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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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Dashti F, Raisi A, Pourali G, Razavi ZS, Ravaei F, Sadri Nahand J, Kourkinejad-Gharaei F, Mirazimi SMA, Zamani J, Tarrahimofrad H, Hashemian SMR, Mirzaei H. A computational approach to design a multiepitope vaccine against H5N1 virus. Virol J 2024; 21:67. [PMID: 38509569 PMCID: PMC10953225 DOI: 10.1186/s12985-024-02337-7] [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: 11/23/2023] [Accepted: 03/07/2024] [Indexed: 03/22/2024] Open
Abstract
Since 1997, highly pathogenic avian influenza viruses, such as H5N1, have been recognized as a possible pandemic hazard to men and the poultry business. The rapid rate of mutation of H5N1 viruses makes the whole process of designing vaccines extremely challenging. Here, we used an in silico approach to design a multi-epitope vaccine against H5N1 influenza A virus using hemagglutinin (HA) and neuraminidase (NA) antigens. B-cell epitopes, Cytotoxic T lymphocyte (CTL) and Helper T lymphocyte (HTL) were predicted via IEDB, NetMHC-4 and NetMHCII-2.3 respectively. Two adjuvants consisting of Human β-defensin-3 (HβD-3) along with pan HLA DR-binding epitope (PADRE) have been chosen to induce more immune response. Linkers including KK, AAY, HEYGAEALERAG, GPGPGPG and double EAAAK were utilized to link epitopes and adjuvants. This construct encodes a protein having 350 amino acids and 38.46 kDa molecular weight. Antigenicity of ~ 1, the allergenicity of non-allergen, toxicity of negative and solubility of appropriate were confirmed through Vaxigen, AllerTOP, ToxDL and DeepSoluE, respectively. The 3D structure of H5N1 was refined and validated with a Z-Score of - 0.87 and an overall Ramachandran of 99.7%. Docking analysis showed H5N1 could interact with TLR7 (docking score of - 374.08 and by 4 hydrogen bonds) and TLR8 (docking score of - 414.39 and by 3 hydrogen bonds). Molecular dynamics simulations results showed RMSD and RMSF of 0.25 nm and 0.2 for H5N1-TLR7 as well as RMSD and RMSF of 0.45 nm and 0.4 for H5N1-TLR8 complexes, respectively. Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) confirmed stability and continuity of interaction between H5N1-TLR7 with the total binding energy of - 29.97 kJ/mol and H5N1-TLR8 with the total binding energy of - 23.9 kJ/mol. Investigating immune response simulation predicted evidence of the ability to stimulate T and B cells of the immunity system that shows the merits of this H5N1 vaccine proposed candidate for clinical trials.
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Affiliation(s)
- Fatemeh Dashti
- School of Medicine, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
| | - Arash Raisi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
| | - Ghazaleh Pourali
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Islamic Republic of Iran
| | - Zahra Sadat Razavi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
| | - Fatemeh Ravaei
- School of Medicine, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
| | - Fatemeh Kourkinejad-Gharaei
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
- Department of Infectious Diseases, Emam Reza Hospital, Sirjan School of Medical Sciences, Sirjan, Islamic Republic of Iran
| | - Seyed Mohammad Ali Mirazimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran
| | - Javad Zamani
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Islamic Republic of Iran
| | - Hossein Tarrahimofrad
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Islamic Republic of Iran.
| | - Seyed Mohammad Reza Hashemian
- Chronic Respiratory Diseases Research Center (CRDRC), National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Islamic Republic of Iran.
