The pH-dependence of the peptidase activity of aminoacylase.

Aminoacylase is a potent peptidase around pH 8.5. The pH dependence of the Km values reveals that only dipeptides with uncharged N-terminal amino acids are substrates of the enzyme. The Km values reflect the hydrophobicity of the N-terminal amino acids. Calculated on the basis of unprotonated peptides they are pH independent. Hydrophobic, deprotonated amino acids are competitive inhibitors of the enzyme, tryptophan and norleucine being the strongest inhibitors. Inhibitor constants with glycylalanine as substrate have been determined for several amino acids. From the present results it may be deduced that the N-terminal amino acids of dipeptides are bound at a strongly hydrophobic site.     

Comparison of the Effect of Calpain Inhibitors on Two Extralysosomal Proteinases: The Multicatalytic Proteinase Complex and m-Calpain

Abstract: The potencies of three peptide aldehyde inhibitors of calpain (calpain inhibitors 1 and 2 and calpeptin) as inhibitors of four catalytic activities of the multicatalytic proteinase complex (MPC) were compared with their potencies as inhibitors of m-calpain. The chymotrypsinlike activity (cleavage after hydrophobic amino acids) and the caseinolytic activity (degradation of β-casein) of MPC were strongly inhibited by calpain inhibitors 1 and 2 (IC₅₀ values in the low micromolar range). Cleavage by MPC after acidic amino acids (peptidylglutamyl-peptide bond hydrolyzing activity) and basic amino acids (trypsinlike activity) was inhibited less effectively, declining moderately with increasing concentrations of calpain inhibitors 1 and 2. Calpeptin only weakly inhibited the four MPC activities, yet was the most potent inhibitor of m-calpain. These results indicate that caution must be exercised when calpain inhibitors 1 and 2 are used to infer calpain function. Calpeptin may be a better choice for such studies, although its effect on other cysteine or serine proteinases remains to be determined.     

Design, synthesis, and evaluation of trifluoromethyl ketones as inhibitors of SARS-CoV 3CL protease

A series of trifluoromethyl ketones as SARS-CoV 3CL protease inhibitors was developed. The inhibitors were synthesized in four steps from commercially available compounds. Three different amino acids were explored in the P1-position and in the P2-P4 positions varying amino acids and long alkyl chain were incorporated. All inhibitors were evaluated in an in vitro assay using purified enzyme and fluorogenic substrate peptide. One of the inhibitors showed a time-dependent inhibition, with a K(i) value of 0.3 microM after 4h incubation.     

Endogenous inhibitors of human placental prostaglandin dehydrogenase.

The presence of endogenous inhibitors of NAD(+)-dependent 15-hydroxyprostaglandin dehydrogenase (PGDH) has been indicated by increasing total activity after the initial purification step of PGDH in human placenta. Based on this observation, we tried to characterize and analyze endogenous inhibitors of PGDH in human placenta in this study. The inhibitors were extracted from the supernatant by precipitation at pH 5.2 and partially purified by acetone precipitation and by thin layer chromatography. The inhibitors were stable to heating at 100 degrees C for 10 min, and to trypsin digestion. The pattern of inhibition was competitive with regard to PGE2 and uncompetitive with regard to NAD at pH 8.0. The Ki value for PGE2 was 18.9 microM. Analysis by gas chromatography and mass spectrometry indicated that the inhibitors consisted of fatty acids which were palmitic, stearic, oleic and linoleic acids. Myristic, palmitic and stearic acids were confirmed to exert an inhibitory action on PGDH and showed a competitive inhibition pattern. Stearic acid was less potent in inhibition than other fatty acids. These findings suggest that intracellular fatty acids may play a unique role in the control of PGDH activity.     

Structure of malonic acid-based inhibitors bound to human neutrophil collagenase. A new binding mode explains apparently anomalous data.

