Design and synthesis of a series of serine derivatives as small molecule inhibitors of the SARS coronavirus 3CL protease

Article abstract of DOI:10.1016/j.bmc.2016.01.052

Synthesis of serine derivatives having the essential functional groups for the inhibitor of SARS 3CL protease and evaluation of their inhibitory activities using SARS 3CL R188I mutant protease are described. The lead compounds, functionalized serine derivatives, were designed based on the tetrapeptide aldehyde and Bai's cinnamoly inhibitor, and additionally performed with simulation on GOLD softwear. Structure activity relationship studies of the candidate compounds were given reasonable inhibitors ent-3 and ent-7k against SARS 3CL R188I mutant protease. These inhibitors showed protease selectivity and no cytotoxicity.

Full text of DOI:10.1016/j.bmc.2016.01.052

Accepted Manuscript
Design and synthesis of a series of serine derivatives as small molecule inhibitors
of the SARS coronavirus 3CL protease
Hiroyuki Konno, Masaki Wakabayashi, Daiki Takanuma, Yota Saito, Kenichi
Akaji
PII:
S0968-0896(16)30066-9
DOI:
http://dx.doi.org/10.1016/j.bmc.2016.01.052
BMC 12795
Reference:
Bioorganic & Medicinal Chemistry
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Accepted Date:
13 January 2016
26 January 2016
27 January 2016
Please cite this article as: Konno, H., Wakabayashi, M., Takanuma, D., Saito, Y., Akaji, K., Design and synthesis
of a series of serine derivatives as small molecule inhibitors of the SARS coronavirus 3CL protease, Bioorganic &
Medicinal Chemistry (2016), doi: http://dx.doi.org/10.1016/j.bmc.2016.01.052
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Design and synthesis of a series of serine derivatives as small molecule inhibitors of the
SARS coronavirus 3CL protease
Hiroyuki Konno,1,* Masaki Wakabayashi,1 Daiki Takanuma,1 Yota Saito,1 Kenichi
Akaji2, *
1Department of Biological Engineering, Graduate School of Science and Technology,
Yamagata University, Yonezawa, Yamagata 992-8510, Japan
2Department of Medicinal Chemistry, Kyoto Pharmaceutical University, Yamashina-ku,
Kyoto 607-8414, Japan
Author information
*Corresponding author
Tel & FAX +81-(0)238-26-3131 (H. Konno)
e-mail konno@yz.yamagata-u.ac.jp (H. Konno), akaji@mb.kyoto-phu.ac.jp (K. Akaji)
Abstract-----Synthesis of serine derivatives having the essential functional groups for the
inhibitor of SARS 3CL protease and evaluation of their inhibitory activities using SARS
3CL R188I mutant protease are described. The lead compounds, functionalized serine
derivatives, were designed based on the tetrapeptide aldehyde and Bai’s cinnamoly
inhibitor, and additionally performed with simulation on GOLD softwear. Structure
activity relationship studies of the candidate compounds were given reasonable inhibitors
ent-3 and ent-7k against SARS 3CL R188I mutant protease. These inhibitors showed
protease selectivity and no cytotoxicity.
Key words: SARS CoV, SARS 3CL protease, serine derivative, docking simulation,
cathepsin B, cytotoxicity
1. Introduction
Severe acute respiratory syndrome (SARS) is a contagious respiratory disease to
humans that is caused by the SARS coronavirus (SARS-CoV). In 2003, an atypical
pneumonia due to SARS-CoV lead to progressive respiratory failure in over 8,000
individuals and 800 deaths within a few months.1-3 Thereafter, the SARS epidemic was
1

successfully controlled, but potential reemergence of pandemic SARS-CoV continues to
be a risk, and new strains of SARS or a SARS-like virus could potentially be more
infectious than the strains that led to the 2003 outbreak. Two human coronaviruses,
NJ63 and HKU1, have been identified in patients around the world since 2003.4-6 A
more recently identified human coronavirus, Middle East Respiratory Syndrome
coronavirus (MERS-CoV), has infected 114 people since April 2012 with a nearly 50%
mortality rate, and this number keeps rising daily.7,8 Two Asian bat coronaviruses,
BtCoV-HKU4 and BtCoV-HKU5, have been shown to be the closest relations to
MERS-CoV.9 The possibility of a future SARS-like pandemic remains, and no vaccines
or antiviral agents have yet been developed to prevent or treat SARS-like infections.10
SARS-CoV is a novel human coronavirus featuring the largest positive-stranded
RNA genome known to date (27kb for pp1a and 31 kb for pp1b). The key enzyme in the
processing of polyproteins translated by the viral RNA genome of SARS-CoV is a
33kDa protease called 3C-like protease (3CL protease). SARS 3CL protease is a
cysteine protease containing a Cys-His catalytic dyad. It cleaves precursor polyproteins
at as many as 11 conserved sites involving a conserved Gln at the P1 position and a
small amino acid (Ser, Ala, or Gly) at the P’1 position. Due to its functional importance
in the viral life cycle, SARS 3CL protease is considered to be an attractive target for
drug design to treat SARS.
A variety of inhibitors against the SARS 3CL protease have been reported in the
literature for the past decade, including substrate-based peptidemimetic,11 fravonoid
derivatives,12 tannin derivatives,13 ML188,14 isatin derivatives,15 and decaisoquinolin,16 etc.
However, no effective therapeutic drug or vaccine has been developed to date although
many candidate anti-SARS CoV agents have been identified.
In the previous study, we reported that design and synthesis of the peptide
aldehyde inhibitor Ac-Thr-Val-Cha-His-H (1) showed high inhibitory activity with an
IC50 value of 98 nM toward 3CL R188I mutant protease as a substrate mimetic
concept.17-18 The inhibitor (1) was optimized by the screening of P1, P2 and P4 site
residues
of
the
previous
reported
peptide
aldehyde
inhibitor
Ac-Ser-Ala-Val-Leu-Gln(Me)2-H, except at the P3 site where the side-chain directed
outside and made no interactions with the protease guided by the X-ray crystal structure
of the lead compound that bound the R188I mutant SARS 3CL protease. The
interactions of inhibitor (1) at the P1 and P2 sites with the protease seemed very
2

effective. Additionally, a new synthetic method using acetal to aldehyde conversion via
thioacetal formation was described to afford the C-terminal peptide aldehyde.19-20
Side chain structures at the P1, P2 and P4 sites and C-terminus aldehyde as the
thiol capture of tetrapeptide inhibitor (1) were thought to have a critical role in its potent
inhibitory activity. In contrast, there is generally enzymatic digestion of peptide chains
and -proton racemization and/or low specificity of aldehyde functionality. To develop
non-peptidyl small molecular inhibitors of the SARS 3CL protease focusing on the P1,
P2 and P4 site interactions, we aimed to design and synthesize serine derivatives having
the essential functional groups and evaluated their inhibitory activity in the present
study. Serine, a commercially available proteinogenic amino acid, has three variant
reaction sites; alcohol, amine and carboxylic acid, which can be orthogonally connected
to various functional groups (Fig. 1).
Fig. 1. Ac-Thr-Val-Cha-His-H (1) and concept for serine derivative
2. Results and Discussion
Design
To determine whether a series of serine derivatives could adopt an energetically
favorable conformation mimicking a tetrapeptide inhibitor (1), we performed a variety
of molecular mechanics calculations with SPARTAN from Wavefunction and docking
simulations of protein interactions by GOLD from CCDC. Firstly, imidazole,
cyclohexyl and hydroxy groups, which were optimized functionalities with potent
biological activities in the previous literature, were connected with L-serine to design
the serine derivative (2a,b) as shown in Scheme 1. However, it did not give good
coverage of the substrate-recognition pocket of 3CL protease (PDB code 3AW1), that is,
the interactions with optimized motifs and the corresponding pockets were different by
binding mode, contrary to expectations. The cyclohexyl group of serine derivative (2)
3

occupied the S1 pocket of the 3CL protease imperatively. Thus, the imidazole and
hydroxy groups of serine derivative (2) expected for the interactions with the S1 and S4
pockets were not effective and consequently the numbers of interaction atom pairs
between the inhibitor (2) and SARS-CoV 3CL protease were diminished. In contrast,
Bai21 reported that the cinnamoyl derivatives inhibited SARS-CoV 3CL protease. In this
case, the Bai’s inhibitor locates deep insides of the S’1, S1 and S2 pockets with
appropriate cinnamoyl functionalities. This result was approximately identified with the
Bai’s simulation employed by the AutoDock 3.0 estimated free energy of binding for
the docking of the Bai’s inhibitor to the SARS 3CL protease (PDB code 1UJ1).
Therefore, we examined molecular docking of the serine derivatives contained together
with benzoyl and aniline moieties to give 2c, which was an attractive ligand for the 3CL
protease. Furthermore, we investigated a reasonable structure for the inhibitor and mode
hybrid compounds with Bai’s and our functionalities on the serine derivative (3). As a
result, we concluded that reasonable structures are N-cinnamoyl derivatives with
benzoate for the side chain on virtual screening by GOLD. Compound 3 has the
following characteristics: (a) Since the substrates by nature have involved small amino
acids (Ser, Ala or Gly) at the P’1 position, it may be preferable to adopt the aromatic
rings. (b) The proper placement of the cyclohexyl ring may be the result of development
of a serine type inhibitor with functionality of the P1 position, as well as stability of
interaction of other positions. (c) The S4 pocket is rather hydrophobic in nature and
therefore the corresponding side chains, namely aromatic, hydrocarbon or neutral
functionalities, make good contact with target regions. (d) Additionally, the region
adjacent to the ester bond of 3 is catalytic thiol functionality (Cys145) of the enzyme
(Scheme 1).
4

