Detoxification of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) by cytochrome P450 enzymes: A theoretical investigation

How does multiple substrate binding lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan? A theoretical study

CYP2D6 is one of the most important metalloenzymes involved in the biodegradation of many drug molecules in the human body. It has been found that multiple substrate binding can lead to substrate inhibition of CYP2D6 metabolizing dextromethorphan (DM), but the corresponding theoretical mechanism is rarely reported. Therefore, we chose DM as the probe and performed molecular dynamics simulations and quantum mechanical calculations on CYP2D6-DM systems to investigate the mechanism of how the multiple substrate binding leads to the substrate inhibition of CYP2D6 metabolizing substrates. According to our results, three gate residues (Arg221, Val374, and Phe483) for the catalytic pocket are determined. We also found that the multiple substrate binding can lead to substrate inhibition by reducing the stability of CYP2D6 binding DM and increasing the reactive activation energy of the rate-determining step. Our findings would help to understand the substrate inhibition of CYP2D6 metabolizing the DM and enrich the knowledge of the drug-drug interactions for the cytochrome P450 superfamily.

Oxidative N-Dealkylation of N,N-Dimethylanilines by Non-Heme Manganese Catalysts

Non-heme manganese(II) complexes [(IndH)MnIICl2] (1) and [(N4Py*)MnII(CH3CN)](ClO4)2 (2) with tridentate isoindoline and pentadentate polypyridyl ligands (IndH = 1,3-bis(2′-pyridylimino)isoindoline; N4Py* = N,N-bis(2-pyridylmethyl)-1,2- di(2-pyridyl)ethylamine) proved to be suitable to catalyze the oxidative demethylation of N,N-dimethylaniline (DMA) with various oxidants such as tert-butyl hydroperoxide (TBHP), peracetic acid (PAA), and meta-chloroperoxybenzoic acid (mCPBA), resulting N-methylaniline (MA) as a main product with N-methylformanilide (MFA) as a result of a free-radical chain process under air. The effect of electron-donating and electron-withdrawing substituents on the aromatic ring on the relative reactivity of the substrates and on the product composition (MA/MFA) was also studied and showed a significant impact on the catalytic N-demethylation reaction. Based on the Hammett correlation with ρ = −0.38 (PAA), −0.45 (mCPBA), and −0.63 (TBHP) for 1 and ρ = −0.38 (PAA) and −0.37 (mCPBA) for 2, an electrophilic intermediate is suggested as the key oxidant. Furthermore, the spectral investigation (UV-Vis) resulted in direct evidence for the formation of a high-valent oxomanganese(IV) and a transient radical cation intermediate, p-Me-DMA•+, suggesting that the initial step in the manganese-catalyzed oxidations is a fast electron-transfer between the amine and the high valent oxometal species. The mechanisms of the subsequent steps are discussed.

Which is the real oxidant in the competitive ligand self-hydroxylation and substrate oxidation, a biomimetic iron(II)-hydroperoxo species or an oxo-iron(IV)-hydroxy one?

Nonheme iron(II)-hydroperoxo species (FeII-(η2-OOH)) 1 and the concomitant oxo-iron(IV)-hydroxyl one 2 are proposed as the key intermediates of a large class of 2-oxoglutarate dependent dioxygenases (e.g., isopenicillin N synthase). Extensive...

Theoretical Investigation on the Elusive Reaction Mechanism of Spirooxindole Formation Mediated by Cytochrome P450s: A Nascent Feasible Charge-Shift C-O Bond Makes a Difference

Spirooxindoles are pivotal biofunctional groups widely distributed in natural products and clinic drugs. However, construction of such subtle chiral skeletons is a long-standing challenge to both organic and bioengineering scientists. The knowledge of enzymatic spirooxindole formation in nature may inspire rational design of new catalysts. To this end, we presented a theoretical investigation on the elusive mechanism of the spiro-ring formation at the 3-position of oxindole mediated by cytochrome P450 enzymes (P450). Our calculated results demonstrated that the electrophilic attack of CpdI, the active species of P450, to the substrate, shows regioselectivity, i.e., the attack at the C9 position forms a tetrahedral intermediate involving an unusual feasible charge-shift C9^δ+-O^δ- bond, while the attack at the C1 position forms an epoxide intermediate. The predominant route is the first route with the charge-shift bonding intermediate due to holding a relatively lower barrier by >5 kcal mol^-1 than the epoxide route, which fits the experimental observations. Such a delocalized charge-shift bond facilitates the formation of a spiro-ring mainly through elongation of the C1-C9 bond to eliminate the aromatization of the tricyclic beta-carboline. Our theoretical results shed profound mechanistic insights for the first time into the elusive spirooxindole formation mediated by P450s.

