Cyclic nucleotide phosphodiesterases (PDEs) are the key enzymes that control the cellular concentration of """"""""second messengers"""""""" adenosine or guanosine 3', 5'-cyclic monophosphate (cAMP or cGMP). The human genome encodes 21 PDE genes and over 60 PDE isoforms categorized into 11 families. All PDEs contain a conserved catalytic domain, but each family possesses individual substrate specificity and selective inhibitors. Selective inhibitors of PDEs have been widely studied as therapeutic agents for various diseases. For example, PDEs inhibitor sildenafil (VIAGRA(tm)) is a drug for erectile dysfunction and PDE3 inhibitor cilostazole (Pletal(tm)) is a drug for intermittent claudication. The wide medical applications of PDE inhibitors have attracted great attention from both academic and industrial research groups. However, it has been mysteries how the similar active sites of PDEs distinguish the different substrates and inhibitors. We hypothesize that the substrate specificity and inhibitor selectivity are determined by both the chemical nature of active site residues and the conformations of the PDE active sites. This proposal chooses cAMP specific PDE4 and cGMP specific PDE5 and PDE9 as the target systems to study the substrate specificity and inhibitor selectivity with approaches of crystallography and protein engineering. The structures of PDE4, PDES and PDE9 in complex with substrate, substrate analogues, and selective inhibitors will be determined. The candidate residues will be switched between PDE4 and PDE5 by a single or multiple mutations for further illustration of the substrate specificity. The structures in this proposal, together with those from the last funding period, will reveal key residues and elements for determination of the substrate specificity and identify potential subpockets contributing to the selective binding of the inhibitors. Since the inhibitor selectivity is a key issue for side effects of drugs, the structures of PDEs in complex with inhibitors will provide templates for design of family- or subfamily-selective inhibitors and ultimately improve the drugs efficiency for treatment of the diseases.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM059791-06
Application #
7101093
Study Section
Macromolecular Structure and Function A Study Section (MSFA)
Program Officer
Flicker, Paula F
Project Start
2000-04-01
Project End
2009-07-31
Budget Start
2006-08-01
Budget End
2007-07-31
Support Year
6
Fiscal Year
2006
Total Cost
$241,669
Indirect Cost
Name
University of North Carolina Chapel Hill
Department
Biochemistry
Type
Schools of Medicine
DUNS #
608195277
City
Chapel Hill
State
NC
Country
United States
Zip Code
27599
Feng, Xiaoqing; Wang, Huanchen; Ye, Mengchun et al. (2018) Identification of a PDE4-Specific Pocket for the Design of Selective Inhibitors. Biochemistry 57:4518-4525
Huang, Manna; Shao, Yongxian; Hou, Jianying et al. (2015) Structural Asymmetry of Phosphodiesterase-9A and a Unique Pocket for Selective Binding of a Potent Enantiomeric Inhibitor. Mol Pharmacol 88:836-45
Tian, Yuanyuan; Cui, Wenjun; Huang, Manna et al. (2014) Dual specificity and novel structural folding of yeast phosphodiesterase-1 for hydrolysis of second messengers cyclic adenosine and guanosine 3',5'-monophosphate. Biochemistry 53:4938-45
Shao, Yong-xian; Huang, Manna; Cui, Wenjun et al. (2014) Discovery of a phosphodiesterase 9A inhibitor as a potential hypoglycemic agent. J Med Chem 57:10304-13
Shang, Na-Na; Shao, Yong-Xian; Cai, Ying-Hong et al. (2014) Discovery of 3-(4-hydroxybenzyl)-1-(thiophen-2-yl)chromeno[2,3-c]pyrrol-9(2H)-one as a phosphodiesterase-5 inhibitor and its complex crystal structure. Biochem Pharmacol 89:86-98
Jansen, Chimed; Wang, Huanchen; Kooistra, Albert J et al. (2013) Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure. J Med Chem 56:2087-96
Wang, Huanchen; Kunz, Stefan; Chen, Gong et al. (2012) Biological and structural characterization of Trypanosoma cruzi phosphodiesterase C and Implications for design of parasite selective inhibitors. J Biol Chem 287:11788-97
Yuan, Qinghui; He, Lin; Ke, Hengming (2012) A potential substrate binding conformation of ýý-lactams and insight into the broad spectrum of NDM-1 activity. Antimicrob Agents Chemother 56:5157-63
Meng, Fei; Hou, Jing; Shao, Yong-Xian et al. (2012) Structure-based discovery of highly selective phosphodiesterase-9A inhibitors and implications for inhibitor design. J Med Chem 55:8549-58
Park, Sung-Jun; Ahmad, Faiyaz; Philp, Andrew et al. (2012) Resveratrol ameliorates aging-related metabolic phenotypes by inhibiting cAMP phosphodiesterases. Cell 148:421-33

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