Enzyme Kinetics of Oxidative Metabolism-Cytochromes P450

Understanding Cytochrome P450 Enzyme Substrate Inhibition and Prospects for Elimination Strategies

Cytochrome P450 (CYP450) enzymes, which are widely distributed and pivotal in various biochemical reactions, catalyze diverse processes such as hydroxylation, epoxidation, dehydrogenation, dealkylation, nitrification, and bond formation. These enzymes have been applied in drug metabolism, antibiotic production, bioremediation, and fine chemical synthesis. Recent research revealed that CYP450 catalytic kinetics deviated from the classic Michaelis-Menten model. A notable substrate inhibition phenomenon that affects the catalytic efficiency of CYP450 at high substrate concentrations was identified. However, the substrate inhibition of various reactions catalyzed by CYP450 enzymes have not been comprehensively reviewed. This review describes CYP450 substrate inhibition examples and atypical Michaelis-Menten kinetic models, and provides insight into mechanisms of these enzymes. We also reviewed 3D structure and dynamics of CYP450 with substrate binding. Outline methods for alleviating substrate inhibition in CYP450 and other enzymes, including traditional fermentation approaches and protein engineering modifications. The comprehensive analysis presented in this study lays the foundation for enhancing the catalytic efficiency of CYP450 by deregulating substrate inhibition.

Drug transporters in drug disposition - highlights from the year 2023

Drug transporter field is rapidly evolving with significant progress in in vitro and in vivo tools and, computational models to assess transporter-mediated drug disposition and drug-drug interactions (DDIs) in humans. On behalf of all coauthors, I am pleased to share the fourth annual review highlighting articles published and deemed influential in the field of drug transporters in the year 2023. Each coauthor independently selected peer-reviewed articles published or available online in the year 2023 and summarized them as shown previously (Chothe et al. 2021; Chothe et al. 2022, 2023) with unbiased perspectives. Based on selected articles, this review was categorized into four sections: (1) transporter structure and in vitro evaluation, (2) novel in vitro/ex vivo models, (3) endogenous biomarkers, and (4) PBPK modeling for evaluating transporter DDIs (Table 1). As the scope of this review is not to comprehensively review each article, readers are encouraged to consult original paper for specific details. Finally, I appreciate all the authors for their time and continued support in writing this review.

Atypical kinetics of cytochrome P450 enzymes in pharmacology and toxicology

Atypical kinetics are observed in metabolic reactions catalyzed by cytochrome P450 enzymes (P450). Yet, this phenomenon is regarded as experimental artifacts in some instances despite increasing evidence challenging the assumptions of typical Michaelis-Menten kinetics. As P450 play a major role in the metabolism of a wide range of substrates including drugs and endogenous compounds, it becomes critical to consider the impact of atypical kinetics on the accuracy of estimated kinetic and inhibitory parameters which could affect extrapolation of pharmacological and toxicological implications. The first half of this book chapter will focus on atypical non-Michaelis-Menten kinetics (e.g. substrate inhibition, biphasic and sigmoidal kinetics) as well as proposed underlying mechanisms supported by recent insights in mechanistic enzymology. In particular, substrate inhibition kinetics in P450 as well as concurrent drug inhibition of P450 in the presence of substrate inhibition will be further discussed. Moreover, mounting evidence has revealed that despite the high degree of sequence homology between CYP3A isoforms (i.e. CYP3A4 and CYP3A5), they have the propensities to exhibit vastly different susceptibilities and potencies of mechanism-based inactivation (MBI) with a common drug inhibitor. These experimental observations pertaining to the presence of these atypical isoform- and probe substrate-specific complexities in CYP3A isoforms by several clinically-relevant drugs will therefore be expounded and elaborated upon in the second half of this book chapter.

The Hydroxylation Position Rather than Chirality Determines How Efavirenz Metabolites Activate Cytochrome P450 46A1 In Vitro

