The kinetics of reversible tight-binding inhibition

Kinetics of phospholipid transfer between liposomes (neutral or negatively charged) and high-density lipoproteins: a spin-label study of early events

The kinetics of spin-labeled phosphatidylcholine transfer between vesicles and HDL particles exhibited a two-phase process, as seen by ESR spectroscopy. The results were analyzed by considering several possible steps in the overall transfer, whose aspects were also studied: (i) micellar complex formation after HDL apolipoprotein-vesicle mixture, (ii) the rate of PC transfer from the micellar complex to HDL, (iii) the rate of the reverse reaction between overloaded HDL particles and other particles such as HDLs, LDLs, and lipid vesicles. The results agree most convincingly with a mechanism in which the diffusion of phospholipids into the HDL-endogenous lipids is the limiting step, occurring as a two-step process. In addition, we observed a negative charge effect on the lipid transfer rates and yields.

Fluoro ketone inhibitors of hydrolytic enzymes

The use of fluoro ketones as inhibitors of hydrolytic enzymes has been investigated. The acetylcholine analogues 6,6-dimethyl-1,1,1-trifluoro-2-heptanone and 3,3-difluoro-6,6-dimethyl-2-heptanone are inhibitors of acetylcholinesterase with Ki values of 16 X 10(-9) M and 1.6 X 10(-9) M, respectively. These fluoro ketones are 10(4)-10(5) times better as inhibitors than the corresponding methyl ketone. Since nucleophiles readily add to fluoro ketones, it is likely that these compounds inhibit acetylcholinesterase by formation of a stable hemiketal with the active-site serine residue. Fluoro ketone substrate analogues are also inhibitors of zinc metallo- and aspartylproteases. 2-Benzyl-4-oxo-5,5,5-trifluoropentanoic acid is an inhibitor of carboxypeptidase A (Ki = 2 X 10(-7) M). Trifluoromethyl ketone dipeptide analogues are good inhibitors of angiotensin converting enzyme. An analogue of pepstatin that contains a difluorostatone residue in place of statine has been prepared and found to be an extremely potent inhibitor of pepsin (Ki = 6 X 10(-11) M). The hydrated ketones are probably the inhibitory species since they are structural mimics of the tetrahedral intermediate that forms during the hydrolysis of peptide substrates.

Purification of an alanine racemase from Streptococcus faecalis and analysis of its inactivation by (1-aminoethyl)phosphonic acid enantiomers

An alanine racemase has been purified some 30 000-fold almost to homogeneity from Gram-positive Streptococcus faecalis NCIB 6459; the enzyme has been purified to the same extent (4000-fold) from an O-carbamyl-D-serine-resistant mutant with a 7-fold higher enzyme level in crude extract. The racemase has one pyridoxal phosphate molecule per 42-kDa subunit, has a Vmax of 3570 units/mg and a Km of 7.8 mM in the L to D direction, and has a Vmax of 1210 units/mg and a Km of 2.2 mM in the D to L direction. The Keq is 0.8 and kcat/Km values are ca. 3 X 10(5) M-1 s-1. The purified enzyme is inhibited in a time-dependent manner by both L- and D-(l-aminoethyl)phosphonates (Ala-P), confirming observations of Atherton et al. in crude extracts of this organism [Atherton, F. R., Hall, M. J., Hassal, C. H., Holmes, S. W., Lambert, R. W., Lloyd, W. J., & Ringrose, P. S. (1980) Antimicrob. Agents Chemother. 18, 897]. Studies with [1-2H]-, [1-3H]-, and [1,2-14C]Ala-P rule out enzymic activation and processing as the basis for irreversible inhibition. Thus, enzyme after exposure to [14C]Ala-P or [alpha-3H]Ala-P and gel filtration contains stoichiometric amounts of radioactive label, but denaturation quantitatively releases intact Ala-P into solution as revealed by high-performance liquid chromatography and cocrystallization with authentic material. The Ala-P isomers are slow binding inhibitors of this racemase as is the alpha,alpha'-dimethyl analogue but not the D or L isomers of the corresponding phosphinate.(ABSTRACT TRUNCATED AT 250 WORDS)

Kinetic study on the initial stage of the fibrinogen-fibrin conversion by thrombin. (III) Effects of competitive inhibitors

By using the turbidimetrical procedure, the inhibition constants, Kip, of competitive inhibitors of thrombin were estimated in systems of fibrinogen-thrombin-inhibitor. In the presence of a competitive inhibitor such as benzamidine, p-aminobenzamidine, tosylarginine methyl ester, MD-805, and antithrombin III-heparin, the turbidity change of reaction mixture was traced on the initial stage of the fibrinogen-fibrin conversion catalyzed by thrombin. The formation rate of the smallest polymer as detectable by turbidimetry was measured from evaluating the induction period of turbidity-time curves. The Kip values thus obtained were a little less than or agreed well with the inhibition constants, Ki, reported on systems of synthetic substrate-thrombin-inhibitor.

