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Ezzemani W, Ouladlahsen A, Altawalah H, Saile R, Sarih M, Kettani A, Ezzikouri S. Identification of novel T-cell epitopes on monkeypox virus and development of multi-epitopes vaccine using immunoinformatics approaches. J Biomol Struct Dyn 2024; 42:5349-5364. [PMID: 37354141 DOI: 10.1080/07391102.2023.2226733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/10/2023] [Indexed: 06/26/2023]
Abstract
Monkeypox virus (MPV) is closely related to the smallpox virus, and previous data from Africa suggest that the smallpox vaccine (VARV) is at least 85% effective in preventing MPV. No multi-epitope vaccine has yet been developed to prevent MPV infection. In this work, we used in silico structural biology and advanced immunoinformatic strategies to design a multi-epitope subunit vaccine against MPV infection. The designed vaccine sequence is adjuvanted with CpG-ODN and includes HTL/CTL epitopes for similar proteins between vaccinia virus (VACV) that induced T-cell production in vaccinated volunteers and the first draft sequence of the MPV genome associated with the suspected outbreak in several countries, May 2022. In addition, the specific binding of the modified vaccine and the immune Toll-like receptor 9 (TLR9) was estimated by molecular interaction studies. Strong interaction in the binding groove as well as good docking scores confirmed the stringency of the modified vaccine. The stability of the interaction was confirmed by a classical molecular dynamics simulation and normal mode analysis. Then, the immune simulation also indicated the ability of this vaccine to induce an effective immune response against MPV. Codon optimization and in silico cloning of the vaccine into the pET-28a (+) vector also showed its expression potential in the E. coli K12 system. The promising data obtained from the various in silico studies indicate that this vaccine is effective against MPV. However, additional in vitro and in vivo studies are still needed to confirm its efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wahiba Ezzemani
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Ahd Ouladlahsen
- Faculté de médecine et de pharmacie, Université Hassan II, Casablanca, Morocco
- Service des maladies infectieuses, CHU Ibn Rochd, Casablanca, Morocco
| | - Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait City, Kuwait
| | - Rachid Saile
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - M'hammed Sarih
- Service de Parasitologie et des Maladies Vectorielles, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Anass Kettani
- Laboratoire de Biologie et Santé (URAC34), Départment de Biologie, Faculté des Sciences Ben Msik, Hassan II University of Casablanca, Casablanca, Morocco
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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Kumar A, Dutt M, Dehury B, Martinez GS, Singh KP, Kelvin DJ. Formulation of next-generation polyvalent vaccine candidates against three important poxviruses by targeting DNA-dependent RNA polymerase using an integrated immunoinformatics and molecular modeling approach. J Infect Public Health 2024; 17:102470. [PMID: 38865776 DOI: 10.1016/j.jiph.2024.102470] [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: 11/24/2023] [Revised: 05/27/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Poxviruses comprise a group of large double-stranded DNA viruses and are known to cause diseases in humans, livestock animals, and other animal species. The Mpox virus (MPXV; formerly Monkeypox), variola virus (VARV), and volepox virus (VPXV) are among the prevalent poxviruses of the Orthopoxviridae genera. The ongoing Mpox infectious disease pandemic caused by the Mpox virus has had a major impact on public health across the globe. To date, only limited repurposed antivirals and vaccines are available for the effective treatment of Mpox and other poxviruses that cause contagious diseases. METHODS The present study was conducted with the primary goal of formulating multi-epitope vaccines against three evolutionary closed poxviruses i.e., MPXV, VARV, and VPXV using an integrated immunoinformatics and molecular modeling approach. DNA-dependent RNA polymerase (DdRp), a potential vaccine target of poxviruses, has been used to determine immunodominant B and T-cell epitopes followed by interactions analysis with Toll-like receptor 2 at the atomic level. RESULTS Three multi-epitope vaccine constructs, namely DdRp_MPXV (V1), DdRp_VARV (V2), and DdRp_VPXV (V3) were designed. These vaccine constructs were found to be antigenic, non-allergenic, non-toxic, and soluble with desired physicochemical properties. Protein-protein docking and interaction profiling analysis depicts a strong binding pattern between the targeted immune receptor TLR2 and the structural models of the designed vaccine constructs, and manifested a number of biochemical bonds (hydrogen bonds, salt bridges, and non-bonded contacts). State-of-the-art all-atoms molecular dynamics simulations revealed highly stable interactions of vaccine constructs with TLR2 at the atomic level throughout the simulations on 300 nanoseconds. Additionally, the outcome of the immune simulation analysis suggested that designed vaccines have the potential to induce protective immunity against targeted poxviruses. CONCLUSIONS Taken together, formulated next-generation polyvalent vaccines were found to have good efficacy against closely related poxviruses (MPXV, VARV, and VPXV) as demonstrated by our extensive immunoinformatics and molecular modeling evaluations; however, further experimental investigations are still needed.
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Affiliation(s)
- Anuj Kumar
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Mansi Dutt
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Budheswar Dehury
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Krishna Pal Singh
- Mahatma Jyotiba Phule Rohilkhand University, Bareilly, Uttar Pradesh, India
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada.
