Mechanism of Selective Aromatic Hydroxylation in the Metabolic Transformation of Paclitaxel Catalyzed by Human CYP3A4.

Paclitaxel (PTX) is heralded as one of the most successful natural-product drugs for the treatment of refractory cancers. In humans, the hepatic metabolic transformation of PTX is primarily mediated by two cytochrome P450 enzymes (P450s): CYP3A4 and CYP2C8. The impact of P450 metabolism on the anticancer effectiveness of PTX is significant. However, the precise mechanism underlying selective P450-catalyzed reactions in PTX metabolism remains elusive. To address this knowledge gap, we conducted molecular docking and molecular dynamics simulations using multiple crystal structures of CYP3A4, which originally contained other ligands. These methods enabled us to determine the most plausible binding structure of PTX within the enzyme. By further employing hybrid quantum mechanics and molecular mechanics calculations, we successfully identified two primary pathways for the reaction between compound I (Cpd I) of CYP3A4 and PTX. One of these pathways involves the formation of an epoxide, while the other proceeds through a ketone intermediate.

The Bonding Nature of Fe-CO Complexes in Heme Proteins.

Although carbon monoxide (CO) has been known to bind to the ferrous heme in cytochrome P450 enzymes (P450s) since the earliest days of P450 research, details on the nature of the ferrous-CO bonding remain elusive. This study employed dispersion-corrected density functional theory (DFT) calculations and DFT-based theoretical analyses to investigate the complexes between CO and a thiolate- or imidazole-ligated heme that contains ferric or ferrous iron. Traditionally, the ferrous-CO bonding in heme systems has been interpreted qualitatively in terms of σ donation and π backdonation. Complementary occupied-virtual orbital pair (COVP) analysis yielded one orbital pair for σ donation and two for π backdonation together with the specific magnitude of their energetic contributions. The charge-transfer effect for these three orbital pairs has nearly the same energetic significance in the ferrous-CO complexes. Therefore, in total, the π-backdonation effect is much greater than the σ-donation effect. In contrast, the σ-donation effect is more significant in the ferric-CO complex because of the less efficient π backdonation. The nature of ferric-CO and ferrous-CO bonding was further scrutinized using the generalized Kohn-Sham energy decomposition analysis (GKS-EDA) scheme, whose results highlighted the significance of various effects in enhancing the Fe-CO bonding for the thiolate- and imidazole-ligated heme groups. In particular, the intrinsic repulsion effect plays a crucial role in promoting the preferential binding of CO toward the ferrous heme and in determining the geometry of the complexes.