Kinetic α-deuterium isotope effects for enzymatic and acid hydrolysis of aryl-β-d-glycopyranosides

The kinetic α-deuterium isotope effect for the enzymatic- and acid-catalyzed hydrolysis of a series of aryl-β-d-[1-²H]glycopyranosides has been measured. The magnitude of the effect indicates a considerable steric hindrance of the anomeric CH (CD) bond in an early transition state for both kinds of reactions. Better leaving aryl groups decrease the isotope effect for the acid-catalyzed hydrolysis, as predicted by the predominant A-1 character of the reaction. In contrast, the α-deuterium effect for the enzymatic-catalyzed reactions is increased by better leaving aglycon groups, suggesting a mechanism with considerable S_N2 characteristics. The isotope effect for the acid hydrolysis of 4-methylumbelliferyl- and 4-methylfenyl-β-d-glucopyranoside has been measured over the temperature range 40–85°C. The results indicate a different temperature dependence of the effect for both β-d-glucopyranosides.     

The chirality selectivity in the uptake of platinum (II) complexes with 1,2-cyclohexanediamine isomers as carrier ligand by human erythrocytes

The uptake kinetics of cisplatin analogs of 1,2-cyclohexanediamine(dach) isomers with various leaving groups, by human erythrocytes in plasma isotonic buffer, were studied. The experimental results showed that the uptake rate constants (k values) decrease with the change of leaving group in the sequence: chloride (Cl) > squaric acid (SA) > oxalate (OX) > demethylcantharic acid (DA), with the same dach isomer as carrier group. It is noteworthy that for the platinum (II) complexes with the same leaving group, the k values always reduce as: 1R, 2R-dach > 1R, 2S-dach > 1S, 2S-dach. This result reflects the chirality selectivity. No differences in reactivity to protein thiols and effects on membrane permeability were found for the R,R-, R,S-, S,S-isomeric complexes. It is proposed that the chirality selectivity in uptake is due to the recognition of the chirality of the platinum complexes by the erythrocyte membrane. The interactions between the chiral platinum complexes and the head groups of the membrane phospholipid molecules are probably involved.     

Model for the exceptional reactivity of peroxiredoxins 2 and 3 with hydrogen peroxide: a kinetic and computational study

Peroxiredoxins (Prx) are thiol peroxidases that exhibit exceptionally high reactivity toward peroxides, but the chemical basis for this is not well understood. We present strong experimental evidence that two highly conserved arginine residues play a vital role in this activity of human Prx2 and Prx3. Point mutation of either ArgI or ArgII (in Prx3 Arg-123 and Arg-146, which are ∼3–4 Å or ∼6–7 Å away from the active site peroxidative cysteine (C_p), respectively) in each case resulted in a 5 orders of magnitude loss in reactivity. A further 2 orders of magnitude decrease in the second-order rate constant was observed for the double arginine mutants of both isoforms, suggesting a cooperative function for these residues. Detailed ab initio theoretical calculations carried out with the high level G4 procedure suggest strong catalytic effects of H-bond-donating functional groups to the C_p sulfur and the reactive and leaving oxygens of the peroxide in a cooperative manner. Using a guanidinium cation in the calculations to mimic the functional group of arginine, we were able to locate two transition structures that indicate rate enhancements consistent with our experimentally observed rate constants. Our results provide strong evidence for a vital role of ArgI in activating the peroxide that also involves H-bonding to ArgII. This mechanism could explain the exceptional reactivity of peroxiredoxins toward H₂O₂ and may have wider implications for protein thiol reactivity toward peroxides.     

Kinetic method for differentiating mechanisms for ligand exchange reactions: application to test for substrate channeling in glycolysis.

