Solvent Isotope Effects in H2O−D2O Mixtures (Proton Inventories) on Serine-Protease-Catalyzed Hydrolysis Reactions. Influence of Oxyanion Hole Interactions and Medium Effects

Proton Bridging in Catalysis by and Inhibition of Serine Proteases of the Blood Cascade System

Inquiries into the participation of short hydrogen bonds in stabilizing transition states and intermediate states in the thrombin, factor Xa, plasmin and activated protein C-catalyzed reactions revealed that specific binding of effectors at Sn, n = 1-4 and S'n, n = 1-3 and at remote exosites elicit complex patterns of hydrogen bonding and involve water networks. The methods employed that yielded these discoveries include; (1) kinetics, especially partial or full kinetic deuterium solvent isotope effects with short cognate substrates and also with the natural substrates, (2) kinetic and structural probes, particularly low-field high-resolution nuclear magnetic resonance (1H NMR), of mechanism-based inhibitors and substrate-mimic peptide inhibitors. Short hydrogen bonds form at the transition states of the catalytic reactions at the active site of the enzymes as they do with mechanism-based covalent inhibitors of thrombin. The emergence of short hydrogen bonds at the binding interface of effectors and thrombin at remote exosites has recently gained recognition. Herein, I describe our contribution, a confirmation of this discovery, by low-field 1H NMR. The principal conclusion of this review is that proton sharing at distances below the sum of van der Waals radii of the hydrogen and both donor and acceptor atoms contribute to the remarkable catalytic prowess of serine proteases of the blood clotting system and other enzymes that employ acid-base catalysis. Proton bridges also play a role in tight binding in proteins and at exosites, i.e., allosteric sites, of enzymes.

Online monitoring of the kinetic isotope effect in chemical reactions with 1H and 19F low-field NMR spectroscopy

The kinetic isotope effect (KIE) describes the change in the rate of a chemical reaction by substituting one of the atoms in the reactants with one of its isotopes. Investigating the KIE and its temperature dependency in reactions renders information for reconstructing chemical processes and confirming the rate-determining step. However, conventional methods to study the KIE, e.g. by calorimetry, conductivity, titration, Raman spectroscopy etc., require calibration and sophisticated handling of the reaction calorimeter, and the data are obtained at irregular and sparse intervals. This current study employs a compact NMR system as an alternative means to determine the temperature dependency of the reaction rate and, thus, the KIE, as well as the activation energy, enthalpy, and entropy of each reaction. Here the neutral hydrolysis of acetic anhydride and ethyl trifluoroacetate was studied in H₂O, D₂O and H₂O-D₂O mixtures with ¹H and ¹⁹F NMR spectroscopy. The activation energies for the hydrolysis of acetic anhydride with D₂O and H₂O were found to be 45 ± 2 kJ mol^-1 and 40 ± 2 kJ mol^-1, respectively. The activation energies of ethyl trifluoroacetate hydrolysis via¹⁹F NMR spectroscopy were determined to 46.7 ± 1 kJ mol^-1 and 54.9 ± 1 kJ mol^-1 for the reaction with H₂O and D₂O, respectively, and via¹H NMR spectroscopy to 48 ± 3 kJ mol^-1 and 55.8 ± 1 kJ mol^-1. The differences in rate constants and activation energies for both reactions in H₂O and D₂O are due to the kinetic isotope effect, involving the breakage and formation of O-H and O-D bonds during the rate-determining step. The proton inventory studies were performed for both the reactions for determining the isotopic fractionation factors for the given transition states of the reactions which help to predict the reaction mechanisms of other similar reactions. The compact NMR system is a relevant and practical tool to unmask precise reaction pathways, by tracing the KIE in real time with densely sampled data, which are essential for obtaining accurate rate constants.

Primary Deuterium Kinetic Isotope Effects From Product Yields: Rationale, Implementation, and Interpretation

A simple and convenient method is described to determine primary deuterium kinetic isotope effects (1°DKIEs) on reactions where the hydron incorporated into the reaction product is derived from solvent water. The 1°DKIE may be obtained by ¹H NMR analyses as the ratio of the yields of H- and D-labeled products from a reaction in 50:50 (v/v) HOH/DOD. The procedures for these ¹H NMR analyses are reviewed. This product deuterium isotope effect (PDIE) is defined as 1/ϕ_EL for fractionation of hydrons between solvent and the transition state for the reaction examined. When the solvent is not the direct hydron donor, it is necessary to correct the PDIE for the fractionation factor ϕ_EL for partitioning of the hydron between the solvent and the direct donor EL. This method was used to determine the 1°DKIE on decarboxylation reactions catalyzed by wild-type orotidine 5'-monophosphate decarboxylase (OMPDC) and by mutants of OMPDC, and then in the determination of the 1°DKIE on the decarboxylation reaction catalyzed by 5-carboxyvanillate decarboxylase. The experimental procedures used in studies on OMPDC and the rationale for these procedures are described.

