Oxygen binding isotope effects of triazole-based HIV-1 reverse transcriptase inhibitors indicate the actual binding site

Binding isotope effects (BIEs) associated with binding of four triazole-based ligands to HIV-1 reverse transcriptase have been calculated at the QM/MM MD level of theory. Two main binding sites: allosteric cavity and RNase H active site, as well as three other sites reported in the literature (the Knuckles, the NNRTI Adjacent, and Incoming Nucleotide Binding) have been considered. The interactions between inhibitors and these protein sites have been quantified by binding free energies obtained from free energy perturbation (FEP) calculations, supported by interaction energy analysis. It has been shown that binding in the allosteric cavity can be distinguished from binding to other sites based on BIEs as it is associated with normal ¹⁸O-BIEs of the carbonyl oxygen atom while binding to RNase H active site is characterized by inverse binding isotope effect (¹⁸O-BIE < 1). For other sites ¹⁸O-BIEs close to unity are predicted. This information points to oxygen binding isotope effects of carbonyl group as indicative of the actual binding site of studied inhibitors.

Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase

The ¹⁸O binding isotope effect allows us to distinguish the actual binding site of an inhibitor in HIV-1 reverse transcriptase.

A theoretical investigation of alpha-carbon kinetic isotope effects and their relationship to the transition-state structure of S(N)2 reactions

[reaction: see text] The transition structures and alpha-carbon 12C/13C kinetic isotope effects for 22 S(N)2 reactions between methyl chloride and a wide variety of nucleophiles have been calculated using the B1LYP/aug-cc-pVDZ level of theory. Anionic, neutral, and radical anion nucleophiles were used to give a wide range of S(N)2 transition states so the relationship between the magnitude of the alpha-carbon kinetic isotope effect and transition-state structure could be determined. The results suggest that the alpha-carbon 12C/13C kinetic isotope effects for S(N)2 reactions will be large (near the experimental maximum) and that the curve relating the magnitude of the KIE to the percent transfer of the alpha-carbon from the nucleophile to the leaving group in the transition state has a broad maximum. This means very similar KIEs will be found for early, symmetric, and late transition states and that one cannot use the magnitude of these KIEs to estimate transition-state structure.

Theoretical evaluation of the hydrogen kinetic isotope effect on the first step of the methylmalonyl-CoA mutase reaction

We have calculated hydrogen kinetic isotope effects (KIEs) for the first step of the methylmalonyl-CoA mutase reaction, including multidimensional tunneling correction at the zero curvature (ZCT) level, and compared them with the experimental values. Both alternative mechanisms of this step, concerted and stepwise, can be accommodated. It turned out to be essential to include Arg207 hydrogen-bonded to the reactant in the mechanism predicting simultaneous breaking of the Co-C bond of AdoCbl and hydrogen atom transfer. The consequence of the stepwise mechanism is a much larger facilitation of the homolytic dissociation of the carbon-cobalt bond by the enzyme than currently appreciated; our results suggest lowering of the activation energy by about 23 kcal mol(-1). We have also shown that large hydrogen KIEs of tunneling origin do not necessarily break the Swain-Schaad equation. Furthermore, when this equation does not hold, the exponent may be smaller in the presence of tunneling than it is at the semi-classical limit, indicating that nonclassical behavior may be a more common phenomenon than expected.

Nitrogen kinetic isotope effects on the decarboxylation of 4-pyridylacetic acid

Nitrogen kinetic isotope effects on the decarboxylation of 4-pyridylacetic acid have been measured in solvents of different polarity and have been found to vary from the inverse value of 0.994 to the normal value of 1.002 upon increase of water content of the binary dioxane--water solvent from 25% to 75% (v/v), respectively. These changes were successfully modeled theoretically and shown to originate from the large inverse nitrogen isotope effect on the equilibrium between acidic and zwitterionic forms.

