TY - JOUR
T1 - PPARα Ligand-Binding Domain Structures with Endogenous Fatty Acids and Fibrates
AU - Kamata, Shotaro
AU - Oyama, Takuji
AU - Saito, Kenta
AU - Honda, Akihiro
AU - Yamamoto, Yume
AU - Suda, Keisuke
AU - Ishikawa, Ryo
AU - Itoh, Toshimasa
AU - Watanabe, Yasuo
AU - Shibata, Takahiro
AU - Uchida, Koji
AU - Suematsu, Makoto
AU - Ishii, Isao
N1 - Funding Information:
We thank Prof. Jerold Chun (Sanford Burnham Prebys Medical Discovery Institute) for helpful comments. S.K. and I.I. acknowledge fundings from Grants-in-Aid for Scientific Research from Japan Society for the Promotion of Sciences (JSPS), Japan (grant numbers: 19K16359 and 16H05107), Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research [BINDS]) from AMED, Japan (grant number: JP19am0101071; support number: 1407), and Showa Pharmaceutical University, Japan. T.O. acknowledges fundings from a Grant-in-Aid for Scientific Research from JSPS (grant number: 18K06081) and Adaptable and Seamless Technology Transfer Program through Target-driven R&D (A-STEP) from Japan Science and Technology Agency, Japan (grant number: JPMJTM19AT). This work was performed under the approval of the Photon Factory Program Advisory Committee, Japan (proposal number: 2018G658). S.K. T.O. and I.I. conceived the study. S.K. T.O. K. Saito, A.H. K. Suda, and T.I. preformed crystal preparation and X-ray crystallography. S.K. and I.I. deposited all PDB data. S.K. A.H. and Y.Y. performed TR-FRET assay. S.K. and A.H. performed CD spectrometry. S.K. T.O. K. Saito, R.I. and T.I. performed crystal structure analyses. Y.W. performed blood drawing. T.S. and K.U. performed lipid analyses. S.K. T.O. K.S. A.H. T.I. Y.W. M.S. and I.I. interpreted data. T.O. and I.I. supervised the study. I.I. wrote the paper, with input from all authors. The authors declare no competing interest.
Funding Information:
We thank Prof. Jerold Chun (Sanford Burnham Prebys Medical Discovery Institute) for helpful comments. S.K. and I.I. acknowledge fundings from Grants-in-Aid for Scientific Research from Japan Society for the Promotion of Sciences ( JSPS ), Japan (grant numbers: 19K16359 and 16H05107 ), Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research [BINDS]) from AMED , Japan (grant number: JP19am0101071 ; support number: 1407), and Showa Pharmaceutical University , Japan. T.O. acknowledges fundings from a Grant-in-Aid for Scientific Research from JSPS (grant number: 18K06081 ) and Adaptable and Seamless Technology Transfer Program through Target-driven R&D (A-STEP) from Japan Science and Technology Agency , Japan (grant number: JPMJTM19AT ). This work was performed under the approval of the Photon Factory Program Advisory Committee, Japan (proposal number: 2018G658).
Publisher Copyright:
© 2020 The Author(s)
PY - 2020/11/20
Y1 - 2020/11/20
N2 - Most triacylglycerol-lowering fibrates have been developed in the 1960s–1980s before their molecular target, peroxisome proliferator-activated receptor alpha (PPARα), was identified. Twenty-one ligand-bound PPARα structures have been deposited in the Protein Data Bank since 2001; however, binding modes of fibrates and physiological ligands remain unknown. Here we show thirty-four X-ray crystallographic structures of the PPARα ligand-binding domain, which are composed of a “Center” and four “Arm” regions, in complexes with five endogenous fatty acids, six fibrates in clinical use, and six synthetic PPARα agonists. High-resolution structural analyses, in combination with coactivator recruitment and thermostability assays, demonstrate that stearic and palmitic acids are presumably physiological ligands; coordination to Arm III is important for high PPARα potency/selectivity of pemafibrate and GW7647; and agonistic activities of four fibrates are enhanced by the partial agonist GW9662. These results renew our understanding of PPARα ligand recognition and contribute to the molecular design of next-generation PPAR-targeted drugs.
AB - Most triacylglycerol-lowering fibrates have been developed in the 1960s–1980s before their molecular target, peroxisome proliferator-activated receptor alpha (PPARα), was identified. Twenty-one ligand-bound PPARα structures have been deposited in the Protein Data Bank since 2001; however, binding modes of fibrates and physiological ligands remain unknown. Here we show thirty-four X-ray crystallographic structures of the PPARα ligand-binding domain, which are composed of a “Center” and four “Arm” regions, in complexes with five endogenous fatty acids, six fibrates in clinical use, and six synthetic PPARα agonists. High-resolution structural analyses, in combination with coactivator recruitment and thermostability assays, demonstrate that stearic and palmitic acids are presumably physiological ligands; coordination to Arm III is important for high PPARα potency/selectivity of pemafibrate and GW7647; and agonistic activities of four fibrates are enhanced by the partial agonist GW9662. These results renew our understanding of PPARα ligand recognition and contribute to the molecular design of next-generation PPAR-targeted drugs.
KW - Biochemistry
KW - Molecular Physiology
KW - Protein Structure Aspects
KW - Structural Biology
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U2 - 10.1016/j.isci.2020.101727
DO - 10.1016/j.isci.2020.101727
M3 - Article
AN - SCOPUS:85095415802
SN - 2589-0042
VL - 23
JO - iScience
JF - iScience
IS - 11
M1 - 101727
ER -