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Shang K, Zhu Y, Tian T, Shi H, Yin Z, He Y, Shi J, Ding J, Zhang F. Development of a novel multi-epitope vaccine for brucellosis prevention. Heliyon 2024; 10:e34721. [PMID: 39148966 PMCID: PMC11325379 DOI: 10.1016/j.heliyon.2024.e34721] [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: 03/13/2024] [Revised: 07/14/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
Brucellosis, a zoonotic disease caused by Brucella, presents a significant threat to both animal and human health. In animals, the disease can lead to infertility, miscarriage, and high fever, while in humans, symptoms may include recurrent fever, fatigue, sweating, hepatosplenomegaly, and joint and muscle pain following infection. Treatment often involves long-term antibiotic therapy, placing a substantial psychological and financial burden on patients. While vaccination is crucial for prevention, current animal vaccines have drawbacks such as residual virulence, and a safe and effective human vaccine is lacking. Hence, the development of a vaccine for brucellosis is imperative. In this study, we utilized bioinformatics methods to design a multi-epitope vaccine targeting Brucella. Targeting Heme transporter BhuA and polysaccharide export protein, we identified antigenic epitopes, including six cytotoxic T lymphocyte (CTL) dominant epitopes, six helper T lymphocyte (HTL) dominant epitopes, one conformation B cell dominant epitope, and three linear B cell dominant epitopes. By linking these epitopes with appropriate linkers and incorporating a Toll-like receptor (TLR) agonist (human beta-defensin-2) and an auxiliary peptide (Pan HLA-DR epitopes), we constructed the multi-epitope vaccine (MEV). The MEV demonstrated high antigenicity, non-toxicity, non-allergenicity, non-human homology, stability, and solubility. Molecular docking analysis and molecular dynamics simulations confirmed the interaction and stability of the MEV with receptors (MHCI, MHCII, TLR4). Codon optimization and in silico cloning validated the translation efficiency and successful expression of MEV in Escherichia coli. Immunological simulations further demonstrated the efficacy of MEV in inducing robust immune responses. In conclusion, our findings suggest that the engineered MEVs have the potential to stimulate both humoral and cellular immune responses, offering valuable insights for the future development of safe and efficient Brucella vaccines.
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Affiliation(s)
- Kaiyu Shang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Yuejie Zhu
- Reproductive Medicine Center, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Tingting Tian
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Huidong Shi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Zhengwei Yin
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Yueyue He
- Department of Immunology, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Juan Shi
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Jianbing Ding
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Fengbo Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
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Zhu X, Wang X, Liu T, Zhang D, Jin T. Design of multi-epitope vaccine against porcine rotavirus using computational biology and molecular dynamics simulation approaches. Virol J 2024; 21:160. [PMID: 39039549 PMCID: PMC11264426 DOI: 10.1186/s12985-024-02440-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
Porcine Rotavirus (PoRV) is a significant pathogen affecting swine-rearing regions globally, presenting a substantial threat to the economic development of the livestock sector. At present, no specific pharmaceuticals are available for this disease, and treatment options remain exceedingly limited. This study seeks to design a multi-epitope peptide vaccine for PoRV employing bioinformatics approaches to robustly activate T-cell and B-cell immune responses. Two antigenic proteins, VP7 and VP8*, were selected from PoRV, and potential immunogenic T-cell and B-cell epitopes were predicted using immunoinformatic tools. These epitopes were further screened according to non-toxicity, antigenicity, non-allergenicity, and immunogenicity criteria. The selected epitopes were linked with linkers to form a novel multi-epitope vaccine construct, with the PADRE sequence (AKFVAAWTLKAAA) and RS09 peptide attached at the N-terminus of the designed peptide chain to enhance the vaccine's antigenicity. Protein-protein docking of the vaccine constructs with toll-like receptors (TLR3 and TLR4) was conducted using computational methods, with the lowest energy docking results selected as the optimal predictive model. Subsequently, molecular dynamics (MD) simulation methods were employed to assess the stability of the protein vaccine constructs and TLR3 and TLR4 receptors. The results indicated that the vaccine-TLR3 and vaccine-TLR4 docking models remained stable throughout the simulation period. Additionally, the C-IMMSIM tool was utilized to determine the immunogenic triggering capability of the vaccine protein, demonstrating that the constructed vaccine protein could induce both cell-mediated and humoral immune responses, thereby playing a role in eliciting host immune responses. In conclusion, this study successfully constructed a multi-epitope vaccine against PoRV and validated the stability and efficacy of the vaccine through computational analysis. However, as the study is purely computational, experimental evaluation is required to validate the safety and immunogenicity of the newly constructed vaccine protein.
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MESH Headings
- Animals
- Swine
- Molecular Dynamics Simulation
- Rotavirus/immunology
- Rotavirus/genetics
- Epitopes, T-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/chemistry
- Computational Biology
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/genetics
- Rotavirus Vaccines/immunology
- Rotavirus Vaccines/chemistry
- Rotavirus Vaccines/genetics
- Rotavirus Infections/prevention & control
- Rotavirus Infections/immunology
- Rotavirus Infections/virology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/genetics
- Vaccines, Subunit/chemistry
- Antigens, Viral/immunology
- Antigens, Viral/genetics
- Antigens, Viral/chemistry
- Molecular Docking Simulation
- Swine Diseases/prevention & control
- Swine Diseases/immunology
- Swine Diseases/virology
- Capsid Proteins/immunology
- Capsid Proteins/genetics
- Capsid Proteins/chemistry
- Vaccine Development
- Immunogenicity, Vaccine
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Affiliation(s)
- Xiaochen Zhu
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China
| | - Xinyuan Wang
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China
| | - Tingting Liu
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China
| | - Dongchao Zhang
- Tianjin Key Laboratory of Agricultural Animal Breeding and Healthy Husbandry, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China.
