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 <b>Cpd I</b> (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 <b>Cpd I</b> (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 d_<i>z</i>² orbital of heme-iron. This was aided by the back-bonding between filled d_<i>xz</i> 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

Density Functional Study on the Cytochrome-Mediated <i>S</i>‑Oxidation: Identification of Crucial Reactive Intermediate on the Metabolic Path of Thiazolidinediones

<i>S</i>-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 (<b>TZD</b>) ring metabolism involving initial <i>S</i>-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 <b>TZD</b> ring metabolism is a subject of interest. The <i>S</i>-oxidation of the <b>TZD</b> ring and the formation of the isocyanate intermediate (<b>ISC</b>) 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 <i>S</i>-oxidation, fate of the sulfoxide product (<b>TZDSO</b>), ring cleavage to <b>ISC</b>, and formation of nucleophilic adducts. The process of <i>S</i>-oxidation was explored by using <b>Cpd I</b> (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 <b>TZDSO</b> to <b>ISC</b> (studied at B3LYP/6-311++G­(2df,3pd)//B3LYP/6-31+G­(d)) required a novel protonated intermediate, <b>TZDSOH</b>^<b>+</b>. The effect of higher basis sets (6-311+G­(d,p), aug-cc-pvqz) on this conversion was studied. <b>TZDSOH</b>^<b>+</b> was observed to be more reactive and thermodynamically accessible than <b>ISC</b>, indicating that <b>TZDSOH</b>^<b>+</b> is the actual reactive intermediate leading to toxicity of the <b>TZD</b> class of compounds

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 <b>Cpd I</b> [(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 <b>Cpd I</b>. 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 <i>S</i>-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

C–H Bond Functionalization Under Metalation–Deprotonation Process: Regioselective Direct Arylation of 3‑Aminoimidazo[1,2‑<i>a</i>]pyrazine

Concerted metalation deprotonation (CMD) approach with appropriate proton shuttle precursor, base, and solvent (PivOH–K₂CO₃–toluene) has rendered a regioselective Pd-catalyzed C6-arylation of 3-aminoimidazo­[1,2-<i>a</i>]­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

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-<i>O</i>-benzylated thioglycosides on grinding with an acceptor sugar in the presence of In­(OTf)₃ yield the corresponding <i>O</i>-glycosides efficiently. The latter in the case of a difficult secondary alcohol was nearly exclusive (>98%) in 1,2-<i>cis</i>-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 β-d-galactopyranosides observed by TEM could be rationalized by molecular modeling