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3
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Kumar A, Misra G, Mohandas S, Yadav PD. Multi-epitope vaccine design using in silico analysis of glycoprotein and nucleocapsid of NIPAH virus. PLoS One 2024; 19:e0300507. [PMID: 38728300 PMCID: PMC11086869 DOI: 10.1371/journal.pone.0300507] [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: 12/09/2023] [Accepted: 02/29/2024] [Indexed: 05/12/2024] Open
Abstract
According to the 2018 WHO R&D Blueprint, Nipah virus (NiV) is a priority disease, and the development of a vaccine against NiV is strongly encouraged. According to criteria used to categorize zoonotic diseases, NiV is a stage III disease that can spread to people and cause unpredictable outbreaks. Since 2001, the NiV virus has caused annual outbreaks in Bangladesh, while in India it has caused occasional outbreaks. According to estimates, the mortality rate for infected individuals ranges from 70 to 91%. Using immunoinformatic approaches to anticipate the epitopes of the MHC-I, MHC-II, and B-cells, they were predicted using the NiV glycoprotein and nucleocapsid protein. The selected epitopes were used to develop a multi-epitope vaccine construct connected with linkers and adjuvants in order to improve immune responses to the vaccine construct. The 3D structure of the engineered vaccine was anticipated, optimized, and confirmed using a variety of computer simulation techniques so that its stability could be assessed. According to the immunological simulation tests, it was found that the vaccination elicits a targeted immune response against the NiV. Docking with TLR-3, 7, and 8 revealed that vaccine candidates had high binding affinities and low binding energies. Finally, molecular dynamic analysis confirms the stability of the new vaccine. Codon optimization and in silico cloning showed that the proposed vaccine was expressed to a high degree in Escherichia coli. The study will help in identifying a potential epitope for a vaccine candidate against NiV. The developed multi-epitope vaccine construct has a lot of potential, but they still need to be verified by in vitro & in vivo studies.
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Affiliation(s)
- Anoop Kumar
- Molecular Diagnostic Laboratory, National Institute of Biologicals, Noida, Uttar Pradesh, India
| | - Gauri Misra
- Molecular Diagnostic Laboratory, National Institute of Biologicals, Noida, Uttar Pradesh, India
| | - Sreelekshmy Mohandas
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
| | - Pragya D. Yadav
- Maximum Containment Laboratory, ICMR-National Institute of Virology, Microbial Containment Complex, Pashan, Pune, India
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4
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Al‐Madhagi H, Kanawati A, Tahan Z. Design of multi-epitope chimeric vaccine against Monkeypox virus and SARS-CoV-2: A vaccinomics perspective. J Cell Mol Med 2024; 28:e18452. [PMID: 38801408 PMCID: PMC11129729 DOI: 10.1111/jcmm.18452] [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: 03/20/2024] [Revised: 05/05/2024] [Accepted: 05/11/2024] [Indexed: 05/29/2024] Open
Abstract
The current era we experience is full with pandemic infectious agents that no longer threatens the major local source but the whole globe. Almost the most emerging infectious agents are severe acute respiratory syndrome coronavirus-2 (SARS CoV-2), followed by monkeypox virus (MPXV). Since no approved antiviral drugs nor licensed active vaccines are yet available, we aimed to utilize immunoinformatics approach to design chimeric vaccine against the two mentioned viruses. This is the first study to deal with design divalent vaccine against SARS-CoV-2 and MPXV. ORF8, E and M proteins from Omicron SARS-CoV-2 and gp182 from MPXV were used as the protein precursor from which multi-epitopes (inducing B-cell, helper T cells, cytotoxic T cells and interferon-ɣ) chimeric vaccine was contrived. The structure of the vaccine construct was predicted, validated, and docked to toll-like receptor-2 (TLR-2). Moreover, its sequence was also used to examine the immune simulation profile and was then inserted into the pET-28a plasmid for in silico cloning. The vaccine construct was probable antigen (0.543) and safe (non-allergen) with strong binding energy to TLR-2 (-1169.8 kcal/mol) and found to have significant immune simulation profile. In conclusion, the designed chimeric vaccine was potent and safe against SARS-CoV-2 and MPXV, which deserves further consideration.
