1
|
Lani R, Thariq IM, Suhaimi NS, Hassandarvish P, Abu Bakar S. From defense to offense: Modulating toll-like receptors to combat arbovirus infections. Hum Vaccin Immunother 2024; 20:2306675. [PMID: 38263674 DOI: 10.1080/21645515.2024.2306675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/14/2024] [Indexed: 01/25/2024] Open
Abstract
Arboviruses are a significant threat to global public health, with outbreaks occurring worldwide. Toll-like receptors (TLRs) play a crucial role in the innate immune response against these viruses by recognizing pathogen-associated molecular patterns and initiating an inflammatory response. Significantly, TLRs commonly implicated in the immune response against viral infections include TLR2, TLR4, TLR6, TLR3, TLR7, and TLR8; limiting or allowing them to replicate and spread within the host. Modulating TLRs has emerged as a promising approach to combat arbovirus infections. This review summarizes recent advances in TLR modulation as a therapeutic target in arbovirus infections. Studies have shown that the activation of TLRs can enhance the immune response against arbovirus infections, leading to increased viral clearance and protection against disease. Conversely, inhibition of TLRs can reduce the excessive inflammation and tissue damage associated with arbovirus infection. Modulating TLRs represents a potential therapeutic strategy to combat arbovirus infections.
Collapse
Affiliation(s)
- Rafidah Lani
- Department of Medical Microbiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Ilya Maisarah Thariq
- Tropical Infectious Diseases Research and Education Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Nuramira Syazreen Suhaimi
- Tropical Infectious Diseases Research and Education Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Pouya Hassandarvish
- Tropical Infectious Diseases Research and Education Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Sazaly Abu Bakar
- Tropical Infectious Diseases Research and Education Centre, Universiti Malaya, Kuala Lumpur, Malaysia
| |
Collapse
|
2
|
Agarwal S, Harsukhbhai Chandpa H, Naskar S, Lal Meena C, Kumar Panda A, Meena J. Dominant B cell-T cell epitopes instigated robust immune response in-silico against Scrub Typhus. Vaccine 2024; 42:3899-3915. [PMID: 38719691 DOI: 10.1016/j.vaccine.2024.04.082] [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: 02/28/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 06/14/2024]
Abstract
Scrub typhus, a potentially life-threatening infectious disease, is attributed to bacteria Orientia tsutsugamushi (O. tsutsugamushi). The transmission of this illness to humans occurs through the bite of infected chiggers, which are the larval forms of mites belonging to the genus Leptotrombidium. In this research, we developed a subunit vaccine specifically designed to target outer membrane proteins. Immunodominant cytotoxic T-lymphocytes (CTLs), B- lymphocytes (BCLs), and major histocompatibility complex (MHC)- II epitopes were identified using machine learning and bioinformatics approaches. These epitopes were arranged in different combinations with the help of suitable linkers like AAY, KK, GPGPG and adjuvant (cholera toxin B) that resulted in a vaccine construct. Physiochemical properties were assessed, where the predicted solubility (0.571) was higher than threshold value. Tertiary structure was predicted using I-TASSER web server and evaluated using Ramachandran plot (94 % residues in most favourable region) and z-score (-6.04), which had shown the structure to have good stability and residue arrangement. Molecular docking with immune receptors, Toll-like receptor (TLR)-2 and -4 showed good residue interaction with 13 and 5 hydrogen bonds respectively. Molecular dynamics simulations of receptor-ligand complex provided the idea about the strong interaction having 1.524751 × 10-5 eigenvalue. Amino acid sequence of vaccine was converted to nucleotide sequence and underwent codon optimization. The optimized codon sequence was used for in-silico cloning, which provided idea about the possibility of synthesis of vaccine using E. coli as host. Overall, this study provided a promising blueprint for a scrub typhus vaccine, although experimental validation is needed for confirmation. Furthermore, it is crucial to acknowledge that while bioinformatics provides valuable insights, in-vitro and in-vivo studies are imperative for a comprehensive evaluation of vaccine candidate. Thus, the integration of computational predictions with empirical research is essential to validate the efficacy, safety, and real-world applicability of the designed vaccine against Scrub Typhus. Nevertheless, the findings are good to carry forward for in-vitro and in-vivo investigations.
