Structures and Conformations of Estrogen-Related Ligands

Structures of ligands (Figure 2) were retrieved from the PubChem database [60 (link)]: 17β-estradiol (ID: 5757), estrone (ID: 5870), DES (ID: 448537), tamoxifen (ID: 2733526), endoxifen (ID: 10090750) and afimoxifene (ID: 449459). For accurate 3D ligand model generation and conformational sampling, all ligands were subjected to structure refinement, tautomeric and ionization state prediction, and an optimization procedure using LigPrep suite [61 ] in Schrödinger software with application of the OPLS3e force field. Protonated states were generated at pH 7.4 ± 1.0 with implementation of the Epik algorithm version 4.4 [62 (link)]. For each ligand, 32 possible stereo-isomeric forms were set.

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Moldogazieva N.T., Ostroverkhova D.S., Kuzmich N.N., Kadochnikov V.V., Terentiev A.A, & Porozov Y.B. (2020). Elucidating Binding Sites and Affinities of ERα Agonists and Antagonists to Human Alpha-Fetoprotein by In Silico Modeling and Point Mutagenesis. International Journal of Molecular Sciences, 21(3), 893.

Publication 2020

17β estradiol Afimoxifene Endoxifen Estrone Isomeric Ligand Tamoxifen

Corresponding Organization : Sechenov University

Other organizations : Lomonosov Moscow State University, Research Institute of Influenza, ITMO University, Pirogov Russian National Research Medical University

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Variable analysis

independent variables

Structure refinement
Tautomeric and ionization state prediction
Optimization procedure using LigPrep suite
Application of the OPLS3e force field
Generation of protonated states at pH 7.4 ± 1.0 with Epik algorithm version 4.4
Setting 32 possible stereo-isomeric forms for each ligand

dependent variables

3D ligand model generation and conformational sampling

control variables

PH 7.4 ± 1.0

controls

No positive or negative controls were explicitly mentioned.

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