5XKM

Crystal structure of human phosphodiesterase 2A in complex with 6-methyl-N-(1-(4-(trifluoromethoxy)phenyl)propyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide

Summary for 5XKM

• Entry DOI: 10.2210/pdb5xkm/pdb
• Descriptor: cGMP-dependent 3',5'-cyclic phosphodiesterase, MAGNESIUM ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: hydrolase, hydrolase inhibitor, pde2a
• Biological source: Homo sapiens (Human)
• Cellular location: Isoform PDE2A3: Cell membrane ; Lipid-anchor . Isoform PDE2A2: Mitochondrion matrix . Isoform PDE2A1: Cytoplasm . Isoform 5: Mitochondrion : O00408
• Total number of polymer chains: 6
• Total formula weight: 244249.29

Authors

Oki, H.,Kondo, M.,Snell, G.,Lane, W. (deposition date: 2017-05-08, release date: 2017-08-16, Last modification date: 2024-03-27)

Primary citation

Mikami, S.,Sasaki, S.,Asano, Y.,Ujikawa, O.,Fukumoto, S.,Nakashima, K.,Oki, H.,Kamiguchi, N.,Imada, H.,Iwashita, H.,Taniguchi, T.
Discovery of an Orally Bioavailable, Brain-Penetrating, in Vivo Active Phosphodiesterase 2A Inhibitor Lead Series for the Treatment of Cognitive Disorders.
J. Med. Chem., 60:7658-7676, 2017

PubMed Abstract: Herein, we describe the discovery of a potent, selective, brain-penetrating, in vivo active phosphodiesterase (PDE) 2A inhibitor lead series. To identify high-quality leads suitable for optimization and enable validation of the physiological function of PDE2A in vivo, structural modifications of the high-throughput screening hit 18 were performed. Our lead generation efforts revealed three key potency-enhancing functionalities with minimal increases in molecular weight (MW) and no change in topological polar surface area (TPSA). Combining these structural elements led to the identification of 6-methyl-N-((1R)-1-(4-(trifluoromethoxy)phenyl)propyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide (38a), a molecule with the desired balance of preclinical properties. Further characterization by cocrystal structure analysis of 38a bound to PDE2A uncovered a unique binding mode and provided insights into its observed potency and PDE selectivity. Compound 38a significantly elevated 3',5'-cyclic guanosine monophosphate (cGMP) levels in mouse brain following oral administration, thus validating this compound as a useful pharmacological tool and an attractive lead for future optimization.

PubMed: 28759228
DOI: 10.1021/acs.jmedchem.7b00709

Experimental method

X-RAY DIFFRACTION (2.16 Å)