Bitopic Ligands and Metastable Binding Sites: Opportunities for G Protein-Coupled Receptor (GPCR) Medicinal Chemistry

Fronik, Philipp; Gaiser, Birgit I; Pedersen, Daniel Sejer

doi:10.1021/acs.jmedchem.6b01601

Cited by 86 publications

(118 citation statements)

References 93 publications

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“…6 ). This observation corroborates with previous investigation of the binding mechanism of GPCR ligands using molecular dynamics simulation 72 , showing the presence of transient binding sites also called metastable binding sites or ligand-entry sites as potential allosteric sites 37 . In particular, a metastable binding site was proposed for adenosine bound to A 2A R 73 .…”

Section: Discussionsupporting

confidence: 92%

Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor

Igonet¹,

Raingeval²,

Cecon³

et al. 2018

Sci Rep

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Structural studies of integral membrane proteins have been limited by the intrinsic conformational flexibility and the need to stabilize the proteins in solution. Stabilization by mutagenesis was very successful for structural biology of G protein-coupled receptors (GPCRs). However, it requires heavy protein engineering and may introduce structural deviations. Here we describe the use of specific calixarenes-based detergents for native GPCR stabilization. Wild type, full length human adenosine A2A receptor was used to exemplify the approach. We could stabilize native, glycosylated, non-aggregated and homogenous A2AR that maintained its ligand binding capacity. The benefit of the preparation for fragment screening, using the Saturation-Transfer Difference nuclear magnetic resonance (STD-NMR) experiment is reported. The binding of the agonist adenosine and the antagonist caffeine were observed and competition experiments with CGS-21680 and ZM241385 were performed, demonstrating the feasibility of the STD-based fragment screening on the native A2A receptor. Interestingly, adenosine was shown to bind a second binding site in the presence of the agonist CGS-21680 which corroborates published results obtained with molecular dynamics simulation. Fragment-like compounds identified using STD-NMR showed antagonistic effects on A2AR in the cAMP cellular assay. Taken together, our study shows that stabilization of native GPCRs represents an attractive approach for STD-based fragment screening and drug design.

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Section: Discussionsupporting

confidence: 92%

Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor

Igonet¹,

Raingeval²,

Cecon³

et al. 2018

Sci Rep

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“…S5A ). The presence of a small cavity at the entrance of the orthosteric binding site [named extracellular ( Dror et al , 2011 ) or membrane ( Stanley et al , 2016 ) vestibule or secondary ( Gonzalez et al , 2011 ) or metastable ( Fronik et al , 2017 ) binding site] has been described. To further evaluate the proposed binding of MDAN-21 (NTI in the orthosteric binding site of δ-OR and OXY in the extracellular vestibule or secondary binding site of μ-OR), we performed two additional MD replicas starting at this conformation.…”

Section: Resultsmentioning

confidence: 99%

The size matters? A computational tool to design bivalent ligands

Pérez‐Benito

Henry²,

Matsoukas

et al. 2018

Bioinformatics

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MotivationBivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs). They contain two pharmacophoric units that simultaneously bind in their corresponding binding sites, connected with a spacer chain. Here, we report a molecular modelling tool that links the pharmacophore units via the shortest pathway along the receptors van der Waals surface and then scores the solutions providing prioritization for the design of new bivalent ligands.ResultsBivalent ligands of known dimers of GPCRs, PROTACs and a model bivalent antibody/antigen system were analysed. The tool could rapidly assess the preferred linker length for the different systems and recapitulated the best reported results. In the case of GPCR dimers the results suggest that in some cases these ligands might bind to a secondary binding site at the extracellular entrance (vestibule or allosteric site) instead of the orthosteric binding site.Availability and implementationFreely accessible from the Molecular Operating Environment svl exchange server (https://svl.chemcomp.com/).Supplementary information Supplementary data are available at Bioinformatics online.

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“…Albeit the existence of GPCRs meta-stable binding sites have not been experimentally proved yet, they are largely accepted in light of the increasing number of computational insights. [6][7][8] The presence of energetically stable meta-binding sites, alternative to the canonical orthosteric one, could open the scenario in which a ligand can simultaneously recognize the same receptor with a stoichiometry other than 1 : 1. In recent crystallographic structures, class A GPCRs contemporary bound orthosteric and allosteric ligands.…”

Section: Introductionmentioning

confidence: 99%

Could Adenosine Recognize its Receptors with a Stoichiometry Other than 1 : 1?

Deganutti

Salmaso

Moro

2018

Molecular Informatics

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One of the most largely accepted concepts in the G protein-coupled receptors (GPCRs) field is that the ligand, either agonist or antagonist, recognizes its receptor with a stoichiometry of 1 : 1. Recent experimental evidence, reporting ternary complexes formed by GPCR:orthosteric: allosteric ligands, has complicated the ligand-receptor 1 : 1 binding scenario. Molecular modeling simulations have been used to retrieve insights on the whole ligand-receptor recognition process, beyond information on the final bound state provided by experimental techniques. The simulation of adenosine binding pathways towards the A adenosine receptor highlighted the presence of alternative binding sites (meta-binding sites) beside the canonical orthosteric one, mainly in proximity to the extracellular vestibule. In light of all these considerations, we investigated the possibility that a second molecule of adenosine engages its receptor when this is already in the holo form, generating a ternary complex with a stoichiometry of 2 : 1. Unexpectedly, supervised molecular dynamics (SuMD) simulations showed that the A adenosine receptor could bind the second molecule of adenosine in one of the possible meta-binding sites as well as into its orthosteric site. The formation of this ternary complex, which favored the formation of the intracellular "ionic lock" between R102 (3.50) and E228 (6.30), could putatively be framed in the context of a negative allosteric regulation.

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Bitopic Ligands and Metastable Binding Sites: Opportunities for G Protein-Coupled Receptor (GPCR) Medicinal Chemistry

Cited by 86 publications

References 93 publications

Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor

Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor

The size matters? A computational tool to design bivalent ligands

Could Adenosine Recognize its Receptors with a Stoichiometry Other than 1 : 1?

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