Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors: Prime side chromane-containing inhibitors

Article abstract of DOI:10.1016/j.bmcl.2013.06.006

The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine (HEA) BACE inhibitors is described. Variation of the P1′ region provided selectivity over Cat-D with a series of 2,2-dioxo-isothiochromanes and optimi

Full text of DOI:10.1016/j.bmcl.2013.06.006

Bioorganic & Medicinal Chemistry Letters 23 (2013) 4674–4679
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Design and synthesis of hydroxyethylamine (HEA) BACE-1 inhibitors:
Prime side chromane-containing inhibitors
a
a,
a
a
a
Raymond A. Ng a, , Minghua Sun , Simeon Bowers , Roy K. Hom , Gary D. Probst , Varghese John ,
Lawrence Y. Fang a, Michel Maillard a, Andrea Gailunas a, Louis Brogley a, R. Jeffrey Neitz a, Jay S. Tung a,
Michael A. Pleiss a, Andrei W. Konradi a, Hing L. Sham a, Michael S. Dappen a, Marc Adler b, Nanhua Yao b,
Wes Zmolek c, David Nakamura c, Kevin P. Quinn c, John-Michael Sauer c, Michael P. Bova c, Lany Ruslim c,
Dean R. Artis b, Ted A. Yednock a,b,c
⇑
⇑
a Department of Chemical Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA
b Department of Molecular Design, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA
c Department of Pharmacological Sciences, Elan Pharmaceuticals, 180 Oyster Point Boulevard, South San Francisco, CA 94080, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
The structure activity relationship of the prime region of conformationally restricted hydroxyethylamine
(HEA) BACE inhibitors is described. Variation of the P10 region provided selectivity over Cat-D with a ser-
ies of 2,2-dioxo-isothiochromanes and optimization of the P20 substituent of chromane–HEA(s) with
polar substituents provided improvements in the compound’s in vitro permeability. Significant potency
gains were observed with small aliphatic substituents such as methyl, n-propyl, and cyclopropyl when
placed at the C-2 position of the chromane.
Received 3 December 2012
Revised 27 May 2013
Accepted 3 June 2013
Available online 11 June 2013
Keywords:
Beta-secratase inhibitor
BACE-1
Ó 2013 Elsevier Ltd. All rights reserved.
Alzheimer’s disease
Cat-D
Chromane
Hydroxyethylamine
It is estimated that by 2050, one in eighty five persons world-
wide will be living with Alzheimer’s disease (AD), a progressive
neurodegenerative disorder.1 This high global burden necessitates
treatments that slow or halt AD progression. Alzheimer’s disease is
pathologically associated with the formation of extracellular insol-
uble amyloid plaques composed of b-amyloid peptides (Ab).2 The
Ab-peptides are in turn generated from sequential proteolytic
cleavage of the b-amyloid precursor protein (b-APP) by the action
Asp32 respectively while the difluoroaryl occupies the S1 pocket.
The cyclohexyl and tert-butyl substituents fill the S10 and S20 pock-
ets respectively. Aryl cycloalkyl amines such as 1 (Fig. 1) possess
excellent potency against BACE-1 but suffer from low permeability
and consequently, poor brain exposure. In order to address this
limitation, we decided to investigate conformational restriction
around the cyclohexyl amine portion of the molecule in order to
reduce the number of rotatable bonds in the inhibitor.9 Cyclization
of the S10 portion of the inhibitor with the aryl ring would lead to
compounds such as 2 (Fig. 1) which is intriguing since the disposi-
tion of substitution into the S10 pocket would be different than that
found in aryl cyclohexyl HEAs. Since there are sequence differences
between BACE-1 and the closely related protein, Cathepsin-D
(Cat-D), in the S10 pocket this provided an opportunity to gain
selectivity and therefore avoid potential toxicity.10 The poor phar-
macokinetic properties of the HEAs could potentially be addressed
by incorporating heteroatoms into the new bicyclic ring system.
The SAR of the conformationally restricted analogs was initially
explored with a tetralin ring system and since the P20 substituent is
crucial to providing potency, this region of the inhibitor was ex-
plored first. As in the cyclohexyl amine series, larger lipophilic sub-
stituents were more potent than smaller substituents (Table 1), but
of two aspartic acid proteases, b-secretase (BACE-1) and c-secre-
tase.3,4 BACE-1 null mice were found to be unable to produce Ab
in the brain but were otherwise healthy and fertile.5 Consequently,
BACE-1 inhibitors have been intensely investigated by many labo-
ratories as potential AD modifying therapeutics.6
We have recently disclosed a series of BACE-1 inhibitors based
upon the hydroxyethylamine (HEA) scaffold7 with cyclohexyl
amine 18 (Fig. 1) being a typical example of the class. The general
binding mode of these compounds to BACE-1 is shown in Figure 1.8
The hydroxyl and protonated amino group bind to Asp228 and
⇑
Corresponding authors. Tel.: +1 650 616 2630; fax: +1 650 794 2387 (S.B.).
