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

Abstract

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.

Structure-based discovery of selective positive allosteric modulators of antagonists for the M 2 muscarinic acetylcholine receptor

“…This was far from certain to us at the outset of this project. Unlike orthosteric sites, whose relatively constrained structures have proven amenable to docking screens ( 48 – 56 ), the mAChR allosteric sites are less defined sterically, are open to bulk solvent, and are more conformationally labile in response to orthosteric ligand binding than are the orthosteric sites themselves. Nonetheless, 3 of 13 docking-prioritized molecules from the initial screen acted as modulators of antagonist (hit rate of 23%).…”

Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

“…Structures of 64 unique GPCRs have been solved, providing opportunities to use molecular modeling to accelerate drug discovery. Structurebased virtual screens of large chemical libraries against GPCRs, followed by experimental testing of top-scoring compounds, have successfully identified leads of many therapeutic targets, including biogenic amine [3][4][5][6][7][8], purine [9], peptide [10,11] and protein-binding receptors [12]. The fact that molecular docking can be used to search chemical libraries with >100 million compounds [8] and identify ligands with hit rates as high as 73% [4] suggests that virtual screening can make important contributions to drug discovery.…”

The role of small-angle scattering in structure-based screening applications

“…On the other hand, the lengthy process involved in establishing crystallization conditions for novel proteins imposes a significant limitation on applicability of crystallographic methods, if these have not been found in previous available studies. This biases their application towards known and well-studied systems (Zheng et al, 2015), particularly in membrane-bound scenarios such as G-protein coupled receptors (Ranganathan et al, 2017). Given that transporters and membrane-bound receptors are critical to major cellular processes and thus highly attractive targets, crystallographic screening remains an important source of structural information.…”