Inhibitory potentials of phytocompounds from<i>Ocimum gratissimum</i>against anti-apoptotic BCL-2 proteins associated with cancer: an integrated computational study

Gyebi, Gideon A.; Ogunyemi, Oludare M.; Ibrahim, Ibrahim M.; Afolabi, Saheed O.; Ojo, Rotimi Johnson; Ejike, Uju D. I.; Adebayo, Joseph O.

doi:10.1080/2314808x.2022.2106095

Cited by 4 publications

(2 citation statements)

References 59 publications

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“…The resulting calculation showed the increasing SASA value of the all studied complex systems at the beginning of the simulation, which is then relatively steady. The increase in this value may indicate that the protein is unfolded during simulation 17 . The 5M8Rgermacrene D has shown a relatively less extent, indicating more stability than the others.…”

Section: Alterations In Solvent Accessibilitymentioning

confidence: 99%

“…Preliminary information regarding this information is needed before conducting research in a wet laboratory. For this reason, computational-based studies, including chemometrics and molecular docking study followed by molecular dynamic simulations, could be used [15][16][17] . Our study aims to characterize the EOs from emprit and red ginger based on their components through chemometric analysis, namely principle component analysis (PCA) and heatmap with dendrogram.…”

Section: Introductionmentioning

confidence: 99%

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Component Discrimination and Anti-skin-aging Potency of Emprit and Red Ginger Essential Oil: Chemometric, Molecular Docking and Molecular Dynamics Study

Badrunanto,

Asoka,

Wahyuni

et al. 2023

Valensi

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Emprit and red ginger essential oils (EOs) are natural sources of antioxidants that have the potential to be used in cosmetics, one of which is as an anti-skin-aging. The aim of this study was to determine the component differences and anti-skin-aging potential of the two EOs. The components were determined by GC-MS, while discrimination was done by chemometric. The potential of the components as the anti-skin-aging were evaluated by molecular docking and molecular dynamics (MD) simulations. A total 66 components were identified in both EOs, where eucalyptol (17.92%) and camphene (15.12%) were the main component in emprit and red ginger, respectively. Chemometric analysis revealed two discriminant clusters highlighting their dissimilarity with germacrene D and α-zingiberene are the key markers for differentiation. The docking and MD simulations were demonstrated the four main components of emprit EO, namely α-curcumene, α-zingiberene, β-bisabolene and β-sesquiphellandrene, have the best docking scores and interact with the enzymes with a relatively stable interaction. AdmetSAR evaluation of the four components has shown good bioavailability and declared safe. This study succeeded in revealing two ginger EOs differences based on their components and demonstrated the emprit ginger EO was more promising as a natural anti-skin-aging agent for further research.

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Section: Alterations In Solvent Accessibilitymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Component Discrimination and Anti-skin-aging Potency of Emprit and Red Ginger Essential Oil: Chemometric, Molecular Docking and Molecular Dynamics Study

Badrunanto,

Asoka,

Wahyuni

et al. 2023

Valensi

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Apoptotic Potential of Iloneoside from Gongronema latifolium Benth against Prostate Cancer Cells Using In Vitro and In Silico Approach

Gyebi,

Afolabi,

Ogunyemi

et al. 2024

Cell Biochem Biophys

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Prostate cancer is a major cause of cancer-related mortality in men worldwide. The anti-proliferative activity of Gongronema latifolium leaf extracts on some cancer cells has been reported. Herein, we investigated the growth inhibitory effect of the Gongronema latilolium leaf methanol extract and isolated pregnane (iloneoside) against prostate cancer cell lines using the MTT cell proliferation assay, apoptosis quantification, cell cycle analysis using flow cytometry and computational analysis molecular docking, molecular dynamics simulation (MDs), binding free energy computation and cluster analysis. In addition, UPLC-ESI-TOFMS chemical fingerprinting of previously isolated compounds was performed. The extract inhibited the growth of the cell lines with an IC50 of 49.3 µg/ml and 28.4 µg/ml for 24 h and 48 h, respectively, for PC3; and 43.7 µg/ml and 22.3 µg/ml for 24 h and 48 h, respectively, for DU145. Iloneoside demonstrated low inhibitory activities against PC3 and DU145 (IC50 > 80 μM). Apoptotic quantification and cell cycle analysis further showed that iloneoside induced apoptosis in a few cells at a dose of 200 uM. The ensemble-based molecular docking of the iloneoside to BCL-XL and BCL-2 proteins, and docking to MCL-1, BCL-A1 and BFL-1 proteins, respectively, presented binding energies of −7.22 ± 0.5, −8.12 ± 0.55, −7.1, −7.2 and −6.3 kcal/mol, while the MM/PBSA binding free energy was −25.72 ± 7.22 and −27.76 ± 11.32 kcal/mol for BCL-XL and BCL-2 proteins. Furthermore, iloneoside was stable during the 100 ns MDs analysis, while the clustering of the MDs trajectories showed that the interactions were strongly preserved. Iloneoside, in part, or in synergy with other constituents, may be responsible for the antiproliferative activities of the leaf, subject to further investigation.

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Ocimum gratissimum L. leaf flavonoid-rich extracts reduced the expression of p53 and VCAM in streptozotocin-induced cardiomyopathy rats

Ajiboye,

Famusiwa,

Falode

et al. 2024

Phytomedicine Plus

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Inhibitory potentials of phytocompounds fromOcimum gratissimumagainst anti-apoptotic BCL-2 proteins associated with cancer: an integrated computational study

Cited by 4 publications

References 59 publications

Component Discrimination and Anti-skin-aging Potency of Emprit and Red Ginger Essential Oil: Chemometric, Molecular Docking and Molecular Dynamics Study

Component Discrimination and Anti-skin-aging Potency of Emprit and Red Ginger Essential Oil: Chemometric, Molecular Docking and Molecular Dynamics Study

Apoptotic Potential of Iloneoside from Gongronema latifolium Benth against Prostate Cancer Cells Using In Vitro and In Silico Approach

Ocimum gratissimum L. leaf flavonoid-rich extracts reduced the expression of p53 and VCAM in streptozotocin-induced cardiomyopathy rats

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