A mathematical study was performed on a set of phosphonic acid derivatives that are substrates for thyroid hormone receptor beta (TRbeta) and thyroid hormone receptor alpha (TRalpha), three-dimensional quantitative structure-activity relationship (3D-QSAR) models using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods were employed to investigate the structural requirements for this series of compounds with improved activity. Some descriptors were also employed to significantly improve the performance of the derived models. The CoMFA model for TRbeta exhibited Rcv(2) of 0.612, Rpred(2) of 0.7218, whereas CoMSIA model showed Rcv(2) of 0.621, R(2)pred of 0.7358; the CoMFA model for TRalpha displayed Rcv(2) of 0.678, Rpred(2) of 0.6424, and the CoMSIA model had Rcv(2) of 0.671, Rpred(2) of 0.6932, which indicate that the constructed models are statistically significant. The derived contour maps further pointed out the regions where interactive fields may influence the activity. In order to validate the QSAR models and explore the origin of the selectivity at the amino acid level, molecular docking was developed, and the results indicate that Arg282, Arg320, Asn331, Gly332, Thr329 and His435 for TRbeta, but Ala225, Arg228, Met259, Arg262 and His381 for TRalpha, respectively are important residues. The information obtained from the QSAR models can be used in the design of more potent TR agonists.
Wang, F-F., Yang, W. W., Shi, Y-H., & Le, G-W. (2015). Molecular determinants of thyroid hormone receptor selectivity in a series of phosphonic acid derivatives: 3D-QSAR analysis and molecular docking. Chemico-Biological Interactions, 240, 324 - 335. https://doi.org/10.1016/j.cbi.2015.09.008