6K0T

Crystal Structure of PPARgamma Ligand Binding Domain in complex with dibenzooxepine derivative compound-17

Summary for 6K0T

• Entry DOI: 10.2210/pdb6k0t/pdb
• Descriptor: Peroxisome proliferator-activated receptor gamma, Peroxisome proliferator-activated receptor gamma coactivator 1-alpha, 3-[(1~{E})-1-[8-[(8-chloranyl-2-cyclopropyl-imidazo[1,2-a]pyridin-3-yl)methyl]-3-fluoranyl-6~{H}-benzo[c][1]benzoxepin-11-ylidene]ethyl]-4~{H}-1,2,4-oxadiazol-5-one, ... (4 entities in total)
• Functional Keywords: ppargamma, ligand binding domain, pparg modulator, cancer, nuclear protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 69309.13

Authors

Suzuki, M.,Yamamoto, K.,Takahashi, Y.,Saito, J. (deposition date: 2019-05-07, release date: 2019-10-30, Last modification date: 2024-11-06)

Primary citation

Yamamoto, K.,Tamura, T.,Nakamura, R.,Hosoe, S.,Matsubara, M.,Nagata, K.,Kodaira, H.,Uemori, T.,Takahashi, Y.,Suzuki, M.,Saito, J.I.,Ueno, K.,Shuto, S.
Development of a novel class of peroxisome proliferator-activated receptor (PPAR) gamma ligands as an anticancer agent with a unique binding mode based on a non-thiazolidinedione scaffold.
Bioorg.Med.Chem., 27:115122-115122, 2019

PubMed Abstract: We previously identified dibenzooxepine derivative 1 as a potent PPARγ ligand with a unique binding mode owing to its non-thiazolidinedione scaffold. However, while 1 showed remarkably potent MKN-45 gastric cancer cell aggregation activity, an indicator of cancer differentiation-inducing activity induced by PPARγ activation, we recognized that 1 was metabolically unstable. In the present study, we identified a metabolically soft spot, and successfully discovered 3-fluoro dibenzooxepine derivative 9 with better metabolic stability. Further optimization provided imidazo[1,2-a]pyridine derivative 17, which showed potent MKN-45 gastric cancer cell aggregation activity and excellent PK profiles compared with 9. Compound 17 exerted a growth inhibitory effect on AsPC-1/AG1 pancreatic tumor in mice. Furthermore, the decrease in the hematocrit (an indicator of localized edema, a serious adverse effect of PPARγ ligands) was tolerable even with oral administration at 200 mg/kg in healthy mice.

PubMed: 31623970
DOI: 10.1016/j.bmc.2019.115122

Experimental method

X-RAY DIFFRACTION (1.84 Å)