Scheme 1. Virtual screening of the serine derivatives for SARS-CoV 3CL protease
(PDB code 3AW1) on GOLD softwear.
Chemistry
In view of the promising computational evaluation of the serine derivative (3) in
terms of tetrapeptide mimetics, we plan to synthesize the target molecules. To evaluate
inhibitory activity of the serine derivative (3) against SARS-CoV 3CL protease, a
structure activity relationship study using the serine derivatives was attempted. As
depicted in Scheme 2, the serine derivatives attached with three functionalities were
prepared. Each coupling partner to introduce the functionalities is shown in Tables 1, 2
and 3. Coupling of Fmoc-L-Ser(tBu)-OH and amines as a P1 moiety with WSC/HOBt
followed by the deprotection of Fmoc group by 20% piperidine/DMF gave the serine
amide derivative (4) at acceptable chemical yields. The P4 moiety was introduced by
coupling with carboxylic acid in the presence of coupling reagents or acylation using
carboxylic anhydride or acyl chloride to afford diamide derivatives. Subsequently,
treatment of TFA for the deprotection of the t-butyl group gave alcohol (5) at moderate
yields. Finally, the esterification of a hydroxy group of 5 with a variety of acyl reagents
was performed to give novel serine derivatives (6, 7 and 8) for evaluation of the small
molecular inhibitors against SARS 3CL protease. Purification of all crude compounds
was performed by silica gel column chromatography. The chemical structures for
1
13
synthetic compounds were mainly determined by H and C NMRs, IR and mass
5

spectra (Scheme 2).
Scheme 2. Synthetic outline for the preparation of serine derivatives (6a-o and 7b-o).
As depicted in Table 1, five cyclic functionalities were attached to the carboxylic
acid of the serine template. As mentioned above, this was to investigate the importance
of cyclohexane ring defined as the P1 position. Treatment of Fmoc-L-Ser(tBu)-OH and
cyclohexylamine with WSC/HOBt and continuous Fmoc-deprotection afforded 4a in
97% yield (entry 1). Under the above-mentioned conditions, Fmoc-L-Ser(tBu)-OH was
subjected to a coupling reaction with piperidine, morpholine, benzylamine or
cyclohexylmethylamine to give 4b-e. Despite the poor yields in entries 2 and 4, it was
available for the evaluation of inhibitory activities (Table 1).
Table 1. Coupling of the P2 position and Fmoc-deprotection of Fmoc-Ser(tBu)-OH
aminea
entry
Product
4a (97%)
4b (26%)
4c (91%)
4d (19%)
4e (48%)
1
2
3
4
5
cyclohexylamine
piperidine
morpholine
benzylamine
cyclohexylmethylamine
a Reagent and conditions: 1) amine, WSC, HOBt, CH2Cl2, 2) 20% piperidine/CH2Cl2.
To optimize P4 functionality, a variety of carboxylic acids, especially
-unsaturated carboxylic acids for 4a, were introduced. Coupling of 4a and cinnamic
acid with HATU22/HOAt23/DIPEA in CH2Cl2 (condition A) followed by treatment with
6

TFA for deprotection of the t-butyl group afforded 5a in 38% yield (entry 1). Treatment
of 4a with 3-(p-hydroxyphenyl)propanoic acid in the presence of HATU/HOAt/DIPEA
in CH2Cl2 also gave 5b in 79% yield after removal of t-butyl group (entry 2). Since 5c
was not isolated by the condition of HATU/HOAt, we found that DMT-MM (condition
B)24 as a coupling reagent was moderate to give 5c in 37% yield over 2 steps (entry 3).
In an attempt to improve the chemical yields for the coupling reaction of cinnamic acid
derivative and amines, we knew that HATU or DMT-MM as the coupling reagents were
useful in preliminary studies. For this reason, a series of cinnamoyl derivatives (5d,
5f-o) were also prepared under identical conditions at moderate yields (entry 6-15). In
addition, acylation of 4a with benzoyl chloride (condition C) was successfully
performed to yield 5e without any problems (entry 5) (Table 2).
Table 2. Coupling of P4 position and deprotection of t-butyl group
entry
subst
conditionsa
product
entry
subst
conditionsa
product
1
4a
A
5a (38%)
9
4a
A
A
A
5i (69%)
2
3
4
5
4a
4a
4a
4a
A
B
5b (79%) 10
5c (37%) 11
5d (43%) 12
5e (80%) 13
4a
4a
4b
4c
5j (55%)
5k (29%)
5l (26%)
5m(91%)
A
A
C
A
A
A
A
6
4a
5f (7%)
14
4d
4e
5n (19%)
5o (48%)
7
8
4a
4a
A
5g (23%) 15
5h (29%)
A
aReagents and conditions: 1) conditions A, B or C, DIPEA, CH2Cl2, rt, 2) 50% TFA/CH2Cl2, rt. A: HATU,
HOAt, B: DMT-MM, C: Et3N, DMAP
For the structure-activity relationship study of P’1 functionality of serine
7

derivatives, we prepared the serine derivatives (3), (6a-o) and (7b-o) as depicted in
Table 3. Acylation of the substrates (5a-o) was employed the Shiina25 and Yamaguchi26
conditions for the coupling of carboxylic acids or acyl chloride and acetic anhydride
reagents. Using commercially available acyl chlorides and Ac2O as the acyl reagent gave
the corresponding esters (3), (6c), (6d), (6g), (6h), (6i) and (6o) at moderate yields
(entries 1, 4, 5, 8-10, 16). Esterification of 5a with N-acetyl-L-histidine by the Shiina
reagent NMBA/DMAP afforded the His-compound (6a) at an extremely low yield
(entry 2). In this case, 2-nitro-6-methylbenzote as a by-product was given at a moderate
yield and it was difficult to improve the chemical yield even after attempting several
conditions. Preparation of a pGlu-compound (6b), isonicotine (6e) and nicotine (6j) also
resulted in similar situations (entries 3, 6, 11). The Yamaguchi protocol was performed
to give 6f and 6k (entry 7, 12) and also acyl chlorides prepared by
3,4,5-trimethoxybenzolic acid, 3-phenylpropanoic acid or cinnamic acid with oxalyl
chloride in the presence of DMF in situ reacted with 5a to afford 6l, 6m and 6n at low
yields (entries 13-15). On the other hand, the treatment of a variety of alcohols (5b-o)
with BzCl/Et3N/DMAP in CH2Cl2 converted to benzoyl esters (7b-o). Chemical yields
of benzoyl esters (7b-o) were variable by used substrates (entry 17-30) (Table 3).
Table 3. Coupling of the P’1 position for the inhibitors
conditionsa
conditionsa
entry subst
product
entry
16
subst
product
1
2
3
4
5
5a
5a
5a
5a
5a
3 (71%)
5a
6o (36%)
A
A
6a (3%)
6b (25%)
6c (78%)
6d (43%)
17
18
19
20
5b
5c
5d
5e
7b (7%)
7c (17%)
7d (22%)
7e (43%)
A
B
D
A
A
A
A
A
8

6
5a
5a
5a
5a
5a
5a
5a
5a
5a
5a
6e (47%)
6f (27%)
6g (70%)
6h (64%)
6i (26%)
6j (47%)
6k (95%)
6l (4%)
21
22
23
24
25
26
27
28
29
30
5f
5g
5h
5i
7f (57%)
7g (37%)
7h (19%)
7i (57%)
7j (52%)
7k (81%)
7l (44%)
7m(75%)
7n (44%)
7o (57%)
A
A
A
A
A
A
A
A
A
A
B
C
7
8
A
9
Ac2O
A
10
11
12
13
14
15
5j
A
5k
5l
B
C
D
5m
5n
5o
6m(13%)
6n (26%)
B
D
aA: carboxylic acid chloride or acetic anhydride, DMAP, Et3N, CH2Cl, B: carboxylic acid, NMBA,
DMAP, Et3N, CH2Cl2, C: carboxylic acid, 2,4,6-trichlorobenzoic acid chloride, DMAP, DIPEA, CH2Cl2,
D: carboxylic acid, (COCl)2, DMF.
Biological assay
The inhibition of SARS 3CL R188I mutant protease was determined by the
previous procedure using a synthetic decapeptide with the S01 cleavage sequence as a
substrate. Synthetic L-serine derivatives from several structural subclasses were
investigated; 5a, cinnamoyl-L-serine derivatives (6a-o) with modification at the P’1
position (Table 4), benzoyl-L-serine derivatives (7b-k) with modification at the P4
position (Table 5).
As depicted in Table 4, inhibitory potency of the synthesized cinnamoyl-L-serine
9

derivatives (6a-o) with modification at the P’1 position was evaluated as IC50 values.
The simulated compound (3) as a control exhibited an IC50 value of 125 M (entry 14).
Since the IC50 value of a previous reported peptide aldehyde (1) was reported to be 98
nM, imidazole of histidine or -lactam of pyroglutamic acid were important
functionalities. However 6a and 6b that had been coupled with 5a and His or pGlu
showed low inhibitory activities as expected from the docking simulations (entries 2, 3).
For optimization of the P’1 functional group of 6, different acyl units; alkyl, phenyl and
pyridyl groups, were examined. Aliphatic groups-containing compounds (6c), (6g) and
(6h) showed lower inhibitory activities than 3 (entries 4, 8, 9). Pyridyl derivatives (6e),
(6j) and (6k) were also similar (entries 6, 11, 12). Aromatic rings with nitro, chloride
and methoxy groups (6f), (6i) and (6l) gave moderate results (entries 7, 10, 13).
Phenylacetate (6d) also showed lower inhibitory activity than 3 (entry 5). In contrast,
conversion of the phenylpropionate or cinnnamoyl groups at a P’1 site would be
expected to have a dramatic effect on inhibitory activity. Especially, the cinnamoyl
compound (6n) showed potent inhibitory activity at an IC50 value of 85 M (entry 16).
In addition, a 2-methyl-6-nitrophenyl derivative (6o) showed good potential as a 3CL
protease inhibitor (entry 17). The IC50 value of saturated compound (6m) was decreased
in comparison with those of the fixed unsaturated derivative (6n) (entry 15). These
results suggest that serine type derivatives containing optimized functionalities would be
useful as 3CL protease inhibitors. As the correlations between IC50 and ClogP, we could
assume that 3, 6m, 6n and 6o with potent inhibitory activities tend relatively to have
high lipophilicity with the ClogP values of 4.82~5.28 (Table 4).
Table 4. Inhibitory activities of 5a and cinnamoy-L-serine derivatives (6a-o) with
modification at the P’1 position
a
a
IC50
ClogPb
2.233
IC50
ClogPb
4.312
entry compd
5a
R3
entry
10
compd
R3
H
1
1500
6i
250
10