- Tianjin Engineering Technology Center of Livestock Pathogen Detection and Genetic Engineering Vaccine, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China.
| | - Tianming Jin
- Tianjin Key Laboratory of Animal Molecular Breeding and Biotechnology, Institute of Animal Science and Veterinary, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.
- Tianjin Engineering Technology Center of Livestock Pathogen Detection and Genetic Engineering Vaccine, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin, 300392, China.
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3
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Biswas R, Swetha RG, Basu S, Roy A, Ramaiah S, Anbarasu A. Designing multi-epitope vaccine against human cytomegalovirus integrating pan-genome and reverse vaccinology pipelines. Biologicals 2024; 87:101782. [PMID: 39003966 DOI: 10.1016/j.biologicals.2024.101782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/13/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024] Open
Abstract
Human cytomegalovirus (HCMV) is accountable for high morbidity in neonates and immunosuppressed individuals. Due to the high genetic variability of HCMV, current prophylactic measures are insufficient. In this study, we employed a pan-genome and reverse vaccinology approach to screen the target for efficient vaccine candidates. Four proteins, envelope glycoprotein M, UL41A, US23, and US28, were shortlisted based on cellular localization, high solubility, antigenicity, and immunogenicity. A total of 29 B-cell and 44 T-cell highly immunogenic and antigenic epitopes with high global population coverage were finalized using immunoinformatics tools and algorithms. Further, the epitopes that were overlapping among the finalized B-cell and T-cell epitopes were linked with suitable linkers to form various combinations of multi-epitopic vaccine constructs. Among 16 vaccine constructs, Vc12 was selected based on physicochemical and structural properties. The docking and molecular simulations of VC12 were performed, which showed its high binding affinity (-23.35 kcal/mol) towards TLR4 due to intermolecular hydrogen bonds, salt bridges, and hydrophobic interactions, and there were only minimal fluctuations. Furthermore, Vc12 eliciting a good response was checked for its expression in Escherichia coli through in silico cloning and codon optimization, suggesting it to be a potent vaccine candidate.
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Affiliation(s)
- Rhitam Biswas
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Rayapadi G Swetha
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biosciences, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Soumya Basu
- Department of Biotechnology, NIST University, Berhampur, 761008, Odisha, India
| | - Aditi Roy
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biosciences, SBST, VIT, Vellore, 632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology (SBST), Vellore Institute of Technology (VIT), Vellore, 632014, Tamil Nadu, India; Department of Biotechnology, SBST, VIT, Vellore, 632014, Tamil Nadu, India.
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4
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Al-Zayadi FQJ, Shakir AS, Kareem AS, Ghasemian A, Behmard E. Design of a novel multi-epitope vaccine against Marburg virus using immunoinformatics studies. BMC Biotechnol 2024; 24:45. [PMID: 38970027 PMCID: PMC11227231 DOI: 10.1186/s12896-024-00873-2] [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: 03/13/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024] Open
Abstract
Marburg virus (MARV) is a highly contagious and virulent agent belonging to Filoviridae family. MARV causes severe hemorrhagic fever in humans and non-human primates. Owing to its highly virulent nature, preventive approaches are promising for its control. There is currently no approved drug or vaccine against MARV, and management mainly involves supportive care to treat symptoms and prevent complications. Our aim was to design a novel multi-epitope vaccine (MEV) against MARV using immunoinformatics studies. In this study, various proteins (VP35, VP40 and glycoprotein precursor) were used and potential epitopes were selected. CTL and HTL epitopes covered 79.44% and 70.55% of the global population, respectively. The designed MEV construct was stable and expressed in Escherichia coli (E. coli) host. The physicochemical properties were also acceptable. MARV MEV candidate could predict comprehensive immune responses such as those of humoral and cellular in silico. Additionally, efficient interaction to toll-like receptor 3 (TLR3) and its agonist (β-defensin) was predicted. There is a need for validation of these results using further in vitro and in vivo studies.
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Affiliation(s)
| | - Ali S Shakir
- College of Dentistry, University of Al-Qadisiyah, Diwaniyah, Iraq
| | - Ahmed Shayaa Kareem
- Department of Medical Laboratories Techniques, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Babylon, 66002, Iraq
| | - Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran.
| | - Esmaeil Behmard
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran.
