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Oladipo EK, Oyelakin OD, Aiyelabegan AO, Olajide EO, Olatayo VO, Owolabi KP, Shittu YB, Olugbodi RO, Ajala HA, Rukayat RA, Olayiwola DO, Irewolede BA, Jimah EM, Oloke JK, Ojo TO, Ajani OF, Iwalokun BA, Kolawole OM, Ariyo OE, Adediran DA, Olufemi SE, Onyeaka H. Exploring computational approaches to design mRNA Vaccine against vaccinia and Mpox viruses. Immun Inflamm Dis 2024; 12:e1360. [PMID: 39150224 PMCID: PMC11328121 DOI: 10.1002/iid3.1360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Messenger RNA (mRNA) vaccines emerged as a powerful tool in the fight against infections. Unlike traditional vaccines, this unique type of vaccine elicits robust and persistent innate and humoral immune response with a unique host cell-mediated pathogen gene expression and antigen presentation. METHODS This offers a novel approach to combat poxviridae infections. From the genome of vaccinia and Mpox viruses, three key genes (E8L, E7R, and H3L) responsible for virus attachment and virulence were selected and employed for designing the candidate mRNA vaccine against vaccinia and Mpox viral infection. Various bioinformatics tools were employed to generate (B cell, CTL, and HTL) epitopes, of which 28 antigenic and immunogenic epitopes were selected and are linked to form the mRNA vaccine construct. Additional components, including a 5' cap, 5' UTR, adjuvant, 3' UTR, and poly(A) tail, were incorporated to enhance stability and effectiveness. Safety measures such as testing for human homology and in silico immune simulations were implemented to avoid autoimmunity and to mimics the immune response of human host to the designed mRNA vaccine, respectively. The mRNA vaccine's binding affinity was evaluated by docking it with TLR-2, TLR-3, TLR-4, and TLR-9 receptors which are subsequently followed by molecular dynamics simulations for the highest binding one to predict the stability of the binding complex. RESULTS With a 73% population coverage, the mRNA vaccine looks promising, boasting a molecular weight of 198 kDa and a molecular formula of C8901H13609N2431O2611S48 and it is said to be antigenic, nontoxic and nonallergic, making it safe and effective in preventing infections with Mpox and vaccinia viruses, in comparison with other insilico-designed vaccine for vaccinia and Mpox viruses. CONCLUSIONS However, further validation through in vivo and in vitro techniques is underway to fully assess its potential.
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Affiliation(s)
- Elijah K Oladipo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Laboratory of Molecular Biology, Immunology and Bioinformatics, Department of Microbiology, Adeleke University, Ede, Osun State, Nigeria
| | - Olanrewaju D Oyelakin
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Abdulsamad O Aiyelabegan
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Elizabeth O Olajide
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Molecular Biology and Biotechnology Department, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Victoria O Olatayo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Kaothar P Owolabi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Yewande B Shittu
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Rhoda O Olugbodi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Hezekiah A Ajala
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Raji A Rukayat
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Deborah O Olayiwola
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife A Irewolede
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Esther M Jimah
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Julius K Oloke
- Department of Natural Sciences, Precious Cornerstone University, Ibadan, Oyo State, Nigeria
| | - Taiwo O Ojo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Olumide F Ajani
- African Centre for Disease Control HQ, Addis Ababa, Ethiopia
| | - Bamidele A Iwalokun
- Molecular Biology and Biotechnology Department, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Olatunji M Kolawole
- Department of Microbiology, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olumuyiwa E Ariyo
- Department of Medicine, Infectious Disease and Tropical Medicine Unit, Federal Teaching Hospital, Ido Ekiti, Ekiti State, Nigeria
| | - Daniel A Adediran
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Seun E Olufemi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
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Oladipo EK, Ojo TO, Elegbeleye OE, Bolaji OQ, Oyewole MP, Ogunlana AT, Olalekan EO, Abiodun B, Adediran DA, Obideyi OA, Olufemi SE, Salamatullah AM, Bourhia M, Younous YA, Adelusi TI. Exploring the nuclear proteins, viral capsid protein, and early antigen protein using immunoinformatic and molecular modeling approaches to design a vaccine candidate against Epstein Barr virus. Sci Rep 2024; 14:16798. [PMID: 39039173 PMCID: PMC11263613 DOI: 10.1038/s41598-024-66828-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/04/2024] [Indexed: 07/24/2024] Open
Abstract
