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Elekofehinti OO, Adetoyi IR, Popoola HO, Ayodeji FO, Taiwo FA, Akinjiyan MO, Koledoye OF, Iwaloye O, Adegboyega AE. Discovery of potential epidermal growth factor receptor inhibitors from black pepper for the treatment of lung cancer: an in-silico approach. In Silico Pharmacol 2024; 12:28. [PMID: 38601803 PMCID: PMC11001845 DOI: 10.1007/s40203-024-00197-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 02/02/2023] [Accepted: 02/16/2024] [Indexed: 04/12/2024] Open
Abstract
A tyrosine kinase receptor known as epidermal growth factor receptor (EGFR) is one of the main tumour markers in many cancer types and also plays a crucial role in cell proliferation, differentiation, angiogenesis, and apoptosis, which is a result of the auto-phosphorylations (kinase activity enhancement) that trigger signals involved in different cellular processes. Due to the discovery that non-small cell lung cancer (NSCLC) is a cause of this kinase activity enhancement, so far, several inhibitors have been tested against EGFR, but the side effects of these inhibitors necessitate an urgent measure to come up with an inhibitor that will be more specific to the cancer cells and not affect self-cells. This study was conducted to evaluate the efficacy of 37 compounds derived from Piper nigrum against EGFR using computer-aided drug design. Based on molecular docking, induced-fit docking, calculation of free binding energy, pharmacokinetics, QSAR prediction, and MD simulation. We propose five (5) lead compounds (clarkinol A, isodihydrofutoquinol B, Burchellin, kadsurin B, and lancifolin C) as a novel inhibitor, with clarkinol A demonstrating the highest binding affinity (-7.304 kcal/mol) with EGFR when compared with the standard drug (erlotinib). They also showed significant moderation for parameters investigated for a good pharmacokinetic profile, with a reliable R2 coefficient value predicted using QSAR models. The MD simulation of clarkinol A was found to be stable within the EGFR binding pocket throughout the 75 ns simulation run time. The findings showed that clarkinol A derived from Piper nigrum is worth further investigation and consideration as a possible EGFR inhibitor for the treatment of lung cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00197-1.
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Affiliation(s)
- Olusola Olalekan Elekofehinti
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
- Teady Bioscience Research Laboratory, C28, Plural Gardens Estate, Akure, Ondo State Nigeria
| | - Ifeoluwa Rachael Adetoyi
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
- Teady Bioscience Research Laboratory, C28, Plural Gardens Estate, Akure, Ondo State Nigeria
| | - Hannah Oluwaseun Popoola
- Phytomedicine Biochemical Pharmacology and Toxicology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
| | - Folasade Oluwatobiloba Ayodeji
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
- Teady Bioscience Research Laboratory, C28, Plural Gardens Estate, Akure, Ondo State Nigeria
| | - Foluso Adeola Taiwo
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
- Teady Bioscience Research Laboratory, C28, Plural Gardens Estate, Akure, Ondo State Nigeria
| | - Moses Orimoloye Akinjiyan
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
- Teady Bioscience Research Laboratory, C28, Plural Gardens Estate, Akure, Ondo State Nigeria
| | - Omowunmi Funmilayo Koledoye
- Phytomedicine Biochemical Pharmacology and Toxicology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
| | - Opeyemi Iwaloye
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo State Nigeria
- Teady Bioscience Research Laboratory, C28, Plural Gardens Estate, Akure, Ondo State Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Plateau State Nigeria
- Bioinformatics Unit, Jaris Computational Biology Centre, Jos, Plateau State Nigeria
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Chike-Ekwughe A, Adegboyega AE, Johnson TO, Adebayo AH, Ogunlana OO. In vitro and in silico inhibitory validation of Tapinanthus cordifolius leaf extract on alpha-glucosidase in the management of type 2 diabetes. J Biomol Struct Dyn 2024; 42:2512-2524. [PMID: 37293926 DOI: 10.1080/07391102.2023.2212791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/16/2023] [Indexed: 06/10/2023]
Abstract
The anti-diabetic properties of medicinal plants are becoming more widely recognized. To identify potential anti-diabetic agents for diabetes drug discovery, the current study used in vitro and in silico approaches to assess the alpha glucosidase inhibitory activities of Tapinanthus cordifolius (TC) leaf extracts and its bioactive components respectively. In vitro alpha glucosidase inhibitory assay was carried out on TC extract and fractions at various concentrations (50-1600 µg/mL), and the compounds with alpha glucosidase inhibitory potentials were identified using molecular docking, pharmacophore modelling, and molecular dynamics simulation. The crude extract exhibited the highest activity with an IC50 value of 248 μg/mL. Out of the 42 phytocompounds of the extract, α-Tocopherol-β-d-mannoside gave the lowest binding energy of -6.20 Kcal/mol followed by, 5-Ergosterol (-5.46 kcal/mol), Acetosyringone (-4.76 kcal/mol), and Benzaldehyde, 4-(Ethylthio)-2,5-Dimethoxy-(-4.67 kcal/mol). The selected compounds interacted with critical active site amino acid residues of alpha-glucosidase, just like the reference ligand. Molecular dynamics simulation revealed the formation of a stable complex between α-glucosidase and α-Tocopherol-β-d-mannoside, with ASP 564 sustaining two hydrogen bond connections for 99.9 and 75.0% of the simulation duration, respectively. Therefore, the selected TC compounds, especially α-Tocopherol-β-d-mannoside might be explored for future research and development as diabetic medicines.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Amarachi Chike-Ekwughe
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Science, College of Health Sciences, University of Jos, Jos, Nigeria
- Bioinformatics Unit, Jaris Computational Biology Centre, Jos, Nigeria
| | - Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Science, College of Health Sciences, University of Jos, Jos, Nigeria
- Bioinformatics Unit, Jaris Computational Biology Centre, Jos, Nigeria
| | - Abiodun Humphrey Adebayo
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
| | - Olubanke Olujoke Ogunlana
- Department of Biochemistry, College of Science and Technology, Covenant University, Ota, Ogun State, Nigeria
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Ojo OA, Adegboyega AE, Taiwo OA, Olowosoke CB, Johnson GI, Umedum NL, Onuh K, Adeduro MN, Nwobodo VO, Elekan AO, Alemika TE, Johnson TO. Lead optimization of Allium sativum L. compounds for PTP1B inhibition in diabetes treatment: in silico molecular docking and dynamics simulation. J Biomol Struct Dyn 2023:1-15. [PMID: 38109128 DOI: 10.1080/07391102.2023.2294179] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 12/14/2022] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has been identified as a promising drug target for the development of diabetes medications via an inhibition mechanism. Using a computational approach, this study investigates the binding mechanism of lead optimized natural compounds from Allium sativum against the human PTP1B. The molecular docking, induced-fit docking, and binding free energy calculations were analyzed using Schrödinger Suite 2021-2. MD simulation, and gene enrichment analysis was achieved via the Desmond module of Schrödinger to identify best compounds as inhibitors against PTP1B in diabetes management. The docking scores of the lead optimized compounds were good; 5280443_121 from apigenin had the best binding score of -9.345 kcal/mol, followed by 5280443_129 with a binding score of -9.200 kcal/mol, and 5280863_177 from kaempferol had a binding score of -8.528 kcal/mol, followed by 5280863_462 with a binding score of -8.338 kcal/mol. The