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Structure-based discovery of A2A adenosine receptor ligands.

Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA - J. Med. Chem. (2010)

Bottom Line: We used molecular docking to screen a 1.4 million compound database against the X-ray structure computationally and tested 20 high-ranking, previously unknown molecules experimentally.Of these 35% showed substantial activity with affinities between 200 nM and 9 microM.For the most potent of these new inhibitors, over 50-fold specificity was observed for the A(2A) versus the related A(1) and A(3) subtypes.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Chemistry, University of California, 1700 4th Street, Box 2550, San Francisco, California 94158, USA.

ABSTRACT
The recent determination of X-ray structures of pharmacologically relevant GPCRs has made these targets accessible to structure-based ligand discovery. Here we explore whether novel chemotypes may be discovered for the A(2A) adenosine receptor, based on complementarity to its recently determined structure. The A(2A) adenosine receptor signals in the periphery and the CNS, with agonists explored as anti-inflammatory drugs and antagonists explored for neurodegenerative diseases. We used molecular docking to screen a 1.4 million compound database against the X-ray structure computationally and tested 20 high-ranking, previously unknown molecules experimentally. Of these 35% showed substantial activity with affinities between 200 nM and 9 microM. For the most potent of these new inhibitors, over 50-fold specificity was observed for the A(2A) versus the related A(1) and A(3) subtypes. These high hit rates and affinities at least partly reflect the bias of commercial libraries toward GPCR-like chemotypes, an issue that we attempt to investigate quantitatively. Despite this bias, many of the most potent new ligands were novel, dissimilar from known ligands, providing new lead structures for modulation of this medically important target.

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Representative dose−response curves for displacement of binding of the radiolabeled A2A AR agonist 3 by compounds 9, 10, and 11.
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fig2: Representative dose−response curves for displacement of binding of the radiolabeled A2A AR agonist 3 by compounds 9, 10, and 11.

Mentions: The 20 compounds selected from the docking screen were tested for binding in a radioligand displacement assay. Seven of these molecules inhibited binding by ≥40% at 20 μM, corresponding to a “hit rate” of 35%. Subsequent dose−response curves were well-behaved, with Ki values varying from 200 nM to 8.8 μM (Table 1 and Figure 2). Four of the ligands, 9, 10, 11 and 13, were counterscreened for colloidal aggregation, a common mechanism of artifactual inhibition.(51) No colloidal particles were observed at 10 μM, by dynamic light scattering, for 9 and 13, nor did they inhibit cruzain at the same concentration. For compounds 10 and 11, particles were observed at 10 μM, but for 10 these appeared to be precipitant rather than colloids and this compound did not inhibit cruzain up to 10 μM. For compound 11 particles were observed at 10 μM, as was enzyme inhibition, but this inhibition was not reversible by detergent, inconsistent with colloidal aggregation. Furthermore, no inhibition of AmpC β-lactamase was observed up to 10 μM for 9 and 11. Taken together with the well-behaved dose−response curves (Figure 2), these results indicate that the molecules are well behaved, classical binding ligands.


Structure-based discovery of A2A adenosine receptor ligands.

Carlsson J, Yoo L, Gao ZG, Irwin JJ, Shoichet BK, Jacobson KA - J. Med. Chem. (2010)

Representative dose−response curves for displacement of binding of the radiolabeled A2A AR agonist 3 by compounds 9, 10, and 11.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2865168&req=5

fig2: Representative dose−response curves for displacement of binding of the radiolabeled A2A AR agonist 3 by compounds 9, 10, and 11.
Mentions: The 20 compounds selected from the docking screen were tested for binding in a radioligand displacement assay. Seven of these molecules inhibited binding by ≥40% at 20 μM, corresponding to a “hit rate” of 35%. Subsequent dose−response curves were well-behaved, with Ki values varying from 200 nM to 8.8 μM (Table 1 and Figure 2). Four of the ligands, 9, 10, 11 and 13, were counterscreened for colloidal aggregation, a common mechanism of artifactual inhibition.(51) No colloidal particles were observed at 10 μM, by dynamic light scattering, for 9 and 13, nor did they inhibit cruzain at the same concentration. For compounds 10 and 11, particles were observed at 10 μM, but for 10 these appeared to be precipitant rather than colloids and this compound did not inhibit cruzain up to 10 μM. For compound 11 particles were observed at 10 μM, as was enzyme inhibition, but this inhibition was not reversible by detergent, inconsistent with colloidal aggregation. Furthermore, no inhibition of AmpC β-lactamase was observed up to 10 μM for 9 and 11. Taken together with the well-behaved dose−response curves (Figure 2), these results indicate that the molecules are well behaved, classical binding ligands.

Bottom Line: We used molecular docking to screen a 1.4 million compound database against the X-ray structure computationally and tested 20 high-ranking, previously unknown molecules experimentally.Of these 35% showed substantial activity with affinities between 200 nM and 9 microM.For the most potent of these new inhibitors, over 50-fold specificity was observed for the A(2A) versus the related A(1) and A(3) subtypes.

View Article: PubMed Central - PubMed

Affiliation: Department of Pharmaceutical Chemistry, University of California, 1700 4th Street, Box 2550, San Francisco, California 94158, USA.

ABSTRACT
The recent determination of X-ray structures of pharmacologically relevant GPCRs has made these targets accessible to structure-based ligand discovery. Here we explore whether novel chemotypes may be discovered for the A(2A) adenosine receptor, based on complementarity to its recently determined structure. The A(2A) adenosine receptor signals in the periphery and the CNS, with agonists explored as anti-inflammatory drugs and antagonists explored for neurodegenerative diseases. We used molecular docking to screen a 1.4 million compound database against the X-ray structure computationally and tested 20 high-ranking, previously unknown molecules experimentally. Of these 35% showed substantial activity with affinities between 200 nM and 9 microM. For the most potent of these new inhibitors, over 50-fold specificity was observed for the A(2A) versus the related A(1) and A(3) subtypes. These high hit rates and affinities at least partly reflect the bias of commercial libraries toward GPCR-like chemotypes, an issue that we attempt to investigate quantitatively. Despite this bias, many of the most potent new ligands were novel, dissimilar from known ligands, providing new lead structures for modulation of this medically important target.

Show MeSH
Related in: MedlinePlus