We have derived analytical expressions for the kinetics of the two mechanisms involved in ligand substitution reactions. These mechanisms are (i) a dissociative mechanism in which the leaving ligand is first dissociated prior to the binding of the incoming ligand and (ii) an associative mechanism where a ternary complex is formed between the incoming ligand and the complex containing the leaving ligand. The equations obtained provide the theoretical basis for differentiating these two mechanisms on the basis of their kinetic patterns of the displacement reactions. Analysis of these equations shows that an associative mechanism can only generate an increasing kinetic pattern for the observed pseudo-first-ordered rate constants as a function of increasing concentration of the incoming ligand and plateaus, in most cases, at a value higher than the off-rate constant of the leaving ligand. However, a dissociative mechanism can generate either an increasing or a decreasing (kapp decreases with increasing concentrations of the incoming ligand) kinetic pattern, depending on the magnitudes of the individual rate constants involved, and, in either case, it will plateau at kapp equal to the koff of the leaving ligand. Therefore, the decreasing kinetic pattern is a hallmark for a dissociative mechanism. This general method was used to settle the dispute of whether NADH is transferred directly via the enzyme-enzyme complex between glycerol-3-phosphate dehydrogenase (GPDH; EC 1.1.1.8) and L-lactate dehydrogenase (LDH; EC 1.1.1.27).(ABSTRACT TRUNCATED AT 250 WORDS)     

The theory and application of transition state pK(a) values: the reaction of papain with a series of trimethylene disulphide reactivity probes

For many years methods to describe the structure of the transition state for a reaction have been sought. Most commonly these structures have been inferred from kinetic isotope effects. We report here for the first time the application of transition state pK(a) values to describe the relationship between molecular recognition and the transition state for the catalytic mechanism of papain. The background to the theory is presented and applied to the reactions of papain with a series of trimethylene disulphide reactivity probes. The common feature of these reactions is a loss in reactivity on ionization of the imidazolium cation for those probes containing molecular recognition features and an increase in reactivity on ionization of the electrostatic switch residue. The use of transition state pK(a) values enhances this information by providing details regarding the protonic distribution within the transition state. This has led to the reconsideration of the effect of the electrostatic switch ionization and the role of the hydrogen bond formed between the catalytic-site imidazolium cation and the leaving group of the reaction in the catalytic mechanism of papain.     

Assessing site-isolation of amine groups on aminopropyl-functionalized SBA-15 silica materials via spectroscopic and reactivity probes

The average degree of separation and the accessibility of aminopropyl groups on SBA-15 silica materials prepared using different silane grafting approaches are compared. Three specific synthetic approaches are used: (1) the traditional grafting of 3-aminopropyltrimethoxysilane in toluene, (2) a protection/deprotection method using benzyl- or trityl-spacer groups, and (3) a cooperative dilution method where 3-aminopropyltrimethoxysilane and methyltrimethoxysilane are co-condensed on the silica surface as a silane mixture. The site-isolation and accessibility of the amine groups are probed via three methods: (a) evaluation of pyrene groups adsorbed onto the solids using fluorescence spectroscopy, (b) the reactions of chlorodimethyl(2,3,4,5-tetramethyl-2,4-cyclopentadien-1-yl)silane (Cp′Si(Me)₂Cl) and chloro(cyclopenta-2,4-dienyl)dimethylsilane (CpSi(Me)₂Cl) with the tethered amine sites, and (c) comparison of the reactivity of zirconium constrained-geometry-inspired catalysts (CGCs) prepared using the Cp′Si(Me)₂-modified aminosilicas in the catalytic polymerization of ethylene to produce poly(ethylene). The spectroscopic probe of site-isolation suggests that both the protection/deprotection method and the cooperative dilution method yield similarly isolated amine sites that are markedly more isolated than sites on traditional aminosilica. In contrast, both reactivity probes show that the protection/deprotection strategy leads to more uniformly accessible amine groups. It is proposed that the reactivity probes are more sensitive tests for accessibility and site-isolation in this case.     

