Antimicrobial Activity, in silico Molecular Docking, ADMET and DFT Analysis of Secondary Metabolites from Roots of Three Ethiopian Medicinal Plants

Anza, Mathewos; Endale, Milkyas; Cardona, Luz; Cortés, Diego; Eswaramoorthy, Rajalakshmanan; Zueco, Jesús; Rico, Hortensia; Trelis, María; Abarca, Belén

doi:10.2147/aabc.s323657

Cited by 28 publications

(18 citation statements)

References 38 publications

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“…Auto Grid generated these maps before the docking run. The interaction energy between the ligand atom and the receptor was calculated for the entire binding site, which is discretized using a grid for each ligand atom type (Anza et al, 2021; Lončarić et al, 2020). The binding affinity of the ligands was calculated, and the docked poses were observed using Pymol software ver 1.7.…”

Section: Methodsmentioning

confidence: 99%

Nimbin analog N2 alleviates high testosterone induced oxidative stress in CHO cells and alters the expression of Tox3 and Dennd1a signal transduction pathway involved in the PCOS zebrafish

Sudhakaran

Rajesh

Murugan

et al. 2022

Phytotherapy Research

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Polycystic ovarian syndrome (PCOS) is a hormonal disorder that causes enlargement of ovaries and follicular maturation arrest, which lacks efficient treatment. N2, a semi-natural triterpenoid from the neem family, was already reported to have antioxidant and antiinflammatory properties in our previous report. This study investigated the anti-androgenic property of N2 on testosterone-induced oxidative stress in Chinese Hamster Ovarian cells (CHO) and PCOS zebrafish model. The testosterone exposure disrupted the antioxidant enzymes and ROS level and enhanced the apoptosis in both CHO cells and PCOS zebrafish. However, N2 significantly protected the CHO cells from ROS and apoptosis. N2 improved the Gonado somatic index (GSI) and upregulated the expression of the SOD enzyme in zebrafish ovaries. Moreover, the testosterone-induced follicular maturation arrest was normalized by N2 treatment in histopathology studies. In addition, the gene expression studies of Tox3 and Denndla in zebrafish demonstrated that N2 could impair PCOS condition. Furthermore, to confirm the N2 activity, the in-silico studies were performed against PCOS susceptible genes Tox3 and Dennd1a using molecular docking and molecular dynamic simulations. The results suggested that N2 alleviated the oxidative stress and apoptosis in-vitro and in-vivo and altered the expression of PCOS key genes.

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Section: Methodsmentioning

confidence: 99%

Nimbin analog N2 alleviates high testosterone induced oxidative stress in CHO cells and alters the expression of Tox3 and Dennd1a signal transduction pathway involved in the PCOS zebrafish

Sudhakaran

Rajesh

Murugan

et al. 2022

Phytotherapy Research

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show abstract

“…Additionally, a large energy gap increases the global hardness of compounds as follows: Ia>Ib>IIa>IIb, and their chemical reactivity decrease in the reverse order: Ia<Ib<IIa<IIb [28]. These results show that all compounds exhibit a low energy gap, suggesting a significant intramolecular charge from HOMO to LUMO groups and high chemical reactivity [29,30]. Besides, like electronegativity and hardness, the electrophilicity index ω, as an indicator of reactivity, measures the stabilization energy when the system acquires an additional electronic charge [31].…”

Section: Discussionmentioning

confidence: 84%

“…The Molecular Docking on perfluorinated derivatives Ia-b and IIa-b against Human DNA Topoisomerase II α (PDB ID 3QX3) indicates that compounds Ib, and IIa-b show a strong binding affinity towards the mentioned target (Table 5) with binding energy values ranging from -8.1 to -10.0 Kcal/mol compared to vosaroxin (−6.2 kcal/mol) [29]. S-(perfluoro-[1, 1'-biphenyl]-4-yl)-L-cysteine (IIa) and S-(perfluoro-[1, 1'-biphenyl]-4-yl)-L-glutathione (IIb) present the higher binding affinity -9.5 and 10.0 Kcal/mol.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, human topoisomerase II alpha (PDB ID: 3QX3) was used to test the bioactivity of synthesized linker cargoes. The protein preparation was performed using the reported protocol [29,50], removing the crystallized ligand, cofactors, and water molecules. AutoDock graphical interface was employed to set the grid for molecular docking simulation whose lengths are 90, 90 and 90, pointing in x, y, and z directions for 3QX3.…”

