Alteration in substrate specificity of horse liver alcohol dehydrogenase by an acyclic nicotinamide analog of NAD(+).

A new, acyclic NAD-analog, acycloNAD(+) has been synthesized where the nicotinamide ribosyl moiety has been replaced by the nicotinamide (2-hydroxyethoxy)methyl moiety. The chemical properties of this analog are comparable to those of ß-NAD(+) with a redox potential of -324mV and a 341nm λmax for the reduced form. Both yeast alcohol dehydrogenase (YADH) and horse liver alcohol dehydrogenase (HLADH) catalyze the reduction of acycloNAD(+) by primary alcohols. With HLADH 1-butanol has the highest Vmax at 49% that of ß-NAD(+). The primary deuterium kinetic isotope effect is greater than 3 indicating a significant contribution to the rate limiting step from cleavage of the carbon-hydrogen bond. The stereochemistry of the hydride transfer in the oxidation of stereospecifically deuterium labeled n-butanol is identical to that for the reaction with ß-NAD(+). In contrast to the activity toward primary alcohols there is no detectable reduction of acycloNAD(+) by secondary alcohols with HLADH although these alcohols serve as competitive inhibitors. The net effect is that acycloNAD(+) has converted horse liver ADH from a broad spectrum alcohol dehydrogenase, capable of utilizing either primary or secondary alcohols, into an exclusively primary alcohol dehydrogenase. This is the first example of an NAD analog that alters the substrate specificity of a dehydrogenase and, like site-directed mutagenesis of proteins, establishes that modifications of the coenzyme distance from the active site can be used to alter enzyme function and substrate specificity. These and other results, including the activity with α-NADH, clearly demonstrate the promiscuity of the binding interactions between dehydrogenases and the riboside phosphate of the nicotinamide moiety, thus greatly expanding the possibilities for the design of analogs and inhibitors of specific dehydrogenases.

Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates.

Bovine CD38/NAD(+)glycohydrolase (bCD38) catalyses the hydrolysis of NAD(+) into nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose (cADPR). We solved the crystal structures of the mono N-glycosylated forms of the ecto-domain of bCD38 or the catalytic residue mutant Glu218Gln in their apo state or bound to aFNAD or rFNAD, two 2'-fluorinated analogs of NAD(+). Both compounds behave as mechanism-based inhibitors, allowing the trapping of a reaction intermediate covalently linked to Glu218. Compared to the non-covalent (Michaelis) complex, the ligands adopt a more folded conformation in the covalent complexes. Altogether these crystallographic snapshots along the reaction pathway reveal the drastic conformational rearrangements undergone by the ligand during catalysis with the repositioning of its adenine ring from a solvent-exposed position stacked against Trp168 to a more buried position stacked against Trp181. This adenine flipping between conserved tryptophans is a prerequisite for the proper positioning of the N1 of the adenine ring to perform the nucleophilic attack on the C1' of the ribofuranoside ring ultimately yielding cADPR. In all structures, however, the adenine ring adopts the most thermodynamically favorable anti conformation, explaining why cyclization, which requires a syn conformation, remains a rare alternate event in the reactions catalyzed by bCD38 (cADPR represents only 1% of the reaction products). In the Michaelis complex, the substrate is bound in a constrained conformation; the enzyme uses this ground-state destabilization, in addition to a hydrophobic environment and desolvation of the nicotinamide-ribosyl bond, to destabilize the scissile bond leading to the formation of a ribooxocarbenium ion intermediate. The Glu218 side chain stabilizes this reaction intermediate and plays another important role during catalysis by polarizing the 2'-OH of the substrate NAD(+). Based on our structural analysis and data on active site mutants, we propose a detailed analysis of the catalytic mechanism.

CD38 induces apoptosis of a murine pro-B leukemic cell line by a tyrosine kinase-dependent but ADP-ribosyl cyclase- and NAD glycohydrolase-independent mechanism.

