhubaneswar, Odisha, India
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Identification of B and T Cell Epitopes to Design an Epitope-Based Peptide Vaccine against the Cell Surface Binding Protein of Monkeypox Virus: An Immunoinformatics Study. J Immunol Res 2023; 2023:2274415. [PMID: 36874624 PMCID: PMC9977553 DOI: 10.1155/2023/2274415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/07/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Background Although the monkeypox virus-associated illness was previously confined to Africa, recently, it has started to spread across the globe and become a significant threat to human lives. Hence, this study was designed to identify the B and T cell epitopes and develop an epitope-based peptide vaccine against this virus's cell surface binding protein through an in silico approach to combat monkeypox-associated diseases. Results The analysis revealed that the cell surface binding protein of the monkeypox virus contains 30 B cell and 19 T cell epitopes within the given parameter. Among the T cell epitopes, epitope "ILFLMSQRY" was found to be one of the most potential peptide vaccine candidates. The docking analysis revealed an excellent binding affinity of this epitope with the human receptor HLA-B∗15:01 with a very low binding energy (-7.5 kcal/mol). Conclusion The outcome of this research will aid the development of a T cell epitope-based peptide vaccine, and the discovered B and T cell epitopes will facilitate the creation of other epitope and multi-epitope-based vaccines in the future. This research will also serve as a basis for further in vitro and in vivo analysis to develop a vaccine that is effective against the monkeypox virus.
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Shah SZ, Jabbar B, Mirza MU, Waqas M, Aziz S, Halim SA, Ali A, Rafique S, Idrees M, Khalid A, Abdalla AN, Khan A, Al-Harrasi A. An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean-Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target. Vaccines (Basel) 2022; 11:61. [PMID: 36679906 PMCID: PMC9867508 DOI: 10.3390/vaccines11010061] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022] Open
Abstract
Crimean-Congo haemorrhagic fever (CCHF), caused by Crimean-Congo haemorrhagic fever virus (CCHFV), is a disease of worldwide importance (endemic yet not limited to Asia, Middle East, and Africa) and has triggered several outbreaks amounting to a case fatality rate of 10-40% as per the World Health Organization. Genetic diversity and phylogenetic data revealed that the Asia-1 genotype of CCHFV remained dominant in Pakistan, where 688 confirmed cases were reported between the 2012-2022 period. Currently, no approved vaccine is available to tackle the viral infection. Epitope-based vaccine design has gained significant attention in recent years due to its safety, timeliness, and cost efficiency compared to conventional vaccines. In the present study, we employed a robust immunoinformatics-based approach targeting the structural glycoproteins G1 and G2 of CCHFV (Asia-1 genotype) to design a multi-epitope vaccine construct. Five B-cells and six cytotoxic T-lymphocytes (CTL) epitopes were mapped and finalized from G1 and G2 and were fused with suitable linkers (EAAAK, GGGS, AAY, and GPGPG), a PADRE sequence (13 aa), and an adjuvant (50S ribosomal protein L7/L12) to formulate a chimeric vaccine construct. The selected CTL epitopes showed high affinity and stable binding with the binding groove of common human HLA class I molecules (HLA-A*02:01 and HLA-B*44:02) and mouse major histocompatibility complex class I molecules. The chimeric vaccine was predicted to be an antigenic, non-allergenic, and soluble molecule with a suitable physicochemical profile. Molecular docking and molecular dynamics simulation indicated a stable and energetically favourable interaction between the constructed antigen and Toll-like receptors (TLR2, TLR3, and TLR4). Our results demonstrated that innate, adaptive, and humoral immune responses could be elicited upon administration of such a potent muti-epitope vaccine construct. These results could be helpful for an experimental vaccinologist to develop an effective vaccine against the Asia-1 genotype of CCHFV.