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Affiliation(s)
- Haitham Al‐Madhagi
- Biochemical Technology Program, Faculty of Applied SciencesDhamar UniversityDhamarYemen
| | - Adeela Kanawati
- Division of Biochemistry, Chemistry DepartmentUniversity of AleppoAleppoSyria
| | - Zaher Tahan
- Division of Microbiology, Biology DepartmentUniversity of AleppoAleppoSyria
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Ahmed A, Zaib S, Bhat MA, Saeed A, Altaf MZ, Zahra FT, Shabir G, Rana N, Khan I. Acyl pyrazole sulfonamides as new antidiabetic agents: synthesis, glucosidase inhibition studies, and molecular docking analysis. Front Chem 2024; 12:1380523. [PMID: 38694406 PMCID: PMC11061460 DOI: 10.3389/fchem.2024.1380523] [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: 02/01/2024] [Accepted: 03/11/2024] [Indexed: 05/04/2024] Open
Abstract
Diabetes mellitus is a multi-systematic chronic metabolic disorder and life-threatening disease resulting from impaired glucose homeostasis. The inhibition of glucosidase, particularly α-glucosidase, could serve as an effective methodology in treating diabetes. Attributed to the catalytic function of glucosidase, the present research focuses on the synthesis of sulfonamide-based acyl pyrazoles (5a-k) followed by their in vitro and in silico screening against α-glucosidase. The envisaged structures of prepared compounds were confirmed through NMR and FTIR spectroscopy and mass spectrometry. All compounds were found to be more potent against α-glucosidase than the standard drug, acarbose (IC50 = 35.1 ± 0.14 µM), with IC50 values ranging from 1.13 to 28.27 µM. However, compound 5a displayed the highest anti-diabetic activity (IC50 = 1.13 ± 0.06 µM). Furthermore, in silico studies revealed the intermolecular interactions of most potent compounds (5a and 5b), with active site residues reflecting the importance of pyrazole and sulfonamide moieties. This interaction pattern clearly manifests various structure-activity relationships, while the docking results correspond to the IC50 values of tested compounds. Hence, recent investigation reveals the medicinal significance of sulfonamide-clubbed pyrazole derivatives as prospective therapeutic candidates for treating type 2 diabetes mellitus (T2DM).
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Affiliation(s)
- Atteeque Ahmed
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Aamer Saeed
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Zain Altaf
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Fatima Tuz Zahra
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ghulam Shabir
- Department of Chemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
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Zahid LU, Zaib S, Saeed A, Alharbi HY, Aljohani MS, Alharbi O, Rana N, Khan I, Shabir G, Ahmed A, Saleem A, Awwad NS, Ibrahium HA. Synthesis, Glucosidase Inhibition, and In Silico Modeling Analysis of Highly Fluorinated 2-Imino-1,3-thiazolines in Search of Potent Antidiabetic Agents. ACS OMEGA 2024; 9:15603-15614. [PMID: 38585118 PMCID: PMC10993276 DOI: 10.1021/acsomega.4c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 04/09/2024]
Abstract
In the present work, 2-imino-1,3-thiazolines featuring highly fluorinated fragments were synthesized through a straightforward cyclization of diversely substituted thioureas with 2-bromo-1-(4-fluorophenyl)ethan-1-one. The target compounds were obtained in good yields, and structures were established by FTIR and 1H- and 13C NMR spectroscopic methods. The in vitro biological assay revealed that all the compounds significantly obstruct the α-glucosidase. Compound 6d (3-fluoro-N-(3-(2-fluorophenyl)-4-(4-fluorophenyl)thiazol-2(3H)-ylidene)benzamide) showed the highest antidiabetic potential with an IC50 value of 1.47 ± 0.05 μM. In addition, computational analysis revealed the binding energy of -11.1 kcal/mol for 6d which was lower than the positive standard, acarbose (-7.9 kcal/mol). Several intermolecular interactions between the active site residues and 6d highlight the significance of 2-imino-1,3-thiazoline core in attaining the potent efficacy and making these compounds a valuable pharmacophore in drug discovery.
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Affiliation(s)
- Lutf ullah Zahid
- Department
of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sumera Zaib
- Department
of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Aamer Saeed
- Department
of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Hussam Y. Alharbi
- Department
of Chemistry, Faculty of Science, Taibah
University, Yanbu 46423, Saudi Arabia
| | - Majed S. Aljohani
- Department
of Chemistry, Faculty of Science, Taibah
University, Yanbu 46423, Saudi Arabia
| | - Osama Alharbi
- Department
of Chemistry, Faculty of Science, Taibah
University, Madinah 42353, Saudi Arabia
| | - Nehal Rana
- Department
of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Imtiaz Khan
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Ghulam Shabir
- Department
of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Atteeque Ahmed
- Department
of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Arslan Saleem
- Department
of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Nasser S. Awwad
- Chemistry
Department, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Hala A. Ibrahium
- Biology
Department, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, 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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Hemmati S, Saeidikia Z, Seradj H, Mohagheghzadeh A. Immunomodulatory Peptides as Vaccine Adjuvants and Antimicrobial Agents. Pharmaceuticals (Basel) 2024; 17:201. [PMID: 38399416 PMCID: PMC10892805 DOI: 10.3390/ph17020201] [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: 01/06/2024] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/25/2024] Open
Abstract
The underdevelopment of adjuvant discovery and diversity, compared to core vaccine technology, is evident. On the other hand, antibiotic resistance is on the list of the top ten threats to global health. Immunomodulatory peptides that target a pathogen and modulate the immune system simultaneously are promising for the development of preventive and therapeutic molecules. Since investigating innate immunity in insects has led to prominent achievements in human immunology, such as toll-like receptor (TLR) discovery, we used the capacity of the immunomodulatory peptides of arthropods with concomitant antimicrobial or antitumor activity. An SVM-based machine learning classifier identified short immunomodulatory sequences encrypted in 643 antimicrobial peptides from 55 foe-to-friend arthropods. The critical features involved in efficacy and safety were calculated. Finally, 76 safe immunomodulators were identified. Then, molecular docking and simulation studies defined the target of the most optimal peptide ligands among all human cell-surface TLRs. SPalf2-453 from a crab is a cell-penetrating immunoadjuvant with antiviral properties. The peptide interacts with the TLR1/2 heterodimer. SBsib-711 from a blackfly is a TLR4/MD2 ligand used as a cancer vaccine immunoadjuvant. In addition, SBsib-711 binds CD47 and PD-L1 on tumor cells, which is applicable in cancer immunotherapy as a checkpoint inhibitor. MRh4-679 from a shrimp is a broad-spectrum or universal immunoadjuvant with a putative Th1/Th2-balanced response. We also implemented a pathway enrichment analysis to define fingerprints or immunological signatures for further in vitro and in vivo immunogenicity and reactogenicity measurements. Conclusively, combinatorial machine learning, molecular docking, and simulation studies, as well as systems biology, open a new opportunity for the discovery and development of multifunctional prophylactic and therapeutic lead peptides.
