The pH dependencies of individual rate constants in papain-catalyzed reactions

Drug discovery for a new generation of covalent drugs

INTRODUCTION

The design of target-specific covalent inhibitors is conceptually attractive because of increased biochemical efficiency through covalency and increased duration of action that outlasts the pharmacokinetics of the agent. Although many covalent inhibitors have been approved or are in advanced clinical trials to treat indications such as cancer and hepatitis C, there is a general tendency to avoid them as drug candidates because of concerns regarding immune-mediated toxicity that can arise from indiscriminate reactivity with off-target proteins.

AREAS COVERED

The review examines potential reason(s) for the excellent safety record of marketed covalent agents and advanced clinical candidates for emerging therapeutic targets. A significant emphasis is placed on proteomic techniques and chemical/biochemical reactivity assays that aim to provide a systematic rank ordering of pharmacologic selectivity relative to off-target protein reactivity of covalent inhibitors.

EXPERT OPINION

While tactics to examine selective covalent modification of the pharmacologic target are broadly applicable in drug discovery, it is unclear whether the output from such studies can prospectively predict idiosyncratic immune-mediated drug toxicity. Opinions regarding an acceptable threshold of protein reactivity/body burden for a toxic electrophile and a non-toxic electrophilic covalent drug have not been defined. Increasing confidence in proteomic and chemical/biochemical reactivity screens will require a retrospective side-by-side profiling of marketed covalent drugs and electrophiles known to cause deleterious toxic effects via non-selective covalent binding.

Mercury chloride decreases the water permeability of aquaporin-4-reconstituted proteoliposomes

BACKGROUND INFORMATION

Mercurials inhibit AQPs (aquaporins), and site-directed mutagenesis has identified Cys(189) as a site of the mercurial inhibition of AQP1. On the other hand, AQP4 has been considered to be a mercury-insensitive water channel because it does not have the reactive cysteine residue corresponding to Cys(189) of AQP1. Indeed, the osmotic water permeability (P(f)) of AQP4 expressed in various types of cells, including Xenopus oocytes, is not inhibited by HgCl2. To examine the direct effects of mercurials on AQP4 in a proteoliposome reconstitution system, His-tagged rAQP4 [corrected] (rat AQP4) M23 was expressed in Saccharomyces cerevisiae, purified with an Ni2+-nitrilotriacetate affinity column, and reconstituted into liposomes with the dilution method.

RESULTS

The water permeability of AQP4 proteoliposomes with or without HgCl2 was measured with a stopped-flow apparatus. Surprisingly, the P(f) of AQP4 proteoliposomes was significantly decreased by 5 microM HgCl2 within 30 s, and this effect was completely reversed by 2-mercaptoethanol. The dose- and time-dependent inhibitory effects of Hg2+ suggest that the sensitivity to mercury of AQP4 is different from that of AQP1. Site-directed mutagenesis of six cysteine residues of AQP4 demonstrated that Cys(178), which is located at loop D facing the intracellular side, is a target responding to Hg2+. We confirmed that AQP4 is reconstituted into liposome in a bidirectional orientation.

CONCLUSIONS

Our results suggest that mercury inhibits the P(f) of AQP4 by mechanisms different from those for AQP1 and that AQP4 may be gated by modification of a cysteine residue in cytoplasmic loop D.

