Nuclear receptor engineering based on novel structure activity relationships revealed by farnesyl pyrophosphate

Nuclear receptors (NRs) comprise the second largest protein family targeted by currently available drugs, acting via specific ligand interactions within the ligand binding domain (LBD). Hence, a better understanding of these NR:ligand interactions is of therapeutic relevance. Recently, farnesyl pyrophosphate (FPP)--an important metabolic intermediate of the cholesterol pathway--was shown to be a unique promiscuous NR ligand, activating a subset of NR family members and inhibiting wound healing in skin. FPP exhibits a significant degree of promiscuity in its activity across different NR family members. The current study was initiated with an aim to identify general ligand-receptor structure-activity relationships that operate over a broad range of NR family members. Docking, an in silico high throughput tool for ligand-receptor structure visualization was used for this study. Docking of FPP to the 3D structures of the LBDs of a diverse set of NRs revealed an electrostatic pyrophosphate contact with a conserved arginine in the NR family, a hydrophobic farnesyl contact with NR helix-12 and a ligand binding pocket volume between 300-400Å 3 as the minimal requirements for FPP activation of any NR. Lack of any of these structural features renders a given NR resistant to FPP activation. We used these predicted novel structure-activity relationships to rationally design and successfully engineer several mutant human estrogen receptors that retain responsiveness to estradiol but no longer respond to FPP. These results have implications for NR-specific ligand design.