Metabolic activation mechanism of 2,2',3,3',6,6'-hexachlorobiphenyl (PCB136) by cytochrome P450 2B6: A QM/MM approach

Cytochrome P450 enzymes (CYPs) play an essential role in the bio-transformation of polychlorinated biphenyls (PCBs). The present work implemented quantum mechanic/molecular mechanic methods (QM/MM) and density functional theory (DFT) to study the metabolic activation of 2,2',3,3',6,6'-hexachlorobiphenyl (PCB136) catalyzed by CYP2B6. Electrophilic additions at the C^α and C^β positions generate different active intermediates. The electrophilic addition energy barrier of C^β is 10.9 kcal/mol higher than that of C^α, and C^α is the preferred site for the electrophilic addition reaction. Based on the previous experimental studies, this work investigated the mechanism of converting active intermediates into OH-PCB136, which has high toxicity in a non-enzymatic environment. Structural analysis via the electrostatic and noncovalent interactions indicates that Phe108, Ile114, Phe115, Phe206, Phe297, Ala298, Leu363, Val367, TIP32475 and TIP32667 play crucial roles in substrate recognition and metabolism. The analysis suggests that the halogen-π interactions are important factors for the metabolism of CYP2B6 to halogenated environmental pollutants. This work improved the understanding of the metabolism and activation process of chiral PCBs, and can be used as a guide to improve the microbial degradation efficiency of PCB136.

Interactive Regulation between Aliphatic Hydroxylation and Aromatic Hydroxylation of Thaxtomin D in TxtC: A Theoretical Investigation

TxtC is an unusual bifunctional cytochrome P450 that is able to perform sequential aliphatic and aromatic hydroxylation of the diketopiperazine substrate thaxtomin D in two distinct sites to produce thaxtomin A. Though the X-ray structure of TxtC complexed with thaxtomin D revealed a binding mode for its aromatic hydroxylation, the preferential hydroxylation site is aliphatic C₁₄. It is thus intriguing to unravel how TxtC accomplishes such two-step catalytic hydroxylation on distinct aliphatic and aromatic carbons and why the aliphatic site is preferred in the hydroxylation step. In this work, by employing molecular docking and molecular dynamics (MD) simulation, we revealed that thaxtomin D could adopt two different conformations in the TxtC active site, which were equal in energy with either the aromatic C₂₀-H or aliphatic C₁₄-H pointing toward the active Cpd I oxyferryl moiety. Further ONIOM calculations indicated that the energy barrier for the rate-limiting hydroxylation step on the aliphatic C₁₄ site was 9.6 kcal/mol more favorable than that on the aromatic C₂₀ site. The hydroxyl group on the monohydroxylated intermediate thaxtomin B C₁₄ site formed hydrogen bonds with Ser280 and Thr385, which induced the l-Phe moiety to rotate around the C_β-C_γ bond of the 4-nitrotryptophan moiety. Thus, it adopted an energetically favorable conformation with aromatic C₂₀ adjacent to the oxyferryl moiety. In addition, the hydroxyl group induced solvent water molecules to enter the active site, which propelled thaxtomin B toward the heme plane and resulted in heme distortion. Based on this geometrical layout, the rate-limiting aromatic hydroxylation energy barrier decreased to 15.4 kcal/mol, which was comparable to that of the thaxtomin D aliphatic hydroxylation process. Our calculations indicated that heme distortion lowered the energy level of the lowest Cpd I α-vacant orbital, which promoted electron transfer in the rate-limiting thaxtomin B aromatic hydroxylation step in TxtC.

Importance of substituents in ring opening: a DFT study on a model reaction of thiazole to thioamide

Thiazole ring is an important active molecular skeleton of drugs. Thiazole in natural products and drugs are usually harmlessly eliminated. However, hepatotoxic reactions may occur due to the biological activation of thiazole to produce reactive thioamide. A typical example is hepatotoxic sudoxicam and safety meloxicam. The only structural difference between them is a methyl group on C5 position of thiazole in meloxicam. The molecular basis for the difference remains unknown and the bioactivation mechanism of the thiazole ring is still obscure. Quantum chemical calculations were performed to elucidate the activation mechanism of the thiazole ring under P450 catalysis, and the influence of the substituents on the activation pathways of thiazole ring was also studied. The calculated results show that the activation of thiazole is closely related to the substituents on the thiazole and spin state of Cpd I. The thiazole and substituted thiazole directly open the ring when catalyzed by doublet spin state Cpd I that catalyzed by the quartet spin state Cpd I can open the ring directly or indirectly, which is related to the substituents. Thiazoles modified with electron-donating substituents mainly undergo direct ring opening, while thiazoles modified with electron-withdrawing groups or weak electron-donating groups mainly undergo indirect ring-opening process accompanied by intermediate formation. The research results laid the foundation for the design of thiazole ring drugs, and also laid a theoretical foundation for the study of reducing the toxicity of thiazole ring drugs.