E-mail address: simeongbowers@gmail.com (S. Bowers).
0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.06.006

R. A. Ng et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4674–4679
4675
S1'
S1'
Y
S1
S1
F
F
NHAc
OH
NHAc
OH
X
R
F
N
H
F
N
H
S2'
S2'
1
2
BACE-1 IC50 = 47 nM
Cat-D IC50 = 25 nM
Papp = 7 nm/s
P-gp efflux ratio = 19
pKa = 8.1
Figure 1. Binding mode of the HEA’s.
Table 1
O
O
I
O
SAR of P20 perturbations in tetralin–HEA12
a
b
HO
HO
HO
F
NHAc
F
N
H
9
10
11
OH
O
R
F
H2N
HCl
a
b
c,d
#
R
BACE-1 IC50 (nM)
Cat-D IC50 (nM)
NHBoc
O
+
3
4
5
6
7
8
Ethyl
n-Butyl
CH2CHMe2
tert-Butyl
CH2tert-Butyl
CH2Ph
538
574
93
378
45
126
77
Nd
74
F
12
13
F
8
251
4705
NHAc
OH
O
Nd = not determined.
a
F
N
H
Ref. 13.
Ref. 14.
e,f,g
b
14
interestingly, in contrast to the cyclohexyl amines, the neopentyl
P20 substituent (7) appeared to provide the greatest potency
against BACE-1. Molecular modeling showed a slight twisting of
the tetralin ring compared to compound 1, thereby placing the
tert-butyl of the neopentyl group into S20. Although tetralin 7
was equipotent to cyclohexyl-HEA 1 (IC50 = 45 nM) it still lacks suf-
ficient passive permeability required for brain exposure
(Papp = 3 nm/s).11 Additionally, tetralin–HEAs 3–8 show greater
potency in inhibiting Cat-D than BACE-1.
It is known that highly lipophilic molecules that possess a basic
amine exhibit a affinity towards membranes.15 Compound 7 has a
measured logP of 4.9 and a pKa of 8.9, it is possible that the poor
permeability of these analogs is due to the compound partitioning
into the membrane8 In order to overcome this liability, we envi-
sioned introducing heteroatoms into the tetralin ring in order to
lower lipophilicity and to enhance the permeability of the
inhibitor.16
An exemplary synthetic route to prepare these analogs is shown
in Scheme 1. Regioselective iodination of commercially available
(R)—chromanol 9, followed by Kumada coupling with neopentyl-
MgCl provided chromanol 11. Conversion of the (R)-alcohol to
(S)-amine 12 was carried out by azide displacement followed by
reduction. Alkylation of the amine with epoxide 1317 and subse-
quent deprotection and acetylation afforded 14.
Scheme 1. Reagents and conditions: (a) I2, HgO, CH2Cl2, rt, (59%); (b) neopentyl-
MgCl, Pd(dppf)2Cl2, THF, 0 °C to rt (59%); (c) DPPA, DBU, PhMe, 0 °C to rt; (d) (1)
LiAlH4, THF, 0 °C, (2) HCl, dioxane (70% for two-steps); (e) (1) NaOH, (2) 13, iPrOH,
85 °C (82%); (f) HCl, dioxane, 0 °C to rt; (g) NMO, AcOH, HOBt, CH2Cl2, rt (61% for
two-steps).
potency by 15-fold (compound 14) but, interestingly, chromane
15 proved to be equipotent to tetralin 7 while isochromane 16 lost
significant potency. Since the S10 pocket in BACE-1 is primary
hydrophilic while that of Cat-D is primarily hydrophobic18 the
placement of polar substituents into the P1’ region of the molecule
may improve the selectivity of the inhibitor. Molecular modeling
suggested that a sulfone placed in the S10 pocket would be able
to make close contact with Lys227, Arg235, and Thr329 (Fig. 2)
and therefore a series of sulfones were prepared (17–19, Table 2).
As observed with the tetralin series, larger P20 substituents were
more potent than smaller alkyl groups but while the most potent
analog 19, had similar potency to tetralin 7, the sulfone analogs
did possess improved selectivity over Cat-D.
