Screening the possible anti-cancer constituents of Hibiscus rosa-sinensis flower to address mammalian target of rapamycin: an in silico molecular docking, HYDE scoring, dynamic studies, and pharmacokinetic prediction

Rasul, Hezha O.; Aziz, Bakhtyar K.; Ghafour, Dlzar D; Kıvrak, Arif

doi:10.1007/s11030-022-10556-9

Cited by 25 publications

(5 citation statements)

References 73 publications

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“…The utilization of PyMOL facilitated the visualization and assessment of the active pocket structures [52] . To assess the effectiveness of the docking approach, the root‐mean‐square deviation (RMSD) was calculated by re‐docking the crystal ligand into the target protein [53–55] . The interactions between the chosen proteins and ligand molecules were visualized and examined using PyMOL [56] .…”

Section: Methodsmentioning

confidence: 99%

“…[52] To assess the effectiveness of the docking approach, the rootmean-square deviation (RMSD) was calculated by re-docking the crystal ligand into the target protein. [53][54][55] The interactions between the chosen proteins and ligand molecules were visualized and examined using PyMOL. [56] Furthermore, the Protein-Ligand Interaction Profiler (PLIP) [57] was employed to analyze the overall count of non-covalent interactions present in the protein-ligand complexes.…”

Section: Molecular Docking Studiesmentioning

confidence: 99%

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Carbon Dots from Tire Waste for the Photodegradation of Methyl Orange Dye, Antimicrobial Activity, and Molecular Docking Study

Mohammad

2023

Chemistry & Biodiversity

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In this study, solvothermal pathway was employed for the synthesis of P, N codoped C‐dot using tire waste as a sustainable source of carbon and nitrogen. Comprehensive analyses encompassing X‐ray diffraction (XRD) analysis, Transmission Electron Microscopy (TEM), FT‐IR, cyclic voltammetry, and UV‐Vis spectra were used to assess the crystalline structure, purity, size, fluorescence up‐conversion, and morphological attributes of the nanomaterial. Subsequently, the produced C‐dots were evaluated for their efficacy in the photocatalytic degradation of methylene blue and methyl orange dyes, demonstrating notable success in degrading MO within eight hours in the visible region. Furthermore, the nanomaterial was applied for carrying out agar disk‐diffusion assays against a spectrum of microorganisms. Results revealed substantial inhibition zones against Methicillin‐Resistant Staphylococcus aureus (MRSA), Escherichia coli, and Pseudomonas aeruginosa. Elucidating the antimicrobial mechanism, molecular‐docking simulations were excuted using on AutoDock Vina with designated ligands. The results indicated a strong binding affinity of the C‐dots with certain proteins associated with antibacterial activity. This observation suggests that the synthesized C‐dots effectively engage with the active sites of these proteins, indicating their potential as promising antibacterial agents. Importantly, this study implies that C‐dots do not induce protein denaturation, thereby warranting further investigation of their utility as antibacterial agents.

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Section: Methodsmentioning

confidence: 99%

Section: Molecular Docking Studiesmentioning

confidence: 99%

Carbon Dots from Tire Waste for the Photodegradation of Methyl Orange Dye, Antimicrobial Activity, and Molecular Docking Study

Mohammad

2023

Chemistry & Biodiversity

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“…Therefore, identifying small molecules capable of inhibiting TNFα could be therapeutically beneficial in treating neurodegenerative disorders associated with chronic inflammation. Here, we utilized SeeSAR, a structure-based drug design software tool, to study the interaction between yohimbine and TNFα [68,69]. Our analysis has demonstrated that yohimbine exhibits a stable interaction with TNFα, as indicated by a Hyde score of -1.0 kJ/mol, suggesting favourable binding.…”

Section: Molecular Docking Of Tnfα-yohimbinementioning

confidence: 99%

In Silico Identification of a Potential TNF-Alpha Binder Using a Structural Similarity: A Potential Drug Repurposing Approach to the Management of Alzheimer’s Disease

