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

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

Components of Src and its activation mechanisms.

<p>(A) SH2 binds to the phosphorylated Tyr530 and SH3 binds with prolines on the linker domain, effectively locking the Src in an inactive closed conformation. (B) Src is activated when Tyr530 is dephosphorylated and Tyr416 within the catalytic domain is autophosphorylated.</p

Spatial contour of test ligands to generated CoMFA maps.

<p>Map areas favoring and disfavoring steric fields are represented respectively in green and yellow. Saracatinib (A), Isopraeroside IV (B), and 9HGF (C) contoured well to the bioactivity map. A benzene ring of aurantiamide was located within the steric disfavoring region (D), suggesting lower bioactivity than it other tested ligands.</p

Ligplot diagrams illustrating protein-ligand interactions during docking.

<p>(A) Saracatinib, (B) Isopraeroside IV, (C) 9HFG, and (D) aurantiamide. Hydrophobic interactions are represented by red spokes radiating towards the ligand atoms they contact. Ligands are represented in purple. C, N, O, and Cl atoms are represented in black, blue, red, and green, respectively. Pink backgrounds highlight amino acids of the small lobe (267–337), and blue background highlight those belonging to the large lobe (340–520). Hydrophobic interactions shown in this illustration are calculated through the Ligplot algorithm.</p

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

CoMFA and CoMSIA models constructed from 53 known Src kinase inhibitors¹.

1<p>: Structures and inhibitory activities adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0033728#pone.0033728-Noronha1" target="_blank">[54]</a>.</p><p>ONC: Optimal number of components.</p><p>S: Steric.</p><p>SEE: Standard error of estimate.</p><p>E: Electrostatic.</p><p>F: F-test value.</p><p>H: Hydrophobic.</p><p>PLS: partial least squares.</p><p>D: Donor.</p>*<p>: Optimum prediction model.</p><p>A: Acceptor.</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

Summary of interaction type, location, and frequency of test ligands following docking and MD simulation.

*<p>: each letter denotes one interaction.</p><p>π: pi-interaction.</p><p>H: H-bond.</p