Ogunyemi Michael - Academia.edu (original) (raw)
Papers by Ogunyemi Michael
Journal of Applied Pharmaceutical Science, 2019
Journal of Biomolecular Structure and Dynamics, 2020
Computers in Biology and Medicine
An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissi... more An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissimum was screened against the active region of 3-Chymotrypsin-Like Protease (3CLpro) of SARS-CoV-2 in silico. Based on docking scores and reference inhibitors, a hit- list of 21 phytocompounds, with binding energies ranging from − 7.2 to -8.0 kcal/mol, was initially generated. Further docking against the 3CLpro of related coronaviruses (SARS-CoV and MERSCoV), docking to 5 different representative conformations generated from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories, and in silico drug-likeness analyses, revealed two drug-like terpenoid structures as promising non-covalent inhibitors of SARS-CoV-2 3CLPro viz: neoandrographolide and vernolide. These terpenoid structures are accommodated within the substrate-binding pocket, and interacted with the catalytic dyad, the oxyanion loop (residues 138–145), and the S1/S2 subsites of the enzyme activ...
Computers in Biology and Medicine
An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissi... more An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissimum was screened against the active region of 3-Chymotrypsin-Like Protease (3CLpro) of SARS-CoV-2 in silico. Based on docking scores and reference inhibitors, a hit- list of 21 phytocompounds, with binding energies ranging from − 7.2 to -8.0 kcal/mol, was initially generated. Further docking against the 3CLpro of related coronaviruses (SARS-CoV and MERSCoV), docking to 5 different representative conformations generated from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories, and in silico drug-likeness analyses, revealed two drug-like terpenoid structures as promising non-covalent inhibitors of SARS-CoV-2 3CLPro viz: neoandrographolide and vernolide. These terpenoid structures are accommodated within the substrate-binding pocket, and interacted with the catalytic dyad, the oxyanion loop (residues 138–145), and the S1/S2 subsites of the enzyme activ...
Computers in Biology and Medicine
An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissi... more An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissimum was screened against the active region of 3-Chymotrypsin-Like Protease (3CLpro) of SARS-CoV-2 in silico. Based on docking scores and reference inhibitors, a hit- list of 21 phytocompounds, with binding energies ranging from − 7.2 to -8.0 kcal/mol, was initially generated. Further docking against the 3CLpro of related coronaviruses (SARS-CoV and MERSCoV), docking to 5 different representative conformations generated from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories, and in silico drug-likeness analyses, revealed two drug-like terpenoid structures as promising non-covalent inhibitors of SARS-CoV-2 3CLPro viz: neoandrographolide and vernolide. These terpenoid structures are accommodated within the substrate-binding pocket, and interacted with the catalytic dyad, the oxyanion loop (residues 138–145), and the S1/S2 subsites of the enzyme active site. With the aid of an array of hydrogen bonds and hydrophobic interactions with residues 142–145, these phytocompounds may stabilize the conformation of the §exible oxyanion loop; and thereby interfere with the tetrahedral oxyanion intermediate formation during proteolytic cleavage. Molecular dynamics simulation and binding free energy calculation further revealed that the terpenoid-enzyme complexes exhibit strong interactions and structural stability, which could be adapted for experimental models.
Bioactive components of dietary herbs and spices are promising chemopreventive agents in cancer. ... more Bioactive components of dietary herbs and spices are promising chemopreventive agents in cancer. This study focused on evaluating the binding characteristics of some previously reported compounds from clove to some key metabolic regulators (AMPK, Akt1, PI3K, and LKB1) in cancer. To this end, the crystal structures of receptors and the ligands were retrieved from the protein databank and PubChem database respectively, prepared using Autodock tools and docked using BINDSURF in order to find the binding sites and characterize the ligand-protein complexes. Results revealed that, limonin, oleanolic acid, myricetin and isohamnetin exhibited higher affinity binding than the standard drug metformin with the proteins. Evaluation of ligand-protein complexes revealed involvement of multiple interactions such as hydrogen bonds, hydrophobic interactions and van der Waals forces, depending on the amino acid composition of binding sites and chemical properties of the compounds. While limonin exhibits hydrogen bonding with specific amino acid residues of AMPK (ARG 298 and SER 241 ), PI3K (HIS 295 and ARG 849 ), and LKB1 (ARG 55 , SER 58 , and ARG 18 ); isorhamnetin bonds with AMPK (SER 255 , SER 315 , HIS 297 HIS 150 and SER 313 ) and AKT1 (THR 211 and THR 82 ); and oleanolic acid bonds with PI3K (ALA 822 , LEU 823 , SER 824 , ILE 828 and GLU 880 ) and LKB1 (ASN 42 and ASP 124 ). In conclusion, limonin, isorhamnetin, and Oleanolic acid from clove, which exhibited high affinity interactions with multiple metabolic regulators in silico may be exploited as important nutraceuticals in targeting Warburg effects in cancer. However, in vitro and in vivo studies are needed to validate such a claim.
Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): an in silico screening of alkaloids and terpenoids from African medicinal plants, 2020
The novel coronavirus disease 2019 (COVID-19) caused by SARS-COV-2 has raised myriad of global co... more The novel coronavirus disease 2019 (COVID-19) caused by SARS-COV-2 has raised myriad of global concerns. There is currently no FDA approved antiviral strategy to alleviate the disease burden. The conserved 3-chymotrypsin-like protease (3CLpro), which controls coronavirus replication is a promising drug target for combating the coronavirus infection. This study screens some African plants derived alkaloids and terpenoids as potential inhibitors of coronavirus 3CLpro using in silico approach. Bioactive alkaloids (62) and terpenoids (100) of plants native to Africa were docked to the 3CLpro of the novel SARS-CoV-2. The top twenty alkaloids and terpenoids with high binding affinities to the SARS-CoV-2 3CLpro were further docked to the 3CLpro of SARS-CoV and MERS-CoV. The docking scores were compared with 3CLpro-referenced inhibitors (Lopinavir and Ritonavir). The top docked compounds were further subjected to ADEM/Tox and Lipinski filtering analyses for drug-likeness prediction analysis. This ligand-protein interaction study revealed that more than half of the top twenty alkaloids and terpenoids interacted favourably with thecoronaviruses3CLpro, and had binding affinities that surpassed that of lopinavir and ritonavir. Also, a highly defined hit-list of seven compounds (10-Hydroxyusambarensine, Cryptoquindoline, 6-Oxoisoiguesterin, 22-Hydroxyhopan-3-one, Cryptospirolepine, Isoiguesterin and 20-Epibryonolic acid) were identified. Furthermore, four non-toxic, druggable plant derived alkaloids (10-Hydroxyusambarensine, and Cryptoquindoline) and terpenoids (6-Oxoisoiguesterin and 22Hydroxyhopan-3-one), that bind to the receptor-binding site and catalytic dyad of SARS-CoV-2 3CLpro were identified from the predictive ADME/tox and Lipinski filter analysis. However, further experimental analyses are required for developing these possible leads into natural anti-COVID-19 therapeutic agents for combating the pandemic.
Tomatoes are a unique functional food and a natural reservoir of many health promoting nutrients,... more Tomatoes are a unique functional food and a natural reservoir of many health promoting nutrients, antioxidants, dietary fibres and chemopreventive nutraceuticals. They are particularly rich in lycopene which has been associated with the prevention of cardiovascular disease and cancers of the prostate and the gastrointestinal tract. As an important vegetable worldwide, tomatoes have drawn the attention of many researchers. Thus, numerous investigations have been conducted and various improvement strategies applied for enhancing the functionality of this medicinal food geared towards disease prevention, global health and well-being. Molecular breeding has produced a number of tomato lines with enhanced levels of lycopene, β-carotene and xanthophylls. Over expression of certain genes have generated tomato fruits with enhanced ascorbic acid levels and folate accumulation up to 25-fold. Plant hormone technology has been used to enhance tomato minerals, antioxidant vitamins, lycopene, β-carotene, flavonoids and phenolic compounds in tomato fruit tissues. Manipulation in soilless culture solutions is valuable for enhancing the antioxidative capacity of tomatoes, vitamin C, flavonoids, lycopene, and β-carotene in fresh fruits. In addition, the spraying of nutrients, such as potassium, in field conditions has a strong stimulatory effect on lycopene contents of tomatoes. Transgenic strategies are also being adopted. These strategies offer a rapid way to introduce desirable traits into the phenotype and differ from other approaches in that novel genetic information is introduced directly into the plant's genome. An important and current trend in the improvement of functional foods is to shift from enhancing single nutritional compounds towards enhancing multiple nutrients and phytochemicals in order to harness their synergistic interactions. This could be achieved by the use of strategies having pleitropic effects such as bioregulators, multigene engineering and regulative genetic elements. However, the full potential of these technologies has not been realised and the relative gap between risk assessment and regulatory threshold desires much attention. These biotechnological strategies for enhancing