top two lead optimized compounds, docked better than the standard PTP1B inhibitor (-7.155 kcal/mol), suggesting them as potent inhibitors than the standard PTP1B inhibitor. The outcomes of the induced-fit docking were consistent with the increased binding affinity used in the Glide computation of the five conformed poses between the derivatives (5280443_121, 5280443_129, 5280863_177, and 5280863_462) and the protein (PTP1B). Based on the binding fee energies (MM-GBSA), the lead optimized compounds from kaempferol exhibited more stability than those from apigenin. In the pharmacophore development, all the models exhibit good results across the different metrics. The best performing model with five of five matches on a 1.34 and 1.33 phase score was DDRRR_1, DDRRR_2, and DDDRR_1. The average BEDROC value (= 160.9) was 1, while the average EF 1% value across all models was 101. There were no substantial conformational modifications during the MD simulation process, indicating that the apigenin derivatives (5280443_121) was stable in the protein's active site in 100 ns. IGF1R, EGFR, INSR, PTPN1, SRC, JAK2, GRB2, BCAR1, and IRS1 are among the 11 potential targets found in the protein-protein interaction (PPI) of A. sativum against PTP1B that may be important in A. sativum's defense against PTP1B. Sixty-four (64) pathways were found by KEGG pathway enrichment analysis to be potentially involved in the anti-PTP1B of A. sativum. Consequently, data obtained indicates the effectiveness of the in silico studies in identifying potential lead compounds in A. sativum against PTP1B target.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Oluwafemi Adeleke Ojo
- Bowen University SDG 03 (Good Health and Wellbeing Research Group), Iwo, Nigeria
- Phytomedicine, Molecular Toxicology, and Computational Biochemistry Research Laboratory (PMTCB-RL), Department of Biochemistry, Bowen University, Iwo, Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
| | | | - Christopher Busayo Olowosoke
- Department of Biotechnology, Federal University of Technology, Ondo, Nigeria
- Department of Biotechnology, Chrisland University, Abeokuta, Nigeria
| | - Grace Inioluwa Johnson
- Jaris Computational Biology Centre, Jos, Nigeria
- College of Health Sciences, University of Jos, Jos, Nigeria
| | - Ngozi Lillian Umedum
- Department of Organic and Medicinal Chemistry, Nnamdi Azikwe University, Akwa, Anambra, Nigeria
| | - Kingsley Onuh
- Department of Biotechnology, Nigerian Defence Academy, Kaduna
| | - Mary Nneka Adeduro
- Department of Pharmaceutical Chemistry, Univervisty of Lagos, Lagos, Nigeria
| | | | - Ayodele O Elekan
- Department of Biochemistry, Adekunle Ajasin University, Ondo, Nigeria
| | | | - Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
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Johnson TO, Adegboyega AE, Johnson GI, Umedum NL, Bamidele OD, Elekan AO, Tarkaa CT, Mahe A, Abdulrahman A, Adeyemi OE, Okafor D, Yusuf AJ, Atewolara-Odule OC, Ogunmoye AO, Ishaya T. Uncovering the inhibitory potentials of Phyllanthus nivosus leaf and its bioactive compounds against Plasmodium lactate dehydrogenase for malaria therapy. J Biomol Struct Dyn 2023; 41:9787-9796. [PMID: 36411736 DOI: 10.1080/07391102.2022.2146750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/06/2022] [Indexed: 11/23/2022]
Abstract
Malaria control efforts have been hampered due to the emergence of resistant malaria parasite strains and the coinciding events of Covid-19. The quest for more effective and safe treatment alternatives is driving a slew of new studies that must be accelerated if malaria can be overcome. Due to its reported antimalarial activity, we studied the effects of extract and fractions of Phyllanthus nivosus leaf on Plasmodium lactate dehydrogenase (pLDH) activity using an in vitro assay. This was followed by an anti-plasmodial study using Plasmodium berghei-infected mice and an in silico identification of the plant's phytochemicals with possible pLDH-inhibitory activity. The activity of pLDH was significantly reduced in the presence of ethanol extract and various solvent fractions of Phyllanthus nivosus leaf, with the ethyl acetate fraction having the best inhibitory activity, which was comparable to that of the standard drug (chloroquine). The ethyl acetate fraction at 100 and 200 mg/Kg also suppressed the parasitaemia of Plasmodium berghei-infected mice by 76 and 80% respectively. Among the 53 compounds docked against pLDH, (-)-alpha-Cadinol, (+)-alpha-phellandrene, and spathulenol, all terpenes from the ethyl acetate fraction of P. nivosus leaf extract, demonstrated docking scores comparable to that of chloroquine. The three chemicals, like chloroquine, displayed important molecular interactions with the amino acid residues of the enzyme's NADH-binding site. According to the in silico ADMET study, the three terpenes have suitable drug-like abilities, pharmacokinetic features, and safety profiles. Hence, they could be considered for further development as antimalarial drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Biotechnology Research Unit, Jaris Computational Biology Center, Jos, Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Biotechnology Research Unit, Jaris Computational Biology Center, Jos, Nigeria
| | - Grace I Johnson
- Biotechnology Research Unit, Jaris Computational Biology Center, Jos, Nigeria
- College of Health Sciences, University of Jos, Jos, Nigeria
| | - Ngozi L Umedum
- Department of Pure and Industrial Chemistry, Nnamdi Azikiwe University, Awka, Anambra State, Nigeria
| | - Olasunkanmi D Bamidele
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin, Nigeria
| | - Ayodele O Elekan
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Nigeria
| | - Christopher T Tarkaa
- Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | - Asma'u Mahe
- Department of Biochemistry, Federal University, Dutse, Jigawa State, Nigeria
| | - Adamu Abdulrahman
- Department of Pharmacognosy and Drug Development, Ahmadu Bello University, Zaria, Nigeria
| | - Olugbenga E Adeyemi
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Desmond Okafor
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Amina J Yusuf
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | | | | | - Tanko Ishaya
- Department of Computer Science, University of Jos, Jos, Nigeria
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Johnson TO, Adeyemi OE, Adegboyega AE, Olomu SA, Enokela F, Ibrahim S, Gwantu B, Afolayan B, Stephen K, Eseola AO, Plass W, Adeyemi OS. Elucidation of the anti-plasmodial activity of novel imidazole and oxazole compounds through computational and in vivo experimental approaches. J Biomol Struct Dyn 2023; 41:9013-9021. [PMID: 36310100 DOI: 10.1080/07391102.2022.2139761] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Received: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
The development of resistance to conventional antimalarial therapies, along with the unfavorable impact of the COVID-19 pandemic on the global malaria fight, necessitates a greater focus on the search for more effective antimalarial drugs. Targeting a specific enzyme of the malaria parasite to alter its metabolic pathways is a reliable technique for finding antimalarial drug candidates. In this study, we used an in silico technique to test four novel imidazoles and an oxazole derivative for inhibitory potential against Plasmodium lactate dehydrogenase (pLDH), a unique glycolytic enzyme necessary for parasite survival and energy production. The promising imidazole compounds and the oxazole derivative were then tested for anti-plasmodial efficacy in Plasmodium berghei-infected mice. With a binding energy of -6.593 kcal/mol, IM-3 had the best docking score against pLDH, which is close to that of NADH (-6.758 kcal/mol) and greater than that of chloroquine (-3.917 kcal/mol). The test compounds occupied the enzyme's NADH binding site, with IM-3 forming four hydrogen bonds with Thr-101, Pro-246, His-195 and Asn-140. Infected mice treatment with IM-3, IM-4 and OX-1 exhibited significantly reduced parasitemia over a four-day treatment period when compared to the infected untreated animals. At 5, 10 and 20 mg/kg, IM-3 demonstrated the highest anti-plasmodial activity, suppressing parasitemia by 86.13, 97.71 and 94.11%, respectively. PCV levels were restored by IM-3 and IM-4, and the three selected compounds reduced the lipid peroxidation induced by P. berghei infection in mice. Thus, these compounds may be considered for further development as antimalarial medicines.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | - Segun Afolabi Olomu
