High-throughput screening of enzyme inhibitors: simultaneous determination of tight-binding inhibition constants and enzyme concentration.

Active site titration by a reversible tight-binding inhibitor normally depends on prior knowledge of the inhibition constant. Conversely, the determination of tight-binding inhibition constants normally requires prior knowledge of the active enzyme concentration. Often, neither of these quantities is known with sufficient accuracy. This paper describes experimental conditions under which both the enzyme active site concentration and the tight-binding inhibition constant can be determined simultaneously from a single dose-response curve. Representative experimental data are shown for the inhibition of human kallikrein.

A broad spectrum Kunitz type serine protease inhibitor secreted by the hookworm Ancylostoma ceylanicum.

Although blood-feeding hookworms infect over a billion people worldwide, little is known about the molecular mechanisms through which these parasitic nematodes cause gastrointestinal hemorrhage and iron deficiency anemia. A cDNA corresponding to a secreted Kunitz type serine protease inhibitor has been cloned from adult Ancylostoma ceylanicum hookworm RNA. The translated sequence of the A. ceylanicum Kunitz type inhibitor 1 (AceKI-1) cDNA predicts a 16-amino acid secretory signal sequence, followed by a 68-amino acid mature protein with a molecular mass of 7889 daltons. Recombinant protein (rAceKI-1) was purified from induced lysates of Escherichia coli transformed with the rAceKI-1/pET 28a plasmid, and in vitro studies demonstrate that rAceKI-1 is a tight binding inhibitor of the serine proteases chymotrypsin, pancreatic elastase, neutrophil elastase, and trypsin. AceKI-1 inhibitory activity is present in soluble protein extracts and excretory/secretory products of adult hookworms but not the infective third stage larvae. The native AceKI-1 inhibitor has been purified to homogeneity from soluble extracts of adult A. ceylanicum using size exclusion and reverse-phase high pressure liquid chromatography. As a potent inhibitor of mammalian intestinal proteases, AceKI-1 may play a role in parasite survival and the pathogenesis of hookworm anemia.

High-throughput screening of enzyme inhibitors: automatic determination of tight-binding inhibition constants.

Determination of tight-binding inhibition constants by nonlinear least-squares regression requires sufficiently good initial estimates of the best-fit values. Normally an initial estimate of the inhibition constant must be provided by the investigator. This paper describes an automatic procedure for the estimation of tight-binding inhibition constants directly from dose-response data. Because the procedure does not require human intervention, it was incorporated into an algorithm for high-throughput screening of enzyme inhibitors. A suitable computer program is available electronically (http://www.biokin.com). Representative experimental data are shown for the inhibition of human mast-cell tryptase.

Fixed-point methods for computing the equilibrium composition of complex biochemical mixtures.

The fixed-point algebraic method [Storer and Cornish-Bowden (1976) Biochem. J. 159, 1-5] for computing the concentrations at equilibrium of complex biochemical mixtures fails for many binding stoichiometries, especially those that include molecular self-association. A typical example is the monomer-dimer-tetramer equilibrium. This paper reports two main results. First, the above algorithm is analysed theoretically to predict for which binding stoichiometries it succeeds and for which it will fail. Secondly, an alternative algorithm is described for self-associating biochemical systems. Illustrative examples are based on the dimeric proteinase from HIV.

Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase.

A computer program with the code name DYNAFIT was developed for fitting either the initial velocities or the time course of enzyme reactions to an arbitrary molecular mechanism represented symbolically by a set of chemical equations. Seven numerical tests and five graphical tests are applied to judge the goodness of fit. Experimental data on the inhibition of the dissociative dimeric proteinase from HIV were used in four test examples. A set of initial velocities was analyzed to see if a tight-binding inhibitor could bind to the HIV proteinase monomer. Three different sets of progress curves were analyzed (i) to determine the kinetic properties of an irreversible inhibitor, (ii) to investigate the dissociation and denaturation mechanism for the protease dimer, and (iii) to investigate the inhibition mechanism for a transient inhibitor. The program is available by anonymous ftp via uwmml.pharmacy.wisc.edu and on the World Wide Web via http://uwmml.pharmacy.wisc.edu.

