Insight into the Structural Determinants of Imidazole Scaffold-Based Derivatives as P38 MAP Kinase Inhibitors by Computational Explorations

C.      Huang; Y.      Li; H.      Ren; J.      Wang; L.      Shao; S.      Zhang; G.      Li; L.      Yang

Abstract

P38 kinase plays a vital role in the inflammation mediated by tumor necrosis factor-α and interleukin-1β pathways, and thus the inhibitors of p38 kinase provide effective approach for the treatment of inflammatory diseases. Presently, a combined study of threedimensional quantitative structure-activity relationship, molecular docking and molecular dynamics (MD) was undertaken to explore the structural insights of 174 2-thioimidazole compounds influencing the p38α inhibitory activities. Both the ligand-based resultant comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models exhibited satisfactory predictability (with Q2=0.475, R2 ncv=0.774, R2 pre=0.668 and Q2=0.504, R2 ncv=0.745, R2 pre=0.709, respectively). Furthermore, good consistency was observed between the 3D-QSAR models, docking and MD results. Our findings are: i) hydrogen bonding and steric size of the molecules play crucial roles in the mechanisms of action that a medium-sized bulky substituent on the 2-position, an electropositive H-bond donor substituent on the 6-position of the pyridine ring are favorable for increasing the inhibition activity; ii) 2- Thioimidazole derivatives may bind to the p38α kinase with a “lobster” active conformation, which is fixed by four hydrogen bonds they formed with the adjacent residues (Lys53, Gly110, Met109 and Ala157) and two hydrophobic interactions (in hydrophobic pockets I and II respectively) in p38α binding site. These models and the derived information may afford valuable clues for design of new potent p38α inhibitors.

Keywords: Imidazoles, P38α, inhibitor, 3D-QSAR, CoMFA, CoMSIA, PLS, molecular docking, MD, lobster active conformation