Cross-linking of CD38 on hematopoietic cells induces activation, proliferation and differentiation of mature T and B cells and mediates apoptosis of myeloid and lymphoid progenitor cells. In addition to acting as a signaling receptor, CD38 is also an enzyme capable of producing several calcium-mobilizing metabolites, including cyclic adenosine diphosphate ribose (cADPR). It has been previously postulated that the calcium-mobilizing metabolites produced by CD38 may regulate its receptor-based activities. To test this hypothesis, we examined whether the enzyme activity of CD38 controls the apoptosis of an anti-CD38-stimulated leukemic B cell. We show that anti-CD38-induced apoptosis of Ba/F3 cells, a murine pro-B cell line, is not affected by blocking the calcium-mobilizing activity of cADPR or by inhibiting intracellular or extracellular calcium mobilization. In addition, we demonstrate that blocking CD38 enzyme activity with 2'-deoxy-2'-fluoro-nicotinamide arabinoside adenine dinucleotide has no effect on apoptosis and that Ba/F3 cells expressing catalytically inactive mutant forms of CD38 still undergo apoptosis upon CD38 cross-linking. Instead, we find that anti-CD38-induced apoptosis is dependent on tyrosine kinase and caspase activation, and that this process appears to be potentiated by the presence of membrane microdomains. Thus, the receptor-mediated functions of CD38 can be separated from its enzyme activity in a murine leukemic cell line, suggesting that CD38 plays multiple, but independent, biologic roles.

Extracellular NAD+ regulates intracellular free calcium concentration in human monocytes.

Ca(2+) ions play a critical role in the biochemical cascade of signal transduction pathways, leading to the activation of immune cells. In the present study, we show that the exposure of freshly isolated human monocytes to NAD(+) results in a rapid concentration-dependent elevation of [Ca(2+)](i) (intracellular free Ca(2+) concentration) caused by the influx of extracellular Ca(2+). NAD(+) derivatives containing a modified adenine or nicotinamide ring failed to trigger a Ca(2+) increase. Treating monocytes with ADPR (ADP-ribose), a major degradation product of NAD(+), also resulted in a rise in [Ca(2+)](i). Selective inhibition of CD38, an NAD-glycohydrolase that generates free ADPR from NAD(+), does not abolish the effect of NAD(+), excluding the possibility that NAD(+) might act via ADPR. The NAD(+)-induced Ca(2+) response was prevented by the prior addition of ADPR and vice versa, indicating that both compounds share some mechanisms mediating the rise in [Ca(2+)](i). NAD(+), as well as ADPR, were ineffective when applied following ATP, suggesting that ATP controls events that intersect with NAD(+) and ADPR signalling.

Mechanism of nicotinamide inhibition and transglycosidation by Sir2 histone/protein deacetylases.

Silent information regulator 2 (Sir2) enzymes catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins have been shown to regulate gene silencing, metabolic enzymes, and life span. Recently, nicotinamide has been implicated as a direct negative regulator of cellular Sir2 function; however, the mechanism of nicotinamide inhibition was not established. Sir2 enzymes are multifunctional in that the deacetylase reaction involves the cleavage of the nicotinamide-ribosyl, cleavage of an amide bond, and transfer of the acetyl group ultimately to the 2'-ribose hydroxyl of ADP-ribose. Here we demonstrate that nicotinamide inhibition is the result of nicotinamide intercepting an ADP-ribosyl-enzyme-acetyl peptide intermediate with regeneration of NAD+ (transglycosidation). The cellular implications are discussed. A variety of 3-substituted pyridines was found to be substrates for enzyme-catalyzed transglycosidation. A Brönsted plot of the data yielded a slope of +0.98, consistent with the development of a nearly full positive charge in the transition state, and with basicity of the attacking nucleophile as a strong predictor of reactivity. NAD+ analogues including beta-2'-deoxy-2'-fluororibo-NAD+ and a His-to-Ala mutant were used to probe the mechanism of nicotinamide-ribosyl cleavage and acetyl group transfer. We demonstrate that nicotinamide-ribosyl cleavage is distinct from acetyl group transfer to the 2'-OH ribose. The observed enzyme-catalyzed formation of a labile 1'-acetylated-ADP-fluororibose intermediate using beta-2'-deoxy-2'-fluororibo-NAD+ supports a mechanism where, after nicotinamide-ribosyl cleavage, the carbonyl oxygen of acetylated substrate attacks the C-1' ribose to form an initial iminium adduct.

Reactions of Charged Substrates. 8. The Nucleophilic Substitution Reactions of (4-Methoxybenzyl)dimethylsulfonium Chloride.

