Using molecular docking analysis to discovery Dregea sinensis Hemsl. potential mechanism of anticancer, antidepression, and immunoregulation

Abstract

Background:Dregea sinensis Hemsl. plant of the genus Dregea volubilis (Asclepiadaceae), plays a vital role in anticancer, antidepression, and immunoregulation. Steroidal glycosides are the main constituents of this herb, which were significant biological active ingredients.Objective:The objective of this study is to recognize the mechanism of anticancer, antidepression, and immunoregulation of D. sinensis Hemsl.Materials and Methods:Seventy-two steroidal glycosides of D. sinensis Hemsl. were evaluated on the docking behavior of tumor-associated proteins (PI3K, Akt, mTOR), depression-related proteins (MAO-A, MAO-B) and immune-related proteins (tumor necrosis factor-α [TNF-α], tumor necrosis factor receptor 2 [TNFR2], interleukin-2Rα [IL-2Rα]) using Discovery Studio version 3.1 (Accelrys, San Diego, USA).Results:The molecular docking analysis revealed that mostly steroidal glycosides of D. sinensis Hemsl. exhibited powerful interaction with the depression-related protein (MAO-A) and the immune-related proteins (TNFR2, IL-2Rα). Some ligands exhibited high binding energy for the tumor-associated proteins (PI3K, Akt, mTOR) and the immune-related protein (TNF-α), but MAO-B showed none interaction with the ligands.Conclusion:This study has paved better understanding of steroidal glycosides from D. sinensis Hemsl. as potential constituents to the prevention of associated cancer, depression and disorders of immunoregulation.SUMMARY The ligand database was consist of 72 steroidal glycosides from Dregea sinensis HemslSteroidal glycosides had the potential to dock with the tumor-associated proteins (PI3K, Akt, mTOR)Steroidal glycosides were bounded with MAO-A rather than MAO-B, accorded with the inhibitor selectivity of MAOs, can be considered as potent candidate inhibitors of MAO-A72 ligands got high interaction with TNFR2 and IL-2Rα, regard the steroidal glycoside as powerful candidate inhibitors of TNFR2 and IL-2Rα. Abbreviations used: PI3K: Phosphatidyl inositol 3-kinase; Akt: Protein kinase B; mTOR: Mammalian target of rapamycin; MAO-A: Monoamine oxidase A; MAO-B: Monoamine oxidase B; TNF-α: Tumor necrosis factor α; TNFR2: Tumor necrosis factor receptor 2; IL-2Rα: The alpha subunit (CD25) of the interleukin-2 receptor; DS: Discovery Studio; PDB: Protein Database Bank; 3D: three-dimensional.

Tanshinone IIA confers protection against myocardial ischemia/reperfusion injury by inhibiting ferroptosis and apoptosis via VDAC1

“…The molecular docking simulation was performed using Discovery Studio 4.5 software ( 26 ). The three-dimensional structure of VDAC1 for molecular docking was obtained from AlphaFold database (UniProt ID: P21796) ( 27 ) and the structure of TSN was obtained from PubChem (PubChem CID: 164676) ( 28 ).…”

Bupleurum marginatum Wall.ex DC in Liver Fibrosis: Pharmacological Evaluation, Differential Proteomics, and Network Pharmacology

“…The mobile phase A contained 0.1% formic acid (v/v) in water, whereas ACN was used as mobile phase B. Peptides were separated using a C18 column (1.8 μm, 0.15 × 1.00 mm) at an eluent flow rate of 300 nL/min using a linear 198 min gradient consisting of 2–25% B over 182 min, 25–35% B over 4 min, 35–90% B over 2 min, and 90% B over 1 min. The mass spectrum sampling method was performed using a data-dependent model as described elsewhere (Liu et al, 2017a ). In brief, the medium isolation width was m/z 1.0, and the mass ranges of the MS1 and MS2 scans were set at 350–1600 in high sensitivity mode (resolution = 30,000).…”

Conserved B-cell epitope identification of envelope glycoprotein (GP120) HIV-1 to develop multi-strain vaccine candidate through bioinformatics approach

“…16 The result of docking simulation was used to analyze the chemical bond interaction and position on the peptide-BCR complex through Discovery Studio 2017. 17 Molecular dynamic simulations were carried out through CABSflex 2.0 server (http://biocomp.chem.uw.edu.pl/CABSflex2/index) to determine stable RMSF of vaccine candidate peptides in hotspot interaction with BCR activity. 18…”