Paper Citing NAMD - Abstract
Dagliyan, Onur; Kavakli, I. Halil; Turkay, Metin
Classification of Cytochrome P450 Inhibitors with Respect to Binding Free Energy and pIC(50) Using Common Molecular Descriptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 49:2403-2411, OCT 2009
Virtual screening of chemical libraries following experimental assays of drug candidates is a common procedure in structure based drug discovery. However, the relationship between binding free energies and biological activities (pIC(50)) of drug candidates is sfill an unsolved issue that limits the efficiency and speed of drug development processes. In this study, the relationship between them is investigated based on a common molecular descriptor set for human cytochrome P450 enzymes (CYPs). CYPs play an important role in drug-drug interactions, drug metabolism, and toxicity. Therefore, in silico prediction of CYP inhibition by drug candidates is one of the major considerations in drug discovery. The combination of partial leastsquares regression (PLSR) and a variety of classification algorithms were employed by considering this relationship as a classification problem. Our results indicate that PLSR with classification is a powerful tool to predict more than one output such as binding free energy and pIC(50) simultaneously. PLSR with mixedinteger linear programming based hyperboxes predicts the binding free energy and pIC(50) with a mean accuracy of 87.18% (min: 81.67% max: 97.05%) and 88.09% (min: 79.83% max: 92.90%), respectively, for the cytochrome p450 superfamily using the common 6 molecular descriptors with a 10-fold cross- val idati on.
