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Bandyopadhyay S, Abiodun OA, Ogboo BC, Kola-Mustapha AT, Attah EI, Edemhanria L, Kumari A, Jaganathan R, Adelakun NS. Polypharmacology of some medicinal plant metabolites against SARS-CoV-2 and host targets: Molecular dynamics evaluation of NSP9 RNA binding protein. J Biomol Struct Dyn 2022; 40:11467-11483. [PMID: 34370622 DOI: 10.1080/07391102.2021.1959401] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Medicinal plants as rich sources of bioactive compounds are now being explored for drug development against COVID-19. 19 medicinal plants known to exhibit antiviral and anti-inflammatory effects were manually curated, procuring a library of 521 metabolites; this was virtually screened against NSP9, including some other viral and host targets and were evaluated for polypharmacological indications. Leads were identified via rigorous scoring thresholds and ADMET filtering. MM-GBSA calculation was deployed to select NSP9-Lead complexes and the complexes were evaluated for their stability and protein-ligand communication via MD simulation. We identified 5 phytochemical leads for NSP9, 23 for Furin, 18 for ORF3a, and 19 for IL-6. Ochnaflavone and Licoflavone B, obtained from Lonicera japonica (Japanese Honeysuckle) and Glycyrrhiza glabra (Licorice), respectively, were identified to have the highest potential polypharmacological properties for the aforementioned targets and may act on multiple pathways simultaneously to inhibit viral entry, replication, and disease progression. Additionally, MD simulation supports the robust stability of Ochnaflavone and Licoflavone B against NSP9 at the active sites via hydrophobic interactions, H-bonding, and H-bonding facilitated by water. This study promotes the initiation of further experimental analysis of natural product-based anti-COVID-19 therapeutics.
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Affiliation(s)
- Suritra Bandyopadhyay
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, India.,Homi Bhabha National Institute (HBNI), BARC Training School Complex, Mumbai, India
| | | | - Blessing Chinweotito Ogboo
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka
| | - Adeola Tawakalitu Kola-Mustapha
- Department of Pharmaceutics, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin, Nigeria.,College of Pharmacy, Alfaisal University Riyadh, Saudi Arabia
| | - Emmanuel Ifeanyi Attah
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka
| | - Lawrence Edemhanria
- Department of Chemical Sciences, Samuel Adegboyega University, Ogwa, Nigeria
| | | | - Ravindran Jaganathan
- SriSamraj Health Services Pvt. Ltd, Tindivanam, Tamilnadu, India.,Pre-clinical Department, Faculty of Medicine, Royal College of Medicine Perak, Universiti Kuala Lumpur (UniKL-RCMP), Malaysia
| | - Niyi S Adelakun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria.,Bio-Assay and Cheminformatics Unit, Molecular and Simulations, Ado-Ekiti, Ekiti State, Nigeria
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Kikiowo B, Ogunleye AJ, Iwaloye O, Ijatuyi TT, Adelakun NS, Alashe WO. Induced Fit Docking and Automated QSAR Studies Reveal the ER-α Inhibitory Activity of Cannabis sativa in Breast Cancer. Recent Pat Anticancer Drug Discov 2021; 16:273-284. [PMID: 33563181 DOI: 10.2174/1574892816666210201115359] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/04/2020] [Accepted: 12/23/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Breast Cancer (BC), a common death-causing disease and the deadliest cancer next to lung cancer, is characterized by an abnormal growth of cells in the tissues of the breast. BC chemotherapy is marked by targeting the activities of some receptors such as Estrogen Receptor alpha (ER-α). At present, one of the most commonly used and approved marketed therapeutic drug for BC is tamoxifen. Despite the short term success of tamoxifen usage, its long time treatment has been associated with significant side effects. Therefore, there is a pressing need for the development of novel anti-estrogens for the prevention and treatment of BC. OBJECTIVE In this study, we evaluate the inhibitory effect of Cannabis Sativa phyto-constituents on ER-α. METHOD Glide and Induced Fit Docking followed by ADME, Automated QSAR and Binding free energy (ΔGbind) studies were used to evaluate the anti-breast cancer and ER-α inhibitory activity of Cannabis sativa, which has been reported to be effective in inhibiting breast cancer cell proliferation. RESULTS Phyto-constituents of Cannabis sativa possess lower docking scores and good ΔGbind when compared to that of tamoxifen. ADME and AutoQSAR studies revealed that our lead compounds demonstrated the properties required to make them promising therapeutic agents. CONCLUSION The results of this study suggest that Naringenin, Dihydroresveratrol, Baicalein, Apigenin and Cannabitriol could have relatively better inhibitory activity than tamoxifen and could be a better and patent therapeutic candidate in the treatment of BC. Further research such as in vivo and/or in vitro assays could be conducted to attest the ability of these compounds.
