Molecular simulation-based 3D structural construction of olfactory receptor with agonist binding

Olfactory receptors (ORs) form the largest subfamily of class A G protein-coupled receptors (GPCRs); however, only a few 3D structures of ORs have been determined. Structure-based virtual screening and improved structural insights are required to effectively identify novel odor molecules and elucidate their binding modes along with mechanisms of activation and inactivation. Herein, we propose a protocol to provide an active state model for the target OR (OR9Q2) with agonist molecules using AlphaFold2, molecular simulations, and virtual screening. Furthermore, we extracted ligand-stable bound sections using the ligand-stable duration (LSD) protocol defined in this study to analyze conformational ensembles of complex structures. We constructed promising complex structures and demonstrated their reliability by calculating the area under the receiver operating characteristic (ROC) curve in virtual screening tests using experimentally validated active and inactive compounds. This study offers a reliable structure-based screening protocol for olfactory receptors, which can subsequently aid novel odorant discovery and advancing fragrance, flavour, and biosensor industries.