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Research Themes Protein design

Design and Discovery: Virtual Drug Screening

SBKB [doi:10.1038/sbkb.2012.180]
Technical Highlight - January 2014
Short description: Optimized crystal structure-based models yield diverse hits in a virtual screen targeting G protein-coupled receptor allosteric and orthosteric ligand-binding sites.

D3RDopa model for allosteric ligand screening, with dopamine shown in space-filling spheres. Compound #26, a new allosteric negative modulator of dopamine signaling (pIC50 = 6.31), is shown in a stick representation with yellow carbon atoms. Figure courtesy of Seva Katrich.

G protein-coupled receptors (GPCRs) are involved in numerous signaling pathways, making these transmembrane proteins potential key targets of therapeutic drugs. Recent advances in the crystallography of membrane proteins have given researchers multiple views of these notoriously difficult-to-study proteins, prompting virtual ligand screens (VLS) albeit with reportedly varied success rates. To address the utility of VLS, Katritch and colleagues (PSI GPCR Network), in collaboration with researchers from the Melbourne Institute of Pharmaceutical Sciences, Australia, screened for ligands targeting binding sites of the dopamine D3 receptor (D3R).

First, the authors performed ligand-guided receptor optimization to generate models of a D3R binding pocket in the apo (D3RAPO) and dopamine-bound (D3RDopa) states, the latter for the screening of ligands targeting a putative allosteric site. Though optimization of the D3RAPO model only slightly altered residue positions in the main orthosteric binding site (r.m.s. deviation of ∼0.9Å), validation with known D3R ligands revealed improved results.

Using these optimized models, the researchers performed VLS on a library of 4.1 million compounds. After eliminating closely related compounds and those similar to known D3R ligands, they tested the 25 top-scoring candidates for each model. Using a Ki cutoff of 10 μM in binding assays, they obtained hit rates of 56% and 32% for the D3RAPO and D3RDopa candidate sets, respectively.

In functional assays measuring the effect of candidate allosteric ligands on dopamine-induced phosphorylation of ERK1/2, two compounds had no effect, two increased phosphorylation, and the rest decreased phosphorylation to various degrees, revealing the range of functionality among identified ligands. Importantly, this approach proved its mettle with the identification of a putative novel class of D3R allosteric ligands. Thus, VLS with optimized structure-based models can be an effective complement to current drug discovery approaches as more GPCR structures become available.

Irene Kaganman

References

  1. J.R. Lane et al. Structure-based ligand discovery targeting orthosteric and allosteric pockets of dopamine receptors.
    Mol. Pharmacol. 84, 794-807 (2013). doi:10.1124/mol.113.088054

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