2
6a
6b
6c
6d
6e
6f
>3200 1.485
>1600 2.116
11
12
13
14
15
16
17
6j
6k
6l
180
175
170
125
120
85
3.382
3.482
4.584
4.826
5.226
5.284
4.878
3
4
650
650
560
550
450
400
4.187
4.748
3.482
6.085
4.367
3.129
5
3
6
6m
6n
6o
7
8
9
6g
6h
65
a M
bClogP was calculated by ChemBio3D Ultra 12.0 (PerkinElmer)
To achieve further optimization using a serine template, a structure activity
relationship study of the P4 functionality (R2) of a lead compound (3) was conducted.
The aliphatic pivaloyl-containing compound (7b) substituted the cinnamoyl group of 3
showed no inhibitory activity and introduction of a phenyl-2-propenate (7c) and benzoyl
group (7e) did not make a significant contribution (entries 1, 2 and 4). Next, modified
cinnamoyl groups were designed because the moiety of the P4 site was replaced with
the methoxy connecting cinnamoyl group to permit the moiety to fit into the S4 pocket
more tightly than 3. Although each 2- or 3-methoxy functionalities were not effective
(compounds 7d, 7f, entries 3 and 5), the inhibitors containing 3- and/or 4-methoxy
groups on a phenyl ring at the P4 site exhibited markedly increased inhibitory activity
(entries 6, 7, 8). The IC50 value of 7k was 74 M and so the results suggested that a
planar aromatic ring and its hydrophobic functionality were essential factors to produce
a reasonable 3CL protease inhibitor (entry 10). The correlations between IC50 and ClogP
11

are difficult to explain because these compounds are close in molecular formula (Table
5).
Table 5. Inhibitory activities of benzoyl-L-serine derivatives (7b-k) with modification at
the P4 position
a
a
IC50
ClogPb
2.955
IC50
ClogPb
4.484
entry compd
R2
entry compd
R2
1
7b
7c
7d
7e
7f
>3200
500
6
7g
7h
7i
154
100
98
2
4.673
4.745
3.968
4.745
7
4.484
4.745
6.304
4.126
3
240
8
4
5
220
9
7j
95
155
10
7k
74
a M
bClogP was calculated by ChemBio3D Ultra 12.0 (PerkinElmer)
To investigate the importance of the cyclohexyl group of 3 at the P1 site, we
evaluated four derivatives combined with different amines; piperidine for 7l, morpholine
for 7m, benzylamine for 7n and cyclohexylmethylamine for 7o. As a result, 7l and 7m
showed no inhibitory activities. These compounds are shorter in terms of one carbon
length of the P1 site than 3 and therefore the P1 position of the inhibitor showed
decreased flexibility as expected and hardly fit the S1 pocket. On the other hand,
aromatic benzyl amine (compound 7n) has a planer structure, which led to moderate
inhibitory activity. Attempts to use cyclohexylmethylamine for 7o was acceptable to
show IC50 = 180 M. It is suggested that the cyclohexyl structure at a P1 site strictly
12

interacts with the hydrophobic S1 pocket. As mentioned above, we optimized the
functionalities at the P’1, P1 and P4 sites of an L-serine template based on reference
compound 3, which was guided by virtual screening on GOLD. P’1 and P4 sites are
preferred for their similar characteristics of aromatic rings, an sp2 planer structure and
hydrophobicity.
Next, the inhibitory activities of the selected serine derivatives with the D-form
were evaluated based on the IC50 values. The IC50 values and tPSA of selected inhibitors
are summarized in Table 6. Preparation of D-serine derivatives was performed by
synthetic protocols of the corresponding L-serine compounds without any problems.
Fmoc-D-Ser(tBu)-OH as a starting material was selected and a 5 step sequence was
performed as shown in Scheme 2. Interestingly, there were no extreme variants for IC50
values between the L- and D-forms except for 6n (entry 6). Both enantiomers of 5a, 6a
and 7l showed no inhibitory activities (entries 1, 2 and 3). The inhibitory activity of the
L-forms of 6h, 7o, 6j, 7n, 6k and 6o showed a tendency to be more potent than those of
the D-forms (entries 4, 5, 7-10). In contrast, 7i, 7h, 7j, 7k and 3, which exhibited potent
inhibitory activities against the 3CL protease, tended to have D-forms with more potent
activities than L-forms (entries 11-15). We guessed the enantiomers of 7i, 7h, 7j, 7k and
3 fitted the active site of 3CL protease via different binding modes, that is, the P’1 site
functionalities interact with the S4 pocket and consequently P4 site groups located in
the S’1 pocket. These serine derivatives have high flexibility and therefore two
hydrophobic spaces of the 3CL protease are recognized in a rigorous manner. The
enantiomer of 3 (ent-3) exhibited the most potent inhibitory activity (IC50 = 30 M) in
the evaluated compounds. Though there are no correlation between the IC50 value and
tPSA in Table 6, these tPSA values were acceptable toward the protease inhibitor for
the target of catalytic domain (Table 6).
Table 6. Inhibitory activities of D-serine derivatives
a
a
IC50
tPSA b
78.43
75.71
138.0
84.50
IC50
tPSAb
96.86
136.3
93.73
103.0
entry
compd
ent-5a
ent-7l
ent-6a
ent-6h
entry
9
compd
ent-6k
ent-6o
ent-7i
1
2
3
4
>1600
>1600
1600
550
210
100
85
10
11
12
ent-7h
80
13

5
ent-7o
ent-6n
ent-6j
ent-7n
430
340
240
225
84.50
84.50
96.86
84.50
13
14
15
ent-7j
ent-7k
ent-3
68
65
30
110.8
112.2
84.50
6
7
8
aM
btPSA was calculated by ChemBio3D Ultra 12.0 (PerkinElmer)
The binding mode of 7k, ent-7k and ent-3 to SARS 3CL protease was predicted
by docking simulations using GOLD from CCDC. These results suggest that reasonable
inhibitors assessed by docking simulation can be designed and lead effectively to
acceptable structures. Interestingly, the interactions between the enzyme and both
enantiomers of serine derivatives were similar. In other words, the functionalities at the
P’1, P1 and P4 sites of the D-serine template were located on the S’1, S1 and S4 pockets,
respectively. This suggests the flexibility of backbones and recognition of the
functionalities for serine type inhibitors. Therefore, the enantiomers of the designed
compounds were also significant candidates as SARS 3CL protease inhibitors.
Moreover, we may consider that D-serine plays a critical role in digestion by proteases
(Fig. 2).
A
B
C
D
14

Fig. 2. Docking simulation of selected inhibitors bound to SARS 3CL protease (PDB
code 3AW1) using GOLD from CCDC. Molecular graphic image shown using PyMOL
from Schrödinger; oxygen (red) and nitrogen (blue) of inhibitors; Cys145 (red) of
SARS 3CL protease. (A) Surface mode with 7k, (B) with ent-7k, (C) with ent-3, (D)
model of interaction with ent-3.
It is important to have enzyme selectivity for the development of protease
inhibitors. We investigated inhibition of cathepsin B,27 which is a mammalian cysteine
protease involved in numerous pathological processes. The cysteine protease inhibitor
E-64 was hardly inhibited against SARS 3CL protease in our previous report. E-64,
miraziridine A28 and tokaramide A29 were reasonable inhibitors to bind the active site of
cathepsin B. For this reason, the inhibitors of SARS 3CL protease are thought to show
specificity against endogenous protease. Therefore, we attempted to evaluate the
inhibitory activity of the serine derivatives against cathepsin B. The inhibitory activity
toward cathepsin B was determined with an assay using a Z-Arg-Arg-MCA substrate
developed by Hiwasa et al.30-31 The inhibition potency of serine derivatives was screened
for cathepsin B inhibition at 1.0 mM concentration and subsequently, the IC50 values
were determined only for the selected compounds. The reasonable inhibitors, 3, 7i, 7j,
7h and 7k and its enantiomers, for SARS 3CL R188I mutant protease and 6m, 7f and
7g, which had good potential as cathepsin B inhibitors, are shown in Table 8. As a result,
the serine derivatives that exhibited potent inhibitory activity against SARS 3CL
protease showed relatively less potent inhibitory effects against cathepsin B activity and
had high protease selectivity (entries 1-10). On the other hand, three compounds were
extracted by the screening for a cathepsin B inhibitor (entries 11-13). These compounds
were useless for SARS 3CL protease inhibition (Table 7).
Table 7. Inhibitory activities against cathpsin B
Inhibitiona
Inhibitiona
22%
entry compd
entry
compd
ent-7h
7k
1
2
3
34%
8
9
NIb
ent-3
21%
15

3
4
5
6
7
7i
ent-7i
7j
36%
44%
35%
19%
NIb
10
11
12
13
ent-7k
6m
7f
70%
82%
67%
88%
ent-7j
7h
7g
aInhibitory activity was measured by 1 mM
bNI: no inhibition
The inhibitory activities of selected serine derivatives, 6m, 7f and 7g, were
evaluated using the corresponding IC50 values. The IC50 value of synthetic 7f was 170
M. Comparing IC50 values against SARS 3CL protease and cathepsin B, it was
strongly suggested that the inhibitory activity is attributable mainly to the ester site of
7f.32 The results are consistent with the structural data on 7f in a complex with cathepsin
B, which suggests that the P1 site of 7f can easily adopt a conformation that is similar to
the binding mode of E-64d. Although the P2 site had a rather weak effect compared
with the P1 site, the inhibitory activity of 7f was about 10 times that of 3. To estimate
the inhibitory mechanism, an inhibitory kinetics experiment with 7f was performed by
making a Lineweaver-Burk plot. The rate of cleavage for different amounts of substrate
by cathepsin B in the absence or presence of 7f (100, 500 M) was monitored using
Fluorescence spectrometer and consequently competitive inhibition toward cathepsin B
was assessed.
Cytotoxicity against Hela cells
The cytotoxic ability of serine derivatives was also important because any protease
inhibitor needs to have an orthogonal relationship between anti-virus activity and
cytotoxicity. A cytotoxicity assay was performed against HeLa cells using synthesized
serine derivatives for cytotoxicity alongside rotenone, which served as the control. The
cytotoxicities of these compounds were determined by measuring live-cell
succinate-tetrazolium reductase activity (MTT assay). Although the serine derivatives,
both enantiomers of 3, 7i, 7j, 7h and 7k at 200 M concentrations were evaluated
against Hela cells (5000 cells), the cell death ratio caused by these compounds was less
than 20% and therefore showed practically no cytotoxicity.
16

