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  1. Article ; Online: Atomistic simulations suggest dietary flavonoids from Beta vulgaris (beet) as promising inhibitors of human angiotensin-converting enzyme and 2-alpha-adrenergic receptors in hypertension.

    Adetunji, Joy A / Ogunyemi, Oludare M / Gyebi, Gideon A / Adewumi, Anuoluwapo E / Olaiya, Charles O

    Bioinformatics advances

    2023  Volume 3, Issue 1, Page(s) vbad133

    Abstract: Motivation: Beta vulgaris: Results: Structure-based virtual screening against angiotensin-converting enzyme revealed that, Cochliophilin A (-9.0 Kcal/mol), Miraxanthin (-8.3 Kcal/mol), and quercimeritrin (-9.7 Kcal/mol) had lower docking scores than ... ...

    Abstract Motivation: Beta vulgaris
    Results: Structure-based virtual screening against angiotensin-converting enzyme revealed that, Cochliophilin A (-9.0 Kcal/mol), Miraxanthin (-8.3 Kcal/mol), and quercimeritrin (-9.7 Kcal/mol) had lower docking scores than the reference lisinopril (-7.9 Kcal/mol). These compounds exhibited dual binding tendency as they also ranked top compounds upon screening against adrenergic receptor. The thermodynamic parameters computed from the resulting trajectories obtained from the 100 ns full atomistic molecular dynamics simulation revealed structural stability and conformational flexibility of the ligand-receptor complexes as indicated by the RMSD, RMSF, RoG, SASA, and H-bond calculations. The molecular mechanics with generalized Born and surface area solvation binding energy calculations revealed that the proteins exhibit considerable binding energy with the phytochemicals in a dynamic environment. Furthermore, the hit compounds possess good physicochemical properties and drug-likeness. Overall, cochliophilin and quercimeritrin are promising dual-target directed flavonoids from
    Availability and implementation: All data was provided in the manuscript.
    Language English
    Publishing date 2023-09-22
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbad133
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  2. Article ; Online: Amyloid β fibrils disruption by kolaviron: Molecular docking and extended molecular dynamics simulation studies.

    Adewole, Kayode Ezekiel / Gyebi, Gideon A / Ibrahim, Ibrahim M

    Computational biology and chemistry

    2021  Volume 94, Page(s) 107557

    Abstract: Garcinia kola (GK) produces notable effects against neurodegenerative conditions, including experimentally-induced Alzheimer's disease (AD). These remarkable effects are basically attributable to kolaviron (KV), a bioflavonoid constituent of this seed. ... ...

    Abstract Garcinia kola (GK) produces notable effects against neurodegenerative conditions, including experimentally-induced Alzheimer's disease (AD). These remarkable effects are basically attributable to kolaviron (KV), a bioflavonoid constituent of this seed. Specifically, it has been reported that in AD models, KV produces interesting neuroprotective effects, being able to diminish associated neurotoxicity, via modulation of antioxidative, inflammatory and other disease modifying processes. Intriguingly, the effect of KV on amyloid-beta (Aβ) aggregation and disruption of preformed Aβ fibrils have not been studied. In this study, we have described a thorough computational study on the mechanism of action of KV as an Aβ fibrils disruptor at molecular level. We used comprehensive in silico docking evaluations and extended molecular dynamics simulation to mimic KV/Aβ fibrils system. Results indicate that KV was able to move within the Aβ fibrils, binding with important residues and components in the Aβ peptide identified to be vital for stabilizing preformed fibrils. KV destabilized the assembled Aβ fibrils, indicating the ability KV as a potential anti-amyloidogenic agent. Furthermore, this work highlighted the possibility of identifying new multifunctional phytocompounds as potent AD drugs.
    MeSH term(s) Amyloid beta-Peptides/antagonists & inhibitors ; Amyloid beta-Peptides/chemistry ; Flavonoids/chemistry ; Flavonoids/pharmacology ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation
    Chemical Substances Amyloid beta-Peptides ; Flavonoids ; kolaviron (PX7M0YV62G)
    Language English
    Publishing date 2021-08-05
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2021.107557
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  3. Article ; Online: Antispasmodic Effect of

    Akinmurele, Opeyemi Josephine / Sonibare, Mubo Adeola / Elujoba, Anthony A / Ogunlakin, Akingbolabo Daniel / Yeye, Oloruntoba Emmanuel / Gyebi, Gideon Ampoma / Ojo, Oluwafemi Adeleke / Alanzi, Abdullah R

    Molecules (Basel, Switzerland)

    2023  Volume 28, Issue 20

    Abstract: Background: Alstonia boonei: Method: The freeze-dried aqueous Stem back extract of : Results: The Stem back crude extract, DCM, ethyl acetate, and aqueous fractions showed antispasmodic activity on high-potassium-induced (K: Conclusion: The ... ...

