pK values for active site residues of carboxypeptidase A

Progress in the Enantioselective Synthesis of Sulfur (VI) Compounds

In recent years, there has been a notable surge in the prominence of enantioenriched sulfur(VI) compounds within the chemical science, particularly in the realm of bioactive molecules. However, the synthesis of these enantioenriched sulfur(VI) compounds has posed significant challenges, necessitating the exploration of diverse synthetic methods. Accordingly, this review aims to provide an in-depth analysis of the latest advancements in the synthesis of sulfoximines, sulfonimidate esters, sulfonimidamides, and sulfonimidoyl halides, with a focus on developments since 1971.

Insights into Catalytic Hydrolysis of Organophosphonates at M-OH Sites of Azolate-Based Metal Organic Frameworks

Organophosphorus nerve agents, a class of extremely toxic chemical warfare agents (CWAs), have remained a threat to humanity because of their continued use against civilian populations. To date, Zr(IV)-based metal organic framework (MOFs) are the most prevalent nerve agent hydrolysis catalysts, and relatively few reports disclose MOFs containing nodes with other Lewis acidic transition metals. In this work, we leveraged this synthetic tunability to explore how the identity of the transition metal node in the M-MFU-4l series of MOFs (M = Zn, Cu, Ni, Co) influences the catalytic performance toward the hydrolysis of the nerve agent simulant dimethyl (4-nitrophenyl)phosphate (DMNP). Experimental studies reveal that Cu-MFU-4l exhibits the best performance in this series with a half-life for hydrolysis of ∼2 min under these conditions. In contrast, both Ni- and Co-MFU-4l demonstrate significantly slower reactivity toward DMNP, as they both fail to surpass 30% conversion of DMNP after 1 h under analogous conditions. Further modification of the active site within Cu-MFU-4l is possible, and we found that although the identity of the anion coordinated to the Cu(II)-X (X = Cl^-, HCOO^-, ClO₄^-, NO₃^-) active site has little influence on the catalytic performance, reduction of the Cu(II) sites yields nodes that contain Cu(I) ions in a trigonal geometry with open metal sites, leading to remarkable catalytic activity with a half-life for hydrolysis less than 2 min. Computational studies indicate the Cu(I) sites exhibit stronger binding affinities than Cu(II) to both water and DMNP, which corroborates the experimental results.

Metallo-β-Lactamase Inhibitors Inspired on Snapshots from the Catalytic Mechanism

β-Lactam antibiotics are the most widely prescribed antibacterial drugs due to their low toxicity and broad spectrum. Their action is counteracted by different resistance mechanisms developed by bacteria. Among them, the most common strategy is the expression of β-lactamases, enzymes that hydrolyze the amide bond present in all β-lactam compounds. There are several inhibitors against serine-β-lactamases (SBLs). Metallo-β-lactamases (MBLs) are Zn(II)-dependent enzymes able to hydrolyze most β-lactam antibiotics, and no clinically useful inhibitors against them have yet been approved. Despite their large structural diversity, MBLs have a common catalytic mechanism with similar reaction species. Here, we describe a number of MBL inhibitors that mimic different species formed during the hydrolysis process: substrate, transition state, intermediate, or product. Recent advances in the development of boron-based and thiol-based inhibitors are discussed in the light of the mechanism of MBLs. We also discuss the use of chelators as a possible strategy, since Zn(II) ions are essential for substrate binding and catalysis.

Overcoming differences: The catalytic mechanism of metallo-β-lactamases

Metallo-β-lactamases are the latest resistance mechanism of pathogenic and opportunistic bacteria against carbapenems, considered as last resort drugs. The worldwide spread of genes coding for these enzymes, together with the lack of a clinically useful inhibitor, have raised a sign of alarm. Inhibitor design has been mostly impeded by the structural diversity of these enzymes. Here we provide a critical review of mechanistic studies of the three known subclasses of metallo-β-lactamases, analyzed at the light of structural and mutagenesis investigations. We propose that these enzymes present a modular structure in their active sites that can be dissected into two halves: one providing the attacking nucleophile, and the second one stabilizing a negatively charged reaction intermediate. These are common mechanistic elements in all metallo-β-lactamases. Nucleophile activation does not necessarily requires a Zn(II) ion, but a Zn(II) center is essential for stabilization of the anionic intermediate. Design of a common inhibitor could be therefore approached based in these convergent mechanistic features despite the structural differences.

