Mechanism for ribonucleotide reductase inactivation by the anticancer drug gemcitabine

Gemcitabine (2',2'-difluoro-2'-deoxycytidine, dFdC) is a very promising anticancer drug, already approved for clinical use in three therapeutic indications. It is metabolized intracellularly to 5'-diphosphate (dFdCDP), which is known to be a potent inhibitor of ribonucleotide reductase (RNR). Although several nucleotide analogs show in vitro capacity of RNR inactivation, none has shown the in vivo efficacy of dFdCDP. Accordingly, the experimental data suggests that its mechanism of inhibition is different from the other known RNR suicide inhibitors. Enzyme inhibition in the absence of reductive species leads to complete loss of the essential radical in subunit R2, and formation of a new nucleotide-based radical. Interestingly, however, the presence of the reductants does not prevent inhibition--the radical is not lost but the targeted subunit of RNR becomes R1, which is inactivated possibly by alkylation. We have conducted a theoretical study, which led us to the first proposal of a possible mechanism for RNR inhibition by dFdCDP in the absence of reductants. This mechanism turned out to be very similar to the natural substrate reduction pathway and only deviates from the natural course after the formation of the well-known disulphide bridge. This deviation is caused precisely by the F atom in the beta-face, only present in this inhibitor. The essential radical in R2 is lost, and so is the enzyme catalytic activity. The nucleotide-based radical that constitutes the end product of our mechanism has been suggested in the literature as a possible candidate for the one detected experimentally. In fact, all experimental data available has been reproduced by the theoretical calculations performed here.     

Enzyme ribonucleotide reductase: unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives

Several 2'-substituted-2'-deoxyribonucleotides are potent inactivators of the enzyme ribonucleotide reductase (RNR), by destroying the essential tyrosyl radical located in subunit R2 or/and covalently alkylating the subunit R1. In the absence of external reductants, the inactivation is achieved by alkylation of subunit R1 by a methylene-3(2H)-furanone. The furanone is generated in solution through degradation of a keto-deoxyribonucleotide intermediate, produced during the inhibitory mechanism of a wide group of 2'-substituted inhibitors, and is easily detected experimentally by UV spectroscopy. Interestingly, the same keto-deoxyribonucleotide is also a proposed intermediate of the normal substrate pathway, but by some unknown reason, it does not dissociate from the active site and does not inactivate the enzyme. Therefore, if the currently accepted mechanism for substrate reduction is correct, there must be some specific reason that makes such a reactive intermediate behave differently, not dissociating from the active site during substrate reduction. In this article, we propose to validate the current substrate mechanism by showing that the keto-deoxyribonucleotide dissociates from the active site only in the case of the inhibitors, and therefore, it corresponds to a viable intermediate in the substrate mechanism. Furthermore, we answer unexplained experimental observations that concern the predomination of the normal reduction mechanism over the abnormal ketone formation in the FdNDP and the release of F(-), either in the normal or in the abnormal turnover. For that purpose, we have investigated the interaction between the enzyme and this keto-deoxyribonucleotide generated from the normal substrate and from two widely studied representative inhibitors. A model containing 140 atoms was used to represent the desired structures. The results allowed us to conclude that the solvation free energy of the 2'-substituents, its influence inside the active site, and the charge transfer mechanism from a protein side chain to solution are the thermodynamic driving forces for the intermediate dissociation and subsequent RNR inhibition. Such charge transfer cannot be accomplished by the natural substrate, preventing its dissociation. These results elucidate a paradox which has been unexplained for more than 20 years and further validates both the proposed substrate and inhibition chemical mechanisms.     

One-pot synthesis of 2-trifluoromethylchromones

We report a simple and suitable method for the preparation of useful 2-trifluoromethylchromones in one step, in high yields and avoiding the use of solvents. We were able to detect the intermediate of this reaction. Furthermore a mechanism for the formation of the 7-methoxy-3-trifluoroacetyl-2-trifluoromethylchromone through the unexpected double trifluoroacetylation of 4-methoxy-2-hydroxyacetophenone followed by dehydration is also proposed. All compounds are fully identified and characterized by spectroscopic techniques.     

