7RAN

5-HT2AR bound to a novel agonist in complex with a mini-Gq protein and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)

Summary for 7RAN

• Entry DOI: 10.2210/pdb7ran/pdb
• EMDB information: 24378
• Descriptor: 5-hydroxytryptamine receptor 2A, G protein subunit q (Gi2-mini-Gq chimera), Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, ... (6 entities in total)
• Functional Keywords: 5-ht2a receptor, serotonin receptor, g protein, gpcr, novel agonist, cryoem, membrane protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 5
• Total formula weight: 142403.71

Authors

Barros-Alvarez, X.,Kim, K.,Panova, O.,Roth, B.L.,Skiniotis, G. (deposition date: 2021-07-02, release date: 2022-07-06, Last modification date: 2024-10-23)

Primary citation

Kaplan, A.L.,Confair, D.N.,Kim, K.,Barros-Alvarez, X.,Rodriguiz, R.M.,Yang, Y.,Kweon, O.S.,Che, T.,McCorvy, J.D.,Kamber, D.N.,Phelan, J.P.,Martins, L.C.,Pogorelov, V.M.,DiBerto, J.F.,Slocum, S.T.,Huang, X.P.,Kumar, J.M.,Robertson, M.J.,Panova, O.,Seven, A.B.,Wetsel, A.Q.,Wetsel, W.C.,Irwin, J.J.,Skiniotis, G.,Shoichet, B.K.,Roth, B.L.,Ellman, J.A.
Bespoke library docking for 5-HT 2A receptor agonists with antidepressant activity.
Nature, 610:582-591, 2022

PubMed Abstract: There is considerable interest in screening ultralarge chemical libraries for ligand discovery, both empirically and computationally. Efforts have focused on readily synthesizable molecules, inevitably leaving many chemotypes unexplored. Here we investigate structure-based docking of a bespoke virtual library of tetrahydropyridines-a scaffold that is poorly sampled by a general billion-molecule virtual library but is well suited to many aminergic G-protein-coupled receptors. Using three inputs, each with diverse available derivatives, a one pot C-H alkenylation, electrocyclization and reduction provides the tetrahydropyridine core with up to six sites of derivatization. Docking a virtual library of 75 million tetrahydropyridines against a model of the serotonin 5-HT receptor (5-HTR) led to the synthesis and testing of 17 initial molecules. Four of these molecules had low-micromolar activities against either the 5-HT or the 5-HT receptors. Structure-based optimization led to the 5-HTR agonists (R)-69 and (R)-70, with half-maximal effective concentration values of 41 nM and 110 nM, respectively, and unusual signalling kinetics that differ from psychedelic 5-HTR agonists. Cryo-electron microscopy structural analysis confirmed the predicted binding mode to 5-HTR. The favourable physical properties of these new agonists conferred high brain permeability, enabling mouse behavioural assays. Notably, neither had psychedelic activity, in contrast to classic 5-HTR agonists, whereas both had potent antidepressant activity in mouse models and had the same efficacy as antidepressants such as fluoxetine at as low as 1/40th of the dose. Prospects for using bespoke virtual libraries to sample pharmacologically relevant chemical space will be considered.

PubMed: 36171289
DOI: 10.1038/s41586-022-05258-z

Experimental method

ELECTRON MICROSCOPY (3.45 Å)