Allosteric Control: Establishing the Nexus of Structure and Catalytic Power

University Of Iowa, Iowa City IA

Investigators

Abstract

ABSTRACT Allosterically active enzymes are flexible for a number of reasons. Understanding the changes in macromolecular dynamics due to small molecule complexation and the enzyme's catalytic power is often the key to unlocking better avenues for drug lead development, and can often yield insights into the raison d'être for such flexibility. Glutamate racemases (GR) and the executioner caspases-7 (C7) are two such systems, both coveted and validated drug targets, the former for antimicrobials and the latter for Parkinson's and inflammatory diseases. Interestingly, the similarities between the two are manifold. We have employed a range of experimental and computational approaches to elucidate their respective allosteric mechanisms and to discover novel drug lead compounds that exploit these requisite dynamics. GR is essential to a wide variety of microbes, and an excellent antimicrobial drug target: D-glutamate, an essential component of the peptidoglycan layer of bacterial cell walls is synthesized by bacterial GRs. A large body of biological and pharmacological studies have established GR's essentiality. A particularly attractive GR system for understanding long range allosteric mechanisms is the GR from H. pylori, (HpGR; a target for gastric cancer). Early allosteric hits against HpGR were not able to move beyond the laboratory for reasons related to the nature of the enzyme's allsoteric pockets. A compounding factor is that a mechanism of action, by which occupancy of the cryptic allosteric pocket remotely leads to inhibition, has heretofore remained elusive. This is a trend that has plagued allosteric drug discovery in general. Our research program has made progress in addressing these knowledge gaps by employing both experimental biophysical and computational approaches. Our simulations on HpGR and C7 complexes have found that key global motions are dampened when allosteric drugs are bound. Critical networks involving their catalytic Cys/His dyads remain non-productively trapped. In the case of C7 our group has developed the first drug-like allosteric inhibitors, and have determined high resolution structures of these complexes that show how the Cys/His catalytic dyads are distorted, including a disorientation of C7's oxyanion hole. In the case of HpGR, we have used these structural and computational insights to design a novel series of drug-like inhibitors that have excellent MIC values against clinically relevant drug-resistant H. pylori strains. Our goal is to elucidate the relationships between catalytic determinants and global enzyme dynamics driven by small molecule complexation. Understanding how catalytic potential and dynamics are being altered will clarify why allosteric drugs are inhibiting these pharmacologically important enzymes. This proposal will develop a new kind of metric, the Allosteric Structure Activity Relationship (ASAR), for which we have an excellent start on both HpGR and C7. Closing these gaps via development of ASARs, will be accomplished by linking experimental and computational horizons which are not often employed together.