Epoxidation and 1,2-dihydroxylation of alkenes by a nonheme iron model system - DFT supports the mechanism proposed by experiment

The FeII complexes of two isomeric pentadentate bispidine ligands in the presence of H2O2 are catalytically active for the epoxidation and 1,2-dihydroxylation of cyclooctene (bispidine = 3,7-diazabicyclo[3.3.1]nonane; the two isomeric pentadentate bispidine ligands discussed here have two tertiary amine and three pyridine donors). The published spectroscopic and mechanistic data, which include an extensive set of 18O labeling experiments, suggest that the FeIV=O complex is the catalytically active species, which produces epoxide as well as cis- and trans-1,2-dihydroxylated products. Several observations from the published experimental study are addressed with hybrid density functional methods and, in general, the calculations support the proposed, for nonheme iron model systems novel mechanism, where the formation of a radical intermediate emerges from the reaction of the FeIV=O oxidant and cyclooctene. The calculations suggest that the S = 1 ground state of the FeIV=O complex reacts with cyclooctene in a stepwise reaction, leading to the formation of a carbon-based radical intermediate. This radical is captured by O2 from air to produce the majority of the epoxide products in an aerobic atmosphere. Under anaerobic conditions, the produced epoxide product is due to the cyclization of the radical intermediate. Several possible spin states (ST = 3, 2, 1, 0) of the radical intermediate are close in energy. As a result of the substantial energy barrier, calculated for the ST = 3 spin ground state, a spin-crossover during the cyclization step is assumed, and a possible two-state scenario is found, where the S = 2 state of the FeIV=O complex participates in the catalytic mechanism. The 1,2-dihydroxylation proceeds, as suggested by experiment, via an unprecedented pathway, where the radical intermediate is captured by a hydroxyl radical, the source of which is FeIII-OOH, and this reaction is barrierless. The calculations suggest that dihydroxylation can also occur by a direct oxidation pathway from FeIII-OOH. The strikingly different reactivities observed with the two isomeric bispidine FeII complexes are rationalized on the basis of structural and electronic differences.     

Mechanistic aspects of the abstraction of an allylic hydrogen in the chlorine atom reaction with 2-methyl-1,3-butadiene (isoprene)

The different channels for the abstraction of an allylic hydrogen in the chlorine atom reaction with isoprene were explored using ab initio methodology. It is shown that the metathesis reaction proceeds through an association-elimination mechanism in which a weakly bound intermediate (HCl.C(5)H(7)(*)) is formed first (formal addition). Further evolution by HCl elimination leads to the final C(5)H(7)(*) radical. QCISD(T)/aug-cc-pVDZ//MP2/6-31G(d,p) calculations show that for two of the possible pathways the barrier heights involved are moderate and the formation of the intermediates are exergonic (DeltaG < 0). Therefore, the mechanism proposed is both kinetically and thermodynamically feasible. The pressure dependence experimentally observed for the Cl + isoprene reaction can be rationalized in terms of the association-elimination mechanism proposed.     

Theoretical study on the inhibition of ribonucleotide reductase by 2'-mercapto-2'-deoxyribonucleoside-5'-diphosphates

Ribonucleotide reductase (RNR) is responsible for the reduction of ribonucleotides into the correspondent 2'-deoxyribonucleotides in the only physiological process that yields the monomers of DNA. The enzyme has thus become an attractive target for chemotherapies that fight proliferation-based diseases, specifically cancer and infections by some viruses and parasites. 2'-Mercapto-2'-deoxyribonucleoside-5'-diphosphates (SHdNDP) are mechanism-based inhibitors of RNR and therefore potential chemotherapeutic agents for those indications. Previous experimental studies established the in vitro and in vivo activity of SHdNDP. In the in vitro studies, it was observed that the activity was dependent on the oxidative status of the medium, with the inactivation of RNR only occurring when molecular oxygen was available. To better understand the mechanism involved in RNR inactivation by SHdNDP, we performed theoretical calculations on the possible reactions between the inhibitors and the RNR active site. As a result, we propose the possible mechanistic pathways for the chemical events that occur in the absence and in the presence of O2. They correspond to a refinement and a complement of those proposed in the literature.     

9-Mercaptodethiobiotin is generated as a ligand to the [2Fe-2S]+ cluster during the reaction catalyzed by biotin synthase from Escherichia coli

Biotin synthase catalyzes formation of the thiophane ring through stepwise substitution of a sulfur atom for hydrogen atoms at the C9 and C6 positions of dethiobiotin. Biotin synthase is a radical S-adenosylmethionine (SAM) enzyme that reductively cleaves S-adenosylmethionine, generating 5'-deoxyadenosyl radicals that initially abstract a hydrogen atom from the C9 position of dethiobiotin. We have proposed that the resulting dethiobiotinyl radical is quenched by the μ-sulfide of the nearby [2Fe-2S](2+) cluster, resulting in coupled formation of 9-mercaptodethiobiotin and a reduced [2Fe-2S](+) cluster. This reduced FeS cluster is observed by electron paramagnetic resonance spectroscopy as a mixture of two orthorhombic spin systems. In the present work, we use isotopically labeled 9-mercaptodethiobiotin and enzyme to probe the ligand environment of the [2Fe-2S](+) cluster in this reaction intermediate. Hyperfine sublevel correlation spectroscopy (HYSCORE) spectra exhibit strong cross-peaks demonstrating strong isotropic coupling of the nuclear spin with the paramagnetic center. The hyperfine coupling constants are consistent with a structural model for the reaction intermediate in which 9-mercaptodethiobiotin is covalently coordinated to the remnant [2Fe-2S](+) cluster.     