The inhibition of ornithine transcarbamoylase from Escherichia coli W by phaseolotoxin

The mechanism of inhibition of ornithine transcarbamoylase by the bacterial toxin phaseolotoxin [N-delta-(phosphosulphamyl)ornithylalanylhomoarginine] was investigated. Ornithine transcarbamoylase was purified by affinity chromatography from Escherichia coli W argR- by using N-delta-(phosphonoacetyl)ornithine as the ligand. Under steady-state conditions phaseolotoxin inhibition was reversible and exhibited mixed kinetics with respect to carbamoyl phosphate. The apparent Ki and apparent K'i were 0.2 microM and 10 microM respectively. Inhibition with respect to ornithine was noncompetitive, with an apparent Ki of 0.9 microM. These data are consistent with competitive binding of phaseolotoxin to the carbamoyl phosphate-binding site of the enzyme. The toxin also appears to be able to bind to the enzyme-carbamoyl phosphate complex, although, since K'i is 50 times greater than Ki, this event is kinetically much less significant. In the presence of phaseolotoxin ornithine transcarbamoylase exhibited a transient phase of activity before a steady state. This is consistent with low rates of association and dissociation for the toxin with enzyme and the enzyme-toxin complex. Rate constants of 2.5 X 10(4)M-1 X s-1 and 5 X 10(-3)s-1 were estimated for the association and dissociation constants respectively.

Inhibition of aspartate aminotransferase by hydrazinosuccinate

DL-Hydrazinosuccinic acid was synthesized by the reaction of DL-bromosuccinic acid with hydrazine. The compound strongly inhibited aspartate aminotransferase and gave 50% inhibition at 1.3 microM when added simultaneously with L-aspartate to an assay mixture containing enzyme. Incubation of the enzyme with the compound prior to assay resulted in a much stronger inhibition, which proceeded time-dependently. The inhibition was protectable with L-aspartate and was substantially reversed by dialysis.

Kinetic study on the slow inhibition of epidermis tyrosinase by m-coumaric acid

The inhibition by m-coumaric acid of oxidation of L-dopa by epidermis tyrosinase (monophenol,dihydroxy-L-phenylalanine:oxygen oxidoreductase, EC 1.14.18.1) is characterized by a prolonged transient phase. Kinetic data correspond to that for a postulated mechanism that involves rapid formation of a reduced enzyme-m-coumaric acid complex that subsequently undergoes a relatively slow reversible reaction. An overall inhibition constant for m-coumaric acid of 0.05 mM was calculated. The value of the Ki for the dissociation of m-coumaric acid from the rapidly formed complex was calculated as 0.53 mM. The first-order rate constants for the slow isomerization of the enzyme-inhibitor complex were calculated as 3.0 +/- 0.1 min-1 for the forward step and 0.31 +/- 0.06 min-1 for the reverse step.

Kinetics of methotrexate binding to dihydrofolate reductase from Neisseria gonorrhoeae

The kinetics of methotrexate inhibition of dihydrofolate reductase from Neisseria gonorrhoeae have been investigated. Methotrexate was shown to be a tight-binding inhibitor (Kt = 13 pM) competitive with dihydrofolate. However, "stoichiometric" or "pseudoirreversible" inhibition could not be demonstrated. Progress curves of inhibited assays quickly attained steady state regardless of the order of substrate addition, indicating that methotrexate association and dissociation processes were rapid. Kinetic techniques were used to measure the rate of methotrexate dissociation from the enzyme-NADPH-methotrexate ternary complex. At 30 degrees, the first-order off-rate constant (koff) was calculated to be 0.56 min-1. This value is approximately 40-fold greater than the dissociation rate constant of methotrexate for Escherichia coli dihydrofolate reductase. At lower temperatures, progress curves of methotrexate-inhibited gonococcal enzyme assays displayed marked increases in both curvature and the time to reach steady state. At 9 degrees, the methotrexate dissociation rate was slow enough (koff = 0.04 min-1) so that initial velocities of the reaction could be measured, and under these conditions methotrexate inhibition was shown to be "stoichiometric".