Crystal structure of reaction intermediates in pyruvate class II aldolase: substrate cleavage, enolate stabilization, and substrate specificity

Crystal structures of divalent metal-dependent pyruvate aldolase, HpaI, in complex with substrate and cleavage products were determined to 1.8-2.0 Å resolution. The enzyme·substrate complex with 4-hydroxy-2-ketoheptane-1,7-dioate indicates that water molecule W2 bound to the divalent metal ion initiates C3-C4 bond cleavage. The binding mode of the aldehyde donor delineated a solvent-filled capacious binding locus lined with predominantly hydrophobic residues. The absence of direct interactions with the aldehyde aliphatic carbons accounts for the broad specificity and lack of stereospecific control by the enzyme. Enzymatic complex structures formed with keto acceptors, pyruvate, and 2-ketobutyrate revealed bidentate interaction with the divalent metal ion by C1-carboxyl and C2-carbonyl oxygens and water molecule W4 that is within close contact of the C3 carbon. Arg(70) assumes a multivalent role through its guanidinium moiety interacting with all active site enzymatic species: C2 oxygen in substrate, pyruvate, and ketobutyrate; substrate C4 hydroxyl; aldehyde C1 oxygen; and W4. The multiple interactions made by Arg(70) stabilize the negatively charged C4 oxygen following proton abstraction, the aldehyde alignment in aldol condensation, and the pyruvate enolate upon aldol cleavage as well as support proton exchange at C3. This role is corroborated by loss of aldol cleavage ability and pyruvate C3 proton exchange activity and by a 730-fold increase in the dissociation constant toward the pyruvate enolate analog oxalate in the R70A mutant. Based on the crystal structures, a mechanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis that facilitates reversible aldol cleavage. The same reaction mechanism promotes decarboxylation of oxaloacetate.

pH dependence studies provide insight into the structure and mechanism of thimet oligopeptidase (EC 3.4.24.15)

Thimet oligopeptidase (EC 3.4.24.15; TOP) is a Zn(II) endopeptidase implicated in physiological regulation of processes involving neuropeptides. The present study clarifies the active site structure and mechanism of catalysis of TOP. The enzyme exhibited a bell-shaped pH dependence of activity having an acidic limb due to a protonation event with a pK(a) of 5.7 and a basic limb with pK(a) of 8.8. The acidic limb can be attributed to protonation of a residue affecting k(cat) while the alkaline limb may be due to conformational change. Mutation of Tyr612 to Phe resulted in more than 400-fold decrease in activity. This result, supported by modeling studies, implicates Tyr612 in transition state stabilization analogous to the role of His231 of thermolysin.

Alkaline phosphatase revisited: hydrolysis of alkyl phosphates

Escherichia coli alkaline phosphatase (AP) is the prototypical two metal ion catalyst with two divalent zinc ions bound approximately 4 A apart in the active site. Studies spanning half a century have elucidated many structural and mechanistic features of this enzyme, rendering it an attractive model for investigating the potent catalytic power of bimetallic centers. Unfortunately, fundamental mechanistic features have been obscured by limitations with the standard assays. These assays generate concentrations of inorganic phosphate (P(i)) in excess of its inhibition constant (K(i) approximately 1 muM). This tight binding by P(i) has affected the majority of published kinetic constants. Furthermore, binding limits k(cat)/K(m) for reaction of p-nitrophenyl phosphate, the most commonly employed substrate. We describe a sensitive (32)P-based assay for hydrolysis of alkyl phosphates that avoids the complication of product inhibition. We have revisited basic mechanistic features of AP with these alkyl phosphate substrates. The results suggest that the chemical step for phosphorylation of the enzyme limits k(cat)/K(m). The pH-rate profile and additional results suggest that the serine nucleophile is active in its anionic form and has a pK(a) of < or = 5.5 in the free enzyme. An inactivating pK(a) of 8.0 is observed for binding of both substrates and inhibitors, and we suggest that this corresponds to ionization of a zinc-coordinated water molecule. Counter to previous suggestions, inorganic phosphate dianion appears to bind to the highly charged AP active site at least as strongly as the trianion. The dependence of k(cat)/K(m) on the pK(a) of the leaving group follows a Brønsted correlation with a slope of beta(lg) = -0.85 +/- 0.1, differing substantially from the previously reported value of -0.2 obtained from data with a less sensitive assay. This steep leaving group dependence is consistent with a largely dissociative transition state for AP-catalyzed hydrolysis of phosphate monoesters. The new (32)P-based assay employed herein will facilitate continued dissection of the AP reaction by providing a means to readily follow the chemical step for phosphorylation of the enzyme.