In recent years, the consumption of nutraceuticals, natural plant foods, and the use of nutrition... more In recent years, the consumption of nutraceuticals, natural plant foods, and the use of nutritional therapy and phytotherapy have become progressively popular to improve health, and to prevent and treat diseases. This study investigated the cardioprotective and hepatoprotective effects of some nutraceuticals from Vernonia amygdalina namely, β-sitosterol (BSS), β-sitosterol glucoside (BSSG) and BSS: BSSG mixture on certain parameters in hypertensive wistar albino rats. Hypertension was induced with Cadmium Chloride and the biochemical analyses of serum were carried out following treatment with BSS, BSSG, BSS:BSSG mixture and lisinopril. Serum urea, creatinine, calcium and electrolytes levels were assayed using appropriate standard methods as tests for renal function, while alkaline phosphatase (ALP), aspartate transaminase (AST) and alanine aminotransferase (ALT) served as enzyme indices of the liver function. The effect on the serum lipid profile was also assessed. Data collected were expressed as mean ± SEM and analysed using one-way ANOVA. The sodium levels had a significant (p<0.05) reduction in BSS and BSS:BSSG mixture treated rats. BSS treatment also gave a significant (p<0.05) decrease in triglyceride and total cholesterol levels while BSSG treatment gave 60.4% increase in HDL-Cholesterol levels and increased HDL-Cholesterol: LDL-Cholesterol ratio. Generally, treatments with the phytosterols reduced the levels of serum AST, ALT, ALP and tends to maintain urea and creatinine basal levels while lisinopril significantly increased (p<0.05) serum urea and creatinine levels. Tissue sections from phytosteroltreated groups show no visible lesion as against those from hypertensive rats that show areas of extensive necrosis. This study revealed that these nutraceuticals possess cardioprotective and hepatoprotective properties, with possible practical application in the management of cardiovascular diseases (CVDs). [Olaiya CO, Choudhary MI, Ogunyemi OM, Nwauzoma AB. Nutraceuticals from Bitter Leaf (Vernonia amygdalina Del.) Protects against Cadmium Chloride induced Hypertension in Albino Rats. Nat Sci 2013;11(6):136-145]. (ISSN: 1545-0740). http://www.sciencepub.net/nature. 16
Journal of Applied Pharmaceutical Science, 2019
Journal of Biomolecular Structure and Dynamics, 2020
Computers in Biology and Medicine
An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissi... more An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissimum was screened against the active region of 3-Chymotrypsin-Like Protease (3CLpro) of SARS-CoV-2 in silico. Based on docking scores and reference inhibitors, a hit- list of 21 phytocompounds, with binding energies ranging from − 7.2 to -8.0 kcal/mol, was initially generated. Further docking against the 3CLpro of related coronaviruses (SARS-CoV and MERSCoV), docking to 5 different representative conformations generated from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories, and in silico drug-likeness analyses, revealed two drug-like terpenoid structures as promising non-covalent inhibitors of SARS-CoV-2 3CLPro viz: neoandrographolide and vernolide. These terpenoid structures are accommodated within the substrate-binding pocket, and interacted with the catalytic dyad, the oxyanion loop (residues 138–145), and the S1/S2 subsites of the enzyme activ...
Computers in Biology and Medicine
An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissi... more An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissimum was screened against the active region of 3-Chymotrypsin-Like Protease (3CLpro) of SARS-CoV-2 in silico. Based on docking scores and reference inhibitors, a hit- list of 21 phytocompounds, with binding energies ranging from − 7.2 to -8.0 kcal/mol, was initially generated. Further docking against the 3CLpro of related coronaviruses (SARS-CoV and MERSCoV), docking to 5 different representative conformations generated from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories, and in silico drug-likeness analyses, revealed two drug-like terpenoid structures as promising non-covalent inhibitors of SARS-CoV-2 3CLPro viz: neoandrographolide and vernolide. These terpenoid structures are accommodated within the substrate-binding pocket, and interacted with the catalytic dyad, the oxyanion loop (residues 138–145), and the S1/S2 subsites of the enzyme activ...
