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Two‐ and Three‐dimensional Quantitative Structure‐activity Relationship Models Based on Conformer Structures

In three‐dimensional (3D)‐quantitative structure‐activity relationship (QSAR) analysis, the chemical structure of a studied molecule is typically optimized assuming its presence in a vacuum environment. However, in practical scenarios, the environment of even the most stable molecules contains water, proteins, and other species; therefore, their actual structures significantly differ from those in vacuum and have multiple structures. Herein, both two‐dimensional and 3D molecular descriptors, which accepted the existence of multiple conformers, were calculated, and a conformer‐based 3D‐QSAR model (C3D‐QSAR) that considered the chemical structures of conformers was developed. The prediction accuracy of the C3D‐QSAR method determined by analyzing the data sets obtained for the angiotensin‐converting enzyme and dihydrofolate reductase inhibitors was found to be higher than those of the existing QSAR models.