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Alharbi M, Alshammari A, Alsabhan JF, Alzarea SI, Alshammari T, Alasmari F, Alasmari AF. A novel vaccine construct against Zika virus fever: insights from epitope-based vaccine discovery through molecular modeling and immunoinformatics approaches. Front Immunol 2024; 15:1426496. [PMID: 39050858 PMCID: PMC11267680 DOI: 10.3389/fimmu.2024.1426496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/05/2024] [Indexed: 07/27/2024] Open
Abstract
The Zika virus (ZIKV) is an emerging virus associated with the Flaviviridae family that mainly causes infection in pregnant women and leads to several abnormalities during pregnancy. This virus has unique properties that may lead to pathological diseases. As the virus has the ability to evade immune response, a crucial effort is required to deal with ZIKV. Vaccines are a safe means to control different pathogenic infectious diseases. In the current research, a multi-epitope-based vaccination against ZIKV is being designed using in silico methods. For the epitope prediction and prioritization phase, ZIKV polyprotein (YP_002790881.1) and flavivirus polyprotein (>YP_009428568.1) were targeted. The predicted B-cell epitopes were used for MHC-I and MHC-II epitope prediction. Afterward, several immunoinformatics filters were applied and nine (REDLWCGSL, MQDLWLLRR, YKKSGITEV, TYTDRRWCF, RDAFPDSNS, KPSLGLINR, ELIGRARVS, AITQGKREE, and EARRSRRAV) epitopes were found to be probably antigenic in nature, non-allergenic, non-toxic, and water soluble without any toxins. Selected epitopes were joined using a particular GPGPG linker to create the base vaccination for epitopes, and an extra EAAAK linker was used to link the adjuvant. A total of 312 amino acids with a molecular weight (MW) of 31.62762 and an instability value of 34.06 were computed in the physicochemical characteristic analysis, indicating that the vaccine design is stable. The molecular docking analysis predicted a binding energy of -329.46 (kcal/mol) for TLR-3 and -358.54 (kcal/mol) for TLR-2. Moreover, the molecular dynamics simulation analysis predicted that the vaccine and receptor molecules have stable binding interactions in a dynamic environment. The C-immune simulation analysis predicted that the vaccine has the ability to generate both humoral and cellular immune responses. Based on the design, the vaccine construct has the best efficacy to evoke immune response in theory, but experimental analysis is required to validate the in silico base approach and ensure its safety.
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Affiliation(s)
- 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
| | - Jawza F. Alsabhan
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sami I. Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Aljouf, Saudi Arabia
| | - Talal Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fawaz Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F. Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Samman N, Mohabatkar H, Behbahani M, Ganjlikhani Hakemi M. Bioinformatics design of a peptide vaccine containing sarcoma antigen NY-SAR-35 epitopes against breast cancer and evaluation of its immunological function in BALB/c mouse model. PLoS One 2024; 19:e0306117. [PMID: 38923980 PMCID: PMC11207152 DOI: 10.1371/journal.pone.0306117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
The development of a cancer vaccine has become an essential focus in the field of medical biotechnology and immunology. In our study, the NY-SAR-35 cancer/testis antigen was targeted to design a novel peptide vaccine using bioinformatics tools, and BALB/c mice were used to evaluate the vaccine's immunological function. This evaluation involved assessing peptide-specific IgG levels in the serum via ELISA and measuring the levels of IFN-γ, IL-4, and granzyme B in the supernatant of cultured splenocytes. The final vaccine construct consisted of two T lymphocyte epitopes linked by the AAY linker. This construct displayed high antigenicity, non-allergenicity, non-toxicity, stability, and ability to induce IFN-γ and IL-4. It showed stable dynamics with both human MHC-I and II molecules, as well as mouse MHC-II molecules, and revealed strong Van der Waals and electrostatic energies. Emulsifying our peptide vaccine in incomplete Freund's adjuvant resulted in a remarkable increase in the levels of IgG. The splenocytes of mice that received the combination of peptide and adjuvant displayed a noteworthy increase in IFN-γ, IL-4, and granzyme B secretion. Additionally, their lymphocytes exhibited higher proliferation rates compared to the control group. Our data demonstrated that our vaccine could stimulate a robust immune response, making it a promising candidate for cancer prevention. However, clinical trials are necessary to assess its efficacy in humans.
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Affiliation(s)
- Nour Samman
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hassan Mohabatkar
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mandana Behbahani
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Mazdak Ganjlikhani Hakemi
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
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Moin AT, Rani NA, Patil RB, Robin TB, Ullah MA, Rahim Z, Rahman MF, Zubair T, Hossain M, Mollah AKMM, Absar N, Hossain M, Manchur MA, Islam NN. In-silico formulation of a next-generation polyvalent vaccine against multiple strains of monkeypox virus and other related poxviruses. PLoS One 2024; 19:e0300778. [PMID: 38758816 PMCID: PMC11101047 DOI: 10.1371/journal.pone.0300778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/05/2024] [Indexed: 05/19/2024] Open
Abstract
Mpox (formerly known as monkeypox) virus and some related poxviruses including smallpox virus pose a significant threat to public health, and effective prevention and treatment strategies are needed. This study utilized a reverse vaccinology approach to retrieve conserved epitopes for monkeypox virus and construct a vaccine that could provide cross-protection against related viruses with similar antigenic properties. The selected virulent proteins of monkeypox virus, MPXVgp165, and Virion core protein P4a, were subjected to epitope mapping for vaccine construction. Two vaccines were constructed using selected T cell epitopes and B cell epitopes with PADRE and human beta-defensins adjuvants conjugated in the vaccine sequence. Both constructs were found to be highly antigenic, non-allergenic, nontoxic, and soluble, suggesting their potential to generate an adequate immune response and be safe for humans. Vaccine construct 1 was selected for molecular dynamic simulation studies. The simulation studies revealed that the TLR8-vaccine complex was more stable than the TLR3-vaccine complex. The lower RMSD and RMSF values of the TLR8 bound vaccine compared to the TLR3 bound vaccine suggested better stability and consistency of hydrogen bonds. The Rg values of the vaccine chain bound to TLR8 indicated overall stability, whereas the vaccine chain bound to TLR3 showed deviations throughout the simulation. These results suggest that the constructed vaccine could be a potential preventive measure against monkeypox and related viruses however, further experimental validation is required to confirm these findings.
