Toxicity Originating from Thiophene Containing Drugs: Exploring the Mechanism using Quantum Chemical Methods.

Drug metabolism of thiophene containing substrates by cytochrome P450s (CYP450) leads to toxic side effects, for example, nephrotoxicity (suprofen, ticlopidine), hepatotoxicity (tienilic acid), thrombotic thrombocytopenic purpura (clopidogrel), and aplastic anemia (ticlopidine). The origin of toxicity in these cases has been attributed to two different CYP450 mediated metabolic reactions: S-oxidation and epoxidation. In this work, the molecular level details of the bioinorganic chemistry associated with the generation of these competitive reactions are reported. Density functional theory was utilized (i) to explore the molecular mechanism for S-oxidation and epoxidation using the radical cationic center Cpd I [(iron(IV)-oxo-heme porphine system with SH(-) as the axial ligand, to mimic CYP450s] as the model oxidant, (ii) to establish the 3D structures of the reactants, transition states, and products on both the metabolic pathways, and (iii) to examine the potential energy (PE) profile for both the pathways to determine the energetically preferred toxic metabolite formation. The energy barrier required for S-oxidation was observed to be 14.75 kcal/mol as compared to that of the epoxidation reaction (13.23 kcal/mol) on the doublet PE surface of Cpd I. The formation of the epoxide metabolite was found to be highly exothermic (-23.24 kcal/mol), as compared to S-oxidation (-8.08 kcal/mol). Hence, on a relative scale the epoxidation process was observed to be thermodynamically and kinetically more favorable. The energy profiles associated with the reactions of the S-oxide and epoxide toxic metabolites were also explored. This study helps in understanding the CYP450-catalyzed toxic reactions of drugs containing the thiophene ring at the atomic level.

Importance of cytochromes in cyclization reactions: quantum chemical study on a model reaction of proguanil to cycloguanil.

Proguanil, an anti-malarial prodrug, undergoes cytochrome P450 catalyzed biotransformation to the pharmacologically active triazine metabolite (cycloguanil), which inhibits plasmodial dihydrofolate reductase. This cyclization is catalyzed by CYP2C19 and many anti-malarial lead compounds are being designed and synthesized to exploit this pathway. Quantum chemical calculations were performed using the model species (Cpd I for active species of cytochrome and N4-isopropyl-N6-methylbiguanide for proguanil) to elucidate the mechanism of the cyclization pathway. The overall reaction involves the loss of a water molecule, and is exothermic by approximately 55 kcal/mol, and involves a barrier of approximately 17 kcal/mol. The plausible reaction pathway involves the initial H-radical abstraction from the isopropyl group by Cpd I, followed by two alternative paths- (i) oxygen rebound to provide hydroxyl derivative and (ii) loss of additional H-radical to yield 1,3,5-triazatriene, which undergoes cyclization. This study helped in understanding the role of the active species of cytochromes in this important cyclization reaction.

In(III) triflate-mediated solvent-free synthesis and activation of thioglycosides by ball milling and structural analysis of long chain alkyl thioglycosides by TEM and quantum chemical methods.

Conventional solution-phase synthesis of thioglycosides from glycosyl acetates and thiols in the presence of In(III) triflate as reported for benzyl thioglucoside failed when applied to the synthesis of phenolic and alkyl thioglycosides. But, it was achieved in high efficiency and diastereospecificity with ease by solvent-free grinding in a ball mill. The acetates in turn were also obtained by the homogenization of free sugars with stoichiometric amounts of acetic anhydride and catalytic In(OTf)3 in the mill as neat products. Per-O-benzylated thioglycosides on grinding with an acceptor sugar in the presence of In(OTf)3 yield the corresponding O-glycosides efficiently. The latter in the case of a difficult secondary alcohol was nearly exclusive (>98%) in 1,2-cis-selectivity. In contrast, the conventional methods for this purpose require use of a coreagent such as NIS along with the Lewis acid to help generate the electrophilic species that actually is responsible for the activation of the thioglycoside donor in situ. The distinctly different self-assembling features of the peracetylated octadecyl 1-thio-α- and ß-D-galactopyranosides observed by TEM could be rationalized by molecular modeling.

Mechanism-based inactivation of cytochromes by furan epoxide: unraveling the molecular mechanism.

