Discovery of potent iminoheterocycle BACE1 inhibitors

Article abstract of DOI:10.1016/j.bmcl.2014.10.006

The synthesis of a series of iminoheterocycles and their structure-activity relationships (SAR) as inhibitors of the aspartyl protease BACE1 will be detailed. An effort to access the S3 subsite directly from the S1 subsite initially yielded compounds with sub-micromolar potency. A subset of compounds from this effort unexpectedly occupied a different binding site and displayed excellent BACE1 affinities. Select compounds from this subset acutely lowered Aβ₄₀ levels upon subcutaneous and oral administration to rats.

Full text of DOI:10.1016/j.bmcl.2014.10.006

Bioorganic & Medicinal Chemistry Letters 24 (2014) 5455–5459
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Discovery of potent iminoheterocycle BACE1 inhibitors
⇑
John P. Caldwell , Robert D. Mazzola, James Durkin, Joseph Chen, Xia Chen, Leonard Favreau,
Matthew Kennedy, Reshma Kuvelkar, Julie Lee, Nansie McHugh, Brian McKittrick, Peter Orth,
Andrew Stamford, Corey Strickland, Johannes Voigt, Liyang Wang, Lili Zhang, Qi Zhang, Zhaoning Zhu
Merck Research Laboratories, 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
The synthesis of a series of iminoheterocycles and their structure–activity relationships (SAR) as inhibi-
tors of the aspartyl protease BACE1 will be detailed. An effort to access the S3 subsite directly from the S1
subsite initially yielded compounds with sub-micromolar potency. A subset of compounds from this
effort unexpectedly occupied a different binding site and displayed excellent BACE1 affinities. Select com-
pounds from this subset acutely lowered Ab40 levels upon subcutaneous and oral administration to rats.
Ó 2014 Elsevier Ltd. All rights reserved.
Received 5 September 2014
Revised 29 September 2014
Accepted 2 October 2014
Available online 23 October 2014
Keywords:
Alzheimer’s disease
b-Secretase
BACE
Aspartyl protease inhibitors
Structure-based drug design
A widely pursued strategy for the potential treatment of Alzhei-
mer’s disease is inhibiting the production of neurotoxic b-amyloid
(Ab) peptides, especially Ab40,42. The first step in generation of Ab
involves cleavage of amyloid precursor protein (APP) by BACE1.1
Potent inhibitors of BACE1 should halt Ab production thereby
reducing the neurotoxic Ab oligomers and plaques. Non-peptidic
BACE1 inhibitors have been reported by our labs and others and
offer the most promising avenue to the discovery of orally bioavail-
able, brain penetrant inhibitors.2,3
In earlier accounts, we reported on the rational design of com-
pound 1 from a fragment screening hit.2 The amidine portion of the
iminohydantoin core forms a critical hydrogen bond network with
the catalytic diad (Asp32 and Asp228) of the BACE1 enzyme. Addi-
tionally, the initial design strategy focused on the optimization of
four subsites (S20, S1, S2, and S3) to afford a potent compound,
Ki = 27 nM (see Fig. 1).4 Unfortunately, this compound had low
plasma exposure in an oral rat pharmacokinetic assay. Consistent
with a strategy to maximize the probability of identifying inhibi-
tors with high CNS exposure, we sought to explore variants of 1
that would access S3 directly through S1, eliminating the need
for occupation of S2 and inherently lowering the MW and cLogP.2d
This work will detail the synthesis of these compounds and high-
light the salient structure–activity relationships.
Key to construction of the proposed S1–S3 iminohydantoins
was the use of the oxazolidinone intermediate 3 (Scheme 1).2d
Elaboration of 3 through alkylation with the appropriate allyl
bromide offered many opportunities to access S3 from S1. Scheme 2
shows the approach to S1 piperidine and pyrrolidine systems. For
O
NH
NH
N
N
HN
O
1
BACE1 Ki =27 nM
⇑
Corresponding author. Tel.: +1 908 740 5199.
E-mail address: john.caldwell@merck.com (J.P. Caldwell).
Figure 1. X-ray of 1 in the active site of BACE1.
http://dx.doi.org/10.1016/j.bmcl.2014.10.006
0960-894X/Ó 2014 Elsevier Ltd. All rights reserved.

