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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ghafoor D, Zeb A, Ali SS, Ali M, Akbar F, Ud Din Z, Ur Rehman S, Suleman M, Khan W. Immunoinformatic based designing of potential immunogenic novel mRNA and peptide-based prophylactic vaccines against H5N1 and H7N9 avian influenza viruses. J Biomol Struct Dyn 2024; 42:3641-3658. [PMID: 37222664 DOI: 10.1080/07391102.2023.2214228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023]
Abstract
Influenza viruses are the most common cause of serious respiratory illnesses worldwide and are responsible for a significant number of annual fatalities. Therefore, it is crucial to look for new immunogenic sites that might trigger an effective immune response. In the present study, bioinformatics tools were used to design mRNA and multiepitope-based vaccines against H5N1 and H7N9 subtypes of avian influenza viruses. Several Immunoinformatic tools were employed to extrapolate T and B lymphocyte epitopes of HA and NA proteins of both subtypes. The molecular docking approach was used to dock the selected HTL and CTL epitopes with the corresponding MHC molecules. Eight (8) CTL, four (4) HTL, and Six (6) linear B cell epitopes were chosen for the structural arrangement of mRNA and of peptide-based prophylactic vaccine designs. Different physicochemical characteristics of the selected epitopes fitted with suitable linkers were analyzed. High antigenic, non-toxic, and non-allergenic features of the designed vaccines were noted at a neutral physiological pH. Codon optimization tool was used to check the GC content and CAI value of constructed MEVC-Flu vaccine, which were recorded to be 50.42% and 0.97 respectively. the GC content and CAI value verify the stable expression of vaccine in pET28a + vector. In-silico immunological simulation the MEVC-Flu vaccine construct revealed a high level of immune responses. The molecular dynamics simulation and docking results confirmed the stable interaction of TLR-8 and MEVC-Flu vaccine. Based on these parameters, vaccine constructs can be regarded as an optimistic choice against H5N1 and H7N9 strains of the influenza virus. Further experimental testing of these prophylactic vaccine designs against pathogenic avian influenza strains may clarify their safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dawood Ghafoor
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, CAS Key Laboratory of Special Pathogens, Wuhan Institute of Virology, Wuhan, Hubei, China
| | - Adnan Zeb
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Shujait Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fazal Akbar
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Zia Ud Din
- Center for Advanced Studies in Vaccinology and Biotechnology, University of Balochistan Quetta, Quetta, Pakistan
| | - Shoaib Ur Rehman
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Muhammad Suleman
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
| | - Wajid Khan
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Khyber Pakhtunkhwa, Pakistan
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da Silva MK, Campos DMDO, Akash S, Akter S, Yee LC, Fulco UL, Oliveira JIN. Advances of Reverse Vaccinology for mRNA Vaccine Design against SARS-CoV-2: A Review of Methods and Tools. Viruses 2023; 15:2130. [PMID: 37896907 PMCID: PMC10611333 DOI: 10.3390/v15102130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
mRNA vaccines are a new class of vaccine that can induce potent and specific immune responses against various pathogens. However, the design of mRNA vaccines requires the identification and optimization of suitable antigens, which can be challenging and time consuming. Reverse vaccinology is a computational approach that can accelerate the discovery and development of mRNA vaccines by using genomic and proteomic data of the target pathogen. In this article, we review the advances of reverse vaccinology for mRNA vaccine design against SARS-CoV-2, the causative agent of COVID-19. We describe the steps of reverse vaccinology and compare the in silico tools used by different studies to design mRNA vaccines against SARS-CoV-2. We also discuss the challenges and limitations of reverse vaccinology and suggest future directions for its improvement. We conclude that reverse vaccinology is a promising and powerful approach to designing mRNA vaccines against SARS-CoV-2 and other emerging pathogens.
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Affiliation(s)
- Maria Karolaynne da Silva
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
| | - Daniel Melo de Oliveira Campos
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
| | - Shopnil Akash
- Department of Pharmacy, Daffodil International University, Sukrabad, Dhaka 1207, Bangladesh;
| | - Shahina Akter
- Bangladesh Council of Scientific & Industrial Research (BCSIR), Dhaka 1205, Bangladesh;
| | - Leow Chiuan Yee
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Kota Bharu 11800, Kelantan, Malaysia;
| | - Umberto Laino Fulco
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
| | - Jonas Ivan Nobre Oliveira
- Department of Biophysics and Pharmacology, Bioscience Center, Federal University of Rio Grande do Norte, Natal 59064-741, RN, Brazil (D.M.d.O.C.)
