Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the “artificial enrichment” and “analogue bias” of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD.

The 5-hydroxytryptamine 1A (5-HT_1A) serotonin receptor has been an attractive target for treating mood and anxiety disorders such as schizophrenia. We have developed binary classification quantitative structure–activity relationship (QSAR) models of 5-HT_1A receptor binding activity using data retrieved from the PDSP K_i database. The prediction accuracy of these models was estimated by external 5-fold cross-validation as well as using an additional validation set comprising 66 structurally distinct compounds from the World of Molecular Bioactivity database. These validated models were then used to mine three major types of chemical screening libraries, i.e., drug-like libraries, GPCR targeted libraries, and diversity libraries, to identify novel computational hits. The five best hits from each class of libraries were chosen for further experimental testing in radioligand binding assays, and nine of the 15 hits were confirmed to be active experimentally with binding affinity better than 10 μM. The most active compound, Lysergol, from the diversity library showed very high binding affinity (K_i) of 2.3 nM against 5-HT_1A receptor. The novel 5-HT_1A actives identified with the QSAR-based virtual screening approach could be potentially developed as novel anxiolytics or potential antischizophrenic drugs.

Antibody-drug conjugates (ADCs) represent a mechanistically defined class of targeted therapeutics that combine monoclonal antibodies with cytotoxic payloads to achieve selective delivery to antigen-expressing carcinoma cells. Conventional ADC development has primarily relied on empirical screening and structure-based design, often limited by incomplete structural information, non-systematic linker–payload selection, and constraints in experimental throughput. Computational methods, including artificial intelligence and machine learning (AI/ML) are increasingly being integrated into ADC discovery and optimization workflows (i.e., AI-driven ADC Design) to address these limitations. This review is organized into six sections: (1) the progression from traditional modeling approaches to AI-driven design of individual ADC components; (2) the application of deep learning (DL) to antibody structure prediction and identification of optimal conjugation sites; (3) the use of AI/ML models for forecasting pharmacokinetic properties and toxicity profiles; (4) emerging generative algorithms for antibody sequence diversification and affinity optimization; (5) case studies demonstrating the integration of computational tools with experimental pipelines, including systems that link in silico predictions to high-throughput validation; and (6) persistent challenges, including data sparsity, model interpretability, validation complexity, and regulatory considerations. The review concludes with a discussion of future directions, emphasizing the role of multimodal data integration, reinforcement learning (RL), and closed-loop design frameworks to support iterative ADC development.

Recent highly expected structural characterizations of agonist‐bound and antagonist‐bound beta‐2 adrenoreceptor (β2AR) by X‐ray crystallography have been widely regarded as critical advances to enable more effective structure‐based discovery of GPCRs ligands. It appears that this very important development may have undermined many previous efforts to develop 3D theoretical models of GPCRs. To address this question directly, we have compared several historical β2AR models versus the inactive state and nanobody‐stabilized active state of β2AR crystal structures in terms of their structural similarity and effectiveness of use in virtual screening for β2AR specific agonists and antagonists. Theoretical models, incluing both homology and de novo types, were collected from five different groups who have published extensively in the field of GPCRs modeling. All models were built before X‐ray structures became available. In general, β2AR theoretical models differ significantly from the crystal structure in terms of TMH definition and the global packing. Nevertheless, surprisingly, several models afforded hit rates resulting from virtual screening of large chemical library enriched by known β2AR ligands that exceeded those using X‐ray structures. The hit rates were particularly higher for agonists. Furthemore, the screening performance of models is associated with local structural quality, such as the RMSDs for binding pocket residues and the ability to capture accurately, most if not all critical protein/ligand interactions. These results suggest that carefully built models of GPCRs could capture critical chemical and structural features of the binding pocket, and thus may be even more useful for practical structure‐based drug discovery than X‐ray structures. Proteins 2012.