Designing Out PXR Activity on Drug Discovery Projects: A Review of Structure-Based Methods, Empirical and Computational Approaches

Abstract

This perspective discusses the role of pregnane xenobiotic receptor (PXR) in drug discovery and the impact of its activation on CYP3A4 induction. The use of structural biology to reduce PXR activity on drug discovery projects has become more common in recent years. Analysis of this work highlights several important molecular interactions, and the resultant structural modifications to reduce PXR activity are summarized. The computational approaches undertaken to support the design of new drugs devoid of PXR activation potential are also discussed. Finally, the SAR of empirical design strategies to reduce PXR activity is reviewed, and the key SAR transformations are discussed and summarized. In conclusion, this perspective demonstrates that PXR activity can be greatly diminished or negated on active drug discovery projects with the knowledge now available. This perspective should be useful to anyone who seeks to reduce PXR activity on a drug discovery project.

The Nuclear Receptor PXR in Chronic Liver Disease

“…As in other NRs, PXR is endowed with three domains, i.e., the N-terminus ligand-independent transactivation domains (AF-1), the DNA-binding domain (DBD), and a ligand-binding region (LBD) at the C-terminus, which is also responsible for the heterodimerization with retinoid X receptor (RXR) ( Figure 1 a). An additional ligand-dependent transactivation domain, named activation function 2 (AF-2), is located within the ligand binding domain [ 1 , 5 , 18 ]. Beyond the presence of PXR splicing and transcript variants, the finely tuned regulation of PXR transcriptional activity is due to the great variety of its ligands, including endobiotic compounds (pregnane, steroids, bile acids, vitamins) and xenobiotics (macrolide antibiotics, antifungals, toxins, and environmental pollutants) [ 4 , 14 ].…”

“…As for other NRs, the first event leading to PXR activation consists in the binding of the ligand to the receptor LBD [ 19 ]. This binding site, normally characterized by an “α-helical sandwich”, has a unique five-stranded β-sheet that acts as a homodimerization site, forming tryptophan-zipper interactions [ 1 , 18 ]. Mutations of specific tryptophan residues (Trp223 and 225) within the structure of the PXR homodimer interface reduces its ability to interact with the steroid receptor coactivator-1 (SRC-1), leading to an impaired transcriptional activity of PXR [ 18 , 19 ].…”

“…This binding site, normally characterized by an “α-helical sandwich”, has a unique five-stranded β-sheet that acts as a homodimerization site, forming tryptophan-zipper interactions [ 1 , 18 ]. Mutations of specific tryptophan residues (Trp223 and 225) within the structure of the PXR homodimer interface reduces its ability to interact with the steroid receptor coactivator-1 (SRC-1), leading to an impaired transcriptional activity of PXR [ 18 , 19 ]. The flexible and large ligand-binding pocket of PXR (from 1000 Å to 1540 Å, after ligand binding) is characterized by four distinct regions, i.e., a hydrophobic cage, a polar margin, a hydrophobic portion, and a polar duct [ 7 , 18 , 20 ].…”

“…Mutations of specific tryptophan residues (Trp223 and 225) within the structure of the PXR homodimer interface reduces its ability to interact with the steroid receptor coactivator-1 (SRC-1), leading to an impaired transcriptional activity of PXR [ 18 , 19 ]. The flexible and large ligand-binding pocket of PXR (from 1000 Å to 1540 Å, after ligand binding) is characterized by four distinct regions, i.e., a hydrophobic cage, a polar margin, a hydrophobic portion, and a polar duct [ 7 , 18 , 20 ]. As stated before, xenobiotics could take advantage of LBD flexibility to interact with the PXR receptor.…”

“…As stated before, xenobiotics could take advantage of LBD flexibility to interact with the PXR receptor. For example, rifampicin interacts with 18 residues of the LBD, forming hydrogen bonds with Ser247, His407, and Gln285, while the HIV reverse transcriptase inhibitor PNU-142721 uses the hydrophobic cage to connect with PXR, through a π–π bond with Phe288 [ 18 ]. Some species-related differences observed in the affinity of PXR ligands could be ascribable to the low homology (73%) of the ligand-binding pocket of PXR between human and mouse [ 21 ].…”