Collapse
Affiliation(s)
- Shalini Agarwal
- 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
| | - Shovan Naskar
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India
| | - Chhuttan Lal Meena
- Drug Design Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Amulya Kumar Panda
- Panacea Biotec Limited, Mohan Cooperative Industrial Estate, Badarpur New Delhi 110044, India
| | - Jairam Meena
- ImmunoEngineering and Therapeutics Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005, India.
| |
Collapse
|
3
|
Roy A, Swetha RG, Basu S, Biswas R, Ramaiah S, Anbarasu A. Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1. 3 Biotech 2024; 14:176. [PMID: 38855144 PMCID: PMC11153438 DOI: 10.1007/s13205-024-04022-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Herpes simplex virus type-1 (HSV-1), the etiological agent of sporadic encephalitis and recurring oral (sometimes genital) infections in humans, affects millions each year. The evolving viral genome reduces susceptibility to existing antivirals and, thus, necessitates new therapeutic strategies. Immunoinformatics strategies have shown promise in designing novel vaccine candidates in the absence of a clinically licensed vaccine to prevent HSV-1. However, to encourage clinical translation, the HSV-1 pan-genome was integrated with the reverse-vaccinology pipeline for rigorous screening of universal vaccine candidates. Viral targets were screened from 104 available complete genomes. Among 364 proteins, envelope glycoprotein D being an outer membrane protein with a high antigenicity score (> 0.4) and solubility (> 0.6) was selected for epitope screening. A total of 17 T-cell and 4 B-cell epitopes with highly antigenic, immunogenic, non-toxic properties and high global population coverage were identified. Furthermore, 8 vaccine constructs were designed using different combinations of epitopes and suitable linkers. VC-8 was identified as the most potential vaccine candidate regarding chemical and structural stability. Molecular docking revealed high interactive affinity (low binding energy: - 56.25 kcal/mol) of VC-8 with the target elicited by firm intermolecular H-bonds, salt-bridges, and hydrophobic interactions, which was validated with simulations. Compatibility of the vaccine candidate to be expressed in pET-29(a) + plasmid was established by in silico cloning studies. Immune simulations confirmed the potential of VC-8 to trigger robust B-cell, T-cell, cytokine, and antibody-mediated responses, thereby suggesting a promising candidate for the future of HSV-1 prevention. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04022-6.
Collapse
Affiliation(s)
- Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Rayapadi G. Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, Odisha 761008 India
| | - Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biosciences, SBST, VIT, Vellore, Tamil Nadu 632014 India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632014 India
- Department of Biotechnology, SBST, VIT, Vellore, Tamil Nadu 632014 India
| |
Collapse
|
4
|
Miranda-López A, González-Ortega O, Govea-Alonso DO, Betancourt-Mendiola L, Comas-García M, Rosales-Mendoza S. Rational design and production of a chimeric antigen targeting Zika virus that induces neutralizing antibodies in mice. Vaccine 2024; 42:3674-3683. [PMID: 38749821 DOI: 10.1016/j.vaccine.2024.04.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/14/2024] [Accepted: 04/25/2024] [Indexed: 06/07/2024]
Abstract
The Zika virus (ZIKV) is considered a public health problem worldwide due to its association with the development of microcephaly and the Guillain-Barré syndrome. Currently, there is no specific treatment or vaccine approved to combat this disease, and thus, developing safe and effective vaccines is a relevant goal. In this study, a multi-epitope protein called rpZDIII was designed based on a series of ZIKV antigenic sequences, a bacterial carrier, and linkers. The analysis of the predicted 3D structure of the rpZDIII chimeric antigen was performed on the AlphaFold 2 server, and it was produced in E. coli and purified from inclusion bodies, followed by solubilization and refolding processes. The yield achieved for rpZDIII was 11 mg/L in terms of pure soluble recombinant protein per liter of fermentation. rpZDIII was deemed immunogenic since it induced serum IgG and IgM responses in mice upon subcutaneous immunization in a three-dose scheme. Moreover, sera from mice immunized with rpZDIII showed neutralizing activity against ZIKV. Therefore, this study reveals rpZDIII as a promising immunogen for the development of a rationally designed multi-epitope vaccine against ZIKV, and completion of its preclinical evaluation is guaranteed.