3. Conclusion
Inhibitory activities of ent-3 against SARS 3CL protease and cathepsin B showed
an IC50 value of 30 M and no inhibition at 1 mM concentration, respectively. Moreover,
ent-7k has inhibitory effects with IC50 = 65 M for SARS 3CL protease and IC50 = 500
M for cathepsin B. These results indicate high specificity between the two proteases.
In addition, the ent-3 and ent-7k inhibitors showed no cytotoxicity and therefore have
good potential as drugs. Ent-3 and ent-7k were chosen for the next stages and
designated as SK23 and SK69, respectively (Fig. 4).
Fig. 4. Optimized inhibitors ent-3 (SK23) and ent-7k (SK69)
In conclusion, we found effective serine derivatives toward the SARS 3CL
protease inhibitor by the combination of docking simulation and a structure activity
relationship study. Consequently, two attractive inhibitors, ent-3 (SK23) and ent-7k
(SK69), which were derived from the tetrapeptide aldehyde (1) and Bai’s inhibitor were
produced. These inhibitors showed protease selectivity and no cytotoxicity and therefore
a useful methodology using a serine template will facilitate drug design. Especially, we
testified that ent-3 (SK23) derived from the virtual screening was most reasonable
inhibitor. To improve the inhibitory activity against the SARS 3CL protease, molecular
design and evaluation are now underway.
Experimental
General information
All solvents were reagent grade. CH2Cl2 was distilled from CaH2. All commercial
reagents were of the highest purity available. Amino acid derivatives were purchased
from Watanabe Chemical Industries. Other chemicals were purchased from Aldrich,
Wako chemical and Nacalai tesque. Optical rotations were determined with a JASCO
DIP-371 polarimeter at the sodium D line. IR spectra of sample were obtained as films
1
13
with a HORIBA FT-720 spectrometer. H (400 and 500 MHz) and C NMR (100 and
17

125 MHz) were determined on a JNM-ECX400 and JNM-ECX500. Chemical shifts are
reported in ppm with reference to tetramethylsilane [1H NMR: TMS (0.00)], or solvent
signals [1H NMR: CDCl3 (7.26), MeOH-d4 (3.30); 13C NMR: CDCl3 (77.16), MeOH-d4
(50.05)]. Mass spectra were recorded on a JEOL AccuTOF JMS-T100LC (ESI).
Analytical TLC was performed on Merck Silica gel 60F254. Crude products were
purified by column chromatography on Silica Gel 60N [Kanto, particle size, (spherical,
neutral) 63-210 m or 100-200 m]. HPLC system (monitored at 220 nm) equipped
with Cosmosil 5C18 AR-II column (4.6×150 mm) using MeCN in 0.1% aqueous TFA.
Absorbance for enzyme inhibition assay was measured with the HITACHI F-7000.
Absorbance for cytotoxicity assay was measured with the CORONA MTP-310Lab.
Coupling of P4 position and tBu-deprotection of amine
(S)-N-Cinnamoylserinecyclohexylamide (5a) To a solution of amine (4a) (4.45 g, 11.3
mmol) in CH2Cl2 were added cinnamic acid (3.35 g, 22.6 mmol), HATU (8.59 g, 22.6
mmol), HOAt (3.08 g, 22.6 mmol) and DIPEA (7.80 ml, 45.2 mmol) and the mixture
was stirred at room temperature for 8 h. After CH2Cl2 and H2O were added to the
solution, the organic layer was washed with brine and dried over MgSO4. Organic layer
was evaporated in vacuo and the residue was purified by silica gel column
chromatography (hexane:AcOEt=4:1) to give L-serine derivative (6.16 g, 16.5 mmol).
To a solution of L-serine derivative was added TFA (3.0 ml) at room temperature. After
being stirred for 2 h, the TFA was carried out azeotropic removal with MeOH and
CH2Cl2 in vacuo. The residue was purified by silica gel column chromatography (CHCl3)
to give alcohol (5a) (1.36 g, 4.30 mmol, 38%) as a white powder, mp 185-188℃. [α]25
D
-78°(c 0.13, CHCl3). IR (film) ν cm-1: 3276, 2930, 1645, 1618, 1542, 1215, 1052, 975,
max
1
752, 666. H NMR (500 MHz, CDCl3) δ: 1.15-1.36 (6H, m), 1.56-1.72 (3H, m),
1.82-1.91 (2H, m), 3.69-3.77 (2H, m), 4.17 (1H, dd, J=12.0, 3.0 Hz), 4.57 (1H, t, J=3.5
Hz), 6.51 (1H, d, J=15.0 Hz), 7.36-7.37 (3H, m), 7.49-7.51 (2H, m), 7.65 (1H, d, J=16.0
Hz). 13C NMR (125 MHz, CDCl3) δ: 24.7, 25.6, 32.8, 32.9, 48.5, 53.8, 63.1, 90.6, 119.7,
128.1, 129.1, 130.3, 134.6, 142.5, 166.9, 170.4. HR-MS (ESI) m/z: Calcd for
C18H24N2O3Na [M+Na]+ 339.1658, Found 339.1700. ent-5a: mp 183-185℃. [α]27 +79° (c
D
0.27, CHCl3), HRMS (ESI) Found 339.1668.
(S)-N-(p-Hydroxyphenyl)propionylserinecyclohexylamide (5b) (0.261 g, 0.780 mmol,
79 %) as an oil. [α]28 -2.7°(c 0.75, MeOH). IR (film) ν cm-1: 3290, 2935, 2858, 1671,
D
max
18

1
1516, 1452, 1352, 1202, 1132, 1026, 892, 833, 758. H NMR (500 MHz, CD3OD) δ:
1.20-1.85 (10H, m), 2.61 (2H, t, J=8.0 Hz), 2.79 (2H, t, J=8.0 Hz), 3.61-3.88 (5H, m),
4.04-4.06 (1H, m), 4.30-4.33 (1H, m), 4.42-4.46 (1H, m), 6.65 (2H, d, J=8.5 Hz), 6.97
13
(2H, d, J=8.0 Hz). C NMR (100 MHz, CD3OD) δ: 24.8, 25.2, 30.5, 32.3, 37.7, 48.3,
55.4, 61.8, 114.9, 129.0, 131.5, 155.5, 169.8, 174.1. HR-MS (ESI) m/z: Calcd for
C18H26N2O4Na [M+Na]+ 357.1790, Found 357.1800.
(S)-N-(E)-4-phenylbut-2-enoicserinecyclohexylamide (5c) (0.278 g, 0.841 mmol,
37 %) as a white powder, mp 150-152℃. [α]26 -3.0°(c 0.10, CHCl3). IR (film) ν cm-1:
D
max
1
3282, 3059, 2933, 2854, 1749, 1655, 1583, 1545, 1475, 1456. H NMR (400 MHz,
CD3OD) δ: 1.11-1.88 (11H, m), 4.58-4.67 (1H, m), 3.93 (2H, s), 4.36-4.42 (1H, m),
4.51-4.56 (1H, m), 6.33 (1H, d, J=16.0 Hz), 6.53 (1H, d, J=16.0 Hz), 7.17-7.21 (1H, m),
7.26-7.29 (2H, m), 7.37 (2H, d, J=7.2 Hz). 13C NMR (100 MHz, CD3OD) δ: 24.8, 25.3,
26.3, 32.3, 37.8, 39.5, 54.3, 55.5, 57.4, 61.8, 122.5, 126.0, 127.2, 128.2, 133.5, 167.6,
170.0, 172.7. HR-MS (ESI) m/z: Calcd for C19H26N2O3Na [M+Na]+ 353.1841, Found
353.1805.
(S)-N-(E)-4’-Methoxy-3-phenylprop-2-enoicserinecyclohexylamide (5d) (0.228 g,
0.659 mmol, 43%) as a yellow powder, mp 226-228℃. [α]23 +1.0°(c 0.10, CHCl3). IR
D
1
(film) ν cm-1: 3282, 2933, 2856, 2777, 1724, 1657, 1603, 1552, 1485, 1412. H NMR
max
(400 MHz, CDCl3) δ: 1.10-1.92 (11H, m), 4.02 (3H, s), 4.08-4.22 (2H, m), 4.51-4.54
(1H, m), 6.37 (1H, d, J=15.6 Hz), 6.89 (2H, d, J=9.2 Hz), 7.45 (2H, d, J=8.7 Hz), 7.60
13
(1H, d, J=15.6 Hz). C NMR (100 MHz, CDCl3) δ: 24.8, 25.3, 32.3, 48.7, 54.5, 55.6,
57.5, 61.8, 62.0, 114.0, 117.6, 129.2, 129.2, 140.8, 150.2, 161.4, 167.8, 169.8, 169.9,
170.2. HR-MS (ESI) m/z: Calcd for C19H26N2O4Na [M+Na]+ 369.1790, Found 369.1783.
(S)-N-Benzoylserinecyclohexylamide (5e) (0.247 g, 0.851 mmol, 80%) as a white
powder, mp189-191℃. [α]28 +26°(c 0.10, CHCl3). IR (film) ν cm-1: 3290, 3072, 2933,
D
max
1
2854, 2355, 2326, 1635, 1548, 1489, 1448. H NMR (400 MHz, CDCl3) δ: 1.10-1.95
(11H, m), 3.48-3.79 (2H, m), 4.23-4.28 (1H, m), 4.52-4.56 (1H, m), 7.43-7.56 (3H, m),
13
7,81 (2H, d, J=11.6 Hz); C NMR (100 MHz, CDCl3) δ: 24.8, 25.3, 32.3, 48.3, 56.0,
62.0, 127.2, 128.3, 131.6, 133.8, 168.7, 170.1. HR-MS (ESI) m/z: Calcd for
C16H22N2O3Na [M+Na]+ 313.1528, Found 313.1514.
(S)-N-(E)-2’-Methoxy-3-phenylprop-2-enoicserinecyclohexylamide (5f) (34.0 mg,
98.2 mol, 7.0%) as a white powder, mp 189-192℃. [α]25 +6.0°(c 0.10, MeOH). IR (film)
D
1
ν cm-1: 3282, 2933, 2846, 1649, 1539, 1489, 1452, 1248, 1201, 1180; H NMR (400
max
19