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Festus Enokela
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Sherifat Ibrahim
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Bernard Gwantu
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Bukola Afolayan
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Kamo Stephen
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Abiodun Omokehinde Eseola
- Department of Chemical Sciences, Redeemer's University, Ede, Nigeria
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Winfried Plass
- Institute of Inorganic and Analytical Chemistry, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Oluyomi Stephen Adeyemi
- Landmark University SDG 3 (Good Health & Well-being Research Group), Landmark University, Nigeria
- Department of Biochemistry, Medicinal Biochemistry and Toxicology Laboratory, Landmark University, Nigeria
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Oluyori AP, Olanipekun BE, Adeyemi OS, Egharevba GO, Adegboyega AE, Oladeji OS. Molecular docking, pharmacophore modelling, MD simulation and in silico ADMET study reveals bitter cola constituents as potential inhibitors of SARS-CoV-2 main protease and RNA dependent-RNA polymerase. J Biomol Struct Dyn 2023; 41:1510-1525. [PMID: 34996336 DOI: 10.1080/07391102.2021.2024883] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 01/24/2023]
Abstract
A mini survey was employed in the search of herbs and spices which people believe could prevent them from contracting COVID-19. Phytochemicals which have been earlier implicated for the bioactivity of the afore-mentioned herbs and spices were identified through literature search. The phytochemicals were then subjected to pharmacore modelling, molecular docking and molecular dynamics simulation in order to identify phytochemicals that could serve as inhibitors of 3-Chymotryprin-like protease and RNA dependent-RNA polymerase of SARS-CoV-2. The drug-likeness and toxicity profile of the phytochemicals were afterwards predicted via ADMET studies. The mini survey showed ginger, garlic, bitter cola, as the lead-herbs which could find application in anti- COVID-19 therapy. Literature search revealed 27 phytochemicals were implicated for bioactivity of these herbs. Of these 27 phytoconstituents that were docked with 3-chymotrypsin-like protease and RNA dependent-RNA polymerase, the constituents of bitter cola had lower docking scores than other phytochemicals. MD simulation results showed that Garcinia biflavonoid I displayed less comformational changes and the better binding free energy. Also, the garcinia biflavonoids had relatively safe ADMET predictions. Hence, Garcinia biflavonoids and some other constituents of bitter cola could be further modified so as to obtain safe pharmaceutical intervention for the COVID-19 challenge.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abimbola Peter Oluyori
- Good Health and Well-Being Research Group, Landmark University SDG 3, Omu Aran, Nigeria.,Department of Physical Sciences, Landmark University, Omu Aran, Nigeria
| | | | - Oluyomi Stephen Adeyemi
- Good Health and Well-Being Research Group, Landmark University SDG 3, Omu Aran, Nigeria.,Department of Biochemistry, Landmark University, Omu Aran, Nigeria
| | - Godshelp Osas Egharevba
- Good Health and Well-Being Research Group, Landmark University SDG 3, Omu Aran, Nigeria.,Department of Physical Sciences, Landmark University, Omu Aran, Nigeria
| | | | - Oluwole Solomon Oladeji
- Good Health and Well-Being Research Group, Landmark University SDG 3, Omu Aran, Nigeria.,Department of Physical Sciences, Landmark University, Omu Aran, Nigeria
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Ugwah-Oguejiofor CJ, Chukwuka EP, Onifade OF, Agu ST, Adegboyega AE, Johnson GI, Ogunsuyi OI, Johnson TO. Computational assessment of chemicals from Morinda citrifolia as potential inhibitors of B-Raf kinase in hepatocellular carcinoma treatment. J Biomol Struct Dyn 2023; 41:13271-13286. [PMID: 36709454 DOI: 10.1080/07391102.2023.2172459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
Abstract
Hepatocellular carcinoma (HCC) is a tumour pathology that lacks specific treatment and is predominantly resistant to chemotherapy. The inhibitory activity of Morinda citrifolia, an evergreen tree commonly called Noni, against various carcinomas especially HCC is widely acclaimed. This study was to assess the phytochemical constituents of the plant for inhibitory activity against B-Raf kinase (3C4C) in order to design drugs for HCC treatment. Molecular docking, pharmacophore modelling, induced-fit docking, molecular dynamics (MD) simulations and ADMET predictions were the computational techniques employed in this study to detect potential inhibitors of B-Raf kinase from 135 compounds of Morinda citrifolia. Soranjidiol, Thiamine, Lucidin, 2-Methyl-1,3,5-Trihydroxyanthraquinone and Rubiadin were the five top-scoring compounds ranging from -8.39 to -8.22 kcal/mol, however, the standard ligand, PLX4720, scored -11.26 kcal/mol. The five compounds, like PLX4720 demonstrated hydrogen bond interactions with active site amino acid residues such as GLN 530, CYS 532 and ASP 594. The main energy contributor to the interactions between the compounds and B-Raf kinase were pi-stacking, hydrogen bond, van der Waals and covalent energy. Better docking scores obtained in the induced-fit docking further validates the inhibitory potential of the Soranjidiol against the flexible protein. In MD simulations, Soranjidiol revealed good stability in the active site of the protein since significant conformational changes were not evident. These five compounds, unlike the standard compound, demonstrated adequate druglike properties and good safety profiles. Therefore, further studies should be undertaken so as to develop them into drugs against HCC.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Chinenye Jane Ugwah-Oguejiofor
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University Sokoto, Sokoto State, Nigeria
| | - Emeka Patrick Chukwuka
- Maternity and Children Hospital, Al Mubarraz, Al Ahsa, KSA
- National Postgraduate Medical College of Nigeria, Ijanikin, Lagos, Nigeria
| | - Olayinka Fisayo Onifade
- Department of Chemical and Food Sciences, Bells University of Technology Ota, Ogun State, Nigeria
| | - Solomon Tsekohol Agu
- Dept of Veterinary Physiology and Biochemistry, Federal University of Agriculture, Makurdi, Benue State, Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Bioinformatics unit, Jaris Computational Biology Centre, Jos, Nigeria
| | - Grace Inioluwa Johnson
- Faculty of Medical Sciences, College of Health Sciences, University of Jos, Jos, Plateau State, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
| | - Olusegun Ifeoluwa Ogunsuyi
- Department of Biological Sciences, College of Basic and Applied Sciences, Mountain Top University, Pakuro, Ogun State, Nigeria
| | - Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
