6BOD

TBK1 in complex with ethyl ester analog of amlexanox


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Carboxylic Acid Derivatives of Amlexanox Display Enhanced Potency toward TBK1 and IKKepsilonand Reveal Mechanisms for Selective Inhibition.

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

(2018) Mol Pharmacol 94: 1210-1219

  • DOI: 10.1124/mol.118.112185
  • Primary Citation of Related Structures:  
    6BNY, 6BOD, 6BOE, 5W5V

  • PubMed Abstract: 
  • Chronic low-grade inflammation is a hallmark of obesity, which is a risk factor for the development of type 2 diabetes. The drug amlexanox inhibits I κ B kinase ε (IKK ε ) and TANK binding kinase 1 (TBK1) to promote energy expe ...

    Chronic low-grade inflammation is a hallmark of obesity, which is a risk factor for the development of type 2 diabetes. The drug amlexanox inhibits I κ B kinase ε (IKK ε ) and TANK binding kinase 1 (TBK1) to promote energy expenditure and improve insulin sensitivity. Clinical studies have demonstrated efficacy in a subset of diabetic patients with underlying adipose tissue inflammation, albeit with moderate potency, necessitating the need for improved analogs. Herein we report crystal structures of TBK1 in complex with amlexanox and a series of analogs that modify its carboxylic acid moiety. Removal of the carboxylic acid or mutation of the adjacent Thr156 residue significantly reduces potency toward TBK1, whereas conversion to a short amide or ester nearly abolishes the inhibitory effects. IKK ε is less affected by these modifications, possibly due to variation in its hinge that allows for increased conformational plasticity. Installation of a tetrazole carboxylic acid bioisostere improved potency to 200 and 400 nM toward IKK ε and TBK1, respectively. Despite improvements in the in vitro potency, no analog produced a greater response in adipocytes than amlexanox, perhaps because of altered absorption and distribution. The structure-activity relationships and cocrystal structures described herein will aid in future structure-guided inhibitor development using the amlexanox pharmacophore for the treatment of obesity and type 2 diabetes.


    Organizational Affiliation

    Program in Chemical Biology (T.S.B.), Life Sciences Institute (T.S.B., L.C., J.J.G.T.), Departments of Medicinal Chemistry (X.G., H.D.S., J.J.G.T.), Pharmacology (J.J.G.T.), Biological Chemistry (J.J.G.T.), and Vahlteich Medicinal Chemistry Core, College of Pharmacy (X.G., H.D.S.), University of Michigan, Ann Arbor, Michigan; Institute for Diabetes and Metabolic Health (S.M.R., A.V.G., A.R.S.), Departments of Medicine (S.M.R., A.R.S.) and Pharmacology (A.V.G., A.R.S.), University of California, San Diego, La Jolla, California; and Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana (J.J.G.T.) jtesmer@purdue.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase TBK1A660Homo sapiensMutation(s): 0 
Gene Names: TBK1NAK
EC: 2.7.11.1
Find proteins for Q9UHD2 (Homo sapiens)
Explore Q9UHD2 
Go to UniProtKB:  Q9UHD2
NIH Common Fund Data Resources
PHAROS  Q9UHD2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E0P
Query on E0P

Download CCD File 
A
ethyl 2-amino-5-oxo-7-(propan-2-yl)-5H-[1]benzopyrano[2,3-b]pyridine-3-carboxylate
C18 H18 N2 O4
PFDJAEKKGJFCNL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.228 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.314α = 90
b = 134.314β = 90
c = 85.275γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



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 StatesR01 DK100319

Revision History 

  • Version 1.0: 2018-09-26
    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