Probing functional interactions between cytochromes P450 with principal component analysis of substrate saturation profiles and targeted proteomics

High-Throughput Assay of Cytochrome P450-Dependent Drug Demethylation Reactions and Its Use to Re-Evaluate the Pathways of Ketamine Metabolism

In a search for a reliable, inexpensive, and versatile technique for high-throughput kinetic assays of drug metabolism, we elected to rehire an old-school approach based on the determination of formaldehyde (FA) formed in cytochrome P450-dependent demethylation reactions. After evaluating several fluorometric techniques for FA detection, we chose the method based on the Hantzsch reaction with acetoacetanilide as the most sensitive, robust, and adaptable to high-throughput implementation. Here we provide a detailed protocol for using our new technique for automatized assays of cytochrome P450-dependent drug demethylations and discuss its applicability for high-throughput scanning of drug metabolism pathways in the human liver. To probe our method further, we applied it to re-evaluating the pathways of metabolism of ketamine, a dissociative anesthetic and potent antidepressant increasingly used in the treatment of alcohol withdrawal syndrome. Probing the kinetic parameters of ketamine demethylation by ten major cytochrome P450 (CYP) enzymes, we demonstrate that in addition to CYP2B6 and CYP3A enzymes, which were initially recognized as the primary metabolizers of ketamine, an important role is also played by CYP2C19 and CYP2D6. At the same time, the involvement of CYP2C9 suggested in the previous reports was deemed insignificant.

Deciphering Microbial Diversity and Functional Codes of Traditional Fermented Whole Grain Tianpei from Typical Regions of China

Whole grains are a crucial part of healthy and sustainable diets, attracting great attention. Tianpei is a popular traditional fermented whole grain food and beverage from China. It is suitable for all ages with lots of health benefits. However, its microflora and their functions, relations between microbial taxa and functions with Tianpei properties, were still little informed, limiting the fermentation optimization and quality improvement. In this study, the characteristics and distribution of the microbial flora taxa and their functions of the fermented whole grain Tianpei from typical regions of China were mainly deciphered through metagenomic methods. Phyla Mucoromycota, Firmicutes, Ascomycota, and Proteobacteria were the most abundant. Rhizopus, Limosilactobacillus, and Lactobacillus were the most abundant genera. Microbial COG functions carbohydrate transport and metabolism (mainly including fructose, galactose, glucose, L-arabinose, and mannose) and amino acid transport and metabolism (mainly including arginine, asparagine, glutamine, and glycine) kept a high abundance. PCA (Principal Component Analysis) illustrated that the microbial community and their functions of every Tianpei sample clustered individually based on the analysis, NR, related with the factors of raw material and sources. The microbial taxa, microbial functions, and the Tianpei properties were significantly correlated. Rhizopus, Limosilactobacillus, and Lactobacillus contributed most COG functions in Tianpei samples. Analysis of quorum sensing, pfam, secretion protein, probio, and cytochromes P450 were also annotated and found among Tianpei microbial communities. A sum of 105 probiotics were classified, mainly belonging to Lactobacillus, Leuconostoc, Acetobacter, Bacillus, Bifidobacterium, Pediococcus, etc. Tianpei samples made in the library with the most abundant and functional microbial key taxa strains—Rhizophus oryzae, Lactobacillus plantarum, and Limosilactobacillus fermentum—showed rich nutrient chemicals. The results indicate that microbial taxa and their functions could determine Tianpei properties. Thus, the quality /nutrients, flavor, and industrial production of Tianpei could be further investigated, promoted, and improved in the future based on the characteristics of these microbial taxa and their functions, such as the regulations of the main carbohydrate and AA. The study will also lay a foundation for the fermentative characteristics and condition technology of fermented whole grain food.

Exploring the Interactome of Cytochrome P450 2E1 in Human Liver Microsomes with Chemical Crosslinking Mass Spectrometry

Aiming to elucidate the system-wide effects of the alcohol-induced increase in the content of cytochrome P450 2E1 (CYP2E1) on drug metabolism, we explored the array of its protein-protein interactions (interactome) in human liver microsomes (HLM) with chemical crosslinking mass spectrometry (CXMS). Our strategy employs membrane incorporation of purified CYP2E1 modified with photoreactive crosslinkers benzophenone-4-maleimide and 4-(N-succinimidylcarboxy)benzophenone. Exposure of bait-incorporated HLM samples to light was followed by isolating the His-tagged bait protein and its crosslinked aggregates on Ni-NTA agarose. Analyzing the individual bands of SDS-PAGE slabs of thereby isolated protein with the toolset of untargeted proteomics, we detected the crosslinked dimeric and trimeric complexes of CYP2E1 with other drug-metabolizing enzymes. Among the most extensively crosslinked partners of CYP2E1 are the cytochromes P450 2A6, 2C8, 3A4, 4A11, and 4F2, UDP-glucuronosyltransferases (UGTs) 1A and 2B, fatty aldehyde dehydrogenase (ALDH3A2), epoxide hydrolase 1 (EPHX1), disulfide oxidase 1α (ERO1L), and ribophorin II (RPN2). These results demonstrate the exploratory power of the proposed CXMS strategy and corroborate the concept of tight functional integration in the human drug-metabolizing ensemble through protein-protein interactions of the constituting enzymes.

Assembling the P450 puzzle: on the sources of nonadditivity in drug metabolism

There is an increasing number of indications of an oversimplification in the premise that the cumulative properties of the human drug-metabolizing ensemble represent a simple aggregate of the properties of the constituting enzymes. Recent studies of the functional effects of hetero-association of multiple cytochrome P450 species and their interactions with metabolically related enzymes revealed a tight integration in the drug-metabolizing ensemble. In our opinion, the sources of interindividual variability in drug metabolism can be elucidated only when considering this ensemble as a multienzyme system, the functional parameters of which are determined by interactions between its constituents. In this article, we present a conceptual model providing a mechanistic explanation for the functional effects of the interactions between multiple P450 species and propose a clue to understanding the nonadditive behavior of the drug-metabolizing ensemble.

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.