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Affiliation(s)
- Abu Tayab Moin
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | - Nurul Amin Rani
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Rajesh B. Patil
- Department of Pharmaceutical Chemistry, Sinhgad Technical Education Society’s, Sinhgad College of Pharmacy, Maharashtra, India
| | - Tanjin Barketullah Robin
- Faculty of Biotechnology and Genetic Engineering, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Md. Asad Ullah
- Faculty of Biological Sciences, Department of Biotechnology and Genetic Engineering, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Zahidur Rahim
- Department of Zoology, Jahangirnagar University, Dhaka, Bangladesh
| | - Md. Foyzur Rahman
- Department of Pharmacy, Dhaka International University, Dhaka, Bangladesh
| | | | - Mohabbat Hossain
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
| | | | - Nurul Absar
- Faculty of Basic Medical and Pharmaceutical Sciences, Department of Biochemistry and Biotechnology, University of Science & Technology Chittagong, Khulshi, Chittagong, Bangladesh
| | - Mahboob Hossain
- Department of Mathematics and Natural Sciences, Microbiology Program, School of Data and Sciences, BRAC University, Dhaka, Bangladesh
| | - Mohammed Abul Manchur
- Faculty of Biological Sciences, Department of Microbiology, University of Chittagong, Chattogram, Bangladesh
| | - Nazneen Naher Islam
- Faculty of Biological Sciences, Department of Genetic Engineering and Biotechnology, Laboratory of Clinical Genetics, Genomics and Enzyme Research (LCGGER), University of Chittagong, Chattogram, Bangladesh
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Karkashan A. Immunoinformatics assisted profiling of West Nile virus proteome to determine immunodominant epitopes for the development of next-generation multi-peptide vaccine. Front Immunol 2024; 15:1395870. [PMID: 38799422 PMCID: PMC11116617 DOI: 10.3389/fimmu.2024.1395870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Emerging infectious diseases represent a significant threat to global health, with West Nile virus (WNV) being a prominent example due to its potential to cause severe neurological disorders alongside mild feverish conditions. Particularly prevalent in the continental United States, WNV has emerged as a global concern, with outbreaks indicating the urgent need for effective prophylactic measures. The current problem is that the absence of a commercial vaccine against WNV highlights a critical gap in preventive strategies against WNV. This study aims to address this gap by proposing a novel, multivalent vaccine designed using immunoinformatics approaches to elicit comprehensive humoral and cellular immune responses against WNV. The objective of the study is to provide a theoretical framework for experimental scientists to formulate of vaccine against WNV and tackle the current problem by generating an immune response inside the host. The research employs reverse vaccinology and subtractive proteomics methodologies to identify NP_041724.2 polyprotein and YP_009164950.1 truncated flavivirus polyprotein NS1 as the prime antigens. The selection process for epitopes focused on B and T-cell reactivity, antigenicity, water solubility, and non-allergenic properties, prioritizing candidates with the potential for broad immunogenicity and safety. The designed vaccine construct integrates these epitopes, connected via GPGPG linkers, and supplemented with an adjuvant with the help of another linker EAAAK, to enhance immunogenicity. Preliminary computational analyses suggest that the proposed vaccine could achieve near-universal coverage, effectively targeting approximately 99.74% of the global population, with perfect coverage in specific regions such as Sweden and Finland. Molecular docking and immune simulation studies further validate the potential efficacy of the vaccine, indicating strong binding affinity with toll-like receptor 3 (TLR-3) and promising immune response profiles, including significant antibody-mediated and cellular responses. These findings present the vaccine construct as a viable candidate for further development and testing. While the theoretical and computational results are promising, advancing from in-silico predictions to a tangible vaccine requires comprehensive laboratory validation. This next step is essential to confirm the vaccine's efficacy and safety in eliciting an immune response against WNV. Through this study, we propose a novel approach to vaccine development against WNV and contribute to the broader field of immunoinformatics, showcasing the potential to accelerate the design of effective vaccines against emerging viral threats. The journey from hypothesis to practical solution embodies the interdisciplinary collaboration essential for modern infectious disease management and prevention strategies.