MHz, CDCl3) δ: 1.07-1.95 (11H, m), 3.62-3.78 (2H, m), 3.89 (3H, s), 4.19 (1H, dd,
J=12.0, 2.8 Hz), 4.48-4.54 (1H, m), 6.65 (1H, d, J=16.0 Hz), 6.86-6.99 (2H, m),
13
7.30-7.37 (1H, m), 7.47 (1H, d, J=8.0 Hz), 7.88 (1H, d, J=16.0 Hz); C NMR (100
MHz, CDCl3) δ: 22.9, 24.8, 25.3, 29.3, 32.3, 54.7, 55.6, 62.0, 111.1, 120.4, 123.5, 128.1,
131.0, 136.4, 158.4, 167.8, 170.1. HR-MS (ESI) m/z: Calcd for C19H26N2O4Na [M+Na]+
369.1790, Found 369.1799.
(S)-N-(E)-3’,4’-Dimethoxy-3-phenylprop-2-enoicserinecyclohexylamide (5g) (0.100
g, 0.266 mmol, 23 %) as a yellow powder, mp 220℃. [α]26 +28°(c 0.10, MeOH). IR (film)
D
1
ν cm-1: 3276, 3099, 3001, 2931, 2846, 1643, 1610, 1543, 1514, 1452. H NMR (400
max
MHz, CDCl3) δ: 1.09-1.94 (11H, m), 3.66-3.81 (1H, m), 3.89 (6H, s), 6.43 (1H, d,
J=16.0 Hz), 6.80-6.89 (1H, m), 7.00-7.04 (1H, m), 7.08 (1H, d, J=6.4 Hz), 7.58 (1H, d,
J=16.0 Hz). 13C NMR (100 MHz, CDCl3) δ: 24.7, 25.5, 32.6, 38.8, 48.4, 54.0, 56.1, 63.2,
109.6, 111.1, 117.3, 122.5, 127.4, 142.4, 149.3, 151.0, 167.3; HR-MS (ESI) m/z: Calcd
for C20H28N2O5Na [M+Na]+ 399.1896, Found 399.1907.
(S)-N-(E)-3’,5’-Dimethoxy-3-phenylprop-2-enoicserinecyclohexylamide (5h) (0.236
g, 0.627 mmol, 29%) as a white powder, mp 175-177℃. [α]26 +22°(c 0.10, CHCl3). IR
D
1
(film) ν cm-1: 3269, 2924, 2846, 2355, 2326, 1647, 1606, 1558, 1541, 1522. H NMR
max
(400 MHz, CDCl3) δ: 1.10-1.92 (11H, m), 3.62-3.76 (1H, m), 3.83 (6H, s), 4.12-4.21
(1H, m), 4.48-4.56 (1H, m), 6.41 (1H, d, J=16.0 Hz), 6.47 (1H, s), 6.65 (2H, s), 7.56
13
(1H, d, J=15.3 Hz). C NMR (100 MHz, CDCl3) δ: 24.7, 25.5, 29.8, 32.8, 35.1, 48.3,
53.4, 55.5, 57.1, 63.0, 100.0, 102.0, 104.2, 105.9, 120.1, 126.3, 136.4, 142.3, 143.0,
161.1. HR-MS (ESI) m/z: Calcd for C20H28N2O5Na [M+Na]+ 399.1896, Found 399.1872.
(S)-N-(E)-3’-Methoxy-3-phenylprop-2-enoicserinecyclohexylamide (5i) (0.290 g,
0.838 mmol, 69% in 2 steps) as a white powder, mp 180-181℃. [α]26 +25°(c 0.10, MeOH).
D
1
IR (film) ν cm-1: 3269, 3086, 2931, 2854, 1647, 1620, 1577, 1547, 1491, 1448; H
max
NMR (400 MHz, CDCl3) δ: 1.11-2.11 (11H, m), 3.63-3.68 (1H, m), 3.83 (3H, s),
4.19-4.25 (1H, m), 4.46-4.50 (1H, m), 6.45 (1H, d, J=16.0 Hz), 6.76-6.83 (1H, m), 6.92
(1H, dd, J=8.8, 2.8 Hz), 7.03 (1H, s), 7.11 (1H, d, J=8.0 Hz), 7.62 (1H, d, J=16.0 Hz).
13C NMR (100 MHz, MeOH-d4) δ: 24.8, 25.3, 32.3, 54.4, 55.7, 62.0, 112.6, 115.3, 120.1,
120.5, 129.6, 136.3, 140.9, 160.2, 161.4, 167.1, 170.1. HR-MS (ESI) m/z: Calcd for
C19H26N2O4Na [M+Na]+ 369.1790, Found 369.1798.
(S)-N-(E)-4’-hydroxy-3-phenylprop-2-enoicserinecyclohexylamide (5j) (0.170 g,
0.511 mmol, 55%) as a white powder, mp 220-222℃. IR (film) ν cm-1: 3338, 3269, 2918,
max
20

2854, 2495, 2432, 1655, 1641, 1606, 1570. 1H NMR (400 MHz, MeOH-d4) δ: 1.10-1.90
(11H, m), 3.60-3.68 (1H, m), 3.76 (1H, d, J=5.2 Hz), 4.49 (1H, t, J=6.0 Hz), 6.52 (1H, d,
J=15.6 Hz), 6.77 (2H, d, J=8.7 Hz), 7.41 (2H, d, J=8.7 Hz), 7.46 (1H, d, J=15.6 Hz). 13C
NMR (100 MHz, MeOH-d4) δ: 24.8, 25.3, 32.3, 48.6, 55.6, 62.0, 115.4, 116.6, 126.2,
129.4, 141.2, 159.4, 167.8, 170.1. HR-MS (ESI) m/z: Calcd for C18H24N2O4Na [M+Na]+
355.1634, Found 355.1639.
(S)-N-(E)-3’,4’,5’-Trimethoxy-3-phenylprop-2-enoicserinecyclohexylamide
(5k)
(0.104 g, 0.256 mmol, 29%) as a white powder, mp 156-162℃. [α]26 +31°(c 0.10, MeOH).
D
1
IR (film) ν cm-1: 3298, 2933, 2846, 1649, 1616, 1583, 1542, 1506, 1452, 1419. H
max
NMR (400 MHz, CDCl3) δ: 1.09-1.96 (11H, m), 3.60-3.78 (4H, m), 3.84 (9H, s), 4.10
(1H, dd, J=8.4, 4.0 Hz), 4.57-4.64 (1H, m), 6.44 (1H, d, J=16.0 Hz), 6.70 (2H, s), 7.04
(1H, d, J=8.0 Hz), 7.12 (1H, d, J=5.6 Hz), 7.52 (1H, d, J=16.0 Hz). 13C NMR (100 MHz,
CDCl3) δ: 24.7, 25.5, 32.8, 48.6, 54.4, 56.2, 61.0, 63.4, 105.2, 119.3, 130.0, 140.0, 142.1,
153.5, 166.8, 169.9. HR-MS (ESI) m/z: Calcd for C21H30N2O6Na [M+Na]+ 429.2002,
Found 429.2009.
(S)-N-Cinnamoylserinepiperidineamide (5l) (95.4 mg, 26%) as an oil, [α]25 +16° (c
D
0.40, MeOH). IR (film) ν cm-1: 3286, 3060, 3027, 2939, 2860, 2245, 1660, 1608, 1549,
max
1
1450. H NMR (400 MHz, CDCl3) δ: 1.53-1.69 (6H, m), 3.50-3.56 (2H, m), 3.58-3.66
(1H, m), 3.82 (2H, s), 5.06-5.11 (1H, m), 6.50 (1H, d, J=16.0 Hz), 7.32-7.38 (3H, m),
7.46-7.51 (2H, m), 7.62 (1H, d, J=16.0 Hz). 13C NMR (100 MHz, CDCl3) δ: 24.4, 25.6,
26.5, 43.6, 47.0, 50.9, 52.0, 119.9, 128.0, 128.9, 130.0, 142.1, 166.5, 168.2. HR-MS
(ESI) m/z: Calcd for C17H22N2O3Na [M+Na]+ 325.1528, Found 325.1540. ent-5l: [α]25
D
-16° (c 0.20, MeOH). HR-MS (ESI) m/z: Found 325.1514.
(S)-N-Cinnamoylserinemorpholineamide (5m) (196 mg, 0.644 mmol, 91%) as an oil,
[α]25 +8.5° (c 0.55, CHCl3). IR (film) ν cm-1: 3303, 3059, 3016, 2966, 2931, 2862,
D
max
2368, 2305, 1736, 1620. 1H NMR (400 MHz, CDCl3) δ: 3.57-3.74 (8H, m), 3.79 (1H, dd,
J=11.2, 4.0 Hz), 3.88 (1H, dd, J=11.6, 4.8 Hz), 4.38 (1H, s), 5.06-5.15 (1H, m), 6.52
(1H, d, J=16.0 Hz), 7.30-7.40 (3H, m), 7.44-7.52 (2H, m), 7.62 (1H, d, J=16.0 Hz). 13C
NMR (100 MHz, CDCl3) δ: 42.8, 46.4, 51.1, 64.1, 66.7, 119.9, 128.7, 130.1, 134.5,
142.3, 166.4, 169.3. HR-MS (ESI) m/z: Calcd for C16H20N2O4Na [M+Na]+ 327.1321,
Found 327.1286. ent-5m: [α]27 -7.1° (c 0.20, CHCl3). HR-MS (ESI) m/z: Found
D
327.1302.
(S)-N-Cinnamoylserinebenzylamide (5n) (111 mg, 0.342 mmol, 19%) as an oil. [α]26
D
21