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Johnson TO, Akinsanmi AO, Ejembi SA, Adeyemi OE, Oche JR, Johnson GI, Adegboyega AE. Modern drug discovery for inflammatory bowel disease: The role of computational methods. World J Gastroenterol 2023; 29:310-331. [PMID: 36687123 PMCID: PMC9846937 DOI: 10.3748/wjg.v29.i2.310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Inflammatory bowel diseases (IBDs) comprising ulcerative colitis, Crohn’s disease and microscopic colitis are characterized by chronic inflammation of the gastrointestinal tract. IBD has spread around the world and is becoming more prevalent at an alarming rate in developing countries whose societies have become more westernized. Cell therapy, intestinal microecology, apheresis therapy, exosome therapy and small molecules are emerging therapeutic options for IBD. Currently, it is thought that low-molecular-mass substances with good oral bio-availability and the ability to permeate the cell membrane to regulate the action of elements of the inflammatory signaling pathway are effective therapeutic options for the treatment of IBD. Several small molecule inhibitors are being developed as a promising alternative for IBD therapy. The use of highly efficient and time-saving techniques, such as computational methods, is still a viable option for the development of these small molecule drugs. The computer-aided (in silico) discovery approach is one drug development technique that has mostly proven efficacy. Computational approaches when combined with traditional drug development methodology dramatically boost the likelihood of drug discovery in a sustainable and cost-effective manner. This review focuses on the modern drug discovery approaches for the design of novel IBD drugs with an emphasis on the role of computational methods. Some computational approaches to IBD genomic studies, target identification, and virtual screening for the discovery of new drugs and in the repurposing of existing drugs are discussed.
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Affiliation(s)
| | | | | | | | - Jane-Rose Oche
- Department of Biochemistry, University of Jos, Jos 930222, Plateau, Nigeria
| | - Grace Inioluwa Johnson
- Faculty of Clinical Sciences, College of Health Sciences, University of Jos, Jos 930222, Plateau, Nigeria
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Okoh OS, Yakubu A, Adegboyega AE, Uti DE, Obeten UN, Agada SA, Oluwaloni F, Johnson GI, Mela LP, Asomadu RO, Iwaloye O, Johnson TO, Orji OU. Identification of some bioactive compounds from Trignonella foenumgraecum as possible inhibitors of PPARϒ for diabetes treatment through molecular docking studies, pharmacophore modelling and ADMET profiling: An in-silico study. PLoS One 2023; 18:e0284210. [PMID: 37200359 DOI: 10.1371/journal.pone.0284210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/24/2023] [Indexed: 05/20/2023] Open
Abstract
Oral antidiabetic agents including the peroxisome proliferator-activated receptor gamma (PPARγ) agonists are available for the clinical management of diabetes mellitus (DM) but most are characterized by many adverse effects. In this study, we explore the antidiabetic properties of phytoconstituents from Trigonellafeonumgraecum (Fabaceae) as potential agonist of PPARγ; using in silico molecular docking, molecular mechanics generalized surface area (MM/GBSA)free binding energy prediction, Pharmacophore modeling experiment, and Pharmacokinetic/ toxicity analysis. One hundred and forty (140) compounds derived from Trigonellafeonumgraecum were screened by molecular docking against protein target PDB 3VI8. Results obtained from binding affinity (BA) and that of binding free energy (BFE) revealed five 5 compounds; arachidonic acid (CID_10467, BA -10.029, BFE -58.9), isoquercetin (CID_5280804, BA -9.507kcal/mol, BFE -56.33), rutin (CID_5280805, BA -9.463kcal/mol, BFE -56.33), quercetin (CID_10121947, BA -11.945kcal/mol, BFE -45.89) and (2S)-2-[[4-methoxy-3-[(pyrene-1-carbonylamino)methyl]phenyl]methyl]butanoic acid (CID_25112371, BA -10.679kcal/mol, BFE -45.73); and were superior to the standard; Rosiglitazone with a docking score of -7.672. Hydrogen bonding was notable in the protein-ligand complex interaction, with hydrophobic bond, polar bond and pipi stacking also observed. Their Pharmacokinetic/ toxicity profile showed varying druggable characteristics, but; arachidonic acid had the most favorable characteristics. These compounds are potential agonists of PPARγ and are considered as antidiabetic agents after successful experimental validation.
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Affiliation(s)
| | | | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Science, University of Jos, Jos, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
| | - Daniel Ejim Uti
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, Federal University of Health Sciences, Otukpo, Benue State, Nigeria
| | - Uket Nta Obeten
- Department of Chemistry/Biochemistry and Molecular Biology, Alex Ekwueme Federal University, Ndufu-Alike Ikwo, Abakaliki, Ebonyi State, Nigeria
| | - Samuel Ali Agada
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, Federal University of Health Sciences, Otukpo, Benue State, Nigeria
| | - Folusho Oluwaloni
- Department of Biotechnology, Federal Institute of Industrial Research, Oshodi, Lagos, Nigeria
| | - Grace Inioluwa Johnson
- Jaris Computational Biology Centre, Jos, Nigeria
- Faculty of Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Leonard Paul Mela
- Department of Clinical Pharmacology and Therapeutics, College of Medical Sciences, University of Maiduguri, Maiduguri, Nigeria
| | | | - Opeyemi Iwaloye
- Jaris Computational Biology Centre, Jos, Nigeria
- Bioinformatics and molecular biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Ondo, Nigeria
| | - Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Science, University of Jos, Jos, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
| | - Obasi Uche Orji
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Ebonyi State, Nigeria
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10
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Johnson TO, Adegboyega AE, Ojo OA, Yusuf AJ, Iwaloye O, Ugwah-Oguejiofor CJ, Asomadu RO, Chukwuma IF, Ejembi SA, Ugwuja EI, Alotaibi SS, Albogami SM, Batiha GES, Rajab BS, Conte-Junior CA. A Computational Approach to Elucidate the Interactions of Chemicals From Artemisia annua Targeted Toward SARS-CoV-2 Main Protease Inhibition for COVID-19 Treatment. Front Med (Lausanne) 2022; 9:907583. [PMID: 35783612 PMCID: PMC9240657 DOI: 10.3389/fmed.2022.907583] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/12/2022] [Indexed: 12/23/2022] Open
Abstract
The inhibitory potential of Artemisia annua, a well-known antimalarial herb, against several viruses, including the coronavirus, is increasingly gaining recognition. The plant extract has shown significant activity against both the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the novel SARS-CoV-2 that is currently ravaging the world. It is therefore necessary to evaluate individual chemicals of the plant for inhibitory potential against SARS-CoV-2 for the purpose of designing drugs for the treatment of COVID-19. In this study, we employed computational techniques comprising molecular docking, binding free energy calculations, pharmacophore modeling, induced-fit docking, molecular dynamics simulation, and ADMET predictions to identify potential inhibitors of the SARS-CoV-2 main protease (Mpro) from 168 bioactive compounds of Artemisia annua. Rhamnocitrin, isokaempferide, kaempferol, quercimeritrin, apigenin, penduletin, isoquercitrin, astragalin, luteolin-7-glucoside, and isorhamnetin were ranked the highest, with docking scores ranging from −7.84 to −7.15 kcal/mol compared with the −6.59 kcal/mol demonstrated by the standard ligand. Rhamnocitrin, Isokaempferide, and kaempferol, like the standard ligand, interacted with important active site amino acid residues like HIS 41, CYS 145, ASN 142, and GLU 166, among others. Rhamnocitrin demonstrated good stability in the active site of the protein as there were no significant conformational changes during the simulation process. These compounds also possess acceptable druglike properties and a good safety profile. Hence, they could be considered for experimental studies and further development of drugs against COVID-19.