Tettevi,

Kuevi,

Sumabe

et al. 2024

BioMed Research International

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Introduction. Alzheimer’s disease (AD) is a neurodegenerative disorder with no conclusive remedy. Yohimbine, found in Rauwolfia vomitoria, may reduce brain inflammation by targeting tumour necrosis factor-alpha (TNFα), implicated in AD pathogenesis. Metoserpate, a synthetic compound, may inhibit TNFα. The study is aimed at assessing the potential utility of repurposing metoserpate for TNFα inhibition to reduce neuronal damage and inflammation in AD. The development of safe and effective treatments for AD is crucial to address the growing burden of the disease, which is projected to double over the next two decades. Methods. Our study repurposed an FDA-approved drug as TNFα inhibitor for AD management using structural similarity studies, molecular docking, and molecular dynamics simulations. Yohimbine was used as a reference compound. Molecular docking used SeeSAR, and molecular dynamics simulation used GROMACS. Results. Metoserpate was selected from 10 compounds similar to yohimbine based on pharmacokinetic properties and FDA approval status. Molecular docking and simulation studies showed a stable interaction between metoserpate and TNFα over 100 ns (100000 ps). This suggests a reliable and robust interaction between the protein and ligand, supporting the potential utility of repurposing metoserpate for TNFα inhibition in AD treatment. Conclusion. Our study has identified metoserpate, a previously FDA-approved antihypertensive agent, as a promising candidate for inhibiting TNFα in the management of AD.

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“…Furthermore, in silico studies are being run on less-explored compounds of Hibiscus species. On the one hand, mTOR binding affinities were found for stigmastadienol, lupeol, and taraxasterol acetate-all present in Hibiscus rosa-sinensis [263]. On the other hand, the estrogenic activity of polyphenols such as pelargonidin, delphinidin, cyanidin, and hibiscetin has proven to bind to the ER-α subunit more efficiently than cancer drugs such as Tamoxifen and Raloxifene and with a more favorable toxicological profile [264].…”

Section: Ficus Deltoidea Lmentioning

confidence: 99%

Advances in Molecular Regulation of Prostate Cancer Cells by Top Natural Products of Malaysia

Prieto

Hanafi

2023

CIMB

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Prostate cancer (PCa) remains both a global health burden and a scientific challenge. We present a review of the molecular targets driving current drug discovery to fight this disease. Moreover, the preventable nature of most PCa cases represents an opportunity for phytochemicals as chemopreventive when adequately integrated into nutritional interventions. With a renovated interest in natural remedies as a commodity and their essential role in cancer drug discovery, Malaysia is looking towards capitalizing on its mega biodiversity, which includes the oldest rainforest in the world and an estimated 1200 medicinal plants. We here explore whether the list of top Malay plants prioritized by the Malaysian government may fulfill the potential of becoming newer, sustainable sources of prostate cancer chemotherapy. These include Andrographis paniculate, Centella asiatica, Clinacanthus nutans, Eurycoma longifolia, Ficus deltoidea, Hibiscus sabdariffa, Marantodes pumilum (syn. Labisia pumila), Morinda citrifolia, Orthosiphon aristatus, and Phyllanthus niruri. Our review highlights the importance of resistance factors such as Smac/DIABLO in cancer progression, the role of the CXCL12/CXCR4 axis in cancer metastasis, and the regulation of PCa cells by some promising terpenes (andrographolide, Asiatic acid, rosmarinic acid), flavonoids (isovitexin, gossypin, sinensetin), and alkylresorcinols (labisiaquinones) among others.

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Screening the possible anti-cancer constituents of Hibiscus rosa-sinensis flower to address mammalian target of rapamycin: an in silico molecular docking, HYDE scoring, dynamic studies, and pharmacokinetic prediction

Cited by 25 publications

References 73 publications

Carbon Dots from Tire Waste for the Photodegradation of Methyl Orange Dye, Antimicrobial Activity, and Molecular Docking Study

Carbon Dots from Tire Waste for the Photodegradation of Methyl Orange Dye, Antimicrobial Activity, and Molecular Docking Study

In Silico Identification of a Potential TNF-Alpha Binder Using a Structural Similarity: A Potential Drug Repurposing Approach to the Management of Alzheimer’s Disease

Advances in Molecular Regulation of Prostate Cancer Cells by Top Natural Products of Malaysia

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