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Affiliation(s)
- Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Kuala Lumpur 56000, Malaysia
| | - Zahra Saeidikia
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran;
| | - Hassan Seradj
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran;
| | - Abdolali Mohagheghzadeh
- Department of Phytopharmaceuticals, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran;
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Yılmaz Çolak Ç. In silico analysis of virulence factors of Streptococcus uberis for a chimeric vaccine design. In Silico Pharmacol 2024; 12:7. [PMID: 38187875 PMCID: PMC10771410 DOI: 10.1007/s40203-023-00181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Streptococcus uberis is one of the causative agents of bovine mastitis, which has detrimental effects on animal health and the dairy industry. Despite decades of research, the requirement for effective vaccines against the disease remains unmet. The goal of this study was to create a multi-epitope vaccine using five virulence factors of S. uberis through the reverse vaccinology approach, which has been employed due to its high efficiency and applicability. Plasminogen activator A (PauA), glyceraldehyde-3-phosphate dehydrogenase C (GapC), C5a peptidase, S. uberis adhesion molecule (SUAM), and sortase A (SrtA) were selected for the T cytotoxic (CTL) and B cell epitope analyses as they were extensively studied in S. uberis or other pathogens. Eighteen CTL and ten B cell epitopes that were antigenic, non-toxic, and non-allergenic were selected in order to design a chimeric vaccine candidate that in silico analysis revealed to be potentially immunogenic, non-allergenic, and stable. Molecular docking analysis of the vaccine candidate with Toll-like receptor (TLR) 2 and TLR 4 revealed stable interactions between the candidate and the immune receptors. Meanwhile, the stability of the docked complexes was confirmed using normal mode analysis. Additionally, in silico immune simulation of the vaccine candidate demonstrated the stimulation of primary immune responses, indicating that the chimeric protein can hold promise as a viable vaccine candidate for preventing S. uberis mastitis. Moreover, the current study can provide a background for designing epitope-based vaccines based on the explored epitopes.
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Anuraga G, Lang J, Xuan DTM, Ta HDK, Jiang JZ, Sun Z, Dey S, Kumar S, Singh A, Kajla G, Wang WJ, Wang CY. Integrated bioinformatics approaches to investigate alterations in transcriptomic profiles of monkeypox infected human cell line model. J Infect Public Health 2024; 17:60-69. [PMID: 37992435 DOI: 10.1016/j.jiph.2023.10.035] [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: 06/20/2023] [Revised: 09/15/2023] [Accepted: 10/30/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The recent re-emergence of the monkeypox (mpox) epidemic in nonendemic regions has raised concerns regarding a potential global outbreak. The mpox virus (MPV) is a smallpox-like virus belonging to the genus Orthopoxvirus (family: Poxviridae). Although studies suggest that MPV infection suppresses the Toll-like receptor-3- and tumor necrosis factor-α-related signaling pathways, whether MPV regulates other immune-related pathways remains unclear. METHODS In this study, two distinct temporal patterns were used for establishing an MPV-infected human immortal epithelial cancer cell line (HeLa). These two durations 2 and 12 h of incubation were selected to identify the coregulated genes and pathways affected by MPV infection. RESULTS The use of the Gene Ontology framework, Kyoto Encyclopedia of Genes and Genome database, and MetaCore software yielded valuable insights. Specifically, various pathways were found to be enriched in HeLa cells infected with MPV for 2 and 12 h. These pathways included Notch, CD40, CD95, hypoxia-inducible factor-1-α, interleukin (IL)- 1, IL-6, phosphoinositide 3-kinase, nuclear factor-κB, mitogen-activated protein kinase, and oxidative stress-induced signalling pathways. Clusters and pathways of metabolism and viral replication cycles were significantly associated with the 2-hour infection group. This association was identified based on the regulation of genes such as HSPG2, RHPN2, MYL1, ASPHD2, CA9, VIPR1, SNX12, MGC2752, SLC25A1, PEX19, and AREG. Furthermore, clusters and pathways related to immunity and cell movement were found to be associated with the 12-hour infection group. This association was identified based on the regulation of genes such as C1orf21, C19orf48, HRK, IL8, GULP1, SCAND2, ATP5C1, FEZ1, SGSH, TACC2, CYP4X1, MMP1, CPB1, P2RY13, WDR27, PRPF4, and ENDOD1. CONCLUSIONS This study can improve our understanding of the mechanisms underlying the pathophysiology and post-infection sequelae of mpox. Our findings provide valuable insights into the various modes of MPV infection.