Collapse
Affiliation(s)
- Arleth Miranda-López
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, México
| | - Omar González-Ortega
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, México; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210 México
| | - Dania O Govea-Alonso
- Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210 México
| | - Lourdes Betancourt-Mendiola
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, México; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210 México
| | - Mauricio Comas-García
- Sección de Microscopía de Alta Resolución, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210, México; Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Parque Chapultepec 1570, San Luis, S.L.P., San Luis Potosí 78210, México.
| | - Sergio Rosales-Mendoza
- Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, Av. Dr. Manuel Nava 6, SLP 78210, México; Sección de Biotecnología, Centro de Investigación en Ciencias de la Salud y Biomedicina, Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, Lomas 2ª. Sección, San Luis Potosí 78210 México.
| |
Collapse
|
5
|
Sarfraz A, Qurrat-Ul-Ain Fatima S, Shehroz M, Ahmad I, Zaman A, Nishan U, Tayyab M, Sheheryar, Moura AA, Ullah R, Ali EA, Shah M. Decrypting the multi-genome data for chimeric vaccine designing against the antibiotic resistant Yersinia pestis. Int Immunopharmacol 2024; 132:111952. [PMID: 38555818 DOI: 10.1016/j.intimp.2024.111952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Yersinia pestis, the causative agent of plague, is a gram-negative bacterium that can be fatal if not treated properly. Three types of plague are currently known: bubonic, septicemic, and pneumonic plague, among which the fatality rate of septicemic and pneumonic plague is very high. Bubonic plague can be treated, but only if antibiotics are used at the initial stage of the infection. But unfortunately, Y. pestis has also shown resistance to certain antibiotics such as kanamycin, minocycline, tetracycline, streptomycin, sulfonamides, spectinomycin, and chloramphenicol. Despite tremendous progress in vaccine development against Y. pestis, there is no proper FDA-approved vaccine available to protect people from its infections. Therefore, effective broad-spectrum vaccine development against Y. pestis is indispensable. In this study, vaccinomics-assisted immunoinformatics techniques were used to find possible vaccine candidates by utilizing the core proteome prepared from 58 complete genomes of Y. pestis. Human non-homologous, pathogen-essential, virulent, and extracellular and membrane proteins are potential vaccine targets. Two antigenic proteins were prioritized for the prediction of lead epitopes by utilizing reverse vaccinology approaches. Four vaccine designs were formulated using the selected B- and T-cell epitopes coupled with appropriate linkers and adjuvant sequences capable of inducing potent immune responses. The HLA allele population coverage of the T-cell epitopes selected for vaccine construction was also analyzed. The V2 constructs were top-ranked and selected for further analysis on the basis of immunological, physicochemical, and immune-receptor docking interactions and scores. Docking and molecular dynamic simulations confirmed the stability of construct V2 interactions with the host immune receptors. Immune simulation analysis anticipated the strong immune profile of the prioritized construct. In silico restriction cloning ensured the feasible cloning ability of the V2 construct in the expression system of E. coli strain K12. It is anticipated that the designed vaccine construct may be safe, effective, and able to elicit strong immune responses against Y. pestis infections and may, therefore, merit investigation using in vitro and in vivo assays.
Collapse
Affiliation(s)
- Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | | | - Muhammad Shehroz
- Department of Bioinformatics, Kohsar University Murree, Murree 47150, Pakistan
| | - Iqra Ahmad
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan 66000, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Muhammad Tayyab
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture Peshawar, Pakistan
| | - Sheheryar
- Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
| | | | - Riaz Ullah
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Essam A Ali
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohibullah Shah
- Department of Biochemistry, Bahauddin Zakariya University, Multan 66000, Pakistan.
| |
Collapse
|
6
|
Sarvmeili J, Baghban Kohnehrouz B, Gholizadeh A, Shanehbandi D, Ofoghi H. Immunoinformatics design of a structural proteins driven multi-epitope candidate vaccine against different SARS-CoV-2 variants based on fynomer. Sci Rep 2024; 14:10297. [PMID: 38704475 PMCID: PMC11069592 DOI: 10.1038/s41598-024-61025-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The ideal vaccines for combating diseases that may emerge in the future require more than simply inactivating a few pathogenic strains. This study aims to provide a peptide-based multi-epitope vaccine effective against various severe acute respiratory syndrome coronavirus 2 strains. To design the vaccine, a library of peptides from the spike, nucleocapsid, membrane, and envelope structural proteins of various strains was prepared. Then, the final vaccine structure was optimized using the fully protected epitopes and the fynomer scaffold. Using bioinformatics tools, the antigenicity, allergenicity, toxicity, physicochemical properties, population coverage, and secondary and three-dimensional structures of the vaccine candidate were evaluated. The bioinformatic analyses confirmed the high quality of the vaccine. According to further investigations, this structure is similar to native protein and there is a stable and strong interaction between vaccine and receptors. Based on molecular dynamics simulation, structural compactness and stability in binding were also observed. In addition, the immune simulation showed that the vaccine can stimulate immune responses similar to real conditions. Finally, codon optimization and in silico cloning confirmed efficient expression in Escherichia coli. In conclusion, the fynomer-based vaccine can be considered as a new style in designing and updating vaccines to protect against coronavirus disease.
