Recently, Histone Lysine Specific Demethylase 1 (LSD1) was regarded as a promising anticancer target for the novel drug discovery. And several small molecules as LSD1 inhibitors in different structures have been reported. In this work, we carried out a molecular modeling study on the 6-aryl-5-cyano-pyrimidine fragment LSD1 inhibitors using three-dimensional quantitative structure–activity relationship (3D-QSAR), molecular docking and molecular dynamics simulations. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were used to generate 3D-QSAR models. The results show that the best CoMFA model has q2 = 0.802, r2ncv = 0.979, and the best CoMSIA model has q2 = 0.799, r2ncv = 0.982. The electrostatic, hydrophobic and H-bond donor fields play important roles in the models. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. Molecular dynamics simulations results reveal that the complex of the ligand and the receptor protein are stable at 300 K. All the results can provide us more useful information for our further drug design.Download high-res image (64KB)Download full-size image

A series of fluoro-substituted imipramines and its analogues, 6a–6e, were synthesized and evaluated for their in vitro local anesthetic activity. Compound 6b was found to have potency, onset, and duration of action comparable to those of lidocaine (lidocaine hydrochloride, CAS:6108-05-0). Dissociation constants (pKa) of these compounds have been determined to be 7.6–7.9.