Modulation of transplanaramine platinum complex reactivity by systematic modification of carrier and leaving groups

Transplatinum planaramine complexes with carboxylate ligands as leaving groups, trans-[Pt(O₂CR)₂(L)(L′)] (L = L′ = pyridine; L = NH₃, L′ = pyridine, isoquinoline, thiazole, quinoline, etc.), are potential anticancer complexes with cytotoxicity in some cases equivalent to that of cisplatin. The carboxylate complexes are, as a family, very water-soluble and surprisingly stable towards hydrolysis - resembling carboplatin in their reactivity. Their pharmacological properties can be systematically modified by steric and electronic effects of the donor groups as well as in the leaving carboxylate ligands. Previously, we have recognized the leaving group formate as having appropriate kinetics for bioligand substitution [1]. In this paper we directly compared the effect on biological properties of a pyridine versus isoquinoline-based carrier group. Binding to calf thymus DNA was similar for both compounds but the distortions produced on DNA, as assessed by T_m (melting temperature) and an ethidium bromide fluorescence reporter assay, were more marked for the isoquinoline ligand. Model studies with 5′-GMP (5′-guanosinemonophosphate) confirmed these trends, with the product trans-[Pt(5′-GMP)₂(NH₃)(isoquinoline)] showing evidence of restricted rotation caused by steric hinderance of three rigid planar rings on the central platinum. A cross-linking assay on pUC19 plasmid confirmed a higher % of interstrand adducts for the isoquinoline compound. This “enhanced” reactivity was matched by higher cytotoxicity in HCT116 human colon tumor cells, and also with enhanced cellular accumulation. Thus, a combination of systematic biophysical and biological studies indicates that trans-[Pt(O₂CH)₂(NH₃)(isoquinoline)] has the most promising range of chemical and biological properties for further development and examination.     

The impact of oxacarbenium ion conformers on the stereochemical outcome of glycosylations

The search for stereoselective glycosylation reactions has occupied synthetic carbohydrate chemists for decades. Traditionally, most attention has been focused on controlling the S_N2-like substitution of anomeric leaving groups as highlighted by Lemieux’s in situ anomerization protocol and by the discovery of anomeric triflates as reactive intermediates in the stereoselective formation of β-mannosides. Recently, it has become clear that also S_N1-like reaction pathways can lead to highly selective glycosylation reactions. This review describes some recent examples of stereoselective glycosylations in which oxacarbenium ions are believed to be at the basis of the selectivity. Special attention is paid to the stereodirecting effect of substituents on a pyranosyl ring with an emphasis on the role of the C-5 carboxylate ester in the condensations of mannuronate ester donors.     

Models of Water-Assisted Hydrolyses of Methyl Formate, Formamide, and Urea from Combined DFT-SCRF Calculations

In this work we present theoretical studies of the hydrolytic reaction of methyl formate, formamide and urea with one water molecule. The studied systems contain two additional water molecules which can act as bifunctional acid-base catalysts. These water molecules catalyze proton transfers between the primary reacting species. Our models describe the concerted transfer of two protons in every reaction step. The calculations have been carried out with the Becke3LYP/6-31G* method. Unspecific solvation effects have been included by means of a polarizable continuum model. Substrate reactivity differences as well as preferences for different reaction pathways can be discussed with the aid of these molecular systems. The studied alternative mechanisms include the common addition-elimination mechanism via a tetrahedral intermediate, and a concerted S_N-like mechanism without a reaction intermediate. Our results suggest that the proved decreasing substrate reactivity in the order ester, amide, urea is caused by a rising resonance stabilization of the reaction centre, and not by a different positive partial charge of the carbonyl carbon. It is also concluded, that the probability of a concerted addition of a nucleophile and elimination of a leaving group without a tetrahedral intermediate rises in the order ester, amide, urea. The ordering of reactivity is not influenced by this behaviour.     

Immunochemical studies of type IV and two group-like (Z) carbohydrate antigens of minute streptococci

Analysis of purified fractions of formamide extracts of Z₄IV and 8650 (Z₅) bacteria gave as composition rhamnose, glucose, galactose and N-acetyl-glucosamine in molar ratio’s for Z₄ antigen 9:0:2:5, for type IV antigen 4:4:4:1 and for Z₅ antigen 8:2:2:3. In contradistinction with other polysaccharide type antigens of minute streptococci all type IV reactivity was recovered from the buffer eluate of a DEAE cellulose column. The Z₅ antigen was present in both the water and the buffer eluate. Precipitin and inhibition reactions indicate that the serological reactions between both strains are cross reactions based on the presence of galactose in the determinant groups of type IV, group Z₄ and group Z₅ antigens. Inhibition reactions also suggest a role of β-galactosyl-glucose as immunodominant group of the Z₅ determinant. Partial acid hydrolysis of type IV antigen yielded four oligosaccharides. Analyses and inhibition reactions show that probably both trisaccharides β-galactosyl-glucosyl-galactose and β-galactosyl-glucosyl-rhamnose are determinant groups of the type IV antigen.     