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Affiliation(s)
- Alaa Karkashan
- Department of Biological Sciences, College of Sciences, University of Jeddah, Jeddah, Saudi Arabia
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Ullah A, Ul Haq M, Iqbal M, Irfan M, Khan S, Muhammad R, Ullah A, Khurram M, Alharbi M, Alasmari AF, Ahmad S. A computational quest for identifying potential vaccine candidates against Moraxella lacunata: a multi-pronged approach. J Biomol Struct Dyn 2024; 42:2976-2989. [PMID: 37177816 DOI: 10.1080/07391102.2023.2212793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
Moraxella lacunata is an emerging gram-negative bacterium that is responsible for multiple nosocomial infections. The bacterium is evolving resistance to several antibiotics, and currently, no effective licensed vaccines are available, which warrants the search for new therapeutics. A multi-epitope-based vaccine has been designed for M. lacunata. The complete proteome of M. lacunata contains 10,110 core proteins. Subcellular localization analysis revealed the presence of five proteins in the extracellular matrix, while 19 proteins were predicted to be located in the outer membrane, and 21 proteins were predicted to be located in the periplasmic region. Only two proteins, the type VI secretion system tube protein (Hcp) and the transporter substrate-binding domain-containing protein, were selected for epitope prediction as they fulfilled all the criteria for being potential vaccine candidates. Shortlisted epitopes from the selected proteins were fused together using "GPGPG" linkers to overcome the limitations of single-epitope vaccines. Next, the cholera toxin-B adjuvant was attached to the peptide epitope using an EAAAK linker. Docking analysis was performed to examine the interaction between the vaccine and immune cell receptors, revealing robust intermolecular interactions and a stable binding conformation. Molecular dynamics simulation findings revealed no drastic changes in the binding conformation of complexes during the simulation period. The net binding free energy of vaccine-receptor complexes was estimated using the molecular mechanics energies combined with the Poisson-Boltzmann and surface area continuum solvation (MM-PBSA) method. The reported values were -586.38 kcal/mol, -283.74 kcal/mol, and -296.88 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. Furthermore, the molecular mechanics energies combined with the generalized Born and surface area continuum solvation (MM-GBSA) analysis predicted binding free energies of -596.69 kcal/mol, -287.39 kcal/mol, and -298.28 kcal/mol for the TLR-4-vaccine complex, MHC-I-vaccine complex, and MHC-II-vaccine complex, respectively. The theoretical vaccine design proposed in the study could potentially serve as a powerful therapeutic against targeted pathogens, subject to validation through experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Mahboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, Pakistan
| | - Madiha Iqbal
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Muhammad Irfan
- College of Dentistry, Department of Oral Biology, University of Florida, Gainesville, FL, USA
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Amin Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | | | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah F Alasmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
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10
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Yu H, Gu X, Wang D, Wang Z. Brucella infection and Toll-like receptors. Front Cell Infect Microbiol 2024; 14:1342684. [PMID: 38533384 PMCID: PMC10963510 DOI: 10.3389/fcimb.2024.1342684] [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: 11/22/2023] [Accepted: 01/17/2024] [Indexed: 03/28/2024] Open
Abstract
Brucella consists of gram-negative bacteria that have the ability to invade and replicate in professional and non-professional phagocytes, and its prolonged persistence in the host leads to brucellosis, a serious zoonosis. Toll-like receptors (TLRs) are the best-known sensors of microorganisms implicated in the regulation of innate and adaptive immunity. In particular, TLRs are transmembrane proteins with a typical structure of an extracellular leucine-rich repeat (LRR) region and an intracellular Toll/interleukin-1 receptor (TIR) domain. In this review, we discuss Brucella infection and the aspects of host immune responses induced by pathogens. Furthermore, we summarize the roles of TLRs in Brucella infection, with substantial emphasis on the molecular insights into its mechanisms of action.
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Affiliation(s)
- Hui Yu
- Inner Mongolia Key Laboratory of Disease-Related Biomarkers, The Second Affiliated Hospital, Baotou Medical College, Baotou, China
- School of Basic Medicine, Baotou Medical College, Baotou, China
| | - Xinyi Gu
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Danfeng Wang
- The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Zhanli Wang
- Inner Mongolia Key Laboratory of Disease-Related Biomarkers, The Second Affiliated Hospital, Baotou Medical College, Baotou, China
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11
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Dhanushkumar T, Selvam PK, M E S, Vasudevan K, C GPD, Zayed H, Kamaraj B. Rational design of a multivalent vaccine targeting arthropod-borne viruses using reverse vaccinology strategies. Int J Biol Macromol 2024; 258:128753. [PMID: 38104690 DOI: 10.1016/j.ijbiomac.2023.128753] [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: 07/29/2023] [Revised: 11/17/2023] [Accepted: 12/09/2023] [Indexed: 12/19/2023]
Abstract