Ion trap tandem mass spectrometry study of dexamethasone transformation products on light activated TiO2 surface

The photocatalytic transformation of dexamethasone and the formation of its intermediate compounds have been studied using titanium dioxide as a photocatalyst. The degradation of dexamethasone occurs easily through the formation of several hydroxy derivatives whose characterization has been made by HPLC/MS/MS. Even if both oxidative and reductive processes can be operating, only oxidative products have been identified in air saturated aqueous suspensions. A pattern of reaction pathways accounting for the observed intermediates is proposed. The obtained experimental evidence may be rationalized postulating the existence of a double initial mechanism. A single oxidation step resulting from the attack by one ·OH radical leading to the formation of five hydroxy-derivatives and a concomitant attack involving two ·OH radicals leading to the hydroxylation of the quinoid moiety of the molecule.     

Ion trap tandem mass spectrometry study of dexamethasone transformation products on light activated TiO2 surface

The photocatalytic transformation of dexamethasone and the formation of its intermediate compounds have been studied using titanium dioxide as a photocatalyst. The degradation of dexamethasone occurs easily through the formation of several hydroxy derivatives whose characterization has been made by HPLC/MS/MS. Even if both oxidative and reductive processes can be operating, only oxidative products have been identified in air saturated aqueous suspensions. A pattern of reaction pathways accounting for the observed intermediates is proposed. The obtained experimental evidence may be rationalized postulating the existence of a double initial mechanism. A single oxidation step resulting from the attack by one ·OH radical leading to the formation of five hydroxy-derivatives and a concomitant attack involving two ·OH radicals leading to the hydroxylation of the quinoid moiety of the molecule.     

Exploring the intermediates of photochemical CO2 reduction: reaction of Re(dmb)(CO)3 COOH with CO2

We have investigated the reaction of Re(dmb)(CO)(3)COOH with CO(2) using density functional theory, and propose a mechanism for the production of CO. This mechanism supports the role of Re(dmb)(CO)(3)COOH as a key intermediate in the formation of CO. Our new experimental work supports the proposed scheme.     

Steric and electronic substitution effects on the thermal oxidation of 5-carboethoxy-2-oxo-1,2,3,4-tetrahydropyridines

Various 4-aryl substituted 5-carboethoxy-2-oxo-1,2,3,4-tetrahydropyridines were oxidized to their corresponding 4-aryl-5-carboethoxy-2-oxo-1,2-dihydropyridines by potassium peroxydisulfate in aqueous acetonitrile under thermal conditions. The products were obtained in good to excellent yields. Based on the proposed mechanism, the removal of the hydrogen from the C₄-atom of the heterocyclic ring by the hydroxyl radical formed in situ is occurred in the rate determining step, which is influenced by the steric and electronic effects of the substituted aryl group attached to this atom and also the stability of the radical intermediate involved in the oxidation reaction. The experimental results were supported by the computational studies.     

HNNC radical and its role in the CH+N2 reaction

A previously unreported channel in the spin-allowed reaction path for the CH+N2 reaction that involves the HNNC radical is presented. The structures and energetics of the HNNC radical and its isomers HCNN and HNCN and the relevant intermediates and transition states that are involved in the proposed mechanism are obtained at the coupled cluster singles and doubles level of theory with noniterative triples correction (CCSD(T)) using a converging series of basis sets aug-cc-pVDZ, aug-cc-pVTZ, and aug-cc-pVQZ. The aug-cc-pVQZ basis is used for all the final single point energy calculations using the CCSD(T)/aug-cc-pVTZ optimized geometries. We find the HNNC radical to have a heat of formation of DeltafH0 (HNNC)=116.5 kcal mol(-1). An assessment of the quality of computed data of the radical species HNCN and HCNN is presented by comparison with the available experimental data. We find that HNNC can convert to HNCN, the highest barrier in this path being 14.5 kcal mol(-1) above the energy of the CH+N2 reactants. Thus, HNNC can play a role in the high-temperature spin-allowed mechanism for the reaction of CH+N2 proposed by Moskaleva, Xia, and Lin (Chem. Phys. Lett. 2000, 331, 269).     