Collapse
Affiliation(s)
- Javad Sarvmeili
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, 51666, Iran
| | | | - Ashraf Gholizadeh
- Department of Animal Biology, University of Tabriz, Tabriz, 51666, Iran
| | - Dariush Shanehbandi
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 51666, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, 33131, Iran
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Ganji M, Bakhshi S, Ahmadi K, Shoari A, Moeini S, Ghaemi A. Rational design of B-cell and T-cell multi epitope-based vaccine against Zika virus, an in silico study. J Biomol Struct Dyn 2024; 42:3426-3440. [PMID: 37190978 DOI: 10.1080/07391102.2023.2213339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Abstract
The Zika virus (ZKV) is a single-stranded positive-sense, enveloped RNA virus. Zika infection during pregnancy can cause congenital microcephaly, Guillain-Barré syndrome, miscarriage, and other CNS abnormalities. The world needs safe and effective vaccinations to fight against ZIKV infection since vaccination is generally regarded as one of the most effective ways to prevent infectious diseases. In the present work, we used immunoinformatics and docking studies to construct a vaccine containing multi-epitopes using the structural and non-structural proteins of ZKV. The structural models of ZKV proteins (PrE, PrM, NS1, and NS2A) were constructed using Pyre2 and RaptorX servers. The epitopes of B-cell, T-cell (HTL and CTL), and IFN-γ were predicted, and each epitope's immunogenic nature and physiochemical properties were confirmed. As an adjuvant, the CPG-Oligodeoxynucleotide, an agonist of Toll-like receptor 9 (TLR9), is associated to cytotoxic T-lymphocytes (CTL) epitopes via PAPAP linker. To assess the binding affinity and the tendency of the designed vaccine to induce an immune response through TLR9, molecular docking was done. In the next step, molecular dynamics (MD) simulation to 100 nanoseconds (ns) was used to evaluate the stability of the interaction of the designed vaccine with TLR9. The designed vaccine is predicted to be highly antigenic, non-toxic, soluble, and stable with low flexibility in MD simulation. MD studies indicated that the finalized vaccine-TLR9 docked complex was stable during simulation time. The vaccine construct is able to stimulate both humoral and cellular immune responses. We suppose that our constructed model of the vaccine may have the ability to induce the host immune response against ZKV. Further studies, including in vitro and in vivo experimental analyses, are needed to prove the constructed vaccine's efficacy with multi-epitopes.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mahmoud Ganji
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Shohreh Bakhshi
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Alireza Shoari
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, USA
| | - Soheila Moeini
- Department of Surgery, Faculty of Medicine, McGill University, Montréal, Québec, Canada
| | - Amir Ghaemi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
9
|
Gupta Y, Baranwal M, Chudasama B. Zika virus precursor membrane peptides induce immune response in peripheral blood mononuclear cells. Hum Immunol 2024; 85:110761. [PMID: 38272735 DOI: 10.1016/j.humimm.2024.110761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/25/2023] [Accepted: 01/17/2024] [Indexed: 01/27/2024]
Abstract
Zika virus is a re-merging flavivirus allied to serious mental health conditions in the fetuses. There is currently no preventives or treatment available for Zika infection. In this work, we have extended the in silico analysis by performing the molecular docking of previous reported three conserved Zika virus precursor membrane (prM) peptides (MP1, MP2 and MP3) with HLA complex (pHLA) and T cell receptors (TCR) and also evaluated the peptide specific immune response in human peripheral blood mononuclear cells (PBMC). Most of the CD8+ and CD4+ T cell peptides-HLA complexes demonstrated good binding energies (ΔG) and HADDOCK scores in molecular docking analysis. Immunogenic response of peptides is measured as human peripheral blood mononuclear cell (PBMC) proliferation and interferon-gamma (IFN-γ) production using a 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and a sandwich enzyme-linked immunosorbent assay (ELISA) respectively on ten different healthy blood samples. Peptide MP3 exhibited significant results in eight (cell proliferation) and seven (IFN-γ secretion) healthy volunteers' blood samples out of ten. Additionally, peptides MP1 and MP2 presented significant cell proliferation and IFN-γ release in six healthy blood samples. Thus, the outcomes from in silico and in vitro studies showed the immunogenic potential of peptides which need to validated in different experimental system before considering as candidate vaccine against Zika virus infection.
