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Title: Structural basis for selective inhibition of human PKG Iα by the balanol-like compound N46

Abstract

Activation of protein kinase G (PKG) Iα in nociceptive neurons induces long-term hyperexcitability that causes chronic pain. Recently, a derivative of the fungal metabolite balanol, N46, has been reported to inhibit PKG Iα with high potency and selectivity and attenuate thermal hyperalgesia and osteoarthritic pain. Here, we determined co-crystal structures of the PKG Iα C-domain and cAMP-dependent protein kinase (PKA) Cα, each bound with N46, at 1.98 Å and 2.65 Å, respectively. N46 binds the active site with its external phenyl ring, specifically interacting with the glycine-rich loop and the αC helix. Phe-371 at the PKG Iα glycine-rich loop is oriented parallel to the phenyl ring of N46, forming a strong π-stacking interaction, whereas the analogous Phe-54 in PKA Cα rotates 30° and forms a weaker interaction. Structural comparison revealed that steric hindrance between the preceding Ser-53 and the propoxy group of the phenyl ring may explain the weaker interaction with PKA Cα. The analogous Gly-370 in PKG Iα, however, causes little steric hindrance with Phe-371. Moreover, Ile-406 on the αC helix forms a hydrophobic interaction with N46 whereas its counterpart in PKA, Thr-88, does not. Substituting these residues in PKG Iα with those in PKA Cα increases the IC50more » values for N46, whereas replacing these residues in PKA Cα with those in PKG Iα reduces the IC50, consistent with our structural findings. In conclusion, our results explain the structural basis for N46-mediated selective inhibition of human PKG Iα and provide a starting point for structure-guided design of selective PKG Iα inhibitors.« less

Authors:
 [1];  [2];  [3];  [3];  [4]
  1. Baylor College of Medicine, Houston, TX (United States). Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Berkeley Center for Structural Biology
  3. Univ. of California, San Diego, CA (United States). Dept. of Medicine
  4. Baylor College of Medicine, Houston, TX (United States). Verna and Marrs McLean Dept. of Biochemistry and Molecular Biology, and Dept. of Pharmacology and Chemical Biology
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1484208
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biological Chemistry
Additional Journal Information:
Journal Volume: 293; Journal Issue: 28; Journal ID: ISSN 0021-9258
Publisher:
American Society for Biochemistry and Molecular Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Qin, Liying, Sankaran, Banumathi, Aminzai, Sahar, Casteel, Darren E., and Kim, Choel. Structural basis for selective inhibition of human PKG Iα by the balanol-like compound N46. United States: N. p., 2018. Web. doi:10.1074/jbc.RA118.002427.
Qin, Liying, Sankaran, Banumathi, Aminzai, Sahar, Casteel, Darren E., & Kim, Choel. Structural basis for selective inhibition of human PKG Iα by the balanol-like compound N46. United States. doi:10.1074/jbc.RA118.002427.
Qin, Liying, Sankaran, Banumathi, Aminzai, Sahar, Casteel, Darren E., and Kim, Choel. Wed . "Structural basis for selective inhibition of human PKG Iα by the balanol-like compound N46". United States. doi:10.1074/jbc.RA118.002427. https://www.osti.gov/servlets/purl/1484208.
@article{osti_1484208,
title = {Structural basis for selective inhibition of human PKG Iα by the balanol-like compound N46},
author = {Qin, Liying and Sankaran, Banumathi and Aminzai, Sahar and Casteel, Darren E. and Kim, Choel},
abstractNote = {Activation of protein kinase G (PKG) Iα in nociceptive neurons induces long-term hyperexcitability that causes chronic pain. Recently, a derivative of the fungal metabolite balanol, N46, has been reported to inhibit PKG Iα with high potency and selectivity and attenuate thermal hyperalgesia and osteoarthritic pain. Here, we determined co-crystal structures of the PKG Iα C-domain and cAMP-dependent protein kinase (PKA) Cα, each bound with N46, at 1.98 Å and 2.65 Å, respectively. N46 binds the active site with its external phenyl ring, specifically interacting with the glycine-rich loop and the αC helix. Phe-371 at the PKG Iα glycine-rich loop is oriented parallel to the phenyl ring of N46, forming a strong π-stacking interaction, whereas the analogous Phe-54 in PKA Cα rotates 30° and forms a weaker interaction. Structural comparison revealed that steric hindrance between the preceding Ser-53 and the propoxy group of the phenyl ring may explain the weaker interaction with PKA Cα. The analogous Gly-370 in PKG Iα, however, causes little steric hindrance with Phe-371. Moreover, Ile-406 on the αC helix forms a hydrophobic interaction with N46 whereas its counterpart in PKA, Thr-88, does not. Substituting these residues in PKG Iα with those in PKA Cα increases the IC50 values for N46, whereas replacing these residues in PKA Cα with those in PKG Iα reduces the IC50, consistent with our structural findings. In conclusion, our results explain the structural basis for N46-mediated selective inhibition of human PKG Iα and provide a starting point for structure-guided design of selective PKG Iα inhibitors.},
doi = {10.1074/jbc.RA118.002427},
journal = {Journal of Biological Chemistry},
number = 28,
volume = 293,
place = {United States},
year = {2018},
month = {5}
}

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Figures / Tables:

Figure 1 Figure 1: Domain organizations and overall structures of N46 bound PKG Iα and PKA Cα. A, the domain organizations of PKG Iα and PKA Cα . The catalytic domains used for crystallization are shaded in orange and labeled with the corresponding residue numbers. Phosphorylated residues are indicated (PKG Iα T517more » and PKA Cα S139/T197/S338). B and C, overall structures of the PKG I Cα– 46 (B) and PKA Cα –N46 (C) complexes. The N-and C termini are labeled with the corresponding residue numbers. The structures are rendered as cartoons, with N46 shown as sticks. The small and large lobes are colored gray and tan, respectively. Atoms in N46 are colored as follows: carbons, yellow; oxygen, red; nitrogen, blue; fluorine, cyan. Enlarged views show Fo-Fc omit maps of N46 (contoured at 3.0 σ level).« less

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    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.