Comparative metabolism of gelsenicine in liver microsomes from humans, pigs, goats and rats

RATIONALE

Gelsemium elegans (G. elegans) is highly toxic to humans and rats but has insecticidal and growth-promoting effects on pigs and goats. However, the mechanisms behind the toxicity differences of G. elegans are unclear. Gelsenicine, isolated from G. elegans, has been reported to be a toxic alkaloid.

METHODS

In this study, the in vitro metabolism of gelsenicine was investigated and compared for the first time using human (HLM), pig (PLM), goat (GLM) and rat (RLM) liver microsomes and high-performance liquid chromatography/mass spectrometry (HPLC/MS).

RESULTS

In total, eight metabolites (M1-M8) were identified by using high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (HPLC/QqTOF-MS). Two main metabolic pathways were found in the liver microsomes of the four species: demethylation at the methoxy group on the indole nitrogen (M1) and oxidation at different positions (M2-M8). M8 was identified only in the GLM. The degradation ratio of gelsenicine and the relative percentage of metabolites produced during metabolism were determined by high-performance liquid chromatography/tandem mass spectrometry (HPLC/QqQ-MS/MS). The degradation ratio of gelsenicine in liver microsomes decreased in the following order: PLM ≥ GLM > HLM > RLM. The production of M1 decreased in the order of GLM > PLM > RLM > HLM, the production of M2 was similar among the four species, and the production of M3 was higher in the HLM than in the liver microsomes of the other three species.

CONCLUSIONS

Based on these results, demethylation was speculated to be the main gelsenicine detoxification pathway, providing vital information to better understand the metabolism and toxicity differences of G. elegans among different species.

Theoretical study on the mechanism of N- and α-carbon oxidation of lapatinib catalyzed by cytochrome P450 monooxygenase

Lapatinib, an orally active dual tyrosine kinase inhibitor, is efficacious in combination therapy with capecitabine for advanced metastatic breast cancer. Despite its importance, it has been associated with hepatotoxicity observed in clinical trials and postmarketing surveillance. The mechanisms of hepatotoxicity at the chemical and cellular levels may link to drug metabolism. In this study, the N- and α-carbon oxidation processes of lapatinib catalyzed by CYP3A4 were explored by density functional theory method. The calculation results show that oxidation of C₆ is the primary metabolic process and carboxylic acid is the main metabolic product. Both hydroxylation of C₈ and subsequent formation of primary amines are feasible. However, it is not easy for the primary amines to form active metabolites nitroso, which indicates that there are other paths for the production of nitroso. Carboxylic acid is not the main metabolite of N₇ oxidation because of higher hydrolysis energy barrier of intermediate nitrone. It is worthy to study subsequent N-hydroxylation and its downstream reaction, which may be the main pathway for the formation of nitroso. These results lay the foundation for drug design and optimization.

Spin states of Mn(III) meso-tetraphenylporphyrin chloride assessed by density functional methods

The present work assessed several exchange-correlation functionals (including GGA, meta-GGA and hybrid functionals), in combination with a variety of basis sets and effective core potentials (ECP) for their ability to predict the ground spin state of Mn(III) meso-tetraphenylporphyrin chloride complex, labeled Mn(III)TPPCl, for which experimental data support the quintet high spin state. Geometry optimization of Mn(III)TPPCl was performed for three possible spin states (singlet state, LS; triplet state, IS; and quintet state, HS) at the TPSSh level using the LANL2DZ ECP for Mn and the 6-311G(d) basis set for C, N, Cl and H. Afterwards, single-point energy calculations were conducted by applying 18 exchange-correlation functionals (BLYP, B3LYP, PW91, BPW91, BP86, OLYP, OPBE, OPW91, O3LYP, PBE0, PBEh1PBE, HSEH1PBE, TPSS, TPSSh, M06 L, M06, M062X and M06HF). The influence of the basis set for the metal center was assessed using a smaller group of functionals and varying between the Pople basis set 6-31G(d), its newer formulation m6-31G(d) and the larger Def2-QZVP basis set. All functionals in combination with Pople basis sets predict the quintet state as the ground spin state. In addition, the BLYP, BP86, BPW91, PW91, PBEh1PBE, TPSS and TPSSh functionals predicted the IS lying at most ~60 kJ mol^-1 above the HS, which agrees with the reference data. Results including Def2-QZVP basis set were inconsistent, since only BLYP and B3LYP predict HS as the ground spin state. The recommended methodology for the treatment of such systems seems to be exchange-correlations functionals with few or none Hartree-Fock exchange and modest size basis sets. Graphical Abstract MnTPPCl molecule and the energy ordering of its spin states assessed by 18 functionals.