Overcoming the Pregnane X Receptor Liability: Rational Design to Eliminate PXR-Mediated CYP Induction

Abstract

The pregnane X receptor (PXR) regulates expression of proteins responsible for all three phases required for the detoxification mechanism, which include CYP450 enzymes, phase II enzymes, and multidrug efflux pumps. Therefore, PXR is a prominent receptor that is responsible for xenobiotic excretion and drug-drug interactions. Pyrimidinone 1 is an antagonist of the calcium sensing receptor (CaSR) and a strong activator of PXR. Repeat oral administration revealed diminished exposures over time, which prohibited further progression. A medicinal chemistry campaign was initiated to understand and abolish activation of PXR in order to increase systemic exposures. Rational structure-activity relationship investigations utilizing cocrystal structures and a de novo pharmacophore model resulted in compounds devoid of PXR activation. These studies culminated in the first orally active CaSR antagonist 8 suitable for progression. Cocrystallography, the pharmacophore model employed, and additional observations reported herein supported rational elimination of PXR activation and have applicability across diverse chemical classes to help erase PXR-driven drug-drug interactions.

Figure 1

Role of PXR in the regulation of xenobiotic metabolism.

Scheme 1. Synthesis of 2-(3-Fluoro-2-hydroxyphenyl)-6-methyl-5-(5-methylthien-2-yl)-3-(2-phenylethyl)-4(3H)-pyrimidinone (1)

Reagents and conditions: (i) benzyl bromide, K₂CO₃, DMF; (ii) NaOH, MeOH, H₂O; (iii) ethyl chloroformate, TEA, THF, NH₄OH; (iv) 10% Pd/C, 40 psi, EtOH; (v) phenethylamine, Et₂O, reflux; (vi) Ti(iPrO)₄, e, reflux; (vii) benzyl bromide, K₂CO₃, DMF; (viii) Br₂, AcOH; (ix) Pd(PPh₃)₄, EtOH, H₂O, Na₂CO₃, 5-methylthiophene-2-boronic acid, microwave.

Figure 2

(a) Structure of compound 2. (b, c) Cocrystal structures showing pocket residues in contact with and in proximity to the bound ligand.

Figure 3

(a) Structure of compound 2 anchored via the two polar residues His407 and Gln285, with the benzyl group sandwiched by Phe288 and Thr299. (b) Structure of T0901317 displaying H-bond interactions of the sulfonyl group with Gln285 and His407 and interactions of the phenyl group with Phe281 and Leu209.

Figure 4

(a) Pharmacophore model displaying key residues engaged binding to a diverse group of compounds. Purple and green spheres represent H-bond and hydrophobic interactions, respectively, while the size of each sphere reflects number of compounds. Distances captured between residues/spaces are depicted. (b) Average distances between the three key groups of hydrophobic residues.

Figure 5

(a) Cocrystal structure of compound 2 depicting key interactions. (b) Docked structure of compound 2. Both the docked and crystal structures show the critical H-bonds between compound 2 and residues Gln285 and His407.

Figure 6

(a) Pharmacophore-model-informed SAR strategy. (b) Docked structure of compound 8 (magenta) supporting elimination of PXR affinity (overlaid with the docked structure of compound 1 in yellow).

Figure 7

Structures and in vitro data of pyrimidinone-based CaSR antagonists 1–8.

Figure 8

(a) Plots of MW and cLogD (pH 7.4) for compounds from the GSK compound collection. (b) Binning of MW and cLogD (pH 7.4) for the GSK compounds. Color coding reflects PXR activity (% maximum response), with red, yellow, and green corresponding to >70% (high), 30–70% (medium), and <30% (low) induction relative to 10 μM rifampicin, respectively (SI pp S8 and S9). (c) Exemplary functional groups observed as PXR activators.