QSAR-Based Computational Approaches to Accelerate the Discovery of Sigma-2 Receptor (S2R) Ligands as Therapeutic Drugs

S2R overexpression is associated with various forms of cancer as well as both neuropsychiatric disorders (e.g., schizophrenia) and neurodegenerative diseases (Alzheimer's disease: AD). In the present study, three ligand-based methods (QSAR modeling, pharmacophore mapping, and shape-based screening) were implemented to select putative S2R ligands from the DrugBank library comprising 2000+ entries. Four separate optimization algorithms (i.e., stepwise regression, Lasso, genetic algorithm (GA), and a customized extension of GA called GreedGene) were adapted to select descriptors for the QSAR models. The subsequent biological evaluation of selected compounds revealed that three FDA-approved drugs for unrelated therapeutic indications exhibited sub-1 uM binding affinity for S2R. In particular, the antidepressant drug nefazodone elicited a S2R binding affinity Ki = 140 nM. A total of 159 unique S2R ligands were retrieved from 16 publications for model building, validation, and testing. To our best knowledge, the present report represents the first case to develop comprehensive QSAR models sourced by pooling and curating a large assemblage of structurally diverse S2R ligands, which should prove useful for identifying new drug leads and predicting their S2R binding affinity prior to the resource-demanding tasks of chemical synthesis and biological evaluation.

Automated summary

S2R overexpression is associated with various diseases and disorders, including cancer, neuropsychiatric disorders, and neurodegenerative diseases. This study used three ligand-based methods to select putative S2R ligands and four optimization algorithms to choose descriptors for QSAR models. Results showed that three FDA-approved drugs exhibited sub-1 uM binding affinity for S2R, with the antidepressant drug nefazodone showing a Ki of 140 nM. The report represents the first comprehensive QSAR models developed from a large assemblage of structurally diverse S2R ligands, providing a useful tool for identifying new drug leads.