Cysteinyl proteinases and their selective inactivation

The affinity-labeling of cysteinyl proteinases may now be carried out with a number of peptide-derived reagents with selectivity, particularly for reactions carried out in vitro. These reagents have been described with emphasis on their selectivity for cysteine proteinases and lack of action on serine proteinases, the most likely source of side reactions among proteinases. Perhaps a crucial feature of this selectivity is an enzyme-promoted activation due to initial formation of a hemiketal, which may destabilize the reagent. Prominent among the reagent types that have this class selectivity are the peptidyl diazomethyl ketones, the acyloxymethyl ketones, the peptidylmethyl sulfonium salts, and peptidyl oxides analogous to E-64. The need for specific inhibitors capable of inactivating the target enzyme in intact cells and animals is inevitably pushing the biochemical application of these inhibitors into more complex molecular environments where the possibilities of competing reactions are greatly increased. In dealing with the current state and potential developments for the in vivo use of affinity-labeling reagents of cysteine proteinases, the presently known variety of cysteinyl proteinases had to be considered. Therefore this chapter has, at the same time, attempted to survey these proteinases with respect to specificity and gene family. The continual discovery of new proteinases will increase the complexity of this picture. At present the lysosomal cysteine proteinases cathepsins B and L and the cytoplasmic calcium-dependent proteinases are reasonable goals for a fairly complete metabolic clarification. The ability of investigators to inactivate individual members of this family in vivo, possibly without complications due to concurrent inactivation of serine proteinases by improvements in reagent specificity, is increasing. Among the cysteine proteinases, at least those of the papain super family, hydrophobic interactions in the S2 and S3 subsites are important and some specificity has been achieved by taking advantage of topographical differences among members of this group. Some of this has probably involved surface differences removed from the regions involved in proteolytic action. The emerging cysteine proteinases include some which, in contrast to the papain family, have a pronounced specificity in S1 for the binding of basic side chains, familiar in the trypsin family of serine proteinases. At least a potential conflict with serine proteinases can be avoided by choice of a covalent bonding mechanism. The departing group region, has not been exploited. As a sole contributor to binding, this region may be rather limited as a source of specificity.(ABSTRACT TRUNCATED AT 400 WORDS)

The Consequences of Lysosomotropism on the Design of Selective Cathepsin K Inhibitors

Many drug candidates contain a basic functional group that results in lysosomotropism--the accumulation of drug in the acidic lysosomes of a cell. When evaluating inhibitors of lysosomal enzymes, such as the cathepsins, this physical property can have a dramatic impact on the functional selectivity of the test compounds. A basic P3 substituent in cathepsin K inhibitors provides a means of achieving potent and selective enzyme inhibition. To evaluate the whole-cell selectivity of the basic cathepsin K inhibitor L-006235, we identified the irreversible pan-selective cathepsin probe BIL-DMK and used it to design whole-cell enzyme-occupancy assays. These cell-based assays showed a dramatic reduction in selectivity against cathepsins B, L, and S relative to the selectivities observed in enzyme assays. Two-photon confocal fluorescence microscopy showed punctated subcellular localization of L-006235, which colocalized with BODIPY-labelled Lysotracker, consistent with compound lysosomotropism. To address this potential problem, a series of potent cathepsin K inhibitors was developed by replacing the P2--P3 amide bond with a metabolically stable trifluoroethylamine moiety. X-ray crystallography has identified the binding of this functional group to active-site residues in cathepsin K. This modification resulted in increased potency and selectivity that allowed the removal of the basic P3 substituent. The resulting nonbasic inhibitor L-873724 is a 0.2 nM inhibitor of cathepsin K with cathepsin B, L, and S potencies that were not shifted between purified enzyme and whole-cell assays; thus indicating that this compound is not lysosomotropic. L-873724 exhibits excellent pharmacokinetics and is orally active in a monkey model of osteoporosis at 3 mg kg(-1) q.d.

Nuclear magnetic resonance studies on the pKa values and interaction of ionizable groups in bromelain inhibitor VI from pineapple stem

Bromelain inhibitor VI (BI-VI), a cysteine proteinase inhibitor from pineapple stem, is a unique double-chain molecule composed of two distinct domains A and B. In order to clarify the molecular mechanism of the proteinase-inhibitor interaction, we investigated the electrostatic properties of this inhibitor. The inhibitory activity toward bromelain was revealed to be maximal at pH 3-4 and the gross conformation to be stable over a wide range of pH. Based on these results, pH titration experiments were performed on the proton resonances of BI-VI in the pH range of 1.5-9.9, and pKa values (pKexp) were determined for all carboxyl groups and alpha-amino groups. The pKexp were also compared with theoretical values calculated from the NMR-derived structures of BI-VI. The electrostatic surface potential map constructed using the pKexp values revealed that BI-VI possesses continuous negatively charged and scattered positively charged regions on the molecular surface and both regions appear to serve for docking properly with a basic target enzyme. Furthermore, it was suggested that the ionic interaction of the inhibitor with the target enzyme is primarily important for the inhibition, which seems to involve some carboxyl groups in the inhibitor and a thiol group in the proteinase.