Solvent-dependent transition states for decarboxylations

The rate constants and kinetic isotope effects for decarboxylation of 4-pyridylacetic acid depend strongly on whether the solvent is water or dioxane, and the present paper interprets this finding. We calculate the solvent dependence of the free energy barrier and of the (13)C and (18)O kinetic isotope effects using a quantum mechanical solvation model based on class IV charges and semiempirical atomic surface tensions. The calculations provide a consistent interpretation of the experimental results, which provides a striking confirmation of the soundness of the solvation modeling. Even more significantly, the agreement of theory and experiment gives us confidence in the physical picture of the reaction provided by the model. This indicates that the location of the transition state, as measured by the length of the breaking C--C bond, is 0.24 A later than the gas phase in dioxane and 0.37 A later than the gas phase in water. Charge development at the transition state also depends strongly on the solvent; in particular the CO(2) moiety is 0.07 electronic charge units more negative at the transition state in dioxane than in water.

Chlorine kinetic isotope effects on the haloalkane dehalogenase reaction

We have found chlorine kinetic isotope effects on the dehalogenation catalyzed by haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 to be 1.0045 +/- 0.0004 for 1,2-dichloroethane and 1.0066 +/- 0.0004 for 1-chlorobutane. The latter isotope effect approaches the intrinsic chlorine kinetic isotope effect for the dehalogenation step. The intrinsic isotope effect has been modeled using semiempirical and DFT theory levels using the ONIOM QM/QM scheme. Our results indicate that the dehalogenation step is reversible; the overall irreversibility of the enzyme-catalyzed reaction is brought about by a step following the dehalogenation.

Hydroxyl radical reaction with melatonin molecule: a computational study

Theoretical calculations of the HO* radical reaction with the melatonin molecule were performed. Reaction pathways with C2, C3, C4, C6 and C7 as the target carbon atoms and corresponding radical adducts were studied. Low activation energies of all adducts suggest that these reactions should occur quite easily and with rather low selectivity. C2 carbon as the most probable site of attack and C3 as the least probable one are proposed.

Tritium secondary kinetic isotope effect on phenylalanine ammonia-lyase-catalyzed reaction

The mechanism by which phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the reversible elimination of ammonia from phenylalanine yielding (E)-cinnamic acid has gained much attention in the recent years. Dehydroalanine is essential for the catalysis. It was assumed that this prostetic group acts as the electrophile, leading to a covalently bonded enzyme-intermediate complex with quarternary nitrogen of phenylalanine. Recently, an alternative mechanism has been suggested in which the enzyme-intermediate complex is formed in a Friedel-Crafts reaction between dehydroalanine and orthocarbon of the aromatic ring. Using semiempirical calculations we have shown that these two alternative mechanisms can be distinguished on the basis of the hydrogen secondary kinetic isotope effect when tritium label is placed in the orthopositions. Our calculations indicated also that the kinetic isotope effect measured using ring-labeled d(5)-phenylalanine could not be used to differentiate these alternative mechanisms. Measured secondary tritium kinetic isotope effect shows strong dependence on the reaction progress, starting at the inverse value of k(H)/k(T) = 0.85 for 5% conversion and reaching the normal value of about 1.15 as the conversion increases to 20%. This dependence has been interpreted in terms of a complex mechanism with initial formation of the Friedel-Crafts type intermediate.

13C and (15)N Kinetic Isotope Effects on the Decarboxylation of 3-Carboxybenzisoxazole. Theory vs Experiment

Nitrogen and carbon kinetic isotope effects were measured on the decarboxylation of 3-carboxybenzisoxazole at room temperature. The nitrogen isotope effect in acetone is 1.0312 +/- 0.0006. The carbon isotope effect shows no dependence on the solvent polarity: 1.0448 +/- 0.0007 in 1,4-dioxane, 1.0445 +/- 0.0001 in acetonitrile, 1.0472 +/- 0.0013 in DMF, and 1.0418 +/- 0.0027 in water. These isotope effects were modeled theoretically at the semiempirical (AM1, PM3, SAM1) and ab initio (up to B3LYP/6-31++G) levels. The comparison of the theoretical and experimental results leads to the conclusion that none of the theory levels employed is capable of quantitatively predicting these isotope effects.

Theoretical calculations of heavy-atom isotope effects

An overview of calculations of isotope effects on biochemical and chemical reactions using quantum chemistry methods is presented . Usefulness of different levels of theoretical scrutiny for such calculations is critically discussed.

