Classification Analysis of P-Glycoprotein Substrate Specificity

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Abstract
Prediction of P-glycoprotein substrate specificity (SPGP) can be viewed as a constituent part of a compound's “pharmaceutical profiling” in drug design. This task is difficult to achieve due to several factors that raised many contradictory opinions: (i) the disparity between the SPGP values obtained in different assays, (ii) the confusion between Pgp substrates and inhibitors, (iii) the confusion between lipophilicity and amphiphilicity of Pgp substrates, and (iv) the dilemma of describing class-specific relationships when Pgp has no binding sites of high ligand specificity. In this work, we compiled SPGP data for 1000 compounds. All data were represented in a binary format, assigning SPGP=1 for substrates and SPGP=0 for non-substrates. Each value was ranked according to the reliability of experimental assay. Two data sets were considered. Set 1 included 220 compounds with SPGP from polarized transport across MDR1 transfected cell monolayers. Set 2 included the entire list of 1000 compounds, with SPGP values of generally lower reliability. Both sets were analysed using a stepwise classification structure–activity relationship (C-SAR) method, leading to derivation of simple rules for crude estimation of SPGP values. The obtained rules are based on the following factors: (i) compound's size expressed through molar weight or volume, (ii) H-accepting given by the Abraham's β (that can be crudely approximated by the sum of O and N atoms), and (iii) ionization given by the acid and base pKa values. Very roughly, SPGP can be estimated by the “rule of fours”. Compounds with (N+O)≥8, MW>400 and acid pKa > 4 are likely to be Pgp substrates, whereas compounds with (N+O)≤4, MWpKa<8 are likely to be non-substrates. The obtained results support the view that Pgp functioning can be compared to a complex “mini-pharmacokinetic” system with fuzzy specificity. This system can be described by a probabilistic version of Abraham's solvation equation, suggesting a certain similarity between Pgp transport and chromatographic retention. The chromatographic model does not work in the case of “marginal” compounds with properties close to the “global” physicochemical cut-offs. In the latter case various class-specific rules must be considered. These can be associated with the “amphiphilicity” and “biological similarity” of compounds. The definition of class-specific effects entails construction of the knowledge base that can be very useful in ADME profiling of new drugs.

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