• Bulletin of the Korean Chemical Society
• /
• v.32 no.1
• /
• pp.251-262
• /
• 2011

Human ether-a-go-go related gene (hERG) potassium channel blockade, an undesirable side effect which might cause sudden cardiac death, is one of the major concerns facing the pharmaceutical industry. The purpose of this study is to develop an in silico QSAR model which uncovers the structural parameters of T-type calcium channel blockers to reduce hERG blockade. Comparative molecular similarity indices analysis (CoMSIA) was conducted on a series of piperazine and benzimidazole derivatives bearing methyl 5-(ethyl(methyl)amino)-2-isopropyl-2-phenylpentanoate moieties, which was synthesized by our group. Three different alignment methods were applied to obtain a reliable model: ligand based alignment, pharmacophore based alignment, and receptor guided alignment. The CoMSIA model with receptor guided alignment yielded the best results : $r^2$ = 0.955, $q^2$ = 0.781, $r^2_{pred}$ = 0.758. The generated CoMSIA contour maps using electrostatic, hydrophobic, H-bond donor, and acceptor fields explain well the structural requirements for hERG nonblockers and also correlate with the lipophilic potential map of the hERG channel pore.

• Journal of the Korean Chemical Society
• /
• v.29 no.5
• /
• pp.522-532
• /
• 1985

The reactions of p-nitrophenyldiphenylphosphate (p-NPDPP) with anions of benzimidazole (BI) and its 2-alkyl derivatives (R-BI) are strongly catalyzed by the micelles of cetyltrimethyl ammonium bromide (CTABr). On the other hand, the first order rate constants $(k'_{R-BI^-})$ and the second order rate constants $(k_{m(R-BI^-)})$ of the reactions mediated by R-$BI^-$in the micellar pseudophase are much smaller than those mediated by $BI^-$. In order to explain the slower rates of the micellar reactions mediated by R-$BI^-$, we compared the concentration-ratios ([R-$BI^-$]/[$BI^-$]) with the first order rate constant-ratios $(k'_{R-BI^-}/k'_{BI^-})$ and the second order constant-ratios $(k_{m(R-BI^-)}/k_{m(BI^-)})$ for the reactions taking place in the micellar pseudophase. The rate constant-ratios were much smaller than the concentration-ratios. For example in a 5 ${\times}10^{-4}$M butyl-BI solution, the two ratios were 0.089 and 0.430 (for the first order) respectively, and in a $10^{-4}$M butyl-BI solution the former was 0.100 (for the second order). This predicts that the reactivities of R-$BI^-$ in the micellar pseudophase are much smaller than that of $BI^-$. Based on the values of several kinetic parameters measured for dephosphorylation of p-NPDPP mediated by R-$BI^-$, a schemetic model is proposed. Due to the hydrophobicity and the steric effect of the alkyl substituents, these groups would penetrate into the core of the micelle for stabilization by van der Waals interaction with long cetyl groups of CTABr. Consequently, the movements of R-$BI^-$ bound to the micelle should be restricted, leading to decreased collison frequencies between the nucleophiles and p-NPDPP. We refer this as an "anchor effect". This effect became more predominent when a larger alky group in R-BI was employed and when a greater concentration of R-BI was used.