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Affiliation(s)
- Syed Zawar Shah
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Usman Mirza
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Muhammad Waqas
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar 25130, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra 21120, Pakistan
| | - Shazia Rafique
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Muhammad Idrees
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box 114, Jazan 45142, Saudi Arabia
- Medicinal and Aromatic Plants and Traditional Medicine Research Institute, National Center for Research, P.O. Box 2404, Khartoum 11111, Sudan
| | - Ashraf N. Abdalla
- Department of Pharmacology and Toxicology, College of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz 616, Oman
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Moezzi MS, Derakhshandeh A, Hemmatzadeh F. Immunoinformatics analysis of candidate proteins for controlling bovine paratuberculosis. PLoS One 2022; 17:e0277751. [PMID: 36409703 PMCID: PMC9678287 DOI: 10.1371/journal.pone.0277751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/02/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Paratuberculosis is debilitating chronic enteritis usually characterized by diarrhea, decreased milk production, and progressive cachexia. Mycobacterium avium subspecies paratuberculosis (MAP) causes significant economic losses by affecting dairy herds globally. Development of protective vaccines is considered as one of the most effective controlling measures for MAP infections. In the current study, hydrophilic parts of MAP2191 and FAP-P proteins as two vaccine candidates were analyzed using immunoinformatics approaches. METHODS After selecting the most hydrophilic parts of MAP2191 and FAP-P, helper and cytotoxic T-cell epitopes of ht-MAP2191 and ht-FAP-P were identified. The immunogenic, toxicity and physicochemical properties were assessed. Secondary structures of these proteins were predicted, and their tertiary structures were modeled, refined, and validated. Linear and conformational epitopes of corresponding B-cells were recognized. Then ht-MAP2191 and ht-FAP-P epitopes were employed for molecular docking simulations. RESULTS The results indicated that ht-MAP2191 and ht-FAP-P were immunogenic, non-allergenic, and non-toxic and possess potent T-cell and B-cell epitopes. Eventually, these protein constructs were docked favorably against TLR4. CONCLUSION According to the findings, ht-MAP2191 and ht-FAP-P could be effective protein-based vaccine candidates for paratuberculosis. It should be noted that to examine their efficacy, further in vitro and in vivo experiments are underway.
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Affiliation(s)
- Maryam Sadat Moezzi
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Abdollah Derakhshandeh
- Department of Pathobiology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
- * E-mail:
| | - Farhid Hemmatzadeh
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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Hermawan A, Damai FI, Martin L, Chrisdianto M, Julianto NM, Pramanda IT, Gustiananda M. Immunoinformatics Analysis of Citrullinated Antigen as Potential Multi-peptide Lung Cancer Vaccine Candidates for Indonesian Population. Int J Pept Res Ther 2022; 28:162. [PMID: 36406283 PMCID: PMC9648882 DOI: 10.1007/s10989-022-10467-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2022] [Indexed: 11/12/2022]
Abstract
Non-small-cell lung cancer (NSCLC) is the most common lung cancer which has the highest mortality rate in Indonesia. One of the trends in treating cancer is by utilizing peptide vaccines, an immunotherapeutic approach that aims to stimulate the cell-mediated adaptive immune system to recognize cancer-associated peptides. Currently, no peptide vaccines are available in the market for NSCLC treatment. Therefore, this project aims to develop a multi-epitope peptide-based vaccine for NSCLC utilizing citrullinated peptides. Citrullination is a post-translational modification that occurs in cancer cells during autophagy that functions to induce immune responses towards modified self-epitopes such as tumor cells, through activation of PAD enzymes within the APC and target cells. It was found that introducing a common citrullinated neo-antigen peptide such as vimentin and enolase to the immune system could stimulate a higher specific CD4+ T cell response against NSCLC. Moreover, carcinoembryonic antigen (CEA), an antigen that is highly expressed in cancer cells, is also added to increase the vaccine’s specificity and to mobilize both CD4+ and CD8+ T cells. These antigens bind strongly to the MHC Class II alleles such as HLA-DRB1*07:01 and HLA-DRB*11:01, which are predominant alleles in Indonesian populations. Through in silico approach, the peptides generated from CEA, citrullinated vimentin and enolase, were analyzed for their MHC binding strength, immunogenicity, ability to induce IFNγ response, and population coverage. It is expected that the immunodominant antigens presentation is able to induce a potent immune response in NSCLC patients in Indonesia, resulting in tumor eradication.
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Affiliation(s)
- Angelika Hermawan
- Biomedicine Department, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Fedric Intan Damai
- Biotechnology Department, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Leon Martin
- Biotechnology Department, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Matthew Chrisdianto
- Biotechnology Department, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | | | - Ihsan Tria Pramanda
- Biotechnology Department, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | - Marsia Gustiananda
- Biomedicine Department, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
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32
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Huang S, Zhang C, Li J, Dai Z, Huang J, Deng F, Wang X, Yue X, Hu X, Li Y, Deng Y, Wang Y, Zhao W, Zhong Z, Wang Y. Designing a multi-epitope vaccine against coxsackievirus B based on immunoinformatics approaches. Front Immunol 2022; 13:933594. [PMID: 36439191 PMCID: PMC9682020 DOI: 10.3389/fimmu.2022.933594] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 10/18/2022] [Indexed: 12/11/2023] Open
Abstract
Coxsackievirus B (CVB) is one of the major viral pathogens of human myocarditis and cardiomyopathy without any effective preventive measures; therefore, it is necessary to develop a safe and efficacious vaccine against CVB. Immunoinformatics methods are both economical and convenient as in-silico simulations can shorten the development time. Herein, we design a novel multi-epitope vaccine for the prevention of CVB by using immunoinformatics methods. With the help of advanced immunoinformatics approaches, we predicted different B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes, respectively. Subsequently, we constructed the multi-epitope vaccine by fusing all conserved epitopes with appropriate linkers and adjuvants. The final vaccine was found to be antigenic, non-allergenic, and stable. The 3D structure of the vaccine was then predicted, refined, and evaluated. Molecular docking and dynamics simulation were performed to reveal the interactions between the vaccine with the immune receptors MHC-I, MHC-II, TLR3, and TLR4. Finally, to ensure the complete expression of the vaccine protein, the sequence of the designed vaccine was optimized and further performed in-silico cloning. In conclusion, the molecule designed in this study could be considered a potential vaccine against CVB infection and needed further experiments to evaluate its safety and efficacy.
