A substrate variant as a high-affinity, reversible inhibitor: insight from the X-ray structure of cilastatin bound to membrane dipeptidase.
An analysis of the X-ray structure of cilastatin bound to membrane dipeptidase, together with docking studies, is presented here to reveal how a simple amide may act as a high-affinity, reversible, amidase inhibitor. Cilastatin binds as a normal substrate and is orientated in a perfect near-attack conformer for formation of a tetrahedral intermediate with the zinc-bound water/hydroxide. This intermediate is fated, however, only to revert to its starting components as scission of the amide bond is prevented by the precise fit of cilastatin within the active site. The cilastatin alkyl end groups that are tightly buttressed against amino acid residues on opposite sides of the active site, are aligned along the C-N reaction coordinate axis thereby preventing collapse of the intermediate via rupture of the C-N bond. Such a feature could have more general applicability in the explicit design of substrate variants as selective, tight-binding, and reversible inhibitors.
Smyth
Timothy P
TP
Department of Chemical and Environmental Sciences, Univeristy of Limerick, National Technological Park, County Limerick, Ireland. timothy.smyth@ul.ie
Wall
J Gerard
JG
Nitanai
Yasushi
Y
D000581:Amidohydrolases / Q000037:antagonists & inhibitors; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D015377:Cilastatin / Q000737:chemistry* / Q000378:metabolism* / Q000494:pharmacology; D018360:Crystallography, X-Ray; D004150:Dipeptidases / Q000378:metabolism*; D004791:Enzyme Inhibitors / Q000494:pharmacology; D017998:Leukotriene D4 / Q000037:antagonists & inhibitors; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation
D004791:Enzyme Inhibitors; D015377:Cilastatin; D017998:Leukotriene D4; D004150:Dipeptidases; D000581:Amidohydrolases