Collapse
Affiliation(s)
- Yogita Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India.
| | - Bhupendra Chudasama
- School of Physics & Materials Science, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| |
Collapse
|
10
|
Hakami MA. An immunoinformatics and structural vaccinology approach to design a novel and potent multi-epitope base vaccine targeting Zika virus. BMC Chem 2024; 18:31. [PMID: 38350946 PMCID: PMC10865692 DOI: 10.1186/s13065-024-01132-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
Zika virus is an infectious virus, that belongs to Flaviviridae family, which is transferred to humans through mosquito vectors and severely threatens human health; but, apart from available resources, no effective and secure vaccine is present against Zika virus, to prevent such infections. In current study, we employed structural vaccinology approach to design an epitope-based vaccine against Zika virus, which is biocompatible, and secure and might trigger an adaptive and innate immune response by using computational approaches. We first retrieved the protein sequence from National Center for Biotechnology Information (NCBI) database and carried out for BLAST P. After BLAST P, predicted protein sequences were shortlisted and checked for allergic features and antigenic properties. Final sequence of Zika virus, with accession number (APO40588.1) was selected based on high antigenic score and non-allergenicity. Final protein sequence used various computational approaches including antigenicity testing, toxicity evaluation, allergenicity, and conservancy assessment to identify superior B-cell and T-cell epitopes. Two B-cell epitopes, five MHC-six MHC-II epitopes and I were used to construct an immunogenic multi-epitope-based vaccine by using suitable linkers. A 50S ribosomal protein was added at N terminal to improve the immunogenicity of vaccine. In molecular docking, strong interactions were presented between constructed vaccine and Toll-like receptor 9 (- 1100.6 kcal/mol), suggesting their possible relevance in the immunological response to vaccine. The molecular dynamics simulations ensure the dynamic and structural stability of constructed vaccine. The results of C-immune simulation revealed that constructed vaccine activate B and T lymphocytes which induce high level of antibodies and cytokines to combat Zika infection. The constructed vaccine is an effective biomarker with non-sensitization, nontoxicity; nonallergic, good immunogenicity, and antigenicity, however, experimental assays are required to verify the results of present study.
Collapse
Affiliation(s)
- Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Riyadh, Saudi Arabia.
| |
Collapse
|
11
|
Kumari S, Kessel A, Singhal D, Kaur G, Bern D, Lemay-St-Denis C, Singh J, Jain S. Computational identification of a multi-peptide vaccine candidate in E2 glycoprotein against diverse Hepatitis C virus genotypes. J Biomol Struct Dyn 2023; 41:11044-11061. [PMID: 37194293 DOI: 10.1080/07391102.2023.2212777] [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: 06/15/2022] [Accepted: 12/11/2022] [Indexed: 05/18/2023]
Abstract
Hepatitis C Virus (HCV) is estimated to affect nearly 180 million people worldwide, culminating in ∼0.7 million yearly casualties. However, a safe vaccine against HCV is not yet available. This study endeavored to identify a multi-genotypic, multi-epitopic, safe, and globally competent HCV vaccine candidate. We employed a consensus epitope prediction strategy to identify multi-epitopic peptides in all known envelope glycoprotein (E2) sequences, belonging to diverse HCV genotypes. The obtained peptides were screened for toxicity, allergenicity, autoimmunity and antigenicity, resulting in two favorable peptides viz., P2 (VYCFTPSPVVVG) and P3 (YRLWHYPCTV). Evolutionary conservation analysis indicated that P2 and P3 are highly conserved, supporting their use as part of a designed multi-genotypic vaccine. Population coverage analysis revealed that P2 and P3 are likely to be presented by >89% Human Leukocyte Antigen (HLA) molecules from six geographical regions. Indeed, molecular docking predicted the physical binding of P2 and P3 to various representative HLAs. We designed a vaccine construct using these peptides and assessed its binding to toll-like receptor 4 (TLR-4) by molecular docking and simulation. Subsequent analysis by energy-based and machine learning tools predicted high binding affinity and pinpointed the key binding residues (i.e. hotspots) in P2 and P3. Also, a favorable immunogenic profile of the construct was predicted by immune simulations. We encourage the scientific community to validate our vaccine construct in vitro and in vivo.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Shweta Kumari
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Amit Kessel