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Affiliation(s)
- Sichao Huang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Congcong Zhang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Jianing Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zongmao Dai
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Jingjing Huang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Fengzhen Deng
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Xumeng Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Xinxin Yue
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Xinnan Hu
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yuxuan Li
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yushu Deng
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yanhang Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Wenran Zhao
- Department of Cell Biology, Harbin Medical University, Harbin, China
| | - Zhaohua Zhong
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Yan Wang
- Department of Microbiology, Harbin Medical University, Harbin, China
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Zaib S, Akram F, Liaqat ST, Altaf MZ, Khan I, Dera AA, Uddin J, Khan A, Al-Harrasi A. Bioinformatics approach for the construction of multiple epitope vaccine against omicron variant of SARS-CoV-2. Sci Rep 2022; 12:19087. [PMID: 36352060 PMCID: PMC9645332 DOI: 10.1038/s41598-022-23550-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
The World Health Organization categorized SARS-CoV-2 as a variant of concern, having numerous mutations in spike protein, which have been found to evade the effect of antibodies stimulated by the COVID-19 vaccine. The susceptibility to omicron variant by immunization-induced antibodies are direly required for risk evaluation. To avoid the risk of arising viral illness, the construction of a specific vaccine that triggers the production of targeted antibodies to combat infection remains highly imperative. The aim of the present study is to develop a particular vaccine exploiting bioinformatics approaches which can target B- and T-cells epitopes. Through this approach, novel epitopes of the S protein-SARS-CoV-2 were predicted for the development of a multiple epitope vaccine. Multiple epitopes were selected on the basis of toxicity, immunogenicity and antigenicity, and vaccine subunit was constructed having potential immunogenic properties. The epitopes were linked with 3 types of linker EAAAK, AAY and GPGPG for vaccine construction. Subsequently, vaccine structure was docked with the receptor and cloned in a pET-28a (+) vector. The constructed vaccine was ligated in pET-28a (+) vector in E. coli using the SnapGene tool for the expression study and a good immune response was observed. Several computational tools were used to predict and analyze the vaccine constructed by using spike protein sequence of omicrons. The current study identified a Multi-Epitope Vaccine (MEV) as a significant vaccine candidate that could potentially help the global world to combat SARS-CoV-2 infections.
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Affiliation(s)
- Sumera Zaib
- grid.444936.80000 0004 0608 9608Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590 Pakistan
| | - Fatima Akram
- grid.444936.80000 0004 0608 9608Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590 Pakistan
| | - Syed Talha Liaqat
- grid.444936.80000 0004 0608 9608Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590 Pakistan
| | - Muhammad Zain Altaf
- grid.444936.80000 0004 0608 9608Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, 54590 Pakistan
| | - Imtiaz Khan
- grid.5379.80000000121662407Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Ayed A. Dera
- grid.412144.60000 0004 1790 7100Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Jalal Uddin
- grid.412144.60000 0004 1790 7100Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, 62529 Kingdom of Saudi Arabia
| | - Ajmal Khan
- grid.444752.40000 0004 0377 8002Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
| | - Ahmed Al-Harrasi
- grid.444752.40000 0004 0377 8002Natural and Medical Sciences Research Center, University of Nizwa, 616 Nizwa, Oman
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Salod Z, Mahomed O. Mapping Potential Vaccine Candidates Predicted by VaxiJen for Different Viral Pathogens between 2017-2021-A Scoping Review. Vaccines (Basel) 2022; 10:1785. [PMID: 36366294 PMCID: PMC9695814 DOI: 10.3390/vaccines10111785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 09/29/2023] Open
Abstract
Reverse vaccinology (RV) is a promising alternative to traditional vaccinology. RV focuses on in silico methods to identify antigens or potential vaccine candidates (PVCs) from a pathogen's proteome. Researchers use VaxiJen, the most well-known RV tool, to predict PVCs for various pathogens. The purpose of this scoping review is to provide an overview of PVCs predicted by VaxiJen for different viruses between 2017 and 2021 using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic Reviews extension for Scoping Reviews (PRISMA-ScR) guidelines. We used the term 'vaxijen' to search PubMed, Scopus, Web of Science, EBSCOhost, and ProQuest One Academic. The protocol was registered at the Open Science Framework (OSF). We identified articles on this topic, charted them, and discussed the key findings. The database searches yielded 1033 articles, of which 275 were eligible. Most studies focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), published between 2020 and 2021. Only a few articles (8/275; 2.9%) conducted experimental validations to confirm the predictions as vaccine candidates, with 2.2% (6/275) articles mentioning recombinant protein expression. Researchers commonly targeted parts of the SARS-CoV-2 spike (S) protein, with the frequently predicted epitopes as PVCs being major histocompatibility complex (MHC) class I T cell epitopes WTAGAAAYY, RQIAPGQTG, IAIVMVTIM, and B cell epitope IAPGQTGKIADY, among others. The findings of this review are promising for the development of novel vaccines. We recommend that vaccinologists use these findings as a guide to performing experimental validation for various viruses, with SARS-CoV-2 as a priority, because better vaccines are needed, especially to stay ahead of the emergence of new variants. If successful, these vaccines could provide broader protection than traditional vaccines.