Displacement reactions on the title compound (1) occur only for nucleophiles with intermediate hardness. Nucleophiles that react display a range of mechanisms. 1 reacts with the neutral nucleophile pyridine-d(5) through a mixed S(N)1/S(N)2 mechanism; salt added to control ionic strength affects the rate for the unimolecular process, but has no effect on the bimolecular rate constant. The mechanism of displacement by N(3)(-) and SO(3)(2)(-) depends on the presence or absence of exogenous salt. At constant ionic strength, the mechanism is mixed S(N)1/S(N)2 over most of the range of [Nu]. With nucleophile only present, plots of k(obsd) vs [Nu] exhibit severe breaks that are not the result of salt effects. Analysis of rate constants and product ratios suggests that at low [Nu] reaction occurs simultaneously through concerted Hughes-Ingold S(N)2 and preassociation-concerted mechanisms. At high [Nu], displacement occurs only through the preassociation-concerted mechanism. Comparison of these results with data for gas-phase dissociation of benzyl dimethylsulfoniums and with solution results for benzyl pyridiniums suggests that the intrinsic stability of the intermediate does not necessarily determine the mechanism.

Reactions of Charged Substrates. 6. The Methoxymethyl Carbenium Ion Problem. 1. A Semiempirical Study of the Kinetic and Thermodynamic Stabilities of Linear and Cyclic Oxo- and Thiocarbenium Ions Generated from Pyridinium and Dimethylanilinium Ions.

AM1-calculated energy profiles for dissociation of (methoxymethyl)pyridinium and dimethylanilinium ion substrates show that the methoxymethyl carbenium ion is not sufficiently stable to exist as an intermediate on the reaction coordinate for this model reaction. [(Thiomethoxy)methyl]pyridinium ion, however, has a distinct transition state because of the stability of the resulting ion-neutral complex. The complete potential energy surfaces for water displacement on the methoxymethyl substrate with either pyridine or dimethylaniline as the leaving group show distinct transition states and very flat surfaces for the ion-neutral complexes in which interaction of the carbenium ion with both leaving group and nucleophile is stabilizing. Secondary systems studied, including linear methoxy and thiomethoxy substrates, 5- and 6-membered cyclic oxo and thio substrates, and ribosyl-, xylopyranosyl-, and glucopyranosylpyridinium ions yield ion-neutral complexes with sufficient intrinsic stability to exist as intermediates. Comparison with solution data, primarily activation entropy and Brønsted coefficients, suggests that the sugar oxocarbenium ions, either as distinct, solvent-equilibrated intermediates or elements of ion-neutral complexes, are formed by unimolecular dissociation of the respective substrates in solution.

Reactions of Charged Substrates. 7. The Methoxymethyl Carbenium Ion Problem. 2. A Semiempirical Study of the Kinetic and Thermodynamic Stabilities of Linear and Cyclic Oxo- and Thiocarbenium Ions Generated from Aldehyde Hydrates, Hemiacetals, Acetals, and Methyl Ribosides and Glucosides.

Factors affecting the cleavage of the carbon-oxygen bond in linear and cyclic aldehyde hydrates, heimacetals, acetals, and methyl ribosides and glucosides have been investigated using semiempirical calculations (AM1 and PM3). (For some systems, low- and high-level ab initio energies are available for comparison with the semiempirical results. With one exception, the results obtained by the two methods show excellent agreement in relative energies and trends in reactivity.) The effects on reactivity and stability caused by substituting a sulfur for the alpha oxygen in the oxocarbenium ion were also studied. In general, systems that can have an antiperiplanar alignment of lone pairs on the leaving group and potential oxocarbenium ion oxygens undergo spontanteous cleavage. An examination of various conformers of the leaving group relative to the potential oxocarbenium oxygen shows, however, that lone pair repulsion and steric factors for MeOH as the leaving group are more important than the antiperiplanar effect for bond cleavage. All compounds in which the alpha-oxygen in the potential carbenium ion is replaced by sulfur undergo spontaneous cleavage regardless of the leaving group or structure of the compound. Energy profiles, DeltaH(), and DeltaH(R) values show that linear and cyclic thiocarbenium ions are much more stable than the corresponding oxocarbenium ions. Comparison of results for methyl ribosides and glucosides with results for corresponding pyridinium substrates suggests that both should hydrolyze through an A-1 mechanism. General-acid catalysis with hydronium as the acid was studied. With solution results, the computations suggest that substrates with either a good leaving group or stable oxocarbenium ion react with rate-limiting proton transfer from the acid to the leaving group but that substrates with both a good leaving group and stable carbenium ion react with concerted proton transfer and bond cleavage.

Reactions of Charged Substrates. 5. The Solvolysis and Sodium Azide Substitution Reactions of Benzylpyridinium Ions in Deuterium Oxide.