Principles of hydroxamate inhibition of metalloproteases: carboxypeptidase A

Hydroxamic acids of structure RCON(OH)CH(2)CH(CH(2)C(6)H(5))CO(2)H induce micromolar competitive inhibition of catalysis for the enzyme carboxypeptidase A. Enzyme affinity depends on the nature of the acyl group, for RCO equaling HCO, CH(3)CO, FCH(2)CO, F(2)CHCO, F(3)CCO, CH(3)OCH(2)CO, or CH(3)OCO. In acid dissociation these residues yield hydroxamic acid pK(a) values that vary from 7.6 to 10.3. Profiles of inhibitory pK(i) plotted versus pH indicate characteristically a maximum effectiveness near neutrality. Weaker binding to enzyme is generally displayed in either acidic or alkaline solution, with the position of the alkaline limb of the profiles depending on the pK(a) of the inhibitor. A reverse-protonation pattern of association with the enzyme is indicated, in which the hydroxamate anion of the inhibitor displaces a relatively acidic H(2)O ligand (pK(a) of 6) from the active-site zinc ion of carboxypeptidase A. The metal-coordinating, N-substituted hydroxamic acid functional groups exist in solution as a mixture of syn and anti rotamers, with relative abundances that depend on their pK(a). A pyrrolidinone analogue having a conformationally syn-fixed cyclohydroxamic acid was not an especially potent inhibitor. Structure-activity relationships suggest design criteria for hydroxamic acid inhibitors in order to provide most effective binding with metalloenzymes.

pK(a) calculations for class C beta-lactamases: the role of Tyr-150

The Poisson-Boltzmann method was used to compute the pK(a) values of titratable residues in a set of class C beta-lactamases. In these calculations, the pK(a) of the phenolic group of residue Tyr150 is the only one to stand out with an abnormally low value of 8.3, more than one pK(a) unit lower than the measured reference value for tyrosine in solution. Other important residues of the catalytic pocket, such as the conserved Lys67, Lys315, His314, and Glu272 (hydrogen-bonded to the ammonium group of Lys315), display normal protonation states at neutral pH. pK(a) values were also computed in catalytically impaired beta-lactamase mutants. Comparisons between the relative k(cat) values and the Tyr150 pK(a) value in these mutants revealed a striking correlation. In active enzymes, this pK(a) value is always lower than the solution reference value while it is close to normal in inactive enzymes. These results thus support the hypothesis that the phenolate form of Tyr150 is responsible for the activation of the nucleophilic serine. The possible roles of Lys67 and Lys315 during catalysis are also discussed.

Synergistic inhibition of carboxypeptidase A by zinc ion and imidazole

Zinc ion in solution yields a 560-fold enhancement in the kinetic inhibition of carboxypeptidase A by the simple heterocycle imidazole, behavior attributed to formation of a ternary complex of the three species. However, the effect is partially negated by formation of less-inhibitory Zn2+(C3H4N2)2-4 coordination complexes, providing for the enzyme an anomalous profile of catalytic rate versus imidazole concentration.

