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Computational models to predict blood–brain barrier permeation and CNS activity

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Abstract

The blood–brain permeation of a structurally diverse set of 281 compounds was modeled using linear regression and a multivariate genetic partial least squares (G/PLS) approach. Key structural features affecting the logarithm of blood–brain partitioning (logBB) were captured through statistically significant quantitative structure–activity relationship (QSAR) models. These relationships reveal the importance of logP, polar surface area, and a variety of electrotopological indices for accurate predictions of logBB. The best models reveal an excellent correlation (r > 0.9) for a training set of 58 compounds. Likewise, the comparison of the average logBB values obtained from an ensemble of QSAR models with experimental values also verifies the statistical quality of the models (r > 0.9). The models provide good agreement (r ∼ 0.7) between the predicted logBB values for 34 molecules in the external validation set and the experimental values. To further validate the models for use during the drug discovery process, a prediction set of 181 drugs with reported CNS penetration data was used. A >70% success rate is obtained by using any of the QSAR models in the qualitative prediction for CNS permeable (active) drugs. A lower success rate (∼60%) was obtained for the best model for CNS impermeable (inactive) drugs. Combining the predictions obtained from all the models (consensus) did not significantly improve the discrimination of CNS active and CNS inactive molecules. Finally, using the therapeutic classification as a guiding tool, the CNS penetration capability of over 2000 compounds in the Synthline® database was estimated. The results were very similar to the smaller set of 181 compounds.

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  1. Govindan Subramanian

    Present address: Transtech Pharma, 41702 Mendenhall Oaks Parkway, High Point, NC, 27265, USA

Authors and Affiliations

  1. Medicinal Chemistry Department, Albany Molecular Research, Inc., 21 Corporate Circle, P.O. Box 15098, Albany, NY, 12212-5098, USA

    Govindan Subramanian & Douglas B. Kitchen

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  1. Govindan Subramanian
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  2. Douglas B. Kitchen
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Subramanian, G., Kitchen, D.B. Computational models to predict blood–brain barrier permeation and CNS activity. J Comput Aided Mol Des 17, 643–664 (2003). https://doi.org/10.1023/B:JCAM.0000017372.32162.37

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  • DOI: https://doi.org/10.1023/B:JCAM.0000017372.32162.37

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