As a novel approach to drug discovery involving neuronal nicotinic acetylcholine receptors (nAChRs), our laboratory targeted nonagonist binding sites (i.e., noncompetitive binding sites, negative allosteric binding sites) located on nAChRs. Cultured bovine adrenal cells were used as neuronal models to investigate interactions of 67 analogs of methyllycaconitine (MLA) on native ␣34* nAChRs. The availability of large numbers of structurally related molecules presents a unique opportunity for the development of pharmacophore models for noncompetitive binding sites. Our MLA analogs inhibited nicotinemediated functional activation of both native and recombinant ␣34* nAChRs with a wide range of IC 50 values (0.9 -115 M). These analogs had little or no inhibitory effects on agonist binding to native or recombinant nAChRs, supporting noncompetitive inhibitory activity. Based on these data, two highly predictive 3D quantitative structure-activity relationship (comparative molecular field analysis and comparative molecular similarity index analysis) models were generated. These computational models were successfully validated and provided insights into the molecular interactions of MLA analogs with nAChRs. In addition, a pharmacophore model was constructed to analyze and visualize the binding requirements to the analog binding site. The pharmacophore model was subsequently applied to search structurally diverse molecular databases to prospectively identify novel inhibitors. The rapid identification of eight molecules from database mining and our successful demonstration of in vitro inhibitory activity support the utility of these computational models as novel tools for the efficient retrieval of inhibitors. These results demonstrate the effectiveness of computational modeling and pharmacophore development, which may lead to the identification of new therapeutic drugs that target novel sites on nAChRs.The physiological roles of neuronal nicotinic acetylcholine receptors (nAChRs) in synaptic release of acetylcholine and their involvement in the modulation of other important neurotransmitters such as norepinephrine, serotonin, GABA, glutamate, and dopamine make nAChRs prime targets for therapeutic interventions. In addition, nAChRs have been linked to pain, epilepsy, and many neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, and psychiatric disorders, such as depression and schizophrenia. The development of new drugs to target these receptors has been slow for several reasons: 1) multiple subtypes of nAChRs are expressed in the central and peripheral nervous systems; 2) few drugs are available that selectively target nAChR subtypes; and 3) information on the physiological roles of specific nAChR subtypes is limited. A key approach to provide a better understanding of physiological processes and pathophysiological conditions involving