Although 25-fold selectivity for BACE-1 over Cat-D was realized
with sulfones 17, the addition of heteroatoms into the tetralin ring
was not sufficient for imparting enough passive permeability for
adequate CNS exposure. For example, although compound 17 pos-
sessed a more desirable basicity and lipophilicity (pKa = 5.8 and
logP = 3.2), it still showed poor permeability, (Papp = 3 nM/s)11
compared to 7.
,
The SAR for this group of analogs is summarized in Table 2.
Insertion of an N-methyl group into the tetralin ring decreased

4676
R. A. Ng et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4674–4679
Table 2
O
I
O
Introduction of heteroatoms into tetralin-ring12
a,b,c
d
BocHN
BocHN
F
10
Y
NHAc
X
R
O
F
N
20
21
H
OH
f
O
O
a
b
e,f
BocHN
BocHN
#
X
Y
R
BACE-1 IC50 (nM)
Cat-D IC50 (nM)
7
CH2
NMe
O
CH2
CH2
CH2
CH2
CH2
CH2
CH2
O
SO2
SO2
SO2
CH2tert-Butyl
CH2tert-Butyl
CH2tert-Butyl
CH2tert-Butyl
Ethyl
45
643
46
19,700
116
127
8
68
12
Nd
2844
940
362
14
15
16
17
18
19
F
F
F
23
22
O
O
Isopropyl
CH2tert-Butyl
42
g,h,i
BocHN
BocHN
j
20
Nd = not determined.
a
Ref. 13.
Ref. 14.
b
Br
CN
24
25
O
26
R = isoPropyl
k
BocHN
27 R = cyclopentyl
28 R = 2-THF
20
29 R = 3-THF
OR
Scheme 2. Reagents and conditions: (a) DPPA, DBU, 0 °C to rt (%); (b) LiAlH4, Et2O,
0 °C; (c) Boc2O, Et3N, CH2Cl2 (99%); (d) isopropenylacetate, ((o-tolyl)3P)PdCl2,
CH3OSnBu3, PhMe, 100 °C (26%); (e) MeMgBr, THF, 0 °C; (f) DAST, PhMe, ꢀ78 °C
(78% for two-steps); (g) nBuLi, PhMe, DMF, rt (50%); (h) NaBH4, MeOH, 0 °C; (i) PBr3,
CH2Cl2, rt (86% for two-steps); (j) isobutyronitrile, LDA, THF (63%); (k) R’OH, CuI,
Cs2CO3, 1,10-phenanthroline, 90 °C, 2–4 days (40–45%).
ate chromanes in hand, removal of the Boc group and coupling
with epoxide 13 as previously discussed (Scheme 1) led to the
preparation of the corresponding chromane-HEAs (Table 3).
The SAR for the P20 modifications are shown in Table 3. As ob-
8
served with our cycloalkyl HEA series of BACE inhibitors replac-
ing one or two methyls of the neopentyl group with fluorine (30
and 31) incrementally improved the in vitro membrane permeabil-
ity, albeit potency dropped 3–4 fold. Incorporating a cyano group
(32) onto the P20 side chain also provided an increase in permeabil-
ity while maintaining potency (BACE-1 IC50 = 60 nM). Replacement
of the neopentyl group with an isopropyloxy (35) group improved
permeability fourfold (Papp = 112 nm/s) but also caused a 10-fold
loss in potency. In an attempt to further increase the potency of
the ethers, larger substituents were incorporated (36–38) but
unfortunately these modifications lead to disappointing decreases
in potency. Since improvement on ligand permeability was possi-
ble, albeit with potency loss, modification of the chromane to im-
prove potency was next explored.
Molecular modeling suggested that there would be sufficient
space in the S10 pocket to accommodate up to a 3-atom substituent
when placed on the C-2 position of the chromane ring and this
additional hydrophobic contact could possibly increase the com-
pound’s potency. Chromanes with substituents at C-2 could be
conveniently prepared by reacting acetophenone 39 with an
appropriate aldehyde or ketone to give chromanone 40 (Scheme 3).
Corey–Bakshi–Shibata reduction of the chromanone provided alco-
hol 41 in 95% ee. Alcohol protection followed by Negishi coupling
with neopentyl-ZnBr gave 42. Deprotection of the alcohol followed
treatment with DPPA and azide reduction gave aminochromane
intermediate 43. Alkylation with epoxide 13 followed by deprotec-
tion and acetylation gave the desired analogs.
Figure 2. Model of compound 18 with BACE-1. The compound forms three H-bond
between the sulfone and S1’ pocket of BACE-1. The H-bonds are: Lys227 (2.9 Å),
Arg235 (3.2 Å), and Thr329 (2.9 Å).