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Affiliation(s)
- Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
- *Correspondence: Titilayo Omolara Johnson
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
- Jaris Computational Biology Centre, Jos, Nigeria
| | - Oluwafemi Adeleke Ojo
- Phytomedicine, Molecular Toxicology, and Computational Biochemistry Research Group, Department of Biochemistry, Bowen University, Iwo, Nigeria
| | - Amina Jega Yusuf
- Department of Pharmaceutical and Medicinal Chemistry, Faculty of Pharmaceutical Sciences Usmanu Danfodiyo University, Sokoto, Nigeria
| | - Opeyemi Iwaloye
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, Akure, Nigeria
| | - Chinenye Jane Ugwah-Oguejiofor
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, Sokoto, Nigeria
| | | | - Ifeoma Felicia Chukwuma
- Department of Biochemistry, Faculty of Biological Sciences, University of Nigeria, Nsukka, Nigeria
| | - Stephen Adakole Ejembi
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria
| | - Emmanuel Ike Ugwuja
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Sarah M. Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Bodour S. Rajab
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Carlos Adam Conte-Junior
- Technological Development Support Laboratory (LADETEC), Center for Food Analysis (NAL), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
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11
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Aja PM, Awoke JN, Agu PC, Adegboyega AE, Ezeh EM, Igwenyi IO, Orji OU, Ani OG, Ale BA, Ibiam UA. Hesperidin abrogates bisphenol A endocrine disruption through binding with fibroblast growth factor 21 (FGF-21), α-amylase and α-glucosidase: an in silico molecular study. J Genet Eng Biotechnol 2022; 20:84. [PMID: 35648239 PMCID: PMC9160168 DOI: 10.1186/s43141-022-00370-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/03/2021] [Accepted: 05/20/2022] [Indexed: 12/03/2022]
Abstract
Background Fibroblast growth factor 21 (FGF-21), alpha-amylase, and alpha-glucosidase are key proteins implicated in metabolic dysregulations. Bisphenol A (BPA) is an environmental toxicant known to cause endocrine dysregulations. Hesperidin from citrus is an emerging flavonoid for metabolic diseases management. Through computational approach, we investigated the potentials of hesperidin in abrogating BPA interference in metabolism. The 3D crystal structure of the proteins (FGF-21, α-amylase, and α-glucosidase) and the ligands (BPA and hesperidin) were retrieved from the PDB and PubChem database respectively. Using Autodock plugin Pyrx, molecular docking of the ligands and individual proteins were performed to ascertain their binding affinities and their potentials to compete for the same binding site. Validation of the docking study was considered as the ability of the ligands to bind at the same site of each proteins. The docking poses were visualized using UCSF Chimera and Discovery Studio 2020, respectively to reveal each of the protein-ligands interactions within the binding pockets. Using SwissAdme and AdmeSar servers, we further investigated hesperidin’s ADMET profile. Hesperidin used was purchased commercially. Results Hesperidin and BPA competitively bound to the same site on each protein. Interestingly, hesperidin had greater binding affinities (Kcal/mol) − 5.80, − 9.60, and − 9.60 than BPA (Kcal/mol) − 4.40, − 7.20, − 7.10 for FGF-21, α-amylase, and α-glucosidase respectively. Visualizations of the binding poses showed that hesperidin interacted with stronger bonds than BPA within the proteins’ pockets. Although hesperidin violated Lipinski rule of five, this however can be optimized through structural modifications. Conclusions Hesperidin may be an emerging natural product with promising therapeutic potentials against metabolic and endocrine derangement.
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Affiliation(s)
- P M Aja
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - J N Awoke
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria. .,Interdisciplinary Biomedical Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK.
| | - P C Agu
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - A E Adegboyega
- Department of Biochemistry, Faculty of Medical Sciences, University of Jos/Jaris Computational Biology Centre, Jos, Nigeria
| | - E M Ezeh
- Department of Chemical Engineering, Nnamdi Azikiwe University, Awka, Nigeria
| | - I O Igwenyi
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - O U Orji
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - O G Ani
- Nutrition and Exercise Physiology, University of Missouri, Columbia, United States of America
| | - B A Ale
- Department of Biochemistry, University of Nigeria Nsukka, Nsukka, Nigeria
| | - U A Ibiam
- Department of Biochemistry, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
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12
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Abodunrin OP, Onifade OF, Adegboyega AE. Therapeutic capability of five active compounds in typical African medicinal plants against main proteases of SARS-CoV-2 by computational approach. Inform Med Unlocked 2022; 31:100964. [PMID: 35647264 PMCID: PMC9125996 DOI: 10.1016/j.imu.2022.100964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 01/28/2022] [Revised: 05/05/2022] [Accepted: 05/11/2022] [Indexed: 12/03/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a pandemic cause of Corona Virus Disease (COVID-19), that has claimed numerous human lives across the globe. Main protease being the active protein of SARS-CoV-2 requires urgent mitigating effect against the spread of the virus. The therapeutic roles of the active compounds present in ten typical African medicinal plants were investigated in this study. Five active compounds Curcuma longa (Curcumin and Bisdethoxy curcumin), Garcinia kola (kolaviron), Zingiber officinale (Gingerol) and Vernonia amygdalina (Artemisinin) were selected and docked against Main protease through receptor grid generation, protein ligand docking, receptor ligand complex pharmacophore and binding free energy. The results obtained revealed Curcumin had the highest binding score of -8.628 kcal/mol while artermisinin presented the least with -4.123 kcal/mol. The outcome of the pharmacokinetic prediction in this study revealed high transport capacity across the gastrointestinal tract and high blood brain barrier permeability for curcumin, bisdemethoxy curcumin, gingerol and artemisinin. The exemption is gingerol with low LD50 value (250 mg/kg), the LD50 of all active compounds ranged from 2000 to 4228 mg/kg. Adsorption, distribution, metabolism, excretion and toxicity (ADMET) properties exhibited by all compounds portrayed them as non-hepatotoxic, non-cytotoxic, non-mutagenic and non-carcinogenic. The active compounds exhibited drug-likeness features against Main protease of Covid-19.
