Prediction of Progestin Affinity for the Human Progesterone Receptor Based on Corrected RBA Data

  • A.V. Mikurova Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
  • V.S. Skvortsov Institute of Biomedical Chemistry, 10 Pogodinskaya str., Moscow, 119121 Russia
Keywords: MM-PBSA; molecular dynamics; molecular docking; affinity; progesterone receptor


The modeling of complexes of 3 sets of steroid and nonsteroidal progestins with the ligand-binding domain of the nuclear progesterone receptor was performed. Molecular docking procedure, long-term simulation of molecular dynamics and subsequent analysis by MM-PBSA (MM-GBSA) were used to model the complexes. Using the characteristics obtained by the MM-PBSA method two data sets of steroid compounds obtained in different scientific groups a prediction equation for the value of relative binding activity (RBA) was constructed. The RBA value was adjusted so that in all samples the actual activity was compared with the progesterone activity. The third data set of nonsteroidal compounds was used as a test. The resulted equation showed that the prediction results could be applied to both steroid molecules and nonsteroidal progestins.


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