Drugs carrying an unsaturated C═C center (such as furans) form reactive epoxide metabolites and cause irreversible mechanism-based inactivation (MBI) of cytochrome P450 (CYP450) activity, through covalent modification of amino acid residues. Though this reaction is confirmed to take place in the active site of CYPs, the details of the reactions of furan (epoxidation and epoxide ring opening), the conditions under which MBI may occur, the residues involved, the importance of the heme center, etc. have yet to be explored. A density functional theory (DFT) study was carried out (i) to elucidate the reaction pathways for the generation of furan epoxide metabolite from furan ring by the model oxidant Cpd I (iron(IV)-oxo heme-porphine radical cation, to mimic the catalytic domain of CYPs) and (ii) to explore different reactions of the furan epoxide metabolite. The energy profiles of the competitive pathways and the conditions facilitating MBI of CYPs by the reactive epoxide metabolite are reported. The rate-determining step for the overall metabolic pathway leading to MBI was observed to be the initial epoxidation, requiring ∼12 kcal/mol under the enzymatic conditions. The covalent adducts (inactivator complexes) are highly stable (∼-46 to -70 kcal/mol) and may be formed due to the reaction between furan epoxide and nucleophilic amino acid residues such as serine/threonine, preferably after initial activation by basic amino acids.

Carbene generation by cytochromes and electronic structure of heme-iron-porphyrin-carbene complex: a quantum chemical study.

Carbene-heme-iron-porphyrin complexes generated from cytochrome P450 (CYP450)-mediated metabolism of compounds containing methylenedioxyphenyl (MDP) moiety lead to the mechanism-based inhibition (MBI) of CYPs. This coordination complex is termed as the metabolic-intermediate complex (MIC). The bioinorganic chemistry of MDP carbenes has been studied using quantum chemical methods employing density functional theory (B3LYP functional with implicit solvent corrections) to (i) analyze the characteristics of MDP-carbene in terms of singlet-triplet energy difference, protonation, and dimerization energies, etc.; (ii) determine the electronic structure and analyze the Fe-carbene interactions; and (iii) elucidate the potential reaction pathways for the generation of carbene, using Cpd I (iron(IV)-oxo-porphine with SH(-) as the axial ligand) as the model oxidant to mimic the activity of CYP450. The results show that MDP-carbenes are sufficiently stable and nucleophilic, leading to the formation of stable MIC (-40.35 kcal/mol) on the doublet spin state, formed via interaction between σ(LP) of carbene and empty dz(2) orbital of heme-iron. This was aided by the back-bonding between filled d(xz) orbital of heme-iron and the empty p orbital of carbene. The mechanistic pathway proposed in the literature for the generation of MDP-carbene (CH hydroxylation followed by water elimination) was studied, and observed to be unfavorable, owing to the formation of highly stable hydroxylated product (-57.12 kcal/mol). An intriguing pathway involving hydride ion abstraction and proton transfer followed by water elimination step was observed to be the most probable pathway.

Metabolic-intermediate complex formation with cytochrome P450: theoretical studies in elucidating the reaction pathway for the generation of reactive nitroso intermediate.

Mechanism-based inhibition (MBI) of cytochrome P450 (CYP) can lead to drug-drug interactions and often to toxicity. Some aliphatic and aromatic amines can undergo biotransformation reactions to form reactive metabolites such as nitrosoalkanes, leading to MBI of CYPs. It has been proposed that the nitrosoalkanes coordinate with the heme iron, forming metabolic-intermediate complex (MIC), resulting in the quasi-irreversible inhibition of CYPs. Limited mechanistic details regarding the formation of reactive nitroso intermediate and its coordination with heme-iron have been reported. A quantum chemical analysis was performed to elucidate potential reaction pathways for the generation of nitroso intermediate and the formation of MIC. Elucidation of the energy profile along the reaction path, identification of three-dimensional structures of reactive intermediates and transition states, as well as charge and spin density analyses, were performed using the density functional B3LYP method. The study was performed using Cpd I [iron (IV-oxo] heme porphine with SH(-) as the axial ligand) to represent the catalytic domain of CYP, simulating the biotransformation process. Three pathways: (i) N-oxidation followed by proton shuttle, (ii) N-oxidation followed by 1,2-H shift, and (iii) H-abstraction followed by rebound mechanism, were studied. It was observed that the proton shuttle pathway was more favorable over the whole reaction leading to reactive nitroso intermediate. This study revealed that the MIC formation from a primary amine is a favorable exothermic process, involving eight different steps and preferably takes place on the doublet spin surface of Cpd I. The rate-determining step was identified to be the first N-oxidation of primary amine.

C-H bond functionalization under metalation-deprotonation process: regioselective direct arylation of 3-aminoimidazo[1,2-a]pyrazine.