Regiochemical and stereochemical evidence for enzyme-initiated catalysis in dual positional specific maize lipoxygenase-1

Dual positional specific maize lipoxygenase-1 catalyzed the formation of racemic mixtures of four possible regioisomers and was strongly inhibited by the radical scavenger, 4-hydroxy-2,2,6,6-tetramethyl-1-piperidinoxy radical. Molecular modeling studies indicated that the oxygen-binding cavity is segregated from the substrate-binding cavity. The data suggest that a bis-allylic radical reaction intermediate is generated enzymatically, released from the enzyme active site, and subsequently oxygenated outside of the enzyme active site by a nonenzymatic mechanism.     

The pyrolysis of CCl4 and C2Cl6 in the gas phase. Mechanistic modeling by thermodynamic and kinetic parameter estimation

A detailed radical reaction mechanism is proposed to describe the thermal reactions of CCl₄ and C₂Cl₆ in the gas phase quantitatively. A consistent set of activation energies and preexponential factors for all elementary reactions, in combination with enthalpies of formation and entropies for all species involved, is computer optimized to fit experimental pressure-rise curves and concentration profiles. For this purpose new experimental results on the pyrolysis of CCl₄ are used, together with published kinetic data on the pyrolysis of C₂Cl₆ (in the absence and in the presence of Cl₂). © 1996 John Wiley & Sons, Inc.     

Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle

Recently, a new branch of fatty acid metabolism has been opened by the novel phosphatase activity found in the N-terminal domain of the, hence bifunctional, soluble epoxide hydrolase (sEH). Importantly, this finding has also provided a new site for drug targeting in sEH's activity regulation. Classical MD and hybrid Car-Parrinello QM/MM calculations have been performed to investigate the reaction mechanism of the phosphoenzyme intermediate formation in the first step of the catalysis. The results support a concerted multi-event reaction mechanism: (1) a dissociative in-line nucleophilic substitution for the phosphoryl transfer reaction; (2) a double proton transfer involved in the formation of a good leaving group in the transition state. The presence of a water bridge in the substrate/enzyme complex allowed an efficient proton shuttle, showing its key role in speeding up the catalysis. The calculated free energy of the favored catalytic pathway is approximately 19 kcal/mol, in excellent agreement with experimental data.     

Photofragment imaging study of the CH2CCH2OH radical intermediate of the OH+allene reaction

These velocity map imaging experiments characterize the photolytic generation of one of the two radical intermediates formed when OH reacts via an addition mechanism with allene. The CH2CCH2OH radical intermediate is generated photolytically from the photodissociation of 2-chloro-2-propen-1-ol at 193 nm. Detecting the Cl atoms using [2+1] resonance-enhanced multiphoton ionization evidences an isotropic angular distribution for the Cl+CH2CCH2OH photofragments, a spin-orbit branching ratio for Cl(2P1/2):Cl(2P3/2) of 0.28, and a bimodal recoil kinetic energy distribution. Conservation of momentum and energy allows us to determine from this data the internal energy distribution of the nascent CH2CCH2OH radical cofragment. To assess the possible subsequent decomposition pathways of this highly vibrationally excited radical intermediate, we include electronic structure calculations at the G3//B3LYP level of theory. They predict the isomerization and dissociation transition states en route from the initial CH2CCH2OH radical intermediate to the three most important product channels for the OH+allene reaction expected from this radical intermediate: formaldehyde+C2H3, H+acrolein, and ethene+CHO. We also calculate the intermediates and transition states en route from the other radical adduct, formed by addition of the OH to the center carbon of allene, to the ketene+CH3 product channel. We compare our results to a previous theoretical study of the O+allyl reaction conducted at the CBS-QB3 level of theory, as the two reactions include several common intermediates.     