    Abstract Background: Alstonia boonei
    Method: The freeze-dried aqueous Stem back extract of
    Results: The Stem back crude extract, DCM, ethyl acetate, and aqueous fractions showed antispasmodic activity on high-potassium-induced (K
    Conclusion: The isolated compounds boonein and β-amyrin could serve as starting materials for the development of antispasmodic drugs.
    MeSH term(s) Rats ; Animals ; Humans ; Alstonia/chemistry ; Plant Extracts/pharmacology ; Plant Extracts/chemistry ; Parasympatholytics/pharmacology ; Water ; Potassium
    Chemical Substances Plant Extracts ; Parasympatholytics ; ethyl acetate (76845O8NMZ) ; beta-amyrin (KM8353IPSO) ; Water (059QF0KO0R) ; Potassium (RWP5GA015D)
    Language English
    Publishing date 2023-10-13
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 1413402-0
    ISSN 1420-3049 ; 1431-5165 ; 1420-3049
    ISSN (online) 1420-3049
    ISSN 1431-5165 ; 1420-3049
    DOI 10.3390/molecules28207069
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  4. Article ; Online: Evaluation of Antimalarial Activity of Ethanolic Extract of

    Nwonuma, Charles Obiora / Balogun, Elizabeth Abiodun / Gyebi, Gideon Ampoma

    Journal of evidence-based integrative medicine

    2023  Volume 28, Page(s) 2515690X231165104

    Abstract: In Nigeria, ...

    Abstract In Nigeria,
    MeSH term(s) Mice ; Animals ; Antimalarials ; Annona/chemistry ; Apigenin ; Luteolin ; Molecular Docking Simulation ; Plant Extracts/pharmacology ; Ethanol
    Chemical Substances Antimalarials ; Apigenin (7V515PI7F6) ; Luteolin (KUX1ZNC9J2) ; Plant Extracts ; Ethanol (3K9958V90M)
    Language English
    Publishing date 2023-04-05
    Publishing country United States
    Document type Journal Article
    ISSN 2515-690X
    ISSN (online) 2515-690X
    DOI 10.1177/2515690X231165104
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: In silico

    Oyeyemi, Ifeoluwa Temitayo / Adewole, Kayode Ezekiel / Gyebi, Gideon Ampoma

    Journal of biomolecular structure & dynamics

    2023  Volume 41, Issue 21, Page(s) 12225–12241

    Abstract: ... Nymphaea ... ...

    Abstract Nymphaea lotus
    MeSH term(s) Hypoglycemic Agents/pharmacology ; Molecular Dynamics Simulation ; Nymphaea ; Molecular Docking Simulation ; Anti-Inflammatory Agents/pharmacology ; Phytochemicals/pharmacology ; Diabetes Mellitus
    Chemical Substances Hypoglycemic Agents ; Anti-Inflammatory Agents ; Phytochemicals
    Language English
    Publishing date 2023-01-16
    Publishing country England
    Document type Journal Article
    ZDB-ID 49157-3
    ISSN 1538-0254 ; 0739-1102
    ISSN (online) 1538-0254
    ISSN 0739-1102
    DOI 10.1080/07391102.2023.2166591
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  6. Article ; Online: Correction: Phytochemical analysis, in vitro and in silico effects from Alstonia boonei De Wild stem bark on selected digestive enzymes and adipogenesis in 3T3‑L1 preadipocytes.

