6CQ0

TBK1 in Complex with Dimethyl Amino Analog of Amlexanox

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Design, synthesis, and biological activity of substituted 2-amino-5-oxo-5H-chromeno[2,3-b]pyridine-3-carboxylic acid derivatives as inhibitors of the inflammatory kinases TBK1 and IKK epsilon for the treatment of obesity.

Beyett, T.S., Gan, X., Reilly, S.M., Gomez, A.V., Chang, L., Tesmer, J.J.G., Saltiel, A.R., Showalter, H.D.

(2018) Bioorg Med Chem 26: 5443-5461

  • DOI: 10.1016/j.bmc.2018.09.020
  • Primary Citation of Related Structures:  
    6CQ0, 6CQ4, 6CQ5

  • PubMed Abstract: 

    • The non-canonical IκB kinases TANK-binding kinase 1 (TBK1) and inhibitor of nuclear factor kappa-B kinase ε (IKKε) play a key role in insulin-independent pathways that promote energy storage and block adaptive energy expenditure during obesity. Utilizing docking calculations and the x-ray structure of TBK1 bound to amlexanox, an inhibitor of these kinases with modest potency, a series of analogues was synthesized to develop a structure activity relationship (SAR) around the A- and C-rings of the core scaffold ...

    The non-canonical IκB kinases TANK-binding kinase 1 (TBK1) and inhibitor of nuclear factor kappa-B kinase ε (IKKε) play a key role in insulin-independent pathways that promote energy storage and block adaptive energy expenditure during obesity. Utilizing docking calculations and the x-ray structure of TBK1 bound to amlexanox, an inhibitor of these kinases with modest potency, a series of analogues was synthesized to develop a structure activity relationship (SAR) around the A- and C-rings of the core scaffold. A strategy was developed wherein R 7 and R 8 A-ring substituents were incorporated late in the synthetic sequence by utilizing palladium-catalyzed cross-coupling reactions on appropriate bromo precursors. Analogues display IC 50 values as low as 210 nM and reveal A-ring substituents that enhance selectivity toward either kinase. In cell assays, selected analogues display enhanced phosphorylation of p38 or TBK1 and elicited IL-6 secretion in 3T3-L1 adipocytes better than amlexanox. An analogue bearing a R 7 cyclohexyl modification demonstrated robust IL-6 production in 3T3-L1 cells as well as a phosphorylation marker of efficacy and was tested in obese mice where it promoted serum IL-6 response, weight loss, and insulin sensitizing effects comparable to amlexanox. These studies provide impetus to expand the SAR around the amlexanox core toward uncovering analogues with development potential.

    Organizational Affiliation: 

    Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States; Vahlteich Medicinal Chemistry Core, University of Michigan, Ann Arbor, MI 48109, United States. Electronic address: showalh@umich.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase TBK1A660Homo sapiensMutation(s): 0 
Gene Names: TBK1, NAK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHD2 (Homo sapiens)
Explore Q9UHD2 
Go to UniProtKB:  Q9UHD2
PHAROS:  Q9UHD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHD2
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F8M (Subject of Investigation/LOI)
Query on F8M
Download Ideal Coordinates CCD File 
B [auth A]2-amino-7-[3-(dimethylamino)propyl]-5-oxo-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxylic acid
C18 H19 N3 O4
UFHZMIKXSGTKFX-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
F8M BindingDB:  6CQ0 IC50: 3760 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.803α = 90
b = 134.803β = 90
c = 85.503γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK100319
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK060591
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesDK60597

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-12-25
    Changes: Author supporting evidence