Research provides a scaffolding to selectively target drug failure processes

Cytochrome P450 (CYP) protein degrades more than 80% of all Food and Drug Administration (FDA) approved drugs, reducing their efficacy. However, how to prevent CYP from doing this without target off effects has previously been confusing researchers.

Scientists at St. Jude Children’s Research Hospital have designed a new drug framework that selectively targets one of the most important CYP proteins, CYP3A4. Structural insights in this work provide a roadmap for future drug developers to better assess drug interactions and selectively target CYP proteins. The findings are published in Nature Communications.

CYP3A4 breaks down drugs that treat a variety of health conditions, including the anti-cancer drug paclitaxel and nilmatorelvir for the treatment of Covid-19. CYP3A4 inhibitors are generally co-administered to reduce the effectiveness of CYP3A4. This includes Ritonavir combined with Paxlovid’s Nirmatrelvir for mild Covid-19 treatment. However, such CYP3A4 inhibitors affect similar but different CYP3A5 due to the covalent functions of the two proteins, including large, promiscuous binding sites, in addition to other unintended CYPs.

Unintended inhibition of CYP3A5 and other CYPs can have dramatic effects if not considered.

“When using non-selective CYP3A inhibitors to maintain the efficacy of CYP3A4 metabolicized drugs, unnecessary inhibition of other CYPs will dangerously increase plasma levels of drugs metabolized by unintended CYPs.”

To address the need for a more selective CYP3A4 inhibitor, researchers conducted high-throughput screens to trim 9299 candidate compounds into a panel of three inhibitor scaffolds that achieve selective and potent CYP3A4 inhibition.

Structural studies reveal key loops within binding pockets

Researchers used X-ray crystallography to investigate the mechanisms behind selectivity. Structural comparisons of CYP3A4 and CYP3A5 reveal a loop at the end of the CYP3A5 protein (its C-terminus), which acts as a physical barrier.

“CYP3A5 has a narrower binding pocket, and CYP3A4 inhibitors prevent binding,” says Chen.

Using this information, researchers optimized inhibitor structures to maximize selectivity and potency. One of the optimized inhibitors, SCM-08, showed a 46-fold difference in CYP3A4 inhibition versus CYP3A5 and CYP3A5, circumventing other CYP proteins involved in target-off target binding of existing CYP inhibitors.

SCM-08 may serve as an important launch point for further designing selective CYP3A4 inhibitors.

“Our goal is to improve efficacy but maintain the selectivity of CYP3A4 selection inhibitors,” Chen said. “These compounds are the starting point for achieving that. This is feasible due to the structural basis of selectivity we have revealed.”

The first authors of this study are Jingheng Wang, Stanley Nithianantham, Sergio Chai, Young-Hwan Jung, and St. This is Jude. Other authors of this study are Lae Yang, Han Wee Ong, Yong Li, Yi Hwang Chang, Darcy Miller, and St. Jude.