UC San Diego

Metalloenzymes are enzymes that require one or more metal ion cofactors for catalytic activity. These enzymes have been estimated to represent up to one-third of the proteome, and are responsible for carrying out a broad range of functions relevant to life. Despite their ubiquity, the metalloenzyme family has been largely underrepresented in terms of drug discovery efforts, with only ~67 drugs having attained FDA approval for metalloenzyme inhibition. To develop new metalloenzyme inhibitors, the Cohen laboratory has developed a library of metal-binding pharmacophores (MBPs) containing ~350 small molecules ideally suited for metalloenzyme inhibitor development. These compounds act by coordinating to the metal ion cofactor necessary for metalloenzyme activity, thereby blocking off the active site and preventing further enzymatic activity. By screening this MBP library against disease relevant metalloenzymes, it is possible to identify MBP scaffolds with both high affinity and specificity for target metalloenzymes. Then through a series of rational fragment growth and structural activity relationship studies, it is possible to elaborate these fragment MBPs into full-length inhibitors.

To further improve this library and facilitate the use of MBPs as metalloenzyme inhibitors, the work described in this thesis has sought to improve the druglikeness of MBP fragments. Chapter 2 deals with a case study of expanding the hydroxypyridinethione (HOPTO) MBP scaffold to by creating sublibrary of HOPTO isostere and analogue compounds designed to enhance the druglikeness of the HOPTO MBP. Chapter 3 then takes this expanded HOPTO sublibrary, and applies it towards drug discovery efforts against human Insulin Degrading Enzyme (IDE), a target relevant for both Type 2 diabetes and neurodegeneration. This work resulted in the discovery of a new, sulfonamide HOPTO inhibitor of IDE. In Chapter 4, this HOPTO sublibrary, as well as a set of derivatized 8-hydroxyquinoline compounds, were applied against New Delhi Metallo-ß-lactamase-1 (NDM-1), a mononuclear Zn2+ metalloenzyme responsible for ß-lactam antibiotic resistance. Finally, Chapter 5 deals with the use of MBPs to develop new inhibitors of human Arginase-1, a dinuclear Mn2+ metalloenzyme relevant to cancer immunotherapy. In this work, catechol, oxazoline, and hydroxamic acid scaffolds were all explored as MBP warheads against this target.