Cited by 217Pharmacological Receptor Mechanisms and EffectsReceptor Mechanisms and SignalingComputational Drug Discovery Methods

Structures of the σ2 receptor enable docking for bioactive ligand discovery

Open access
Alon, Assaf, Lyu, Jiankun, Braz, Joao M., Tummino, Tia A., Craik, Veronica, O’Meara, Matthew J., Webb, Chase M., Radchenko, Dmytro S. +8 more·2021·Nature

Published version of a preprint

Abstract

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.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41586-021-04175-x

Cites

92 of 92 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Cited by

Sorted by citations

Authors
Alon, A., Lyu, J., Braz, J. M., Tummino, T. A., Craik, V., O’Meara, M. J., Webb, C. M., Radchenko, D. S., Moroz, Y. S., Huang, X.-P., Liu, Y., Roth, B. L., Irwin, J. J., Basbaum, A. I., Shoichet, B. K., & Kruse, A. C.
Affiliations
  • Harvard University (US)
  • University of California, San Francisco (US)
  • University of Michigan (US)
  • Taras Shevchenko National University of Kyiv (UA)
  • University of North Carolina at Chapel Hill (US)
Corresponding author
  • Basbaum, Allan I.
  • Shoichet, Brian K.
  • Kruse, Andrew C.
Venue
Nature
Published
2021-12-08
Volume
600
Issue
7890
Pages
759-764
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W4200289210
Cited by
211
References
92
Citations by year
2026: 24 · 2025: 41 · 2024: 49 · 2023: 55 · 2022: 37 · 2021: 5
FWCI
11.93
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • U.S. Department of Energy (DE‐ AC02‐06CH11357, Contract No. DE-AC02-06CH11357., AC02‐06CH11357, 06CH11357, No. DE-AC02-06CH11357, DE-AC02-)
  • Sanofi
  • Vallee Foundation
  • National Institutes of Health (ACB-12002, 1s10od012289-01a1, DE-AC02–06CH11357, AGM-12006)
  • Defense Advanced Research Projects Agency (HR0011, HR0011-19-2-0020)
  • Office of Science (Contract No. DE-AC02-06CH11357, AC02‐06CH11357, DE-AC02, No. DE-AC02-06CH11357., 06CH11357, DE-AC02-06CH11357)
  • National Cancer Institute (DE-AC02-06CH11357, ACB12002, AGM-12006)
  • National Institute of General Medical Sciences (S10 OD012289, R01GM133836, R01GM119185, P41GM103311, DE-AC02-06CH11357, AGM-12006, ACB-12002, T32GM007175, P30GM138396, R35GM122481, AGM-12006, P30GM138396)
  • National Institute of Neurological Disorders and Stroke (R35NS097306)
  • Argonne National Laboratory (DE- AC02-06-CH11357, DE-AC02, AC02–06CH11357, No. DE-AC02-06CH11357, 06CH11357, Contract No. DE-AC02-06CH11357., S10 OD012289)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pharmacological Receptor Mechanisms and Effects
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
  • Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
Keywords
sigma-2 receptor, crystal structure, virtual screening, structure-based drug design, protein-ligand docking, neuropathic pain, mechanical hypersensitivity, spared nerve injury model, nociception
MeSH terms
Animals, Ligands, Neuralgia, Structure-Activity Relationship, Receptors, sigma, Mice

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review