X‑ray Crystal Structure of Phosphodiesterase 2 in Complex with a Highly Selective, Nanomolar Inhibitor Reveals a Binding-Induced Pocket Important for Selectivity
To better understand the structural origins of inhibitor selectivity of human phosphodieasterase families (PDEs 1–11), here we report the X-ray crystal structure of PDE2 in complex with a highly selective, nanomolar inhibitor (BAY60-7550) at 1.9 Å resolution, and the structure of apo PDE2 at 2.0 Å r...
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Published in | Journal of the American Chemical Society Vol. 135; no. 32; pp. 11708 - 11711 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
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American Chemical Society
14.08.2013
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Abstract | To better understand the structural origins of inhibitor selectivity of human phosphodieasterase families (PDEs 1–11), here we report the X-ray crystal structure of PDE2 in complex with a highly selective, nanomolar inhibitor (BAY60-7550) at 1.9 Å resolution, and the structure of apo PDE2 at 2.0 Å resolution. The crystal structures reveal that the inhibitor binds to the PDE2 active site by using not only the conserved glutamine-switch mechanism for substrate binding, but also a binding-induced, hydrophobic pocket that was not reported previously. In silico affinity profiling by molecular docking indicates that the inhibitor binding to this pocket contributes significantly to the binding affinity and thereby improves the inhibitor selectivity for PDE2. Our results highlight a structure-based design strategy that exploits the potential binding-induced pockets to achieve higher selectivity in the PDE inhibitor development. |
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AbstractList | To better understand the structural origins of inhibitor selectivity of human phosphodieasterase families (PDEs 1-11), here we report the X-ray crystal structure of PDE2 in complex with a highly selective, nanomolar inhibitor (BAY60-7550) at 1.9 Å resolution, and the structure of apo PDE2 at 2.0 Å resolution. The crystal structures reveal that the inhibitor binds to the PDE2 active site by using not only the conserved glutamine-switch mechanism for substrate binding, but also a binding-induced, hydrophobic pocket that was not reported previously. In silico affinity profiling by molecular docking indicates that the inhibitor binding to this pocket contributes significantly to the binding affinity and thereby improves the inhibitor selectivity for PDE2. Our results highlight a structure-based design strategy that exploits the potential binding-induced pockets to achieve higher selectivity in the PDE inhibitor development. |
Author | Zhu, Jian Dai, Dandan Huang, Qiang Yang, Qiqi |
AuthorAffiliation | Fudan University Shanghai Medicilon Inc |
AuthorAffiliation_xml | – name: Fudan University – name: Shanghai Medicilon Inc |
Author_xml | – sequence: 1 givenname: Jian surname: Zhu fullname: Zhu, Jian – sequence: 2 givenname: Qiqi surname: Yang fullname: Yang, Qiqi – sequence: 3 givenname: Dandan surname: Dai fullname: Dai, Dandan – sequence: 4 givenname: Qiang surname: Huang fullname: Huang, Qiang email: huangqiang@fudan.edu.cn |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23899287$$D View this record in MEDLINE/PubMed |
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Snippet | To better understand the structural origins of inhibitor selectivity of human phosphodieasterase families (PDEs 1–11), here we report the X-ray crystal... To better understand the structural origins of inhibitor selectivity of human phosphodieasterase families (PDEs 1-11), here we report the X-ray crystal... |
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SubjectTerms | Binding Sites Crystallography, X-Ray Cyclic Nucleotide Phosphodiesterases, Type 2 - chemistry Cyclic Nucleotide Phosphodiesterases, Type 2 - metabolism Humans Imidazoles - chemistry Imidazoles - pharmacology Molecular Docking Simulation Phosphodiesterase Inhibitors - chemistry Phosphodiesterase Inhibitors - pharmacology Protein Binding Triazines - chemistry Triazines - pharmacology |
Title | X‑ray Crystal Structure of Phosphodiesterase 2 in Complex with a Highly Selective, Nanomolar Inhibitor Reveals a Binding-Induced Pocket Important for Selectivity |
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