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J Mol Graph Model. 2003 Jan;21(4):273-87.

Hydrogen bonding descriptors in the prediction of human in vivo intestinal permeability.

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Department of Medicinal Chemistry, BMC, Uppsala University, SE-751 23 Uppsala, Sweden.


Hydrogen bonding has been identified as an important parameter for describing drug permeability. Recently, we derived models for predicting intestinal permeability using the hydrogen bonding descriptors polar surface area (PSA) and number of hydrogen bond donors (HBD), and a lipophilicity descriptor [J. Med. Chem. 41 (1998) 4939]. We have now explored other types of hydrogen bonding descriptors to see if these improve the models. Both an experimental hydrogen bonding descriptor, deltalogP, and calculated descriptors, based either on semiempirical calculations or on experimentally derived hydrogen bond strength values of small molecules, were used. Principal component analyses (PCA) were performed in order to characterize the different parameters, using both a drug data set and a data set of small non-drug-like molecules for which deltalogP-values had been published. For a set of diverse drug molecules, for which human intestinal permeability data was available, a PLS-analysis was performed to study the correlation of permeability to the different hydrogen bonding parameters. No correlation could be identified between deltalogP and human intestinal permeability in this data set. However, the combination of a hydrogen bond donor descriptor, a general hydrogen bonding descriptor and a lipophilicity descriptor enabled the prediction of human intestinal permeability, whereas hydrogen bond acceptor descriptors were found to be less important. The obtained models successfully predicted the intestinal permeability values of two external data sets.

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