PMID: 21531720 , Related PDB ids: 3ARO, 3ARP, 3ARQ, 3ARR, 3ARS, 3ART, 3ARU, 3ARV, 3ARW, 3ARX, 3ARY, 3ARZ, 3AS0, 3AS1, 3AS2, 3AS3

Authors:

Pantoom S, Vetter IR, Prinz H, Suginta W

Title:

Potent family-18 chitinase inhibitors: x-ray structures, affinities, and binding mechanisms.

Journal:

J Biol Chem. 2011 Jul 8;286(27):24312-23. Epub 2011 Apr 29.

Abstract:

Six novel inhibitors of Vibrio harveyi chitinase A (VhChiA), a family-18 chitinase homolog, were identified by in vitro screening of a library of pharmacologically active compounds. Unlike the previously identified inhibitors that mimicked the reaction intermediates, crystallographic evidence from 14 VhChiA-inhibitor complexes showed that all of the inhibitor molecules occupied the outer part of the substrate-binding cleft at two hydrophobic areas. The interactions at the aglycone location are well defined and tightly associated with Trp-397 and Trp-275, whereas the interactions at the glycone location are patchy, indicating lower affinity and a loose interaction with two consensus residues, Trp-168 and Val-205. When Trp-275 was substituted with glycine (W275G), the binding affinity toward all of the inhibitors dramatically decreased, and in most structures two inhibitor molecules were found to stack against Trp-397 at the aglycone site. Such results indicate that hydrophobic interactions are important for binding of the newly identified inhibitors by the chitinase. X-ray data and isothermal microcalorimetry showed that the inhibitors occupied the active site of VhChiA in three different binding modes, including single-site binding, independent two-site binding, and sequential two-site binding. The inhibitory effect of dequalinium in the low nanomolar range makes this compound an extremely attractive lead compound for plausible development of therapeutics against human diseases involving chitinase-mediated pathologies.