Inhibitors of the tyrosine kinase EphB4. Part 2: Structure-based discovery and optimisation of 3,5-bis substituted anilinopyrimidines

Bioorganic and Medicinal Chemistry Letters

Volumn 18, Issue 21, 2008, Pages 5717-5721

  Bardelle, Catherine ^a   Coleman, Tanya ^a   Cross, Darren ^a   Davenport, Sara ^a   Kettle, Jason G ^a   Ko, Eun Jung ^a   Leach, Andrew G ^a   Mortlock, Andrew ^a   Read, Jon ^a   Roberts, Nicola J ^a   Robins, Peter ^a   Williams, Emma J ^a  

^a ASTRAZENECA   (United Kingdom)

Author keywords

EphB4; Pyrimidine; Structure based design; Tyrosine kinase

Indexed keywords

ANILINOPYRIMIDINE DERIVATIVE; EPHRIN RECEPTOR A4; PROTEIN TYROSINE KINASE; PYRIMIDINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CRYSTALLOGRAPHY; DRUG CONFORMATION; DRUG DESIGN; DRUG POTENCY; DRUG SYNTHESIS; ENZYME INHIBITION;

MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN KINASE INHIBITORS; PYRIMIDINES; RECEPTOR, EPHB4;

EID: 54049137918     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmcl.2008.09.087     Document Type: Article

References (20)

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6. 1 with approximate cell dimensions a = 46.0, b = 53.5, c = 61.4 Ǻ and β = 110.9°. The first complex structure was solved by molecular replacement using a model of EphB2 (PDB code 1JPA); subsequent structure solution used the newly determined EphB4 complex structures as models. Detailed protein preparation and other experimental protocols are included in the Supplementary Material to this paper.
7. 5 2 (resolution 1.7 Ǻ, R-factor 0.238) and 7 (resolution 1.9 Ǻ, R-factor 0.184) have been deposited in the PDB with accession codes 2VWU, 2VWV and 2VWW, respectively.
8. EphB4 crystals were soaked in 0.5 μl compound 1 (100 mg/ml) plus 4.5 μl reservoir solution. The 1.65 Ǻ structure was refined to R = 16.6% and deposited with PDB accession code 2VWX. Data collection protocol and statistics are available in the Supplementary Material.
9. Complex crystal structures with compounds 2, 3, 4 and 5 were determined at 1.65 Ǻ (except compound 4 at 2.1 Ǻ) and refined to R = 18.7%, 16.8%, 18.4% and 17.1%. PDB deposition codes are 2VWY, 2VWZ, 2VX0, 2VX1, respectively. Statistics and protocols for both parts 1 and 2 of this publication series are included in the Supplementary Material.
10. Occupancies were roughly estimated by balancing the atomic temperature factors in the two alternate ligand models and were not refined.
11. This simplistic argument ignores any impact on potency from changes in lipophilicity and/or de-solvation penalties when adding an additional substituent.
12. For detailed synthetic procedures see: Kettle, J. G.; Read, J.; Leach, A.; Barlaam, B. C.; Ducray, R.; Lambert-Van Der Brempt, C. M. P.; PCT Int. Appl. WO2007085833.
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15. The assay detects inhibitors of recombinant EphB4-mediated phosphorylation of a polypeptide substrate in presence of magnesium-ATP using Alphascreen (Packard Bioscience) luminescence detection technology. For full details see Ref. 12.
16. CHO-K1 cells were engineered to stably express an EphB4-Myc-His construct. The endpoint assay used a sandwich ELISA to detect EphB4 phosphorylation status. Myc-tagged EphB4 from treated cell lysate were captured via an anti-c-Myc antibody and the phosphorylation status of captured EphB4 was then measured using a generic phosphotyrosine antibody. For further details see Ref. 8.
17. In this limited data set the correlation between number of hydrogen-bond donors and Clog P is weak.
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19. N-[4-[3-(6,7-Dimethoxy-3,4-dihydro-1H-isoquinolin-2-yl)propoxy]phenyl]-9 -oxo-10H-acridine-4-carboxamide was used, an analogue of the known BCRP and PGP inhibitor Elacridar, see: Dodic, N.; Dumaitre, B.; Daugan, A.; Pianetti, P. J. Med. Chem. 1995, 38, 2418-2426.
20. This does not rule out the possibility of reduced permeability in conjunction with efflux for the less cell potent inhibitors 10 and 16.