Equilibrium isotope effect on ternary complex formation of [1-18O]oxamate with NADH and lactate dehydrogenase

An equilibrium isotope effect on association of [1-18O]oxamate to form a ternary complex with lactate dehydrogenase and NADH of 0.9840 +/- 0.0027 has been measured by equilibrium dialysis and whole molecule isotope ratio mass spectrometry. Semiempirical calculations of vibrational frequencies using various models for solvent were shown to predict an inverse equilibrium isotope effect on association. However, the calculated effect cannot be directly attributed to one specific normal mode or vibrational force constant. Analysis of the carboxylate interaction with the guanidinium ion showed that the ionic interaction increased the torsional force constant for rotation about the carbon-carbon bond of oxamate. The minimum energy geometry for oxamate interacting with methyl guanidinium predicts that the plane of the oxamate carboxylate will be at an oblique angle to the plane defined by the guanidinium nitrogens. The combination of experimental and calculated equilibrium isotope effects on association holds the potential to improve the characterization of the interaction of ligands with protein active sites.

Theoretical calculations of heavy-atom isotope effects

An overview of calculations of isotope effects on biochemical and chemical reactions using quantum chemistry methods is presented. Usefulness of different levels of theoretical scrutiny for such calculations is critically discussed.

Kinetic isotope effects on substrate association: reactions of phosphoenolpyruvate with phosphoenolpyruvate carboxylase and pyruvate kinase

Kinetic isotope effects on association have been measured using the remote label methodology developed by O'Leary and Marlier (1979). The isotope effect on V/KA for the first substrate in an obligatorily ordered mechanism is an isotope effect on its second-order rate constant for association with the enzyme. With phosphoenolpyruvate carboxylase the 18(V/KPEP) when the bridging O is labeled decreases from 1.0056 +/- 0.0007 to 0.9943 +/- 0.0002 as the concentration of bicarbonate, the second substrate, increases from 2 to 200 mM. With pyruvate kinase the 18(V/KPEP) decreases from 1.0024 +/- 0.0014 to 0.9928 +/- 0.0027 as the concentration of ADP increases from 1.5 to 30 mM. These inverse kinetic isotope effects are best understood as arising from an isotope effect on the rate constant for forming the Michaelis complex of enzyme and substrate. The inverse value suggests that the bridging oxygen is in a vibrationally stiffer environment in the transition state for the association reaction.

Semiempirical calculations of the oxygen equilibrium isotope effect on binding of oxamate to lactate dehydrogenase

Semiempirical methods have been used in an attempt to predict theoretically the experimentally observed value of 0.9840 for the oxygen isotope effect on binding of oxamate to lactate dehydrogenase. The overall strategy involved vibrational analysis of oxamate in two different environments; that of the active site residues and in aqueous solution. The comparison of calculated values with the experimentally determined isotope effect proved the AM1 Hamiltonian to be superior to the PM3 Hamiltonian in this modelling. While most tested methods of accounting for solvent effects on the vibrational frequencies of the solute yielded similar results it turned out that what was crucial for the purpose of determination of the isotope effect was the model of oxamate in the active site of the enzyme. In particular, the major factor responsible for the inverse value of this isotope effect can be ascribed to the formation of an ordered, bifurcated hydrogen bond between the oxamate carboxylate and the guanidinium group of the active site histidine.

Investigation of the enzymatic mechanism of yeast orotidine-5'-monophosphate decarboxylase using 13C kinetic isotope effects

