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J Chem Inf Model. 2016 May 23;56(5):924-9. doi: 10.1021/acs.jcim.6b00005. Epub 2016 May 2.

Simple Predictive Models of Passive Membrane Permeability Incorporating Size-Dependent Membrane-Water Partition.

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Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.
Schrödinger, Inc., 120 West 45th Street, 17th Floor, New York, New York 10036, United States.


We investigate the relationship between passive permeability and molecular size, in the context of solubility-diffusion theory, using a diverse compound set with molecular weights ranging from 151 to 828, which have all been characterized in a consistent manner using the RRCK cell monolayer assay. Computationally, each compound was subjected to extensive conformational search and physics-based permeability prediction, and multiple linear regression analyses were subsequently performed to determine, empirically, the relative contributions of hydrophobicity and molecular size to passive permeation in the RRCK assay. Additional analyses of Log D and PAMPA data suggest that these measurements are not size selective, a possible reason for their sometimes weak correlation with cell-based permeability.

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