Discovery of a small-molecule inhibitor of Dvl–CXXC5 interaction by computational approaches
The Wnt/β-catenin signaling pathway plays a significant role in the control of osteoblastogenesis and bone formation. CXXC finger protein 5 (CXXC5) has been recently identified as a negative feedback regulator of osteoblast differentiation through a specific interaction with Dishevelled (Dvl) protein. It was reported that targeting the Dvl–CXXC5 interaction could be a novel anabolic therapeutic target for osteoporosis. In this study, complex structure of Dvl PDZ domain and CXXC5 peptide was simulated with molecular dynamics (MD). Based on the structural analysis of binding modes of MD-simulated Dvl PDZ domain with CXXC5 peptide and crystal Dvl PDZ domain with synthetic peptide–ligands, we generated two different pharmacophore models and applied pharmacophore-based virtual screening to discover potent inhibitors of the Dvl–CXXC5 interaction for the anabolic therapy of osteoporosis. Analysis of 16 compounds selected by means of a virtual screening protocol yielded four compounds that effectively disrupted the Dvl–CXXC5 interaction in the fluorescence polarization assay. Potential compounds were validated by fluorescence spectroscopy and nuclear magnetic resonance. We successfully identified a highly potent inhibitor, BMD4722, which directly binds to the Dvl PDZ domain and disrupts the Dvl–CXXC5 interaction. Overall, CXXC5–Dvl PDZ domain complex based pharmacophore combined with various traditional and simple computational methods is a promising approach for the development of modulators targeting the Dvl–CXXC5 interaction, and the potent inhibitor BMD4722 could serve as a starting point to discover or design more potent and specific the Dvl–CXXC5 interaction disruptors.
KeywordsWnt/β-catenin signaling pathway Dvl–CXXC5 interaction Pharmacophore Virtual screening Molecular dynamics simulation Nuclear magnetic resonance
This work was supported by the Ministry of Knowledge Economy through Korea Research Institute of Chemical Technology (SI-1205, SI-1304, SI-1404), and Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2016R1A6A3A04010213).
- 9.Kim HY, Yoon JY, Yun JH, Cho KW, Lee SH, Rhee YM, Jung HS, Lim HJ, Lee H, Choi J, Heo JN, Lee W, No KT, Min D, Choi KY (2015) CXXC5 is a negative-feedback regulator of the Wnt/[beta]-catenin pathway involved in osteoblast differentiation. Cell Death Differ 22(6):912–920. https://doi.org/10.1038/cdd.2014.238 CrossRefGoogle Scholar
- 11.Kim MS, Yoon SK, Bollig F, Kitagaki J, Hur W, Whye NJ, Wu YP, Rivera MN, Park JY, Kim HS, Malik K, Bell DW, Englert C, Perantoni AO, Lee SB (2010) A novel Wilms tumor 1 (WT1) target gene negatively regulates the WNT signaling pathway. J Biol Chem 285(19):14585–14593. https://doi.org/10.1074/jbc.M109.094334 CrossRefGoogle Scholar
- 14.Grandy D, Shan J, Zhang X, Rao S, Akunuru S, Li H, Zhang Y, Alpatov I, Zhang XA, Lang RA, Shi DL, Zheng JJ (2009) Discovery and characterization of a small molecule inhibitor of the PDZ domain of dishevelled. J Biol Chem 284(24):16256–16263. https://doi.org/10.1074/jbc.M109.009647 CrossRefGoogle Scholar
- 17.Fujii N, You L, Xu Z, Uematsu K, Shan J, He B, Mikami I, Edmondson LR, Neale G, Zheng J, Guy RK, Jablons DM (2007) An antagonist of dishevelled protein-protein interaction suppresses β-catenin–dependent tumor cell growth. Can Res 67(2):573–579. https://doi.org/10.1158/0008-5472.can-06-2726 CrossRefGoogle Scholar
- 21.Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, November 11–17Google Scholar
- 27.Schrodinger LLC (2010) The PyMOL molecular graphics system, version 1.3r1Google Scholar