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Affiliation(s)
- Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya, East Java 60234, Indonesia
| | - Jilu Lang
- Peking University Shenzhen Hospital Cardiovascular Surgery and Department of Cardiac Vascular Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, People's Republic of China
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Jia-Zhen Jiang
- Emergency Department, Huashan Hospital North, Fudan University, Shanghai 201508, People's Republic of China
| | - Zhengda Sun
- Kaiser Permanente, Northern California Regional Laboratories, The Permanente Medical Group, 1725 Eastshore Hwy, Berkeley, CA 94710, USA
| | - Sanskriti Dey
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Sachin Kumar
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Faculty of Biotechnology and Applied Sciences, Shoolini University of Biotechnology and Management Sciences, Himachal Pradesh, India
| | - Ayushi Singh
- Faculty of Biotechnology and Applied Sciences, Shoolini University of Biotechnology and Management Sciences, Himachal Pradesh, India
| | - Gagan Kajla
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; Faculty of Biotechnology and Applied Sciences, Shoolini University of Biotechnology and Management Sciences, Himachal Pradesh, India
| | - Wei-Jan Wang
- Department of Biological Science and Technology, College of Life Sciences, China Medical University, Taichung, Taiwan; Cancer Biology and Precision Therapeutics Center and Research Center for Cancer Biology, China Medical University, Taichung, Taiwan.
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya, East Java 60234, Indonesia; TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan.
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11
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Ramprasadh SV, Rajakumar S, Srinivasan S, Susha D, Sharma S, Chourasiya R. Computer-Aided Multi-Epitope Based Vaccine Design Against Monkeypox Virus Surface Protein A30L: An Immunoinformatics Approach. Protein J 2023; 42:645-663. [PMID: 37615828 DOI: 10.1007/s10930-023-10150-4] [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] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
Monkeypox, a viral zoonotic disease resembling smallpox, has emerged as a significant national epidemic primarily in Africa. Nevertheless, the recent global dissemination of this pathogen has engendered apprehension regarding its capacity to metamorphose into a sweeping pandemic. To effectively combat this menace, a multi-epitope vaccine has been meticulously engineered with the specific aim of targeting the cell envelope protein of Monkeypox virus (MPXV), thereby stimulating a potent immunological response while mitigating untoward effects. This new vaccine uses T-cell and B-cell epitopes from a highly antigenic, non-allergenic, non-toxic, conserved, and non-homologous A30L protein to provide protection against the virus. In order to ascertain the vaccine design with the utmost efficacy, protein-protein docking methodologies were employed to anticipate the intricate interactions with Toll-like receptors (TLR) 2, 3, 4, 6, and 8. This meticulous approach led the researchers to discern an optimal vaccine architecture, bolstered by affirmative prognostications derived from both molecular dynamics (MD) simulations and immune simulations. The current research findings indicate that the peptides ATHAAFEYSK, FFIVVATAAV, and MNSLSIFFV exhibited antigenic properties and were determined to be non-allergenic and non-toxic. Through the utilization of codon optimization and in-silico cloning techniques, our investigation revealed that the prospective vaccine exhibited a remarkable expression level within Escherichia coli. Moreover, upon conducting immune simulations, we observed the induction of a robust immune response characterized by elevated levels of both B-cell and T-cell mediated immunity. Moreover, as the initial prediction with in-silico techniques has yielded promising results these epitope-based vaccines can be recommended to in vitro and in silico studies to validate their immunogenic properties.
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Affiliation(s)
- S V Ramprasadh
- Department of Bioinformatics, BioNome, Bangalore, 560043, India
| | | | - S Srinivasan
- Department of Bioinformatics, BioNome, Bangalore, 560043, India
| | - D Susha
- Department of Bioinformatics, BioNome, Bangalore, 560043, India
| | - Sameer Sharma
- Department of Bioinformatics, BioNome, Bangalore, 560043, India.
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12
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Lucena-Neto FD, Falcão LFM, Vieira-Junior AS, Moraes ECS, David JPF, Silva CC, Sousa JR, Duarte MIS, Vasconcelos PFC, Quaresma JAS. Monkeypox Virus Immune Evasion and Eye Manifestation: Beyond Eyelid Implications. Viruses 2023; 15:2301. [PMID: 38140542 PMCID: PMC10747317 DOI: 10.3390/v15122301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Monkeypox virus (MPXV), belonging to the Poxviridae family and Orthopoxvirus genus, is closely related to the smallpox virus. Initial prodromal symptoms typically include headache, fever, and lymphadenopathy. This review aims to detail various ocular manifestations and immune evasion associated with the monkeypox viral infection and its complications, making it appropriate as a narrative review. Common external ocular manifestations of MPXV typically involve a generalized pustular rash, keratitis, discharges, and dried secretions related to conjunctival pustules, photophobia, and lacrimation. Orthopoxviruses can evade host immune responses by secreting proteins that antagonize the functions of host IFNγ, CC and CXC chemokines, IL-1β, and the complement system. One of the most important transcription factors downstream of pattern recognition receptors binding is IRF3, which controls the expression of the crucial antiviral molecules IFNα and IFNβ. We strongly recommend that ophthalmologists include MPXV as part of their differential diagnosis when they encounter similar cases presenting with ophthalmic manifestations such as conjunctivitis, blepharitis, or corneal lesions. Furthermore, because non-vaccinated individuals are more likely to exhibit these symptoms, it is recommended that healthcare administrators prioritize smallpox vaccination for at-risk groups, including very young children, pregnant women, older adults, and immunocompromised individuals, especially those in close contact with MPXV cases.