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Divya Singhal
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Gurpreet Kaur
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, Punjab, India
| | - David Bern
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Claudèle Lemay-St-Denis
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein, Function, Engineering and Applications, Québec, QC, Canada
- CGCC, Center in Green Chemistry and Catalysis, Montréal, QC, Canada
| | - Jasdeep Singh
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
| | - Sahil Jain
- University Institute of Biotechnology, Chandigarh University, Mohali, Punjab, India
- Department of Biochemistry and Molecular Biology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
12
|
Gupta Y, Baranwal M, Chudasama B. Immunoinformatics-Based Identification of the Conserved Immunogenic Peptides Targeting of Zika Virus Precursor Membrane Protein. Viral Immunol 2023; 36:503-519. [PMID: 37486711 DOI: 10.1089/vim.2023.0015] [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] [Indexed: 07/25/2023] Open
Abstract
Zika virus infections lead to neurological complications such as congenital Zika syndrome and Guillain-Barré syndrome. Rising Zika infections in newborns and adults have triggered the need for vaccine development. In the current study, the precursor membrane (prM) protein of the Zika virus is explored for its functional importance and design of epitopes enriched conserved peptides with the usage of different immunoinformatics approach. Phylogenetic and mutational analyses inferred that the prM protein is highly conserved. Three conserved peptides containing multiple T and B cell epitopes were designed by employing different epitope prediction algorithms. IEDB population coverage analysis of selected peptides in six different continents has shown the population coverage of 60-99.8% (class I HLA) and 80-100% (class II HLA). Molecular docking of selected peptides/epitopes was carried out with each of class I and II HLA alleles using HADDOCK. A majority of peptide-HLA complex (pHLA) have HADDOCK scores found to be comparable and more than native-HLA complex representing the good binding interaction of peptides to HLA. Molecular dynamics simulation with best docked pHLA complexes revealed that pHLA complexes are stable with RMSD <5.5Å. Current work highlights the importance of prM as a strong antigenic protein and selected peptides have the potential to elicit humoral and cell-mediated immune responses.
Collapse
Affiliation(s)
- Yogita Gupta
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Bhupendra Chudasama
- School of Physics & Materials Science, Thapar Institute of Engineering and Technology, Patiala, India
| |
Collapse
|
13
|
Yousaf H, Naz A, Zaman N, Hassan M, Obaid A, Awan FM, Azam SS. Immunoinformatic and reverse vaccinology-based designing of potent multi-epitope vaccine against Marburgvirus targeting the glycoprotein. Heliyon 2023; 9:e18059. [PMID: 37534001 PMCID: PMC10391973 DOI: 10.1016/j.heliyon.2023.e18059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 06/30/2023] [Accepted: 07/05/2023] [Indexed: 08/04/2023] Open
Abstract
Marburg virus (MARV) has been a major concern since its first outbreak in 1967. Although the deadly BSL-4 pathogen has been reported in few individuals with sporadic outbreaks following 1967, its rarity commensurate the degree of disease severity. The virus has been known to cause extreme hemorrhagic fever presenting flu-like symptoms (as implicated in COVID-19) with a 90% case fatality rate (CFR). After a number of plausible evidences, it has been observed that the virus usually originates from African fruit bat, Rousettus aegyptiacus, who themselves do not indicate any signs of illness. Thus, efforts have been made in the recent years for a universal treatment of the infection, but till date, no such vaccine or therapeutics could circumvent the viral pathogenicity. In an attempt to formulate a vaccine design computationally, we have explored the entire proteome of the virus and found a strong correlation of its glycoprotein (GP) in receptor binding and subsequent role in infection progression. The present study, explores the MARV glycoprotein GP1 and GP2 domains for quality epitopes to elicit an extended immune response design potential vaccine construct using appropriate linkers and adjuvants. Finally, the chimeric vaccine wass evaluated for its binding affinity towards the receptors via molecular docking and molecular dynamics simulation studies. The rare, yet deadly zoonotic infection with mild outbreaks in recent years has flustered an alarming future with various challenges in terms of viral diseases. Thus, our study has aimed to provide novel insights to design potential vaccines by using the predictive framework.
