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In summary, we report the structure-based design of novel P1–
P3 linked macrocyclic BACE-1 inhibitors based on crystallographic
data obtained for the open-chain compound 1. In agreement with
modeling studies, the 15- and 16-membered macrocycles 3b and
3d were more active compared to their open-chain analogues 2a
and b, without increasing their molecular weight. The binding
mode of 3b to BACE-1 was confirmed by crystallographic analysis.
Sufficient occupancy of P1 by methyl substitution of the alkyl chain
appeared necessary to reach submicromolar BACE-1 inhibition.
The macrocyclization alone did not improve cellular potency.
Notably, the reduction of the peptidic character of the macrocyclic
inhibitors by methylation of the P2/3 amide retained the enzy-
matic activity but did not improve the cellular activity to the same
level. The macrocyclic inhibitors proved also to be weakly to mod-
erately selective over the related aspartyl protease CathD.
12. (a) Hannesian, S.; Yun, H.; Hou, Y.; Yang, G.; Bayrakdarian, M.; Therrien, E.;
Moitessier, N.; Roggo, S.; Veenstra, S.; Tintelnot-Blomley, M.; Rondeau, J.-M.;
Ostermeier, C.; Strauss, A.; Ramage, P.; Paganetti, P.; Neumann, U.; Betschart, C.
J. Med. Chem. 2005, 48, 5175; (b) The cellular activity was determined in
Chinese Hamster Ovary cells, stably transfected with human wild-type APP.
Acknowledgments
Compounds (0.003–10 lM) were incubated with adherent cells in 96 well
plates (n = 3 for each concentration) for 24 h. Supernatant concentration of
amyloid peptide 1–40 was analyzed using Europium-labeled beta-1 (N-
terminus) and XL-665 labeled 25H10 (C-terminus) in-house antibody and
homogenous time resolved fluorescence detection on a PHERAstar instrument
(BMG Labtech, Offenburg, Germany). Cell viability was determined using MTT
staining.
For the BACE complex with 3b, X-ray data collection was per-
formed at the Swiss Light Source, Paul Scherrer Institut, Villigen,
Switzerland. We are grateful to the machine and beamline groups
whose outstanding efforts have made this experiment possible.
We thank C. McCarthy for proofreading the manuscript.
13. Turner, R. T., III; Koelsch, G.; Hong, L.; Castanheira, P.; Gosh, A.; Tang, J.
Biochemistry 2001, 40, 10001.
14. X-ray coordinates for the complex of BACE with inhibitors 1 and 3b have been
under PDB ID: 3DUY and 3DV1.
Supplementary data
15. Reid, R. C.; Kelso, M. J.; Scanlon, M. J.; Fairlie, D. P. J. Am. Chem. Soc. 2002, 124,
5673.
Supplementary data associated with this article can be found, in
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608; (b) Tyndall, J. D. A.; Reid, R. C.; Tyssen, D. P.; Jardine, D. K.; Todd, B.;
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S.-H.; Alewood, P. F.; Birch, C. J.; Martin, J. L.; Fairlie, D. P. J. Med. Chem. 2000,
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