Overview of Inhibitor Design

An important feature of long spacer zinc-endoproteases like thermolysin, as revealed by comparisons of the free enzyme and that complexed with inhibitors [40,41] is that conformational change is an essential component for catalytic activity. A similar conformational change is also probable [15,18,26] for the short spacer family, although a definite confirmation must await more structural information on equivalent free and inhibited proteins of this class. 

In spite of the overall similarity of tertiary structure, a detailed analysis of the binding of inhibitors (Fig. 10), shows important differences in inhibitor-binding properties between the classes. In the short spacer family, the inhibitor is bound in an extended conformation while in the thermolysin family inhibitors adopt a twisted conformation. The contrasting requirements of the two classes is illustrated by the selectivity of the classical non-specific zinc-pro-tease inhibitor phosphoramidon which is active in nanomolar concentrations against the thermolysin-like enzymes [28] but has little or no inhibitory activity against the enzymes of the short spacer family [42]. 

In contrast, for inhibitors interacting with members of short consensus zinc endoprotease family, like the matrixins [17,19-23,25], the subsites P2 and P3 are suitably orientated for bridging. Molecules having the essential zinc-binding functionality and macrolactams span- 

EQWT KDTTGTK] LVAAB IGBSLG B ELW . LVAAB FGBAMG H 

In an analogous manner, inhibitors bearing substituents at the carbon spacer between the zinc ligand and the alpha centre of the PI subsite have different enzyme-inhibitor interactions with separate members of the MMP family. The crystal structure of the synthetic inhibitor RO32-0554 (5) (Fig. 13) complexed with fibroblast collagenase indicates a favorable interaction between the imide oxygen of the naphthalimide group of the inhibitor and an 

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