Reaction intermediate analogues for enolase

A number of compounds that appear to be analogues of the aci form of the normal carbanion intermediate are good inhibitors of yeast enolase. These include (3-hydroxy-2-nitropropyl)phosphonate (I), the ionized (pK = 8.1) nitronate form of which in the presence of 5 mM Mg2+ has a Ki of 6 nM, (nitroethyl)phosphonate (III) (pK = 8.5; Ki of the nitronate in the presence of 5 mM Mg2+ = 1 microM), phosphonoacetohydroxamate (IV) (pK = 10.2; Ki with saturating Mg2+ for the ionized form = 15 pM), and (phosphonoethyl)nitrolate (VII) (Ki at 1 mM Mg2+ = 14 nM). The oxime of phosphonopyruvate (VI) has a pH-independent Ki of 75 microM. I, IV, VI, and VII are slow binding inhibitors. All of these compounds are trigonal at the position analogous to C-2 of 2-phosphonoglycerate and contain a phosphono group, but a negatively charged metal ligand at the position isosteric with the hydroxyl attached to C-3 of 2-phosphoglycerate (as in IV) appears to contribute more to binding than a nitro group isosteric with the carboxyl of 2-phosphoglycerate (I and III). These data support the carbanion mechanism for enolase and suggest that the 3-hydroxyl of 2-phosphoglycerate is directly coordinated to Mg2+ prior to being eliminated to give phosphoenolpyruvate.

Cathepsin D from pig myometrium. Characterization of the proteinase

The purification of cathepsin D from pig uterus by two-step affinity chromatography on concanavalin A- and pepstatin-Sepharose was described previously [Afting & Becker (1981) Biochem. J. 197, 519-522]. In this paper, chemical and physical properties of the proteinase are presented. The purified enzyme showed three bands on SDS (sodium dodecyl sulphate)/polyacrylamide-gel electrophoresis, one main band corresponding to an Mr of 31 000 and two minor bands with Mr values of 43 000 and 15 000 respectively. Gel filtration on Bio-gel P-150 and sedimentation-diffusion equilibrium studies give an Mr for the main band of about 35 000. The pI of the enzyme was determined to be 7.2. Haemoglobin was the best substrate, with a Km value of 6.4 X 10(-6)M. It was hydrolysed with a pH optimum between 3.0 and 3.3 for a substrate concentration of 100 microM. The proteinase was stable over the pH range of 3.5-6.5. At pH 6 the enzyme showed stability up to a temperature of 50 degrees C; at pH 3 the activity was already decreased below 40 degrees C. Carbohydrate studies resulted in the staining of all three bands on an SDS/polyacrylamide gel by thymol/H2SO4. After treatment with endo-beta-N-acetylglucosaminidase H, all three bands were shifted to a region of lower Mr. Of various inhibitors tested, only pepstatin was strongly inhibiting, with a Ki of 2.1 X 10(-9)M.

Estimation of the elimination half-life of the monoamine oxidase inhibitor cimoxatone in rat brain on the basis of ex vivo inhibition data

Cimoxatone is a reversible mixed-type selective inhibitor of monoamine oxidase-A. For a mixed-type inhibitor, it can be shown that (vo-vi)/Vi is proportional to the inhibitor concentration. This relationship has been used to estimate the t 1/2 of the elimination of cimoxatone in rat brain after a single dose of inhibitor. t 1/2 values, estimated with three monoamine oxidase substrates, were in the range 3.9-4.8 h, in reasonable agreement with t 1/2 values determined from the plasma and brain concentration/time curves of cimoxatone.

Metabolic resistance: the protection of enzymes against drugs which are tight-binding inhibitors by the accumulation of substrate

Blockade of a metabolic pathway by interaction of a drug with a particular 'target enzyme' results in depletion of essential end-products of the pathway and accumulation of intermediates prior to the blockade. Metabolic resistance to a particular drug can arise if the substrate of the inhibited enzyme accumulates to levels sufficiently high to compete effectively with the inhibitor, leading to restoration of full activity of the metabolic pathway after a transitory delay. Such resistance has recently been demonstrated in vitro for the interaction of the tight-binding inhibitor N-phosphonacetyl-L-aspartate (PAcAsp) with the aspartate transcarbamoylase activity of the trifunctional protein which initiates pyrimidine biosynthesis in mammals [Christopherson, R. I. and Jones, M. E. (1980) J. Biol. Chem. 255, 11381-11395]. Carbamoyl phosphate, the product of the carbamoyl phosphate synthetase activity of this trifunctional protein, accumulates to a sufficiently high concentration that the inhibitory effect of PAcAsp is effectively abolished. We have developed a theoretical model for metabolic resistance which quantitatively accounts for these experimental data. This model has been used to simulate the interaction between the following potential or proven anti-cancer drugs and their target enzyme, under conditions similar to those which would occur in vivo: PAcAsp with aspartate transcarbamoylase; various OMP analogues [the 5'-monophosphates of 6-azauridine, pyrazofurin and 1-(beta-D-ribofuranosyl)-barbituric acid] with OMP decarboxylase; 5-fluorodeoxyUMP with thymidylate synthase; methotrexate with dihydrofolate reductase; and deoxycoformycin with adenosine deaminase.

