D. A. Cogan et al. / Bioorg. Med. Chem. Lett. 18 (2008) 3251–3255
3255
Table 3. Relationship between physicochemical properties and potency in human whole blood for select compounds
Compound
Tm (ꢂC)
Human whole
blood IC50 (nM)
Solubility in pH 7.4
buffer (lg/mL)
Caco-2 Papp. · 10À6 (cm/s)
Plasma protein
binding (%)
BIRB796
63.5
60.5
59.9
57.3
780
260
210
83
1.0
bqla
2.0
10
b
99
92
66
66
12
24
28
7.4
13
13.9
a Below quantifiable limit: 0.1 lg/ml.
b Insufficient solubility for assay.
S.; Boehm, J.; Lee, J. C. Nature Rev. Drug Discov. 2003, 2,
717; (d) Ono, K.; Han, J. Cell. Signal. 2000, 12, 1.
2. (a) Dominguez, C.; Powers, D. A.; Tamayo, N. Curr.
Opin. Drug Disc. Dev. 2005, 8, 421; (b) Nikas, S. N.;
Drosos, A. A. Curr. Opin. Invest. Drugs 2004, 5, 1205; (c)
Cirillo, P. F.; Pargellis, C.; Regan, J. Curr. Topics Med.
Chem. 2002, 2, 1021.
is compound 28, whose IC50 in whole blood is 83 nM de-
spite having a Tm 3 ꢂC lower than 12.
Efficacy in the human whole blood assay can be attrib-
uted to a variety of factors, including plasma protein
binding (affinity and kinetics), and membrane perme-
ability, that should be dependant upon a compound’s
physicochemical properties. Table 3 indicates how solu-
bility, permeability, and plasma protein binding relate to
whole blood potency for select compounds. While it ap-
pears that permeability is not a determining factor for
these compounds, the extent of protein binding does
have an impact. As a result, compound 28 is almost
10-fold more potent in whole blood than BIRB 796 de-
spite having a Tm more than 6 ꢂC lower.
3. (a) Klinkhoff, A. Drugs 2004, 64, 1267; (b) Barry, J.;
Kirby, B. Expert Opin. Biol. Ther. 2004, 4, 975.
4. (a) Regan, J.; Breitfelder, S.; Cirillo, P.; Gilmore, T.;
Graham, A. G.; Hickey, E. R.; Klaus, B.; Madwed, J.;
Moriak, M.; Moss, N.; Pargellis, C. A.; Pav, S.; Proto, A.;
Swinamer, A.; Tong, L.; Torcellini, C. J. Med. Chem.
2002, 45, 2994; (b) Regan, J.; Capolino, A.; Cirillo, P. F.;
Gilmore, T.; Graham, A. G.; Hickey, E.; Kroe, R. R.;
Madwed, J.; Moriak, M.; Nelson, R.; Pargellis, C. A.;
Swinamer, A.; Torcellini, C.; Tsang, M.; Moss, N. J. Med.
Chem. 2003, 46, 4676.
It is worth noting that the compounds from this series
typically demonstrate a high level of kinase selectivity,
even among kinases that the naphthyl ureas typically in-
hibit. For example, whereas BIRB 796 has an IC50 for
Jnk2a of 6 nM, the IC50 for compound 28 is 1.1 lM.
In addition, 28 does not demonstrate activity against
the following kinases at 3 lM: MKK1, ERK2, JNK1,
p38c, p38d, MAPKAP-K1a, MAPKAP-K2, MSK1,
PRAK, PKA, PKCa, PDK1, PKBdPH, SGK, S6K1,
GSK3b, ROCK-II, AMPK, CHK1, CK2, PHOS. KI-
NASE, CDK2/cyclin A, CK1, DYRK1A, PP2A, and
NEK6, and the following tested at 10 lM: Btk, Eck,
EGFR, FGFR3, Hek, HGFR, IGF1R, IR, Itk, JAK3,
Lyn, Syk, TXK, VEGFR1.
5. Pargellis, C. A.; Tong, L.; Churchill, L.; Cirillo, P.;
Gilmore, T.; Graham, A. G.; Grob, P. M.; Hickey, E.
R.; Moss, N.; Pav, S.; Regan, J. Nat. Struct. Biol. 2002,
9, 268.
6. (a) Goldberg, D.; Hao, M.-H.; Qian, K. C.; Swinamer, A.
D.; Gao, D. A.; Xiong, Z.; Sarko, C.; Berry, A.; Lord, J.;
Magolda, R. L.; Fadra, T.; Kroe, R. R.; Kukulka, A.;
Madwed, J. B.; Martin, L.; Pargellis, C.; Skow, D.; Song,
J. J.; Tan, Z.; Torcellini, C. A.; Zimmitti, C. S.; Yee, N.
K.; Moss, N. J. Med. Chem. 2007, 50, 4016; (b) Wang, R.;
Gao, Y.; Lai, L. J. Mol. Model 2000, 6, 498.
7. SAR at this region will be disclosed in future publications.
8. A 2.8 ꢂC change in thermal denaturation temperature
corresponds to approximately a 10-fold change in binding
affinity. However, it must be noted that this relationship
was developed for pyrazole naphthyl urea-based inhibitors
(e.g., BIRB 796), and if the thermodynamics of binding for
this class of inhibitors is significantly different, this
relationship may be an approximation. Kroe, R. R.;
Regan, J.; Proto, A.; Peet, G. W.; Roy, T.; Dickert, L.;
Fuschetto, N.; Pargellis, C. A.; Ingraham, R. H. J. Med.
Chem. 2003, 46, 4669.
Our de novo design strategy has provided access to an
additional structurally distinct class of p38 inhibitors.
This work highlights an example of using computer-
aided drug design to generate ideas, and molecular mod-
eling to refine these ideas into viable lead structures. The
design provided potent p38 inhibitors that were amena-
ble to analogue synthesis, allowing the further improve-
ment in physicochemical properties and potency in
human whole blood.
9. The coordinates have been deposited in the RSCB protein
databank (RCSB ID code rcsb047198 and PDB ID code
3CTQ).
10. Fitzgerald, C. E.; Patel, S. B.; Becker, J. W.; Cameron, P.
M.; Zaller, D.; Pikounis, V. B.; O’Keefe, S. J.; Scapin, G.
Nature: Struct. Biol. 2003, 10, 764.
References and notes
11. Compounds 26 and 27 were prepared from their N-Boc
piperidine analogues via Boc-removal (HCl/dioxane; 66%
yield) and reductive amination (formaldehyde, 1% HOAc
in methanol, NaCNBH3, 25% yield).
1. (a) Wagner, G.; Laufer, S. Med. Res. Rev. 2006, 26, 1; (b)
Saklatvala, J. Curr. Opin. Pharm. 2004, 4, 372; (c) Kumar,