5TO8

Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation 3D Report Full Report



Literature

Selectivity switch between FAK and Pyk2: Macrocyclization of FAK inhibitors improves Pyk2 potency.

Farand, J.Mai, N.Chandrasekhar, J.Newby, Z.E.Van Veldhuizen, J.Loyer-Drew, J.Venkataramani, C.Guerrero, J.Kwok, A.Li, N.Zherebina, Y.Wilbert, S.Zablocki, J.Phillips, G.Watkins, W.J.Mourey, R.Notte, G.T.

(2016) Bioorg Med Chem Lett 26: 5926-5930

  • DOI: 10.1016/j.bmcl.2016.10.092
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Herein, we describe the synthesis of Pyk2 inhibitors via macrocyclization of FAK and dual Pyk2-FAK inhibitors. We identified macrocycle 25a as a highly potent Pyk2 inhibitor (IC 50 =0.7nM), with ∼175-fold improvement in Pyk2 potency as com ...

    Herein, we describe the synthesis of Pyk2 inhibitors via macrocyclization of FAK and dual Pyk2-FAK inhibitors. We identified macrocycle 25a as a highly potent Pyk2 inhibitor (IC 50 =0.7nM), with ∼175-fold improvement in Pyk2 potency as compared to its acyclic counterpart. In many cases, macrocyclization improved Pyk2 potency while weakening FAK potency, thereby improving the Pyk2/FAK selectivity ratio for this structural class of inhibitors. Various macrocyclic linkers were studied in an attempt to optimize Pyk2 selectivity. We observed macrocyclic atropisomerism during the synthesis of 19-membered macrocycles 10a-d, and successfully obtained crystallographic evidence of one atropisomer (10a-AtropB) preferentially bound to Pyk2.


    Organizational Affiliation

    Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein-tyrosine kinase 2-beta
A
282Homo sapiensMutation(s): 0 
Gene Names: PTK2BFAK2PYK2RAFTK
EC: 2.7.10.2
Find proteins for Q14289 (Homo sapiens)
Go to UniProtKB:  Q14289
NIH Common Fund Data Resources
PHAROS  Q14289
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7FM
Query on 7FM

Download CCD File 
A
25-(methylsulfonyl)-8-(trifluoromethyl)-5,17,18,21,22,23,24,25-octahydro-12H-7,11-(azeno)-16,13-(metheno)pyrido[3,2-i]pyrrolo[1,2-q][1,3,7,11,17]pentaazacyclohenicosin-20(6H)-one
C25 H26 F3 N7 O3 S
FOLRUTAUDNCQAE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7FMIC50:  3.0999999046325684   nM  BindingDB
7FMIC50:  3.0999999046325684   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.625α = 90
b = 93.565β = 93.85
c = 43.214γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-10-17 
  • Released Date: 2016-12-21 
  • Deposition Author(s): Newby, Z.E.

Revision History 

  • Version 1.0: 2016-12-21
    Type: Initial release