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. 2013 Feb;10(2):140-6.
doi: 10.1038/nmeth.2324. Epub 2013 Jan 6.

A Pharmacological Organization of G Protein-Coupled Receptors

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Free PMC article

A Pharmacological Organization of G Protein-Coupled Receptors

Henry Lin et al. Nat Methods. .
Free PMC article

Abstract

Protein classification typically uses structural, sequence or functional similarity. Here we introduce an orthogonal method that organizes proteins by ligand similarity, focusing on the class A G-protein-coupled receptor (GPCR) protein family. Comparing a ligand-based dendrogram to a sequence-based one, we identified GPCRs that were distantly linked by sequence but were neighbors by ligand similarity. Experimental testing of the ligands predicted to link three of these new pairs confirmed the predicted association, with potencies ranging from low nanomolar to low micromolar. We also predicted hundreds of non-GPCRs closely related to GPCRs by ligand similarity and confirmed several cases experimentally. Ligand similarities among these targets may reflect the conservation of identical ligands among unrelated receptors, which signal in different time domains. Our method integrates these apparently disparate receptors into chemically coherent circuits and suggests which of these receptors may be targeted by individual ligands.

Conflict of interest statement

Competing Financial Interest

BKS declares a competing financial interest: he is the founder of SeaChange Pharmaceuticals, which uses chemoinformatics for target prediction. All other authors declare no competing interests.

Figures

Figure 1
Figure 1
Dendrograms of human GPCRs with annotated ligands from ChEMBL. Organization based on (a) sequence similarity in the binding site and (b) ligand set similarity based on SEA E-values. Color coding is based on chemistry of their endogenous ligands (i.e. Bioamines (blue), melatonins (gold), lipids (green), peptides (black), purinergics (dark blue), adenosines (light blue), orphans (red).).
Figure 2
Figure 2
Dose-response curves of new GPCR cross-activities. (a–e) Radioligand competition binding assay: compound 1 at HTR2B (a) and OPRK (b), compound 2 at NPY5R (c), compound 3 at MTR1B (d) and NPY5R (e). Data represent mean values ± s.e.m, performed on triplicate experiments.
Figure 3
Figure 3
Non-GPCRs (orange) highly-related to particular GPCRs by ligand similarity (color code is as in Figure 1). Bolded targets have known ligands that bind to both the GPCR and non-GPCR target. Links that share known messengers are labeled in black in parenthesis.
Figure 4
Figure 4
Dose-response curves of new GPCR cross-activities with non-GPCRs. Testing new GPCR cross-activities with non-GPCRs. β-Arrestin Recruitment Tango Assay: compound 4 at CXCR2 (a), competition binding assay: compound 5 at α2c Adrenergic receptor (b), compound 6 at CNR1 (c) and CNR2 (d). Data represent mean values ± s.e.m, performed on triplicate experiments.

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