5456
J. P. Caldwell et al. / Bioorg. Med. Chem. Lett. 24 (2014) 5455–5459
Ph Br
H3CO2C
H3CO2C
NHCbz
NHCbz
a, b
c, d
HO
O
NCbz
HO
O
NH2
a, b, c
O
12
13
14
(S)/(R):1/1
2
3
NBoc
NBoc
H3CO2C
NH2
N
Scheme 1. Reagents and conditions: (a) 5% Rh/C with 50% H2O, 5% Pt/C, MeOH/
H2O/concd HCl aq, 60 psi H2, rt, 97%; (b) CbzOSu, dioxane/H2O, Et3N, rt, 95%; and (c)
BF3–OEt2, PhCH(OMe)2, THF, ꢀ78 °C then rt, 70%.
e, f
NH
g - j
O
(R)-14
1
3
TBSO
HO
(R)-15
(R)-16
O
O
Ph
NCbz
H3CO2C
NH2
N
CO2CH3
a - e
Br
O
k, l
f
O
NH
g,h
g, h, i
(S)-14
(R)-16
1
3
BocN
S
N
CH3
N
HO
Boc
5
HO
6
4
(S)-17
(S)-16
N
N
O
H3CO2C
S
i
NH2
NBoc
NH
j
NH
NH
NBoc
NH
H
H
H
N
N
m
n, o
O
O
BocN
BocN
BocN
7
(S)-8
(R)-8
O
(S)-16
H2N
19
18
N
O
N
S
N
O
S
O
H
Ph
NH
l
NH
NCbz
k
H
NH
NH
H
Br
O
O
+
p, b, j
HN
TBSO
RN
RN
26, 28-32, 34
20
21
(R)-10
(R)-9
H3CO2C
H3CO2C
NHCbz
NH2
CO2Me
steps
N
NH
N
O
O
NH
NH
k, l
q, r, s
H
H
NH
HO
HO
N
Bn
22
RN
32 and 34
RN
33 and 35
23
NBoc
NH
11
NH
NH
N
N
O
t, u
O
Scheme 2. Reagents and conditions: (a) 1-chloroethyl chloroformate, toluene, heat;
(b) HCl aq, CH3OH, heat; (c) Boc2O, Et3N, CH2Cl2, rt, a–c: 48% three steps; (d) DIBAL-
H, THF, ꢀ78 °C then rt, 73%; (e) PPh3, imidazole, Br2, 76%; (f) KHMDS, 3, THF, ꢀ78 °C,
60%; (g) LiOCH3, CH3OH, rt, 92%; (h) Pd(OH)2, H2 1 atm, MeOH, 99%; (i) MeNCS,
DIEA, THF, rt, 80%; (j) TFA, CH2Cl2, rt, 97%; (k) N-derivatization; (l) NH4OH, CH3OH,
t-BuO2H, rt, 35–60%.
R1
HN
H2N
24
Scheme 3. Reagents and conditions: (a) LiHMDS, 3, THF, ꢀ78 °C; (b) LiOCH3,
CH3OH, rt, a–b: 80% two steps; (c) Pd/C, K2CO3, t-BuO2H, CH2Cl2, 25–60%; (d) NaBH4,
CH3OH, 0 °C then rt, 96%; (e) TBSCl, imidazole, rt, 95%; (f) Pd(OH)2/C, H2, rt, 99%; (g)
MeNCS, DIEA, THF, rt, 79%; (h) NH4OH, CH3OH, t-BuO2H, rt; (i) Boc2O; CH2Cl2, rt, h–
i: 79% two steps; (j) TBAF, THF, rt; (k) [DiPFc-Rh(cod)]BF4, CH2Cl2, 55 psi H2, 77%; (l)
5% Rh/C, 5% Pd/C, 55 psi H2, AcOH, rt, 99%; (m) Dess–Martin reagent, CH2Cl2, rt, 93%;
(n) MP-CNBH4, DMBNH2, cat. AcOH, DCE, rt, 96%; (o) 5% Pd(OH)2/C, HCO2NH4,
CH3OH, rt, 93%; (p) LiHMDS, THF, ꢀ78 °C; (q) BocNHC(S)NHCH3, DIEA, THF, 82%; (r)
DIAD, PPh3, 3-pyC(O)N3, THF, rt, 90%;11 (s) 5% Pd/C, H2 CH3OH, rt, 99%; (t) N-
derivatization; and (u) TFA, CH2Cl2, rt, 95%.