Mechanical effects on the kinetics of the HIV proteinase deactivation.

The proteinase from HIV undergoes rapid and irreversible deactivation caused by mild mechanical stirring. Both the free enzyme and the ternary Michaelis complex disappear in two separate first-order processes, with half-times of 3.0 and 0.8 minutes, respectively. Ignoring these deactivation steps distorts the results of kinetic analyses.

Inhibition of human steroid 5alpha reductases type I and II by 6-aza-steroids: structural determinants of one-step vs two-step mechanism.

We have discovered that 17beta-[N,N-(diethyl)carbamoyl]-6-azaandrost-4-en-3-one is a time-dependent inhibitor of type II 5alpha-reductase, as is the drug finasteride. Unlike finasteride, the 6-aza-steroid is not a time-dependent inhibitor of type I 5 alpha-reductase. Finasteride inhibition of type II enzyme proceeds in a two-step mechanism. At pH 6 and 37 degrees C, an initial finasteride-reductase complex is formed with a K(i)(app) of 11.9 +/- 4.1 nM. In a second step, an irreversible complex is formed with a rate constant of inactivation of 0.09 +/- 0.01 s(-1). In contrast, the 6-aza-steroid is a reversible inhibitor. From the results of a simplified mathematical analysis, based on the rapid equilibrium approximation, the inhibitor and the enzyme form an initial complex with a K(i) of 6.8 +/- 0.2 nM. The reversible formation of a final complex, with an overall K(i) of 0.07 +/- 0.02 nM, is characterized by a first-order isomerization rate constant 0.0035 +/- 0.0001 s(-1) for the forward step and 0.00025 +/- 0.00006 s(-1) for the backward step. All rate constants for the two-step mechanism were obtained by using a general numerical integration method. The best fit values for the association and dissociation rate constants were 5.0 microM(-1) s(-1) and 0.033 +/- 0.008 s(-1), respectively, and the isomerization rate constants were 0.0035 +/- 0.007 s(-1) and 0.000076 +/- 0.000019 s(-1). These values correspond to an initial K(i) of 6.5 nM and an overall dissociation constant of 0.14 nM. The data presented here show that both finasteride and the 6-aza-steroid analogs are potent against type II 5alpha-reductase, although their mechanisms of inhibition are different.

Increase in fluorescence upon the hydrolysis of tyrosine peptides: application to proteinase assays.

The intrinsic fluorescence of tyrosine increases by a factor of approximately two when the carboxy group is liberated from a peptide bond by hydrolysis. The increase in fluorescence provides a novel way to monitor the hydrolysis of native tyrosine peptides that contain only proteinogenic amino acids. Thus, for example, the hydrolysis by HIV-1 proteinase of a heptapeptide viral protein fragment gag129-135, Ser-Gln-Asn-Tyr-Pro-Ile-Val, was followed continuously at excitation and emission wavelengths 275 and 305 nm. The fluorescence increase is magnified by at least a factor of a thousand when a resonance energy quencher, such as paranitrophenylalanine, is in the vicinity. For example, the peptide Lys-Ala-Arg-Val-Tyr-Phe(p-NO2)-Glu-Ala-Nle-NH2 [Richards et al. (1990) J. Biol. Chem. 265, 7733], widely used for spectrophotometric assays of the HIV-1 proteinase, yields a substrate:product fluorescence ratio greater than 1:1000. Tyrosine-containing substrates of pepsin and trypsin showed similar behavior. The detection limit of the present method is at least one order of magnitude lower than absorbance assays of p-nitrophenylalanine peptides.

Stabilization of HIV proteinase dimer by bound substrate.