Detailed kinetic analysis of a family 52 glycoside hydrolase: a beta-xylosidase from Geobacillus stearothermophilus

Geobacillus stearothermophilus T-6 encodes for a beta-xylosidase (XynB2) from family 52 of glycoside hydrolases that was previously shown to hydrolyze its substrate with net retention of the anomeric configuration. XynB2 significantly prefers substrates with xylose as the glycone moiety and exhibits a typical bell-shaped pH dependence curve. Binding properties of xylobiose and xylotriose to the active site were measured using isothermal titration calorimetry (ITC). Binding reactions were enthalpy driven with xylobiose binding more tightly than xylotriose to the active site. The kinetic constants of XynB2 were measured for the hydrolysis of a variety of aryl beta-D-xylopyranoside substrates bearing different leaving groups. The Br?nsted plot of log k(cat) versus the pK(a) value of the aglycon leaving group reveals a biphasic relationship, consistent with a double-displacement mechanism as expected for retaining glycoside hydrolases. Hydrolysis rates for substrates with poor leaving groups (pK(a) > 8) vary widely with the aglycon reactivity, indicating that, for these substrates, the bond cleavage is rate limiting. However, no such dependence is observed for more reactive substrates (pK(a) < 8), indicating that in this case hydrolysis of the xylosyl-enzyme intermediate is rate limiting. Secondary kinetic isotope effects suggest that the intermediate breakdown proceeds with modest oxocarbenium ion character at the transition state, and bond cleavage proceeds with even lower oxocarbenium ion character. Inhibition studies with several gluco analogue inhibitors could be measured since XynB2 has low, yet sufficient, activity toward 4-nitrophenyl beta-D-glucopyranose. As expected, inhibitors mimicking the proposed transition state structure, such as 1-deoxynojirimycin, bind with much higher affinity to XynB2 than ground state inhibitors.     

Kinetics and mechanism of the oxidative addition of iodomethane to β-diketonatobis(triphenylphosphite)rhodium(I) complexes

The kinetics and mechanism of the oxidative addition of CH₃I to [Rh(β-diketone)(P(OPh)₃)₂] complexes was studied in acetone medium at various temperatures. The experimental rate law is R = k[Rh(β-diketone)(P(OPh₃)₂][CH₃I]. The order of the effect of the β-diketone on the reactivity of the complexes is acac >; BA >; DBM >; TFAA >; TFBA >; HFAA indicating that electronegative substituents of the β-diketone decrease the reactivity of the complexes towards oxidative addition reactions. The volume of activation for some of the reactions was determined in various solvents. The large negative values of the volume and entropy of the activation indicated a mechanism which occurs via a polar transition state.     

The inhibition of morphine: UDP-glucuronyltransferase in rabbit liver microsomes by cyproheptadine.

The reactivity of the non-narcotic substances, cyproheptadine and N-desmethylcyproheptadine with morphine: UDP-glucuronyltransferase was studied in rabbit hepatic microsomal preparations. Cyproheptadine produced a potent competitive inhibition of morphine glucuronidation $\text{in vitro}$ (K_i=0.08 mM) whereas its N-desmethyl derivative was significantly less effective (K_i=0.4 mM). No cyproheptadine glucuronide was formed in these reactions suggesting that cyproheptadine acts as a dead-end inhibitor. Results indicate that the mechanism of the inhibition of morphine: UDP-glucuronyltransferase by cyproheptadine is similar to that produced by opioids and is related to the presence of the N-alkyl group in it structure.     