Orotidine-5'-monophosphate decarboxylase (ODCase) from Saccharomyces cerevisiae displays an observed 13C kinetic isotope effect of 1.0247 +/- 0.0008 at 25 degrees C, pH 6.8. The observed isotope effect is sensitive to changes in the reaction medium, such as pH, temperature, or glycerol content. The value of 1.0494 +/- 0.0006 measured at pH 4.0, 25 degrees C, is not altered significantly by temperature or glycerol, and thus the intrinsic isotope effect for the reaction is apparently being observed under these conditions and decarboxylation is almost entirely rate-determining. These data require a catalytic mechanism with freely reversible binding and one in which a very limited contribution to the overall rate is made by chemical steps preceding decarboxylation; the zwitterion mechanism of Beak and Siegel [Beak, P. & Siegel, B. (1976) J. Am. Chem. Soc. 98, 3601-3606], which involves only protonation of the pyrimidine ring, is such a mechanism. With use of an intrinsic isotope effect of 1.05, a partitioning factor of less than unity is calculated for ODCase at pH 6.0, 25 degrees C. A quantitative kinetic analysis using this result excludes the possibility of an enzymatic mechanism involving covalent attachment of an enzyme nucleophile to C-5 of the pyrimidine ring. The observed isotope effect does not rise to the intrinsic value above pH 8.5; instead, the observed isotope effects at 25 degrees C plotted against pH yield an asymmetric curve that at high pH plateaus at about 1.035. These data, in conjunction with the pH profile of Vmax/km, fit a kinetic model in which an enzyme proton necessary for catalysis is titrated at high pH, thus providing evidence for the catalytic mechanism of Beak and Siegel (1976).

Analogues of NADP(+) as inhibitors and coenzymes for NADP(+) malic enzyme from maize leaves

Structural analogues of the NADP(+) were studied as potential coenzymes and inhibitors for NADP(+) dependent malic enzyme from Zea mays L. leaves. Results showed that 1, N(6)-etheno-nicotinamide adenine dinucleotide phosphate (∈ NADP(+)), 3-acetylpyridine-adenine dinucleotide phosphate (APADP(+)), nicotinamide-hypoxanthine dinucleotide phosphate (NHDP(+)) and β-nicotinamide adenine dinucleotide 2': 3'-cyclic monophosphate (2'3'NADPc(+)) act as alternate coenzymes for the enzyme and that there is little variation in the values of the Michaelis constants and only a threefold variation in Vmax for the five nucleotides. On the other hand, thionicotinamide-adenine dinucleotide phosphate (SNADP(+)), 3-aminopyridine-adenine dinucleotide phosphate (AADP(+)), adenosine 2'-monophosphate (2'AMP) and adenosine 2': 3'-cyclic monophosphate (2'3'AMPc) were competitive inhibitors with respect to NADP(+), while β-nicotinamide adenine dinucleotide 3'-phosphate (3'NADP(+)), NAD(+), adenosine 3'-monophosphate (3'AMP), adenosine 2': 5'-cyclic monophosphate (2'5'AMPc), 5'AMP, 5'ADP, 5'ATP and adenosine act as non-competitive inhibitors. These results, together with results of semiempirical self-consistent field-molecular orbitals calculations, suggest that the 2'-phosphate group is crucial for the nucleotide binding to the enzyme, whereas the charge density on the C4 atom of the pyridine ring is the major factor that governs the coenzyme activity.

Isotope effect evidence for the zinc hydroxide mechanism of carbonic anhydrase catalysis

The carbon kinetic isotope effect on the enzymatic dehydration of HCO3- ion is k12/k13 = 1.011 and is independent, within experimental error, of the addition of sucrose, substitution of D2O for H2O, and substitution of enzyme-bound Zn2+ by Co2+. These results are consistent with a ping-pong mechanism in which proton transfer between enzyme and solvent is separated from HCO3- dehydration. For the dehydration half-reaction, diffusional processes are severalfold faster than dehydration, and the rate-determining step is the dehydration itself. The intrinsic isotope effect is approximately 1.011, indicating that hydration of CO2 occurs by reaction of zinc-bound OH-, rather than zinc-bound H2O.

Carbon isotope effect on dehydration of bicarbonate ion catalyzed by carbonic anhydrase

The carbon-13 kinetic isotope effect on the dehydration of HCO3- by bovine carbonic anhydrase has been measured. To accomplish this, bicarbonate was added to a buffer solution at pH 8 containing carbonic anhydrase under conditions where purging of the product CO2 from the solution is rapid. Measurement of the isotopic composition of the purged CO2 as a function of the concentration of carbonic anhydrase permits calculation of the isotope effect on the enzymic reaction. The isotope effect on the dehydration is k12/k13 = 1.0101 +/- 0.0004. This effect is most consistent with a ping-pong mechanism for carbonic anhydrase action, in which proton transfer to or from the enzyme occurs in a step separate from the dehydration step. Substrate and product dissociation steps are at least 2-3-fold faster than the hydration/dehydration step.