Concerted metalation deprotonation (CMD) approach with appropriate proton shuttle precursor, base, and solvent (PivOH-K(2)CO(3)-toluene) has rendered a regioselective Pd-catalyzed C6-arylation of 3-aminoimidazo[1,2-a]pyrazine, a therapeutically relevant scaffold accessible by multicomponent reaction. The arylation of this heteroarene suffers from competing C5 and C2'-arylation reactions, while the developed process has virtually eliminated these competing arylations. Density functional calculations for CMD C-H activation at C6, C5, C8, and C2' sites imply that the energy barrier with distortion energy penalty as major contributing component influences the regioselectivity.

Density functional study on the cytochrome-mediated S-oxidation: identification of crucial reactive intermediate on the metabolic path of thiazolidinediones.

S-Oxidation is an important cytochrome P450 (CYP450)-catalyzed reaction, and the structural and energetic details of this process can only be studied by using quantum chemical methods. Thiazolidinedione (TZD) ring metabolism involving initial S-oxidation leads to the generation of reactive metabolites (RMs) and subsequent toxicity forcing the withdrawal of the glitazone class of drugs, thus, the study of the biochemical pathway of TZD ring metabolism is a subject of interest. The S-oxidation of the TZD ring and the formation of the isocyanate intermediate (ISC) was implicated as a possible pathway; however, there are several questions still unanswered in this biochemical pathway. The current study focuses on the CYP450-mediated S-oxidation, fate of the sulfoxide product (TZDSO), ring cleavage to ISC, and formation of nucleophilic adducts. The process of S-oxidation was explored by using Cpd I (iron(IV)-oxo porphyrin, to mimic CYP450) at TZVP/6-311+G(d) basis set. The barriers were calculated after incorporating dispersion and solvent corrections. The metabolic conversion from TZDSO to ISC (studied at B3LYP/6-311++G(2df,3pd)//B3LYP/6-31+G(d)) required a novel protonated intermediate, TZDSOH(+). The effect of higher basis sets (6-311+G(d,p), aug-cc-pvqz) on this conversion was studied. TZDSOH(+) was observed to be more reactive and thermodynamically accessible than ISC, indicating that TZDSOH(+) is the actual reactive intermediate leading to toxicity of the TZD class of compounds.

S-oxidation of thiazolidinedione with hydrogen peroxide, peroxynitrous acid, and C4a-hydroperoxyflavin: a theoretical study.

Quantum chemical analysis was carried out to model metabolism of glitazone class of drugs through oxygen transfer process to the sulfur atom of thiazolidinedione ring with different oxidants such as H(2)O(2), HOONO, and C4a-hydroperoxyflavin. Complete optimization (geometric and energy parameters) of all the required structures and transition states on the reaction path was carried out using MP2(full)/6-31+G(d,p). Charge and second-order delocalization analyses of important structures were carried out using the NBO method. The effect of solvent on the oxygen transfer to sulfur of thiazolidinedione was studied by including one, two, or three explicit water molecules. These calculations revealed that explicit solvent (water) effectively contributed in the sulfoxidation of thiazolidinedione and led to remarkable reduction in the energy barrier by ∼10 kcal/mol as compared to the gas phase. These results were found to be consistent with previously reported S-oxidation of dimethyl sulfide. When explicit water molecules were included, solvent molecules stabilize the charge separation at the transition state via specific interactions, and oxidation occurs via stretching of the O-O bond of oxidants and gradual formation of S-O bond. This study is helpful in understanding the metabolite generation due to the S-oxidation process in the glitazone series of antidiabetic drugs under physiological conditions.

Mechanochemical click reaction as a tool for making carbohydrate-based triazole-linked self-assembling materials (CTSAMs).

Various glycosides in which glycosylated triazole residues are anchored on to a central phenyl ring have been prepared under green reaction conditions by a solvent-free mechanochemical method. Some of the glycosides exhibited the ability to form gels when in contact with long chain hydrocarbons, e.g. hexane, heptane and octane, and this property was phase-selective. Thus, from a mixture of hexane-water, the compounds preferably absorbed the alkane to form a gel. The gelation ability was found to increase with an increasing number of substituents on the phenyl ring but only up to tetra-substitution. The hexa-substituted phenyl derivative did not swell in the hydrocarbon solvents investigated. The spontaneous self-assembling properties of these compounds in hexane have been investigated by transmission electron microscopy (TEM). Molecular modelling was used to optimize the structural geometry of these carbohydrate-based triazole-linked self-assembling materials (CTSAMs) and to rationalize their behaviour.