Serine proteinase inhibitors from Vipera ammodytes venom. Isolation and kinetic studies

Three protein inhibitors of serine proteinases were isolated from the crude venom of the long-nosed viper Vipera ammodytes ammodytes by ion-exchange and gel chromatography. Two of them strongly inhibit trypsin (Ki = 3.4 X 10(-10) and 5.6 X 10(-10) M), while the third one primarily inhibits chymotrypsin (Ki = 4.3 X 10(-9) M). Their Mr values are close to 7000, and pI is 9.8 in both trypsin inhibitors and 10.0 in the chymotrypsin inhibitor. The N-terminal group in the former inhibitors is blocked; arginine is the N-terminal amino acid in the latter. Besides trypsin and alpha-chymotrypsin, the trypsin inhibitors also inhibit plasmin, human plasma kallikrein and porcine pancreatic kallikrein. The chymotrypsin inhibitor inhibits trypsin and human plasma kallikrein only weakly and does not inhibit plasmin and porcine pancreatic kallikrein. According to their properties, all three inhibitors belong to the Kunitz-pancreatic trypsin inhibitor family of inhibitors.

NAD-linked L(+)-lactate dehydrogenase from the strict aerobe alcaligenes eutrophus. 2. Kinetic properties and inhibition by oxaloacetate

The L(+)-lactate dehydrogenase (EC 1.1.1.27) of Alcaligenes eutrophus catalyzes the NADH-dependent reduction of pyruvate and a few other 2-oxoacids. The Km values for NADH, NAD, pyruvate and L(+)-lactate are 0.075 mM, 0.130 mM, 0.820 mM and 7.10 mM, respectively. The reaction follows a rapid equilibrium ordered bi-bi mechanism and involves the formation of a dead-end EBQ complex. The competitive inhibition of pyruvate reduction caused by NAD (with respect to NADH) is regarded to be of physiological importance. The enzyme is strongly inhibited by oxaloacetate, oxalate and to a less extent by oxamate. Oxaloacetate was found to be the most powerful inhibitor of the enzyme and exerts an almost complete inhibition of the reduction of pyruvate and some 2-oxoacids at concentrations of 1 microM and less. At 0.1 microM oxaloacetate the inhibition of pyruvate reduction is about 90%. The kinetics of pyruvate reduction in the presence of oxaloacetate is characterized by a burst phase followed by a decreased steady-state velocity. During the burst phase, which lasts from several seconds to some minutes, the enzyme undergoes transition to a less active enzyme form. The inhibition studies revealed the lactate dehydrogenase to be a hysteretic enzyme, due to its slow response to the ligand. The characteristics of the transient were examined. The inhibition of lactate dehydrogenase from A. eutrophus by oxaloacetate is considered to be of great physiological importance, allowing its function only at a low oxaloacetate concentration and consequently at high NADH/NAD ratios.

Purification of pyruvate formate-lyase from Streptococcus mutans and its regulatory properties

Pyruvate formate-lyase (EC 2.3.1.54) from Streptococcus mutans strain JC2 was purified in an anaerobic glove box, giving a single band on disk and sodium dodecyl sulfate electrophoresis. This enzyme was immediately inactivated by exposure to the air. Enzyme activity was unstable even when stored anaerobically, but the activity was restored by preincubating the inactivated crude enzyme with S-adenosyl-L-methionine, oxamate, and reduced for ferredoxin or methylviologen. On the other hand, the purified enzyme was not reactivated. Either D-glyceraldehyde 3-phosphate or dihydroxyacetone phosphate strongly inhibited this enzyme. The inhibitory effects of these compounds were largely influenced by enzyme concentration. The inhibition of these triose phosphates in cooperation with the reactivating effect of ferredoxin and the fluctuations of both the enzyme and the triose phosphate levels may efficiently regulate the pyruvate formate-lyase activity in S. mutans in vivo.