Kinetic characterization of the neutral protease vimelysin from Vibrio sp. T1800

The kinetics of the hydrolysis of dipeptide and tripeptide substrates by the recently discovered neutral protease from Vibrio species T1800 (vimelysin) were studied. In the pH dependence of the apparent second-order rate constant, the pKa2 value of vimelysin (approximately 6.5) was significantly lower than thermolysin (8.3), although the pKa1 (approximately 5.1) values were comparable (5.0). The Kcat/Km(lim) parameter for hydrolysis of Fua-Gly-PheNH2 (Fua = furylacryloyl) was more than sevenfold greater than for Fua-Gly-LeuNH2. This higher specificity for Fua-Gly-PheNH2 was deduced for both Kcat and Km parameters. Fua-Phe-PheNH2 showed the highest Kcat/Km(app) value of the six substrates studied. The discrimination between Phe/Leu at the P1' site was most evident when the P1 site was not sufficiently filled. Reflecting the characteristically high proteolytic activity of vimelysin at lower temperatures [Oda, K., Okayama, K., Okutomi, K., Shimada, M., Sato, R. & Takahashi, S. (1996) Biosci. Biotech. Biochem. 60, 463-467], the Arrhenius plot of the apparent second-order rate constant for the hydrolysis of Fua-Gly-LeuNH2 showed an inverse temperature dependence; higher reaction rates were observed at lower temperatures. This was not merely due to the pKa shift nor to thermal denaturation of the enzyme coupling, but rather to the Kcat(app) parameter, which alone showed an inverse temperature dependence. A model containing two temperature-dependent forms of the active enzyme was postulated to explain this unique temperature dependence.

XAFS studies of carboxypeptidase A: detection of a structural alteration in the zinc coordination sphere coupled to the catalytically important alkaline pKa

X-ray absorption fine structure (XAFS) spectra of carboxypeptidase A (ZnCPD) show progressive spectral changes particularly in the near edge region when the pH is changed from neutral to alkaline values. Both least square fitting and radial distribution function (RDF) data analysis yield two distributions of atoms in the first coordination shell of ZnCPD at all pH values and at both 150 and 297 K. Direct comparison of the first and higher coordination shells of ZnCPD reveals structural differences between pH 7.0 and pH 9.9. At pH 7.0, the zinc ion has four ligand atoms (N or O) at an average distance of 2.024 +/- 0.006 A, and a smaller distribution of 1.3 atoms (N or O) at 2.54 +/- 0.05 A from the zinc ion (from the least square fitting analysis). At pH 9.9, the larger distribution contains four atoms at a 0.022 A shorter distance (2.002 A) from the zinc, while the smaller distribution contains 0.7 atoms at 2.52 +/- 0.06 A. The smaller distribution can be attributed mainly to the contribution of the epsilon 2-oxygen of Glu 72 and to the atoms farther away for which the contribution cannot be fully separated from the first shell peak. The structural changes of ZnCPD at intermediate pHs are consistent with the changes observed at pH 7.0 and pH 9.9. The XAFS Debye-Waller factor shows an increased structural disorder for the four atom distribution at the alkaline pH.(ABSTRACT TRUNCATED AT 250 WORDS)

The effect of pH, temperature, and D2O on the activity of porcine synovial collagenase and gelatinase

The pH dependence of Vmax and Vmax/Km for hydrolysis of Dnp-Pro-Leu-Gly-Leu-Trp-Ala-D-Arg-NH2 at the Gly-Leu bond by porcine synovial collagenase and gelatinase was determined in the pH range 5-10. Both enzymes exhibited bell-shaped dependencies on pH for these two kinetic parameters, indicating that activity is dependent on at least two ionizable groups, one of which must be unprotonated and the other protonated. For collagenase, Vmax/Km data indicate that in the substrate-free enzyme, these groups have apparent pK values of 7.0 and 9.5, while the Vmax profile indicates similar pK values of 6.8 and 10.1 for the enzyme-substrate complex. The corresponding pH profiles of gelatinase were similar to those of collagenase, indicating the importance of groups with apparent pK values of 5.9 and 10.0 for the free enzyme and 5.9 and 11.1 for the enzyme-substrate complex. When these kinetic constants were determined in D2O using the peptide substrate, there was no significant effect on Vmax or Km for collagenase or Km for gelatinase. However, there was a deuterium isotope effect of approximately 1.5 on Vmax for gelatinase. These results indicate that a proton transfer step is not involved in the rate-limiting step for collagenase, but may be limiting with gelatinase. The Arrhenius activation energies for peptide bond hydrolysis of the synthetic peptide as well as the natural substrates were also determined for both enzymes. The activation energy (81 kcal) for hydrolysis of collagen by collagenase was nine times greater than that determined for the synthetic substrate (9.2 kcal). In contrast, the activation energy for hydrolysis of gelatin by gelatinase (26.3 kcal) was only 2.4 times greater than that for the synthetic substrate (11 kcal).