Ligand diversity of human and chimpanzee CYP3A4: activation of human CYP3A4 by lithocholic acid results from positive selection

The Functional Comparison of Eukaryotic Proteomes: Implications for Choosing an Appropriate Model Organism to Probe Human Biology

Phenotypic differences between species are, in significant part, determined by their proteomic diversity. The link between proteomic and phenotypic diversity can be best understood in the context of the various pathways and biological processes in which proteins participate. While the conservation pattern for individual proteins across species is expected to follow the phylogenetic relationships among the species, the diversity patterns of individual pathways may not: certain pathways may be much more conserved among distantly related species than two closely related species, owing to the ecological histories of the species. Thus, a pathway-centric analysis of proteome conservation and diversity has important implications for the appropriate choice of a model organism when investigating specific aspects of human biology. Exploiting the complete genome sequences and protein-coding gene annotations, here we perform a comprehensive gene-set-centric analysis of proteomic diversity between humans and 54 eukaryotic organisms, resulting in a catalog of organisms that are most similar to humans in terms of specific pathways, processes, expression patterns, and diseases. We corroborate our findings using species-specific mass spectrometry data.Our analysis provides a general framework to identify conserved and unique pathways in a group of organisms and a resource to prioritize appropriate model systems to study a specific biological system in a reference organism such as humans.

Hepatic expression of cytochrome P450 enzymes in non-human primate species

Cytochromes P450 (P450) largely remain to be characterized in great apes. Comparative immunochemical detection of drug metabolizing forms of P450s 1A, 2A, 2B, 2C, 2D, 2E, 2J, 3A, 4A, and 4F in liver microsomes from chimpanzees, gorillas, orangutans, gibbons, cynomolgus and rhesus macaques, and common marmosets were carried out.

Enhanced methamphetamine metabolism in rhesus macaque as compared with human: an analysis using a novel method of liquid chromatography with tandem mass spectrometry, kinetic study, and substrate docking

Methamphetamine (MA), which remains one of the widely used drugs of abuse, is metabolized by the cytochrome P450 (P450) family of enzymes in humans. However, metabolism of methamphetamine in macaques is poorly understood. Therefore, we first developed and validated a very sensitive liquid chromatography with tandem mass spectrometry (LC-MS/MS) method using solid phase extraction of rhesus plasma with a lower limit of quantitation at 1.09 ng/ml for MA and its metabolites, 4-hydroxy methamphetamine (4-OH MA), amphetamine (AM), 4-OH amphetamine (4-OH AM), and norephedrine. We then analyzed plasma samples of MA-treated rhesus, which showed >10-fold higher concentrations of AM (∼29 ng/ml) and 4-OH AM (∼28 ng/ml) than MA (∼2 ng/ml). Because the plasma levels of MA metabolites in rhesus were much higher than in human samples, we examined MA metabolism in human and rhesus microsomes. Interestingly, the results showed that AM and 4-OH AM were formed more rapidly and that the catalytic efficiency (Vmax/Km) for the formation of AM was ∼8-fold higher in rhesus than in human microsomes. We further examined the differences in these kinetic characteristics using three selective inhibitors of each human CYP2D6 and CYP3A4 enzymes. The results showed that each of these inhibitors inhibited both d- and l-MA metabolism by 20%-60% in human microsomes but not in rhesus microsomes. The differences between human and rhesus CYP2D6 and CYP3A4 enzymes were further assessed by docking studies for both d and l-MA. In conclusion, our results demonstrated an enhanced MA metabolism in rhesus compared with humans, which is likely to be caused by differences in MA-metabolizing P450 enzymes between these species.