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Indexed by:期刊论文

Date of Publication:2012-08-01

Journal:CURRENT MEDICINAL CHEMISTRY

Included Journals:SCIE、PubMed、Scopus

Volume:19

Issue:23

Page Number:4024-4037

ISSN No.:0929-8673

Key Words:Imidazoles; P38 alpha; inhibitor; 3D-QSAR; CoMFA; CoMSIA; PLS; molecular docking; MD; lobster active conformation

Abstract:P38 kinase plays a vital role in the inflammation mediated by tumor necrosis factor-alpha and interleukin-1 beta pathways, and thus the inhibitors of p38 kinase provide effective approach for the treatment of inflammatory diseases. Presently, a combined study of three-dimensional quantitative structure-activity relationship, molecular docking and molecular dynamics (MD) was undertaken to explore the structural insights of 174 2-thioimidazole compounds influencing the p38 alpha inhibitory activities. Both the ligand-based resultant comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) models exhibited satisfactory predictability (with Q(2)=0.475, R-ncv(2)=0.774, R-pre(2)=0.668 and Q(2)=0.504, R-ncv(2)=0.745, R-pre(2)=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 p38 alpha 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 p38 alpha binding site. These models and the derived information may afford valuable clues for design of new potent p38 alpha inhibitors.