Protein engineering of nitrile hydratase activity of papain: molecular dynamics study of a mutant and wild-type enzyme

The mechanism of hydrolysis of the nitrile (N-acetyl-phenylalanyl-2-amino-propionitrile, I) catalyzed by Gln19Glu mutant of papain has been studied by nanosecond molecular dynamics (MD) simulations. MD simulations of the complex of mutant enzyme with I and of mutant enzyme covalently attached to both neutral (II) and protonated (III) thioimidate intermediates were performed. An MD simulation with the wild-type enzyme.I complex was undertaken as a reference. The ion pair between protonated His159 and thiolate of Cys25 is coplanar, and the hydrogen bonding interaction S(-)(25).HD1-ND1(159) is observed throughout MD simulation of the mutant enzyme.I complex. Such a sustained hydrogen bond is absent in nitrile-bound wild-type papain due to the flexibility of the imidazole ring of His159. The nature of the residue at position 19 plays a critical role in the hydrolysis of the covalent thioimidate intermediate. When position 19 represents Glu, the imidazolium ion of His159-ND1(+).Cys25-S(-) ion pair is distant, on average, from the nitrile nitrogen of substrate I. Near attack conformers (NACs) have been identified in which His159-ImH(+) is positioned to initiate a general acid-catalyzed addition of Cys-S(-) to nitrile. Though Glu19-CO(2)H is distant from nitrile nitrogen in the mutant.I structure, MD simulations of the mutant.II covalent adduct finds Glu19-CO(2)H hydrogen bonded to the thioimide nitrogen of II. This hydrogen bonded species is much less stable than the hydrogen bonded Glu19-CO(2)(-) with mutant-bound protonated thioimidate (III). This observation supports Glu19-CO(2)H general acid catalysis of the formation of mutant.III. This is the commitment step in the Gln19Glu mutant catalysis of nitrile hydrolysis.

Kinetic and titration methods for determination of active site contents of enzyme and catalytic antibody preparations

Kinetic characterization of enzymes and analogous catalysts such as catalytic antibodies requires knowledge of the molarity of functional sites. Various stoichiometric titration methods are available for the determination of active-site concentrations of some enzymes and these are exemplified in the second part of this article. Most of these are not general in that they require the existence of certain types of either intermediate or active-site residues that are susceptible to specific covalent modification. Thus they are not readily applicable to many enzymes and they are rarely available currently for titration of catalytic antibody active sites. In the first part of the article we discuss a general kinetic method for the investigation of active-site availability in preparations of macromolecular catalysts. The method involves steady-state kinetics to provide Vmax and Km and single-turnover first-order kinetics using excess of catalyst over substrate to provide the analogous parameters k(obs)lim and K(m)app. The active-site contents of preparations that contain only active catalyst (Ea) and inert material (Ei) may be calculated as [Ea](T) = Vmax)/k(obs)lim. This is true even if nonproductive binding to E(a) occurs. For polyclonal catalytic antibody preparations, which may contain binding but noncatalytic material (Eb) in addition to Ea and Ei, the significance of Vmax/k(obs)lim is more complex but provides an upper limit to E(a). This can be refined by consideration of the relative values of Km and the equilibrium dissociation constant of EbS. Analysis of the Ea, Eb, Ei system requires the separate determination of Ei. For catalytic antibodies this may be achieved by analytical affinity chromatography using an immobilized hapten or hapten analog and an ELISA procedure to ensure the clean separation of Ei from the Ea + Eb mixture.