Collapse
Affiliation(s)
- Hassan Yousaf
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Anam Naz
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
| | - Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Mubashir Hassan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore (UOL), Lahore, Pakistan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Ayesha Obaid
- Department of Medical Lab Technology, The University of Haripur, Haripur, Pakistan
| | - Faryal Mehwish Awan
- Department of Medical Lab Technology, The University of Haripur, Haripur, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| |
Collapse
|
14
|
Silva AJD, de Jesus ALS, Leal LRS, de Macêdo LS, da Silva Barros BR, de Sousa GF, da Paz Leôncio Alves S, Pena LJ, de Melo CML, de Freitas AC. Whole Yeast Vaccine Displaying ZIKV B and T Cell Epitopes Induces Cellular Immune Responses in the Murine Model. Pharmaceutics 2023; 15:1898. [PMID: 37514084 PMCID: PMC10385271 DOI: 10.3390/pharmaceutics15071898] [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: 05/15/2023] [Revised: 06/30/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Improving antigen presentation is crucial for the success of immunization strategies. Yeasts are classically used as biofactories to produce recombinant proteins and are efficient vehicles for antigen delivery, in addition to their adjuvant properties. Despite the absence of epidemic outbreaks, several vaccine approaches continue to be developed for Zika virus infection. The development of these prophylactic strategies is fundamental given the severity of clinical manifestations, mainly due to viral neurotropism. The present study aimed to evaluate in vivo the immune response induced by P. pastoris recombinant strains displaying epitopes of the envelope (ENV) and NS1 ZIKV proteins. Intramuscular immunization with heat-attenuated yeast enhanced the secretion of IL-6, TNF-α, and IFN-γ, in addition to the activation of CD4+ and CD8+ T cells, in BALB/c mice. P. pastoris displaying ENV epitopes induced a more robust immune response, increasing immunoglobulin production, especially IgG isotypes. Both proposed vaccines showed the potential to induce immune responses without adverse effects, confirming the safety of administering P. pastoris as a vaccine vehicle. Here, we demonstrated, for the first time, the evaluation of a vaccine against ZIKV based on a multiepitope construct using yeast as a delivery system and reinforcing the applicability of P. pastoris as a whole-cell vaccine.
Collapse
Affiliation(s)
- Anna Jéssica Duarte Silva
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | | | - Lígia Rosa Sales Leal
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Larissa Silva de Macêdo
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| | | | | | | | - Lindomar José Pena
- Department of Virology and Experimental Therapy, Instituto Aggeu Magalhães, Oswaldo Cruz Foundation, Recife 50670-901, Brazil
| | | | - Antonio Carlos de Freitas
- Laboratory of Molecular Studies and Experimental Therapy-LEMTE, Department of Genetics, Federal University of Pernambuco, Recife 50670-901, Brazil
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Antonelli AC, Almeida VP, da Fonseca SG. Immunoinformatics Vaccine Design for Zika Virus. Methods Mol Biol 2023; 2673:411-429. [PMID: 37258930 DOI: 10.1007/978-1-0716-3239-0_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Zika virus (ZIKV) is an emerging virus from the Flaviviridae family and Flavivirus genus that has caused important outbreaks around the world. ZIKV infection is associated with severe neuropathology in newborns and adults. Until now, there is no licensed vaccine available for ZIKV infection. Therefore, the development of a safe and effective vaccine against ZIKV is an urgent need. Recently, we designed an in silico multi-epitope vaccine for ZIKV based on immunoinformatics tools. To construct this in silico ZIKV vaccine, we used a consensus sequence generated from ZIKV sequences available in databank. Then, we selected CD4+ and CD8+ T cell epitopes from all ZIKV proteins based on the binding prediction to class II and class I human leukocyte antigen (HLA) molecules, promiscuity, and immunogenicity. ZIKV Envelope protein domain III (EDIII) was added to the construct and B cell epitopes were identified. Adjuvants were associated to increase immunogenicity. Distinct linkers were used for connecting the CD4+ and CD8+ T cell epitopes, EDIII, and adjuvants. Several analyses, such as antigenicity, population coverage, allergenicity, autoimmunity, and secondary and tertiary structures of the vaccine, were evaluated using various immunoinformatics tools and online web servers. In this chapter, we present the protocols with the rationale and detailed steps needed for this in silico multi-epitope ZIKV vaccine design.
Collapse
Affiliation(s)
- Ana Clara Antonelli
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Vinnycius Pereira Almeida
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil
| | - Simone Gonçalves da Fonseca
- Department of Bioscience and Technology, Institute of Tropical Pathology and Public Health, Federal University of Goiás, Goiânia, Goiás, Brazil.
| |
Collapse
|
17
|
Multi-Epitope Vaccine for Monkeypox Using Pan-Genome and Reverse Vaccinology Approaches. Viruses 2022; 14:v14112504. [PMID: 36423113 PMCID: PMC9695528 DOI: 10.3390/v14112504] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Outbreaks of monkeypox virus infections have imposed major health concerns worldwide, with high morbidity threats to children and immunocompromised adults. Although repurposed drugs and vaccines are being used to curb the disease, the evolving traits of the virus, exhibiting considerable genetic dynamicity, challenge the limits of a targeted treatment. A pan-genome-based reverse vaccinology approach can provide fast and efficient solutions to resolve persistent inconveniences in experimental vaccine design during an outbreak-exigency. The approach encompassed screening of available monkeypox whole genomes (n = 910) to identify viral targets. From 102 screened viral targets, viral proteins L5L, A28, and L5 were finalized based on their location, solubility, and antigenicity. The potential T-cell and B-cell epitopes were extracted from the proteins using immunoinformatics tools and algorithms. Multiple vaccine constructs were designed by combining the epitopes. Based on immunological properties, chemical stability, and structural quality, a novel multi-epitopic vaccine construct, V4, was finalized. Flexible-docking and coarse-dynamics simulation portrayed that the V4 had high binding affinity towards human HLA-proteins (binding energy < -15.0 kcal/mol) with low conformational fluctuations (<1 Å). Thus, the vaccine construct (V4) may act as an efficient vaccine to induce immunity against monkeypox, which encourages experimental validation and similar approaches against emerging viral infections.
