Machine learning-based screening of MCF-7 human breast cancer cells and molecular docking analysis of essential oils from Ocimum basilicum against breast cancer

Nguyen, Tan Khanh; Nguyen, Thao Nguyen Le; Nguyen, Kiet Van; Nguyen, Huynh Van Thi; Tran, Linh Thuy Thi; Ngo, Thanh Xuan Thi; Pham, Phu Tran Vinh; Tran, Manh Hung

doi:10.1016/j.molstruc.2022.133627

Cited by 23 publications

(8 citation statements)

References 17 publications

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“…Finally, the molecular interactions between proteins and selected ligands were visualized by Discovery Studio Visualizer 2020, and their 3D and 2D interaction plots were derived. 15…”

Section: Molecular Docking Studymentioning

confidence: 99%

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Integrating in Silico and In Vitro Studies to Screen Anti-Staphylococcus aureus Activity From Vietnamese Ganoderma multiplicatum and Ganoderma sinense

Nguyen

et al. 2023

Natural Product Communications

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Background: Staphylococcus aureus is a nosocomial pathogen responsible for many serious infectious diseases in humans. Finding the anti- S. aureus agents is a time-consuming and costly process. Recently, computational methods have provided a better understanding of the interactions between herbal medicine drug targets to help clinical practitioners rationally design herbal formulae. Methods: In this study, molecular docking simulation was applied to screen a list of natural secondary metabolites from Ganoderma sp. on the protein target S. aureus sortase A. Molecular dynamics models were used to assess the stability of protein–ligand complexes during the first 100 ns. To validate the computational results, 2 Ganoderma species, G. multiplicatum VNKKK1901 and G. sinense VNKKK1902, were tested for antibacterial activity against S. aureus using the disk diffusion method. Results: The results showed that, among the selected compounds, ganosinensin B and ganosinoside A generated the highest binding energy on S. aureus sortase A, and demonstrated strong and stable binding capacity to proteins. In addition, the extracts of G. sinense VNKKK1902 and G. multiplicatum VNKKK1901 were bactericidal, with minimum bactericidal concentration (MBC)/minimum inhibitory concentration (MIC) ratios of 2. Conclusion: Our findings provide the first scientific report on the antibacterial activity of Ganoderma sp., which contain 2 promising compounds, ganosinensin B and ganosinoside A, as potential hits for developing novel drugs capable of supporting treatment of S. aureus infection.

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“…Finally, the molecular interactions between proteins and selected ligands were visualized by Discovery Studio Visualizer 2020, and their 3D and 2D interaction plots were derived. 15…”

Section: Molecular Docking Studymentioning

confidence: 99%

“…Recently, computational methods have provided a better understanding of the interactions between herbal medicine drug targets to help clinical practitioners design herbal formulae rationally. 15 In this study, we investigate anti- S. aureus activity of Ganoderma sp. using a virtual screening method.…”

Section: Introductionmentioning

confidence: 99%

Integrating in Silico and In Vitro Studies to Screen Anti-Staphylococcus aureus Activity From Vietnamese Ganoderma multiplicatum and Ganoderma sinense

Nguyen

et al. 2023

Natural Product Communications

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“…Researchers utilize the MCF‐7R cell line in BC studies to investigate the impact of TAM resistance on BC cells. This cell line is derived from MCF‐7 human BC cells that have developed resistance to TAM [108].…”

Section: Michigan Cancer Foundation – 7 Resistant (Mcf‐7r Cells)mentioning

confidence: 99%

Targeting autophagy with tamoxifen in breast cancer: From molecular mechanisms to targeted therapy

Zamanian

Golmohammadi

Nili‐Ahmadabadi

et al. 2023

Fundamemntal Clinical Pharma

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BackgroundTamoxifen (TAM) is often recommended as a first‐line treatment for estrogen receptor‐positive breast cancer (BC). However, TAM resistance continues to be a medical challenge for BC with hormone receptor positivity. The function of macro‐autophagy and autophagy has recently been identified to be altered in BC, which suggests a potential mechanism for TAM resistance. Autophagy is a cellular stress‐induced response to preserve cellular homeostasis. Also, therapy‐induced autophagy, which is typically cytoprotective and activated in tumor cells, could sometimes be non‐protective, cytostatic, or cytotoxic depending on how it is regulated.ObjectiveThis review explored the literature on the connections between hormonal therapies and autophagy. We investigated how autophagy could develop drug resistance in BC cells.MethodsScopus, Science Direct, PubMed, and Google Scholar were used to search articles for this study.ResultsThe results demonstrated that protein kinases such as pAMPK, BAX, and p‐p70S6K could be a sign of autophagy in developing TAM resistance. According to the study's findings, autophagy plays an important role in BC patients' TAM resistance.ConclusionTherefore, by overcoming endocrine resistance in estrogen receptor‐positive breast tumors, autophagy inhibition may improve the therapeutic efficacy of TAM.

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“…1 The application of in silico procedures supports identifying drug targets, evaluating compounds and protein interactions, pharmacokinetic analysis (ADME), and improving the drug properties of molecules. [2][3][4] These techniques will be a great precursor to new drug development works.…”

Section: Introductionmentioning

confidence: 99%

Xanthine Oxidase Inhibitory Activity of Fatty Acids From Hedyotis pilulifera: In Vitro and In Silico Studies

Nguyen

et al. 2023

Natural Product Communications

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The potential targeting of xanthine oxidase (XO) for the treatment of gout has been explored through animal and human experiments. To identify potential XO inhibitors, a virtual screening method was utilized to examine fatty acids from Hedyotis pilulifera. Molecular docking results demonstrated that all possible configurations of the fatty acid 9,12,13-trihydroxyoctadeca-10 E,15 Z-dienoic acid exhibited a strong binding affinity to XO. In vitro experiment also showed that this compound inhibited XO activity compared to the control compound. Molecular dynamic simulation was used to further investigate the interaction between the ligand and protein. Additionally, ADMET studies revealed that this compound has highly favorable drug-like properties and pharmacokinetics.

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Machine learning-based screening of MCF-7 human breast cancer cells and molecular docking analysis of essential oils from Ocimum basilicum against breast cancer

Cited by 23 publications

References 17 publications

Integrating in Silico and In Vitro Studies to Screen Anti-Staphylococcus aureus Activity From Vietnamese Ganoderma multiplicatum and Ganoderma sinense

Integrating in Silico and In Vitro Studies to Screen Anti-Staphylococcus aureus Activity From Vietnamese Ganoderma multiplicatum and Ganoderma sinense

Targeting autophagy with tamoxifen in breast cancer: From molecular mechanisms to targeted therapy

Xanthine Oxidase Inhibitory Activity of Fatty Acids From Hedyotis pilulifera: In Vitro and In Silico Studies

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