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Affiliation(s)
- Oluwasayo Peter Abodunrin
- Radiation and Health Physics, Physical Sciences Department, Bells University of Technology, Ota, Nigeria
| | - Olayinka Fisayo Onifade
- Phytomedicine, Biochemistry and Bioinformatics, Chemical Sciences Department, Bells University of Technology, Ota, Nigeria
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13
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Olawale F, Iwaloye O, Elekofehinti OO, Kikiowo B, Oluwarotimi EA, Ilesanmi KM, Akinropo ID, Akinlosotu OB, Adegboyega AE, Ologuntere TE. A Multi-target Approach for the Discovery of Anti Breast Cancer Agents from Plants Secondary Metabolites. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180818666210521111535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Cancer is a multifactorial disease with multiple complications involving multiple
proteins. Breast cancer is the most prevalent form of cancer among women. The pathophysiology
of this cancer form has implicated several genetic alterations in its hallmark. Two of the most studied
breast cancer molecular pathways are the cell cycle protein kinases and P13/AKT signaling pathway.
Objective:
Thus, this study identified novel inhibitors through computational screening of a library of
medicinal plant compounds against cyclin-dependent kinase 2 (CDK2), phosphoinositide-3-kinase A
(PI3Ka) and protein kinase B (AKT1).
Methods:
Rigid protein docking via Glide algorithm was applied to identify the hits from 3000 plant
compounds screened against three drug targets involved in breast cancer pathogenesis. A more accurate
and reliable ligand-protein docking called induced fit docking was adopted to extensively improve the
scoring function by ranking favourable binding as top-scoring one.
Results:
Nine hit compounds were identified and found to interact with essential residues at the proteins’
binding sites. Subsequently, the hits pharmacokinetic parameters and toxicity were predicted to
determine their potential as drug candidates and minimise toxic effects. The hit compounds were found
to be non-carcinogenic, and five of them showed a desirable drug-like property. The built predictive
QSAR models with an R2 value of 0.7684, 0.7973 and 0.5649 for CDK2, AKT1 and PI3Ka, respectively,
were adopted to determine the hits inhibitory activity (pIC50) against the screened proteins; and
the predictions revealed compounds with significant activity. Prediction of the hit compounds druglikeness,
pharmacokinetic and toxicity properties by online web servers showed that the compounds are
non-carcinogenic and showed moderate indices for ADMET parameters. The constructed QSAR models
with reliable R2 coefficient value were used to predict the pIC50 of the selected compounds. The
results revealed potent compounds with significant activity.
Concluson:
This study thus provides insight into multi-target protein compounds which could be
explored as chemotherapeutic alternatives in breast cancer treatment.
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Affiliation(s)
- Femi Olawale
- Nano-Gene and Drug Delivery Group, Department of Biochemistry, School of life science, University of Kwazulu Natal, 4000, Durban, South Africa
| | - Opeyemi Iwaloye
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal, University of Technology Akure, Ondo State, Nigeria
| | - Olusola Olalekan Elekofehinti
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal, University of Technology Akure, Ondo State, Nigeria
| | - Babatomiwa Kikiowo
- Department of Biochemistry, Adekunle Ajasin University, Akungba Akoko, Ondo State, Nigeria
| | | | | | | | - Oluwaseun Benedicta Akinlosotu
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal, University of Technology Akure, Ondo State, Nigeria
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14
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Johnson TO, Adegboyega AE, Iwaloye O, Eseola OA, Plass W, Afolabi B, Rotimi D, Ahmed EI, Albrakati A, Batiha GE, Adeyemi OS. Computational study of the therapeutic potentials of a new series of imidazole derivatives against SARS-CoV-2. J Pharmacol Sci 2021; 147:62-71. [PMID: 34294374 PMCID: PMC8141268 DOI: 10.1016/j.jphs.2021.05.004] [Citation(s) in RCA: 7] [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: 01/04/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023] Open
Abstract
Owing to the urgent need for therapeutic interventions against the SARS-coronavirus 2 (SARS-CoV-2) pandemic, we employed an in silico approach to evaluate the SARS-CoV-2 inhibitory potential of newly synthesized imidazoles. The inhibitory potentials of the compounds against SARS-CoV-2 drug targets - main protease (Mpro), spike protein (Spro) and RNA-dependent RNA polymerase (RdRp) were investigated through molecular docking analysis. The binding free energy of the protein-ligand complexes were estimated, pharmacophore models were generated and the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of the compounds were determined. The compounds displayed various levels of binding affinities for the SARS-CoV-2 drug targets. Bisimidazole C2 scored highest against all the targets, with its aromatic rings including the two imidazole groups contributing to the binding. Among the phenyl-substituted 1H-imidazoles, C9 scored highest against all targets. C11 scored highest against Spro and C12 against Mpro and RdRp among the thiophene-imidazoles. The compounds interacted with HIS 41 - CYS 145 and GLU 288 – ASP 289 – GLU 290 of Mpro, ASN 501 of Spro receptor binding motif and some active site amino acids of RdRp. These novel imidazole compounds could be further developed as drug candidates against SARS-CoV-2 following lead optimization and experimental studies.
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Affiliation(s)
- Titilayo O Johnson
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Jos, Jos, Nigeria.
| | | | - Opeyemi Iwaloye
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, Akure
| | - Omokehinde Abiodun Eseola
- Department of Chemical Sciences, Redeemer's University, Ede, Nigeria; Friedrich-Schiller-Universität Jena, Institute of Inorganic and Analytical Chemistry, Humboldtstraße 8, 07743, Jena, Germany
| | - Winfried Plass
- Friedrich-Schiller-Universität Jena, Institute of Inorganic and Analytical Chemistry, Humboldtstraße 8, 07743, Jena, Germany
| | - Boluwatife Afolabi
- Department of Biochemistry, Medicinal Biochemistry, Nanomedicine & Toxicology Laboratory, Landmark University, PMB 1001, Omu-Aran -, 251101, Nigeria
| | - Damilare Rotimi
- Department of Biochemistry, Medicinal Biochemistry, Nanomedicine & Toxicology Laboratory, Landmark University, PMB 1001, Omu-Aran -, 251101, Nigeria
| | - Eman I Ahmed
- Department of Pharmacology and Therapeutics, College of Medicine, Jouf University, Sakaka, 72346, Saudi Arabia; Department of Pharmacology, Faculty of Medicine, Fayoum University, Fayoum, 63511, Egypt
| | - Ashraf Albrakati
- Department of Human Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia.
| | - Gaber E Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Oluyomi Stephen Adeyemi
- Department of Biochemistry, Medicinal Biochemistry, Nanomedicine & Toxicology Laboratory, Landmark University, PMB 1001, Omu-Aran -, 251101, Nigeria.