Proton delivery to ferryl heme in a heme peroxidase: enzymatic use of the Grotthuss mechanism

We test the hypothesized pathway by which protons are passed from the substrate, ascorbate, to the ferryl oxygen in the heme enzyme ascorbate peroxidase (APX). The role of amino acid side chains and bound solvent is demonstrated. We investigated solvent kinetic isotope effects (SKIE) for the wild-type enzyme and several site-directed replacements of the key residues which form the proposed proton path. Kinetic constants for H(2)O(2)-dependent enzyme oxidation to Compound I, k(1), and subsequent reduction of Compound II, k(3), were determined in steady-state assays by variation of both H(2)O(2) and ascorbate concentrations. A high value of the SKIE for wild type APX ((D)k(3) = 4.9) as well as a clear nonlinear dependence on the deuterium composition of the solvent in proton inventory experiments suggest the simultaneous participation of several protons in the transition state for proton transfer. The full SKIE and the proton inventory data were modeled by applying Gross-Butler-Swain-Kresge theory to a proton path inferred from the known structure of APX. The model has been tested by constructing and determining the X-ray structures of the R38K and R38A variants and accounts for their observed SKIEs. This work confirms APX uses two arginine residues in the proton path. Thus, Arg38 and Arg172 have dual roles, both in the formation of the ferryl species and binding of ascorbate respectively and to facilitate proton transfer between the two.

Hydration of acetone in the gas phase and in water solvent

In water solvent, the hydration of acetone proceeds by a cyclic (cooperative) process in which concurrent C–O bond formation and proton transfer to oxygen take place through a solvent and (or) catalyst bridge. Reactivity is determined primarily by the concentration of a reactant complex and not the barrier from this complex. This situation is reversed in the gas phase; although the concentrations of reactive complexes are much higher than in solution, the barriers are also higher and dominant in determining reactivity. Calculations of isotope effects suggest that multiple hydron transfers are synchronous in the gas phase to avoid zwitterionic transition states. In solution, such transition states are stabilized by solvation and hydron transfers can be asynchronous.

SER-HIS-ASP catalytic triad in model non-aqueous solvent environment: A computational study

Emerging new properties and applications of enzymes in organic solvents and ionic liquids are unabating. By applying a combined Quantum Mechanics/Continuum Mechanics computation on a prototypical catalytic triad serine-histidine-aspartate (SER-HIS-ASP) interacting with ethanol or acetonitrile molecules, the major difference between protic and aprotic solvents in effecting transition-state stabilization has been analyzed. Moderately polar aprotic solvent acetonitrile is predicted to be unable to stabilize the transition state in replacing the role of the oxyanion-hole environment, whereas protic ethanol solvent molecules of similar polarity to acetonitrile are adequate in re-gaining the enzymatic activities.

The RNA-Cleaving Bipartite DNAzyme Is a Distinctive Metalloenzyme

Much interest has focused on the mechanisms of the five naturally occurring self-cleaving ribozymes, which, in spite of catalyzing the same reaction, adopt divergent strategies. These ribozymes, with the exception of the recently described glmS ribozyme, do not absolutely require divalent metal ions for their catalytic chemistries in vitro. A mechanistic investigation of an in vitro-selected, RNA-cleaving DNA enzyme, the bipartite, which catalyzes the same chemistry as the five natural self-cleaving ribozymes, found a mechanism of significant complexity. The DNAzyme showed a bell-shaped pH profile. A dissection of metal usage indicated the involvement of two catalytically relevant magnesium ions for optimal activity. The DNAzyme was able to utilize manganese(II) as well as magnesium; however, with manganese it appeared to function complexed to either one or two of those cations. Titration with hexaamminecobalt(III) chloride inhibited the activity of the bipartite; this suggests that it is a metalloenzyme that utilizes metal hydroxide as a general base for activation of its nucleophile. Overall, the bipartite DNAzyme appeared to be kinetically distinct not only from the self-cleaving ribozymes but also from other in vitro-selected, RNA-cleaving deoxyribozymes, such as the 8-17, 10-23, and 614.

Spray-dried amorphous solid dispersions of simvastatin, a low tg drug: in vitro and in vivo evaluations

PURPOSE

To obtain free flowing, stable, amorphous solid dispersions (SDs) of simvastatin (SIM), a drug with relatively lower glass transition temperature (T(g)) by spray drying technique, and to perform comparative in vivo study in rats, which could justify the improvement in rate and extent of in vitro drug release.