The structure-activity relationship of the papain hydrolysis of N-benzoylglycine esters

The relationship between structure and the Michaelis-Menten constants (Km) for the papain hydrolysis of a series of 37 N-benzoylglycine esters was investigated. The series studied comprises a wide range of aromatic and aliphatic esters with a 5000-fold variation in their Km constants and essentially constant kcat values. It was found that the variation in the Km constants could be rationalized by the following quantitative structure-activity relationship (QSAR): log 1/Km = 8.13F + 0.33Z + 1.27II3' + 1.95. In this equation F is the field inductive parameter, II3' is the hydrophobic constant for the more lipophilic of the two possible meta substituents and Z is the Van der Waals distance from oxygen through the end of the molecule, in the direction of the 4 position of the aromatic ester moiety.

Inhibition of papain by nitriles: mechanistic studies using NMR and kinetic measurements

N-(N-acetyl-1-phenylalanyl)aminoacetronitrile is an inhibitor of papain. With 13C NMR spectroscopy we have shown that a reversible covalent adduct is formed with papain. The reversible nature of the covalent-adduct formation was demonstrated with NMR saturation-transfer technique using a DANTE pulse for selective excitation. In addition the covalent adduct was displaced with an aldehyde inhibitor to regenerate the nitrile compound. No hydrolysis of the nitrile was observed. The covalent adduct is most likely a thioimidate formed between the essential thiol and the nitrile. Several p-nitroanilide substrates and their corresponding nitrile inhibitors were examined. A correlation between Ki and kcat/Km was observed. This finding together with the fact that the pH dependence of Ki parallels that of kcat/Km suggests that the interaction of nitriles and papain has considerable transition-state character. In contrast, a nitrile was shown to be an ineffective inhibitor of alpha-chymotrypsin.

Polymers containing enzymatically degradable bonds V. Hydrophilic polymers degradable by papain

Copolymers of N-(2-hydroxypropyl)methacrylamide were prepared, in which synthetic polymer chains are joined by crosslinks containing oligopeptidic sequences degradable with papain, with the general structure P-(Gly)n-X-Y-NH-(CH2)6-NH-Y-X-(Gly)n-P (P is the polymer chain, n = 1,2; X...Phe, Val, Gly; Y...Lys, Gly, Tyr, Ala, Phe). The relationship between the structure of these polymeric substrates and their degradability with papain was investigated viscometrically. It was shown that -Phe-Lys- was the most suitable -X-Y- sequence. Extension of the oligopeptidic sequence by one amino acid residue causes a pronounced rise in the rate of cleavage of the polymeric substrates.

Deuterium isotope effects on papain acylation. Evidence for lack of general base catalysis and for enzyme--leaving-group interaction

The experimental data presented in this paper comprise kinetic deuterium isotope effects on acylation of papain with various substrates when conducted in H2O and 2H2O. With alkyl esters of N-acylamino acids there is no or very little isotope effect, whereas with N-acylamino acid amides the ratio kappa H2O/kappa 2H2O is less than 1, i.e. there is an inverse isotope effect. Similarly, alkylation of papain with methyl bromoacetate exhibits no kinetic isotope effect, whereas for the analogous alkylation with bromoacetamide an inverse isotope effect is observed. It is concluded that (a) general base catalysis does not occur in the acylation of papain and (b) kinetic deuterium isotope effects can be affected substantially by interaction between the substrate leaving group and the enzyme, which has not been considered in previous mechanistic investigations.

Rate constants of individual steps in papain-catalysed reactions

Rate constants for acylation of papain (EC 3.4.22.2) by specific substrates and its subsequent deacylation are derived from kinetic analysis of the reactions in the presence of aminoacetonitrile and methanol. Methyl and ethyl hippurate and methyl N-benzyloxycarbonylglycinate have marginally higher values of rate constants for acylation than for deacylation, while the reverse is true for ethyl N-benzoyl-L-arginate. Both acylation and deacylation are rate-determining for these substrates, while only deacylation irate-determining for methyl-N-acetyl-L-phenylalanylglycinate. Deacylation is the only rate-determining step for p-nitrophenyl esters of hippuric acid, N-benzyloxycarbonylglycine and N-acetyl-L-phenylalanylglycine. These results are discussed in relation to those from inactivation of the enzyme by alkylating agent in the presence of substrate.

