RT Journal Article
T1 Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations.
A1 Ding, Tianyi
A1 Karlov, Dmitry S
A1 Pino-Angeles, Almudena
A1 Tikhonova, Irina G
K1 Allosteric regulation
K1 Allosteric site
K1 Amides
K1 Binding sites
AB Allosteric modulators are called promising candidates in G protein-coupled receptor (GPCR) drug development by displaying subtype selectivity and more specific receptor modulation. Among the allosteric sites known to date, cavities at the receptor-lipid interface represent an uncharacteristic binding location that raises many questions about the ligand interactions and stability, the binding site structure, and how all of these are affected by lipid molecules. In this work, we analyze interactions in the allosteric sites of the PAR2, C5aR1, and GCGR receptors in three lipid compositions using molecular dynamics simulations. In addition, we performed quantum chemical calculations involving the symmetry-adapted perturbation theory (SAPT) and the natural population analysis to quantify the strength of intermolecular interactions. We show that besides classical hydrogen bonds, weak polar interactions such as O-HC, O-Br, and long-range electrostatics with the backbone amides contribute to the stability of allosteric modulators at the receptor-lipid interface. The allosteric cavities are detectable in various membrane compositions. The availability of polar atoms for interactions in such cavities can be assessed by water molecules from simulations. Although ligand-lipid interactions are weak, lipid tails play a role in ligand binding pose stability and the size of allosteric cavities. We discuss physicochemical aspects of ligand binding at the receptor-lipid interface and suggest a compound library enriched by weak donor groups for ligand search in such sites.
PB American Chemical Society
YR 2022
FD 2022-09-30
LK http://hdl.handle.net/10668/22588
UL http://hdl.handle.net/10668/22588
LA en
NO Ding T, Karlov DS, Pino-Angeles A, Tikhonova IG. Intermolecular Interactions in G Protein-Coupled Receptor Allosteric Sites at the Membrane Interface from Molecular Dynamics Simulations and Quantum Chemical Calculations. J Chem Inf Model. 2022 Oct 10;62(19):4736-4747
NO This project made use of computational time on Kelvin-2 (grant no. EP/T022175/1) and JADE and ARCHER2 granted via the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (hecbiosim.ac.uk), supported by EPSRC (grant no. EP/R029407/1 and EP/W03204X/1).I.G.T. participates in the European COST Action CA18133(ERNEST).
DS RISalud
RD Apr 6, 2025