Discovery of TGFBR1 (ALK5) as a potential drug target of quercetin glycoside derivatives (QGDs) by reverse molecular docking and molecular dynamics simulation

Xu, Jiahui; Zhang, Shanshan; Wu, Tao; Fang, Xianying; Zhao, Linguo

doi:10.1016/j.bpc.2021.106731

Cited by 7 publications

(3 citation statements)

References 57 publications

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“…Root-mean-squared fluctuation (RMSF) calculates the increase and decrease of each atom relative to its average position, characterizing the change in structure averaged over time, i.e., giving a characterization of the flexibility of each region of the protein ( Işık et al, 2022 ; Xu et al, 2022 ). All results are shown in Figures 2C–E .…”

Section: Resultsmentioning

confidence: 99%

Two-carbon tethered artemisinin–isatin hybrids: design, synthesis, anti-breast cancer potential, and in silico study

Wang,

Huang,

Yuan

et al. 2023

Front. Mol. Biosci.

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Eleven two-carbon tethered artemisinin–isatin hybrids (4a–k) were designed, synthesized, and evaluated for their antiproliferative activity against MCF-7, MDA-MB-231, and MDA-MB-231/ADR breast cancer cell lines, as well as cytotoxicity toward MCF-10A cells in this paper. Among them, the representative hybrid 4a (IC50: 2.49–12.6 µM) was superior to artemisinin (IC50: 72.4->100 µM), dihydroartemisinin (IC50: 69.6–89.8 µM), and Adriamycin (IC50: 4.46–>100 µM) against the three tested breast cancer cell lines. The structure–activity relationship revealed that the length of the alkyl linker between artemisinin and isatin was critical for the activity, so further structural modification could focus on evaluation of the linker. The in silico studies were used to investigate the mechanism of the most promising hybrid 4a. Target prediction, bioinformatics, molecular docking, and molecular dynamics revealed that the most promising hybrid 4a may exert anti-breast cancer activity by acting on multiple targets such as EGFR, PIK3CA, and MAPK8 and thus participating in multiple tumor-related signaling pathways.

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Section: Resultsmentioning

confidence: 99%

Two-carbon tethered artemisinin–isatin hybrids: design, synthesis, anti-breast cancer potential, and in silico study

Wang,

Huang,

Yuan

et al. 2023

Front. Mol. Biosci.

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“…Binding energy is also an important criterion for considering the interaction between proteins and ligands, and the lowest binding energy is considered to be more stable. Epidermal growth factor receptor (EGFR1), fibroblast growth factor (FGFR1), and matrix metalloproteinase (MMP-1) play important roles in cell proliferation, tissue remodeling, and wound healing [ 20 ]. Thus, it not only helped us to screen for the best peptide sequence FAFQAEIAQLMS, but also further elucidated the mechanism of the significant cell proliferation promotion by PMPPs.…”

Section: Discussionmentioning

confidence: 99%

Investigation of the In Vivo, In Vitro, and In Silico Wound Healing Potential of Pinctada martensii Purified Peptides

et al. 2022

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Previous studies found that both oral and topical administration of enzymatic digestion products < 3 K Da ultrafiltration fractions of Pinctada martensii mantle (PMPs) had pro-healing effects. Thus, we further purified them by Sephadex-G25 and screened them by cellular assays to obtain Pinctada martensii purified peptides (PMPPs). In this study, we explored the mechanism of PMPPs on wound healing by in vivo, in vitro, and in silico experiments. LC-MS/MS results showed that PMPPs consisted of 33 peptides with molecular weights ranging from 758.43 to 2014.04 Da, and the characteristic peptide was Leu-Asp. The results of cellular assays showed that PMPPs promoted the proliferation of human skin fibroblasts (HSF) (135%) and human immortalized keratinocyte (HaCaT) cells (125%) very significantly at 12.5 μg/mL. The in vivo results showed that PMPPs could achieve scarless healing by inhibiting the inflammatory response, accelerating the epithelialization process, and regulating collagen I/III ratio. The optimal peptide sequence FAFQAEIAQLMS of PMPPs was screened for key protein receptors in wound healing (EGFR1, FGFR1, and MMP-1) with the help of molecular docking technique, which also showed to be the key pro-healing active peptide sequence. Therefore, it may provide a therapeutic strategy with great potential for wound healing.

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“…Using the Prime/MM-GBSA computations provided in Schrodinger Suite 2020-3, at pH 7 ± 2 the free binding energy ΔG bind for EGFR-TKIs systems were prepared according to the OPLS3e force field and the VSGB 2.1 solvent model [ 90 , 91 ]. This procedure was implemented as an aid protocol for molecular docking simulations towards the identification of potentially most stable systems for their validation by molecular dynamics simulation (for details, see the supplementary information).…”

Section: Methodsmentioning

confidence: 99%

Repositioning Cannabinoids and Terpenes as Novel EGFR-TKIs Candidates for Targeted Therapy Against Cancer: A virtual screening model using CADD and biophysical simulations

Daoui¹,

Mali²,

Elkhattabi³

et al. 2023

Heliyon

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Discovery of TGFBR1 (ALK5) as a potential drug target of quercetin glycoside derivatives (QGDs) by reverse molecular docking and molecular dynamics simulation

Cited by 7 publications

References 57 publications

Two-carbon tethered artemisinin–isatin hybrids: design, synthesis, anti-breast cancer potential, and in silico study

Two-carbon tethered artemisinin–isatin hybrids: design, synthesis, anti-breast cancer potential, and in silico study

Investigation of the In Vivo, In Vitro, and In Silico Wound Healing Potential of Pinctada martensii Purified Peptides

Repositioning Cannabinoids and Terpenes as Novel EGFR-TKIs Candidates for Targeted Therapy Against Cancer: A virtual screening model using CADD and biophysical simulations

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