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Pharm Res. 2013 Jul;30(7):1790-8. doi: 10.1007/s11095-013-1023-6. Epub 2013 Apr 9.

The use of pseudo-equilibrium constant affords improved QSAR models of human plasma protein binding.

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  • 1Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science & Engineering, Tongji University, 417 Mingjing Building, Shanghai 200092, China.



To develop accurate in silico predictors of Plasma Protein Binding (PPB).


Experimental PPB data were compiled for over 1,200 compounds. Two endpoints have been considered: (1) fraction bound (%PPB); and (2) the logarithm of a pseudo binding constant (lnKa) derived from %PPB. The latter metric was employed because it reflects the PPB thermodynamics and the distribution of the transformed data is closer to normal. Quantitative Structure-Activity Relationship (QSAR) models were built with Dragon descriptors and three statistical methods.


Five-fold external validation procedure resulted in models with the prediction accuracy (R²) of 0.67 ± 0.04 and 0.66 ± 0.04, respectively, and the mean absolute error (MAE) of 15.3 ± 0.2% and 13.6 ± 0.2%, respectively. Models were validated with two external datasets: 173 compounds from DrugBank, and 236 chemicals from the US EPA ToxCast project. Models built with lnKa were significantly more accurate (MAE of 6.2-10.7 %) than those built with %PPB (MAE of 11.9-17.6 %) for highly bound compounds both for the training and the external sets.


The pseudo binding constant (lnKa) is more appropriate for characterizing PPB binding than conventional %PPB. Validated QSAR models developed herein can be applied as reliable tools in early drug development and in chemical risk assessment.

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