Computers in Biology and Medicine
An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissi... more An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissimum was screened against the active region of 3-Chymotrypsin-Like Protease (3CLpro) of SARS-CoV-2 in silico. Based on docking scores and reference inhibitors, a hit- list of 21 phytocompounds, with binding energies ranging from − 7.2 to -8.0 kcal/mol, was initially generated. Further docking against the 3CLpro of related coronaviruses (SARS-CoV and MERSCoV), docking to 5 different representative conformations generated from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories, and in silico drug-likeness analyses, revealed two drug-like terpenoid structures as promising non-covalent inhibitors of SARS-CoV-2 3CLPro viz: neoandrographolide and vernolide. These terpenoid structures are accommodated within the substrate-binding pocket, and interacted with the catalytic dyad, the oxyanion loop (residues 138–145), and the S1/S2 subsites of the enzyme active site. With the aid of an array of hydrogen bonds and hydrophobic interactions with residues 142–145, these phytocompounds may stabilize the conformation of the §exible oxyanion loop; and thereby interfere with the tetrahedral oxyanion intermediate formation during proteolytic cleavage. Molecular dynamics simulation and binding free energy calculation further revealed that the terpenoid-enzyme complexes exhibit strong interactions and structural stability, which could be adapted for experimental models.
Bioactive components of dietary herbs and spices are promising chemopreventive agents in cancer. ... more Bioactive components of dietary herbs and spices are promising chemopreventive agents in cancer. This study focused on evaluating the binding characteristics of some previously reported compounds from clove to some key metabolic regulators (AMPK, Akt1, PI3K, and LKB1) in cancer. To this end, the crystal structures of receptors and the ligands were retrieved from the protein databank and PubChem database respectively, prepared using Autodock tools and docked using BINDSURF in order to find the binding sites and characterize the ligand-protein complexes. Results revealed that, limonin, oleanolic acid, myricetin and isohamnetin exhibited higher affinity binding than the standard drug metformin with the proteins. Evaluation of ligand-protein complexes revealed involvement of multiple interactions such as hydrogen bonds, hydrophobic interactions and van der Waals forces, depending on the amino acid composition of binding sites and chemical properties of the compounds. While limonin exhibits hydrogen bonding with specific amino acid residues of AMPK (ARG 298 and SER 241 ), PI3K (HIS 295 and ARG 849 ), and LKB1 (ARG 55 , SER 58 , and ARG 18 ); isorhamnetin bonds with AMPK (SER 255 , SER 315 , HIS 297 HIS 150 and SER 313 ) and AKT1 (THR 211 and THR 82 ); and oleanolic acid bonds with PI3K (ALA 822 , LEU 823 , SER 824 , ILE 828 and GLU 880 ) and LKB1 (ASN 42 and ASP 124 ). In conclusion, limonin, isorhamnetin, and Oleanolic acid from clove, which exhibited high affinity interactions with multiple metabolic regulators in silico may be exploited as important nutraceuticals in targeting Warburg effects in cancer. However, in vitro and in vivo studies are needed to validate such a claim.
Potential inhibitors of coronavirus 3-chymotrypsin-like protease (3CLpro): an in silico screening of alkaloids and terpenoids from African medicinal plants, 2020
The novel coronavirus disease 2019 (COVID-19) caused by SARS-COV-2 has raised myriad of global co... more The novel coronavirus disease 2019 (COVID-19) caused by SARS-COV-2 has raised myriad of global concerns. There is currently no FDA approved antiviral strategy to alleviate the disease burden. The conserved 3-chymotrypsin-like protease (3CLpro), which controls coronavirus replication is a promising drug target for combating the coronavirus infection. This study screens some African plants derived alkaloids and terpenoids as potential inhibitors of coronavirus 3CLpro using in silico approach. Bioactive alkaloids (62) and terpenoids (100) of plants native to Africa were docked to the 3CLpro of the novel SARS-CoV-2. The top twenty alkaloids and terpenoids with high binding affinities to the SARS-CoV-2 3CLpro were further docked to the 3CLpro of SARS-CoV and MERS-CoV. The docking scores were compared with 3CLpro-referenced inhibitors (Lopinavir and Ritonavir). The top docked compounds were further subjected to ADEM/Tox and Lipinski filtering analyses for drug-likeness prediction analysis. This ligand-protein interaction study revealed that more than half of the top twenty alkaloids and terpenoids interacted favourably with thecoronaviruses3CLpro, and had binding affinities that surpassed that of lopinavir and ritonavir. Also, a highly defined hit-list of seven compounds (10-Hydroxyusambarensine, Cryptoquindoline, 6-Oxoisoiguesterin, 22-Hydroxyhopan-3-one, Cryptospirolepine, Isoiguesterin and 20-Epibryonolic acid) were identified. Furthermore, four non-toxic, druggable plant derived alkaloids (10-Hydroxyusambarensine, and Cryptoquindoline) and terpenoids (6-Oxoisoiguesterin and 22Hydroxyhopan-3-one), that bind to the receptor-binding site and catalytic dyad of SARS-CoV-2 3CLpro were identified from the predictive ADME/tox and Lipinski filter analysis. However, further experimental analyses are required for developing these possible leads into natural anti-COVID-19 therapeutic agents for combating the pandemic.