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15
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Ojo OA, Ojo AB, Okolie C, Nwakama MAC, Iyobhebhe M, Evbuomwan IO, Nwonuma CO, Maimako RF, Adegboyega AE, Taiwo OA, Alsharif KF, Batiha GES. Deciphering the Interactions of Bioactive Compounds in Selected Traditional Medicinal Plants against Alzheimer's Diseases via Pharmacophore Modeling, Auto-QSAR, and Molecular Docking Approaches. Molecules 2021; 26:molecules26071996. [PMID: 33915968 PMCID: PMC8037217 DOI: 10.3390/molecules26071996] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases, for example Alzheimer’s, are perceived as driven by hereditary, cellular, and multifaceted biochemical actions. Numerous plant products, for example flavonoids, are documented in studies for having the ability to pass the blood-brain barrier and moderate the development of such illnesses. Computer-aided drug design (CADD) has achieved importance in the drug discovery world; innovative developments in the aspects of structure identification and characterization, bio-computational science, and molecular biology have added to the preparation of new medications towards these ailments. In this study we evaluated nine flavonoid compounds identified from three medicinal plants, namely T. diversifolia, B. sapida, and I. gabonensis for their inhibitory role on acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and monoamine oxidase (MAO) activity, using pharmacophore modeling, auto-QSAR prediction, and molecular studies, in comparison with standard drugs. The results indicated that the pharmacophore models produced from structures of AChE, BChE and MAO could identify the active compounds, with a recuperation rate of the actives found near 100% in the complete ranked decoy database. Moreso, the robustness of the virtual screening method was accessed by well-established methods including enrichment factor (EF), receiver operating characteristic curve (ROC), Boltzmann-enhanced discrimination of receiver operating characteristic (BEDROC), and area under accumulation curve (AUAC). Most notably, the compounds’ pIC50 values were predicted by a machine learning-based model generated by the AutoQSAR algorithm. The generated model was validated to affirm its predictive model. The best models achieved for AChE, BChE and MAO were models kpls_radial_17 (R2 = 0.86 and Q2 = 0.73), pls_38 (R2 = 0.77 and Q2 = 0.72), kpls_desc_44 (R2 = 0.81 and Q2 = 0.81) and these externally validated models were utilized to predict the bioactivities of the lead compounds. The binding affinity results of the ligands against the three selected targets revealed that luteolin displayed the highest affinity score of −9.60 kcal/mol, closely followed by apigenin and ellagic acid with docking scores of −9.60 and −9.53 kcal/mol, respectively. The least binding affinity was attained by gallic acid (−6.30 kcal/mol). The docking scores of our standards were −10.40 and −7.93 kcal/mol for donepezil and galanthamine, respectively. The toxicity prediction revealed that none of the flavonoids presented toxicity and they all had good absorption parameters for the analyzed targets. Hence, these compounds can be considered as likely leads for drug improvement against the same.
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Affiliation(s)
- Oluwafemi Adeleke Ojo
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
- Correspondence: ; Tel.: +234-703-782-4647
| | - Adebola Busola Ojo
- Department of Biochemistry, Faculty of Sciences, Ekiti State University, Ado-Ekiti PMB 5363, Nigeria;
| | - Charles Okolie
- Department of Microbiology, Landmark University, Omu-Aran PMB 1001, Nigeria; (C.O.); (I.O.E.)
| | - Mary-Ann Chinyere Nwakama
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | - Matthew Iyobhebhe
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | | | - Charles Obiora Nwonuma
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | - Rotdelmwa Filibus Maimako
- Medicinal Biochemistry and Biochemical Toxicology Group, Department of Biochemistry, Landmark University, Omu-Aran PMB 1001, Nigeria; (M.-A.C.N.); (M.I.); (C.O.N.); (R.F.M.)
| | | | | | - Khalaf F. Alsharif
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira 22511, Egypt;
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16
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Duru CE, Duru IA, Adegboyega AE. In silico identification of compounds from Nigella sativa seed oil as potential inhibitors of SARS-CoV-2 targets. Bull Natl Res Cent 2021; 45:57. [PMID: 33727782 PMCID: PMC7952832 DOI: 10.1186/s42269-021-00517-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The growing number of cases, severity and fatality of the COVID-19 pandemic, coupled with the fact that no cure has been found has made infected individuals especially in Africa, to resort to the consumption of different natural products to alleviate their condition. One of such plant materials that have been consumed to remedy the severity of this viral infection is the oil of Nigella sativa seed commonly called black seed oil. In this study, we extracted and characterized the oil from this seed using gas chromatography coupled to a mass selective detector to identify the component phytochemicals. Site-directed multiligand docking of the identified compounds was performed on SARS-CoV-2 molecular targets- Replicase polyprotein 1a, RNA binding protein of NSP9, ADP ribose phosphatase of NSP3, 3-chymotrypsin-like protease 3CLpro, and RNA-dependent RNA polymerase RDRP, and ACE2-angiotensin-converting enzyme from the Homo sapiens. RESULTS The binding affinity of caryophyllene oxide was the highest on 3CLpro (- 6.0 kcal/mol), NSP3 (- 6.3 kcal/mol), NSP9 (- 6.3 kcal/mol), and RDRP (- 6.9 kcal/mol) targets, while α-bergamotene gave the best binding affinity on RPIA (5.7 kcal/mol) target. The binding affinity of β-bisabolene on the ACE2 target (- 8.0 kcal/mol) was almost the same as Remdesivir (- 8.1 kcal/mol). The ADMET properties of these three phytochemicals showed that they are good drug leads for these SARS-CoV-2 receptors. CONCLUSION The findings from this study strongly indicate that the reported recovery from COVID-19 infection claimed by patients who consumed black seed oil could be linked to the presence of caryophyllene oxide, α-bergamotene, and β-bisabolene in this natural product.