the piperidines, upon deprotonation of 3 with KHMDS and treat-
ment with 5 (generated from 4 in a straightforward manner5,6),
1,10-oxazolidinone 6 was produced with retention of stereochemis-
try in a manner consistent with literature precedent.7 Methanoly-
sis and hydrogenation of 6 furnished the aminoester 7 as a
diastereomeric mixture of Boc-protected piperidines. After subse-
quent cyclization to the corresponding thiohydantoins 8, the
diastereomerically pure compounds were obtained by silica gel
chromatography. The Boc-piperidines were individually deprotec-
ted, and the resulting piperidines 9 were elaborated through a vari-
ety of standard N-derivatization chemistries (reductive amination,
amidation and sulfonylation). These thiohydantoins 10 were
subjected to oxidative amination conditions to prepare the final
iminohydantoin targets (representative sequence shown for the
(R)-isomer in Scheme 2). Derivatives of both diastereomers of
the S1-piperidine were explored. The S1-pyrrolidinyl analogs were
prepared in an similar fashion starting with the benzyl-protected
2,5-dihydropyrrole ester 11 (Scheme 2, bottom section).8
In a concurrent effort to explore the S1-aminocyclohexane vari-
ants (Scheme 3), oxazolidone 3 was alkylated with 12, oxidized to
the en-one,9 and then reduced to form a mixture of alcohol diaste-
reomers 14. Since the position of the hydroxyl group as an allyl
alcohol offered the opportunity to set the desired C1(R)-stereo-

J. P. Caldwell et al. / Bioorg. Med. Chem. Lett. 24 (2014) 5455–5459
5457
chemistry at the cyclohexyl stereocenter, we separated the alco-
hols to provide pure diastereoisomers 14. Hydrogenation of the
TBS-protected derivative of alcohol (R)-14 proceeded cis relative
to the bulky silyl protecting group, whereas hydroxyl-directed
hydrogenation of (S)-14 provided (S)-17. As desired, both transfor-
mations provided the (R)-stereochemistry at the C1 cyclohexyl.
Aminoesters (R)-15 and (S)-17 were separately elaborated to
the Boc-protected iminohydantoins 16, and the alcohol moieties
were then oxidized to give the corresponding cyclohexanone 18.
To obtain the (R)-aminocyclohexane of 19, cyclohexanone 18 was
treated with 2,4-dimethoxybenzylamine (DMBNH2) under reduc-
tive amination conditions. The resulting diastereomers were sepa-
rated (product d.r. = (S)/(R):1/2), and the DMB group was
deprotected under hydrogenation conditions.10 Amine (R)-19 was
converted to the corresponding amides (43–45), ureas (46–53),
and N-arylated targets (54–55).
Once the correct diastereomer was validated through BACE1 Ki
determination (vide infra), we developed an alternative stream-
lined synthesis (Scheme 3, bottom section). In this new route, oxa-
zolidinone 20 was prepared from 2 and then alkylated with chiral
allyl bromide 21, which contained the TBS-protected-(S)-hydroxyl
such that the C3-cyclcohexyl stereocenter was installed far earlier
in the synthesis. After methanolysis of the oxazolidinone and TBAF
deprotection, cyclohexenol 22 was subjected to a one-pot sequen-
tial hydrogenation to (a) set the C1-cyclohexyl (R)-stereocenter
through hydroxyl-directed hydrogenation, (b) deprotect the N-
benzyl carbamate, and (c) reduce the phenethyl to the cyclohexyl-
ethyl to produce 23. Aminoester 23 was elaborated to the Boc-pro-
tected iminohydantoin, treated with an azide transfer reagent with
inversion of stereochemistry at C3, and reduced to the aminocyclo-
hexane 24 now possessing the desired (R)-C3-stereochemistry.
Amino derivatives of 24 were produced and Boc-deprotection
afforded the final target compounds.
30, and 31). When amides were explored further, the n-butyl
amide and cyclopentylmethyl amide showed the best potencies
with several examples showing sub-micromolar BACE1 Ki values.
The S1-pyrolidine was slightly more potent than the S1-piperidine.
Table 2 details the results in the S1-cyclohexylamine series. In
general, potencies were significantly better in this series in com-
parison to the heterocycloalkyl series. Reductive amination with
a variety of substrates led to compounds (40–42) with sub-micro-
molar potency. From X-ray crystallographic studies (Fig. 2),13 com-
pounds from both series (e.g., 38 and 41) validated the hypothesis
that we can improve potency by occupying S3 directly from S1.