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Affiliation(s)
- Babatomiwa Kikiowo
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State. Nigeria
| | - Adewale J Ogunleye
- Department of Micrbiology, Adekunle Ajasin University, Akungba-Akoko, Ondo State. Nigeria
| | - Opeyemi Iwaloye
- Department of Biochemistry, Federal University of Technology, Akure, Ondo State. Nigeria
| | - Taiwo T Ijatuyi
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State. Nigeria
| | - Niyi S Adelakun
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State. Nigeria
| | - Wasiu O Alashe
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State. Nigeria
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Omotuyi OI, Nash O, Safronetz D, Ojo AA, Ogunwa TH, Adelakun NS. T-705-modified ssRNA in complex with Lassa virus nucleoprotein exhibits nucleotide splaying and increased water influx into the RNA-binding pocket. Chem Biol Drug Des 2019; 93:544-555. [PMID: 30536557 DOI: 10.1111/cbdd.13451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/18/2018] [Accepted: 11/24/2018] [Indexed: 12/28/2022]
Abstract
Lassa virus infection is clinically characterized by multiorgan failure in humans. Without an FDA-approved vaccine, ribavirin is the frontline drug for the treatment but with attendant toxicities. 6-Fluoro-3-hydroxy-2-pyrazinecarboxamide (T-705) is an emerging alternative drug with proven anti-Lassa virus activity in experimental model. One of the mechanisms of action is its incorporation into nascent single-strand RNA (ssRNA) which forms complex with Lassa nucleoprotein (LASV-NP). Here, using molecular dynamics simulation, the structural and electrostatics changes associated with LASV-NP-ssRNA complex have been studied when none, one, or four of its bases has been substituted with T-705. The results demonstrated that glycosidic torsion angle χ (O4'-C1'-N1-C2) rotated from high-anti- (-110° and -60°) to the syn- conformation (+30) with increased T-705 substitution. Similarly, increased T-705 substitution resulted in increased splaying (55°-70°), loss of ssRNA-LASV-NP H-bond interaction, increased water influx into the ssRNA-binding pocket, and decreased electrostatic potentials of ssRNA pocket. Furthermore, strong positively correlated motion observed between α6 residues (aa: 128-145) and its contact ssRNA bases (5-7) is weakened in Apo biosystem and transitioned into anticorrelated motions in ssRNA-bound LASV-NP biosystem. Finally, LASV genome may become more accessible to cellular ribonuclease access with T-705 incorporation due to loss of NP interaction.