Viruses transmitted by arthropods, such as Dengue, Zika, and Chikungunya, represent substantial worldwide health threats, particularly in countries like India. The lack of approved vaccines and effective antiviral therapies calls for developing innovative strategies to tackle these arboviruses. In this study, we employed immunoinformatics methodologies, incorporating reverse vaccinology, to design a multivalent vaccine targeting the predominant arboviruses. Epitopes of B and T cells were recognized within the non-structural proteins of Dengue, Zika, and Chikungunya viruses. The predicted epitopes were enhanced with adjuvants β-defensin and RS-09 to boost the vaccine's immunogenicity. Sixteen distinct vaccine candidates were constructed, each incorporating epitopes from all three viruses. FUVAC-11 emerged as the most promising vaccine candidate through molecular docking and molecular dynamics simulations, demonstrating favorable binding interactions and stability. Its effectiveness was further evaluated using computational immunological studies confirming strong immune responses. The in silico cloning performed using the pET-28a(+) plasmid facilitates the future experimental implementation of this vaccine candidate, paving the way for potential advancements in combating these significant arboviral threats. However, further in vitro and in vivo studies are warranted to confirm the results obtained in this computational study, which highlights the effectiveness of immunoinformatics and reverse vaccinology in creating vaccines against major Arboviruses, offering a promising model for developing vaccines for other vector-borne diseases and enhancing global health security.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Prasanna Kumar Selvam
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Santhosh M E
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
| | - Hatem Zayed
- Department of Biomedical Sciences College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Balu Kamaraj
- Department of Dental Education, College of Dentistry, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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12
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Alshiekheid MA, Dou AM, Algahtani M, Al-Megrin WAI, Alhawday YA, Alradhi AE, Bukhari K, Alharbi BF, Algefary AN, Alhunayhani BA, Allemailem KS. Bioinformatics and immunoinformatics assisted multiepitope vaccine construct against Burkholderia anthina. Saudi Pharm J 2024; 32:101917. [PMID: 38226347 PMCID: PMC10788630 DOI: 10.1016/j.jsps.2023.101917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/11/2023] [Indexed: 01/17/2024] Open
Abstract
Burkholderia anthina is a pathogenic bacterial species belonging to the Burkholderiaceae family and it is mainly considered the etiological agent of chronic obstructive pulmonary diseases associated with cystic fibrosis, due to being intrinsic antibiotic resistant making it difficult to treat pulmonary infections. Hence increased rate of antibiotic-resistant bacterial species vaccine development is the priority to tackle this problem. In research work, we designed a multi-epitope-based vaccine construct against B. anthina using reverse vaccinology immunoinformatics and biophysical approaches. Based on the subtractive proteomic screening of core proteins we identified 3 probable antigenic proteins and good vaccine targets namely, type VI secretion system tube protein hcp Burkholderia, fimbria/pilus periplasmic chaperone and fimbrial biogenesis outer membrane usher protein. The selected 3 proteins were used for B and B cells B-derived T-cell epitopes prediction. In epitopes prediction, different epitopes were predicted with various lengths and percentile scores and subjected to further immunoinformatics analysis. In immunoinformatics screening a total number of 06, IDDGNANAL, KTVKPDPRY, SEVESGSAP, YGGDLTVEV, SVSHDTNGR, and GSKADGYQR epitopes were considered good vaccine target candidates and shortlisted for vaccine construct designing. The vaccine construct was designed by joining selected epitopes with the help of a GPGPG linker and additionally linked with cholera toxin b subunit adjuvant to increase the efficacy of the vaccine construct the sequence of the said adjuvant were retrieved from protein data bank through its (PDB ID: 5ELD). The designed vaccine construct was evaluated for its physiochemical properties analysis in which we reported that the vaccine construct comprises 216 amino acids with a molecular weight of 22.37499 kilo Dalton, 15.55 instability index (II) is computed, and this classifies that the vaccine construct is properly stable. VaxiJen v2.0 web server predicted that the vaccine construct is probable antigenic in nature with 0.6320 predicted value. Furthermore AllerTOP v. 2.0 tool predicted that the designed vaccine construct is non allergic in nature. Molecular docking analysis was done for analysis of the binding affinity of the vaccine construct with TLR-2 (PDB ID: 6NIG), the docking results predicted 799.2 kcal/mol binding energy score that represents the vaccine construct has a good binding ability with TLR-2. Moreover, molecular dynamic simulation analysis results revealed that the vaccine construct and immune cell receptor has proper binding stability over various environmental condition, i.e. change in pressure range, temperature, and motion. After each analysis, we observed that the vaccine construct is safe stable, and probably antigenic and could generate an immune response against the target pathogen but in the future, experimental analysis is still needed to verify in silico base results.
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Affiliation(s)
- Maha A. Alshiekheid
- Department of Botany & Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ali M. Dou
- Department of Medical Laboratories, Riyadh Security Forces Hospital, Ministry of Interior, Riyadh 11481, Saudi Arabia
| | - Mohammad Algahtani
- Department of Laboratory & Blood Bank, Security Forces Hospital, P.O. Box 14799, Mecca 21955, Saudi Arabia
| | - Wafa Abdullah I. Al-Megrin
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Yaseer Ali Alhawday
- Department of Medical Microbiology, Qassim University Medical City , Qassim University, Buraydah 51452, Saudi Arabia
| | - Arwa Essa Alradhi
- Regional Laboratory and Central Blood Bank, Hafr Al Batin 39513, Saudi Arabia
| | - Khulud Bukhari
- Department of Microbiology and Parasitology, College of Veterinary Medicine, P. O. Box 1757, Hofuf 36388, Al-Ahsa, King Faisal University, Saudi Arabia
| | - Basmah F. Alharbi
- Department of Basic Health Science, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Ahmed N. Algefary
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Basmah Awwadh Alhunayhani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Khaled S. Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
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13
