Development and Validation of k-Nearest-Neighbor QSPR Models of Metabolic Stability of Drug Candidates

• Published in: Journal of medicinal chemistry 2003-07, Vol.46 (14), p.3013-3020
• Main Authors: Shen, Min, Xiao, Yunde, Golbraikh, Alexander, Gombar, Vijay K, Tropsha, Alexander
• Format: Article
• Language: English
• Subjects: Algorithms; Biological and medical sciences; Drug Stability; General pharmacology; Humans; In Vitro Techniques; Liver - metabolism; Medical sciences; Models, Molecular; Pharmaceutical Preparations - chemistry; Pharmaceutical Preparations - metabolism; Pharmacology. Drug treatments; Physicochemical properties. Structure-activity relationships; Quantitative Structure-Activity Relationship
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm020491t

Computational ADME (absorption, distribution, metabolism, and excretion) models may be used early in the drug discovery process in order to flag drug candidates with potentially problematic ADME profiles. We report the development, validation, and application of quantitative structure−property relationship (QSPR) models of metabolic turnover rate for compounds in human S9 homogenate. Biological data were obtained from uniform bioassays of 631 diverse chemicals proprietary to GlaxoSmithKline (GSK). The models were built with topological molecular descriptors such as molecular connectivity indices or atom pairs using the k-nearest neighbor variable selection optimization method developed at the University of North Carolina (Zheng, W.; Tropsha, A. A novel variable selection QSAR approach based on the k-nearest neighbor principle. J. Chem. Inf. Comput. Sci., 2000, 40, 185−194.). For the purpose of validation, the whole data set was divided into training and test sets. The training set QSPR models were characterized by high internal accuracy with leave-one-out cross-validated R 2 (q 2) values ranging between 0.5 and 0.6. The test set compounds were correctly classified as stable or unstable in S9 assay with an accuracy above 85%. These models were additionally validated by in silico metabolic stability screening of 107 new chemicals under development in several drug discovery programs at GSK. One representative model generated with MolConnZ descriptors predicted 40 compounds to be metabolically stable (turnover rate less than 25%), and 33 of them were indeed found to be stable experimentally. This success (83% concordance) in correctly picking chemicals that are metabolically stable in the human S9 homogenate spells a rapid, computational screen for generating components of the ADME profile in a drug discovery process.