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TitleAlphaFold2 structures guide prospective ligand discovery.
Journal, issue, pagesScience, Page eadn6354, Year 2024
Publish dateMay 16, 2024
AuthorsJiankun Lyu / Nicholas Kapolka / Ryan Gumpper / Assaf Alon / Liang Wang / Manish K Jain / Ximena Barros-Álvarez / Kensuke Sakamoto / Yoojoong Kim / Jeffrey DiBerto / Kuglae Kim / Isabella S Glenn / Tia A Tummino / Sijie Huang / John J Irwin / Olga O Tarkhanova / Yurii Moroz / Georgios Skiniotis / Andrew C Kruse / Brian K Shoichet / Bryan L Roth /
PubMed AbstractAlphaFold2 (AF2) models have had wide impact, but they have had mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ2 and ...AlphaFold2 (AF2) models have had wide impact, but they have had mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ2 and 5-HT2A receptors, testing hundreds of new molecules and comparing results to docking against the experimental structures. Hit rates were high and similar for the experimental and the AF2 structures, as were affinities. The success of docking against the AF2 models was achieved despite differences in orthosteric residue conformations versus the experimental structures. Determination of the cryo-electron microscopy structure for one of the more potent 5HT2A ligands from the AF2 docking revealed residue accommodations that resembled the AF2 prediction. AF2 models may sample conformations that differ from experimental structures but remain low energy and relevant for ligand discovery, extending the domain of structure-based ligand discovery.
External linksScience / PubMed:38753765
MethodsEM (single particle)
Resolution2.8 - 3.0 Å
Structure data

42676

8uwl

EMDB-42676, PDB-8uwl:
5-HT2AR bound to Lisuride in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)
Method: EM (single particle) / Resolution: 2.8 Å

42999

8v6u

EMDB-42999, PDB-8v6u:
5HT2AR-miniGq heterotrimer in complex with a novel agonist obtained from large scale docking
Method: EM (single particle) / Resolution: 3.0 Å

Chemicals

ChemComp-H8G:
N,N-diethyl-N'-[(8alpha)-6-methyl-9,10-didehydroergolin-8-yl]urea / medication*YM / Lisuride


ChemComp, No image

ChemComp-YEQ:
Unknown entry

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / 5-HT2A receptor / serotonin receptor / G protein / GPCR / Lisuride / cryoEM / active state GPCR / heterotrimer / complex / serotonin

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