Reactivity of platinum-based antitumor drugs towards a Met- and His-rich 20mer peptide corresponding to the N-terminal domain of human copper transporter 1

Cellular uptake of platinum-based antitumor drugs is a critical step in the mechanism of the drug action and associated resistance, and deeper understanding of this step may inspire development of novel methods for new drugs with reduced resistance. Human copper transporter 1 (hCtr1), a copper influx protein, was recently found to facilitate the cellular entry of several platinum drugs. In the work reported here, we constructed a Met- and His-rich 20mer peptide (hCtr1-N20) corresponding to the N-terminal domain of hCtr1, which is the essential domain of hCtr1 for transporting platinum drugs. The interactions of the peptide with cisplatin and its analogues, including transplatin, carboplatin, oxaliplatin, and [Pt(l-Met)Cl₂], were explored at the molecular level. Electrospray ionization (ESI) mass spectrometry (MS) data revealed that all of the platinum(II) complexes used in present study can bind to hCtr1-N20 in 1:1 and 2:1 stoichiometry. Four Met residues should be involved in binding to cis-platinum complexes on the basis of the tandem MS spectrometry and previously reported data. Time-dependent 2D [¹H,¹⁵N] heteronuclear single quantum coherence NMR spectra indicate the reaction of cisplatin with hCtr1-N20 is a stepwise process. The intermediate, however, is transient, which is consistent with the ESI-MS results. Time-dependent ESI-MS data revealed that the geometry and the properties of both the leaving and the nonleaving groups of platinum(II) complexes play essential roles in controlling the reactivity and formation of the final products with hCtr1-N20.     

Beta-glucosidase: substrate, solvent, and viscosity variation as probes of the rate-limiting steps

The second-order rate constants (kcat/Km) for the beta-glucosidase-catalyzed hydrolysis of aryl beta-D-glucopyranosides show a bell-shaped dependence of pH. The pKas that characterize this dependence are 4.4 (delta Hion approximately equal to 0) and 6.7 (delta Hion approximately equal to 0). In D2O these pKas are increased by 0.5 (+/- 0.1) unit, but there is no solvent isotope effect on the pH-independent second-order rate constant. Nath and Rydon [Nath, R. L., & Rydon, H. N. (1954) Biochem. J. 57, 1-10] examined the kinetics of the beta-glucosidase-catalyzed hydrolysis of a series of substituted phenyl glucosides. We have extended this study to include glucosides with phenol leaving groups of pKa less than 7. Br?nsted plots for this extended series were nonlinear for both kcat/Km and kcat. Br?nsted coefficients for those compounds with leaving groups of pKa greater than 7 (for kcat/Km) or pKa greater than 8.5 (for kcat) were nearly equal to -1.0, indicating substantial negative charge buildup on the leaving group in the transition state. The nonlinearity indicates an intermediate in the reaction. This was confirmed by partitioning experiments in the presence of methanol as a competing glucose acceptor. A constant product ratio, [methyl glucoside]/[glucose], was found with aryl glucoside substrates varying over 16,000-fold in reactivity (V/K), indicative of a common intermediate. Viscosity variation (in sucrose-containing buffers) was used to probe the extent to which the beta-glucosidase reactions are diffusion-controlled.(ABSTRACT TRUNCATED AT 250 WORDS)     

Reactivity difference between protolytic forms of some macrocyclic chromium(III) complexes in ligand substitution and electron transfer processes

The review provides insight into the mechanism of ligand substitution and electron transfer (from chromium(III) to iron(III)) by comparison of the reactivity of some tetraazamacrocyclic chromium(III) complexes in the conjugate acid-base forms. Use of two geometrical isomers made possible to estimate the influence of geometry and protolytic reactions in trans and cis position towards the leaving group on the rate enhancement. Studies on the reaction rates in different media demonstrated the role played by outer sphere interactions in a monodentate ligand substitution.     

