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Hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens
(2013)
With this work we target the development of a predictictive model for the identification of small molecules which bind to the estrogen receptor alpha and, thus, may act as endocrine disruptors. We propose a combined thermodynamic approach for the estimation of preferential binding modes along with corresponding free energy differences using a linear interaction energy (LIE) ansatz. The LIE model is extended by a Monte Carlo approach for the computation of conformational entropies as recently developed by our group. Incorporating the entropy contribution substantially increased the correlation with experimental affinity values. Both squared coefficients for the fitted data as well as the more meaningful leave-one-out cross-validation of predicted energies were elevated up to rFit2 = 0.87 and qLOO2 = 0.82, respectively. All calculations have been performed on a set of 31 highly diverse ligands regarding their structural properties and affinities to the estrogen receptor alpha. Comparison of predicted ligand orientations with crystallographic data retrieved from the Protein database pdb.org revealed remarkable binding mode predictions.
Commercially available linear alkylbenzenesulfonates (LASs) are a mixture of various homologues and isomers, leading to 20 major species. In this work we investigated the commercial product by liquid chromatography-solid phase extraction-nuclear magnetic resonance spectroscopy-mass spectrometry (LC-SPE-NMR/MS). The commercial product was separated into 17 fractions by liquid chromatography (LC). After chromatographic separation, 5% of the flow was split to a mass spectrometer (MS) while 95% was send to post-column solid phase extraction cartridges for enrichment of the analytes (LC-SPE). After elution from the SPE-cartridges a NMR-spectrometer equipped with a cryo-probe was used for the characterisation of the different LASs species. For the first time H-1-1D and H-H-COSY spectra for 14 LASs species out of 20 major isomers are presented, whereas the 6 remaining species are detected as mixtures in 3 H-1-1D and H-H-COSY spectra. These data were used to correlate the chromatographic retention of the LASs isomers to the substitution pattern of the alkyl chain.