The available Epstein Barr virus vaccine has tirelessly harnessed the gp350 glycoprotein as its target epitope, but the result has not been preventive. Right here, we designed a global multi-epitope vaccine for EBV; with special attention to making sure all strains and preventive antigens are covered. Using a robust computational vaccine design approach, our proposed vaccine is armed with 6-16 mers linear B-cell epitopes, 4-9 mer CTL epitopes, and 8-15 mer HTL epitopes which are verified to induce interleukin 4, 10 & IFN-gamma. We employed deep computational mining coupled with expert intelligence in designing the vaccine, using human Beta defensin-3-which has been reported to induce the same TLRs as EBV-as the adjuvant. The tendency of the vaccine to cause autoimmune disorder is quenched by the assurance that the construct contains no EBNA-1 homolog. The protein vaccine construct exhibited excellent physicochemical attributes such as Aliphatic index 59.55 and GRAVY - 0.710; and a ProsaWeb Z score of - 3.04. Further computational analysis revealed the vaccine docked favorably with EBV indicted TLR 1, 2, 4 & 9 with satisfactory interaction patterns. With global coverage of 85.75% and the stable molecular dynamics result obtained for the best two interactions, we are optimistic that our nontoxic, non-allergenic multi-epitope vaccine will help to ameliorate the EBV-associated diseases-which include various malignancies, tumors, and cancers-preventively.
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Affiliation(s)
- Elijah Kolawole Oladipo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, 232104, Nigeria
| | - Taiwo Ooreoluwa Ojo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Oluwabamise Emmanuel Elegbeleye
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Olawale Quadri Bolaji
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Moyosoluwa Precious Oyewole
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
- Department of Biochemistry, Bowen University, Iwo, 232101, Nigeria
| | - Abdeen Tunde Ogunlana
- Institute of Advanced Medical Research and Training (IAMRAT), College of Medicine, University of Ibadan, Ibadan, 200005, Nigeria
| | - Emmanuel Obanijesu Olalekan
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Bamidele Abiodun
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria
| | - Daniel Adewole Adediran
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
| | | | - Seun Elijah Olufemi
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, 210214, Nigeria
| | - Ahmad Mohammad Salamatullah
- Department of Food Science and Nutrition, College of Food and Agricultural Sciences, King Saud University, 11, P.O. Box 2460, 11451, Riyadh, Saudi Arabia
| | - Mohammed Bourhia
- Laboratory of Therapeutic and Organic Chemistry, Faculty of Pharmacy, University of Montpellier, Montpellier, 34000, France
| | | | - Temitope Isaac Adelusi
- Computational Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, (LAUTECH), Ogbomoso, 210214, Nigeria.
- Department of Surgery, School of Medicine, University of Connecticut Health, Farmington Ave, Farmington, CT, 06030, USA.
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Ojo TO, Elegbeleye OE, Bolaji OQ, Adelusi TI, Oladipo EK, Olawuyi MO, Afolayan BO, Oyaronbi AO, Ogunjobi TT, Oyewole MP, Folorunso KP, Ogunlana AT. Hitting Epstein Barr virus where it hurts: computational methods exploration for siRNA therapy in alleviating Epstein Barr virus-induced multiple sclerosis. Neurogenetics 2024; 25:263-275. [PMID: 38809364 DOI: 10.1007/s10048-024-00764-w] [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: 04/24/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024]
Abstract
Multiple sclerosis (MS), an intricate neurological disorder, continues to challenge our understanding of the pivotal interplay between the immune system and the central nervous system (CNS). This condition arises from the immune system's misdirected attack on nerve fiber protection, known as myelin sheath, alongside nerve fibers themselves. This enigmatic condition, characterized by demyelination and varied clinical manifestations, prompts exploration into its multifaceted etiology and potential therapeutic avenues. Research has revealed a potential connection between Epstein Barr virus (EBV), specifically Epstein Barr Nuclear Antigen 1 (EBNA-1), and MS. The immune response to EBNA-1 antigen triggers the production of anti-EBNA-1 molecules, including IgG that identify a similar amino acid sequence to EBNA-1 in myelin, inadvertently targeting myelin sheath and contributing to MS progression. Currently, no treatment exists for EBNA-1-induced MS apart from symptom management. Addressing this, a novel potential therapeutic avenue utilizing small interference RNAs (siRNA) has been designed. By targeting the conserved EBNA-1 gene sequences in EBV types 1 and 2, five potential siRNAs were identified in our analysis. Thorough evaluations encompassing off-target binding, thermodynamics and secondary structure elucidation, efficacy prediction, siRNA-mRNA sequence binding affinity exploration, melting temperature, and docking of siRNAs with human argonaute protein 2 (AGO2) were conducted to elucidate the siRNAs efficiency. These designed siRNA molecules harnessed promising silencing activity in the EBNA-1 gene encoding the EBNA-1 antigen protein and thus have the potential to mitigate the severity of this dangerous virus.
