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J. V. Allen et al. / Bioorg. Med. Chem. Lett. 21 (2011) 5224–5229
as a compact donor/acceptor is required in conjunction with an
acceptor on the 20 position of the benzyl.
A directed screen of a relatively small number of compounds,
selected for kinase ATP pocket binding potential, yielded a novel
0
series of hit compounds. These were originally designed as hinge0
binders through the carbonyl group of the benzanilide however
SAR studies demonstrated the importance of the 30-OH-Ph and
200-CN-benzyl working co-operatively to deliver maximum inhibi-
tion. Modeling studies suggest a novel binding mode for compound
12, incorporating a water molecule bound between these two
groups and concomitant binding to the ‘hinge’. The compounds
27 and 43 were identified as optimal for rat bio-availability but
were insufficiently potent and inefficient, in both LLE and LE, to
continue further development.
Supplementary data
Supplementary data associated with this article can be found, in
Figure 2. Compound 12 (green) posed into high resolution structure c-Met
structure 3f66, placing 30-OH as binding to Tyr1159. An internal H-bond between
the amide and ether places the 200-CN-benzyl with the 200-CN pointing toward the
30-OH. A c-Met structure (3ccn) was aligned to evaluate this complex and was found
to have the small molecule phenol bound as shown (yellow).
References and notes
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Sattler, M.; Salgia, R. Curr. Oncol. Rep. 2007, 9(2), 102; (b) Birchmeier, C.;
Birchmeier, W.; Gherardi, E.; Vande Woude, G. F. Nature Rev. 2003, 4, 915.
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Birchmeier, W. Nature 1996, 384, 173; (b) Sachs, M.; Brohmann, H.; Zechner, D.;
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Woude, G. F.; Aaronson, S. A. Science 1991, 251, 802.
Starting with the highest resolution co-crystal structure in the
public domain, 3f6624 we sought to model the binding mode of
12 through editing, minimisation and comparison to other c-Met
structures.25 The model has set the 30-OH group as a hinge binder
to Tyr1159 and an internal H-bond is present between the amide
NH and benzyl ether oxygen. The central phenyl ring is tight
against the protein surface with the basic amine side chain pro-
truding into the solvent and near a region of acidic residues (
Fig. 2). Comparing the modeled complex by alignment with pro-
tein-ligand complex 3ccn,23 which contains a small molecule phe-
nolic compound (yellow structure – Figure 2) we see excellent
alignment of the phenolic groups of both compounds. Further-
more, alignment with apo-structure 2g15, offers an explanation
for the activity of 12.26 Figure 3 shows the overlay of two water
molecules in 2g15 (blue spheres). One water molecule aligns with
the 30-OH, both satisfying binding to Tyr1159. The other water re-
sides between carbonyl of met 1160, the 200-CN and the 30-OH sug-
gesting co-operation between these groups is possible. This
binding mode could explain the SAR we have observed for the ser-
ies and our difficulty in finding a replacement for the 30-OH group
5. Potempa, S.; Ridley, A. J. Mol. Biol. Cell 1998, 9, 2185.
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M.; Mendal, D. B. Cancer Res. 2003, 63, 7345; (b) Sattler, M.; Pride, Y. B.; Ma, P.;
Gramlich, J. L.; Chu, S. C.; Quinnan, S. S.; Liang, C.; Podar, K.; Christensen, J. G.;
Salgia, R. Cancer Res. 2003, 63, 5462.
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Kim, K.; Lippy, J.; Lombardo, L. J.; Manne, V.; Oppenheimer, S.; Sack, J. S.;
Schmidt, R. J.; Shen, G.; Stenfanski, K.; Tokarski, J. S.; Trainer, G. L.; Waulet, B. S.;
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13. ‘Privileged’ refers to structural motifs that are known to bind into the ATP
binding pocket of kinases, for example H-bond acceptor/donor pairs that
mimic the purine group of ATP. Amides are known kinase inhibitors, for
example: Baldwin, I.; Bamborough, P.; Haslam, C. G.; Hunjan, S. S.; Longstaff, T.;
Mooney, C. J.; Patel, S.; Quinn, J.; Somers, D. O. Bioorg. Med. Chem. Lett. 2008, 18,
5285.
14. Recombinant GST-wild type c-met (kinase domain residues 1056-1371)
enzyme was titrated in the assay by dilution with enzyme diluent (50 mM
MOPS pH6.8, 0.75 mM MnCl2, 0.1 mM sodium orthovanadate, 10 mM DTT &
0.1% BSA). Test compounds (at 10 mM in dimethylsulphoxide (DMSO)) were
diluted in a dose response manner into 384-well low volume assay plates.
‘Total’ control wells contained 6% DMSO instead of compound, ‘blank’ wells
contained 2
(7.2 M ATP, 24 nM biotin-poly EAY (Glu, Ala, Tyr) (CisBio, Product number
6SGATBBO) in 50 mM MOPS pH6.8, 0.75 mM MnCl2, 0.1 mM sodium
orthovanadate, 10 mM DTT & 0.1% BSA) was then added to all test wells. 5
of freshly diluted enzyme was added to all wells to start the reaction and the
plates incubated at room temperature for 60 min. To stop the reaction 5
ll 0.5 M EDTA instead of compound. 5 ll of substrate/ATP mix
l
Figure 3. Alignment of apo-c-Met structure 2g15 with 12/3f66 virtual complex.
Two water molecules present in 2g15, represented by blue spheres, present a
rationale for potency enhancement of 200-CN-benzyl in combination with 30-OH-Ph.
ll
ll