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Affiliation(s)
- Olaposi I Omotuyi
- Center for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Oyekanmi Nash
- Center for Genomics Research and Innovation, National Biotechnology Development Agency, NABDA/FMST, Abuja, Nigeria
| | - David Safronetz
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Ayodeji A Ojo
- Department of Public and Community Health, Liberty University, Lynchburg, Virginia
| | - Tomisin H Ogunwa
- Center for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria.,School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan
| | - Niyi S Adelakun
- Center for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba-Akoko, Nigeria
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David TI, Adelakun NS, Omotuyi OI, Metibemu DS, Ekun OE, Eniafe GO, Inyang OK, Adewumi B, Enejoh OA, Owolabi RT, Oribamise EI. Molecular docking analysis of phyto-constituents from Cannabis sativa with pfDHFR. Bioinformation 2018; 14:574-579. [PMID: 31223216 PMCID: PMC6563669 DOI: 10.6026/97320630014574] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 11/23/2022] Open
Abstract
Available antimalarial drugs have been associated with numerous side effects, which include skin rashes and myelo-suppression. Therefore, it is of interest to explore compounds from natural source having drug-like properties without side effect. This study focuses on the screening of compounds from Cannabis sativa against malaria Plasmodium falciparum dihydrofolate reductase for antimalarial properties using Glide (Schrodinger maestro 2018-1). The result showed that phytochemicals from Cannabis sativa binds with a higher affinity and lower free energy than the standard ligand with isovitexin and vitexin having a glide score of -11.485 and -10.601 respectively, sophoroside has a glide score of -9.711 which is lower than the cycloguanil (co-crystallized ligand) having a glide score of -6.908. This result gives new perception to the use of Cannabis sativa as antimicrobial agent.
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Affiliation(s)
- Temitope I David
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Niyi S Adelakun
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Olaposi I Omotuyi
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Damilohun S Metibemu
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria.,Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Oluwafemi E Ekun
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Gabriel O Eniafe
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Olumide K Inyang
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Bamidele Adewumi
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Ojochenemi A Enejoh
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Raymond T Owolabi
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
| | - Eunice I Oribamise
- Centre for Biocomputing and Drug Development, AdekunleAjasin University, AkungbaAkoko, Ondo State, Nigeria
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Eniafe GO, Metibemu DS, Omotuyi OI, Ogunleye AJ, Inyang OK, Adelakun NS, Adeniran YO, Adewumi B, Enejoh OA, Osunmuyiwa JO, Shodehinde SA, Oyeneyin OE. Agemone mexicana flavanones; apposite inverse agonists of the β2-adrenergic receptor in asthma treatment. Bioinformation 2018; 14:60-67. [PMID: 29618901 PMCID: PMC5879945 DOI: 10.6026/97320630014060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 11/23/2022] Open
Abstract
Asthma is an inflammatory disease of the airway that poses a major threat to human health. With increase industrialization in the developed and developing countries, the incidence of asthma is on the rise. The β2-adrenergic receptor is an important target in designing anti-asthmatic drugs. The synthetic agonists of the β2-adrenergic receptor used over the years proved effective, but with indispensable side effects, thereby limiting their therapeutic use on a long-term scale. Inverse agonists of this receptor, although initially contraindicated, had been reported to have long-term beneficial effects. Phytochemicals from Agemone mexicana were screened against the human β2-adrenergic receptor in the agonist, inverse agonist, covalent agonist, and the antagonist conformations. Molecular docking of the phyto-constituents showed that the plant constituents bind better to the inverse agonist bound conformation of the protein, and revealed two flavanones; eriodictyol and hesperitin, with lower free energy (ΔG) values and higher affinities to the inverse agonist bound receptor than the co-crystallized ligand. Eriodictyol and hesperitin bind with the glide score of -10.684 and - 9.958 kcal/mol respectively, while the standard compound ICI-118551, binds with glide score of -9.503 kcal/mol. Further interaction profiling at the protein orthosteric site and ADME/Tox screening confirmed the drug-like properties of these compounds.
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Affiliation(s)
- Gabriel O. Eniafe
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Damilohun S. Metibemu
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Olaposi I. Omotuyi
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Adewale J. Ogunleye
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Olumide K. Inyang
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Niyi S. Adelakun
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Yakubu O. Adeniran
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Bamidele Adewumi
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Ojochenemi A. Enejoh
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Joseph O. Osunmuyiwa
- Centre for Biocomputing and Drug Development, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Sidiqat A. Shodehinde
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | - Oluwatoba E. Oyeneyin
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
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