In Silico Investigation of Potential Src Kinase Ligands from Traditional Chinese Medicine

Src kinase is an attractive target for drug development based on its established relationship with cancer and possible link to hypertension. The suitability of traditional Chinese medicine (TCM) compounds as potential drug ligands for further biological evaluation was investigated using structure-based, ligand-based, and molecular dynamics (MD) analysis. Isopraeroside IV, 9alpha-hydroxyfraxinellone-9-O-beta-D-glucoside (9HFG) and aurantiamide were the top three TCM candidates identified from docking. Hydrogen bonds and hydrophobic interactions were the primary forces governing docking stability. Their stability with Src kinase under a dynamic state was further validated through MD and torsion angle analysis. Complexes formed by TCM candidates have lower total energy estimates than the control Sacaratinib. Four quantitative-structural activity relationship (QSAR) in silico verifications consistently suggested that the TCM candidates have bioactive properties. Docking conformations of 9HFG and aurantiamide in the Src kinase ATP binding site suggest potential inhibitor-like characteristics, including competitive binding at the ATP binding site (Lys295) and stabilization of the catalytic cleft integrity. The TCM candidates have significantly lower ligand internal energies and are estimated to form more stable complexes with Src kinase than Saracatinib. Structure-based and ligand-based analysis support the drug-like potential of 9HFG and aurantiamide and binding mechanisms reveal the tendency of these two candidates to compete for the ATP binding site

May disordered protein cause serious drug side effect?

[[abstract]]Insomnia is a self-reported disease where patients lose their ability to initiate and maintain sleep, leading to daytime performance impairment. Several drug targets to ameliorate insomnia symptoms have been discovered; however, these drug targets lead to serious side effects. Thus, we characterize the structural properties of these sleep-related receptors and the clock complex and discuss a possible drug design that will reduce side effects. Computational prediction shows that disordered property is shared. Over 30% of the structure of CLOCK, PER1/2/3, BMAL-1, muscarinic acetylcholine receptor-M1, melatonin receptor and casein kinase I are structurally disordered (the remaining proteins represent <30%). Investigations support the principle that the failures of insomnia drugs might be closely related to the protein architecture. Copyright © 2013 Elsevier Ltd. All rights reserved

Traditional Chinese medicine as dual guardians against hypertension and cancer?

<div><p>This study utilizes the comprehensive traditional Chinese medicine database TCM Database@Taiwan (<a href="http://tcm.cmu.edu.tw/" target="_blank">http://tcm.cmu.edu.tw/</a>) in conjunction with structure-based and ligand-based drug design to identify multi-function Src inhibitors. The three potential TCM candidates identified as having suitable docking conformations and bioactivity profiles were Angeliferulate, (3R)-2′-hydroxy-3′,4′-dimethoxyisoflavan-7-O-beta-D-glucoside (HMID), and 3-[2′,6-dihydroxy-5′-(2-propenyl)[1,1′-biphenyl]3-yl]-(E)-2-propenoic acid (3PA). Molecular dynamics simulation demonstrated that the TCM candidates have more stable interactions with the cleft and in complex with Src kinase compared to Saracatinib. Angeliferulate and HMID, both originated from <i>Angelica sinensis</i>, not only interact with Lys298 and amino acids from different loops in the cleft, but also with Asp407 located on the activation loop. These interactions are important to reduce the opening of the activation loop due to phosphorylation, hence stabilize the Src kinase cleft structure and inhibit activation. The TCM candidates also exhibited high affinity to other cancer-related target proteins (EGFR, HER2, and HSP90). Our observations suggest that the TCM candidates might have multi-targeting effects in hypertension and cancer.</p> <p>An animated Interactive 3D Complement (I3DC) is available in Proteopedia at <a href="http://proteopedia.org/w/Journal:JBSD:14" target="_blank">http://proteopedia.org/w/Journal:JBSD:14</a></p> </div

Mechanisms underlying Src kinase inhibition and activation.

<p>(A) Based on the molecular interactions observed through MD, TCM candidates 9HFG and aurantiamide (A; violet diamond) may inhibit Src kinase activation through different pathways. Aurantiamide binds directly to Lys295, competing with ATP for the binding site. 9HGF also binds to Lys295, but has additional binding with Asp404, which acts similarly to Mg²⁺ found in native Src kinase. (B) The bridging function of Mg²⁺ between Lys295 and Asp404 in native Src kinase.</p

Docking poses of different ligands in Src kinase ATP binding pocket.

<p>Shown are snapshots of (A) Saracatinib,(B) Isopraeroside IV, (C) 9HFG, and (D) aurantiamide during docking simulation with Src kinase. Purple and blue surfaces are added to denote the small lobe (267–337) and large lobe (340–520) of Src kinase, respectively. Hydrogen bonds are shown as dotted green lines and pi-interactions are shown in orange. (A) Pi-interactions with Lys273 and Lys295 are critical for Saracatinib. (B) Isopraeroside IV docks to the outer region of the ATP binding pocket via H-bonds at Ser345 and Asp348. (C) 9HFG structure enables docking in the inner regions of the ATP binding pocket, forming H-bonds with Lys295 and Asp404. (D) Similar to Saracatinib, aurantiamide forms pi-interactions with Lys295, in addition to H-bonds with Ser345 and Asp348.</p

Ligand-protein interactions determined through LigPlot.

1<p>Amino acid residues where hydrophobic interactions are observed are denoted by the “+” symbol.</p><p>A: hydrophobic interaction.</p><p>H1: form one hydrogen bond between ligand and amino acid.</p><p>H2: form two hydrogen bond between ligand and amino acid.</p

H-bond distance and occupancies¹ of different ligands during MD.

1<p>: Occupancy calculated based on the default cut-off distance of 2.5 Å.</p

Adsorption, distribution, metabolism, toxicity properties and predicted pIC₅₀ of Saracatinib and the top three TCM compounds.

*<p>Control.</p>1<p>ADMET Adsorption levels: 0 = Good; 1 = Moderate; 2 = Low; 3 = Very low.</p>2<p>Plasma Protein Binding: 0 = Binding <90% ;1 = Binding >90%; 2 = Binding >95%.</p>3<p>Inhibition probability of Cytochrome P450 2D6 enzyme.</p>4<p>Hepatoxicity: 0 = Nontoxic; 1 = Toxic.</p

Torsion angles of test candidates during MD simulation.

<p>Torsion angle measured is designated by a lower case alphabet which corresponds to the radar chart with the same alphabet. Red numbers indicate the locations where H-bonds are formed. (numbering corresponds to those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033728#pone-0033728-t005" target="_blank">Table 5</a>). Blue lines indicate the torsion angles recorded; the red and gray lines indicate the angle during docking and at time 0 of MD, respectively.</p