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Affiliation(s)
- Zakia Salod
- Discipline of Public Health Medicine, University of KwaZulu-Natal, Durban 4051, South Africa
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Designing an Epitope-Based Peptide Vaccine Derived from RNA-Dependent RNA Polymerase (RdRp) against Dengue Virus Serotype 2. Vaccines (Basel) 2022; 10:vaccines10101734. [PMID: 36298599 PMCID: PMC9611443 DOI: 10.3390/vaccines10101734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
Dengue fever (DF) continues to be one of the tropical and subtropical health concerns. Its prevalence tends to increase in some places in these regions. This disease is caused by the dengue virus (DENV), which is transmitted through the mosquitoes Aedes aegypti and A. albopictus. The treatment of DF to date is only supportive and there is no definitive vaccine to prevent this disease. The non-structural DENV protein, RNA-dependent RNA Polymerase (RdRp), is involved in viral replication. The RdRp-derived peptides can be used in the construction of a universal dengue vaccine. These peptides can be utilized as epitopes to induce immunity. This study was an in silico evaluation of the affinity of the potential epitope for the universal dengue vaccine to dendritic cells and the bonds between the epitope and the dendritic cell receptor. The peptide sequence MGKREKKLGEFGKAKG generated from dengue virus subtype 2 (DENV-2) RdRp was antigenic, did not produce allergies, was non-toxic, and had no homology with the human genome. The potential epitope-based vaccine MGKREKKLGEFGKAKG binds stably to dendritic cell receptors with a binding free energy of −474,4 kcal/mol. This epitope is anticipated to induce an immunological response and has the potential to serve as a universal dengue virus vaccine candidate.
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36
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Aziz S, Almajhdi FN, Waqas M, Ullah I, Salim MA, Khan NA, Ali A. Contriving multi-epitope vaccine ensemble for monkeypox disease using an immunoinformatics approach. Front Immunol 2022; 13:1004804. [PMID: 36311762 PMCID: PMC9606759 DOI: 10.3389/fimmu.2022.1004804] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/27/2022] [Indexed: 11/18/2022] Open
Abstract
The current global outbreak of monkeypox (MPX) disease, caused by Monkeypox virus (MPXV), has resulted in 16 thousand infection cases, five deaths, and has been declared a global health emergency of international concern by the World Health Organization. Given current challenges in the safety of existing vaccines, a vaccine to prevent MPX infection and/or onset of symptoms would significantly advance disease management. In this context, a multi-epitope-based vaccine could be a well-suited approach. Herein, we searched a publicly accessible database (Virus Pathogen Database and Analysis Resource) for MPXV immune epitopes from various antigens. We prioritized a group of epitopes (10 CD8+ T cells and four B-cell epitopes) using a computer-aided technique based on desirable immunological and physicochemical properties, sequence conservation criteria, and non-human homology. Three multi-epitope vaccines were constructed (MPXV-1–3) by fusing finalized epitopes with the aid of appropriate linkers and adjuvant (beta-defensin 3, 50S ribosomal protein L7/L12, and Heparin-binding hemagglutinin). Codon optimization and in silico cloning in the pET28a (+) expression vector ensure the optimal expression of each construct in the Escherichia Coli system. Two and three-dimensional structures of the constructed vaccines were predicted and refined. The optimal binding mode of the construct with immune receptors [Toll-like receptors (TLR2, TLR3, and TLR4)] was explored by molecular docking, which revealed high docking energies of MPXV-1–TLR3 (–99.09 kcal/mol), MPXV-2–TLR3 (–98.68 kcal/mol), and MPXV-3–TLR2 (–85.22 kcal/mol). Conformational stability and energetically favourable binding of the vaccine-TLR2/3 complexes were assessed by performing molecular dynamics simulations and free energy calculations (Molecular Mechanics/Generalized Born Surface Area method). In silico immune simulation suggested that innate, adaptive, and humoral responses will be elicited upon administration of such potent multi-epitope vaccine constructs. The vaccine constructs are antigenic, non-allergen, non-toxic, soluble, topographically exposed, and possess favourable physicochemical characteristics. These results may help experimental vaccinologists design a potent MPX vaccine.