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Affiliation(s)
- Francisco D. Lucena-Neto
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Luiz F. M. Falcão
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Adolfo S. Vieira-Junior
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Evelly C. S. Moraes
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
| | - Joacy P. F. David
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
| | - Camilla C. Silva
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Jorge R. Sousa
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Maria I. S. Duarte
- Department of Infectious Disease, School of Medicine, São Paulo University, São Paulo 01246-904, SP, Brazil;
| | - Pedro F. C. Vasconcelos
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
| | - Juarez A. S. Quaresma
- Department of Infectious Disease, School of Medicine, State University of Pará, Belém 66087-670, PA, Brazil; (F.D.L.-N.); (L.F.M.F.); (A.S.V.-J.); (C.C.S.); (J.R.S.); (P.F.C.V.)
- Department of Infectious Disease, School of Medicine, Federal University of Pará, Belém 66075-110, PA, Brazil; (E.C.S.M.); (J.P.F.D.)
- Department of Infectious Disease, School of Medicine, São Paulo University, São Paulo 01246-904, SP, Brazil;
- Virology Section, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil
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Farzan M, Farzan M, Mirzaei Y, Aiman S, Azadegan-Dehkordi F, Bagheri N. Immunoinformatics-based multi-epitope vaccine design for the re-emerging monkeypox virus. Int Immunopharmacol 2023; 123:110725. [PMID: 37556996 DOI: 10.1016/j.intimp.2023.110725] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND On May 7, 2022, WHO reported a new monkeypox case. By May 2023 over 80,000 cases had been reported worldwide outside previously endemic nations. (This primarily affected the men who have sex with men (MSM) community in rich nations). The present research aims to develop a multi-epitope vaccine for the monkeypox virus (MPXV) using structural and cell surface proteins. METHODS The first part of the research involved retrieving protein sequences. The Immune Epitope Database (IEDB) was then used to analyze the B and T lymphocyte epitopes. After analyzing the sensitizing properties, toxicity, antigenicity, and molecular binding, appropriate linkers were utilizedto connect selected epitopes to adjuvants, and the structure of the vaccine was formulated. Algorithms from the field of immunoinformatics predicted the secondary and tertiary structures of vaccines. The physical, chemical, and structural properties were refined and validated to achieve maximum stability. Molecular docking and molecular dynamic simulations were subsequently employed to assess the vaccine's efficacy. Afterward, the ability of the vaccine to interact with toll-like receptors 3 and 4 (TLR3 and TLR4) was evaluated. Finally, the optimized sequence was then introduced into the Escherichia coli (E. coli) PET30A + vector. RESULTS An immunoinformatics evaluation suggested that such a vaccine might be safe revealed that this vaccine is safe, hydrophilic, temperature- and condition-stable, and can stimulate innate immunity by binding to TLR3 and TLR4. CONCLUSION Our findings suggest that the first step in MPXV pathogenesis is structural and cell surface epitopes. In this study, the most effective and promising epitopes were selected and designed throughprecision servers. Furthermore,through the utilization of multi-epitope structures and a combination of two established adjuvants, this research has the potential to be a landmarkin developing an antiviralvaccine against MPXV. However, additional in vitro and in vivo tests are required to confirm these results.
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Affiliation(s)
- Mahour Farzan
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Mahan Farzan
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Yousef Mirzaei
- Department of Medical Biochemical Analysis, Cihan University-Erbil, Kurdistan Region, Iraq
| | - Sara Aiman
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fatemeh Azadegan-Dehkordi
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
| | - Nader Bagheri
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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14
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Suleman M, Khan SH, Rashid F, Khan A, Hussain Z, Zaman N, Rehman SU, Zhai J, Xue M, Zheng C. Designing a multi-epitopes subunit vaccine against human herpes virus 6A based on molecular dynamics and immune stimulation. Int J Biol Macromol 2023:125068. [PMID: 37245745 DOI: 10.1016/j.ijbiomac.2023.125068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Human Herpesvirus 6A (HHV-6A) is a prevalent virus associated with various clinical manifestations, including neurological disorders, autoimmune diseases, and promotes tumor cell growth. HHV-6A is an enveloped, double-stranded DNA virus with a genome of approximately 160-170 kb containing a hundred open-reading frames. An immunoinformatics approach was applied to predict high immunogenic and non-allergenic CTL, HTL, and B cell epitopes and design a multi-epitope subunit vaccine based on HHV-6A glycoprotein B (gB), glycoprotein H (gH), and glycoprotein Q (gQ). The stability and correct folding of the modeled vaccines were confirmed through molecular dynamics simulation. Molecular docking found that the designed vaccines have a strong binding network with human TLR3, with Kd values of 1.5E-11 mol/L, 2.6E-12 mol/L, 6.5E-13 mol/L, and 7.1E-11 mol/L for gB-TLR3, gH-TLR3, gQ-TLR3, and the combined vaccine-TLR3, respectively. The codon adaptation index values of the vaccines were above 0.8, and their GC content was around 67 % (normal range 30-70 %), indicating their potential for high expression. Immune simulation analysis demonstrated robust immune responses against the vaccine, with approximately 650,000/ml combined IgG and IgM antibody titer. This study lays a strong foundation for developing a safe and effective vaccine against HHV-6A, with significant implications for treating associated conditions.