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Khan A, Sohail S, Yaseen S, Fatima S, Wisal A, Ahmed S, Nasir M, Irfan M, Karim A, Basharat Z, Khan Y, Aurongzeb M, Raza SK, Alshahrani MY, Morel CM, Hassan SS. Exploring and targeting potential druggable antimicrobial resistance targets ArgS, SecY, and MurA in Staphylococcus sciuri with TCM inhibitors through a subtractive genomics strategy. Funct Integr Genomics 2023; 23:254. [PMID: 37495774 DOI: 10.1007/s10142-023-01179-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/14/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023]
Abstract
Staphylococcus sciuri (also currently Mammaliicoccus sciuri) are anaerobic facultative and non-motile bacteria that cause significant human pathogenesis such as endocarditis, wound infections, peritonitis, UTI, and septic shock. Methicillin-resistant S. sciuri (MRSS) strains also infects animals that include healthy broilers, cattle, dogs, and pigs. The emergence of MRSS strains thereby poses a serious health threat and thrives the scientific community towards novel treatment options. Herein, we investigated the druggable genome of S. sciuri by employing subtractive genomics that resulted in seven genes/proteins where only three of them were predicted as final targets. Further mining the literature showed that the ArgS (WP_058610923), SecY (WP_058611897), and MurA (WP_058612677) are involved in the multi-drug resistance phenomenon. After constructing and verifying the 3D protein homology models, a screening process was carried out using a library of Traditional Chinese Medicine compounds (consisting of 36,043 compounds). The molecular docking and simulation studies revealed the physicochemical stability parameters of the docked TCM inhibitors in the druggable cavities of each protein target by identifying their druggability potential and maximum hydrogen bonding interactions. The simulated receptor-ligand complexes showed the conformational changes and stability index of the secondary structure elements. The root mean square deviation (RMSD) graph showed fluctuations due to structural changes in the helix-coil-helix and beta-turn-beta changes at specific points where the pattern of the RMSD and root mean square fluctuation (RMSF) (< 1.0 Å) support any major domain shifts within the structural framework of the protein-ligand complex and placement of ligand was well complemented within the binding site. The β-factor values demonstrated instability at few points while the radius of gyration for structural compactness as a time function for the 100-ns simulation of protein-ligand complexes showed favorable average values and denoted the stability of all complexes. It is assumed that such findings might facilitate researchers to robustly discover and develop effective therapeutics against S. sciuri alongside other enteric infections.
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Affiliation(s)
- Aafareen Khan
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Saman Sohail
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Seerat Yaseen
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Sareen Fatima
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
| | - Ayesha Wisal
- Department of Chemistry, Islamia College Peshawar, Peshawar, 25000, KP, Pakistan
| | - Sufyan Ahmed
- Abbasi Shaheed Hospital, Karachi Medical and Dental College, Karachi, Pakistan
| | - Mahrukh Nasir
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Irfan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Asad Karim
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Zarrin Basharat
- Alpha Genomics (Private) Limited, Islamabad, 44710, Pakistan
| | - Yasmin Khan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan
| | - Muhammad Aurongzeb
- Faculty of Engineering Sciences & Technology, Hamdard University, Karachi, 74600, Pakistan
| | - Syed Kashif Raza
- Faculty of Rehabilitation and Allied Health Sciences (FRAHS), Riphah International University, Faisalabad, Pakistan
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha, 9088, Saudi Arabia
| | - Carlos M Morel
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
| | - Syed S Hassan
- Dr. Panjwani Center for Molecular Medicine, International Center for Chemical and Biological Sciences (ICCBS-PCMD), University of Karachi, Karachi, 75270, Pakistan.
- Centre for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Building "Expansão", 8Th Floor Room 814, Av. Brasil 4036 - Manguinhos, Rio de Janeiro, RJ, 21040-361, Brazil.