    Anyanwu, Gabriel O / Ejike, Uju D / Gyebi, Gideon A / Rauf, Khalid / Nisar-Ur-Rehman / Iqbal, Jamshed / Zaib, Sumera / Usunobun, Usunomena / Onyeneke, Eusebius C / Alotaibi, Badriyah S / El-Saber Batiha, Gaber

    BMC complementary medicine and therapies

    2023  Volume 23, Issue 1, Page(s) 389

    Language English
    Publishing date 2023-10-28
    Publishing country England
    Document type Published Erratum
    ISSN 2662-7671
    ISSN (online) 2662-7671
    DOI 10.1186/s12906-023-04236-w
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  7. Article ; Online: Deciphering the therapeutic role of Kigelia africana fruit in erectile dysfunction through metabolite profiling and molecular modelling

    Femi Olawale / Kolawole Olofinsan / Oludare M. Ogunyemi / Kayode O. Karigidi / Gideon A. Gyebi / Ibrahim M. Ibrahim / Opeyemi Iwaloye

    Informatics in Medicine Unlocked, Vol 37, Iss , Pp 101190- (2023)

    2023  

    Abstract: Kigelia africana herbal products are often used traditionally to treat erectile dysfunction and other sexual complaints, but the underlying mechanism is not yet understood. This study focused on profiling the bioactive constituents of Kigelia africana ... ...

    Abstract Kigelia africana herbal products are often used traditionally to treat erectile dysfunction and other sexual complaints, but the underlying mechanism is not yet understood. This study focused on profiling the bioactive constituents of Kigelia africana fruit (KAF) using spectroscopic techniques and providing the computational models of their interactions with phosphodiesterase (PDE5) and Rho-associated coiled-coil containing protein kinase 2 (ROCK2) targets associated with erectile dysfunction. Integrated FT-IR, HPLC-MS, and GC-MS analysis revealed 152 (C1–C152) KAF compounds with highly diverse functional groups and chemical properties. Molecular docking showed several hit compounds as potential inhibitors of PDE5 and ROCK2. Post docking MMGBSA, QSAR, predictive physicochemical analysis and AdmetSAR analysis revealed that most of the hit compounds are potential drug leads. Among these, hydroxydoxepin (C3) and ritodrine (C131) exhibited the strongest interactions with PDE5, while epigallocatechin 3-O-p-coumarate (C9) and chlorogenic acid (C91) had the strongest interaction with ROCK2. The thermodynamic parameters and trajectory clusters computed from the trajectories obtained from the 100 ns full atomistic molecular dynamic (MD) simulation indicated the structural stability and conformational flexibility of the selected complexes. The MD simulation-based MMPBSA calculation further revealed strong binding affinity and energy contribution by active site residues of PDE5 towards binding the selected KAF compounds. Various computational analyses employed revealed that the catalytic residues Gln817, Val782 and Phe786 of PDE5 exhibited high interaction potential and flexibility towards C3 and C131. Overall, hydroxydoxepin, ritodrine and other phytochemicals in Kigelia africana may account for the therapeutic role of this plant in erectile dysfunction.
    Keywords Kigelia africana ; Erectile dysfunction ; Phytochemical analysis ; Molecular docking and dynamics ; QSAR ; Computer applications to medicine. Medical informatics ; R858-859.7
    Subject code 540
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Dual targeting of cytokine storm and viral replication in COVID-19 by plant-derived steroidal pregnanes: An in silico perspective.

    Gyebi, Gideon A / Ogunyemi, Oludare M / Ibrahim, Ibrahim M / Afolabi, Saheed O / Adebayo, Joseph O

    Computers in biology and medicine

    2021  Volume 134, Page(s) 104406

    Abstract: The high morbidity and mortality rate of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection arises majorly from the Acute Respiratory Distress Syndrome and "cytokine storm" syndrome, which is sustained by an aberrant systemic ... ...

    Abstract The high morbidity and mortality rate of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) infection arises majorly from the Acute Respiratory Distress Syndrome and "cytokine storm" syndrome, which is sustained by an aberrant systemic inflammatory response and elevated pro-inflammatory cytokines. Thus, phytocompounds with broad-spectrum anti-inflammatory activity that target multiple SARS-CoV-2 proteins will enhance the development of effective drugs against the disease. In this study, an in-house library of 117 steroidal plant-derived pregnanes (PDPs) was docked in the active regions of human glucocorticoid receptors (hGRs) in a comparative molecular docking analysis. Based on the minimal binding energy and a comparative dexamethasone binding mode analysis, a list of top twenty ranked PDPs docked in the agonist conformation of hGR, with binding energies ranging between -9.8 and -11.2 kcal/mol, was obtained and analyzed for possible interactions with the human Janus kinases 1 and Interleukins-6 and SARS-CoV-2 3-chymotrypsin-like protease, Papain-like protease and RNA-dependent RNA polymerase. For each target protein, the top three ranked PDPs were selected. Eight PDPs (bregenin, hirundigenin, anhydroholantogenin, atratogenin A, atratogenin B, glaucogenin A, glaucogenin C and glaucogenin D) with high binding tendencies to the catalytic residues of multiple targets were identified. A high degree of structural stability was observed from the 100 ns molecular dynamics simulation analyses of glaucogenin C and hirundigenin complexes of hGR. The selected top-eight ranked PDPs demonstrated high druggable potentials and favourable in silico ADMET properties. Thus, the therapeutic potentials of glaucogenin C and hirundigenin can be explored for further in vitro and in vivo studies.
    Language English
    Publishing date 2021-04-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 127557-4
    ISSN 1879-0534 ; 0010-4825
    ISSN (online) 1879-0534
    ISSN 0010-4825
    DOI 10.1016/j.compbiomed.2021.104406
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    Zs.A 653: Show issues Location:
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  9. Article ; Online: Identification of promising multi-targeting inhibitors of obesity from Vernonia amygdalina through computational analysis.

