Preprint, 2023
Rapid and accurate deorphanization of ligand-receptor pairs using AlphaFold
In: bioRxiv,
Volume 4,
03-29,
Page 2023.03.16.531341,
10.1101/2023.03.16.531341
Contributors (11)
Danneskiold-Samsøe, Niels Banhos
(
0000-0002-2889-5630)
(Corresponding author)
[1]
[2]
Kavi, Deniz
[2]
Jude, Kevin M
(
0000-0002-3675-5136)
[2]
Nissen, Silas Boye
(
0000-0002-9473-4755)
[2]
Wat, Lianna W
(
0000-0001-6998-0594)
[2]
Coassolo, Laetitia
(
0000-0003-2138-4819)
[2]
Zhao, Meng
(
0000-0002-5415-8335)
[2]
Santana-Oikawa, Galia Asae
[2]
Broido, Beatrice Blythe
[2]
Garcia, Kenan Christopher
[2]
Svensson, Katrin Jennifer
(
0000-0001-5376-5128)
(Corresponding author)
[2]
Affiliations
- [1]
University of Copenhagen
[NORA names:
KU University of Copenhagen; University; Denmark; Europe, EU; Nordic; OECD]
- [2]
Stanford University
[NORA names:
United States; America, North; OECD]
Abstract
Secreted proteins are extracellular ligands that play key roles in paracrine and endocrine signaling, classically by binding cell surface receptors. Experimental assays to identify new extracellular ligand-receptor interactions are challenging, which has hampered the rate of novel ligand discovery. Here, using AlphaFold-multimer, we developed and applied an approach for extracellular ligand-binding prediction to a structural library of 1,108 single-pass transmembrane receptors. We demonstrate high discriminatory power and a success rate of close to 90 % for known ligand-receptor pairs where no a priori structural information is required. Importantly, the prediction was performed on de novo ligand-receptor pairs not used for AlphaFold training and validated against experimental structures. These results demonstrate proof-of-concept of a rapid and accurate computational resource to predict high-confidence cell-surface receptors for a diverse set of ligands by structural binding prediction, with potentially wide applicability for the understanding of cell-cell communication.
Keywords
AlphaFold,
applicability,
approach,
assays,
cell surface receptors,
cell-cell communication,
communication,
computational resources,
concept,
deorphanization,
discovery,
discriminatory power,
diverse set,
endocrine,
experimental assays,
experimental structures,
extracellular ligand-receptor interactions,
extracellular ligands,
high discriminatory power,
information,
interaction,
key role,
library,
ligand discovery,
ligand-binding prediction,
ligand-receptor interactions,
ligand-receptor pairs,
ligands,
pairs,
paracrine,
power,
prediction,
proof,
protein,
rate,
receptors,
resources,
results,
role,
secreted proteins,
set,
single-pass transmembrane receptors,
structural information,
structural library,
structure,
success rate,
surface receptors,
training,
transmembrane receptors,
understanding,
wide applicability
Funders