Structural insights into endogenous ligand selectivity and activation mechanisms of FFAR1 and FFAR2

Yudun Ke; Yimiao Huang; Cuiying Yi; Limin Ma; Xiaojing Chu; Beili Wu; Qiang Zhao; Shuo Han

doi:10.1016/j.celrep.2024.115024

Structural insights into endogenous ligand selectivity and activation mechanisms of FFAR1 and FFAR2

Cell Rep. 2024 Dec 24;43(12):115024. doi: 10.1016/j.celrep.2024.115024. Epub 2024 Nov 30.

Authors

Yudun Ke¹, Yimiao Huang¹, Cuiying Yi², Limin Ma², Xiaojing Chu², Beili Wu³, Qiang Zhao⁴, Shuo Han⁵

Affiliations

¹ School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China.
² State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
³ School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China; State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310020, China; School of Life Science and Technology, Shanghai Tech University, Shanghai 201210, China. Electronic address: [email protected].
⁴ School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China; State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China. Electronic address: [email protected].
⁵ State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310020, China. Electronic address: [email protected].

PMID: 39616615
DOI: 10.1016/j.celrep.2024.115024

Abstract

Free fatty acid receptors (FFARs) play critical roles in metabolic regulation and are potential therapeutic targets for metabolic and inflammatory diseases. A comprehensive understanding of the activation mechanisms and endogenous ligand selectivity of FFARs is essential for drug discovery. Here, we report two cryoelectron microscopy structures of the human FFAR1 bound to the endogenous ligand docosahexaenoic acid (DHA) and G_i1 protein as well as FFAR2 in complex with butyrate and G_i1 at 3.2 Å and 3.3 Å resolution, respectively. These structures highlight that distinct locations and sizes of the orthosteric ligand binding pockets are crucial determinants of the endogenous ligand selectivity of this receptor subfamily. Additionally, computational analysis reveals a potential allosteric ligand binding pocket in FFAR2. Furthermore, we observe that the upward movement of helix V upon endogenous ligand binding is responsible for receptor activation. These insights will significantly aid in the development of drugs targeting this receptor family.

Keywords: CP: Molecular biology; FFAR1; FFAR2; GPCR; Structural biology; cryo-EM; free fatty acid receptors; signaling complex.

MeSH terms

Binding Sites
Butyrates / chemistry
Butyrates / metabolism
Cryoelectron Microscopy
Docosahexaenoic Acids / chemistry
Docosahexaenoic Acids / metabolism
GTP-Binding Protein alpha Subunits, Gi-Go / chemistry
GTP-Binding Protein alpha Subunits, Gi-Go / metabolism
HEK293 Cells
Humans
Ligands
Protein Binding
Receptors, Cell Surface / chemistry
Receptors, Cell Surface / metabolism
Receptors, G-Protein-Coupled* / chemistry
Receptors, G-Protein-Coupled* / metabolism

Substances

Receptors, G-Protein-Coupled
Ligands
FFAR2 protein, human
FFAR1 protein, human
Docosahexaenoic Acids
Butyrates
Receptors, Cell Surface
GTP-Binding Protein alpha Subunits, Gi-Go