Tomatoes are a unique functional food and a natural reservoir of many health promoting nutrients,... more Tomatoes are a unique functional food and a natural reservoir of many health promoting nutrients, antioxidants, dietary fibres and chemopreventive nutraceuticals. They are particularly rich in lycopene which has been associated with the prevention of cardiovascular disease and cancers of the prostate and the gastrointestinal tract. As an important vegetable worldwide, tomatoes have drawn the attention of many researchers. Thus, numerous investigations have been conducted and various improvement strategies applied for enhancing the functionality of this medicinal food geared towards disease prevention, global health and well-being. Molecular breeding has produced a number of tomato lines with enhanced levels of lycopene, β-carotene and xanthophylls. Over expression of certain genes have generated tomato fruits with enhanced ascorbic acid levels and folate accumulation up to 25-fold. Plant hormone technology has been used to enhance tomato minerals, antioxidant vitamins, lycopene, β-carotene, flavonoids and phenolic compounds in tomato fruit tissues. Manipulation in soilless culture solutions is valuable for enhancing the antioxidative capacity of tomatoes, vitamin C, flavonoids, lycopene, and β-carotene in fresh fruits. In addition, the spraying of nutrients, such as potassium, in field conditions has a strong stimulatory effect on lycopene contents of tomatoes. Transgenic strategies are also being adopted. These strategies offer a rapid way to introduce desirable traits into the phenotype and differ from other approaches in that novel genetic information is introduced directly into the plant's genome. An important and current trend in the improvement of functional foods is to shift from enhancing single nutritional compounds towards enhancing multiple nutrients and phytochemicals in order to harness their synergistic interactions. This could be achieved by the use of strategies having pleitropic effects such as bioregulators, multigene engineering and regulative genetic elements. However, the full potential of these technologies has not been realised and the relative gap between risk assessment and regulatory threshold desires much attention. These biotechnological strategies for enhancing
In recent years, the consumption of nutraceuticals, natural plant foods, and the use of nutrition... more In recent years, the consumption of nutraceuticals, natural plant foods, and the use of nutritional therapy and phytotherapy have become progressively popular to improve health, and to prevent and treat diseases. This study investigated the cardioprotective and hepatoprotective effects of some nutraceuticals from Vernonia amygdalina namely, β-sitosterol (BSS), β-sitosterol glucoside (BSSG) and BSS: BSSG mixture on certain parameters in hypertensive wistar albino rats. Hypertension was induced with Cadmium Chloride and the biochemical analyses of serum were carried out following treatment with BSS, BSSG, BSS:BSSG mixture and lisinopril. Serum urea, creatinine, calcium and electrolytes levels were assayed using appropriate standard methods as tests for renal function, while alkaline phosphatase (ALP), aspartate transaminase (AST) and alanine aminotransferase (ALT) served as enzyme indices of the liver function. The effect on the serum lipid profile was also assessed. Data collected were expressed as mean ± SEM and analysed using one-way ANOVA. The sodium levels had a significant (p<0.05) reduction in BSS and BSS:BSSG mixture treated rats. BSS treatment also gave a significant (p<0.05) decrease in triglyceride and total cholesterol levels while BSSG treatment gave 60.4% increase in HDL-Cholesterol levels and increased HDL-Cholesterol: LDL-Cholesterol ratio. Generally, treatments with the phytosterols reduced the levels of serum AST, ALT, ALP and tends to maintain urea and creatinine basal levels while lisinopril significantly increased (p<0.05) serum urea and creatinine levels. Tissue sections from phytosteroltreated groups show no visible lesion as against those from hypertensive rats that show areas of extensive necrosis. This study revealed that these nutraceuticals possess cardioprotective and hepatoprotective properties, with possible practical application in the management of cardiovascular diseases (CVDs). [Olaiya CO, Choudhary MI, Ogunyemi OM, Nwauzoma AB. Nutraceuticals from Bitter Leaf (Vernonia amygdalina Del.) Protects against Cadmium Chloride induced Hypertension in Albino Rats. Nat Sci 2013;11(6):136-145]. (ISSN: 1545-0740). http://www.sciencepub.net/nature. 16