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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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Nawaz R, Arif MA, Ahmad Z, Ahad A, Shahid M, Hassan Z, Husnain A, Aslam A, Raza MS, Mehmood U, Idrees M. An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes. BMC Infect Dis 2023; 23:872. [PMID: 38087193 PMCID: PMC10718025 DOI: 10.1186/s12879-023-08870-0] [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: 07/05/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The corona virus SARS-CoV-2 is the causative agent of recent most global pandemic. Its genome encodes various proteins categorized as non-structural, accessory, and structural proteins. The non-structural proteins, NSP1-16, are located within the ORF1ab. The NSP3, 4, and 6 together are involved in formation of double membrane vesicle (DMV) in host Golgi apparatus. These vesicles provide anchorage to viral replicative complexes, thus assist replication inside the host cell. While the accessory genes coded by ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, 9b, 9c, and 10 contribute in cell entry, immunoevasion, and pathological progression. METHODS This in silico study is focused on designing sequence specific siRNA molecules as a tool for silencing the non-structural and accessory genes of the virus. The gene sequences of NSP3, 4, and 6 along with ORF3a, 6, 7a, 8, and 10 were retrieved for conservation, phylogenetic, and sequence logo analyses. siRNA candidates were predicted using siDirect 2.0 targeting these genes. The GC content, melting temperatures, and various validation scores were calculated. Secondary structures of the guide strands and siRNA-target duplexes were predicted. Finally, tertiary structures were predicted and subjected to structural validations. RESULTS This study revealed that NSP3, 4, and 6 and accessory genes ORF3a, 6, 7a, 8, and 10 have high levels of conservation across globally circulating SARS-CoV-2 strains. A total of 71 siRNA molecules were predicted against the selected genes. Following rigorous screening including binary validations and minimum free energies, final siRNAs with high therapeutic potential were identified, including 7, 2, and 1 against NSP3, NSP4, and NSP6, as well as 3, 1, 2, and 1 targeting ORF3a, ORF7a, ORF8, and ORF10, respectively. CONCLUSION Our novel in silico pipeline integrates effective methods from previous studies to predict and validate siRNA molecules, having the potential to inhibit viral replication pathway in vitro. In total, this study identified 17 highly specific siRNA molecules targeting NSP3, 4, and 6 and accessory genes ORF3a, 7a, 8, and 10 of SARS-CoV-2, which might be used as an additional antiviral treatment option especially in the cases of life-threatening urgencies.
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Affiliation(s)
- Rabia Nawaz
- Department of Biological Sciences, Superior University, Lahore, Pakistan.
- Division of Molecular Virology, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Muhammad Ali Arif
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Zainab Ahmad
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Ammara Ahad
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Shahid
- Division of Molecular Virology, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Zohal Hassan
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Ali Husnain
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Ali Aslam
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Saad Raza
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Uqba Mehmood
- Department of Biological Sciences, Superior University, Lahore, Pakistan
| | - Muhammad Idrees
- Division of Molecular Virology, Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Vice chancellor, University of Peshawar, Peshawar, Pakistan
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Al Mamun Khan MA, Ahsan A, Khan MA, Sanjana JM, Biswas S, Saleh MA, Gupta DR, Hoque MN, Sakif TI, Rahman MM, Islam T. In-silico prediction of highly promising natural fungicides against the destructive blast fungus Magnaporthe oryzae. Heliyon 2023; 9:e15113. [PMID: 37123971 PMCID: PMC10130775 DOI: 10.1016/j.heliyon.2023.e15113] [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: 08/03/2022] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Magnaporthe oryzae causes destructive blast disease in more than 50 species of the major cereal crops rice, wheat and maize and destroys food of millions of people worldwide. Application of synthetic chemical fungicides are environmentally hazardous and unreliable in controlling M. oryzae. Conversely, naturally occurring biofungicides with multiple modes of actions are needed to be discovered for combatting the blast fungus. To find the effective biofungicides, we performed molecular docking study of some potential antifungal natural compounds targeting two proteins including a single-stranded DNA binding protein MoSub1 (4AGH), and an effector protein AVR-Pik (5E9G) of M. oryzae that regulates transcription in fungus and/or suppresses the host cell immunity. The thirty-nine natural compounds previously shown to inhibit M. oryzae growth and reproduction were put under molecular docking against these two proteins followed by simulation, free energy, and interaction analysis of protein-ligand complexes. The virtual screening revealed that two alkaloidal metabolites, camptothecin and GKK1032A2 showed excellent binding energy with any of these target proteins compared to reference commercial fungicides, azoxystrobin and strobilurin. Of the detected compounds, GKK1032A2 bound to both target proteins of M. oryzae. Both compounds showed excellent bioactivity scores as compared to the reference fungicides. Results of our computational biological study suggest that both camptothecin and GKK1032A2 are potential fungicides that could also be considered as lead compounds to design novel fungicides against the blast fungus. Furthermore, the GKK1032A2 acted as a multi-site mode of action fungicide against M. oryzae.