(S)-Efavirenz (EFV) is a reverse transcriptase inhibitor and an antiviral drug. In addition, (S)-EFV can interact off target with CYP46A1, the major cholesterol hydroxylating enzyme in the mammalian brain, and allosterically activate CYP46A1 at a small dose in mice and humans. Studies with purified CYP46A1 identified two allosteric sites on the enzyme surface, one for (S)-EFV and the second site for L-glutamate (Glu), a neurotransmitter that also activates CYP46A1 either alone or in the presence of (S)-EFV. Previously, we found that racemic (rac)-7-hydroxyefavirenz, (rac)-8-hydroxyefavirenz, (S)-8-hydroxyefavirenz, and (rac)-8,14-dihydroxyefavirenz, compounds with the hydroxylation positions corresponding to the metabolism of (S)-EFV in the liver, activated CYP46A1 in vitro. Yet, these compounds differed from (S)-EFV in how they allosterically interacted with CYP46A1. Herein, we further characterized (rac)-7-hydroxyefavirenz, (rac)-8-hydroxyefavirenz, (S)-8-hydroxyefavirenz, and (rac)-8,14-dihydroxyefavirenz, and, in addition, (R)-EFV, (S)-7-hydroxyefavirenz, (rac)-7,8-dihydroxyefavirenz, (S)-7,8-dihydroxyefavirenz, and (S)-8,14-dihydroxyefavirenz for activation and binding to CYP46A1 in vitro. We found that the spatial configuration of all tested compounds neither affected the CYP46A1 activation nor the sites of binding to CYP46A1. Yet, the hydroxylation position determined whether the hydroxylated metabolite interacted with the allosteric site for (S)-EFV [(R)-EFV, (rac)-7,8-dihydroxyefavirenz, and (S)-7,8-dihydroxyefavirenz], L-Glu [(rac)- and (S)-8,14-dihydroxyefavirenz], or both [(rac)-7-hydroxyefavirenz, (S)-7-hydroxyefavirenz, (rac)-8-hydroxyefavirenz, and (S)-8-hydroxyefavirenz]. This difference in binding to the allosteric sites determined, in turn, how CYP46A1 activity was changed in the coincubations with (S)-EFV and either its metabolite or L-Glu. The results suggest EFV metabolites that could be more potent for CYP46A1 activation in vivo than (S)-EFV. SIGNIFICANCE STATEMENT: This study found that not only efavirenz but also all its hydroxylated metabolites allosterically activate CYP46A1 in vitro. The enzyme activation depended on the hydroxylation position but not the metabolite spatial configuration and involved either one or two allosteric sites-for efavirenz, L-glutamate, or both. The results suggest that the hydroxylated efavirenz metabolites may differ from efavirenz in how they interact with the CYP46A1 allosteric and active sites.

Midazolam as a Probe for Heterotropic Drug-Drug Interactions Mediated by CYP3A4

Human cytochrome P450 CYP3A4 is involved in the processing of more than 35% of current pharmaceuticals and therefore is responsible for multiple drug-drug interactions (DDI). In order to develop a method for the detection and prediction of the possible involvement of new drug candidates in CYP3A4-mediated DDI, we evaluated the application of midazolam (MDZ) as a probe substrate. MDZ is hydroxylated by CYP3A4 in two positions: 1-hydroxy MDZ formed at lower substrate concentrations, and up to 35% of 4-hydroxy MDZ at high concentrations. The ratio of the formation rates of these two products (the site of metabolism ratio, SOM) was used as a measure of allosteric heterotropic interactions caused by effector molecules using CYP3A4 incorporated in lipid nanodiscs. The extent of the changes in the SOM in the presence of effectors is determined by chemical structure and is concentration-dependent. MD simulations of CYP3A4 in the lipid bilayer suggest that experimental results can be explained by the movement of the F-F' loop and concomitant changes in the shape and volume of the substrate-binding pocket. As a result of PGS binding at the allosteric site, several residues directly contacting MDZ move away from the substrate molecule, enabling the repositioning of the latter for minor product formation.

Complex Cytochrome P450 Kinetics Due to Multisubstrate Binding and Sequential Metabolism. Part 1. Theoretical Considerations

Complexities in P450-mediated metabolism kinetics include multisubstrate binding, multiple-product formation, and sequential metabolism. Saturation curves and intrinsic clearances were simulated for single-substrate and multisubstrate models using derived velocity equations and numerical solutions of ordinary differential equations (ODEs). Multisubstrate models focused on sigmoidal kinetics because of their dramatic impact on clearance predictions. These models were combined with multiple-product formation and sequential metabolism, and simulations were performed with random error. Use of single-substrate models to characterize multisubstrate data can result in inaccurate kinetic parameters and poor clearance predictions. Comparing results for use of standard velocity equations with ODEs clearly shows that ODEs are more versatile and provide better parameter estimates. It would be difficult to derive concentration-velocity relationships for complex models, but these relationships can be easily modeled using numerical methods and ODEs. SIGNIFICANCE STATEMENT: The impact of multisubstrate binding, multiple-product formation, and sequential metabolism on the P450 kinetics was investigated. Numerical methods are capable of characterizing complicated P450 kinetics.