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Affiliation(s)
- Taiwo Ooreoluwa Ojo
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, 210214, Nigeria
| | - Oluwabamise Emmanuel Elegbeleye
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olawale Quadri Bolaji
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Temitope Isaac Adelusi
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Department of Surgery, School of Medicine, University of Connecticut Health, Farmington Ave, Connecticut, 06030, United States of America
| | - Elijah Kolawole Oladipo
- Division of Vaccine Design and Development, Helix Biogen Institute, Ogbomoso, Oyo State, 210214, Nigeria
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, 232104, Nigeria
| | - Matthew Oluwaseun Olawuyi
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Bukola Oluwafunmilayo Afolayan
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Taiwo Temitope Ogunjobi
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Kolade Pelumi Folorunso
- Department of Anatomy, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Abdeen Tunde Ogunlana
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo State, 200005, Nigeria.
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Adelusi TI, Ojo TO, Bolaji OQ, Oyewole MP, Olaoba OT, Oladipo EK. Predicting Plasmodium falciparum kinase inhibitors from antimalarial medicinal herbs using computational modeling approach. In Silico Pharmacol 2023; 12:4. [PMID: 38130691 PMCID: PMC10730500 DOI: 10.1007/s40203-023-00175-z] [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: 08/23/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023] Open
Abstract
Malaria remains a significant public health challenge, with resistance to available drugs necessitating the development of novel therapies targeting invasion-dependent proteins. Plasmodium falciparum calcium-dependent protein kinase 1 (PfCDPK-1) is essential for host erythrocyte invasion and parasite asexual development. This study screened a library of 490 compounds using computational methods to identify potential PfCDPK-1 inhibitors. Three compounds; 17-hydroxyazadiradione, Picracin, and Epicatechin-gallate derived from known antimalarial botanicals, showed potent inhibitory effects on PfCDPK-1. These compounds exhibited better binding affinities (-8.8, -9.1, -9.3 kCal/mol respectively), pharmacokinetics, and physicochemical properties than the purported inhibitory standard of PfCDPK-1, Purfalcamine. Molecular dynamics simulations (50 ns) and molecular mechanics analyses confirmed the stability and binding rigidity of these compounds at the active pocket of PfCDPK-1. The results suggest that these compounds are promising pharmacological targets with potential therapeutic effects for malaria treatment/management without undesirable side effects. Therefore, this study provides new insights into the development of effective antimalarial agents targeting invasion-dependent proteins, which could help combat the global malaria burden. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00175-z.
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Affiliation(s)
- Temitope Isaac Adelusi
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
| | - Taiwo Ooreoluwa Ojo
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
- Genomics unit, Helix Biogen Institute, P.M.B 212102, Ogbomoso, Oyo State Nigeria
| | - Olawale Quadri Bolaji
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
| | - Moyosoluwa Precious Oyewole
- Computational Molecular Biology and Drug Discovery Laboratory, Department of Biochemistry, Ladoke Akintola University of Technology, P.M.B 210214, Ogbomoso, Oyo State Nigeria
| | - Olamide Tosin Olaoba
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211 USA
| | - Elijah Kolawole Oladipo
- Genomics unit, Helix Biogen Institute, P.M.B 212102, Ogbomoso, Oyo State Nigeria
- Laboratory of Molecular Biology, Bioinformatics and Immunology, Department of Microbiology, Adeleke University, Ede, Osun State Nigeria
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