A comprehensive computational analysis of NR2F2/6 receptors for drug repurposing

Abstract

Nuclear Receptors (ORFs) are a small family of transcription factors (15 members) playing a crucial role in regulating various physiological and developmental processes. Within this superfamily, NR2Fs, also known as Chicken Ovalbumin Upstream Promoter Transcription Factor (COUP-TF), is a family of nuclear orphan receptors, due to the lack of endogenous ligands. The NR2Fs are composed of three members: NR2F1 (COUP-TFI, EAR- 3), NR2F2 (COUP-TFII, ARP-1) and NR2F6 (COUP-TFIII, EAR-2). Due to the pivotal functions of NR2Fs in cell growth, they are regarded as promising candidates for the development of novel therapeutic targets in cancer treatment [1]. In the context of the PNRR project, "HEAL ITALIA", a comprehensive computational analysis was conducted on the X-ray crystal structures of the human ligand binding domain of NR2F2 (PDB ID: 3CJW) and the NR2F6 (PDB ID: 8C5L). To date, only compound CIA1 has been identified as an inhibitor of NR2F2 in prostate cancer cell lines (IC50 1.2-7.6 μM). To this aim, the ligand binding domain was mapped identifying potential binding sites, designated as site 1 and site 2. Followed by classic docking with CIA1, molecular dynamics (MD), Binding Pose Metadynamics (BPMD), and Molecular Mechanics-Generalized Born Surface Area continuum solvation (MM-GBSA) were conducted to assess the stability of the complexes NR2F2-CIA in the two sites. For NR2F6 no inhibitor has been identified in the literature. Potential hotspot binding sites were identified and their potential for drug use was predicted. Subsequently, the identified binding sites for NR2F2 and NR2F6 were then used to perform a virtual screening protocol involving pharmacophore models and docking studies on extensive libraries, such as Drugbank, FDA and commercial libraries for drug repurposing.