Section: Molecular Dockingmentioning

confidence: 99%

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A Theoretical and Experimental Study of Cysteine-Based Perfluorinated Derivatives

Chalán-Gualán¹,

Ramos-Tomillero²,

Terencio³

et al. 2022

Preprint

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A series of cysteine-based perfluoroaromatic (hexafluorobenzene (I) and decafluorobiphenyl (II) were synthesized and established as a chemoselective and available core to simple or more complex systems since small molecules to biomolecules with interesting properties. As proof of concept of the potential application of perfluorinated derivatives as non-cleavable linkers, some antibody-perfluorinated conjugates were prepared via thiol, demonstrating that the bioconjugation process doesn’t affect to the macromolecular entity. Besides, some molecular properties of synthesized compounds are evaluated using a combination of spectroscopic characterization (FT-IR and 19F-NMR chemical shifts) and theoretical calculations. Moreover, molecular Docking was also developed to predict cysteine-based hexafluorobenzene and decafluorobiphenyl derivatives’ affinity against topoisomerase Il and cyclooxygenase 2 (COX-2). The results suggested that mainly cysteine-based decafluorobiphenyl derivatives could be potential topoisomerase II α and COX-2 inhibitors, becoming potential anticancer agents and candidates for anti-inflammatory treatment.

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“…Classes I, II, and III have less toxicity, whereas Class IV displays no toxicity [57]. Moreover, PROTOX is a rodent oral toxicity server that is used to determine LD50 values and toxicity classes of potentially cytotoxic agents [58]. Based on the molecular docking drug-likeness data and toxicity data, phytoconstituents were selected for further MD simulation analysis.…”

Section: Toxicity Prediction Of F Vulgare Phytoconstituents By Protox...mentioning

confidence: 99%

An In Silico Investigation to Explore Anti-Cancer Potential of Foeniculum vulgare Mill. Phytoconstituents for the Management of Human Breast Cancer

et al. 2022

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Breast cancer is one of the most prevalent cancers in the world. Traditionally, medicinal plants have been used to cure various types of diseases and disorders. Based on a literature survey, the current study was undertaken to explore the anticancer potential of Foeniculum vulgare Mill. phytoconstituents against breast cancer target protein (PDB ID: 6CHZ) by the molecular docking technique. Molecular docking was done using Autodock/vina software. Toxicity was predicted by the Protox II server and drug likeness was predicted by Molinspiration. 100 ns MD simulation of the best protein-ligand complexes were done using the Amber 18 tool. The present molecular docking investigation has revealed that among the 40 selected phytoconstituents of F. vulgare, α-pinene and D-limonene showed best binding energy (−6 and −5.9 kcal/mol respectively) with the breast cancer target. α-Pinene and D-limonene followed all the parameters of toxicity, and 100 ns MD simulations of α-pinene and D-limonene complexes with 6CHZ were found to be stable. α-Pinene and D-limonene can be used as new therapeutic agents to cure breast cancer.

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Antimicrobial Activity, in silico Molecular Docking, ADMET and DFT Analysis of Secondary Metabolites from Roots of Three Ethiopian Medicinal Plants

Cited by 28 publications

References 38 publications

Nimbin analog N2 alleviates high testosterone induced oxidative stress in CHO cells and alters the expression of Tox3 and Dennd1a signal transduction pathway involved in the PCOS zebrafish

Nimbin analog N2 alleviates high testosterone induced oxidative stress in CHO cells and alters the expression of Tox3 and Dennd1a signal transduction pathway involved in the PCOS zebrafish

A Theoretical and Experimental Study of Cysteine-Based Perfluorinated Derivatives

An In Silico Investigation to Explore Anti-Cancer Potential of Foeniculum vulgare Mill. Phytoconstituents for the Management of Human Breast Cancer

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