Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Jun 4:7:406.
doi: 10.3389/fchem.2019.00406. eCollection 2019.

Deciphering the Allosteric Effect of Antagonist Vismodegib on Smoothened Receptor Deactivation Using Metadynamics Simulation

Xiaoli An  1 , Qifeng Bai  1 , Fang Bai  2 , Danfeng Shi  1 , Huanxiang Liu  2 , Xiaojun Yao  1   3
Affiliations

Deciphering the Allosteric Effect of Antagonist Vismodegib on Smoothened Receptor Deactivation Using Metadynamics Simulation

Xiaoli An et al. Front Chem. .

Abstract

The smoothened receptor (Smo) plays a key role in Hedgehog (Hh) signaling pathway and it has been regarded as an efficacious therapeutic target for basal cell carcinoma (BCC) and medulloblastoma (MB). Nevertheless, the resistance mutation and active mutants of Smo have put forward the requirement of finding more effective inhibitors. Herein, we performed metadynamics simulations on Smo bound with vismodegib (Smo-Vismod) and with cholesterol (Smo-CLR), respectively, to explore the inhibition mechanism of vismodegib. The simulation results indicated that vismodegib-induced shifts of TM5, TM6, and TM7, which permitted the extracellular extension of TM6 and extracellular loop3 (ECL3) to enter the extracellular cysteine-rich domain (CRD) groove. Therefore, an open CRD groove that has not been noticed previously was observed in Smo-Vismod complex. As a consequence, the occupied CRD groove prevents the binding of cholesterol. In addition, the HD and ECLs play crucial roles in the interaction of CRD and TMD. These results reveal that TM5, TM6, and TM7 play important roles in allosteric inhibition the activation of Smo and disrupting cholesterol binding by vismodegib binding. Our results are expected to contribute to understanding the allosteric inhibition mechanism of Smo by vismodegib. Moreover, the detailed conformational changes contribute to the development of novel Smo inhibitors against resistance mutation and active mutants of Smo.

Keywords: allosteric inhibition mechanism; cholesterol; metadynamics simulation; smoothened receptor; vismodegib.

PubMed Disclaimer

Figures

Figure 1
Figure 1
The two-dimensional maps of the free energy surfaces along d1 and d2 of Smo-Vismod (A) and Smo-CLR (B). The marked black triangles represent the position of d1 and d2 of the crystal structures.
Figure 2
Figure 2
(a) The representative structures of Smo-Vismod (forest) and Smo-CLR (marine) at the free-energy minima. (b,c) Hydrophobic interaction formed among CRD groove, HD, TM6 and ECL3 of Smo-CLR and Smo-Vismod respectively; (d) the conformational comparison of CRDs between Smo-Vismod and Smo-CLR; (e) conformational comparison of TMD-sites between Smo-Vismod and Smo-CLR.
Figure 3
Figure 3
The evolution of d1 and d2 along time of Smo-Vismod (A) and Smo-CLR (B). The solvent accessible surface area (SASA) of the hydrophobic pockets consisted of hydrophobic residues of CRD groove, HD, helix VI and ELC3 evolve with time for Smo-Vismod (C) and Smo-CLR (D).
Figure 4
Figure 4
(A,B) The conformational dynamics of ECDs of basins 4 (orange), 3 (yellow-orange), 2 (light green), and 1 (forest) of Smo-Vismod compared with the crystal structure (white). (C) The conformational changes of the CRD. (D) The conformational changes of HD.
Figure 5
Figure 5
(A) The binding mode of vismodegib of the represent structure in free energy minima (forest) varied compared with the crystal structure (white). (B) The RMSD of heavy atoms of vismodegib evolved along with time. (C) The distance between the atom O3 of vismodegib and the atom ND2 of N219 evolved along with time.
Figure 6
Figure 6
The conformational changes of TMD-site. (A) The center mass distance between the side chain of R400 and E518 evolved along with time in the Smo-Vismod (forest) and Smo-CLR (marine). (B) The distance of the extracellular end of TM5 (residues 397-401) and TM7 (residues 515-519) evolved along with time. (C) The scatter plot of dihedral of C, CA, CB, and CG of D473 between the Smo-Vismod and Smo-CLR. (D) The distance of the extracellular end of TM3 (residues 315-319) and TM6 (residues 488-492) evolved along with time. (E) The conformational changes of R400, D473 and E518. (F) The movements of TM5, TM6, and TM7.
Figure 7
Figure 7
(A) The conformational dynamics of ICDs of basins 4 (orange), 3 (yellow-orange), 2 (light green), and 1 (forest) in the Smo-Vismod. (B) The conformational dynamics of ICDs of basins 1 (marine) and 2 (cyan) in Smo-CLR.
Figure 8
Figure 8
The communication between the multiple domains of Smo-Vismod (A) and Smo-CLR (B).
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Arensdorf A. M., Marada S., Ogden S. K. (2016). Smoothened regulation: a tale of two signals. Trends Pharmacol. Sci. 37, 62–72. 10.1016/j.tips.2015.09.001 - DOI - PMC - PubMed
    1. Bai Q., Shen Y., Jin N., Liu H., Yao X. (2014). Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation. Biochim. Biophys. Acta 1840, 2128–2138. 10.1016/j.bbagen.2014.03.010 - DOI - PubMed
    1. Bender M. H., Hipskind P. A., Capen A. R., Cockman M., Credille K. M., Gao H., et al. (2011). Identification and characterization of a novel smoothened antagonist for the treatment of cancer with deregulated hedgehog signaling. Cancer Res. 71, 2819–2819. 10.1158/1538-7445.AM2011-2819 - DOI
    1. Byrne E. F. X., Sircar R., Miller P. S., Hedger G., Luchetti G., Nachtergaele S., et al. . (2016). Structural basis of Smoothened regulation by its extracellular domains. Nature 535, 517–522. 10.1038/nature18934 - DOI - PMC - PubMed
    1. Chen J. K., Taipale J., Cooper M. K., Beachy P. A. (2002a). Inhibition of Hedgehog signaling by direct binding of cyclopamine to Smoothened. Genes Dev. 16, 2743–2748. 10.1101/gad.1025302 - DOI - PMC - PubMed