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Affiliation(s)
- Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Fahad Nasser Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Waqas
- Department of Biotechnology and genetic Engineering, Hazara University, Mansehra, Pakistan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
- *Correspondence: Muhammad Waqas, ; Amjad Ali,
| | - Inam Ullah
- Department of Biotechnology and genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Muhammad Adil Salim
- Microbiology Graduate Group, University of California, Davis, Davis, CA, United States
- Genome Center, University of California, Davis, Davis, CA, United States
| | - Nasir Ali Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, Oman
| | - Amjad Ali
- Department of Biotechnology and genetic Engineering, Hazara University, Mansehra, Pakistan
- *Correspondence: Muhammad Waqas, ; Amjad Ali,
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Novel multi epitope-based vaccine against monkeypox virus: vaccinomic approach. Sci Rep 2022; 12:15983. [PMID: 36156077 PMCID: PMC9510130 DOI: 10.1038/s41598-022-20397-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
While mankind is still dealing with the COVID-19 pandemic, a case of monkeypox virus (MPXV) has been reported to the WHO on May 7, 2022. Monkeypox is a viral zoonotic disease that has been a public health threat, particularly in Africa. However, it has recently expanded to other parts of the world, so it may soon become a global issue. Thus, the current work was planned and then designed a multi-epitope vaccine against MPXV utilizing the cell surface-binding protein as a target in order to develop a novel and safe vaccine that can evoke the desirable immunological response. The proposed MHC-I, MHC-II, and B-cell epitopes were selected to design multi-epitope vaccine constructs linked with suitable linkers in combination with different adjuvants to enhance the immune responses for the vaccine constructs. The proposed vaccine was composed of 275 amino acids and was shown to be antigenic in Vaxijen server (0.5311) and non-allergenic in AllerTop server. The 3D structure of the designed vaccine was predicted, refined and validated by various in silico tools to assess the stability of the vaccine. Moreover, the solubility of the vaccine construct was found greater than the average solubility provided by protein-Sol server which indicating the solubility of the vaccine construct. Additionally, the most promising epitopes bound to MHC I and MHC II alleles were found having good binding affinities with low energies ranging between − 7.0 and − 8.6 kcal/mol. According to the immunological simulation research, the vaccine was found to elicit a particular immune reaction against the monkeypox virus. Finally, the molecular dynamic study shows that the designed vaccine is stable with minimum RMSF against MHC I allele. We conclude from our research that the cell surface-binding protein is one of the primary proteins involved in MPXV pathogenesis. As a result, our study will aid in the development of appropriate therapeutics and prompt the development of future vaccines against MPXV.
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Aiman S, Alhamhoom Y, Ali F, Rahman N, Rastrelli L, Khan A, Farooq QUA, Ahmed A, Khan A, Li C. Multi-epitope chimeric vaccine design against emerging Monkeypox virus via reverse vaccinology techniques- a bioinformatics and immunoinformatics approach. Front Immunol 2022; 13:985450. [PMID: 36091024 PMCID: PMC9452969 DOI: 10.3389/fimmu.2022.985450] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 07/29/2022] [Indexed: 12/15/2022] Open
Abstract
The emerging monkeypox virus (MPXV) is a zoonotic orthopoxvirus that causes infections in humans similar to smallpox. Since May 2022, cases of monkeypox (MPX) have been increasingly reported by the World Health Organization (WHO) worldwide. Currently, there are no clinically validated treatments for MPX infections. In this study, an immunoinformatics approach was used to identify potential vaccine targets against MPXV. A total of 190 MPXV-2022 proteins were retrieved from the ViPR database and subjected to various analyses including antigenicity, allergenicity, toxicity, solubility, IFN-γ, and virulence. Three outer membrane and extracellular proteins were selected based on their respective parameters to predict B-cell and T-cell epitopes. The epitopes are conserved among different strains of MPXV and the population coverage is 100% worldwide, which will provide broader protection against various strains of the virus globally. Nine overlapping MHC-I, MHC-II, and B-cell epitopes were selected to design multi-epitope vaccine constructs linked with suitable linkers in combination with different adjuvants to enhance the immune responses of the vaccine constructs. Molecular modeling and structural validation ensured high-quality 3D structures of vaccine constructs. Based on various immunological and physiochemical properties and docking scores, MPXV-V2 was selected for further investigation. In silico cloning revealed a high level of gene expression for the MPXV-V2 vaccine within the bacterial expression system. Immune and MD simulations confirmed the molecular stability of the MPXV-V2 construct, with high immune responses within the host cell. These results may aid in the development of experimental vaccines against MPXV with increased potency and improved safety.
