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ACS Chem Biol. 2017 Mar 17;12(3):735-745. doi: 10.1021/acschembio.6b00646. Epub 2017 Jan 24.

Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries.

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Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University , SE-106 91 Stockholm, Sweden.
Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland.
G7 Therapeutics AG , Grabenstrasse 11a, 8952 Schlieren, Switzerland.
Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC, Box 596, SE-751 24 Uppsala, Sweden.


Peptide-recognizing G protein-coupled receptors (GPCRs) are promising therapeutic targets but often resist drug discovery efforts. Determination of crystal structures for peptide-binding GPCRs has provided opportunities to explore structure-based methods in lead development. Molecular docking screens of two chemical libraries, containing either fragment- or lead-like compounds, against a neurotensin receptor 1 crystal structure allowed for a comparison between different drug development strategies for peptide-binding GPCRs. A total of 2.3 million molecules were screened computationally, and 25 fragments and 27 leads that were top-ranked in each library were selected for experimental evaluation. Of these, eight fragments and five leads were confirmed as ligands by surface plasmon resonance. The hit rate for the fragment screen (32%) was thus higher than for the lead-like library (19%), but the affinities of the fragments were ∼100-fold lower. Both screens returned unique scaffolds and demonstrated that a crystal structure of a stabilized peptide-binding GPCR can guide the discovery of small-molecule agonists. The complementary advantages of exploring fragment- and lead-like chemical space suggest that these strategies should be applied synergistically in structure-based screens against challenging GPCR targets.

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