Conversion of the active-site cysteine residue of papain into a dehydro-serine, a serine and a glycine residue

Photolysis of papain which had been inhibited with 2-bromo-2',4'-dimethoxyacetophenone regenerated papain, but also formed [deltaSer25]-papain (i.e. papain in which the active-site cysteine residue 25 was replaced by dehydroserine) via the intermediate dehydrocysteine analogue, [deltaCys25]-papain. Reduction with sodium borohydride gave [Ser25]papain. Both [Ser25]papain and [deltaSer25]-papain had binding properties similar to those of papain, but were devoid of enzymic activity. Their fluorescence properties were also investigated. Incubation of [deltaSer25]papain at pH 9.0 gave [Gly25]papain.

Resonance Raman evidence for substrate reorginization in the active site of papain

Resonance Raman spectra were obtained for the acylenzyme 4-dimethylamino-3-nitro(alpha-benzamido)cinnamoyl-papain prepared using the chromophoric substrate methyl 4-dimethylamino-3-nitro(alpha-benzamido)cinnamate. These spectra contained vibrational spectral data of the acyl residue while covalently attached to the active site and could be used to follow directly acylation and deacylation kinetics. Spectra were obtained at pH values ranging from those where the acyl-enzyme is relatively stable (pH 3.0, tau 1/2 congruent to 800 s) to those where it is relatively unstable (pH 9.2, tau 1/2 congruent to 223 s). Throughout this range acyl-enzyme spectra differed completely from that of the free substrate or the product (4-dimethylamino-3-nitro(alpha-benzamido)cinnamic acid) indicating that a structural change occurred on combination with the active site. The spectra are consistent with rearrangement of the alpha-benzamido group in the bound substrate, -NH--C(==O)Ph becoming --N==C(--OX)Ph, where the bonding to oxygen is unknown. Superimposed on these large differences, small changes in acyl-enzyme spectra also occurred as pH was raised to decrease the half-life. All of the above spectral perturbations are consistent with a structural change in the acyl-enzyme which precedes the rate-determining step in deacylation. Thus, deacylation proceeds from an acyl residue structure differing from that of the substrate in solution. Upon acid denaturation the spectrum characteristic of the intermediate reverts to one closely resembling the substrate, demonstrating that a functioning active site is necessary to produce the observed differences. Spectra in D2O of native acyl-enzyme were identical with those in H2O, indicating that the observed differences in rate constant were not due to solvent-induced structural changes. Activated papain purified by crystallization or by affinity chromatography formed the acyl-enzyme. However, the kinetics of formation and deacylation differed between these materials, as did the spectral properties. Small differences in active-site structure are considered to be responsible for this effect, and it is suggested that such spectral perturbations may be useful in directly relating small differences in structure of the substrate in the active site with corresponding differences in kinetics.

Reactions of papain and of low-molecular-weight thiols with some aromatic disulphides. 2,2'-Dipyridyl disulphide as a convenient active-site titrant for papain even in the presence of other thiols