Chromane analog 15 displayed good potency and improved per-
meability (Papp = 30 nm/s)11 compared to tetralin 7 and was
deemed to be a good starting point to further enhance permeability
and potency. We have previously reported the effect of polar P20
substituents on the permeability of cyclohexyl amine series of
BACE-1 inhibitors8 and therefore decided to investigate if similar
substituents would aid in the permeability of the chromanes.
These analogs were prepared as shown in Scheme 2. (R)-6-Iodo-
chroman-4-ol 10 was converted to key intermediate 20 by azide
displacement, reduction, and protection as the Boc-carbamate.
The 6-position of the chromane was diversified by homologation
of 20 with isopropenylacetate to afford ketone 21. Addition of
MeMgBr to ketone 21 generated the corresponding tertiary alco-
hol. This alcohol and ketone 21 were treated with DAST and con-
verted to the corresponding fluorohydrocarbons, which were
later coupled with 19 to prepare 30 and 31. Iodide 20 was also con-
verted to the benzyl bromide 24 by formylation, reduction, and
bromination. Alkylation of isobutyronitrile with benzyl bromide
24 afforded 25. Ethers 26–29 were accessed by Ullmann coupling
of the versatile intermediate 20 with alcohols. With the appropri-

R. A. Ng et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4674–4679
4677
Table 3
SAR of P20 perturbations in chromane–HEA
F
NHAc
OH
O
R
F
N
H
Pappc (nm/s)
a
b
#
R
BACE-1 IC50 (nM)
Cat-D IC50 (nM)
14
30
31
32
33
35
36
37d
38d
CH2tert-Butyl
CH2CMe2F
CH2CMeF2
CH2CMe2CN
CH2CMe2(CHF2)
O-iso-Propyl
O-cyclopentyl
O-(2-tetrahydrofuranyl)
O-(3-tetrahydrofuranyl)
46
148
186
60
1300
414
221
1325
858
12
80
144
70
478
429
145
286
255
30
83
146
64
Nd
112
Nd
110
71
Nd = not determined.
a
Ref. 13.
Ref. 14.
Ref. 11.
b
c
d
1:1 Mixture of epimers at THF stereocenter.
O
OH
O
Table 4
O
Br
Br
SAR of P20 perturbations of chromane–HEA
Br
a
b
R1
R1
F
R1 R2
O
O
OH
R2
R2
NHAc
39
40
41
F
N
H
OTBS
R1
NH2
O
OH
c, d
e,f,g
R1
O
R2
R2
42
43
a
b
R1
R2
BACE-1 IC50 (nM)
Cat-D IC50 (nM)
F
#
R1 R2
O
45
46
47
48c
49
50c
Me
n-Propyl
Me
CH2OMe
CH2OCH2
cycloPropyl
Me
Me
n-Propyl
Me
—
8
6
15
18
1
2
NHAc
h,i,j
F
N
H
OH
9
5
22,506
6
27,105
22
44
H
a
b
c
Ref. 13.
Ref. 14.
1:1 Mixture of epimers.
Scheme 3. Reagents and conditions: (a) R1C(O)R2, pyrrolidine, CH3CN (65%); (b)
(S)-Me-CBS–oxazaborolidine, BH3–DMS, PhMe, 0 °C (64%); (c) TBSCl, imidazole,
DMF (86%); (d) neopentyl–ZnBr, (dppf)2PdCl2, THF, 60 °C; (e) TBAF, THF, rt (72% for
two-steps); (f) DPPA, DBU, 0 °C to rt (70%); (g) LiAlH4, Et2O, 0 °C; (h) 13, iPr2NEt,
iPrOH, 85 °C; (i) HCl, dioxane, 0 °C to rt; (j) (Ac)2NOMe, iPr2NEt, CH2Cl2, rt (10% for
four-steps).
substituents that provided an increase in permeability. Com-
pounds 51–52 (Table 5) were prepared using methods outlined
in Scheme 2 while 53 was prepared starting from 2-hydroxy-5-tri-
fluoromethoxy-acetophenone by employing a similar sequence as
Scheme 3. Compound 54 was prepared via alkylation of 6-hydro-
xy-2,2-dimethyl-4-chromanone with Boc2O in the presence of
Sc(OTf)2,19 followed by elaboration to 54 as in Scheme 3.
Replacement of one or two of the methyl groups of the neopen-
tyl substituent with either fluoro (51) or cyano (52) maintained the
potency of 45 and also maintained a twofold selectivity over Cat-D,
but the increase in the permeability was modest (52 Papp = 25 nm/
s compared to 45 Papp = 3 nm/s). The addition of ethers (52–54)
caused a significant decrease in potency against BACE-1.