Theoretical investigation of reactivities of amines in the <Emphasis Type="Italic">N</Emphasis>-nitrosation reactions by N<Subscript>2</Subscript>O<Subscript>3</Subscript>

N-nitrosamine is a class of carcinogenic, mutagenic, and teratogenic compounds, which can be produced from N-nitrosation of amine by nitrosating agents. N-nitrosation of 19 amines (eight acyclic amines, five heterocyclic amines, and six amines with unsaturated groups) by N₂O₃ was investigated at the CBS-QB3 level of theory. The results indicate that generally the heterocyclic amines have the highest reactivities among the three kinds of amines, whereas the reactivities of the amines with unsaturated and electron-withdrawing groups are relatively low. Frontier molecular orbital analysis indicates that the energy gap between the HOMO of an amine and the LUMO of N₂O₃ has a close connection with the reactivity of an amine. A structure-reactivity relationship of amines in the N-nitrosation reactions by N₂O₃ was established using the stepwise multivariate linear regression. The results indicate that the reactivity of an amine has a definite relationship (R_adj² = 0.947) with the heterolytic bond dissociation energy of R₁R₂N-H bond, energy of HOMO, NBO occupancy of the natural lone pair orbital of N atom, the NBO charge of the N atom, and the pyramidalization angle of an amine. This work will be helpful to gain more insight into the N-nitrosation reactions.     

Synthesis of novel types of copper-bipyridyl porphyrins and characterization of their interactions and reactivity with DNA

The inherent ability to interact with DNA makes cationic metallo-porphyrins attractive targets as antitumor drugs. Many studies describe their interaction with DNA and the mechanism by which they induce DNA cleavage. Since porphyrins can be used as anchors for chemically reactive groups, it is possible to modify them to generate a family of compounds with specific functions. In the present work, we used chemical groups such as copper-bipyridinium (Cu-bpy), which hydrolyze phosphodiester bonds, and a porphyrin core to synthesize two novel Cu₂-bpy-porphyrins. Their interactions with DNA have been characterized using classic spectroscopic methods, and their oxidative and hydrolytic reactivity toward supercoiled plasmid DNA has been studied in vitro. Our results show that Cu₂-bpy-porphyrins interact with DNA via external association and intercalation and that their ability to cleave DNA and the mechanisms depends on the experimental conditions.     

Citrobacter freundii tyrosine phenol-lyase: the role of asparagine 185 in modulating enzyme function through stabilization of a quinonoid intermediate

Asn185 is an invariant residue in all known sequences of TPL and of closely related tryptophanase and it may be aligned with the Asn194 in aspartate aminotransferase. According to X-ray data, in the holoenzyme and in the Michaelis complex Asn185 does not interact with the cofactor pyridoxal 5'-phosphate, but in the external aldimine a conformational change occurs which is accompanied by formation of a hydrogen bond between Asn185 and the oxygen atom in position 3 of the cofactor. The substitution of Asn185 in TPL by alanine results in a mutant N185A TPL of moderate residual activity (2%) with respect to adequate substrates, L-tyrosine and 3-fluoro-L-tyrosine. The affinities of the mutant enzyme for various amino acid substrates and inhibitors, studied by both steady-state and rapid kinetic techniques, were lower than for the wild-type TPL. This effect mainly results from destabilization of the quinonoid intermediate, and it is therefore concluded that the hydrogen bond between Asn185 and the oxygen at the C-3 position of the cofactor is maintained in the quinonoid intermediate. The relative destabilization of the quinonoid intermediate and external aldimine leads to the formation of large amounts of gem-diamine in reactions of N185A TPL with 3-fluoro-L-tyrosine and L-phenylalanine. For the reaction with 3-fluoro-L-tyrosine it was first possible to determine kinetic parameters of gem-diamine formation by the stopped-flow method. For the reactions of N185A TPL with substrates bearing good leaving groups the observed values of k(cat) could be accounted for by taking into consideration two effects: the decrease in the quinonoid content under steady-state conditions and the increase in the quinonoid reactivity in a beta-elimination reaction. Both effects are due to destabilization of the quinonoid and they counterbalance each other. Multiple kinetic isotope effect studies on the reactions of N185A TPL with suitable substrates, L-tyrosine and 3-fluoro-L-tyrosine, show that the principal mechanism of catalysis, suggested previously for the wild-type enzyme, does not change. In the framework of this mechanism the observed considerable decrease in k(cat) values for reactions of N185A TPL with L-tyrosine and 3-fluoro-L-tyrosine may be ascribed to participation of Asn185 in additional stabilization of the keto quinonoid intermediate.