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3
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Roja B, Chellapandi P. Design and characterization of a multi-epitope vaccine against Clostridium botulinum A3 Loch Maree intoxication in humans. Gene 2024; 892:147865. [PMID: 37783297 DOI: 10.1016/j.gene.2023.147865] [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: 06/23/2023] [Revised: 09/03/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
Clostridium botulinum Loch Maree expresses an extremely potent botulinum neurotoxin subtype, A3 causing botulism and several gastrointestinal disorders in mammals. Several recombinant vaccines have been developed for human botulism and no vaccine is currently available for the treatment of diseases caused by other virulence factors. Hence, we designed, constructed, and characterized a multi-epitope vaccine from new virulence proteins identified from this organism using an immunoinformatics approach. The vaccine construct used in this study was designed from 6B cell linear epitopes, 12 cytotoxic T cell lymphocyte epitopes, and 15 helper T cell lymphocyte epitopes, with a defensin adjuvant and adjusting linker sequences. A molecular modeling approach was used to model, refine, and validate the 3D structure of the vaccine construct. Molecular docking studies were performed to determine the stability of the molecular interactions between the vaccine construct and human toll-like receptor 7. The in silico molecular cloning was used to clone a codon-optimized synthetic vaccine gene in pCYB1 vector and expressed in Escherichia coli. The results of this study identified six new virulence proteins: peptidoglycan hydrolase, SCP-like extracellular protein, N-acetylmuramoyl-l-alanine amidase, putative membrane protein, drug/metabolite exporter, and bacillolysin. The top B-cell, cytotoxic T-cell lymphocyte, and helper T-lymphocyte epitopes were predicted from these virulence proteins with greater accuracy and reliability. HLA-A*02:01 and HLA-A*03:01 were identified as HLA-A-binding alleles for cytotoxic T-cell lymphocyte epitopes. DRB1*0110 and DRB1*0115 are the dominant alleles that bind to helper T-cell lymphocyte epitopes. The synthetic gene construct was highly expressed in a heterologous host and produced considerable amounts of antigenic protein. The multi-epitope vaccine is more conservative in the sequence-structure-function link, immunogenic with less allergenicity, and possibly provokes cellular and humoral immunity. The present study suggests that the designed multi-epitope vaccine is a promising prophylactic candidate for the virulence and intoxication caused by subtype A3 strains.
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Affiliation(s)
- B Roja
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - P Chellapandi
- Industrial Systems Biology Lab, Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India.
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Lv Z, Ji F, Song J, Li P, Chen M, Chang J. Predicting the spatial structure of membrane protein and B-cell epitopes of the MPXV_VEROE6 strain of monkeypox virus. Heliyon 2023; 9:e20386. [PMID: 37767496 PMCID: PMC10520823 DOI: 10.1016/j.heliyon.2023.e20386] [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: 10/25/2022] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
By targeting the membrane (M) proteins of monkeypox virus (MPXV) strain VEROE6, we analyzed its evolutionary hierarchy and predicted its dominant antigenic B-cell epitope to provide a theoretical basis for the development of MPXV epitope vaccines and related monoclonal antibodies. In this study, phylogenetic trees were constructed based on the nucleic acid sequences of MPXV and the amino acid sequences of M proteins. The 3D structure of the MPXV_VEROE6 M proteins was predicted with AlphaFold v2.0 and the dominant antigenic B-cell epitopes were comprehensively predicted by analyzing parameters such as flexible segments, the hydrophilic index, the antigenic index, and the protein surface probability. The results showed that the M protein of MPXV_VEROE6 contained 377 amino acids, and their spatial configuration was relatively regular with a turning and random coil structure. The results of a comprehensive multiparameter analysis indicated that possible B-cell epitopes were located in the 23-28, 57-63, 67-78, 80-93, 98-105, 125-131, 143-149, 201-206, 231-237, 261-270, 291-303, and 346-362 amino acid segments. This study elucidated the structural and evolutionary characteristics of MPXV membrane proteins with the aim of providing theoretical information for the development of epitope vaccines, rapid diagnostic reagents, and monoclonal antibodies for monkeypox virus.