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Ullah A, Rehman B, Khan S, Almanaa TN, Waheed Y, Hassan M, Naz T, Ul Haq M, Muhammad R, Sanami S, Irfan M, Ahmad S. An In Silico Multi-epitopes Vaccine Ensemble and Characterization Against Nosocomial Proteus penneri. Mol Biotechnol 2023:10.1007/s12033-023-00949-y. [PMID: 37934390 DOI: 10.1007/s12033-023-00949-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023]
Abstract
Proteus penneri (P. penneri) is a bacillus-shaped, gram-negative, facultative anaerobe bacterium that is primarily an invasive pathogen and the etiological agent of several hospital-associated infections. P. penneri strains are naturally resistant to macrolides, amoxicillin, oxacillin, penicillin G, and cephalosporins; in addition, no vaccines are available against these strains. This warrants efforts to propose a theoretical based multi-epitope vaccine construct to prevent pathogen infections. In this research, reverse vaccinology bioinformatics and immunoinformatics approaches were adopted for vaccine target identification and construction of a multi-epitope vaccine. In the first phase, a core proteome dataset of the targeted pathogen was obtained using the NCBI database and subjected to bacterial pan-genome analysis using bacterial pan-genome analysis (BPGA) to predict core protein sequences which were then used to find good vaccine target candidates. This identified two proteins, Hcp family type VI secretion system effector and superoxide dismutase family protein, as promising vaccine targets. Afterward using the IEDB database, different B-cell and T-cell epitopes were predicted. A set of four epitopes "KGSVNVQDRE, NTGKLTGTR, IIHSDSWNER, and KDGKPVPALK" were chosen for the development of a multi-epitope vaccine construct. A 183 amino acid long vaccine design was built along with "EAAAK" and "GPGPG" linkers and a cholera toxin B-subunit adjuvant. The designed vaccine model comprised immunodominant, non-toxic, non-allergenic, and physicochemical stable epitopes. The model vaccine was docked with MHC-I, MHC-II, and TLR-4 immune cell receptors using the Cluspro2.0 web server. The binding energy score of the vaccine was - 654.7 kcal/mol for MHC-I, - 738.4 kcal/mol for MHC-II, and - 695.0 kcal/mol for TLR-4. A molecular dynamic simulation was done using AMBER v20 package for dynamic behavior in nanoseconds. Additionally, MM-PBSA binding free energy analysis was done to test intermolecular binding interactions between docked molecules. The MM-GBSA net binding energy score was - 148.00 kcal/mol, - 118.00 kcal/mol, and - 127.00 kcal/mol for vaccine with TLR-4, MHC-I, and MHC-II, respectively. Overall, these in silico-based predictions indicated that the vaccine is highly promising in terms of developing protective immunity against P. penneri. However, additional experimental validation is required to unveil the real immune response to the designed vaccine.
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Affiliation(s)
- Asad Ullah
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 2500, Pakistan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Bushra Rehman
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Saifullah Khan
- Institute of Biotechnology and Microbiology, Bacha Khan University, Charsadda, Pakistan
| | - Taghreed N Almanaa
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Yasir Waheed
- Office of Research, Innovation and Commercialization, Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, 44000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, 1401, Lebanon
| | - Muhammad Hassan
- Department of Pharmacy, Bacha Khan University, Charsadda, 24461, Pakistan
| | - Tahira Naz
- Department of Chemical and Life Sciences, Qurtuba University of Science and Technology, Peshawar, Pakistan
| | - Mehboob Ul Haq
- Department of Pharmacy, Abasyn University, Peshawar, 25000, Pakistan
| | - Riaz Muhammad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 2500, Pakistan
| | - Samira Sanami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, 32611, USA
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, 2500, Pakistan.
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Beirut, Lebanon.
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14
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Sarfraz A, Wara TU, Sheheryar, Chen K, Ansari SH, Zaman A, Nishan U, Iqbal A, Ullah R, Ali EA, Shah M, Ojha SC. Structural informatics approach for designing an epitope-based vaccine against the brain-eating Naegleria fowleri. Front Immunol 2023; 14:1284621. [PMID: 37965306 PMCID: PMC10642955 DOI: 10.3389/fimmu.2023.1284621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Primary Amoebic Meningoencephalitis (PAM), a severe lethal brain disease, is caused by a parasite, Naegleria fowleri, also known as the "brain-eating amoeba". The chances of a patient's recovery after being affected by this parasite are very low. Only 5% of people are known to survive this life-threatening infection. Despite the fact that N. fowleri causes a severe, fatal infection, there is no proper treatment available to prevent or cure it. In this context, it is necessary to formulate a potential vaccine that could be able to combat N. fowleri infection. The current study aimed at developing a multi-epitope subunit vaccine against N. fowleri by utilizing immunoinformatics techniques and reverse vaccinology approaches. The T- and B-cell epitopes were predicted by various tools. In order to choose epitopes with the ability to trigger both T- and B-cell-mediated immune responses, the epitopes were put through a screening pipeline including toxicity, antigenicity, cytokine-inductivity, and allergenicity analysis. Three vaccine constructs were designed from the generated epitopes linked with linkers and adjuvants. The modeled vaccines were docked with the immune receptors, where vaccine-1 showed the highest binding affinity. Binding affinity and stability of the docked complex were confirmed through normal mode analysis and molecular dynamic simulations. Immune simulations developed the immune profile, and in silico cloning affirmed the expression probability of the vaccine construct in Escherichia coli (E. coli) strain K12. This study demonstrates an innovative preventative strategy for the brain-eating amoeba by developing a potential vaccine through immunoinformatics and reverse vaccinology approaches. This study has great preventive potential for Primary Amoebic Meningoencephalitis, and further research is required to assess the efficacy of the designed vaccine.
