Kinetics of substrate reaction during irreversible modification of enzyme activity where the modifier is not in great excess of the enzyme

Structure Kinetics Relationships and Molecular Dynamics Show Crucial Role for Heterocycle Leaving Group in Irreversible Diacylglycerol Lipase Inhibitors

Drug discovery programs of covalent irreversible, mechanism-based enzyme inhibitors often focus on optimization of potency as determined by IC₅₀-values in biochemical assays. These assays do not allow the characterization of the binding activity (K_i) and reactivity (k_inact) as individual kinetic parameters of the covalent inhibitors. Here, we report the development of a kinetic substrate assay to study the influence of the acidity (pK_a) of heterocyclic leaving group of triazole urea derivatives as diacylglycerol lipase (DAGL)-α inhibitors. Surprisingly, we found that the reactivity of the inhibitors did not correlate with the pK_a of the leaving group, whereas the position of the nitrogen atoms in the heterocyclic core determined to a large extent the binding activity of the inhibitor. This finding was confirmed and clarified by molecular dynamics simulations on the covalently bound Michaelis–Menten complex. A deeper understanding of the binding properties of covalent serine hydrolase inhibitors is expected to aid in the discovery and development of more selective covalent inhibitors.

Use of a windows program for simulation of the progress curves of reactants and intermediates involved in enzyme-catalyzed reactions

A program that performs simulation of the kinetics of enzyme-catalyzed reactions with up to 32 species is described. The program is written in C++ for MS Windows 95/98/NT and uses a simple text file to define the kinetic model. The use of the program is illustrated with some examples. WES is available free of charge on request from the authors (e-mail: fgarcia@iele-ab.uclm.es).

A simple method for determining kinetic constants of complexing inactivation at identical enzyme and inhibitor concentrations

The kinetics of complexing inactivation at identical enzyme and inhibitor concentrations were analyzed and the equations of product generation were derived when the free enzyme concentration is great, larger or smaller than the dissociation constant of inhibitor, K(I). The kinetic constants can be obtained by fitting the derived equations to the progress curve. Numerical examples show that this method is valid and gives satisfactory results.

Functions of the N-terminal domain of secretory leukoprotease inhibitor

Secretory leukoprotease inhibitor (SLPI) comprises two homologous domains: the C-terminal domain contains the reactive site, while the function of the N-terminal domain remains unknown. In order to elucidate the function of the N-terminal domain, we studied the kinetics of reactions of human leukocyte elastase with two recombinant forms of SLPI: the full-length inhibitor and the C-terminal domain alone. The reactions of elastase with the full-length inhibitor and the C-terminal domain share the same association rate constant, 2 x 10(6) M-1 s-1, but the complex formed with the C-terminal domain is less stable, with a dissociation rate constant of 8 x 10(-4) s-1, 5 times higher than that of the complex with the full-length inhibitor. The binding of the full-length inhibitor to elastase is greatly accelerated by polyanions. In the presence of submicromolar concentrations (1 microgram/mL) of heparin, the association rate constant is increased by more than 1 order of magnitude. The binding of the C-terminal domain alone to elastase shows much lower sensitivity to heparin; in the presence of 5 microM (25 micrograms/mL) heparin, association of the C-terminal domain with elastase reaches a maximum rate of 7 x 10(6) M-1 s-1, about 3 times higher than the rate in the absence of heparin. Similar differential effects of heparin have been observed on the reactions of alpha-chymotrypsin with the two recombinant forms of SLPI.2=

MSR--a program for kinetic analysis of enzyme modification data on PC

A computer program has been written for the kinetic method of substrate reaction (MSR) in enzyme modification studies. The program analyses a series of progress curves that continuously record signals (absorbance, fluorescence emission, etc.) reflecting the concentration changes of substrate or product during enzyme modification in the presence of substrate. After the apparent kinetic parameters are calculated by graphdrawing or curve-fitting method, a series of relevant plots is shown, from which information about the enzyme-inhibitor interaction can be deduced and microscopic kinetic constants calculated.