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Affiliation(s)
- Zhiyuan Lv
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
| | - Feng Ji
- Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Jianzhong Song
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
- Department of Pharmacy, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011,China
| | - Panpan Li
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
| | - Ming Chen
- Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Junmin Chang
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
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Firdaus MER, Mustopa AZ, Ekawati N, Chairunnisa S, Arifah RK, Hertati A, Irawan S, Prastyowati A, Kusumawati A, Nurfatwa M. Optimization, characterization, comparison of self-assembly VLP of capsid protein L1 in yeast and reverse vaccinology design against human papillomavirus type 52. J Genet Eng Biotechnol 2023; 21:68. [PMID: 37222880 DOI: 10.1186/s43141-023-00514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/06/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND Vaccination is the one of the agendas of many countries to reduce cervical cancer caused by the Human papillomavirus. Currently, VLP-based vaccine is the most potent vaccine against HPV, which could be produced by a variety of expression systems. Our study focuses on a comparison of recombinant protein expression L1 HPV52 using two common yeasts, Pichia pastoris and Hansenula polymorpha that have been used for vaccine production on an industrial scale. We also applied bioinformatics approach using reverse vaccinology to design alternative multi-epitope vaccines in recombinant protein and mRNA types. RESULTS Our study found that P. pastoris relatively provided higher level of L1 protein expression and production efficiency compared to H. polymorpha in a batch system. However, both hosts showed self-assembly VLP formation and stable integration during protein induction. The vaccine we have designed exhibited high immune activation and safe in computational prediction. It is also potentially suitable for production in a variety of expression systems. CONCLUSION By monitoring the overall optimization parameter assessment, this study can be used as the basis reference for large-scale production of the HPV52 vaccine.
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Affiliation(s)
- Moh Egy Rahman Firdaus
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
- Current Address: Laboratory of Structural Virology, The International Institute of Molecular Mechanisms and Machines (IMOL), Polish Academy of Sciences, Warsaw, Poland
| | - Apon Zaenal Mustopa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia.
| | - Nurlaili Ekawati
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Sheila Chairunnisa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Rosyida Khusniatul Arifah
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Ai Hertati
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Shasmita Irawan
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Anika Prastyowati
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Arizah Kusumawati
- Directorate of Laboratory Management Research Facilities, Science and Technology Park, National Research and Innovation Agency (BRIN), Bogor, 16911, West Java, Indonesia
| | - Maritsa Nurfatwa
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
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Fontes-Dantas FL, Fernandes GG, Gutman EG, De Lima EV, Antonio LS, Hammerle MB, Mota-Araujo HP, Colodeti LC, Araújo SM, Froz GM, da Silva TN, Duarte LA, Salvio AL, Pires KL, Leon LA, Vasconcelos CCF, Romão L, Savio LEB, Silva JL, da Costa R, Clarke JR, Da Poian AT, Alves-Leon SV, Passos GF, Figueiredo CP. SARS-CoV-2 Spike protein induces TLR4-mediated long-term cognitive dysfunction recapitulating post-COVID-19 syndrome in mice. Cell Rep 2023; 42:112189. [PMID: 36857178 PMCID: PMC9935273 DOI: 10.1016/j.celrep.2023.112189] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/16/2022] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Cognitive dysfunction is often reported in patients with post-coronavirus disease 2019 (COVID-19) syndrome, but its underlying mechanisms are not completely understood. Evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike protein or its fragments are released from cells during infection, reaching different tissues, including the CNS, irrespective of the presence of the viral RNA. Here, we demonstrate that brain infusion of Spike protein in mice has a late impact on cognitive function, recapitulating post-COVID-19 syndrome. We also show that neuroinflammation and hippocampal microgliosis mediate Spike-induced memory dysfunction via complement-dependent engulfment of synapses. Genetic or pharmacological blockage of Toll-like receptor 4 (TLR4) signaling protects animals against synapse elimination and memory dysfunction induced by Spike brain infusion. Accordingly, in a cohort of 86 patients who recovered from mild COVID-19, the genotype GG TLR4-2604G>A (rs10759931) is associated with poor cognitive outcome. These results identify TLR4 as a key target to investigate the long-term cognitive dysfunction after COVID-19 infection in humans and rodents.