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Affiliation(s)
- Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Yahya Alhamhoom
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Fawad Ali
- Department of Biochemistry, Hazara University, Mansehra, Pakistan
| | - Noor Rahman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, KP, Pakistan
- *Correspondence: Noor Rahman, ; Chunhua Li,
| | - Luca Rastrelli
- Dipartimento di Farmacia, University of Salerno, Via Giovanni Paolo II, Fisciano, SA, Italy
| | - Asifullah Khan
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, KP, Pakistan
| | - Qurat ul Ain Farooq
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Abbas Ahmed
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Asif Khan
- Education department, Qurtaba University of Science and Information Technology (QUSIT) Peshawar, Peshawar, Pakistan
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
- *Correspondence: Noor Rahman, ; Chunhua Li,
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Aziz S, Waqas M, Halim SA, Ali A, Iqbal A, Iqbal M, Khan A, Al-Harrasi A. Exploring whole proteome to contrive multi-epitope-based vaccine for NeoCoV: An immunoinformtics and in-silico approach. Front Immunol 2022; 13:956776. [PMID: 35990651 PMCID: PMC9382669 DOI: 10.3389/fimmu.2022.956776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/07/2022] [Indexed: 12/14/2022] Open
Abstract
Neo-Coronavirus (NeoCoV) is a novel Betacoronavirus (β-CoVs or Beta-CoVs) discovered in bat specimens in South Africa during 2011. The viral sequence is highly similar to Middle East Respiratory Syndrome, particularly that of structural proteins. Thus, scientists have emphasized the threat posed by NeoCoV associated with human angiotensin-converting enzyme 2 (ACE2) usage, which could lead to a high death rate and faster transmission rate in humans. The development of a NeoCoV vaccine could provide a promising option for the future control of the virus in case of human infection. In silico predictions can decrease the number of experiments required, making the immunoinformatics approaches cost-effective and convenient. Herein, with the aid of immunoinformatics and reverse vaccinology, we aimed to formulate a multi-epitope vaccine that may be used to prevent and treat NeoCoV infection. Based on the NeoCoV proteins, B-cell, cytotoxic T lymphocyte (CTL), and helper T lymphocyte (HTL) epitopes were shortlisted. Four vaccines (Neo-1-4) were devised by fusing shortlisted epitopes with appropriate adjuvants and linkers. The secondary and three-dimensional structures of final vaccines were then predicted. The binding interactions of these potential vaccines with toll-like immune receptors (TLR-2, TLR-3, and TLR-4) and major histocompatibility complex molecules (MHC-I and II) reveal that they properly fit into the receptors' binding domains. Besides, Neo-1 and Neo-4 vaccines exhibited better docking energies of -101.08 kcal/mol and -114.47 kcal/mol, respectively, with TLR-3 as compared to other vaccine constructs. The constructed vaccines are highly antigenic, non-allergenic, soluble, non-toxic, and topologically assessable with good physiochemical characteristics. Codon optimization and in-silico cloning confirmed efficient expression of the designed vaccines in Escherichia coli strain K12. In-silico immune simulation indicated that Neo-1 and Neo-4 vaccines could induce a strong immune response against NeoCoV. Lastly, the binding stability and strong binding affinity of Neo-1 and Neo-4 with TLR-3 receptor were validated using molecular dynamics simulations and free energy calculations (Molecular Mechanics/Generalized Born Surface Area method). The final vaccines require experimental validation to establish their safety and effectiveness in preventing NeoCoV infections.
