The Retinoid and Non-Retinoid Ligands of the Rod Visual G Protein-Coupled Receptor

Abstract

G protein-coupled receptors (GPCRs) play a predominant role in the drug discovery effort. These cell surface receptors are activated by a variety of specific ligands that bind to the orthosteric binding pocket located in the extracellular part of the receptor. In addition, the potential binding sites located on the surface of the receptor enable their allosteric modulation with critical consequences for their function and pharmacology. For decades, drug discovery focused on targeting the GPCR orthosteric binding sites. However, finding that GPCRs can be modulated allosterically opened a new venue for developing novel pharmacological modulators with higher specificity. Alternatively, focus on discovering of non-retinoid small molecules beneficial in retinopathies associated with mutations in rhodopsin is currently a fast-growing pharmacological field. In this review, we summarize the accumulated knowledge on retinoid ligands and non-retinoid modulators of the light-sensing GPCR, rhodopsin and their potential in combating the specific vision-related pathologies. Also, recent findings reporting the potential of biologically active compounds derived from natural products as potent rod opsin modulators with beneficial effects against degenerative diseases related to this receptor are highlighted here.

Keywords: G protein-coupled receptor; flavonoids; opsin; retinoids; rhodopsin; small molecules.

Figure 1

Schematic representation of rhodopsin photoactivation and regeneration. Light illumination triggers isomerization of rhodopsin’s (Rho) chromophore 11-cis-retinal (11-cis-RAL) to all-trans-retinal (All-trans-RAL) and transition of the receptor to its photoactivated state (Rho*). Eventually, all-trans-retinal dissociates from the retinal-binding pocket resulting in formation of ligand-free opsin and free all-trans-retinal, which is reduced to all-trans-retinol (All-trans-ROL) by retinal dehydrogenases (RDH8 and RDH12). All-trans-retinol is then esterified by lecithin retinol acyltransferase (LRAT) to all-trans-retinyl esters (All-trans-RE) that can be stored in retinosomes or converted to 11-cis-retinol (11-cis-ROL) by retinyl pigment epithelium-specific protein 65 (RPE65) isomerase. Then, 11-cis-retinol is further reduced by RDH5 to 11-cis-retinal that re-associates with opsin forming the visual pigment, rhodopsin.

Figure 2

Retinal-binding site. Shown is the configuration of the residues present within the retinal-binding pocket interacting with 11-cis-retinal within dark-adapted rhodopsin (A) and with all-trans-retinal within photoactivated rhodopsin (B). The upper panels show 2D diagrams for the main interaction networks between the retinal and the residues within the binding pocket. Specific types of interactions are indicated in the legend. The lower panels show the 3D configuration of the retinal and the residues within the retinal-binding pocket. The light-stimulated isomerization of 11-cis-retinal to all-trans-retinal triggers the conformational changes within the protein leading to the rearrangement of the residues within the binding site. The coordinates derived from the X-ray structure of dark state rhodopsin (PDB ID: 1GZM) and photoactivated rhodopsin (PDB ID: 4A4M) were obtained from the Protein Data Bank. The co-crystallization products were removed and the resulted PDB files were opened with the VINA/VegaZZ 3.1.0.21 software [13] and the hydrogen atoms and partial charges were assigned to all atoms. Then, the obtained protein structures were optimized with the NAMD 2.12 software [14], applying CHARMM22 forced field [15]. The final structures were visualized with the Biovia Discovery Studio Visualizer 17.2.0 software and 2D diagrams and 3D representations were obtained by selecting the main atoms that interact with the retinal ligand.

Figure 3

Bioinformatic analysis of the interaction between bovine rod opsin and non-retinoid small molecules. Shown are the molecular docking 2D diagrams of the interactions between rod opsin and YC-001 (A) and quercetin (B) within the orthosteric binding pocket. YC-001 and quercetin could accommodate within the retinal-binding pocket. However, the interaction pattern and the types of interactions that occur in the orthosteric site are different for these compounds. The molecular docking of YC-001 or quercetin to bovine rod opsin (PDB ID: 3CAP) was performed using VINA/VegaZZ 3.1.0.21 software as described in Ortega et al. [20] with 30 iterations for each compound. The resulting complexes were visualized with the Biovia Discovery Studio Visualizer 17.2.0 software and 2D diagrams were obtained by selecting the main atoms that interact with the ligand.

Figure 4

Topological analysis of the potential binding sites for non-retinoid small molecules within the bovine rod opsin structure (PDB ID: 3CAP). The surface analysis was performed with the CASTp 3.0 software [31]. Three main pockets related to protein–drug interaction were identified: (1) the orthosteric site (shown in red), (2) the extracellular pocket between TM5, TM6, and ECL2 (shown in purple), and (3) the cytoplasmic pocket between TM1, TM7, ICL2, and H8 (shown in orange). The crystal structure of ligand-free bovine opsin (PDB ID: 3CAP) was processed as described in Figure 2. Then, the surface topology analysis was performed by using the CASTp 3.0 software available at http://sts.bioe.uic.edu/castp/server3.