+46° (c 0.10, MeOH). IR (film) ν cm-1: 3435, 3400, 3369, 3278, 1645, 1618, 1215,
max
1
1051. H NMR (400 MHz, CDCl3) δ: 3.64-3.72 (1H, m), 4.25-4.31 (1H, m), 4.41-4.49
(2H, m), 4.54-4.60 (1H, m), 4.46 (1H, d, J=16.0 Hz), 6.78 (1H, s), 7.26-7.35 (4H, m),
7.38 (3H, t, J=3.2 Hz), 7.50 (2H, d, J=5.6 Hz), 7.65 (1H, d, J=16.0 Hz). 13C NMR (100
MHz, MeOH-d4) δ: 42.8, 55.9, 61.9, 120.4, 126.8, 127.6, 128.6, 129.6, 134.9, 138.4,
141.1, 167.4, 171.2. HR-MS (ESI) m/z: Calcd for C19H20N2O3Na [M+Na]+ 347.1372,
Found 347.1353. ent-5n: mp 171-176℃. HR-MS (ESI) m/z: Found 347.1361.
(S)-N-Cinnamoylserinecyclohexanemethylamide (5o) (399 mg, 1.21 mmol, 48%) as a
white powder, mp 183-184℃. [α]26 +21°(c 0.10, MeOH), IR (film) ν cm-1: 3273, 3107,
D
max
1
3047, 2922, 2850, 2368, 2326, 1954, 1884, 1651. H NMR (400 MHz, CDCl3) δ:
0.83-0.97 (2H, m), 1.05-1.29 (3H, m), 1.40-1.53 (1H, m), 1.59-1.74 (6H, m), 3.05-3.14
(2H, m), 3.75-3.85 (2H, m), 3.75-3.84 (1H, m), 4.18 (1H, dd, J=12.0, 4.0 Hz), 4.64-4.71
(1H, m), 6.57 (1H, d, J=16.0 Hz), 7.32-7.40 (3H, m), 7.45-7.53 (2H, m), 7.65 (1H, d,
J=16.0 Hz). 13C NMR (100 MHz, CDCl3) δ: 25.8, 26.4, 30.8, 37.8, 38.8, 46.0, 54.2, 63.0,
119.3, 128.1, 129.0, 130.3, 134.3, 142.9, 166.1, 167.4, 171.2. HR-MS (ESI) m/z: Calcd
for C19H26N2O3Na [M+Na]+ 353.1841 Found 353.1818. ent-5o: mp 181-183℃. [α]27 -24°(c
D
0.10, MeOH), HR-MS (ESI) m/z: Found 353.1818.
Coupling of P1’ position for the inhibitors
(S)-N-Cinnamoyl serine(benzoyl)cyclohexylamide (3) To a solution of 5a (19.6 mg,
0.0619 mmol) in CH2Cl2
℃, and the mixture was
stirred at room temperature for 3 h. After CH2Cl2 and H2O were added to the solution,
the organic layer was washed with brine and dried over MgSO4. The solvent was
evaporated in vacuo and the residue was purified by silica gel column chromatography
(hexane:AcOEt=4:1) to give 3 (18.6 mg, 0.0442 mmol, 71%) as a white powder, mp
200-203℃. [α]24 -1.5° (c 0.76, CHCl3). IR (film) ν cm-1: 3282, 2930, 2849, 2364, 1727,
D
max
1
1646, 1617, 1541, 1450, 1270, 1112, 1025, 975, 710. H NMR (400 MHz, CDCl3) δ:
1.09-1.39 (6H, m), 1.66 (2H, m), 1.88 (2H, m), 3.77 (1H, m), 4.60 (1H, dd, J=11.2, 5.6
Hz), 4.71 (1H, dd, J=11.2, 6.4 Hz), 5.00 (1H, q, J=6.0 Hz), 6.50 (1H, d, J=7.2 Hz), 6.52
(1H, d, J=15.6 Hz), 6.97 (1H, d, J=7.6 Hz), 7.36-7.61 (8H, m), 7.64 (1H, d, J=15.6 Hz),
8.02 (2H, d, J=7.6 Hz). 13C NMR (125 MHz, CDCl3) δ: 24.8, 25.5, 32.9, 48.8, 52.8, 64.2,
120.1, 128.1, 128.6, 129.0, 129.9, 130.1, 130.3, 133.4, 133.6, 134.7, 136.8, 141.8, 142.2,
22

166.3, 166.5, 168.2, 170.4. HR-MS (ESI) m/z: Calcd for C25H28N2O4Na [M+Na]+
443.1947, Found 443.1913. ent-3: mp 205-206℃. [α]27 +1.4°(c 0.14, CHCl3). HR-MS
D
(ESI) m/z: Found 443.1906.
(S)-N-Cinnamoylserine{3-(R)-pyroglutamoyl}cyclohexylamide (6b) (10.9 mg,
0.0255 mmol, 25 %). [α]26 +0.87° (c 0.23, CHCl3). IR (film) ν cm-1: 3418, 2933, 2854,
D
max
1
2360, 2341, 1749, 1647, 1558, 1541, 1456, 1192. H NMR (400 MHz, CDCl3) δ:
1.15-1.88 (10H, m), 2.29-2.44 (4H, m), 3.74 (1H, br), 4.28-4.39 (2H, m), 4.53-4.57 (1H,
m), 4.96 (1H, br), 6.51 (1H, d, J=15.6 Hz), 6.79 (1H, d, J=7.2 Hz), 7.12 (1H, d, J=7.2
13
Hz), 7.31-7.50 (6H, m), 7.66 (1H, d, J=15.6 Hz), 7.72 (1H, d, J=16.0 Hz). C NMR
(100 MHz, CDCl3) δ: 24.3, 24.4, 24.9, 25.5, 29.5, 32.9, 48.9, 52.1, 52.3, 65.3, 119.8,
128.0, 129.0, 130.2, 134.5, 142.5, 166.3, 167.5, 171.8, 178.4. HR-MS (ESI) m/z: Calcd
for C23H29N3O6Na [M+Na]+ 450.2005 Found 450.2041.
(S)-N-Cinnamoylserine(butanoyl)cyclohexylamide (6c) (23.6 mg, 0.0611 mmol,
78 %) as a white powder, mp 176-182℃. [α]25 -0.6° (c 0.17, CHCl3). IR (film) ν cm-1:
D
max
1
3282, 3069, 2933, 2855, 1741, 1649, 1620, 1546, 1449, 1344, 1172, 1092, 977. H
NMR (500 MHz, CDCl3) δ: 1.13-1.37 (11H, m), 1.60-1.72 (4H, m), 1.91 (2H, m),
3.73-3.79 (1H, m), 4.29 (1H, dd, J=11.5, 5.0 Hz), 4.49 (1H, dd, J=11.5, 6.0 Hz), 4.79
(1H, q, J=6.3 Hz), 6.13 (1H, br), 6.45 (1H, d, J=15.5 Hz), 6.59 (1H, br), 7.37-7.39 (3H,
13
m), 7.51-7.52 (2H, m), 7.64 (1H, d, J=15.5 Hz). C NMR (125 MHz, CDCl3) δ: 24.9,
25.6, 27.3, 33.1, 39.0, 48.8, 53.0, 64.1, 119.9, 128.1, 129.0, 130.2, 134.6, 142.3, 166.1,
167.8, 178.8. HR-MS (ESI) m/z: Calcd for C22H30N2O4Na [M+Na]+ 409.2103, Found
409.2080.
(S)-N-Cinnamoylserine(phenylacetyl)cyclohexylamide (6d) (18.0 mg, 0.0414 mmol,
67 %) as a white powder, mp 172-177℃. [α]27 0° (c 0.10, MeOH). IR (film) ν cm-1:
D
max
1
3649, 3583, 3282, 3064, 3030, 2931, 2854, 2362, 2312, 1749. H NMR (400 MHz,
CDCl3) δ: 0.95-1.20 (5H, m), 1.21-1.40 (4H, m), 1.52-1.73 (4H, m), 1.76-1.89 (3H, m),
3.67-3.77 (1H, m), 4.27-4.35 (1H, m), 4.46-4.54 (1H, m), 4.73-4.82 (1H, m), 6.09-6.19
(1H, m), 6.34 (1H, d, J=16.0 Hz), 6.49 (1H, d, J=8.0 Hz), 7.26-7.33 (5H, m), 7.34-7.40
13
(3H, m), 7.46-7.52 (1H, m), 7.60 (1H, d, J=16.0 Hz). C NMR (100 MHz, CDCl3) δ:
24.8, 25.5, 32.9, 41.3, 48.7, 52.5, 64.3, 119.9, 127.3, 128.0, 128.8, 129.0, 129.4, 130.1,
133.7,134.6, 142.1, 166.0, 167.6, 171.5. HR-MS (ESI) m/z: Calcd for C26H30N2O4Na
[M+Na]+ 457.2103, Found 457.2079.
(S)-N-Cinnamoylserine(isonicotinoyl)cyclohexylamide (6e) (13.2 mg, 0.0313 mmol,
23