METHODS

Dichloromethane suspensions of SIM either alone or in combination with PVP (1:1 or 1:2 parts by weight) were spray dried with proposed quantity of Aerosil 200 (1:1, 1:1:1, 1:2:2 parts by weight of SIM, Aerosil 200 and PVP, respectively). SDs were characterized initially in comparison with pure drug and corresponding physical mixtures in same ratios by drug content, saturation solubility, SEM, DSC, XRPD, IR, and in vitro drug release. SD 1:2:2 was further subjected to accelerated stability testing and checked for in vitro drug release and presence of crystallinity using DSC and XRPD. In addition, improvement in rate and extent of in vitro drug release from SD 1:2:2 was justified by in vivo study in rats.

RESULTS

Combination of SD and surface adsorption techniques has been attempted to overcome the limitations of spray drying technique for amorphization of low T(g) drugs. Based on powder characteristics, drug content, saturation solubility, and feasibility of processing into tablets; SD 1:2:2 was selected as the optimized formulation. During initial characterization, SEM, DSC, and XRPD analyses confirmed the presence of amorphous form in SD 1:2:2. IR spectroscopy revealed possibility of hydrogen bonding interaction between SIM and PVP in SDs. Also, there was dramatical improvement in rate and extent of in vitro drug release of SD 1:2:2. Insignificant decrease in dissolution was observed with no evidence of crystallinity during accelerated stability studies of SD 1:2:2. Moreover in vivo study in rats also justified the improvement in therapeutic efficacy of SD 1:2:2 over pure SIM.

CONCLUSIONS

Thus, present study demonstrates high potential of spray drying technique for obtaining stable amorphous SDs of low T(g) drugs.

Virtual screening of human 5-aminoimidazole-4-carboxamide ribonucleotide transformylase against the NCI diversity set by use of AutoDock to identify novel nonfolate inhibitors

AICAR transformylase (5-aminoimidazole-4-carboxamide ribonucleotide transformylase) is a folate-dependent activity of the bifunctional protein ATIC (AICAR transformylase and IMP cyclohydrolase) and is responsible for catalyzing the penultimate step of the de novo purine biosynthetic pathway. As such, AICAR transformylase has been proposed as a potential target for antineoplastic drug design. Virtual screening of the human AICAR transformylase active site by use of AutoDock against the NCI diversity set, a library of compounds with nonredundant pharmacophore profiles, has revealed 44 potential inhibitor candidates. In vitro inhibition assay of 16 soluble compounds from this list revealed that eight compounds with novel scaffolds, relative to the general folate template, had micromolar inhibition. Subsequent extension of docking trials on compounds with similar scaffolds from the entire NCI-3D database has unveiled 11 additional inhibitors that were confirmed by the in vitro inhibition assay. In particular, one compound, NSC30171, had nanomolar inhibition (K(i) = 154 nM, IC(50) = 600 nM) against AICAR transformylase. These 19 inhibitors serve as novel templates/scaffolds for development of more potent and specific non-folate-based AICAR transformylase inhibitors.

Solvent deuterium kinetic isotope effects for the methanolyses of neutral CO, PO and PS esters catalyzed by a triazacyclododecane : Zn2+-methoxide complex

The methanolyses of several organophosphate/phosphonate/phosphorothioate esters (O,O-diethyl O-(4-nitrophenyl) phosphate, paraoxon, ; O,O-diethyl S-(3,5-dichlorophenyl) phosphorothioate, ; O-ethyl O-(2-nitro-4-chlorophenyl) methylphosphonate, ; O,O-dimethyl O-(3-methyl-4-nitrophenyl) phosphorothioate, fenitrothion, ; O-ethyl S-(3,5-dichlorophenyl) methylphosphonothioate ) and a carboxylate ester (p-nitrophenyl acetate, ) catalyzed by methoxide and the Zn(2+)((-)OCH(3)) complex of 1,5,9-triazacyclododecane ( : Zn(2+)((-)OCH(3))) were studied in methanol and d(1)-methanol at 25 degrees C. In the case of the methoxide reactions inverse skie's were observed for the series with values ranging from 2 to 1.1, except for where the k(D)/k(H) = 0.90 +/- 0.02. The inverse k(D)/k(H) values are consistent with a direct nucleophilic methoxide attack involving desolvation of the nucleophile with varying extents of resolvation of the TS. With the : Zn(2+)((-)OCH(3)) complex all the skie values are k(D)/k(H) = 1.0 +/- 0.1 except for where the value is 0.79 +/- 0.06. Arguments are presented that the fractionation factors associated with complex : Zn(2+)((-)OCH(3)) are indistinguishable from unity. The skie's for all the complex-catalyzed methanolyses are interpreted as being consistent with an intramolecular nucleophilic attack of the Zn(2+)-coordinated methoxide within a pre-equilibrium metal : substrate complex.

