Structure-BasedVirtual Screening of the NociceptinReceptor: Hybrid Dockingand Shape-Based Approaches for Improved Hit Identification

摘要

The antagonist-bound crystal structure of the nociceptin receptor (NOP), from the opioid receptor family, was recently reported along with those of the other opioid receptors bound to opioid antagonists. We recently reported the first homology model of the ‘active-state’ of the NOP receptor, which when docked with ‘agonist’ ligands showed differences in the TM helices and residues, consistent with GPCR activation after agonist binding. In this study, we explored the use of the active-state NOP homology model for structure-based virtual screening to discover NOP ligands containing new chemical scaffolds. Several NOP agonist and antagonist ligands previously reported are based on a common piperidine scaffold. Given the structure–activity relationships for known NOP ligands, we developed a hybrid method that combines a structure-based and ligand-based approach, utilizing the active-state NOP receptor as well as the pharmacophoric features of known NOP ligands, to identify novel NOP binding scaffolds by virtual screening. Multiple conformations of the NOP active site includingthe flexible second extracellular loop (EL2) loop were generated bysimulated annealing and ranked using enrichment factor (EF) analysisand a ligand–decoy dataset containing known NOP agonist ligands.The enrichment factors were further improved by combining shape-basedscreening of this ligand–decoy dataset and calculation of consensusscores. This combined structure-based and ligand-based EF analysisyielded higher enrichment factors than the individual methods, suggestingthe effectiveness of the hybrid approach. Virtual screening of theCNS Permeable subset of the ZINC database was carried out using theabove-mentioned hybrid approach in a tiered fashion utilizing a ligandpharmacophore-based filtering step, followed by structure-based virtualscreening using the refined NOP active-state models from the enrichmentanalysis. Determination of the NOP receptor binding affinity of aselected set of top-scoring hits resulted in identification of severalcompounds with measurable binding affinity at the NOP receptor, oneof which had a new chemotype for NOP receptor binding. The hybridligand-based and structure-based methodology demonstrates an effectiveapproach for virtual screening that leverages existing SAR and receptorstructure information for identifying novel hits for NOP receptorbinding. The refined active-state NOP homology models obtained fromthe enrichment studies can be further used for structure-based optimizationof these new chemotypes to obtain potent and selective NOP receptorligands for therapeutic development.