Upon the binding of a synthetic nonapeptide substrate, the catalytically active dimeric form of HIV proteinase is strongly stabilized against dissociation into inactive subunits. The dissociation of the ternary Michaelis complex into protein monomers is immeasurably low (apparent dissociation constant in the picomolar range), while the dimer-to-monomer equilibrium dissociation constant at pH 4.7 and at ionic strength 1.0 M is 30.4 +/- 1.6 nM. Consequently, the apparent activity of HIV proteinase depends on the order in which the enzyme and the substrate are added to in vitro assays. Substrate-induced stabilization should be carefully considered in designing kinetic studies of all dissociative retroviral enzymes, the proteinase, the integrase, and the reverse transcriptase.

Kinetic assay for HIV proteinase subunit dissociation.

The kinetics and thermodynamics of the monomer--dimer equilibrium for HIV-1 proteinase are investigated in a concentration jump experiment, at a concentration of the substrate that is substantially lower than the Michaelis constant. Under these conditions the substrate-induced stabilization of the active dimer is suppressed, and the integral rate equation can be obtained in a closed form. Both the monomer--dimer bimolecular association rate constant and the corresponding equilibrium dissociation constant are obtained directly by nonlinear regression analysis of the reaction time-course. In buffers of low ionic strength and in the absence of external ligands (substrates and inhibitors), the equilibrium dissociation constant at 37 degrees C is 440 +/- 52 nM, a value significantly higher than previous estimates obtained at a comparatively high concentration of substrates.

A continuous spectrophotometric direct assay for peptidyl prolyl cis-trans isomerases.

m-Nitrotyrosine incorporated into proline peptides of the general sequence -Xxx-Pro-Tyr(m-NO2)- responds to cis-trans Xxx-Pro conformational transition by changes in the pKa of its side-chain hydroxyl (Garel and Siffert, 1979). We exploited this effect to develop a continuous direct (uncoupled) assay for peptidyl prolyl cis-trans isomerases. Prior to the enzyme assay, the cis-trans equilibrium is perturbed in favor of the cis isomer by dissolving the substrate H-Ala-Ala-Pro-Tyr(m-NO2)-Ala-NH2 in a 470 mM solution of LiCl in trifluoroethanol. Upon addition of substrate to the biological buffer, the conformational equilibrium characteristic for the aqueous medium is restored, and the Ala-Pro isomerization is monitored spectrophotometrically.

Identification of actin and HSP 70 as cyclosporin A binding proteins by photoaffinity labeling and fluorescence displacement assays.

A novel family of cyclosporin A (CsA) binding proteins was identified by using the biologically active, radioiodinated photoaffinity probe [D-Lys-N epsilon-(4-azido-3-[125I]iodophenyl)propionyl)]8-CsA. In addition to cyclophilin, proteins with molecular masses of 43 kDa and approximately 50-55 kDa were labeled in Jurkat extracts and bovine calf thymus. Sequence analysis of the 43-kDa protein purified from calf thymus and subsequent Western analysis of CsA affinity-purified material from Jurkat extracts identified the 43-kDa component as actin. [D-Lys-N epsilon-(5-dimethylamino-1-naphthalenesulfonyl)]8-CsA, a fluorescent analogue of CsA, was prepared and used to measure the binding constants of cyclosporin derivatives to actin by means of a new fluorescence displacement assay. [D-Lys-N epsilon-(5-dimethylamino-1-naphthalenesulfonyl)]8-CsA and [N delta-t-butoxycarbonyl diaminobutyryl)]8-CsA bind to bovine actin at physiologically relevant concentrations, with dissociation constants of 60 +/- 33 and 570 +/- 380 nM, respectively. Because the ATPase fragment of heat shock cognate 70 (HSC 70) is structurally related to actin, the yeast homologue SSA1 was tested and found to be radiolabeled by the cyclosporin A photoaffinity reagent. The binding constant for [D-Lys-N epsilon-(5-dimethylamino-1-naphthalenesulfonyl)]8-CsA to SSA1 was determined and is 53 +/- 48 nM. These results indicate that actin and the 70-kDa heat shock protein family contain a structurally related domain for binding of cyclosporin A-related peptides.