Furthermore, significant potency gains were achieved by
decreasing the basicity of the exocyclic nitrogen through the amide
(43–44) and urea (46–54) derivatives. The benzylamide 45 was
five-fold less potent than the phenyl amide analog 43. Once again,
X-ray crystallography provided valuable insight into these dra-
matic potency differences. Surprisingly, these compounds did not
Table 2
BACE1 affinities of S1-aminocyclohexyl analogs12
NH
N
O
NH
R1
HN
Compound
R1
BACE-1
Ki (nM)
Cat-D
Ki ( M)
l
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
–CH2-c-propyl
–c-Pentyl
–c-Hexyl
–C(O)Ph
–C(O)-4-pyridyl
–C(O)Bn
480
430
230
130
39
585
16
301
10
276
10
3
138
22
14
53.3
>100
63.5
3.8
19.3
3.5
7.1
8.5
>100
2.4
2.5
Table 1 highlights the SAR in the S1-heterocycloalkyl series. In
both the S1 piperidine and S1 pyrrolidine series, there is a prefer-
ence in terms of BACE1 potency for the (R)-stereochemistry at the
tertiary center (cf. 32 vs 33, 34 vs 35, 36 vs 37, and 38 vs 39). Addi-
tionally, amides appeared to be the preferred derivative when
compared to substituted amines, ureas and sulfonamides (cf. 29,
–C(O)NHPh
–C(O)NH-2-Cl-Ph
–C(O)NH-4-Cl-Ph
–C(O)NH-2-MeO-Ph
–C(O)NH-4-MeO-Ph
–C(O)NH-4-CNPh
–C(O)NH-c-hexyl
2-Quinoline–
2-Quinoxaline–
6.9
6.0
25.0
7.5
Table 1
BACE1 affinities of S1-piperidine and pyrrolidine analogs12
N
O
NH
(S)/(R)
NH
NH
N
NH
NH
N
O
RN
O
NH
n
N
HN
Compound
R
n
S/R
BACE-1
Cat-D
Ki(lM)
O
38
41
Ki (lM)
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
Boc
Boc
H
2
2
2
2
2
2
2
2
2
2
2
1
1
1
1
S
R
S
R
R
R
R
R
S
R
S
R
S
R
S
41
29
66
33
>100
>100
>100
>100
2.8
25.5
44.0
28.0
0.87
8.5
H
8.5
7.6
8.5
6.3
3.2
17
0.97
12.4
0.49
17.4
0.64
37
n-(CH2)4CH3
–C(O)NH(CH2)2CH3
–SO2(CH2)3CH3
–C(O)(CH2)3CH3
–C(O)(CH2)3CH3
–C(O)CH2-c-pentyl
–C(O)CH2-c-pentyl
–C(O)(CH2)3CH3
–C(O)(CH2)3CH3
–C(O)CH2-c-pentyl
–C(O)CH2-c-pentyl
23.0
nt
6.0
nt
Figure 2. X-ray of compound 38 (orange) and 41 (cyan) occupying the S3 subsite
directly from S1.
nt = not tested.

NH
NH
NH
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J. P. Caldwell et al. / Bioorg. Med. Chem. Lett. 24 (2014) 5455–5459
Unfortunately, no cortical Ab40 reduction was observed when 53
was dosed to CRND8 mice.12 Although 53 was potent in the enzy-
matic assay (Ki = 22 nM) it suffered from a pronounced cell shift
when tested in the whole cell assay, WCAb40 EC50 = 258 nM.12 Fur-
thermore, when dosed with a known p-glycoprotein (Pgp) inhibi-
tor, the cellular potency improved to 110 nM, the leftward shift
suggesting that 53 was a Pgp substrate.
In summary, employment of a modular synthetic strategy
allowed us to access structurally distinct iminoheterocycles and
enabled rapid SAR exploration of a series of small-molecule BACE1
inhibitors. Our understanding of the SAR was refined through X-
ray crystallographic studies, which showed that a subset of these
inhibitors serendipitously occupied a different subsite of the
BACE1 enzyme. Optimization studies exploiting this unique subsite
led to the discovery of 53, a compound possessing modest expo-
sure that lowered plasma Ab40 levels upon subcutaneous and oral
dosing.
