Structures of the σ2 receptor enable docking for bioactive ligand discovery
The σ 2 receptor has attracted intense interest in cancer imaging 1 , psychiatric disease 2 , neuropathic pain 3 – 5 and other areas of biology 6 , 7 . Here we determined the crystal structure of this receptor in complex with the clinical candidate roluperidone 2 and the tool compound PB28 8 . These...
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| Published in | Nature (London) Vol. 600; no. 7890; pp. 759 - 764 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
23.12.2021
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| Subjects | |
| Online Access | Get full text |
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| Summary: | The σ
2
receptor has attracted intense interest in cancer imaging
1
, psychiatric disease
2
, neuropathic pain
3
–
5
and other areas of biology
6
,
7
. Here we determined the crystal structure of this receptor in complex with the clinical candidate roluperidone
2
and the tool compound PB28
8
. These structures templated a large-scale docking screen of 490 million virtual molecules, of which 484 compounds were synthesized and tested. We identified 127 new chemotypes with affinities superior to 1 μM, 31 of which had affinities superior to 50 nM. The hit rate fell smoothly and monotonically with docking score. We optimized three hits for potency and selectivity, and achieved affinities that ranged from 3 to 48 nM, with up to 250-fold selectivity versus the σ
1
receptor. Crystal structures of two ligands bound to the σ
2
receptor confirmed the docked poses. To investigate the contribution of the σ
2
receptor in pain, two potent σ
2
-selective ligands and one potent σ
1
/σ
2
non-selective ligand were tested for efficacy in a mouse model of neuropathic pain. All three ligands showed time-dependent decreases in mechanical hypersensitivity in the spared nerve injury model
9
, suggesting that the σ
2
receptor has a role in nociception. This study illustrates the opportunities for rapid discovery of in vivo probes through structure-based screens of ultra large libraries, enabling study of underexplored areas of biology.
Crystal structures of the σ
2
receptor are determined and used to perform a docking screen of nearly 500 million molecules, identifying σ
2
-selective ligands and providing insight into the role of σ
2
in neuropathic pain. |
|---|---|
| Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 A.A. performed cloning, mutagenesis, protein purification, SEC-MALS experiments, CD measurements, crystallization, X-ray data collection and processing, structure determination and refinement, radioligand binding, yeast complementation experiments, sterol isomerization enzymatic assay. J.L. conducted the docking, chemoinformatics analyses, docking energy analysis, and ligand picking, assisted in the latter by T.A.T. and B.K.S. J.M.B. conducted and analyzed the mouse allodynia experiments assisted by V.C., as well as the receptor expression experiments, supervised and co-analyzed by A.I.B. M.J.O. conducted the Bayesian analysis of docking scores vs. hit rates; C.M.W. tested molecules for activity against the μOR. X.P.H. and Y.L. tested compounds against the GPCR-ome and other off-targets, with supervision from B.L.R. Y.S.M. supervised the synthesis of molecules from the virtual library, J.J.I. was responsible for the building of the version of the ZINC library that was docked. A.C.K., B.K.S, and A.I.B. supervised the project. The manuscript was written by A.A., J.L., B.K.S, and A.C.K. with input from other authors. These authors contributed equally. Author contributions |
| ISSN: | 0028-0836 1476-4687 1476-4687 |
| DOI: | 10.1038/s41586-021-04175-x |