In summary, using structure based design, we have demon-
strated that selectivity for BACE-1 over Cat-D is possible with
2,2-dioxo-isothiochromanes. Furthermore, the addition of polar
substituents into the P20 region of the inhibitor provided substan-
tial increases in the permeability of the inhibitors. The addition of
alkyl substituents to the C-2 position of the chromane resulted in
As shown in Table 4, 2,2-dimethyl substitution (45) on the chro-
mane boosted the potency fivefold over the des-methyl analog 15
and also provided slight selectivity for BACE-1 over Cat-D. n-Propyl
analogs 46 and 47 were also tolerated but offered no advantage
over gem-dimethyl analog 45. The n-propyl group was replaced
with methoxymethyl ether (48) in order to lower the clogP and in-
crease selectivity over Cat-D. Molecular modeling showed a puta-
tive electrostatic interaction between the ether oxygen of 48
with Arg235 of BACE-1. Gratifyingly, the potency of 48 (IC50 = 9 -
nM; 1:1 mixture of diastereomers) rivaled the potency of 44
although the ether oxygen of 48 did not impart selectivity for
BACE-1. Spiro-oxetane 49 is inactive in both BACE-1 and Cat-D
indicating a poor fit in the S10 pocket, while cyclopropyl analog
50 lost potency compared to gem-dimethyl analog 45.
With the potency of the analogs increased, it remained to com-
bine the more potent C-2-substituted chromanes with the P20

4678
R. A. Ng et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4674–4679
Table 5
SAR of P10/P20 variation
F
R1 R2
NHAc
OH
O
F
N
H
R3
a
b
#
R1
R2
R3
BACE-1 IC50 (nM)
Cat-D IC50 (nM)
Pappc (nm/s)
45
51
52
53
54
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
CH2tert-Butyl
CH2CMeF2
CH2CMe2CN
OCF3
8
9
6
89
690
18
16
8
59
374
3
17
25
12
11
O-tert-Butyl
a
b
c
Ref. 13.
Ref. 14.
Ref. 11.
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single-digit nanomolar inhibitors with moderate permeability and
moderate selectivity over Cat-D. Our progress in balancing po-
tency, good membrane permeability, Cat-D selectivity within our
HEA scaffold will be reported in due course.
Acknowledgement
We would like to thank C. Lorentzen, B. Peterson, W. Chan, and
R. Arslanian for their contributions to this work.
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11. Compounds (5 lM) in mHBSS (pH 7.4) were incubated with MDCK II cell
monolayers for 120 min at 37 °C. Samples were taken from apical and
basolateral chambers, and analyzed using LC/MS/MS.
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13. Compounds serially diluted in DMSO were added to recombinant BACE-1
purified from E. coli in 100 mM sodium acetate buffer containing 0.001%
Tween-20 at pH 4.5 and allowed to incubate for 20 min at room temperature. A
biotinylated peptide substrate, based on the Swedish mutant APP sequence,
containing an Oregon Green moiety at the C-terminus, was added to initiate
the reaction which was allowed to proceed for 3 h at 37 °C. The reaction was
quenched by the addition of a fivefold volume excess of 100 mM sodium
phosphate buffer pH = 7.4 containing
a 1.5 lM final concentration of
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Pleiss, M. A.; Tucker, J. A.; Konradi, A. W.; Sham, H. L.; Jagodzinski, J.; Toth, G.;
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LJL Analyst.
14. The Cathepsin-D was obtained from Sigma (cat. #C8696). Cathepsin-D was first
dissolved with water to a 2 lM concentration and then subsequently with
100 mM sodium acetate buffer pH 4.5 to a 1.8 nM working concentration. A
biotinylated peptide Cathepsin-D substrate was labeled at the C-terminus of
the peptide with an Oregon Green fluorophore. Compounds were serially
diluted threefold in DMSO at a 100ꢁ concentration and then subsequently
diluted 33ꢁ with 100 mM sodium acetate buffer pH 4.5. Compound was added
to Cathepsin-D (0.6 nM final concentration) for 30 min before the addition of
peptide substrate to initiate the reaction. The reaction was allowed to proceed
for 110 min at 37 °C and then quenched by the addition of streptavidin in
200 mM sodium phosphate buffer pH 7.5. The amount of fluorescence
polarization in the well was measured using a LJL Analyst (Perkin Elmer). If
Cathepsin-D cleaves the peptide substrate then polarization will be reduced.
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