N
N
NH
O
O
O
O
N
HN
HN
HN
44
46
NH
NH
N
O
N
HN
53
Acknowledgments
We would like to thank Dr. William Greenlee, Dr. Eric Parker,
and Dr. John Hunter for their support and guidance of this work,
Dr. Jesse Wong for preparation of intermediates, Ron Manning for
genotyping and maintenance of the CRND8 mice, and Dr. Jared
Cumming for suggestions and helpful discussions in the prepara-
tion of this Letter. Use of the IMCA-CAT beamline 17-ID at the
Advanced Photon Source was supported by the companies of the
Industrial Macromolecular Crystallography Association through a
contract with the Center for Advanced Radiation Sources at the
University of Chicago.
Figure 3. X-ray of compounds 44 (cyan), 46 (orange), and 53 (yellow). Note that the
substituents designed to reside in S3 instead occupy a different hydrophobic region
making favorable hydrophobic interactions with the Ile171 and Lys168 residues as
well as forming a hydrogen bond with the carbonyl of Phe169
.
References and notes
Table 3
In vivo evaluation of selected compounds
1. Hardy, J.; Selkoe, D. J. Science 2002, 297, 353.
Compound AUC0–6h (nM-h) Ab40 lowering plasma Ab40 lowering plasma
2. (a) Wang, Y.-S.; Strickland, C.; Voigt, J. H.; Kennedy, M. E.; Beyer, B. M.; Senior,
M. M.; Smith, E. M.; Nechuta, T. L.; Madison, V. S.; Czarniecki, M.; McKittrick, B.
A.; Stamford, A. W.; Parker, E. M.; Hunter, J. C.; Greenlee, W. J.; Wyss, D. F. J.
Med. Chem. 2010, 53, 942; (b) Zhu, Z.; Sun, Z.-Y.; Ye, Y.; Voigt, J.; Strickland, C.;
Smith, E. M.; Cumming, J.; Wang, L.; Wong, J.; Wang, Y.-S.; Wyss, D. F.; Chen, X.;
Kuvelkar, R.; Kennedy, M. E.; Favreau, L.; Parker, E.; McKittrick, B. A.; Stamford,
A. W.; Czarniecki, M.; Greenlee, W. J.; Hunter, J. C. J. Med. Chem. 2010, 53, 951;
(c) Cumming, J. N.; Smith, E. M.; Wang, L.; Misiaszek, J.; Durkin, J.; Pan, J.;
Iserloh, U.; Wu, Y.; Zhu, Z.; Strickland, C.; Voigt, J.; Chen, X.; Kennedy, M. E.;
Kuvelkar, R.; Hyde, L. A.; Cox, K.; Favreau, L.; Czarniecki, M. F.; Greenlee, W. J.;
McKittrick, B. A.; Parker, E. M.; Stamford, A. W. Bioorg. Med. Chem. Lett. 2012, 22,
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Wu, Y.; Misiaszek, J.; Cumming, J. N.; Gilbert, E. J.; Huang, C.; McKittrick, B. A.;
Hong, J.; Guo, T.; Zhu, Z.; Strickland, C.; Orth, P.; Voigt, J. H.; Kennedy, M. E.;
Chen, X.; Kuvelkar, R.; Hodgson, R.; Hyde, L. A.; Cox, K.; Favreau, L.; Parker, E.
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M.; Frederickson, M.; Folmer, R. H. A.; Geschwindner, S.; Koether, G.; Kolmodin,
K.; Krumrine, J.; Mauger, R. C.; Murray, C. W.; Olsson, L. L.; Patel, S.; Spear, N.;
Tian, G. J. Med. Chem. 2007, 50, 5912; (b) Barrow, J. C.; Stauffer, S. R.; Rittle, K. E.;
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Holloway, M. K.; Simon, A. J.; Price, E. A.; Sankaranarayanan, S.; Colussi, D.;
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@ 10 mg/kg
(30 mg/kg, sc) (%)
(30 mg/kg, po)
44
51
53
0
0
306
63
65
65
Not determined
Not determined
55%
occupy the S3 subsite; but, instead occupied a different subsite
altogether (Fig. 3).14 This subsite is a narrow hydrophobic region
which extends into
a solvent-exposed region of the BACE1
enzyme.15 Compounds occupying this subsite make favorable
hydrophobic interactions with the side chains of Ile171 and Lys168
as well as take advantage of a hydrogen bond interaction with
the carbonyl of Phe169. To maximize the probability of identifying
inhibitors with high CNS exposure, urea isosteres 53 and 54 were
prepared to reduce the number of hydrogen bond donors present
in the urea analogs. In Figure 3, superimposition of the X-ray co-
crystal structure of inhibitors 44, 46, and 53 with BACE1 illustrates
that the quinolinyl analog 50 binds in a similar manner as both the
amide 44 and urea 46 analogs. Selectivities of 44, 46, and 53 for
BACE1 versus the closely related aspartyl protease cathepsin D
(Cat-D) were 494-, 546-, and 1111-fold, respectively. As a refer-
ence, the initial lead compound 1 was not selective versus cathep-
sin D (cathepsin D Ki = 31 nM).