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Chatterjee D, Al Rimon R, Chowdhury UF, Islam MR. A multi-epitope based vaccine against the surface proteins expressed in cyst and trophozoite stages of parasite Entamoeba histolytica. J Immunol Methods 2023; 517:113475. [PMID: 37088358 DOI: 10.1016/j.jim.2023.113475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/12/2023] [Accepted: 04/19/2023] [Indexed: 04/25/2023]
Abstract
Entamoeba histolytica, an anaerobic parasite, infects humans and other primates and causes fatal diseases, such as amebiasis, amebic liver abscesses, and many others. Thousands of people are infected and dying due to the need for a proper protective cure, especially in poor sanitizing regions, such as Latin America, Asia, and Africa. Around 10% of the world population is infected by E. histolytica every year. Consequently, novel preventive approaches are required to eliminate the threats of the parasite. A designed vaccine targeting the exposed proteins that are common between cyst and trophozoite stages of the parasite's life cycle would be an effective way to repress the impact of the parasite. Therefore, an in silico bioinformatics approach was performed to design an effective vaccine targeting surface proteins common between both stages of the parasite's life cycle using B-cell and T-cell epitopes. The epitopes derived from the conserved portions of the proteins and their corresponding isomers specific to the parasite suggested that the vaccine could benefit cross-protection. Furthermore, the three-dimensional structure of the designed vaccine was modelled, refined, and validated using multiple bioinformatics tools. The physiological properties and solubility were also predicted using different algorithmic tools and found to be highly soluble in nature. The vaccine was found interactcted with TLR immune receptors, and the stability was observed via dynamics simulation. Codon optimization and cloning were performed for expression analysis. Immune simulation prediction anticipated significant immune responses with a high IgG and IgM antibodies expression, Th and Tc cells population, B-cell population, memory cells, INF-γ, and IL-2 cytokines. Therefore, the constructed multi-epitope putative vaccine can effectively neutralize the parasite's harmful effects.
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Affiliation(s)
- Dipankor Chatterjee
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Razoan Al Rimon
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
| | - Umar Faruq Chowdhury
- Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
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Naveed M, Waseem M, Aziz T, Hassan JU, Makhdoom SI, Ali U, Alharbi M, Alsahammari A. Identification of Bacterial Strains and Development of anmRNA-Based Vaccine to Combat Antibiotic Resistance in Staphylococcus aureus via In Vitro and In Silico Approaches. Biomedicines 2023; 11:biomedicines11041039. [PMID: 37189657 DOI: 10.3390/biomedicines11041039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The emergence of antibiotic-resistant microorganisms is a significant concern in global health. Antibiotic resistance is attributed to various virulent factors and genetic elements. This study investigated the virulence factors of Staphylococcus aureus to create an mRNA-based vaccine that could help prevent antibiotic resistance. Distinct strains of the bacteria were selected for molecular identification of virulence genes, such as spa, fmhA, lukD, and hla-D, which were performed utilizing PCR techniques. DNA extraction from samples of Staphylococcus aureus was conducted using the Cetyl Trimethyl Ammonium Bromide (CTAB) method, which was confirmed and visualized using a gel doc; 16S rRNA was utilized to identify the bacterial strains, and primers of spa, lukD, fmhA, and hla-D genes were employed to identify the specific genes. Sequencing was carried out at Applied Bioscience International (ABI) in Malaysia. Phylogenetic analysis and alignment of the strains were subsequently constructed. We also performed an in silico analysis of the spa, fmhA, lukD, and hla-D genes to generate an antigen-specific vaccine. The virulence genes were translated into proteins, and a chimera was created using various linkers. The mRNA vaccine candidate was produced utilizing 18 epitopes, linkers, and an adjuvant, known as RpfE, to target the immune system. Testing determined that this design covered 90% of the population conservancy. An in silico immunological vaccine simulation was conducted to verify the hypothesis, including validating and predicting secondary and tertiary structures and molecular dynamics simulations to evaluate the vaccine’s long-term viability. This vaccine design may be further evaluated through in vivo and in vitro testing to assess its efficacy.
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Bakkari MA. Targeted Protein-Specific Multi-Epitope-Based Vaccine Designing against Human Cytomegalovirus by Using Immunoinformatics Approaches. Vaccines (Basel) 2023; 11. [PMID: 36851082 DOI: 10.3390/vaccines11020203] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Cytomegaloviruses are emerging pathogenic agents known to cause congenital disorders in humans. In this study, immune epitopes (CTL, B cell and HTL) were screened for highly antigenic target proteins of the Human Cytomegalovirus. These shortlisted epitopes were then joined together through suitable linkers to construct multi epitope-based vaccine constructs (MEVCs). The functionality of each vaccine construct was evaluated through tertiary vaccine structure modelling and validations. Furthermore, physio-chemical properties including allergenicity, antigenicity molecular weight and many others were also predicted. The vaccine designs were also docked with the human TLR-4 receptor to demonstrate the receptor specific affinity and formed interactions. The vaccine peptides sequences were also subjected to codon optimization to confirm the potential vaccines expression in E. coli hosts. Additionally, all the MEVCs were also evaluated for immune response (IgG and IgM) induction. However, further in vivo tests are needed to ensure the efficacy of these vaccine designs.