Matrix metalloproteinases (MMPs) are a family of zinc endopeptidases, which have been implicated in various disease processes. Various classes of MMP inhibitors, including hydroxamic acids, phosphinic acids, and thiols, have been previously described. Most of these mimic peptides, and most likely bind analogous to the corresponding peptide substrates. Among the hydroxamic acids, malonic acid derivatives have been used as MMP inhibitors, although optimization of their inhibition potency was not successful. Here we report the design of malonic acid-based inhibitors using the X-ray structure of a collagenase/inhibitor complex, which revealed a nonsubstrate-like binding mode. The proposed beta-type turn-like conformation for the improved inhibitors was confirmed by X-ray crystallography. The observation of nonsubstrate-like binding confirms the original strategy for structure-based modeling of improved malonic acid inhibitors, and explains kinetic data that are inconsistent with substrate-like binding. Detailed interactions for the improved inhibitors seen in the crystal structure also suggest possibilities for further modifications in cycles of structure based drug design. Indeed, we have designed nonpeptidic inhibitors with approximately 500-fold improved inhibition based on these structures.     

On the importance of decarboxylation in the metabolism of phenylalanine, tyrosine, and tryptophan

After the oral administration of large doses of tyrosine, tryptophan, or phenylalanine to rats, increased plasma levels of these amino acids can be observed. These levels can be further elevated, approximately 2-fold, by administering along with the amino acids, inhibitors of aromatic-l-amino acid decarboxylase. The inhibitors, by themselves, do not alter control plasma levels of the aromatic amino acids. This effect of the inhibitors appears to be specific for amino acids which are substrates of the decarboxylase since they did not further elevate plasma levels of leucine or valine after oral loading of these amino acids. Elevation of plasma tyrosine could also be observed after inhibition of the decarboxylase when tyrosine was administered intraperitoneally or in rats pretreated with antimicrobial agents, indicating that inhibition of decarboxylation by intestinal bacteria was not responsible for the effects. It was shown that the decarboxylase inhibitors do not act by simultaneously inhibiting other major routes of metabolism, such as transamination in the case of tyrosine. These findings indicate that, when tissue levels of tyrosine, phenylalanine, or tryptophan are elevated, decarboxylation becomes a major route for their metabolism.     

Reversible inhibitors of penicillinases.

Reversible competitive inhibitors of a penicillinase, beta-lactamase 1 from Bacillus cereus, were studied. These represent the first inhibitors of a penicillinase that lack the beta-lactam ring. The products of the enzymic reaction, namely penicilloic acids, are inhibitors; their decarboxylation products, the penilloic acids, are also inhibitors, and have somewhat lower Ki values. Inhibitors have been prepared from benzylpenicillin, phenoxymethyl-penicillin, methicillin (2,6-dimethoxybenzamidopenicillanic acid) and 3-hydroxy-4-nitrobenzamidopenicillanic acid. Decarboxylation of the penicilloic acids from benzyl-penicillin, or from phenoxymethylpenicillin, leads to epimerization (at C-5) of the penilloic acid. Nuclear-magnetic resonance spectroscopy at a frequency of 270 MHz can distinguish the epimers. Other competitive inhibitors studied were boric acid, benzene boronic acid and m-aminobenzeneboronic acid. Boric acid itself was the best inhibitor of beta-lactamase I so far found.     

Biaryl diacid inhibitors of human s-PLA2 with anti-inflammatory activity

Twenty-four hydrophobic dicarboxylic acids are described which were evaluated as inhibitors of 14 kDa human platelet phospholipase A2 (HP-PLA2). In general, biarylacetic acid derivatives were found to be more active than biaryl acids or biarylpropanoic acids. More potent inhibitors were obtained when hydrophobic groups were attached to the biaryl acid nucleus using an olefin linkage as compared to an ether linkage. Compounds with larger hydrophobic groups were usually more potent inhibitors of HP-PLA2. Five of the compounds disclosed in this report (2, 4, 28, 36b and 36i) were found to possess significant anti-inflammatory activity in a phorbol ester induced mouse ear edema model of chronic inflammation.     