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Affiliation(s)
- Shahkaar Aziz
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Peshawar, Pakistan
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, Pakistan
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
| | - Amjad Ali
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, Pakistan
| | - Aqib Iqbal
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Peshawar, Pakistan
| | - Maaz Iqbal
- Institute of Biotechnology and Genetic Engineering, the University of Agriculture Peshawar, Peshawar, Pakistan
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-ul-Mouz, Nizwa, Oman
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Zhang J, Li J, Hu K, Zhou Q, Chen X, He J, Yin S, Chi Y, Liao X, Xiao Y, Qin H, Zheng Z, Chen J. Screening Novel Vaccine Candidates for Leishmania Donovani by Combining Differential Proteomics and Immunoinformatics Analysis. Front Immunol 2022; 13:902066. [PMID: 35812381 PMCID: PMC9260594 DOI: 10.3389/fimmu.2022.902066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022] Open
Abstract
Visceral leishmaniasis (VL), also known as kala-azar, is the most dangerous form of leishmaniasis. Currently no effective vaccine is available for clinical use. Since the pathogenicity of different Leishmania strains is inconsistent, the differentially expressed proteins in Leishmania strains may play an important role as virulence factors in pathogenesis. Therefore, effective vaccine candidate targets may exist in the differentially expressed proteins. In this study, we used differential proteomics analysis to find the differentially expressed proteins in two Leishmania donovani strains, and combined with immunoinformatics analysis to find new vaccine candidates. The differentially expressed proteins from L. DD8 (low virulent) and L. 9044 (virulent) strains were analyzed by LC-MS/MS, and preliminarily screened by antigenicity, allergenicity and homology evaluation. The binding peptides of MHC II, IFN-γ and MHC I from differentially expressed proteins were then predicted and calculated for the second screening. IFN-γ/IL-10 ratios and conserved domain prediction were performed to choose more desirable differentially expressed proteins. Finally, the 3D structures of three vaccine candidate proteins were produced and submitted for molecular dynamics simulation and molecular docking interaction with TLR4/MD2. The results showed that 396 differentially expressed proteins were identified by LC-MS/MS, and 155 differentially expressed proteins were selected through antigenicity, allergenicity and homology evaluation. Finally, 16 proteins whose percentages of MHC II, IFN-γ and MHC I binding peptides were greater than those of control groups (TSA, LmSTI1, LeIF, Leish-111f) were considered to be suitable vaccine candidates. Among the 16 candidates, amino acid permease, amastin-like protein and the hypothetical protein (XP_003865405.1) simultaneously had the large ratios of IFN-γ/IL-10 and high percentages of MHC II, IFN-γ and MHC I, which should be focused on. In conclusion, our comprehensive work provided a methodological basis to screen new vaccine candidates for a better intervention against VL and associated diseases.
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Affiliation(s)
- Jianhui Zhang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jiao Li
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Kaifeng Hu
- Department of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Zhou
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Xiaoxiao Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Jinlei He
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Shuangshuang Yin
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yangjian Chi
- Department of Urinary Surgery, Jianou Municipal Hospital of Fujian Province, Jianou, China
| | - Xuechun Liao
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuying Xiao
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hanxiao Qin
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Zhiwan Zheng
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
- *Correspondence: Zhiwan Zheng, ; Jianping Chen,
| | - Jianping Chen
- Department of Pathogenic Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
- *Correspondence: Zhiwan Zheng, ; Jianping Chen,
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Kaushik V, G SK, Gupta LR, Kalra U, Shaikh AR, Cavallo L, Chawla M. Immunoinformatics Aided Design and In-Vivo Validation of a Cross-Reactive Peptide Based Multi-Epitope Vaccine Targeting Multiple Serotypes of Dengue Virus. Front Immunol 2022; 13:865180. [PMID: 35799781 PMCID: PMC9254734 DOI: 10.3389/fimmu.2022.865180] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/05/2022] [Indexed: 02/03/2023] Open
Abstract
Dengue virus (DENV) is an arboviral disease affecting more than 400 million people annually. Only a single vaccine formulation is available commercially and many others are still under clinical trials. Despite all the efforts in vaccine designing, the improvement in vaccine formulation against DENV is very much needed. In this study, we used a roboust immunoinformatics approach, targeting all the four serotypes of DENV to design a multi-epitope vaccine. A total of 13501 MHC II binding CD4+ epitope peptides were predicted from polyprotein sequences of four dengue virus serotypes. Among them, ten conserved epitope peptides that were interferon-inducing were selected and found to be conserved among all the four dengue serotypes. The vaccine was formulated using antigenic, non-toxic and conserved multi epitopes discovered in the in-silico study. Further, the molecular docking and molecular dynamics predicted stable interactions between predicted vaccine and immune receptor, TLR-5. Finally, one of the mapped epitope peptides was synthesized for the validation of antigenicity and antibody production ability where the in-vivo tests on rabbit model was conducted. Our in-vivo analysis clearly indicate that the imunogen designed in this study could stimulate the production of antibodies which further suggest that the vaccine designed possesses good immunogenicity.
