Published today in Nature Communications, first author Andrew Huber, PhD, corresponding author Taosheng Chen, PhD, and second author Wenwei Lin, PhD, St. Jude Department of Chemical Biology and Therapeutics, uncovered a hidden binding pocket on the pregnane X receptor (PXR), paving the way for selective PROTAC therapies that target nuclear receptors while minimizing off-target effects.
A study from St. Jude Children’s Research Hospital uncovered an alternative binding pocket within nuclear receptors, revealing a much-needed new therapy route for this important class of drug targets. The scientists found the “hidden” pocket on the pregnane X receptor (PXR), a protein that drives the unwanted breakdown of chemotherapies. The binding pocket is well-suited for a proteolysis-targeting chimera (PROTAC), a type of protein-degrading molecule. The pocket is present, yet structurally distinct, across all nuclear receptors, allowing the selective design of PROTACs. Targeting this pocket may help overcome the specificity issue common to nuclear receptor drugs. The researchers demonstrated this by designing PROTACs that had high potency against PXR but reduced off-target activity. The findings were published today in Nature Communications.
Nuclear receptors regulate gene expression by binding small molecules via a classical ligand-binding pocket. These proteins are linked to numerous diseases and are the target of 16% of approved small-molecule drugs. Their structural similarities, however, mean that designing drugs to target just one type of nuclear receptor is extremely challenging. One such nuclear receptor, PXR, activates the expression of drug-metabolizing enzymes which prevent toxin build-up in cells but also indiscriminately flag therapeutic drugs for removal from cells. This reduces drug efficacy, requiring clinicians to increase the dosage, which increases the risk of treatment-related toxicity, or add a PXR inhibitor to the treatment, which carries its own risk.
“My lab has had great success in developing PXR inhibitors, but a subtle chemical change or a point mutation in PXR can convert an inhibitor to an activator,” explained corresponding author Taosheng Chen, PhD, PMP, St. Jude Department of Chemical Biology & Therapeutics. “This is dangerous, because the inhibitor itself, if converted to an activator, could not only lose efficacy but have the opposite effect. A PROTAC that destroys the protein, however, wouldn’t have this issue.”
Old PROTAC dog, new therapeutic trick
PROTACs, which bind their targets and recruit cellular protein-degrading machinery, are a promising alternative option to inhibitors. But the deep classical PXR ligand-binding pocket has hindered the rational design of effective PROTACs. Chen decided to see if any already available PROTACs could be repurposed to bind PXR.
They identified one such candidate, MD-224, a PROTAC designed for anticancer therapy. MD-224 effectively degraded PXR but had an unexpected twist. “Mechanism studies showed some strange things, leading us to believe it wasn’t binding to the classical ligand-binding pocket,” said first author Andrew Huber, PhD, Department of Chemical Biology & Therapeutics. “We realized it was binding a cleft outside the deep classical ligand-binding pocket, which allows it to recruit protein-degrading machinery more effectively.”
While MD-224 also bound to other nuclear receptors, only those that share close similarities with PXR were affected. This selectivity could also be tuned. “For typical inhibitors, the selectivity problem exists across multiple nuclear receptor groups, but with this new binding pocket and this particular PROTAC, it’s only for the four most related receptors,” Huber said. “When we modified the compound, we also found we could change the potency among the four, suggesting it is possible to achieve selectivity.”
While Chen continues to explore the best ways to navigate PXR-driven drug metabolism, he is aware of the broader implications of the study. A newly discovered targetable binding pocket opens a world of opportunities for drug discovery. “Our angle is PXR, but the study is very relevant for those who think about other receptors too, such as the androgen receptor,” Chen said. “There are many exciting opportunities for other researchers stemming from what we’ve found.”
Authors and funding
The study’s other authors are Wenwei Lin, Young-Hwan Jung, Shyaron Poudel, Guangwei Yang, Jing Wu, Annalise Carrigan, Vishwajeeth Pagala, Wei Wang, Yingxue Fu, Zuo-Fei Yuan, Stephanie Byrum, Ka Yang, Rebecca Florke Gee, Elizabeth Arnold, Allister Loughran, Jingheng Wang, Shondra Pruett-Miller and Junmin Peng, all of St. Jude.
The study was supported by the National Institutes of Health (R35GM118041, RF1AG064909, P30CA021765, P30DK120531 and R24DK139775), and the American Lebanese Syrian Associated Charities (ALSAC), the fundraising and awareness organization of St. Jude.
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