Inhibitors of metalloendopeptidase EC 3.4.24.15 and EC 3.4.24.16 stabilized against proteolysis by the incorporation of beta-amino acids

The enzyme EC 3.4.24.15 (EP 24.15) is a zinc metalloendopeptidase whose precise function in vivo remains unknown but is thought to participate in the regulated metabolism of a number of specific neuropeptides. The lack of stable and selective inhibitors has hindered the determination of the exact function of EP 24.15. Of the limited number of EP 24.15 inhibitors that have been developed, N-[1-(R,S)-carboxy-3-phenylpropyl]-Ala-Ala-Tyr-p-aminobenzoate (CFP) is the most widely studied. CFP is a potent and specific inhibitor, but it is unstable in vivo due to cleavage between the alanine and tyrosine residues by the enzyme neprilysin (EP 24.11). This cleavage by EP 24.11 generates a potent inhibitor of angiotensin converting enzyme, thereby limiting the use of CFP for in vivo studies. To develop specific inhibitors of EP 24.15 that are resistant to in vitro and potentially in vivo proteolysis by EP 24.11, this study incorporated beta-amino acids replacing the Ala-Tyr scissile alpha-amino acids of CFP. Both C2 and C3 substituted beta-amino acids were synthesized and substituted at the EP 24.11 scissile Ala-Tyr bond. Significant EP 24.15 inhibitory activity was observed with some of the beta-amino acid containing analogues. Moreover, binding to EP 24.11 was eliminated, thus rendering all analogues containing beta-amino acids resistant to degradation by EP 24.11. Selective inhibition of either EP 24.15 or EP 24.16 was also observed with some analogues. The results demonstrated the use of beta-amino acids in the design of inhibitors of EP 24.15 and EP 24.16 with K(i)'s in the low micromolar range. At the same time, these analogues were resistant to cleavage by the related metalloendopeptidase EP 24.11, in contrast to the alpha-amino acid based parent peptide. This study has therefore clearly shown the potential of beta-amino acids in the design of stable enzyme inhibitors and their use in generating molecules with selectivity between closely related enzymes.     

Inhibition of carbonic anhydrase isoforms I,II, IV,VII and XII with carboxylates and sulfonamides incorporating phthalimide/phthalic anhydride scaffolds

We report a panel of carboxylates and sulfonamides incorporating phthalic anhydride and phthalimide moieties in their structure and their interaction with the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). They were synthesized from substituted anthranilic acids and trimellitic anhydride chloride, followed by reaction with primary amines and were tested for the inhibition of five physiologically relevant CA isoforms, the human (h) hCA I, II, IV, VII and XII, some of which are involved in serious pathologies (CA II, IV and XII in glaucoma; CA VII in epilepsy; CA XII in some solid tumors). The carboxylic acids were generally poor inhibitors of isoforms hCA I, II and IV but were highly effective, low nanomolar inhibitors of hCA VII and XII. The sulfonamides inhibited all isoforms significantly, and some of them were sub-nanomolar hCA VII inhibitors, although their isoform selectivity was lower compared to the carboxylates. This study proves that carboxylic acids incorporating a phthalic anhydride/phthalimide based scaffold may lead to isoform-selective inhibitors by applying the tail approach, mostly used up until now for obtaining sulfonamide, sulfamide and sulfamate CA inhibitors.     

Specificity of intestinal brush-border proline transport: cyanine dye studies

The ability of rabbit jejunal brush borders to transport inhibitors of the imino carrier was investigated in membrane vesicles by measuring their ability to depolarize the membrane potential. Membrane potentials were monitored using a voltage-sensitive cyanine dye. Piperidine and pyrrolidine carboxylic acids, which are potent inhibitors of Na+-dependent proline transport (Ki less than 0.5 mM) depolarize the potential in a Na+-dependent, saturable manner indicating transport. On the other hand, N-methylated amino acids, which are fair inhibitors (Ki 2-10 mM), do not depolarize the membrane to any significant extent, but they competitively inhibit the L-proline transport signal. This indicates that these analogs are nontransported inhibitors of the imino carrier. The poor inhibitors niacin and pipolinic acid (Ki greater than 60 mM) depolarize the membrane about twice as much as proline and with low Kf values. This suggests separate carriers for these substrates.     