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Khan T, Muzaffar A, Shoaib RM, Khan A, Waheed Y, Wei DQ. Towards specie-specific ensemble vaccine candidates against mammarenaviruses using optimized structural vaccinology pipeline and molecular modelling approaches. Microb Pathog 2022; 172:105793. [PMID: 36165863 DOI: 10.1016/j.micpath.2022.105793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/16/2022] [Accepted: 09/16/2022] [Indexed: 10/31/2022]
Abstract
Mammarena viruses are emerging pathogenic agents and cause hemorrhagic fevers in humans. These viruses accomplish host immune system evasion to replicate and spread in the host. There are only few available therapeutic options developed for Mammarena Virus (also called MMV). Currently, only a single candidate vaccine called Candid#1 is available against Junin virus. Similarly, the effective treatment Ribavirin is used only in Lassa fever treatments. Herein, immune-informatics pipeline has been used to annotate whole proteome of the seven human infecting Mammarena strains. The extensive immune based analysis reveals specie specific epitopes with a crucial role in immune response induction. This was achieved by construction of immunogenic epitopes (CTL "Cytotoxic T-Lymphocytes", HTL "Helper T-Lymphocytes", and B cell "B-Lymphocytes") based vaccine designs against seven different Mammarena virus species. Furthermore, validation of the vaccine constructs through exploring physiochemical properties was performed to confirm experimental feasibility. Additionally, in-silico cloning and receptor based immune simulation was performed to ensure induction of primary and secondary immune response. This was confirmed through expression of immune factors such as IL, cytokines, and antibodies. The current study provides with novel vaccine designs which needs further demonstrations through potential processing against MMVs. Future studies may be directed towards advanced evaluations to determine the efficacy and safety of the designed vaccines through further experimental procedures.
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Affiliation(s)
- Taimoor Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | | | | | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, PR China.
| | - Yasir Waheed
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, PR China; Peng Cheng National Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China.
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Albutti A. Proteome-Wide and Protein-Specific Multi-Epitope Vaccine Constructs Against the Rift Valley Fever Virus Outbreak Using Integrated Omics Approaches. Front Microbiol 2022; 13:921683. [PMID: 35711778 PMCID: PMC9195176 DOI: 10.3389/fmicb.2022.921683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Rift Valley fever (RVF) is a viral disease caused by a member of the Bunyavirales family causing severe infections in humans. The RVF virus is an enveloped, negative-sense, single-stranded RNA virus that can infect both animals and humans. The symptoms associated with these infections span from minor (fever and headaches) to severe (meningoencephalitis and hemorrhagic fever syndrome) symptoms. Despite the outbreaks of the RVF virus being reported in different parts of the world, no effective therapy is available. Herein, the development of an efficient vaccine is critical for the control of infections associated with the RVF virus. Moreover, computational vaccine approaches are helpful in the design of specific, safe, and stable peptide-based designs when compared to the conventional methods of vaccine development. In this study, the whole proteome of the virus, comprising four proteins (NP, L, GP, and NSP), was screened to find putative vaccine epitope sequences (T cell, B cell, and HTL) specific for each protein. These shortlisted epitopes were then combined with flexible linkers to design protein-specific and proteome-wide immunogenic multi-epitope-based vaccine constructs. The results revealed that these multi-epitope vaccine constructs (MEVCs) are strongly antigenic and non-allergenic in nature. The efficacy of these constructs was further validated by docking with immune receptors, which revealed strong binding interactions with human TLR8. Using the MD simulation approach, the binding stability and residual flexibility of the best vaccine construct (proteome-wide) were confirmed, which revealed stable dynamic and favorable features. Furthermore, in-silico cloning and immune simulation analysis confirmed the expression and production of immune factors, that is, IgM, IgG, and IL-6, against the proposed vaccine designs. Additionally, 3D models of all the MEVC constructs have been developed and evaluated for potential immunization against the RVF virus. Finally, the proteome-wide vaccine candidate (MEVC-PW-RVFV) with the highest immune reinforcement potential provides new insights into the development of future vaccines against the emerging RVF virus.
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Affiliation(s)
- Aqel Albutti
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
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