Structure-based design of non-peptide, carbohydrazide-based cathepsin K inhibitors

Using binding models which were based on the X-ray crystal structure of an amino acid-based active site-spanning inhibitor complexed with cathepsin K, Cbz-leucine mimics have been developed, leading ultimately to the design o f a potent cathepsin K inhibitor free of amino acid components. These mimic s, which consist of a-substituted biphenylacetyl groups in place of Cbz-leu cine moieties, effectively mimic all aspects of the Cbz-leucine moieties wh ich are important for inhibitor binding. The predicted directions of bindin g for the inhibitors were confirmed by mass spectral analysis of their comp lexes with cathepsin K, which gave results consistent with acylation of the enzyme and loss of the acylhydrazine portion of the inhibitor which binds on the S' side of the active site. The binding models were found to be very predictive of relative inhibitor potency as well as direction of inhibitor binding. These results strengthen the validity of a strategy involving ite rative cycles of structure-based design and inhibitor synthesis and evaluat ion for the discovery of non-peptide inhibitors. (C) 1999 Elsevier Science Ltd. All rights reserved.