Exploring the potential of boronic acids as inhibitors of OXA‐24/40 β‐lactamase

β‐lactam antibiotics are crucial to the management of bacterial infections in the medical community. Due to overuse and misuse, clinically significant bacteria are now resistant to many commercially available antibiotics. The most widespread resistance mechanism to β‐lactams is the expression of β‐lactamase enzymes. To overcome β‐lactamase mediated resistance, inhibitors were designed to inactivate these enzymes. However, current inhibitors (clavulanic acid, tazobactam, and sulbactam) for β‐lactamases also contain the characteristic β‐lactam ring, making them susceptible to resistance mechanisms employed by bacteria. This presents a critical need for novel, non‐β‐lactam inhibitors that can circumvent these resistance mechanisms. The carbapenem‐hydrolyzing class D β‐lactamases (CHDLs) are of particular concern, given that they efficiently hydrolyze potent carbapenem antibiotics. Unfortunately, these enzymes are not inhibited by clinically available β‐lactamase inhibitors, nor are they effectively inhibited by the newest, non‐β‐lactam inhibitor, avibactam. Boronic acids are known transition state analog inhibitors of class A and C β‐lactamases, and are not extensively characterized as inhibitors of class D β‐lactamases. Importantly, boronic acids provide a novel way to potentially inhibit class D β‐lactamases. Sixteen boronic acids were selected and tested for inhibition of the CHDL OXA‐24/40. Several compounds were identified as effective inhibitors of OXA‐24/40, with K_i values as low as 5 μM. The X‐ray crystal structures of OXA‐24/40 in complex with BA3, BA4, BA8, and BA16 were determined and revealed the importance of interactions with hydrophobic residues Tyr112 and Trp115. These boronic acids serve as progenitors in optimization efforts of a novel series of inhibitors for class D β‐lactamases.     

Enhancement and inhibition of luminol chemiluminescence by phenolic acids

We explored the behaviour of a series of phenolic acids used as enhancers or inhibitors of luminol chemiluminescence by three different methods to determine if behaviour was associated with phenolic acid structure and redox character. All the phenolic acids inhibited chemiluminescence when hexacyanoferrate(III) was reacted with the phenolic acids before adding luminol. The redox character of these compounds was clearly related to structure. When hexacyanoferrate(III)-luminol-O₂ chemiluminescence was initiated by phenolic acid-luminol mixtures some phenolic acids behaved as enhancers of chemiluminescence, and others as inhibitors. We propose a mechanism to explain these findings. We found direct relationships between the redox character of the phenolic acids and the enhancement or inhibition of the chemiluminescence of the luminol–H₂O₂–peroxidase system and we propose mechanism to explain these phenomena.     

Quantitative structure-activity relationship study on some 5-lipoxygenase inhibitors

A quantitative structure-activity relationship (QSAR) study has been made on some lipoxygenase inhibitors belonging to the series of omega-phenylalkyl hydroxamic acids, omega-naphthylalkyl hydroxamic acids, eicosatetraenoic acids, and 1H.benzimidazole-4-ols. It was found that the hydrophobic character of the molecules and the size of their substituents selectively govern their lipoxygenase inhibitory activity. The enzyme active site possesses a non-heme ferric ion, a hydrophobic domain, and a carboxylic acid binding site. It was found that while the functional group of inhibitors must interact with the ferric ion, the substituent on one side of it would be involved in hydrophobic interaction and that on the other side in van der Waals interaction with the enzyme so leading to an enhancement in the inhibitory activity of the inhibitors.     

Acetoin production as an indicator of growth and metabolic inhibition of Listeria monocytogenes

It has been shown that Listeria monocytogenes produces acetoin from glucose under aerobic conditions. A defined medium with glucose as the sole carbon source was used in an aerobic shake flask culture to reliably produce acetoin. Acetoin, the reactive compound in the Voges-Proskauer test, was assayable in the medium and was used to quantify the metabolic response when inhibitors were added to the medium. Inhibitors such as lactic, acetic, propionic and benzoic acids were used to demonstrate the utility of acetoin production as an indicator of metabolic disruption. With increasing levels of inhibitor, the metabolic and growth responses were measured by acetoin production and optical density change, respectively. Both measurements decreased in a similar manner with increasing inhibitor concentrations. The data also showed the apparent mode of action of the inhibitors. A bacteriostatic effect was observed for the protonated organic acids, acetic (4 mmol l(-1)) and propionic (4 mmol l(-1)), whereas protonated lactic (4 mmol l(-1)) and benzoic (0.16 mmol l(-1)) acids gave an irreversible (apparent bacteriocidal) effect. Lactic, acetic, and propionic acids showed stimulation of metabolic activity at low concentrations, but benzoic did not. Acetoin production is a novel method for quantifying and assessing the mode of action of inhibitors against L. monocytogenes. This system can be used to screen inhibitors for applications in food safety.     