Second-order rate constants and activation values were measured for the reactions with NaN(3) of a series of 4-Y-substituted (Y = MeO, Me, H, Cl, and NO(2)) benzyl 3'-Z-substituted (Z = CN, CONH(2), H, F, Ac) pyridinium chlorides in deuterium oxide. 3'-Cyanopyridine substrates reacted much faster than nicotinamide and pyridine substrates; in the pyridine series the 4-Me, 4-H, and 4-Cl benzyl analogs did not react for up to 6 months at 96()() degrees C in 1.7 M NaN(3). The 3'-cyanopyridine substrates do not exhibit borderline kinetic behavior, but the nicotinamide substrates do. The Hammett plot is flat for the NaN(3) reaction of 3'-cyanopyridine substrates and increasingly V-shaped for the nicotinamide and pyridine substrates. The values of beta(LG) (four-point plot) for the NaN(3) reaction of the 4-MeO benzyl substrates is -1.45, which is usually interpreted as being a very "late" activated complex. Two-point Brønsted "plots" for the other benzyl derivatives and for two N-methylpyridinium ions give values of beta(LG) in the same range. The second-order rate constant and activation values for N-methyl-3'-cyanopyridinium iodide are within the same range as those for the benzyl substrates. For the hydrolysis reaction, the Hammett plot is linear for 3'-cyanopyridine substrates (rho(+) = -1.24) and flat for the nicotinamide substrates. The extent of hydrolysis of 0.005-0.05 M solutions of the 3'-cyanopyridinie substrates depended on the initial concentration of substrate, and hydrolysis was slowed significantly or stopped completely in the presence of exogenous 3-cyanopyridine. These results show that an equilibrium is established among the products for the 4-MeO, 4-Me, 4-H, and 4-Cl substrates; the 4-NO(2) substrate reacted too slowly to discern any difference. Data for the extent of hydrolysis were fitted by an equation derived assuming the equilibrium. Despite this limitation on a classic test of mechanism, the rates and rho values are consistent with direct displacement by solvent and not with a unimolecular process. These results, which are rationalized in terms of the Pross-Shaik model, suggest that there are no ion-dipole complex intermediates in the benzyl series and show that borderline kinetic behavior is a function of leaving group ability and is not necessarily related to a change in mechanism. A computational approach was used to evaluate anomalous beta(LG) values for the hydrolysis and nucleophilic substitution reactions of the methypyridinium ion substrates. It was found that neither the Nu-substrate bond lengths nor the difference in charge matched the beta(LG) values. The value of DeltaDeltaS() of -15 gibbs/mol between (4-methoxybenzyl)-3'-cyanopyridinium chloride and the corresponding dimethylsulfonium chloride in the NaN(3) reaction, which is the result of the solvation of the pyridine at the transition state and the lack of solvation of SMe(2), is used to argue that the source of NAD(+) glycohydrolase "catalysis" of NAD(+) bond cleavage is the result of desolvation of the leaving group upon binding.

Reactions of Charged Substrates. 4. The Gas-Phase Dissociation of (4-Substituted benzyl)dimethylsulfoniums and -pyridiniums.

The relative rates for the gas-phase dissociation RX(+) --> R(+) + X degrees of five (4-Y-substituted benzyl)dimethysulfoniums (Y = MeO, Me, H, Cl, and NO(2)) and 24 (4-Y-substituted benzyl)-3'-Z-pyridiniums (complete series for Z = CN, Cl, CONH(2), and H, and 4-methoxy- and 4-nitrobenzyls for Z = F and CH(3)CO) were measured using liquid secondary ion mass spectrometry. The Hammett plot (vs deltaDeltaG degrees or sigma(+)) is linear for the sulfoniums, but plots for the four pyridinium series have a drastic break between the 4-Cl and 4-NO(2) substrates. Brønsted-like plots for the pyridiniums show a strong leaving group effect only for 4-nitrobenzyls. An analysis of these linear free energy relations with supporting evidence from semiempirical computations suggests that collisionally activated pyridinium substrates dissociate by two pathways, direct dissociation and through an ion-neutral complex intermediate. Comparison of these results with results for the solution reactions of some of these compounds shows that the mechanism is different in the gas and solution phases. Sufficient experimental data are not available to assign a mechanism for dissociation to the sulfonium series, but computational results show characteristics of a direct dissociative mechanism.