Structure-Based Virtual Screening of MT₂ Melatonin Receptor: Influence of Template Choice and Structural Refinement

Abstract

Developing GPCR homology models for structure-based virtual screening requires the choice of a suitable template and refinement of binding site residues. We explored this systematically for the MT2 melatonin receptor, with the aim to build a receptor homology model that is optimized for the enrichment of active melatoninergic ligands. A set of 12 MT2 melatonin receptor models was built using different GPCR X-ray structural templates and submitted to a virtual screening campaign on a set of compounds composed of 29 known melatonin receptor ligands and 2560 drug-like decoys. To evaluate the effect of including a priori information in receptor models, 12 representative melatonin receptor ligands were placed into the MT2 receptor models in poses consistent with known mutagenesis data and with assessed pharmacophore models. The receptor structures were then adapted to the ligands by induced-fit docking. Most of the 144 ligand-adapted MT2 receptor models showed significant improvements in screening enrichments compared to the unrefined homology models, with some template/refinement combinations giving excellent enrichment factors. The discriminating ability of the models was further tested on the 29 active ligands plus a set of 21 inactive or low-affinity compounds from the same chemical classes. Rotameric states of side chains for some residues, presumed to be involved in the binding process, were correlated with screening effectiveness, suggesting the existence of specific receptor conformations able to recognize active compounds. The top MT2 receptor model was able to identify 24 of 29 active ligands among the first 2% of the screened database. This work provides insights into the use of refined GPCR homology models for virtual screening.

A Molecular and Chemical Perspective in Defining Melatonin Receptor Subtype Selectivity

“…Homology modeling approaches have identified a subset of residues and potential structural determinants that appear to be critical for receptor ligand binding [82,109]. However, the reliability of the prediction is susceptible to the degree of similarity between the target sequence and the template of crystallized receptors.…”

“…Comparative analyses of prospective modeled ligand-receptor complexes generated from distinct classes of GPCR templates suggest that 35%–40% sequence identity boundaries are required for reliable homology modeling in general [110]. Although modeling between closely related receptor subtypes, and especially, among the same class of GPCRs is generally successful, distant homology modeling based on a phylogenetically remote receptor template often fails to produce accurate receptor models due to significant deviation in structures [109]. Melatonin shares a low sequence identity with the available crystallized receptor, and hence, receptor modeling is usually accompanied by experimental data from mutagenesis studies.…”

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description

“…Recently Thomas et al developed homology models for the acetylcholine muscarinic receptors M₁R-M₅R, again using the β₂-adrenergic receptor as template, and highlighted how optimizing the binding site with ligand information has a stronger impact on the quality of the final model than target-template sequence similarity [74]. Several other works confirmed the importance of accounting for ligand information during the modeling process [75][76][77][78][79].…”

Novel N-Acetyl Bioisosteres of Melatonin: Melatonergic Receptor Pharmacology, Physicochemical Studies, and Phenotypic Assessment of Their Neurogenic Potential

“…[5][6][7] Among these pharmacophores, there is a wide consensus about the necessity of an oxygen atom attached to the aromatic or heteroaromatic core connected to the acetamido-containing side chain. Deletion of the methoxy group generally provokes a decrease in intrinsic the study to investigate the ability of its dimethylamino substituent to bind human MTRs.…”

“…50 The binding affinities are gathered in Table 1. Retroamides with unsaturated side chains (3)(4)(5)(6) showed the highest affinities, with K i s in the low nano-and sub-nanomolar range. The alkenyl or alkynyl substitution does not significantly affect the potency of compounds.…”