Fingerprint-based in silico models for the prediction of P-glycoprotein substrates and inhibitors

Bioorg Med Chem. 2012 Sep 15;20(18):5388-95. doi: 10.1016/j.bmc.2012.03.045. Epub 2012 Mar 29.


P-Glycoprotein (P-gp, ABCB1) plays a significant role in determining the ADMET properties of drugs and drug candidates. Substrates of P-gp are not only subject to multidrug resistance (MDR) in tumor therapy, they are also associated with poor pharmacokinetic profiles. In contrast, inhibitors of P-gp have been advocated as modulators of MDR. However, due to the polyspecificity of P-gp, knowledge on the molecular basis of ligand-transporter interaction is still poor, which renders the prediction of whether a compound is a P-gp substrate/non-substrate or an inhibitor/non-inhibitor quite challenging. In the present investigation, we used a set of fingerprints representing the presence/absence of various functional groups for machine learning based classification of a set of 484 substrates/non-substrates and a set of 1935 inhibitors/non-inhibitors. Best models were obtained using a combination of a wrapper subset evaluator (WSE) with random forest (RF), kappa nearest neighbor (kNN) and support vector machine (SVM), showing accuracies >70%. Best P-gp substrate models were further validated with three sets of external P-gp substrate sources, which include Drug Bank (n = 134), TP Search (n = 90) and a set compiled from literature (n = 76). Association rule analysis explores the various structural feature requirements for P-gp substrates and inhibitors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATP Binding Cassette Transporter, Subfamily B, Member 1 / antagonists & inhibitors*
  • ATP Binding Cassette Transporter, Subfamily B, Member 1 / chemistry
  • ATP Binding Cassette Transporter, Subfamily B, Member 1 / metabolism
  • Algorithms
  • Computational Biology*
  • Databases, Pharmaceutical
  • Drug Substitution
  • Models, Molecular
  • Molecular Structure


  • ATP Binding Cassette Transporter, Subfamily B, Member 1