1. The u.v.-spectral characteristics of 5,5'-dithiobis-(2-nitrobenzoic acid) (Nbs(2)), 2,2'-dipyridyl disulphide (2-Py-S-S-2-Py), 4,4'-dipyridyl disulphide (4-Py-S-S-4-Py), 5-mercapto-2-nitrobenzoic acid (Nbs), 2-thiopyridone (Py-2-SH) and 4-thiopyridone (Py-4-SH) were determined over a wide range of pH and used to calculate their acid dissociation constants. 2. The reactions of l-cysteine, 2-mercaptoethanol and papain with the above-mentioned disulphides were investigated spectrophotometrically in the pH range 2.5-8.5. 3. Under the conditions of concentration used in this study the reactions of both low-molecular-weight thiols with all three disulphides resulted in the stoicheiometric release of the thiol or thione fragments Nbs, Py-2-SH and Py-4-SH at all pH values. The rates of these reactions are considerably faster at pH8 than at pH4, which suggests that the predominant reaction pathway in approximately neutral media is nucleophilic attack of the thiolate ion on the unprotonated disulphide. 4. The reaction of papain with Nbs(2) is markedly reversible in the acid region, and the pH-dependence of the equilibrium constant for this system in the pH range 5-8 at 25 degrees C and I=0.1 is described by: [Formula: see text] 5. Papain reacts with both 2-Py-S-S-2-Py and 4-Py-S-S-4-Py in the pH range 2.5-8.5 to provide release of the thione fragments, stoicheiometric with the thiol content of the enzyme. 6. Whereas the ratios of the second-order rate constant for the reaction at pH4 to that at pH8 for the cysteine-2-Py-S-S-2-Py reaction (k(pH4)/k(pH8)=0.015) and for the papain-4-Py-S-S-4-Py reaction (k(pH4)/k(pH8)=0.06) are less than 1, that for the papain-2-Py-S-S-2-Py reaction is greater than 1 (k(pH4)/k(pH8)=15). 7. This high reactivity of papain has been shown to involve reaction of the thiol group of cysteine-25, the enzyme's only cysteine residue, which is part of its catalytic site. 8. That this rapid and stoicheiometric reaction of the thiol group of native papain is not shown either by low-molecular-weight thiols or by the thiol group of papain after its active conformation has been destroyed by acid or heat denaturation, strongly commends 2-Py-S-S-2-Py as one of the most useful papain active-site titrants discovered to date. This reagent has been shown to allow accurate titration of papain active sites in the presence of up to 10-fold molar excess of l-cysteine and up to 100-fold molar excess of 2-mercaptoethanol.

Kinetic specificity in papain-catalysed hydrolyses

The specificity of the proteolytic enzyme, papain, for the peptide bond of the substrate adjacent to that about to be cleaved and for the acyl residue of some N-acylglycine derivatives is manifest almost exclusively in the formation of the acyl-enzyme from the enzyme-substrate complex. Models for the enzyme-substrate complex and acyl-enzyme intermediate are suggested that account for these observations. In particular it is suggested that the peptide bond of the substrate adjacent to that about to be cleaved, is bound in the cleft of the enzyme between the NH group of glycine-66 and the backbone C=O group of aspartic acid-158, and provides a sensitive amplification mechanism through which the specificity of the enzyme for hydrophobic amino acids such as l-phenylalanine is relayed. It is also suggested that the distortion in the enzyme-substrate complex and the binding of the peptide bond adjacent to that about to be cleaved are also linked and behave co-operatively, the distortion of the protein facilitating binding and the stronger binding facilitating distortion. The results imply that between the enzyme-substrate complex and the acyl-enzyme a relaxation of the protein conformation must occur.

pH-dependence and structure-activity relationships in the papain-catalysed hydrolysis of anilides

The pH-dependence of the Michaelis-Menten parameters for the papain-catalysed hydrolysis of N-acetyl-l-phenylalanylglycine p-nitroanilide was determined. The equilibrium binding constant, K(s), is independent of pH between 3.7 and 9.3, whereas the acylation constant, k(+2), shows bell-shaped pH-dependence with apparent pK(a) values of 4.2 and 8.2. The effect of substituents in the leaving group on the acylation constant of the papain-catalysed hydrolysis of hippuryl anilides and N-acetyl-l-phenylalanylglycine anilides gives rise in both series to a Hammett rho value of -1.04. This indicates that the enzyme provides electrophilic, probably general-acid, catalysis, as well as the nucleophilic or general-base catalysis previously found. A mechanism involving a tetrahedral intermediate whose formation is general-base-catalysed and whose breakdown is general-acid-catalysed seems most likely. The similarity of the Hammett rho values appears to exclude facilitated proton transfer as a means through which the specificity of papain is expressed.