Y.-J. Wu et al. / Bioorg. Med. Chem. Lett. 19 (2009) 2654–2660
2659
Figure 3. (a) (Left). Binding model of inhibitor 27 (Merck)19 based on its X-ray crystal structure with human BACE-1. (b) (Right) Docked inhibitor 5i (E-isomer) in BACE-1
enzyme. hydrophobic interaction with S3 pocket (light blue circle); H-bonds to SO2 displacing interstitial H2O (red); H-bond to backbone of G230 (yellow) (only in 27);
hydrophobic interaction with T72 side chain (light green circle).
Me
O
O
Me
S
S
S3
S2
HO
S2
N
N
O
O
S3
OH
Ph
5pc
H
N
H
N
H
N
H
N
NH
N
O
OMe
Me
O
O
Me
O
Ph-3,5-di-F
27
4i
6. Wilson, C. A.; Doms, R. W.; Lee, V. M. J. Neurosci. Res. 2003, 74, 761.
7. Shankar, G. M.; Li, S.; Mehta, T. H.; Garcia-Munoz, A.; Shepardson, N. E.; Smith,
I.; Brett, F. M.; Farrell, M. A.; Rowan, M. J.; Lemere, C. A.; Regan, C. M.; Walsh, D.
M.; Sabatini, B. L.; Selkoe, D. J. Nat. Medicine 2008, 14, 837–842.
8. Klyubin, I.; Betts, V.; Welzel, A. T.; Blennow, K.; Zetterberg, H.; Wallin, A.;
Lemere, C. A.; Cullen, W. K.; Peng, Y.; Wisniewski, T.; Selkoe, D. J.; Anwyl, R.;
Walsh, D. M.; Rowan, M. J. J. Neurosci. 2008, 28, 4231.
9. Lundkvist, J.; Naslund, J. Curr. Opin. Pharmacol. 2007, 7, 112.
10. John, V.; Beck, J. P.; Bienkowski, M. J.; Sinha; HeinriksonSinha, R. L. J. Med. Chem.
2003, 46, 4625.
The acetyl,
a-hydroxyethyl and a-methoxyiminoethyl at C-3 gen-
erally enhanced binding affinity in the isophthalamide series pre-
sumably due to the hydrogen bonding network created through
their positive interaction with interstitial water in the enzyme,
as well as hydrophobic interaction with T72 side chain. The isoph-
thalamides with acetyl or
a-hydroxyethyl groups at C-3 also
exhibited optimal cellular activity. However, these substituents
show less pronounced effects in the sulfonamide series because
they occupy the S3 pocket instead of the S2 pocket, as in the case
of isophthalamides. The structure-based optimization for potency
led to several 1,3,5-trisubstituted phenylcarboxyamides with po-
tent cellular activity (IC50s < 100 nM). However, these compounds
were shown to be Pgp substrates and had poor pharmacokinetic
properties.22,23 Our efforts to address both of these liabilities will
be reported in due course.
11. McConlogue, L.; Buttini, M.; Anderson, J. P.; Brigham, E. F.; Chen, K. S.;
Freedman, S. B.; Games, D.; Johnson-Wood, K.; Lee, M.; Zeller, M.; Liu, W.;
Motter, R.; Sinha, S. J. Biol. Chem. 2007, 282, 26326.
12. Maillard, M. C.; Hom, R. K.; Benson, T. E.; Moon, J. B.; Mamo, S.; Bienkowski, M.;
Thomasselli, A. G.; Woods, D. D.; Prince, D. B.; Paddock, D. J.; Emmons, T. L.;
Tucker, J. A.; Dappen, M. S.; Brogley, L.; Thorsett, E. D.; Jewett, N.; Sinha, S.;
Varghese, J. J. Med. Chem. 2007, 50, 776; For recent progress in this area, see:
Charrier, N.; Clarke, B.; Cutler, L.; Demont, E.; Dingwall, C.; Dunsdon, R.; East,
P.; Hawkins, J.; Howes, C.; Hussain, I.; Jeffrey, P.; Maile, G.; Matico, R.; Mosley,
J.; Naylor, A.; O’Brien, A.; Redshaw, S.; Rowland, S.; Soleil, V.; Smith, K. J.;
Sweitzer, S.; Theobald, P.; Vessey, D.; Walter, D. S.; Wayne, G. J. Med. Chem.
2008, 51, 3313; Rizzi, L.; Vaiana, N.; Sagui, F.; Genesio, E.; Pilli, E.; Porcari, V.;
Romeo, S. Protein Pept. Lett. 2009, 16, 86.
Acknowledgments
13. (a) Boy, K. M.; Guernon, J. M.; Shi, J.; Zheng, C.; Liauw, A.; Bronson, J. J.; Macor, J.
E.; Combs, A. P.; Trainor, G.; Decicco, C. P.; Good, A.; Tebben, A. J.; Toyn, J. H.;
Burton, C. R.; Barten, D. M.; Marcinkeviciene, J.; Copeland, R. A.; Muckelbauer, J.
K.; Morin, P. E.; Lentz, K.; Albright, C.; Thompson, L. A. Abstracts of Papers,
233rd ACS National Meeting, Chicago, IL, United States, March 25–29, 2007,
MEDI-235; (b) Thompson, L. A.; Boy, K. M.; Shi, J.; Macor, J. E. U.S. Pat. Appl.
Publ. 2006, US 2006046984 A1.
We thank Carol Krause, Cathy Kieras, Lynn Balanda, Barbara
Robertson and Larry Iben for carrying out biological assays.
14. Rotella, D. Tetrahedron Lett. 1995, 36, 5453.
References and notes
15. Vallin, K. S. A.; Larhed, M.; Hallberg, A. J. Org. Chem. 2001, 66, 4340.
16. Steinhuebel, D.; Palucki, M.; Askin, D.; Dolling, U. Tetrahedron Lett. 2004, 45,
3305.
17. Wu, Y. -J.; He, H. Synlett 2003, 1789.
18. Iben, L. G.; Kopcho, L.; Marcinkeviciene, J.; Zheng, C.; Thompson, L. A.; Albright,
C. F.; Toyn, J. H. Eur. J. Pharmacol. 2008, 593, 10–15.
1. For recent reviews, see: Barten, D. M.; Albright, C. F. Mol. Neurobiol. 2008, 37,
171; Marcello, E.; Epis, R.; Luca, M. D. Eur. J. Pharmacol. 2008, 585, 109; LaFerla,
F. M.; Green, K. N.; Oddo, S. Nat. Rev. Neurosci. 2007, 8, 499.
2. Hardy, J.; Selkoe, D. J. Science 2002, 297, 353–356.
19. Burton, C. R.; Meredith, J. E.; Barten, D. M.; Goldstein, M. E.; Krause, C. M.;
Kieras, C. J.; Sisk, L.; Iben, L. G.; Polson, C.; Thompson, M. W.; Lin, X.; Corsa, J.;
Fiedler, T.; Pierdomenico, M.; Cao, Y.; Roach, A. H.; Cantone, J. L.; Ford, M. J.;
Drexler, D. M.; Olson, R. E.; Yang, M. G.; Bergstrom, C. P.; McElhone, K. E.;
3. Selkoe, D. J. Neuron 1991, 6, 487.
4. Caughey, B.; Lansbury, P. T. Annu. Rev. Neurosci. 2003, 26, 267.
5. Cleary, J. P.; Walsh, D. M.; Hofineister, J. J.; Shankar, G. M.; Kuskowski, M. A.;
Selkoe, D. J.; Ashe, K. H. Nat. Neurosci. 2005, 8, 79.