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Affiliation(s)
- Chidi Edbert Duru
- Surface Chemistry and Environmental Technology (SCENT) Research Unit, Department of Chemistry, Imo State University, Owerri, Imo State Nigeria
| | - Ijeoma Akunna Duru
- Department of Chemistry, Federal University of Technology, Owerri, Imo State Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Medical Sciences, University of Jos, Jos, Plateau State Nigeria
- Africa Center of Excellence in Phytomedicine Research and Development, University of Jos, Jos, Plateau State Nigeria
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Johnson TO, Abolaji AO, Omale S, Longdet IY, Kutshik RJ, Oyetayo BO, Adegboyega AE, Sagay A. Benzo[a]pyrene and Benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide induced locomotor and reproductive senescence and altered biochemical parameters of oxidative damage in Canton-S Drosophila melanogaster. Toxicol Rep 2021; 8:571-580. [PMID: 33777703 PMCID: PMC7985712 DOI: 10.1016/j.toxrep.2021.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 11/24/2020] [Revised: 01/25/2021] [Accepted: 03/06/2021] [Indexed: 01/20/2023] Open
Abstract
Benzo[a]pyrene (B[a]P) is a polycyclic aromatic hydrocarbon (PAH) commonly found in cigarette smoke, automobile exhaust fumes, grilled meat, and smoked food among others. Exposure to B[a]P is associated with a range of toxic effects including developmental, neurological, oxidative, inflammatory, mutagenic, carcinogenic and mortal. Efficient and more affordable experimental models like Drosophila melanogaster could provide more insight into the mechanism of PAH toxicity and help develop new strategies for prevention, diagnosis and treatment of PAH-related conditions. In this study, we examined the induction of some biochemical changes along with mortality and functional senescence by B[a]P and its metabolite, benzo[a]pyrene- 7,8-dihydrodiol-910-epoxide (BPDE) in the Canton-S strain of Drosophila melanogaster, with the aim to establish an alternative assay medium for B[a]P toxicity in flies. Flies were exposed to 2-200 μM of B[a]P and 1-10 μM of BPDE through diet for a seven-day survival assay followed by a four-day treatment to determine the effects of the compounds on negative geotaxis, fecundity and some biochemical parameters of oxidative damage. BPDE significantly reduced the survival rate of flies along the 7 days of exposure whereas B[a]P did not cause any significant change in the survival rate of flies. B[a]P and BPDE significantly reduced the climbing ability of flies after 4 days of exposure. Rate of emergence of flies significantly reduced at 10-200 μM of B[a]P and 5-10 μM of BPDE. Both compounds caused various levels of alterations in the values of reduced glutathione (GSH), total thiol (T-SH), glutathione-S-transferase (GST), catalase (CAT), hydrogen peroxide (H2O2), nitric oxide (NO) and acetylcholinesterase (AChE) of the flies. The compounds also exhibited high binding affinities and molecular interactions with the active site amino acid residues of Drosophila GST and the inhibitor binding site of Drosophila AChE in an in silico molecular docking analysis, with BPDE forming stable hydrogen bonds with AChE. Hence, the Canton-S strain of Drosophila melanogaster could offer a simple and affordable assay medium to study B[a]P toxicity.
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Affiliation(s)
- Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Amos Olalekan Abolaji
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Nigeria
| | - Simeon Omale
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, University of Jos, Jos, Nigeria
- Africa Center of Excellence in Phytomedicine Research and Development, University of Jos, Jos, Nigeria
| | - Ishaya Yohanna Longdet
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Richard Joseph Kutshik
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Bolaji Oyenike Oyetayo
- Department of Biochemistry, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, University of Jos, Jos, Nigeria
| | - Atiene Sagay
- Department of Obstetrics and Gynecology, College of Health Sciences, University of Jos, Jos, Nigeria
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Ojo OA, Adegboyega AE, Johnson GI, Umedum NL, Onuh K, Adeduro MN, Nwobodo VO, Elekan AO, Alemika TE, Johnson TO. Deciphering the interactions of compounds from Allium sativum targeted towards identification of novel PTP 1B inhibitors in diabetes treatment: A computational approach. Informatics in Medicine Unlocked 2021. [DOI: 10.1016/j.imu.2021.100719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Johnson TO, Odoh KD, Nwonuma CO, Akinsanmi AO, Adegboyega AE. Biochemical evaluation and molecular docking assessment of the anti-inflammatory potential of Phyllanthus nivosus leaf against ulcerative colitis. Heliyon 2020; 6:e03893. [PMID: 32426537 PMCID: PMC7226661 DOI: 10.1016/j.heliyon.2020.e03893] [Citation(s) in RCA: 9] [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: 09/24/2019] [Revised: 11/25/2019] [Accepted: 04/28/2020] [Indexed: 02/07/2023] Open
Abstract
Ulcerative colitis (UC) is an inflammation of the colon that can progress to colorectal cancer if left untreated. No medication completely cures UC and natural products are sources of alternative approaches. This study aimed to determine the anti-inflammatory potential of Phyllanthus nivosus leaf extract and fractions in a rat model of ulcerative colitis and to identify the active ingredients. UC was induced in rats by intra-rectal infusion of 1ml of 4% acetic acid (AA) in normal saline. AA exposed groups of rats were treated with 100 mg/kg bodyweight of methanol extract, hexane, ethyl-acetate and butanol fractions orally for four days. Another group received the standard drug - Dexamethasone and control rats were given distilled water only. Some biochemical changes were evaluated and the active ingredients were identified using Gas Chromatography-Mass Spectrometry (GC-MS) followed by molecular docking against interleukin-1-beta converting enzyme (Caspase-1), beta-2 adrenergic receptor (ADRB2), cyclooxygenase-2 (COX-2) and tumour necrosis factor-alpha (TNF-α). Exposure of rat colon to acetic acid significantly altered (p < 0.05) serum levels of tumour necrosis factor-alpha (TNF-α), interleukin - 6 (IL-6), nitric oxide (NO), lipid peroxidation product (malondialdehyde or MDA), reduced glutathione (GSH); and activities of superoxide dismutase (SOD) and catalase (CAT). These alterations were however restored in the rats treated with P. nivosus leaf with the ethyl-acetate fraction displaying the highest ameliorative activity. GC-MS analysis of the ethyl acetate fraction revealed the presence of 40 compounds which when subjected to molecular docking demonstrated varying degrees of binding affinities for the protein targets. Ethyl iso-allocholate demonstrated the highest binding affinity for caspase-1, cholest-22-ene-21-ol, 3,5-dehydro-6- methoxy-, pivalate for ADRB2 and TNF-α; and alpha-cadinol for COX-2. The anti-inflammatory potential of Phyllanthus nivosus leaf as a natural remedy and as a source of new drugs against ulcerative colitis is validated.
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Affiliation(s)
- Titilayo Omolara Johnson
- Department of Biochemistry, Faculty of Medical Sciences, University of Jos, Jos, Nigeria
- Department of Biochemistry, College of Pure and Applied Sciences, Landmark University, Omu-Aran, Nigeria
| | - Kenneth Daniel Odoh
- Department of Biochemistry, Faculty of Medical Sciences, University of Jos, Jos, Nigeria
| | - Charles Obiora Nwonuma
- Department of Biochemistry, College of Pure and Applied Sciences, Landmark University, Omu-Aran, Nigeria
| | - Augustina Oduje Akinsanmi
- Department of Biochemistry, Faculty of Medical Sciences, University of Jos, Jos, Nigeria
- Africa Center of Excellence in Phytomedicine Research and Development, University of Jos, Jos, Nigeria
| | - Abayomi Emmanuel Adegboyega
- Department of Biochemistry, Faculty of Medical Sciences, University of Jos, Jos, Nigeria
- Africa Center of Excellence in Phytomedicine Research and Development, University of Jos, Jos, Nigeria
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