Actinoplanic acids A and B as novel inhibitors of farnesyl-protein transferase

Actinoplanic acids A and B are macrocyclic polycarboxylic acids that are potent reversible inhibitors of farnesyl-protein transferase. Actinoplanic acids A and B were isolated from Actinoplanes sp. MA 7066 while actinoplanic acid B was isolated from both MA 7066 and Streptomyces sp. MA 7099. Actinoplanic acids A and B are competitive with respect to farnesyl diphosphate and are selective inhibitors of farnesyl-protein transferase because they do not inhibit geranylgeranyl-protein transferase type 1 or squalene synthase. MA 7066 is believed to be a novel species of actinomycetes while MA 7099 is believed to be a novel strain of Streptomyces violaceusniger on the basis of morphological, biochemical and chemotaxonomic characteristics as well as its production of actinoplanic acids.     

alpha-Ketocarboxylic acid-based inhibitors of protein tyrosine phosphatases.

A series of aryl alpha-ketocarboxylic acids was synthesized and investigated as inhibitors for the protein tyrosine phosphatase from Yersinia enterocolitica. IC(50) values for these compounds range from 79 to 2700 microM. Larger aromatic groups, and aromatic groups with high electron density, lead to more potent inhibitors. In general, the related aryl alpha-hydroxycarboxylic acids show lower activity.     

Isolation and characterization of calcium oxalate crystal growth inhibitors from human urine

Four acidic polypeptides which inhibit the growth of calcium oxalate crystals have been isolated from normal human urine, and two of these have been characterized with respect to their amino acid and carbohydrate compositions. SDS-Polyacrylamide gel electrophoresis of either of the two latter inhibitors revealed one prominent band that migrated with an apparent molecular weight of 17,500 daltons. γ-Carboxyglutamate is present in these inhibitors, and they contain a total of more than 25% glutamic and aspartic acids and less than 10% of basic amino acids.     

Interaction of tyrosine-phenol-lyase from Citrobacter intermedius with amino acids and their derivatives: factors determining the effectiveness of binding

The inhibition by L-amino acids and their derivatives of tyrosine phenol-lyase is investigated. Tyramine, alpha-phenylethylamine and tryptamine have no detectable inhibition effect and hence are weakly bonded by an active site. The aromatic amino acid amides are competitive inhibitors but do not manifest an enzymatic isotope exchange of alpha-proton in D2O. Free amino acids however are competitive inhibitors and in the majority of cases exchange alpha-proton. The presence of COOH-group is therefore an important feature which determines the binding efficiency and causes the "active" conformation of the amino acid-PLP complex labelising alpha-proton. In the absence of functional and bulky groups in the amino acid side chain the hydrophobicity is found to be the main factor determining the binding efficiency. For these amino acids a correlation exists between-RTlnKi and side chain hydrophobicity. The amino acids bearing the bulky groups, i. e. valine, leucine and isoleucine have reduced binding efficiency. Lysine and arginine bearing positively charged functional groups possess no inhibition effect. Aspartic and glutamic acids are anomalously strong inhibitors taking into consideration low hydrophobicity of their side chains. One can assume that the electrophilic group able to interact with the terminal COO- -group of aspartic and glutamic acids is located in the active site of tyrosine phenollyase.     

Quantitative Structure-Activity Relationship Study on Some 5-Lipoxygenase Inhibitors

Abstract

A quantitative structure-activity relationship (QSAR) study has been made on some lipoxygenase inhibitors belonging to the series of ω-phenylalkyl hydroxamic acids, ω-naphthylalkyl hydroxamic acids, eicosatetraenoic acids, and 1H.benzimidazole-4-ols. It was found that the hydrophobic character of the molecules and the size of their substituents selectively govern their lipoxygenase inhibitory activity. The enzyme active site possesses a non-heme ferric ion, a hydrophobic domain, and a carboxylic acid binding site. It was found that while the functional group of inhibitors must interact with the ferric ion, the substituent on one side of it would be involved in hydrophobic interaction and that on the other side in van der Waals interaction with the enzyme so leading to an enhancement in the inhibitory activity of the inhibitors.