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Affiliation(s)
- Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Sunil Krishnan G
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Lovi Raj Gupta
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Utkarsh Kalra
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, India
- Department of Data Science, Innopolis University, Innopolis, Russia
| | - Abdul Rajjak Shaikh
- Department of Research and Innovation, STEMskills Research and Education Lab Private Limited, Faridabad, India
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
| | - Luigi Cavallo
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
| | - Mohit Chawla
- Kaust Catalysis Center, Physical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Abdul Rajjak Shaikh, ; Luigi Cavallo, ; Mohit Chawla, ;
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Omoniyi AA, Adebisi SS, Musa SA, Nzalak JO, Bauchi ZM, Bako KW, Olatomide OD, Zachariah R, Nyengaard JR. In silico design and analyses of a multi-epitope vaccine against Crimean-Congo hemorrhagic fever virus through reverse vaccinology and immunoinformatics approaches. Sci Rep 2022; 12:8736. [PMID: 35610299 PMCID: PMC9127496 DOI: 10.1038/s41598-022-12651-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/12/2022] [Indexed: 12/16/2022] Open
Abstract
Crimean Congo Hemorrhagic Fever virus (CCHFV) is a deadly human pathogen that causes an emerging zoonotic disease with a broad geographic spread, especially in Africa, Asia, and Europe, and the second most common viral hemorrhagic fever and widely transmitted tick-borne viral disease. Following infection, the patients are presented with a variety of clinical manifestations and a fatality rate of 40%. Despite the high fatality rate, there are unmet clinical interventions, as no antiviral drugs or vaccines for CCHF have been approved. Immunoinformatics pipeline and reverse vaccinology were used in this study to design a multi-epitope vaccine that may elicit a protective humoral and cellular immune response against Crimean-Congo hemorrhagic fever virus infection. Three essential virulent and antigenic proteins (S, M, and L) were used to predict seven CTL and 18 HTL epitopes that were non-allergenic, antigenic, IFN-γ inducing, and non-toxic. The epitopes were connected using linkers and 50S ribosomal protein L7/L12 was used as an adjuvant and raised a multi-epitope vaccine (MEV) that is 567 amino acids long. Molecular docking and simulation of the predicted 3D structure of the MEV with the toll-like (TLR2, TLR3, and TLR4) receptors and major histocompatibility complex (MCH-I and MCH-II) indicate high interactions and stability of the complexes, MM-GBSA free binding energy calculation revealed a favourable protein-protein complex. Maximum MEV expression was achieved with a CAI value of 0.98 through in silico cloning in the Drosophila melanogaster host. According to the immune simulation, IgG1, T-helper cells, T-cytotoxic cells, INF-γ, and IL-2 were predicted to be significantly elevated. These robust computational analyses demonstrated that the proposed MEV is effective in preventing CCHFV infections. However, it is still necessary to conduct both in vitro and in vivo experiments to validate the potential of the vaccine.
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Affiliation(s)
- Akinyemi Ademola Omoniyi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria.
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark.
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark.
| | - Samuel Sunday Adebisi
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Sunday Abraham Musa
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - James Oliver Nzalak
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Zainab Mahmood Bauchi
- Department of Human Anatomy, Faculty of Basic Medical Sciences, Abubakar Tafawa Balewa University, Bauchi, Nigeria
| | - Kerkebe William Bako
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Oluwasegun Davis Olatomide
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Richard Zachariah
- Department of Human Anatomy, Faculty of Basic Medical Science, College of Medical Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Jens Randel Nyengaard
- Department of Clinical Medicine, Core Centre for Molecular Morphology, Section for Stereology and Microscopy, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
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An Immunoinformatic Strategy to Develop New Mycobacterium tuberculosis Multi-epitope Vaccine. Int J Pept Res Ther 2022; 28:99. [PMID: 35573911 PMCID: PMC9086656 DOI: 10.1007/s10989-022-10406-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2022] [Indexed: 11/12/2022]
Abstract
Mycobacterium tuberculosis causes a life-threatening disease known as tuberculosis (TB). In 2021, tuberculosis was the second cause of death after COVID-19 among infectious diseases. Latent life cycle and development of multidrug resistance in one hand and lack of an effective vaccine in another hand have made TB a global health issue. Here, a multi-epitope vaccine have been designed against TB using five new antigenic protein and immunoinformatic tools. To do so, immunodominant MHC-I/MHC-II binding epitopes of Rv2346, Rv2347, Rv3614, Rv3615 and Rv2031 antigenic proteins have been selected using advanced computational procedures. The vaccine was designed by linking ten epitopes from the antigenic proteins and flagellin and TpD as adjuvant. Three-dimensional (3D) structure of the vaccine was modeled, was refined and was evaluated using bioinformatics tools. The 3D structure of the vaccine was docked into the toll-like-receptors (TLR3, 4, 8) to evaluate potential interaction between the vaccine and TLRs. Evaluation of immunological and physicochemical properties of the constructed vaccine have demonstrated the vaccine construct can induce significant humoral and cellular immune responses, the vaccine is non-allergenic and can be recognized by TLR proteins. The immunoinformatic results reported in the present study demonstrates that it is worth following the designed vaccine by experimental investigations.
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Immunoinformatics guided design of a next generation epitope-based vaccine against Kaposi Sarcoma. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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