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Affiliation(s)
- Fabricia L. Fontes-Dantas
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Department of Pharmacology, Institute of Biology, Rio de Janeiro State University, Rio de Janeiro, RJ, Brazil
| | - Gabriel G. Fernandes
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Elisa G. Gutman
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil,Clinical Medicine Post-graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Emanuelle V. De Lima
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Leticia S. Antonio
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mariana B. Hammerle
- Clinical Medicine Post-graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Hannah P. Mota-Araujo
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Lilian C. Colodeti
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Suzana M.B. Araújo
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gabrielle M. Froz
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Talita N. da Silva
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Larissa A. Duarte
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil,Clinical Medicine Post-graduation Program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Andreza L. Salvio
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil
| | - Karina L. Pires
- Neurology Department, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, RJ, Brazil
| | - Luciane A.A. Leon
- Laboratório de Desenvolvimento Tecnológico em Virologia, IOC/FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | | | - Luciana Romão
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luiz Eduardo B. Savio
- Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Jerson L. Silva
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Robson da Costa
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Julia R. Clarke
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
| | - Soniza V. Alves-Leon
- Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, Rio de Janeiro, RJ, Brazil,Division of Neurology, Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
| | - Giselle F. Passos
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
| | - Claudia P. Figueiredo
- School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil,Corresponding author
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Naveed M, Mughal MS, Jabeen K, Aziz T, Naz S, Nazir N, Shahzad M, Alharbi M, Alshammari A, Sadhu SS. Evaluation of the whole proteome to design a novel mRNA-based vaccine against multidrug-resistant Serratia marcescens. Front Microbiol 2022; 13:960285. [PMID: 36329838 PMCID: PMC9624125 DOI: 10.3389/fmicb.2022.960285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
Serratia marcescens, a Gram-negative bacterium, is one of the known disease-causing pathogens. It is resistant to ampicillin, macrolides, cephalosporins, cefotaxime, and ceftazidime. The only antibiotic that has been proven to be effective against S. marcescens is gentamicin. By causing epigenetic alterations, bacteria can also become resistant to all antibiotics. Many epigenetically related proteins were studied, and four proteins were selected in this regard for epitope evaluation and their subsequent use in the development of a messenger ribonucleic acid (mRNA) vaccine. A series of immune-informatics tools used to build this mRNA vaccine elicited cellular and humoral immunity. Molecular docking between epitopes and alleles of the major histocompatibility complex (MHC) was performed. The vaccine was developed using 37 epitopes, an adjuvant that is a TLR-4 agonist known as resuscitation-promoting factor E (RpfE), subcellular trafficking structures, secretion boosters, and linkers. This proposed architecture was found to cover 99.6% of the population during testing. During testing, it was proven that it was both effective and safe. To confirm our idea, we performed an in silico immunological simulation of vaccination. The codon was also optimized to ensure that the mRNA reached the cytoplasm of a human host and underwent efficient translation. TLR-4 and TLR-3 were also docked against the secondary and tertiary structures of the vaccine peptide. Furthermore, the vaccine's stability was confirmed by molecular dynamics simulation. In summary, this vaccine construct can be a potential candidate against S. marcescens and is suitable for in vitro analyses to validate its effectiveness.
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Affiliation(s)
- Muhammad Naveed
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
- *Correspondence: Muhammad Naveed
| | - Muhammad Saad Mughal
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Khizra Jabeen
- Department of Biotechnology, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Tariq Aziz
- Pak-Austria Fachhochschule: Institute of Applied Sciences and Technology, Mang, Pakistan
- Tariq Aziz
| | - Sumaira Naz
- Department of Biochemistry, University of Malakand, Chakdara, Pakistan
| | - Nausheen Nazir
- Department of Biochemistry, University of Malakand, Chakdara, Pakistan
| | - Muhammad Shahzad
- Institute of Basic Medical Sciences, Khyber Medical University, Peshawar, Pakistan
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Satya Sai Sadhu
- Chemistry Department, Northern Michigan University, Marquette, MI, United States
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Designing multi-epitope based peptide vaccine targeting spike protein SARS-CoV-2 B1.1.529 (Omicron) variant using computational approaches. Struct Chem 2022; 33:2243-2260. [PMID: 36160688 PMCID: PMC9485025 DOI: 10.1007/s11224-022-02027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/02/2022] [Indexed: 10/26/2022]
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