4. Coordinates for the X-ray structure of compound 1 complexed with BACE1
have been deposited in the Protein Data Bank (www.rcsb.org), and can be
accessed under PDB 3L5E.
5. Coldham, I.; Crapnell, K. M.; Fernandez, J.-C.; Moseley, J. D.; Rabot, R. J. Org.
Chem. 2002, 67, 6185.
6. Winkler, J. D.; Axten, J.; Hammach, A. H.; Kwak, Y.-S.; Lengweiler, U.; Lucero, M.
J.; Houk, K. N. Tetrahedron 1998, 54, 7045.
7. (a) Karady, S.; Amato, J. S.; Weinstock, L. M. Tetrahedron Lett. 1984, 25, 4373; (b)
Jones, J. B.; Keitz, P.; Cheng, H. J. Org. Chem. 1994, 59, 7671; (c) Eriksson, M.;
Napolitano, E.; Xu, J.; Kapadia, S.; Byrne, D.; Nummy, L.; Grinberg, N.; Shen, S.;
Lee, H.; Farina, V. Chimia 2006, 60, 566.
The amide 44 and urea 46 failed to achieve measurable plasma
levels in rats when dosed orally, however both compounds exhib-
ited modest levels of plasma Ab40 lowering when administered
sub-cutaneously (s.c.) to rats at a dose of 30 mg/kg (Table 3). On
the other hand, we were gratified when quinoline 53 displayed
modest oral bioavailability in a rat pharmacokinetic study at a dose
of 10 mg/kg, p.o.16 Furthermore, compound 53 not only exhibited
Ab40 lowering when dosed s.c. but also upon oral administration.

J. P. Caldwell et al. / Bioorg. Med. Chem. Lett. 24 (2014) 5455–5459
5459
8. Terao, Y.; Kotaki, H. N.; Achiwa, K. Chem. Pharm. Bull. 1985, 33, 2766.
9. Yu, J.-Q.; Corey, E. J. Org. Lett. 2002, 4, 2727.
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11. Papeo, G.; Posteri, H.; Vianello, P.; Varasi, M. Synthesis 2004, 17, 2886.
12. Inhibitor Ki values at purified human BACE1 were determined using a FRET-
peptide substrate hydrolysis assay. Cellular IC50 values for reduction of Ab40
production were determined in stably transfected HEK293-APPswe/lon cells.
The protocols for these assays have been previously described in Ref. 2b (Zhu
et al.). All values reported are the average of a minimum of two independent
determinations. CRND8-APP mice are models for early onset (familial) AD that
express human APP containing both Swedish and London mutations that
enhance the rate of APP cleavage by BACE1 and favor production of Ab42 over
13. Coordinates for the X-ray structure of compounds 38 and 41 complexed with
BACE1 have been deposited in the Protein Data Bank (www.rcsb.org), and can
be accessed under PDB 4R8Y and PDB 4R9, respectively.
14. Coordinates for the X-ray structure of compounds 44, 46, and 54 complexed
with BACE1 have been deposited in the Protein Data Bank (www.rcsb.org), and
can be accessed under PDB 4R92, PDB 4R93 and PDB 4R95, respectively.
15. This subsite was initially reported in a previous account (see Ref. 2b) and
termed the ‘A-site’ as this subsite was occupied by ‘Mode
A inhibitors’.
Serendipitously, we were able to occupy this subsite using ‘Mode B’ inhibitors.
16. Korfmacher, W. A.; Cox, K. A.; Ng, K. J.; Veals, J.; Hsien, Y.; Wainhaus, S.; Broske,
L.; Prelusky, D.; Nomeir, A.; White, R. E. Rapid Commun. Mass. Spectrom. 2001,
15, 335.
Ab40 in the c-secretase cleavage step as described by Hyde, L. A.; Kazdoba, T.