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Discovery of TGFBR1 (ALK5) as a potential drug target of quercetin glycoside derivatives (QGDs) by r

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


Quercetin glycoside derivatives (QGDs) are a class of common compounds with a wide range of biological activities, such as antitumor activities. However, their molecular targets associated with biological activities have not been investigated. In this study, four common QGDs with mutual bioconversion were selected, and studied in the large-scale reverse docking experiments. Network pharmacology analysis showed that most of the four QGDs can bind several potential protein targets that were closely related to breast cancer disease. Among them, a druggable protein, transforming growth factor beta receptor I (TGFBR1/ALK5) was screened via high docking scores for the four QGDs. This protein has been proven to be an important target for the treatment of breast cancer by regulating the proliferation and migration of cancer cells in the past. Subsequently, the molecular dynamics (MD) simulation and MM/GBSA calculation demonstrated that all QGDs could thermodynamically bind with TGFBR1, indicating that TGFBR1 might be one of the potential protein targets of QGDs. Finally, the cytotoxicity test and wound-healing migration assay displayed that isoquercetin, which can perform best in MD experiment, might be a promising agent in the treatment of breast cancer metastasis.



Quercetin, a kind of polyphenolic compounds, is widely distributed in lots of plants including various fruits and vegetables, as well as in several medicinal plants such as Ginkgo biloba, Hypericum perforatum, and elderberry. It shows various biological activities such as antioxidant, anti-inflammatory, antitumor activity, antiangiogenic activity, etc. As same as quercetin, its glycoside derivatives (QGDs), for example, rutin, isoquercitrin, quercitrin, and hyperoside, would exhibit to some extent consistent activity. The only structural differences between quercetin and their glycoside derivatives are different glycosyl groups. Considering minor differences between these compounds and their consistent activities, it is inferred that these derivatives might share a same macromolecule target in vivo.



The chemical structure of quercetin and four common QGDs


Transforming Growth Factor-β (TGF-β) signaling pathway is involved with many cellular processes including cell growth, cell differentiation, apoptosis, and cellular homeostasis. Transforming growth factor β receptor I (TGFBR1) as a serine/threonine protein kinase, is the central propagator of TGF-β signaling pathway. Mutations in this protein have been associated with breast cancer . Moreover, cancer susceptibility and progression can be blocked by TGFBR1 inhibitors. So far, several potent TGFBR1 inhibitors such as LY-2109761 , galunisertib , and SB-431542, have been developed, and some portion come into clinical studies. In addition, TGFBR1 inhibitors have been found to be effective against BRAF-mutant tumor cells. It is supposed that these inhibitors are involved with tumor cell microenvironment. Therefore, it is of significance to discover new potent TGFBR1 inhibitors for the treatment of malignant tumor.



Frequency distribution of docking score of each QGD compound derived from the reverse docking study. A) Rutin; B) Isoquercitrin; C) Quercitrin; D) Hyperoside.


In order to search some protein targets of the QGDs and investigate the correlation of targets among these derivatives, a large-scale reverse docking experiment was conducted. The most widespread and reliable method of virtual screening in the drug design should be molecular docking, which focuses on predicting the binding pose of candidate compounds in defined protein active pockets for scoring and screening out the best binders. Based on the molecular docking, reverse docking can assess the binding affinity of a known small molecule target to a large collection of clinically relevant proteins in known binding-sites, finally screening potential receptor proteins. Currently, there are a large number of databases and online tools available for searching and predicting potential drug targets for specific small molecule. Nevertheless, the accuracy of these tools cannot be comparable to that of the large-scale reverse docking study, especially in the protein target discovery.



The interaction network of “compound-target-pathway” of QGDs. Orange diamond nodes stand for QGDs; blue round nodes stand for known protein targets; yellow rectangle nodes stand for the main related diseases. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)


Although such predicting approach seems to be time-consuming, the prediction of protein targets with relative precision is acceptable. Moreover, further molecular dynamics (MD) study could be used for examining the binding mode of QGDs and internal dynamics changes of the protein to determine the optimal binding pose of the complexes. Due to the fact that the experimental measurement of thermodynamic properties of biomolecular systems is usually expensive and time-consuming, the theoretical calculation of free energy through numerical simulation becomes increasingly important. After verifying that the system is balanced, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) can be used to represent protein-ligand interaction in greater depth. The MM/GBSA is a free energy calculation method with high calculation efficiency and wide application. It calculates the binding free energy and energy decomposition of the molecular dynamic trajectory, and analyzes the contribution of the energy term to determine whether the structure is stable and the main interactions. In this study, the large-scale reverse docking and molecular dynamics (MD) simulation and preliminarily biological assay would be used for identifying potential targets of QGDs.



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

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

Biophysical Chemistry,

2021,

106731,

ISSN 0301-4622,

https://doi.org/10.1016/j.bpc.2021.106731.

(https://www.sciencedirect.com/science/article/pii/S0301462221002143)