Theoretical and Mechanistic Validation of Global Kinetic Parameters of the Inactivation of GABA Aminotransferase by OV329 and CPP-115

• DOI: 10.1021/acschembio.0c00784
• Publication Date: 2021-03-18T21:32:51Z
• Authors: Pathum M. Weerawarna; Matthew J. Moschitto; Richard B. Silverman
• Keywords: Kinetic isotope effect; QM/MM; Limiting

((S)-3-Amino-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (OV329) is a recently discovered inactivator of γ-aminobutyric aminotransferase (GABA-AT), which has 10 times better inactivation efficiency than its predecessor, CPP-115, despite the only structural difference being an endocyclic double bond in OV329. Both compounds are mechanism-based enzyme inactivators (MBEIs), inactivate GABA-AT by similar mechanism. Here, combination variety computational chemistry tools and experimental methods, including quantum mechanical (QM) calculations, molecular dynamic simulations, progress curve analysis, deuterium kinetic isotope effect (KIE) experiments, utilized to comprehensively study mechanism CPP-115 OV329 account for their experimentally obtained global parameters kinact KI. Our first key finding that rate-limiting step deprotonation step, according QM calculations KIE accurately represents enhancement given Second, present shows widely used simple models do not represent geometric criteria step. In contrast, cluster successfully both ground state destabilization transition stabilization, as revealed natural orbital analysis. Furthermore, globally derived KI values inhibitor constants initial binding complexes (Kd) indicate competition with substrate analysis observed effect. The configurational entropy loss accounts between inactivators. approach we describe this work can be employed determine validity process MBEI optimization mechanisms.