47 %) as a white powder, mp 210-212℃. [α]24 -6.1° (c 0.08, CHCl3). IR (film) ν cm-1:
D
max
3282, 2929, 2854, 2360, 2341, 1741, 1645, 1616, 1560, 1539, 1211, 1144, 1066, 974.
1H NMR (400 MHz, CDCl3) δ: 1.09-1.39 (4H, m), 1.59-1.71 (4H, m), 1.89 (2H, m),
3.74-3.81 (1H, m), 4.64-4.72 (2H, m), 5.05 (1H, q, J=6.4 Hz), 6.50 (1H, d, J=15.6 Hz),
6.66 (1H, d, J=7.6 Hz), 6.86 (1H, d, J=7.6 Hz), 7.36-7.37 (3H, m), 7.48-7.50 (2H, m),
7.63 (1H, d, J=15.6 Hz), 7.82 (2H, d, J=6.0 Hz), 8.76 (2H, d, J=5.6 Hz). 13C NMR (125
MHz, CDCl3) δ: 24.8, 25.5, 33.0, 48.9, 52.6, 65.4, 119.8, 123.0, 128.1, 129.1, 130.3,
134.5, 136.9, 142.5, 150.8, 165.1, 166.2, 167.5. HR-MS (ESI) m/z: Calcd for
C24H27N3O4Na [M+Na]+ 444.1899, Found 444.1864.
(S)-N-Cinnamoylserine(2,4,6-trichlorobenzoyl)cyclohexylamide (6f) (9.00 mg,
0.0172 mmol, 27%) as a white powder, mp 208-211℃. [α]26 -19° (c 0.67, CHCl3). IR
D
(film) ν cm-1: 3275, 2931, 2854, 2360, 2330, 1747, 1651, 1620, 1558, 1520, 1458,
max
1
1273, 1119, 1057, 972, 852, 752. H NMR (500 MHz, CDCl3) δ: 1.13-1.38 (4H, m),
1.58-1.69 (4H, m), 1.86-1.90 (2H, m), 3.70-3.79 (1H, m), 4.61 (1H, dd, J=11.5, 5.0 Hz),
4.87 (1H, dd, J=11.5, 6.5 Hz), 4.93 (1H, q, J=6.3 Hz), 6.33 (1H, d, J=8.5 Hz), 6.45 (1H,
d, J=16.0 Hz), 6.62 (1H, d, J=8.0 Hz), 7.34-7.38 (5H, m), 7.49-7.51 (2H, m), 7.65 (1H,
13
d, J=15.5 Hz). C NMR (125 MHz, CDCl3) δ: 24.8, 25.6, 32.9, 48.8, 52.6, 65.4, 119.7,
128.1, 128.3, 129.0, 130.3, 132.8, 134.5, 134.7, 142.6, 164.1, 166.3, 167.5. HR-MS
(ESI) m/z: Calcd for C25H25Cl3N2O4Na [M+Na]+ 545.0778, Found 545.0815.
(S)-N-Cinnamoylserine(pivaloyl)cyclohexylamide (6g) (20.6 mg, 0.0514 mmol, 70%)
as a white powder, mp 183-186℃. [α]28 +0.7° (c 0.28, CHCl3). IR (film) ν cm-1: 3282,
D
max
2932, 2856, 2364, 1737, 1646, 1620, 1547, 1450, 1215, 1155, 979; 1H NMR (400 MHz,
CDCl3) δ: 0.94 (3H, t, J=7.4 Hz), 1.13-1.41 (5H, m), 1.60-1.69 (7H, m), 1.89 (2H, m),
2.32 (2H, t, J=7.2 Hz), 3.78 (1H, m), 4.30 (1H, dd, J=11.4, 5.5 Hz), 4.79 (1H, q, J=6.3
Hz), 6.22 (1H, br), 6.46 (1H, d, J=16.0 Hz), 6.64 (1H, br), 7.37-7.38 (3H, m), 7.51-7.52
(2H, m), 7.64 (1H, d, J=15.6 Hz). 13C NMR (100 MHz, CDCl3) δ: 13.8, 18.5, 24.8, 25.6,
33.0, 36.1, 48.7, 52.9, 63.9, 119.9, 128.1, 129.0, 130.2, 134.6, 142.4, 167.8, 173.9.
HR-MS (ESI) m/z: Calcd for C23H32N2O4Na [M+Na]+ 423.2260, Found 423.2227.
(S)-N-Cinnamoylserine(acetyl)cyclohexylamide (6h) (18.4 mg, 0.0513 mmol, 64%)
as a white powder, mp 191-194℃. [α]26 -3.0° (c 0.81, CHCl3). IR (film) ν cm-1: 3298,
D
max
3098, 3093, 2929, 2854, 2360, 2332, 1743, 1647, 1616, 1558, 1540, 1448, 1375, 1246,
1219, 1080, 1049, 974. 1H NMR (500 MHz, CDCl3) δ: 1.11-1.25 (3H, m), 1.29-1.40 (2H,
m), 1.59-1.61 (1H, m), 1.68-1.73 (2H, m), 1.84-1.94 (2H, m), 2.07 (3H, s), 3.77 (1H, m),
24

4.34 (1H, dd, J=11.5, 5.5 Hz), 4.48 (1H, dd, J=11.5, 6.0 Hz), 4.90 (1H, q, J=6.0 Hz),
6.53 (1H, d, J=16.5 Hz), 6.66 (1H, d, J=8.0 Hz), 6.95 (1H, d, J=8.0 Hz), 7.34-7.36 (3H,
m), 7.47-7.50 (2H, m), 7.47-7.50 (2H, m), 7.64 (1H, d, J=15.5 Hz). 13C NMR (125 MHz,
CDCl3) δ: 21.0, 24.9, 25.6, 33.0, 48.7, 52.6, 64.2, 120.1, 129.0, 130.1, 134.7, 142.1,
166.2, 167.9, 171.0. HR-MS (ESI) m/z: Calcd for C20H26N2O4Na [M+Na]+ 381.1790
Found 381.1793. ent-6h: mp 185-187℃. [α]27 +2.4° (c 0.17, CHCl3). HRMS (ESI) Found
D
381.1749.
(S)-N-Cinnamoylserine(benzoyl)cyclohexylamide (6i) (8.2 mg, 0.0161 mmol, 26%).
[α]28 -11°(c 0.23, CHCl3). IR (film) ν cm-1: 3583, 3282, 2924, 2854, 2360, 2332, 1728,
D
max
1
1645, 1616, 1541, 1458, 1348, 1176. H NMR (500 MHz, CDCl3) δ: 1.25 (6H, m),
1.71-1.74 (2H, m), 1.94 (2H, m), 3.80 (1H, m), 4.72 (1H, dd, J=11.5, 7.0 Hz), 4.76 (1H,
dd, J=11.5, 5.5 Hz), 5.01 (1H, q, J=6.7 Hz), 6.16 (1H, d, J=9.0 Hz), 6.47 (1H, d, J=15.0
Hz), 6.59 (1H, d, J=8.0 Hz), 7.37-7.39 (3H, m), 7.50-7.52 (2H, m), 7.65 (1H, d, J=16.5
Hz), 9.13 (2H, d, J=1.5 Hz), 9.23 (1H, m). HR-MS (ESI) m/z: Calcd for C25H26N4O8Na
[M+Na]+ 533.1648, Found 533.1600.
(S)-N-Cinnamoylserine(nicotinoyl)cyclohexylamide (6j) (13.2 mg, 0.0313 mmol,
47 %) as a white powder, mp 201-202℃. [α]26 -4.0° (c 0.45, CHCl3). IR (film) ν cm-1:
D
max
1
3400, 2931, 2854, 2360, 2332, 1733, 1647, 1618, 1541, 1292, 1211, 1144, 974. H
NMR (400 MHz, CDCl3) δ: 1.13-1.35 (6H, m), 1.68-1.71 (2H, m), 1.87-1.90 (2H, m),
3.73-3.82 (1H, m), 4.64 (1H, dd, J=12.0, 5.6 Hz), 4.73 (1H, dd, J=11.6, 6.0 Hz), 4.98
(1H, q, J=6.4 Hz), 6.30 (1H, d, J=8.4 Hz), 6.48 (1H, d, J=16.0 Hz), 6.71 (1H, d, J=7.6
Hz), 7.35-7.38 (4H, m), 7.48-7.51 (2H, m), 7.64 (1H, d, J=15.6 Hz), 8.28 (1H, dt, J=8.0,
13
2.0 Hz), 8.78 (1H, dd, J=4.8, 1.6 Hz), 9.20 (1H, d, J=1.2 Hz). C NMR (125 MHz,
CDCl3) δ: 24.9, 25.5, 33.0, 48.8, 52.7, 65.0, 119.9, 123.5, 125.7, 128.1, 129.0, 130.2,
134.6, 137.4, 142.5, 151.1, 153.9, 165.2, 166.2, 167.7. HR-MS (ESI) m/z: Calcd for
C24H27N3O4Na [M+Na]+ 444.1899, Found 444.1861. ent-6j: mp 197-201℃. [α]27 +3.0° (c
D
0.38, CHCl3). HRMS (ESI) Found 444.1866.
(S)-N-Cinnamoylserine(picolinoyl)cyclohexylamide (6k) (25.8 mg, 0.0612 mmol,
95 %) as a white powder, mp 202-204℃. [α]28 -6.0° (c 0.19, CHCl3). IR (film) ν cm-1:
D
max
3260, 2933, 2854, 2360, 2341, 1734, 1653, 1622, 1558, 1541, 1290, 1217, 1130, 1090,
1
978. H NMR (500 MHz, CDCl3) δ: 1.10-1.36 (6H, m), 1.56-1.71 (2H, m), 1.83-1.90
(2H, m), 3.74-3.81 (1H, m), 4.51 (1H, q, J=5.8 Hz), 4.86 (1H, q, J=5.7 Hz), 4.97 (1H, q,
J=6.5 Hz), 6.50 (1H, d, J=15.5 Hz), 6.66 (1H, d, J=8.0 Hz), 7.02 (1H, d, J=7.5 Hz),
25