Collapse
|
18
|
Vaccines against Emerging and Neglected Infectious Diseases: An Overview. Vaccines (Basel) 2022; 10:vaccines10091385. [PMID: 36146463 PMCID: PMC9503027 DOI: 10.3390/vaccines10091385] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 12/25/2022] Open
Abstract
Neglected Tropical Diseases (NTDs) are a group of diseases that are highly prevalent in tropical and subtropical regions, and closely associated with poverty and marginalized populations. Infectious diseases affect over 1.6 billion people annually, and vaccines are the best prophylactic tool against them. Along with NTDs, emerging and reemerging infectious diseases also threaten global public health, as they can unpredictably result in pandemics. The recent advances in vaccinology allowed the development and licensing of new vaccine platforms that can target and prevent these diseases. In this work, we discuss the advances in vaccinology and some of the difficulties found in the vaccine development pipeline for selected NTDs and emerging and reemerging infectious diseases, including HIV, Dengue, Ebola, Chagas disease, malaria, leishmaniasis, zika, and chikungunya.
Collapse
|
19
|
Apostolopoulos V, Bojarska J, Feehan J, Matsoukas J, Wolf W. Smart therapies against global pandemics: A potential of short peptides. Front Pharmacol 2022; 13:914467. [PMID: 36046832 PMCID: PMC9420997 DOI: 10.3389/fphar.2022.914467] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/01/2022] [Indexed: 12/20/2022] Open
Affiliation(s)
- Vasso Apostolopoulos
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Immunology Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, VIC, Australia
| | - Joanna Bojarska
- Technical University of Lodz, Department of Chemistry, Institute of General and Ecological Chemistry, Lodz, Poland
- *Correspondence: Joanna Bojarska,
| | - Jack Feehan
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
| | - John Matsoukas
- Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- NewDrug, Patras Science Park, Patras, Greece
| | - Wojciech Wolf
- Technical University of Lodz, Department of Chemistry, Institute of General and Ecological Chemistry, Lodz, Poland
| |
Collapse
|
20
|
In Silico Comparative Analysis of Predicted B Cell Epitopes against Dengue Virus (Serotypes 1–4) Isolated from the Philippines. Vaccines (Basel) 2022; 10:vaccines10081259. [PMID: 36016147 PMCID: PMC9415047 DOI: 10.3390/vaccines10081259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 11/19/2022] Open
Abstract
Dengue is a viral mosquito-borne disease that rapidly spreads in tropical and subtropical countries, including the Philippines. One of its most distinguishing characteristics is the ability of the Dengue Virus (DENV) to easily surpass the innate responses of the body, thus activating B cells of the adaptive immunity to produce virus-specific antibodies. Moreover, Dengvaxia® is the only licensed vaccine for DENV, but recent studies showed that seronegative individuals become prone to increased disease severity and hospitalization. Owing to this limitation of the dengue vaccine, this study determined and compared consensus and unique B cell epitopes among each DENV (1–4) Philippine isolate to identify potential areas of interest for future vaccine studies and therapeutic developments. An in silico-based epitope prediction of forty (40) DENV 1–4 strains, each serotype represented by ten (10) sequences from The National Center for Biotechnology Information (NCBI), was conducted using Kolaskar and Tongaonkar antigenicity, Emini surface accessibility, and Parker hydrophilicity prediction in Immune Epitope Database (IEDB). Results showed that five (5) epitopes were consensus for DENV-1 with no detected unique epitope, one (1) consensus epitope for DENV-2 with two (2) unique epitopes, one (1) consensus epitope for DENV-3 plus two (2) unique epitopes, and two (2) consensus epitopes and one (1) unique epitope for DENV-4. The findings of this study would contribute to determining potential vaccine and diagnostic marker candidates for further research studies and immunological applications against DENV (1–4) Philippine isolates.
Collapse
|