Chemical mechanism of the reaction catalyzed by dihydrofolate reductase from Streptococcus faecium: pH studies and chemical modification

The variation with pH of the kinetic parameters associated with dihydrofolate reductase from Streptococcus faecium has been used to gain information about the chemical mechanism of the reaction catalyzed by the enzyme. The pH dependence of log V/K for dihydrofolate showed that a group with a pK value of 4.7 must be ionized and that a group with a pK value of 6.6 must be protonated for activity. Temperature and solvent perturbation studies indicate that these groups are probably the carboxyls of the glutamate moiety of dihydrofolate and of an aspartate residue on the enzyme, respectively. The similarity of the pH profile and the magnitude of the pK value for the linear competitive inhibitor 2,4-diaminopteridine suggest that the carboxyl group is concerned with the binding of dihydrofolate and its analogues to the enzyme. This conclusion is confirmed by the result that a group with a pK value of 6.7 must be protonated for the binding of methotrexate. It is proposed that the binding involves the formation with N-5 of dihydrofolate or N-1 of methotrexate of a hydrogen bond which has considerable ionic character and which lies within a hydrophobic environment. Further, it is suggested that the same hydrogen acts as an auxiliary catalyst which facilitates hydride transfer from NADPH to dihydrofolate for its conversion to tetrahydrofolate. Evidence to support this suggestion comes from the finding that the V profile is similar to the V/K profile except that the pK of the group which must be protonated for maximum enzyme activity is shifted upward by about 2 pH units. Such an increase in a pK value is consistent with the formation of a hydrogen ionic bond in the ternary enzyme-NADPH-dihydrofolate complex. The results of inactivation experiments with trinitrobenzenesulfonate appear to indicate that a lysine residue is necessary to maintain the enzyme in its active conformation.

Kinetic and e.p.r. studies on the inhibition of xanthine oxidase by alloxanthine (1 H-pyrazolo [3, 4-d] pyrimidine-4,6-diol)

The inhibition by alloxanthine of oxidation of xanthine by xanthine oxidase is characterized by a prolonged transient phase. Kinetic data accord with a mechanism that involves rapid formation of a reduced enzyme-alloxanthine complex that subsequently undergoes a relatively slow-reversible reaction. In this scheme the slowly formed complex cannot be fully reoxidized by oxygen. From the Ki value for the dissociation of alloxanthine from the rapidly formed complex (1.15 microM) and values of 0.37 min-1 and 0.011 min-1 for the forward and reverse rate constants of the slow reaction, an overall inhibition constant for alloxanthine of 35 nM was calculated. A molybdenum (V) e.p.r. signal from the slowly formed reduced enzyme-alloxanthine complex is described. The rate of appearance of this new signal is consistent with this assignment. The signal (the "Alloxanthine signal") was simulated with g1 2,0269, g2 1,9593, g3 11.9444 and shows indications of hyperfine coupling to nitrogen. Similarities between it and the Very Rapid signal are discussed. Close structural analogies between the catalytic intermediate represented by the Very Rapid signal and the inhibitor complex represented by the Alloxanthine signal are suggested.

Dihydrofolate reductase hysteresis and its effect of inhibitor binding analyses

Escherichia coli dihydrofolate reductase was shown to follow slow transient kinetics (hysteresis). Nonlinear reaction velocities were detected during the enzyme assay and required 10-15 min to reach a steady-state rate. The degree of hysteresis was influenced by the enzyme concentration and the order of substrate addition. Incubation of the enzyme with NADPH before addition of dihydrofolate resulted in slow initial velocities that increased up to 2-fold during the course of the assay. Increasing the enzyme concentration from 0.2 to 1 nM resulted in diminished hysteresis. NADPH-initiated reactions were linear at all enzyme concentrations tested. Certain drugs had profound effects on hysteresis. Pyrimethamine practically eliminated the hysteresis of dihydrofolate-started reactions, whereas trimethoprime augmented the non-linearities in the sense that hysteresis was detected in both enzyme- and NADPH-started reactions. The shape of these reaction tracings makes trimethoprim is not a slow-binding inhibitor when assayed under conditions that eliminate hysteresis. Contrary to this, sulfamethoxazole did not affect hysteresis or augment inhibition of the enzyme by trimethoprim. Sulfamethoxazole alone (at 6 mM) did not inhibit the hysteresis and allow reliable determinations of Ki values of both weak and tight binding inhibitors. For example, Ki values for pyrimethamine, trimethoprim, and methotrexate were found to be 214 nM, 1.3 nM, and 0.021 nM, respectively.