Toward an improved understanding of the glutamate mutase system

High-level quantum chemistry calculations have been used to examine the catalytic reactions of adenosylcobalamin-dependent glutamate mutase (GM) with the natural substrate (S)-glutamic acid. We have also examined the rearrangement of (S)-2-hydroxyglutaric acid, (S)-2-thiolglutaric acid, and 2-ketoglutaric acid, all of which have previously been shown to react as substrates or inhibitors of the enzyme. Our calculations support the notion that the 100-fold difference in kcat between glutamate and 2-hydroxyglutarate is associated with the relatively high energy of the glycolyl radical intermediate compared with the glycyl radical. More generally, calculations of radical stabilization energies for a variety of substituted glycyl radical analogues indicate that modifications at the radical center can profoundly affect the relative stability of the resulting radical, leading to important mechanistic consequences. We find that the formation of a thioglycolyl radical, derived from (S)-2-thiolglutaric acid, is highly dependent on the protonation state of sulfur. The neutral radical is found to be of stability similar to that of the glycolyl radical, whereas the S- form of the thioglycolyl radical is much more stable, thus providing a rationalization for the inhibition of the enzyme by the substrate analogue 2-thiolglutarate. Two possible rearrangement pathways have been examined for the reaction of GM with 2-ketoglutaric acid, for which previous experiments had suggested no rearrangement took place. The fragmentation-recombination pathway is associated with a fragmentation step that is very endothermic (by 102.2 kJ mol-1). In contrast, the addition-elimination pathway has significantly lower energy requirements. An alternative possibility, namely, that 2-ketoglutaric acid is bound in its hydrated form, 2,2-dihydroxyglutaric acid, also leads to a pathway with relatively low energy requirements, suggesting that some rearrangement might be expected under such circumstances.     

Cu(111)面上糠醇加氢生成2-甲基呋喃的反应机理

采用广义梯度近似的密度泛函理论并结合平板模型的方法,详细研究了糠醇在Cu(111)面上反应生成2-甲基呋喃的反应历程,优化了糠醇在Cu(111)面的吸附模型,并采用完全线性同步和二次同步变换的方法,对三种可能的反应机理中的各反应步骤进行了过渡态搜索.结果表明,糠醇主要通过支链上OH与Cu(111)面相互作用,易形成ψCH2和ψCH2O中间体(ψ代表呋喃环).糠醇进一步加氢机理很可能为:引入的氢物种明显降低了糠醇分解形成的中间体ψCH2的活化能,并促进了它的形成;中间体ψCH2更易从糠醇中获得H而生成2-甲基呋喃.该过程的控速步骤为ψCH2O*→ψCHO*+H*,活化能为199.0kJ/mol,总反应是2ψCH2OH=ψCH3+ψCHO+H2O.     

Theoretical studies on the mechanism of inhibition of Ribonucleotide Reductase by (E)-2'-Fluoromethylene-2'-deoxycitidine-5'-diphosphate

(E)-2'-Fluoromethylene-2'-deoxycitidine-5'-diphosphate (FMCDP) is a potent time-dependent inactivator of the enzyme Ribonucleotide Reductase, which operates by destructing an essential tyrosil radical and performing a covalent addition to an active site residue. Considerable effort to elucidate the inhibition mechanism has been undertaken in recent years, and some insights have been obtained. Although a mechanistic proposal has been put forward, based on a general paradigm of inhibition of RNR by 2' substituted substrate analogues, details about the mechanism have remained elusive. Namely, the exact residue that adds to the inhibitor is still not identified, although mutagenesis experiments suggest that it should correspond to the E441 residue. In this work, we performed an extensive theoretical exploration of the potential energy surface of a model system representing the active site of RNR with FMCDP, using Density Functional Theory. This study establishes the detailed mechanism of inhibition, which is considerably different from the one proposed earlier. The proposed mechanism is fully consistent with available experimental data. Energetic results reveal unambiguously that the residue adding to the inhibitor is a cysteine, most probably C439, and exclude the possibility of the addition of E441. However, the E441 residue is shown to be essential for inhibition, catalyzing both the major and minor inhibition pathways, in agreement with mutagenesis results. It is shown also that the major mode of inactivation mimics the early stages of the natural substrate pathway.     

Conversion of C5 into C6 cyclic species through the formation of C7 intermediates

We have recently proposed that the addition of C2H2 to the cyclopentadienyl radical can lead to the rapid formation of the cycloheptatrienyl radical and, in succession, of the indenyl radical. These reactions represent an interesting and unexplored route for the enlargement of gas-phase cyclic species. In this work we report ab initio calculations we performed with the aim of investigating in detail the gas-phase reactivity of cycloheptatrienyl and indenyl radicals. We found that the reaction of the cycloheptatrienyl radical with atomic hydrogen can lead to its fast conversion into the more stable benzyl radical. This reaction pathway involves the intermediate formation of heptatriene, norcaradiene, and toluene. Successively we investigated whether this reaction mechanism can be extended to polycyclic aromatic hydrocarbons (PAHs). For this purpose we studied the reaction of C2H2 with the indenyl radical, which can be considered as a superior homologue of the cyclopentadienyl radical. This reaction proceeds through a pathway similar to that proposed for C5H5 but with a reaction rate about an order of magnitude smaller. The present calculations extend thus the previously proposed C5-C7-C9 mechanism to bicyclic PAH and suggest a fast route for the conversion of C5 into C6 cyclic radicals, mediated by the formation of C7 cyclic species.