    Ogunyemi, Oludare M / Gyebi, Gideon A / Ibrahim, Ibrahim M / Esan, Adewale M / Olaiya, Charles O / Soliman, Mohameed M / Batiha, Gaber El-Saber

    Molecular diversity

    2022  Volume 27, Issue 1, Page(s) 1–25

    Abstract: Vernonia amygdalina, a widely consumed West African food herb, can be a boon in the discovery of safe anti-obesity agents given the extensive reports on its anti-obesity and antidiabetic potentials. The main aim of this study was to screen 78 Vernonia- ... ...

    Abstract Vernonia amygdalina, a widely consumed West African food herb, can be a boon in the discovery of safe anti-obesity agents given the extensive reports on its anti-obesity and antidiabetic potentials. The main aim of this study was to screen 78 Vernonia-Derived Phytocompounds (VDPs) against the active site regions of Human Pancreatic Lipase (HPL), Human Pancreatic Amylase and Human Glucosidase (HG) as drug targets associated with obesity in silico. Structure-based virtual screening helped to identify Luteolin 7-O-glucuronoside and Andrographidoid D2 as hit compounds with dual targeting tendency towards the HPL and HG. Analysis of the molecular dynamic simulation trajectory files of the ligand-receptor complexes as computed from the thermodynamic parameters plots showed not only increased flexibility and greater interaction potential of the active site residues of the receptor towards the VDPs as indicated by the root mean square fluctuation but also higher stability as indicated by the root mean square deviation, radius of gyration and number of hydrogen bonds. The cluster analysis further showed that the interactions with important residues were preserved in the dynamic environment. These observations were further verified from Molecular Mechanics Generalized Born Surface Area Analysis, which also showed that residual contributions to the binding free energies were mainly from catalytic residues at the active sites of the enzymes. The hit compounds also feature desirable physicochemical properties and drug-likeness. This study provides in silico evidence for the inhibitory potential of phytochemicals from Vernonia amygdalina against two target enzymes in obesity.
    MeSH term(s) Humans ; Vernonia/chemistry ; Obesity/drug therapy ; Catalytic Domain ; Molecular Dynamics Simulation ; Hydrogen Bonding
    Language English
    Publishing date 2022-02-18
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 1376507-3
    ISSN 1573-501X ; 1381-1991
    ISSN (online) 1573-501X
    ISSN 1381-1991
    DOI 10.1007/s11030-022-10397-6
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    Zs.A 4946: Show issues Location:
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  10. Article: GC-MS chemical profiling, antioxidant, anti-diabetic, and anti-inflammatory activities of ethyl acetate fraction of

    Ojo, Oluwafemi Adeleke / Ogunlakin, Akingbolabo Daniel / Gyebi, Gideon Ampoma / Ayokunle, Damilare IyinKristi / Odugbemi, Adeshina Isaiah / Babatunde, Dare Ezekiel / Ajayi-Odoko, Omolola Adenike / Iyobhebhe, Matthew / Ezea, Samson Chukwuemeka / Akintayo, Christopher Oloruntoba / Ayeleso, Ademola / Ojo, Adebola Busola / Ojo, Omolara Olajumoke

    Frontiers in pharmacology

    2023  Volume 14, Page(s) 1235810

    Abstract: Introduction: ...

    Abstract Introduction:
    Language English
    Publishing date 2023-07-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587355-6
    ISSN 1663-9812
    ISSN 1663-9812
    DOI 10.3389/fphar.2023.1235810
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