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Affiliation(s)
- Asifa Sarfraz
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Tehreem Ul Wara
- Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
| | - Sheheryar
- Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
| | - Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | | | - Aqal Zaman
- Department of Microbiology & Molecular Genetics, Bahauddin Zakariya University, Multan, Pakistan
| | - Umar Nishan
- Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
| | - Anwar Iqbal
- Department of Chemical Sciences, University of Lakki Marwat, Khyber Pakhtunkhwa, Pakistan
| | - 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, Pakistan
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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15
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Sanami S, Nazarian S, Ahmad S, Raeisi E, Tahir Ul Qamar M, Tahmasebian S, Pazoki-Toroudi H, Fazeli M, Ghatreh Samani M. In silico design and immunoinformatics analysis of a universal multi-epitope vaccine against monkeypox virus. PLoS One 2023; 18:e0286224. [PMID: 37220125 DOI: 10.1371/journal.pone.0286224] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/11/2023] [Indexed: 05/25/2023] Open
Abstract
Monkeypox virus (MPXV) outbreaks have been reported in various countries worldwide; however, there is no specific vaccine against MPXV. In this study, therefore, we employed computational approaches to design a multi-epitope vaccine against MPXV. Initially, cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL), linear B lymphocytes (LBL) epitopes were predicted from the cell surface-binding protein and envelope protein A28 homolog, both of which play essential roles in MPXV pathogenesis. All of the predicted epitopes were evaluated using key parameters. A total of 7 CTL, 4 HTL, and 5 LBL epitopes were chosen and combined with appropriate linkers and adjuvant to construct a multi-epitope vaccine. The CTL and HTL epitopes of the vaccine construct cover 95.57% of the worldwide population. The designed vaccine construct was found to be highly antigenic, non-allergenic, soluble, and to have acceptable physicochemical properties. The 3D structure of the vaccine and its potential interaction with Toll-Like receptor-4 (TLR4) were predicted. Molecular dynamics (MD) simulation confirmed the vaccine's high stability in complex with TLR4. Finally, codon adaptation and in silico cloning confirmed the high expression rate of the vaccine constructs in strain K12 of Escherichia coli (E. coli). These findings are very encouraging; however, in vitro and animal studies are needed to ensure the potency and safety of this vaccine candidate.
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Affiliation(s)
- Samira Sanami
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Shahin Nazarian
- Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, United States of America
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University, Peshawar, Pakistan
| | - Elham Raeisi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Muhammad Tahir Ul Qamar
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shahram Tahmasebian
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Department of Physiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Fazeli
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran, Iran
| | - Mahdi Ghatreh Samani
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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16
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Chen Y, Gan Y, Yu J, Ye X, Yu W. Key ingredients in Verbena officinalis and determination of their anti-atherosclerotic effect using a computer-aided drug design approach. FRONTIERS IN PLANT SCIENCE 2023; 14:1154266. [PMID: 37077636 PMCID: PMC10106644 DOI: 10.3389/fpls.2023.1154266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 05/03/2023]
Abstract
Lipid metabolism disorders may considerably contribute to the formation and development of atherosclerosis (AS). Traditional Chinese medicine has received considerable attention in recent years owing to its ability to treat lipid metabolism disorders using multiple components and targets. Verbena officinalis (VO), a Chinese herbal medicine, exhibits anti-inflammatory, analgesic, immunomodulatory, and neuroprotective effects. Evidence suggests that VO regulates lipid metabolism; however, its role in AS remains unclear. In the present study, an integrated network pharmacology approach, molecular docking, and molecular dynamics simulation (MDS) were applied to examine the mechanism of VO against AS. Analysis revealed 209 potential targets for the 11 main ingredients in VO. Further, 2698 mechanistic targets for AS were identified, including 147 intersection targets between VO and AS. Quercetin, luteolin, and kaempferol were considered key ingredients for the treatment of AS based on a potential ingredient target-AS target network. GO analysis revealed that biological processes were primarily associated with responses to xenobiotic stimuli, cellular responses to lipids, and responses to hormones. Cell components were predominantly focused on the membrane microdomain, membrane raft, and caveola nucleus. Molecular functions were mainly focused on DNA-binding transcription factor binding, RNA polymerase II-specific DNA-binding transcription factor binding, and transcription factor binding. KEGG pathway enrichment analysis identified pathways in cancer, fluid shear stress, and atherosclerosis, with lipid and atherosclerosis being the most significantly enriched pathways. Molecular docking revealed that three key ingredients in VO (i.e., quercetin, luteolin, and kaempferol) strongly interacted with three potential targets (i.e., AKT1, IL-6, and TNF-α). Further, MDS revealed that quercetin had a stronger binding affinity for AKT1. These findings suggest that VO has beneficial effects on AS via these potential targets that are closely related to the lipid and atherosclerosis pathways. Our study utilized a new computer-aided drug design to identify key ingredients, potential targets, various biological processes, and multiple pathways associated with the clinical roles of VO in AS, which provides a comprehensive and systemic pharmacological explanation for the anti-atherosclerotic activity of VO.
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Affiliation(s)
- Yuting Chen
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Yuanyuan Gan
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Jingxuan Yu
- Clinical Medical College, Changsha Medical University, Changsha, Hunan, China
| | - Xiao Ye
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Wei Yu
- School of Pharmacy, Xianning Medical College, Hubei University of Science and Technology, Xianning, Hubei, China
- Hubei Engineering Research Center of Traditional Chinese Medicine of South Hubei Province, Xianning, Hubei, China
- *Correspondence: Wei Yu,
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