Improved Prediction of CYP2D6 Catalyzed Drug Metabolism by Taking Variant Substrate Specificities and Novel Polymorphic Haplotypes into Account

Abstract

The polymorphic CYP2D6 enzyme plays a pivotal role in the metabolism of approximately 25% of clinically prescribed drugs. However, the impact of specific genetic variants on the interindividual variability in CYP2D6-mediated drug metabolism remains insufficiently quantified. This translational study sought to address this gap by analyzing the genotypes and phenotypes of patients in two large clinical cohorts, focusing on the metabolism of the CYP2D6 substrates risperidone and desmethyltamoxifen. The analysis incorporated novel polymorphic haplotypes and substrate-specific differences among the CYP2D6.1, CYP2D6.2, and CYP2D6.35 enzyme variants. The study revealed that CYP2D6.2 and CYP2D6.35 exhibit reduced metabolic capacity for these substrates, both in vivo and in an in vitro expression model. This was evidenced by decreased catalytic turnover (Kcat), decreased substrate affinity, and altered substrate docking. Furthermore, novel polymorphic haplotypes on the CYP2D6*1, CYP2D6*2, and CYP2D6*35 backgrounds were identified, each associated with a 30-40% increase in CYP2D6 activity. Incorporating these findings into prediction equations significantly improved the genetic prediction accuracy (R²) for CYP2D6-mediated metabolism of desmethyltamoxifen from 59% to 71% and risperidone, also metabolized by CYP3A4, from 42% to 46%. These results highlight the importance of accounting for drug-specific interactions with enzyme variants and integrating distinct polymorphic haplotypes into CYP pharmacogenomic models and guidelines for better translation into clinical practice.

Figure 1

Effect of CYP2D6.2/CYP2D6.35 vs. CYP2D6.1. Effect of CYP2D6.2/CYP2D6.35 vs. CYP2D6.1 on (a) log ratio [endoxifen]/[desmethyltamoxifen] and log ratio [9‐hydroxyrisperidone]/[risperidone] and on (b) endoxifen and 9‐hydroxyrisperidone levels.

Figure 2

Kinetic analysis of different CYP2D6 enzyme variants. Kinetic analysis of the metabolism of (a) bufuralol, risperidone, and desmethyltamoxifen catalyzed by the different CYP2D6 enzyme variants. Graphs from representative experiments are shown. (b) Binding of desmethyltamoxifen and risperidone to the CYP2D6.1, CYP2D6.2, and CYP2D6.35 variants. Structures of desmethyltamoxifen and risperidone binding to CYP2D6 and its variant enzymes were analyzed using molecular docking as described under Methods. The active site of CYP2D6 is highlighted in the surface with the rainbow spectrum, and the substrate is shown in a red stick. The figure indicates the different modes of substrate binding for each of the CYP2D6 variants.

Figure 3

Schematic representation of the distribution of haplotypes identified on chromosome 22. Schematic representation of the genomic distribution of haplotypes identified on chromosome 22. Haplotypes B1, C2, E, J1, L, and O1. Marked red were significant for log M/P [desmethyltamoxifen]/[endoxifen] among carriers of CYP2D6*1, CYP2D6*2, and CYP2D6*35. Red dots indicate the localization of the significant SNPs from the GWAS that were not grouped into haplotypes.

Figure 4

Effect of haplotypes on log [endoxifen]/[desmethyltamoxifen] ratio. Effect of haplotypes J1, L, C2, E, B1, and O1 on log [endoxifen]/[desmethyltamoxifen] ratio in patients carrying CYP2D6*1 and being heterozygous for CYP2D6*2 or CYP2D6*35. ***P < 0.001, **P < 0.01, *P < 0.05 according to Mann–Whitney U test.

Figure 5

Evaluation of the CYP2D6*2 and CYP2D6*35 haplotype desmethyltamoxifen activity score. Evaluation of the CYP2D6*2 and CYP2D6*35 haplotype activity score based on the desmethyltamoxifen product‐to‐substrate ratio and its relevance to the prediction of CYP2D6 metabolic capacity by CYP2D6 genotype. The improvement in the prediction of the desmethyltamoxifen product‐to‐substrate ratio by CYP2D6 genotype if activity scores for CYP2D6 alleles were revised as provided in Table 3 is illustrated on the plot showing (a) the prediction power based on activity scores taken as currently suggested by the CPIC guidelines, (b) the presently proposed revised activity scores, (c) the presently proposed revised activity scores with discrimination between carriers and non‐carriers of J Haplotype among *2 and *35 carriers.

Figure 6

Evaluation of the CYP2D6*2 and CYP2D6*35 haplotype risperidone activity score. Evaluation of the CYP2D6*2 and CYP2D6*35 haplotype activity score based on risperidone product‐to‐substrate ratios and its relevance to the prediction of CYP2D6 metabolic capacity by CYP2D6 genotype. The improvement in the prediction of the risperidone product‐to‐substrate ratio by CYP2D6 genotype if activity scores for CYP2D6 alleles were revised as provided in Table 1 is illustrated in the plot showing (a) the prediction power based on activity scores taken as currently suggested by the CPIC guidelines, (b) the presently proposed revised activity scores.