Solvent and guest isotope effects on complexation thermodynamics of alpha-, beta-, and 6-amino-6-deoxy-beta-cyclodextrins

The stability constant (K), standard free energy (DeltaG degrees ), enthalpy (DeltaH degrees ), and entropy changes (TDeltaS degrees ) for the complexation of native alpha- and beta-cyclodextrins (CDs) and 6-amino-6-deoxy-beta-CD with more than 30 neutral, positively, and negatively charged guests, including seven fully or partially deuterated guests, have been determined in phosphate buffer solutions (pH/pD 6.9) of hydrogen oxide (H(2)O) or deuterium oxide (D(2)O) at 298.15 K by titration microcalorimetry. Upon complexation with these native and modified CDs, both nondeuterated and deuterated guests examined consistently exhibited higher affinities (by 5-20%) in D(2)O than in H(2)O. The quantitative affinity enhancement in D(2)O versus H(2)O directly correlates with the size and strength of the hydration shell around the charged/hydrophilic group of the guest. For that reason, negatively/positively charged guests, possessing a relatively large and strong hydration shell, afford smaller K(H2O)/K(D2O) ratios than those for neutral guests with a smaller and weaker hydration shell. Deuterated guests showed lower affinities (by 5-15%) than the relevant nondeuterated guests in both H(2)O and D(2)O, which is most likely ascribed to the lower ability of the C-D bond to produce induced dipoles and thus the reduced intracavity van der Waals interactions. The excellent enthalpy-entropy correlation obtained can be taken as evidence for the very limited conformational changes upon transfer of CD complexes from H(2)O to D(2)O.

Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases

Despite the availability of many experimental data and some modeling studies, questions remain as to the precise mechanism of the serine proteases. Here we report molecular dynamics simulations on the acyl-enzyme complex and the tetrahedral intermediate during the deacylation step in elastase catalyzed hydrolysis of a simple peptide. The models are based on recent crystallographic data for an acyl-enzyme intermediate at pH 5 and a time-resolved study on the deacylation step. Simulations were carried out on the acyl enzyme complex with His-57 in protonated (as for the pH 5 crystallographic work) and deprotonated forms. In both cases, a water molecule that could provide the nucleophilic hydroxide ion to attack the ester carbonyl was located between the imidazole ring of His-57 and the carbonyl carbon, close to the hydrolytic position assigned in the crystal structure. In the "neutral pH" simulations of the acyl-enzyme complex, the hydrolytic water oxygen was hydrogen bonded to the imidazole ring and the side chain of Arg-61. Alternative stable locations for water in the active site were also observed. Movement of the His-57 side-chain from that observed in the crystal structure allowed more solvent waters to enter the active site, suggesting that an alternative hydrolytic process directly involving two water molecules may be possible. At the acyl-enzyme stage, the ester carbonyl was found to flip easily in and out of the oxyanion hole. In contrast, simulations on the tetrahedral intermediate showed no significant movement of His-57 and the ester carbonyl was constantly located in the oxyanion hole. A comparison between the simulated tetrahedral intermediate and a time-resolved crystallographic structure assigned as predominantly reflecting the tetrahedral intermediate suggests that the experimental structure may not precisely represent an optimal arrangement for catalysis in solution. Movement of loop residues 216-223 and P3 residue, seen both in the tetrahedral simulation and the experimental analysis, could be related to product release. Furthermore, an analysis of the geometric data obtained from the simulations and the pH 5 crystal structure of the acyl-enzyme suggests that since His-57 is protonated, in some aspects, this crystal structure resembles the tetrahedral intermediate.

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.

The role of the medium in solvent isotope effects on serine protease action

The hydrolysis of N-carbobenzyloxyaminoacyl-O-p-nitrophenyl esters derived from L-leucine, L-phenylalanine, and L-tryptophan, with catalysis by bovine pancreatic α-chymotrypsin at pH 7.00 at 25.00°C in water containing acetonitrile from 15.0% to 60% (v/v), exhibits values of kcat/Km that decrease as the 34th to 36th power of the activity of water and values of kcat that are essentially constant. Solvent isotope effects kcat(H2O)/ kcat(D2O) range from 2.1 to 3.0 with proton inventories (dependences of kcat(n) on n, the atom fraction of deuterium in the water component of the solvent) that are linear, regardless of the amount of acetonitrile in the medium. The isotope effect on kcat thus appears to arise from a single transition-state site and to be little affected by the medium. Contributions from the medium to solvent isotope effects on enzymic reactions clearly exist but appear not to be detectable in the deacylation reactions of acyl chymotrypsins.Key words: solvent isotope effects, proton inventories, medium effects, enzyme catalysis, alpha-chymotrypsin.