Generating a PXR Crystal Structure

At Sygnature Discovery, we thrive on solving complex protein challenges—and our recent success in solving the crystal structure of human Pregnane X Receptor (PXR), is a perfect example of how our expertise can accelerate drug discovery.

Background

The human Pregnane X Receptor (PXR) is a ligand activated nuclear receptor that plays a central role in regulating xenobiotic metabolism. It functions as a master transcriptional regulator of genes involved in drug metabolism and clearance, including key cytochrome P450 enzymes such as CYP3A4 (1-3).

PXR is characterised by a large and highly flexible ligand binding domain (LBD) enabling the recognition of a wide range of structurally and chemically diverse compounds (4-5). Consequently, PXR is involved in the initial phases of drug metabolism but can also contribute to undesirable effects such as drug–drug interactions, reduced efficacy of anticancer treatments, and the accumulation of toxic metabolites (6). As a result, PXR has emerged as an important target in pharmaceutical research, with ongoing efforts aimed at improving drug efficacy and guiding the development of new therapeutic strategies.

Whilst the intrinsic flexibility of PXR underpins its biological function, it also presents challenges for structural biology. In particular, the conformational heterogeneity of the LBD can hinder crystallisation. To overcome this, we expressed the human PXR ligand binding domain (residues 130 – 434) fused to a stabilising coactivator peptide derived from SRC-1. This strategy, widely reported in the literature, promotes conformational stabilisation of the receptor by mimicking coactivator binding, thereby facilitating crystallisation and structural characterisation (1).

Purification and Quality Control

The PXR construct was successfully expressed in E. coli using TB autoinduction media, yielding soluble protein suitable for downstream purification.

Purification was then performed using a twostep workflow:

• Nickel affinity chromatography (IMAC) enabled efficient capture of the His-tagged protein
• Size exclusion chromatography (SEC) provided further polishing and removal of impurities

Following IMAC, SDS-PAGE analysis confirmed the presence of the target protein at ~40 kDa, consistent with the expected molecular weight. To achieve the high level of purity and homogeneity required for crystallography, the IMAC eluate was further purified by size exclusion chromatography (SEC). SEC successfully separated PXR from the higher molecular weight contaminants, producing a well defined main peak corresponding to monomeric PXR. Stringent pooling of fractions was performed to maximise homogeneity, which is essential for crystallography. The final protein batch was highly pure (Figure 1A) and showed excellent agreement between expected and observed molecular mass by mass spectrometry (Δ0.27 Da) confirming sample identity (Figure 1B).

Structural Biology

With the purified PXR fused to the SRC-1 peptide, broad and literature informed crystallisation trials were initiated employing a combination of sitting and hanging drop vapour diffusion methods. The presence of the SRC-1 co-activator peptide was key to stabilising the receptor in an active conformation and reduced the conformational heterogeneity which in turn increased the likelihood of crystal formation, an approach consistent with previously reported PXR structures. The final co-crystal structure, in complex with the cholesterol-lowering agent SR12813, belonged to the space group P212121 and was solved at 1.71 Å resolution using data collected at Diamond Light Source and processed with STARANISO (Figure 2).

The resulting crystal structure provides valuable insights into the architecture of the PXR ligand binding domain and establishes a robust platform for future ligand bound co-crystallisation studies. Importantly, this system enables the screening of client supplied compounds directly against PXR, allowing rapid assessment of binding and structural information to be determined on ligand receptor interactions, binding modes, and key contact residues.

Crucially, our integrated teams at Sygnature Discovery can provide an iterative, structure guided design process for client’s compounds. Following initial screening and co-crystallisation, with PXR or other protein targets of interest, ligand bound structures can guide rational optimisation of compounds to reduce or prevent interactions with PXR and correspondingly guide modifications to improve target protein interactions and hence potency. By combining structural biology with medicinal chemistry expertise in-house, this approach allows rapid, coordinated refinement of compounds based on direct experimental insights.

Together, this platform provides a powerful structure guided approach for compound optimisation, enabling clients to refine chemical scaffolds based on direct experimental evidence and ultimately accelerate the development of safer and more effective therapeutics.

Conclusions

This work demonstrates our ability to deliver high quality structural biology solutions for challenging targets such as nuclear receptors. Key highlights include:

• Rational construct design to stabilise flexible proteins
• Efficient purification workflows yielding highly pure, homogeneous samples
• Excellent analytical characterisation
• Successful crystallisation of a challenging, ligand promiscuous receptor

With its central role in drug metabolism, PXR remains a critical target in drug discovery. Our expertise enables rapid progression from construct design to structural insight, helping clients better understand ligand binding and guide medicinal chemistry efforts.

Whether you’re targeting PXR or another challenging protein, our gene-to-structure workflow and expert team are ready to support your discovery journey.

Get in touch to explore how Sygnature Discovery can accelerate your structural biology goals.

References

1. Carivenc C, Laconde G, Blanc P, Amblard M, Bourguet W, Delfosse V. A two-in-one expression construct for biophysical and structural studies of the human pregnane X receptor ligand-binding domain, a pharmaceutical and environmental target. Acta Crystallogr F Struct Biol Commun. 2025 Mar;81(3):85–94. doi: 10.1107/S2053230X2500069X.
2. Gee RRF, Huber AD, Chen T. Expert Opin Drug Metab Toxicol. 2024;20(1):9–23.
3. Timsit YE, Negishi M. CAR and PXR: the xenobiotic-sensing receptors. Expert Opin Drug Metab Toxicol. 2024;20:9–23.
4. Cheng J, Ma X, Gonzalez FJ. Pregnane X receptor- and CYP3A4-humanized mouse models and their applications. Br J Pharmacol. 2011 Jun;163(3):461–468.
5. Ngan CH, Beglov D, Rudnitskaya AN, Kozakov D, Waxman DJ, Vajda S. The structural basis of pregnane X receptor binding promiscuity. Biochemistry. 2009 Dec 8;48(48):11572–11581.
6. Niu X, Wu T, Li G, Gu X, Tian Y, Cui H. Insights into the critical role of PXR in preventing carcinogenesis and chemotherapeutic drug resistance. Int J Biol Sci. 2022 Jan 1;18(2):742–759.