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Affiliation(s)
- Muhammad Suleman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Syed Hunain Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Farooq Rashid
- Department of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China.
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Zahid Hussain
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Nasib Zaman
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
| | - Shoaib Ur Rehman
- Department of Biotechnology, University of Science and Technology, Bannu, Pakistan
| | - Jingbo Zhai
- Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Medical College, Inner Mongolia Minzu University, Tongliao 028000, China.
| | - Mengzhou Xue
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, 2 Jingba Road, Zhengzhou, Henan 450001, China.
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
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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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Saadh MJ, Ghadimkhani T, Soltani N, Abbassioun A, Daniel Cosme Pecho R, Taha A, Jwad Kazem T, Yasamineh S, Gholizadeh O. Progress and prospects on vaccine development against Monkeypox Infection. Microb Pathog 2023; 180:106156. [PMID: 37201635 DOI: 10.1016/j.micpath.2023.106156] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023]
Abstract
The monkeypox virus (MPOX) is an uncommon zoonotic illness brought on by an orthopoxvirus (OPXV). MPOX can occur with symptoms similar to smallpox. Since April 25, 2023, 110 nations have reported 87,113 confirmed cases and 111 fatalities. Moreover, the outspread prevalence of MPOX in Africa and a current outbreak of MPOX in the U.S. have made it clear that naturally occurring zoonotic OPXV infections remain a public health concern. Existing vaccines, though they provide cross-protection to MPOX, are not specific for the causative virus, and their effectiveness in the light of the current multi-country outbreak is still to be verified. Furthermore, as a sequel of the eradication and cessation of smallpox vaccination for four decades, MPOX found a possibility to re-emerge, but with distinct characteristics. The World Health Organization (WHO) suggested that nations use affordable MPOX vaccines within a framework of coordinated clinical effectiveness and safety evaluations. Vaccines administered in the smallpox control program and conferred immunity against MPOX. Currently, vaccines approved by WHO for use against MPOX are replicating (ACAM2000), low replicating (LC16m8), and non-replicating (MVA-BN). Although vaccines are accessible, investigations have demonstrated that smallpox vaccination is approximately 85% efficient in inhibiting MPOX. In addition, developing new vaccine methods against MPOX can help prevent this infection. To recognize the most efficient vaccine, it is essential to assess effects, including reactogenicity, safety, cytotoxicity effect, and vaccine-associated side effects, especially for high-risk and vulnerable people. Recently, several orthopoxvirus vaccines have been produced and are being evaluated. Hence, this review aims to provide an overview of the efforts dedicated to several types of vaccine candidates with different strategies for MPOX, including inactivated, live-attenuated, virus-like particles (VLPs), recombinant protein, nucleic acid, and nanoparticle-based vaccines, which are being developed and launched.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan; Applied Science Research Center, Applied Science Private University, Amman, Jordan
| | | | - Narges Soltani
- School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Arian Abbassioun
- Department of Virology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | | | - Ali Taha
- Medical Technical College, Al-Farahidi University, Iraq
| | - Tareq Jwad Kazem
- Scientific Affairs Department, Al-Mustaqbal University, 51001, Hillah, Babylon, Iraq
| | - Saman Yasamineh
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
| | - Omid Gholizadeh
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.