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Affiliation(s)
- Md Abdullah Al Mamun Khan
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Asif Ahsan
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka 1209, Bangladesh
- Bio-Bio-1 Bioinformatics Research Foundation, Dhaka, Bangladesh
| | - Jannatul Maowa Sanjana
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Dipali Rani Gupta
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
| | - M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur 1706, Bangladesh
| | - Tahsin Islam Sakif
- Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506-6109, USA
| | - Md Masuder Rahman
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh
- Corresponding author. Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur 1706, Bangladesh.
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Khan MA, Al Mamun Khan MA, Mahfuz AMUB, Sanjana JM, Ahsan A, Gupta DR, Hoque MN, Islam T. Highly potent natural fungicides identified in silico against the cereal killer fungus Magnaporthe oryzae. Sci Rep 2022; 12:20232. [PMID: 36418863 PMCID: PMC9684433 DOI: 10.1038/s41598-022-22217-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Magnaporthe oryzae is one of the most notorious fungal pathogens that causes blast disease in cereals, and results in enormous loss of grain production. Many chemical fungicides are being used to control the pathogen but none of them are fully effective in controlling blast disease. Therefore, there is a demand for the discovery of a new natural biofungicide to manage the blast disease efficiently. A large number of new natural products showed inhibitory activities against M. oryzae in vitro. To find out effective biofungicides, we performed in silico molecular docking analysis of some of the potent natural compounds targeting four enzymes namely, scytalone dehydratase, SDH1 (PDB ID:1STD), trihydroxynaphthalene reductase, 3HNR (PDB ID:1YBV), trehalose-6-phosphate synthase, Tps1 (PDB ID:6JBI) and isocitrate lyase, ICL1 (PDB ID:5E9G) of M. oryzae fungus that regulate melanin biosynthesis and/or appresorium formation. Thirty-nine natural compounds that were previously reported to inhibit the growth of M. oryzae were subjected to rigid and flexible molecular docking against aforementioned enzymes followed by molecular dynamic simulation. The results of virtual screening showed that out of 39, eight compounds showed good binding energy with any one of the target enzymes as compared to reference commercial fungicides, azoxystrobin and strobilurin. Among the compounds, camptothecin, GKK1032A2 and chaetoviridin-A bind with more than one target enzymes of M. oryzae. All of the compounds except tricyclazole showed good bioactivity score. Taken together, our results suggest that all of the eight compounds have the potential to develop new fungicides, and remarkably, camptothecin, GKK1032A2 and chaetoviridin-A could act as multi-site mode of action fungicides against the blast fungus M. oryzae.
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Affiliation(s)
- Md. Arif Khan
- grid.443057.10000 0004 4683 7084Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, 1209 Bangladesh
| | - Md. Abdullah Al Mamun Khan
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - A. M. U. B. Mahfuz
- grid.443057.10000 0004 4683 7084Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, 1209 Bangladesh
| | - Jannatul Maowa Sanjana
- grid.443019.b0000 0004 0479 1356Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Tangail, 1902 Bangladesh
| | - Asif Ahsan
- grid.411511.10000 0001 2179 3896Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202 Bangladesh
| | - Dipali Rani Gupta
- grid.443108.a0000 0000 8550 5526Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706 Bangladesh
| | - M. Nazmul Hoque
- grid.443108.a0000 0000 8550 5526Department of Gynecology, Obstetrics and Reproductive Health, BSMRAU, Gazipur, 1706 Bangladesh
| | - Tofazzal Islam
- grid.443108.a0000 0000 8550 5526Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, 1706 Bangladesh
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Anticipating the Next Chess Move: Blocking SARS-CoV-2 Replication and Simultaneously Disarming Viral Escape Mechanisms. Genes (Basel) 2022; 13:genes13112147. [DOI: 10.3390/genes13112147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic initiated a race to determine the best measures to control the disease and to save as many people as possible. Efforts to implement social distancing, the use of masks, and massive vaccination programs turned out to be essential in reducing the devastating effects of the pandemic. Nevertheless, the high mutation rates of SARS-CoV-2 challenge the vaccination strategy and maintain the threat of new outbreaks due to the risk of infection surges and even lethal variations able to resist the effects of vaccines and upset the balance. Most of the new therapies tested against SARS-CoV-2 came from already available formulations developed to treat other diseases, so they were not specifically developed for SARS-CoV-2. In parallel, the knowledge produced regarding the molecular mechanisms involved in this disease was vast due to massive efforts worldwide. Taking advantage of such a vast molecular understanding of virus genomes and disease mechanisms, a targeted molecular therapy based on siRNA specifically developed to reach exclusive SARS-CoV-2 genomic sequences was tested in a non-transformed human cell model. Since coronavirus can escape from siRNA by producing siRNA inhibitors, a complex strategy to simultaneously strike both the viral infectious mechanism and the capability of evading siRNA therapy was developed. The combined administration of the chosen produced siRNA proved to be highly effective in successfully reducing viral load and keeping virus replication under control, even after many days of treatment, unlike the combinations of siRNAs lacking this anti-anti-siRNA capability. Additionally, the developed therapy did not harm the normal cells, which was demonstrated because, instead of testing the siRNA in nonhuman cells or in transformed human cells, a non-transformed human thyroid cell was specifically chosen for the experiment. The proposed siRNA combination could reduce the viral load and allow the cellular recovery, presenting a potential innovation for consideration as an additional strategy to counter or cope COVID-19.
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