Computational insights into the different catalytic activities of CYP3A4 and CYP3A5 towards schisantherin E

The structural determinants responsible for the different catalytic activities of CYP3A5 and CYP3A4 towards their common substrate schisantherin E were identified by using computational methods. Our results demonstrate that the direct hydrogen bonding interactions and the water‐mediated networks differed in the two complex systems, which resulted in the different binding modes of SE in the active sites of the two isoenzymes.

Abstract

The cytochrome CYP3A4 and CYP3A5 share 84% sequence identity, but they exhibit different catalytic activities towards some substrates. Schisantherin E (SE) was recently identified as a selective substrate of CYP3A5, which exhibited catalytic efficiency that was more than 23 times higher than CYP3A4. At present, however, the structural determinants responsible for the different catalytic activities of the two enzymes towards SE have not been fully understood. In this study, a combination of molecular docking, molecular dynamic simulations, and binding free energy calculation was performed on the CYP3A4/CYP3A5‐SE systems to investigate the issue. The results demonstrate that Ser119 in CYP3A4 and Glu374 in CYP3A5 formed direct hydrogen bonding with SE, respectively. Additionally, one water molecule located between the B‐C loop and the I helix mediated different hydrogen bonding networks between CYP3A4/3A5 and SE. The residue differences (Phe/Leu108 and Leu/Phe210) triggered the distinct conformational changes of the Phe‐cluster residues, especially Phe213 and Phe215, which formed stronger hydrophobic interactions with SE in CYP3A5. The calculated binding free energies were consistent with the experimental results.

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