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17
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Shamim MA, Satapathy P, Padhi BK, Veeramachaneni SD, Akhtar N, Pradhan A, Agrawal A, Dwivedi P, Mohanty A, Pradhan KB, Kabir R, Rabaan AA, Alotaibi J, Al Ismail ZA, Alsoliabi ZA, Al Fraij A, Sah R, Rodriguez-Morales AJ. Pharmacological treatment and vaccines in monkeypox virus: a narrative review and bibliometric analysis. Front Pharmacol 2023; 14:1149909. [PMID: 37214444 PMCID: PMC10196034 DOI: 10.3389/fphar.2023.1149909] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Mpox (earlier known as monkeypox) virus infection is a recognized public health emergency. There has been little research on the treatment options. This article reviews the specific drugs used to treat mpox virus infection and the vaccines used here. Instead of focusing on the mechanistic basis, this review narrates the practical, real-life experiences of individual patients of mpox virus disease being administered these medicines. We conducted a bibliometric analysis on the treatment of the mpox virus using data from several databases like PubMed, Scopus, and Embase. The research on this topic has grown tremendously recently but it is highly concentrated in a few countries. Cidofovir is the most studied drug. This is because it is indicated and also used off-label for several conditions. The drugs used for mpox virus infection include tecovirimat, cidofovir, brincidofovir, vaccinia immune globulin, and trifluridine. Tecovirimat is used most frequently. It is a promising option in progressive mpox disease in terms of both efficacy and safety. Brincidofovir has been associated with treatment discontinuation due to elevated hepatic enzymes. Cidofovir is also not the preferred drug, often used because of the unavailability of tecovirimat. Trifluridine is used topically as an add-on agent along with tecovirimat for ocular manifestations of mpox virus disease. No study reports individual patient data for vaccinia immune globulin. Though no vaccine is currently approved for mpox virus infection, ACAM 2000 and JYNNEOS are the vaccines being mainly considered. ACAM 2000 is capable of replicating and may cause severe adverse reactions. It is used when JYNNEOS is contraindicated. Several drugs and vaccines are under development and have been discussed alongside pragmatic aspects of mpox virus treatment and prevention. Further studies can provide more insight into the safety and efficacy of Tecovirimat in actively progressing mpox virus disease.
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Affiliation(s)
| | - Prakisini Satapathy
- Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Bijaya Kumar Padhi
- Department of Community Medicine, School of Public Health, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Naushaba Akhtar
- Indian Council of Medical Research—Regional Medical Research Centre, Bhubaneswar, India
| | - Anindita Pradhan
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, India
| | - Abhimanyu Agrawal
- Department of Pharmacology, All India Institute of Medical Sciences, Bathinda, India
| | - Pradeep Dwivedi
- Department of Pharmacology, All India Institute of Medical Sciences, Jodhpur, India
- Centre of Excellence for Tribal Health, All India Institute of Medical Sciences, Jodhpur, India
| | - Aroop Mohanty
- All India Institute of Medical Sciences, Gorakhpur, India
| | | | - Russell Kabir
- School of Allied Health, Anglia Ruskin University, Essex, United Kingdom
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Jawaher Alotaibi
- Infectious Diseases Unit, King Faisal Specialist Hospital and Research Center, Department of Medicine, Riyadh, Saudi Arabia
| | - Zainab A. Al Ismail
- Long Term Care Department, Dhahran Long Term Hospital, Dhahran, Saudi Arabia
| | | | - Ali Al Fraij
- Medical Laboratories and Blood Bank Department, Jubail Health Network, Jubail, Saudi Arabia
| | - Ranjit Sah
- Tribhuvan University Teaching Hospital, Institute of Medicine, Kathmandu, Nepal
- Harvard Medical School, Boston, MA, United States
- Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Alfonso J. Rodriguez-Morales
- Faculty of Health Sciences, Universidad Científica del Sur, Lima, Peru
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
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18
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Zaib S, Rana N, Hussain N, Ogaly HA, Dera AA, Khan I. Identification of Potential Inhibitors for the Treatment of Alkaptonuria Using an Integrated In Silico Computational Strategy. Molecules 2023; 28:molecules28062623. [PMID: 36985595 PMCID: PMC10058836 DOI: 10.3390/molecules28062623] [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: 02/07/2023] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Alkaptonuria (AKU) is a rare genetic autosomal recessive disorder characterized by elevated serum levels of homogentisic acid (HGA). In this disease, tyrosine metabolism is interrupted because of the alterations in homogentisate dioxygenase (HGD) gene. The patient suffers from ochronosis, fractures, and tendon ruptures. To date, no medicine has been approved for the treatment of AKU. However, physiotherapy and strong painkillers are administered to help mitigate the condition. Recently, nitisinone, an FDA-approved drug for type 1 tyrosinemia, has been given to AKU patients in some countries and has shown encouraging results in reducing the disease progression. However, this drug is not the targeted treatment for AKU, and causes keratopathy. Therefore, the foremost aim of this study is the identification of potent and druggable inhibitors of AKU with no or minimal side effects by targeting 4-hydroxyphenylpyruvate dioxygenase. To achieve our goal, we have performed computational modelling using BioSolveIT suit. The library of ligands for molecular docking was acquired by fragment replacement of reference molecules by ReCore. Subsequently, the hits were screened on the basis of estimated affinities, and their pharmacokinetic properties were evaluated using SwissADME. Afterward, the interactions between target and ligands were investigated using Discovery Studio. Ultimately, compounds c and f were identified as potent inhibitors of 4-hydroxyphenylpyruvate dioxygenase.
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Affiliation(s)
- Sumera Zaib
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
- Correspondence: (S.Z.); (I.K.)
| | - Nehal Rana
- Department of Basic and Applied Chemistry, Faculty of Science and Technology, University of Central Punjab, Lahore 54590, Pakistan
| | - Nadia Hussain
- Department of Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain P.O. Box 64141, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi P.O. Box 144534, United Arab Emirates
| | - Hanan A. Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha 61421, Saudi Arabia
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Ayed A. Dera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha 62529, Saudi Arabia
| | - Imtiaz Khan
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Correspondence: (S.Z.); (I.K.)
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