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D4 dopamine receptor high-resolution structures enable the discovery of selective agonists

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Science  20 Oct 2017:
Vol. 358, Issue 6361, pp. 381-386
DOI: 10.1126/science.aan5468
  • Fig. 1 Human DRD4-nemonapride complex crystal structure.

    (A) Overview of the DRD4-nemonapride complex structure, with water molecules depicted as red spheres. (B) Conformation of the binding pocket, with nemonapride shown as sticks with magenta carbons. The protein is displayed in cartoon representation, with the 11 contact residues within 4.0 Å from the ligand shown as slate-blue sticks. Structured water molecules are shown as red spheres. Ballesteros-Weinstein numbering is shown in superscript. (C) Diagram of ligand interactions in the binding pocket side chains at a 4.0-Å cutoff. Hydrogen bonds are shown with dashed lines. (D) Side views of the sliced binding pocket in the DRD4-nemonapride and DRD3-eticlopride complexes. The pocket surfaces are colored gray. Ligands are shown as capped sticks with carbons colored magenta (nemonapride) and orange (eticlopride). (E) Structural differences in the EBPs of DRD4 (slate blue) and DRD3 (green). Ligands are colored as in (D). Single-letter abbreviations for the amino acid residues are as follows: A, Ala; C, Cys; D, Asp; E, Glu; F, Phe; G, Gly; H, His; I, Ile; K, Lys; L, Leu; M, Met; N, Asn; P, Pro; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; W, Trp; and Y, Tyr.

  • Fig. 2 Structural and functional details of the DRD4’s allosteric Na+ site.

    (A) Close-ups of respective Na+ allosteric pockets in A2AAR (magenta), δ-OR (green), sodium-free DRD4 (slate blue, left), and sodium-bound DRD4 (slate blue, right). Receptors are shown as transparent cartoons, and residues lining the Na+ cavity are shown as sticks and labeled according to the Ballesteros-Weinstein scheme. Water molecules in the cluster are shown as red spheres. Na+ is displayed as a yellow sphere. The salt bridge between Na+ and D2.50 and hydrogen bonds are shown as gray dotted lines. (B to E) The allosteric effect of graded concentrations of sodium on DAMGO, DADLE, NECA, or dopamine affinity were respectively measured at μ-OR (B), δ-OR (C), A2AAR (D), and DRD4 (E). KB, equilibrium dissociation constant of modulator binding to its allosteric site. Error bars, SEM.

  • Fig. 3 Structure-guided discovery of selective DRD4 agonists.

    (A) Structure-based strategy for discovery of DRD4 chemotypes from docking screens of large virtual libraries (EES, electrostatic energy; EVDW, van der Waals interaction energy; Elig,desol, ligand desolvation energy). (B) Single-point competition binding assay of 10 candidate molecules against the DRD4 antagonist 3H-N-methylspiperone. Each ligand was tested at 5 μM, and the data shown are means ± SEM (n = 3 measurements). (C and D) Docking poses of compounds 3 (C) and 9 (D). DRD4 is shown in tan, and compounds are shown as capped sticks with carbons colored cyan (compound 3) and green (compound 9). Ballesteros-Weinstein numbering is shown in superscript.

  • Fig. 4 Structure-guided compound optimization toward potent and selective DRD4 agonists.

    (A) Overview of structure-guided “analog-by-catalog” optimization toward compound 9-6-24. EC50, median effective concentration. (B and C) Docking poses of compounds 9-6 (B) and 9-6-24 (C). Both optimized analogs have a simplified right-hand linker while maintaining key interactions and occupying the EBP. DRD4 is shown in tan, and compounds are shown as capped sticks with carbons colored pink (compound 9-6) and green (compound 9-6-24). Ballesteros-Weinstein numbering is shown in superscript. (D and E) Normalized concentration-response studies for compounds 9-6 (D) and 9-6-24 (E) in human-cloned DRD4-mediated activation of Gαi/o and arrestin translocation. Error bars, SEM from a minimum of three assays. Details regarding bias factor calculation can be found in the methods. (F and G) Compounds 9-6 (F) and 9-6-24 (G) were screened against 320 nonolfactory GPCRs for agonism in the arrestin recruitment TANGO assay. Each point shows luminescence normalized to the basal level at a given GPCR. Error bars, SEM.

Supplementary Materials

  • D4 dopamine receptor high-resolution structures enable the discovery of selective agonists

    Sheng Wang, Daniel Wacker, Anat Levit, Tao Che, Robin M. Betz, John D. McCorvy, A. J. Venkatakrishnan, Xi-Ping Huang, Ron O. Dror, Brian K. Shoichet, Bryan L. Roth

    Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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    • Materials and Methods 
    • Figs. S1 to S16 
    • Tables S1 to S13 
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    Data S1

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