Fluorescence displacement method for the determination of receptor-ligand binding constants.

The equilibrium constant for the binding of a spectroscopically invisible ligand to its protein receptor can be determined in a competition experiment, by using a structural analog that contains a reporter group (fluorophor). A novel mathematical treatment of the multiple equilibria allows the analysis to be performed under tight-binding conditions. The equilibrium equation for mixtures of two mutually competitive tight-binding ligands can be expressed in a recursive form, a form in which the dependent variable appears on both sides and the solution is found iteratively. The algorithm is also applicable to the special case of weak binding, where the concentration of the bound ligand can be neglected in the mass balance. The fluorescence displacement method is demonstrated on the determination cyclophilin binding to cyclosporin A (CsA), in competition with its fluorescent derivative, [D-Lys(Dns)]8-CsA.

Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equation.

When two or more tight-binding inhibitors are present in an enzyme assay, the equation that relates the initial velocity v to the concentration of reactants cannot be written in an algebraically explicit form. Rather, for n inhibitors it is an implicit polynomial equation of degree n + 1 with respect to v. The complexity of the polynomial coefficients dramatically increases with each added inhibitor. Solving the transcendental rate equation by traditional methods of numerical mathematics has proven tedious because of the sensitivity of these methods to initial estimates and because of the existence of multiple roots. However, the equation can be rearranged into a convenient recursive form, one in which the velocity appears on both sides and the solution is found iteratively. The algebraic form of the recursive rate equation is remarkably simple and differs from the rate equation for classical rather than tight-binding inhibition only by an added term. The numerical stability and the speed of convergence were tested on the case of two competitive inhibitors. Initial estimates of velocity that spanned 12 orders of magnitude converged within five iterations. The velocities computed with the recursive method for a single tight-binding inhibitor were identical with the values predicted by the Morrison equation. The method is used to analyze experimental data for the inhibition of rat liver dihydrofolate reductase by mixtures of the anticancer drug methotrexate and its metabolic precursor form, methotrexate-alpha-aspartate (a prodrug).

Determination of kinetic constants for peptidyl prolyl cis-trans isomerases by an improved spectrophotometric assay.

The kinetic properties and substrate specificity of two well-characterized peptidyl prolyl cis-trans isomerases (PPIases), cyclophilin and the FK-506 binding protein (FKBP), have been previously examined [Fischer, G., Bang, H., Berger, E., & Schellenberger, A. (1984) Biochim. Biophys. Acta 791, 87-97; Harrison, R.K., & Stein, R.L. (1990) Biochemistry 29, 1684-1689; Albers, M.W., Walsh, C.T., & Schreiber, S. L. (1990) J. Org. Chem. 55, 4984-4986]. The chymotrypsin-coupled enzymatic assay employed in these studies suffers from two serious shortcomings. Due to the low equilibrium population of the X-cis-Pro-Phe-pNA isomer (the PPIase substrate), in conjunction with the low solubility of p-nitroaniline generated by chymotrypsin hydrolysis, substrate concentrations in the saturating region are not experimentally attainable. Secondly, the uncatalyzed cis-trans isomerization obscures the interpretation of the initial velocity. As a result of these limitations, the steady-state kinetic parameters (Km,Kcat) have not been determined. Here we introduce an improved version of the spectrophotometric assay and report for the first time the Michaelis constants and turnover numbers for both PPIases with established substrates. The improvements in the experimental conditions originate in a medium-induced increase in the equilibrium population of the cis X-Pro conformer and in conducting the assay at 0 degrees C to suppress the uncatalyzed thermal isomerization. In addition, we present a rigorous mathematical model of the spectrophotometric progress curves that accounts for the contributions of the residual background rate.(ABSTRACT TRUNCATED AT 250 WORDS)