7.36-7.38 (3H, m), 7.49-7.52 (3H, m), 7.64 (1H, d, J=16.5 Hz), 7.86 (1H, dd, J=7.5, 2.0
Hz), 8.14 (1H, d, J=7.5 Hz), 8.72 (1H, dd, J=4.0, 2.0 Hz). 13C NMR (125 MHz, CDCl3)
δ: 24.8, 25.6, 32.8, 32.9, 48.8, 52.4, 65.0, 120.1, 125.6, 127.5, 128.1, 129.0, 130.1, 134.7,
137.4, 142.1, 147.6, 149.8, 164.9, 166.2, 167.8. HR-MS (ESI) m/z: Calcd for
C24H27N3O4Na [M+Na]+ 444.1899, Found 444.1870. ent-6k: mp 205-208℃. HRMS (ESI)
Found 444.1866.
(S)-N-Cinnamoylserine{(E)-3’,4’,5’-trimethoxy-3-phenylprop-2-enly}cyclohexylam
ide (6l)
(E)-3’,4’,5’-trimethoxy-3-phenylprop-2-enoic acid (37.6 mg, 0.158 mmol) at room
temperature in CH2Cl2 under nitrogen atmosphere. The mixture was stirred at room
temperature for 10 min, the solvent was evaporated in vacuo and the residue was added
to the mixture of 5a (50.0 mg, 0.158 mmol), TEA (132 ml, 0.738 mmol) in CH2Cl2 and
stirred at room temperature for 2 h. After CH2Cl2 and H2O were added to the solution,
the organic layer was dried over MgSO4. The solvent was evaporated in vacuo and the
residue was purified by silica-gel column chromatography (CHCl3) to give 6k (3.00 mg,
-229℃. [α]27 -9.8° (c 0.25, CHCl3). IR (film)
D
1
ν cm-1: 3283, 3073, 2931, 2841, 2370, 2337, 1720, 1640, 1621, 1582. H NMR (400
max
MHz, CDCl3) δ: 1.10-1.95 (11H, m), 3.87 (9H, s), 4.47-4.51 (1H, m), 4.60-4.67 (1H, m),
4.81-4.89 (1H, m), 6.21 (1H, d, J=9.6 Hz), 6.34 (1H, d, J=16.0 Hz), 6.47 (1H, d, J=16.0
Hz), 6.68 (1H, d, J=1.6 Hz), 6.73 (2H, s), 7.37 (3H, s), 7.50 (2H, s), 7.60-7.67 (2H, m).
13C NMR (100 MHz, CDCl3) δ: 24.8, 25.5, 33.0, 48.6, 53.0, 56.2, 61.1, 64.2, 105.4,
116.4, 119.9, 128.0, 129.0, 129.7, 130.1, 134.5, 142.2, 146.0, 150.9, 153.5, 166.2, 167.0,
167.8. HR-MS (ESI) m/z: Calcd for C30H37N2O7 [M+H]+ 537.2601 Found 537.2612.
(S)-N-Cinnamoylserine(phenylpropanoyl)cyclohexylamide (6m) (4.2 mg, 9.36 mol,
13%) as an oil. [α]27 -19° (c 0.16, CHCl3). IR (film) ν cm-1: 3286, 2931, 2854, 2360,
D
max
1
1736, 1651, 1624, 1543, 1454, 1362, 1215, 1173, 1080, 976. H NMR (500 MHz,
CDCl3) δ: 1.10-1.39 (6H, m),1.68-1.71 (2H, m), 1.87-1.89 (2H, m), 2.67 (2H, t, J=7.8
Hz), 2.95 (2H, t, J=7.8 Hz), 3.75-3.76 (1H, m), 4.29 (1H, dd, J=12.0, 5.5 Hz), 4.50 (1H,
dd, J=11.5, 6.5 Hz), 4.73 (1H, q, J=6.3 Hz), 6.06 (1H, d, J=8.0 Hz), 6.39 (1H, d, J=15.5
Hz), 6.44 (1H, d, J=7.0 Hz), 7.18-7.21 (2H, m), 7.27-7.30 (3H, m), 7.38-7.40 (3H, m),
7.50-7.52 (2H, m), 7.64 (1H, d, J=15.5 Hz). 13C NMR (125 MHz, CDCl3) δ: 24.8, 25.6,
30.9, 33.0, 35.7, 48.7, 52.8, 64.1, 119.8, 126.5, 128.1, 128.4, 128.7, 129.0, 134.6, 140.4,
142.4, 166.1, 167.7. HR-MS (ESI) m/z: Calcd for C27H32N2O4Na [M+Na]+ 471.2260,
26

Found 471.2264.
(S)-N-Cinnamoyl serine(cinnamoyl)cyclohexylamide (6n) (4.00 mg, 0.00896 mmol,
26%) as a white powder, mp 192-198℃. [α]27 -6.9° (c 0.18, CHCl3). IR (film) ν cm-1:
D
max
1
3279, 2929, 2856, 1716, 1643, 1617, 1541, 1447, 1311, 1172, 975, 769. H NMR (500
MHz, CDCl3) δ: 1.25-1.90 (10H, m), 3.80 (1H, m), 4.47 (1H, dd, J=11.5, 5.0 Hz), 4.63
(1H, dd, J=12.0, 6.5 Hz), 4.84 (1H, q, J=6.2 Hz), 6.21 (1H, br), 6.44 (1H, d, J=16.0 Hz),
6.47 (1H, d, J=15.0 Hz), 6.69 (1H, br), 7.37-7.40 (6H, m), 7.51-7.52 (4H, m), 7.66 (1H,
13
d, J=16.0 Hz), 7.72 (1H, d, J=16.0 Hz), 7.83 (2H, d, J=8.0 Hz). C NMR (125 MHz,
CDCl3) δ: 24.8, 25.6, 29.9, 33.0, 48.7, 53.1, 64.2, 117.2, 119.9, 128.1, 128.4, 129.0,
129.1, 130.2, 130.8, 134.3, 134.7, 142.4, 146.3, 166.2, 167.8. HR-MS (ESI) m/z: Calcd
for C27H30N2O4Na [M+Na]+ 469.2104, Found 469.2078. ent-6n: mp 207-211℃. [α]27
D
+9.0° (c 0.14, CHCl3). HRMS (ESI) Found 469.2064.
(S)-N-Cinnamoylserine(2-methyl-6-nitrobenzoyl)cyclohexylamide (6o) (17.8 mg,
0.0371 mmol, 36%) as a white powder, mp 205-208℃. [α]28 -11° (c 0.23, CHCl3). IR
D
(film) ν cm-1: 3287, 2930, 2849, 2359, 1742, 1645, 1620, 1538, 1450, 1344, 1267,
max
1215, 1112, 1075, 975. 1H NMR (400 MHz, CDCl3) δ: 1.13-1.89 (10H, m), 2.42 (3H, s),
3.74 (1H, m), 4.73 (1H, dd, J=11.6 Hz), 4.82 (1H, dd, J=11.2, 4.8 Hz), 4.89-4.93 (1H,
m), 6.32 (1H, m), 6.52 (1H, d, J=15.2 Hz), 6.60 (1H, m), 7.37-7.39 (3H, m), 7.47-7.57
(4H, m), 7.68 (1H, d, J=16.0 Hz). 13C NMR (100 MHz, CDCl3) δ: 19.4, 24.8, 25.5, 32.9,
48.7, 52.7, 65.4, 119.7, 121.9, 128.2, 129.0, 130.0, 130.3, 136.5, 142.6, 166.4, 167.6.
HR-MS (ESI) m/z: Calcd for C26H29N3O6Na [M+Na]+ 502.1954 Found 502.1971. ent-6o:
mp 205-208℃. [α]27 +12° (c 0.15, CHCl3). HRMS (ESI) Found 502.1926.
D
(S)-N-(E)-4-Phenylbut-2-enoicserine(benzoyl)cyclohexylamide (7c) (11.1 mg, 25.5
mol, 17%) as a white powder, mp 184-186℃. [α]28 +10° (c 0.10, CHCl3). IR (film) ν
D
max
cm-1: 3286, 3064, 3004, 2933, 2854, 2359, 1724, 1647, 1579, 1550. 1H NMR (400 MHz,
CDCl3) δ: 1.02-1.89 (11H, m), 4.72-4.83 (1H, m), 3.92 (2H, s), 4.58-4.73 (2H, m),
4.88-4.96 (1H, m), 6.06 (1H, d, J=7.6 Hz), 6.36 (1H, d, J=7.6 Hz), 7.27-7.37 (1H, m),
7.38-7.43 (2H, m), 7.53-759 (1H, m), 7.93-8.01 (2H, m). 13C NMR (100 MHz, CDCl3) δ:
24.8, 25.4, 33.0, 48.7, 54.4, 55.0, 64.7, 128.6, 129.3, 129.8, 133.6, 166.4, 167.5, 167.9,
172.7. HR-MS (ESI) m/z: Calcd for C26H30N2O4Na [M+Na]+ 457.2103, Found 457.2103.
(S)-N-(E)-4’-Methoxy-3-phenylprop-2-enoicserine(benzoyl)cyclohexylamide (7d)
(5.8 mg, 12.9 mol, 22%) as a white powder, mp 185-187℃. [α]23 +13° (c 0.10, CHCl3).
D
1
IR (film) ν cm-1: 3282, 2925, 2852, 2360, 2333, 1724, 1647, 1577, 1545, 1481. H
max
27

NMR (400 MHz, CDCl3) δ: 1.02-1.90 (11H, m), 3.93 (3H, s), 4.60-4.73 (2H, m),
4.90-4.96 (1H, m), 6.03 (1H, d, J=8.2 Hz), 6.28-6.35 (2H, m), 6.88 (1H, d, J=8.7 Hz),
7.42-7.45 (3H, m), 7.56-7.61 (2H, m), 7.96-8.02 (2H, m). 13C NMR (100 MHz, CDCl3)
δ: 24.8, 25.4, 33.0, 48.7, 54.4, 55.0, 64.7, 128.6, 129.3, 133.6, 166.4, 167.4, 167.9, 172.4,
172.6. HR-MS (ESI) m/z: Calcd for C26H30N2O5Na [M+Na]+ 473.2052, Found 473.2099.
(S)-N-Benzoylserine(benzoyl)cyclohexylamide (7e) (11.5 mg, 0.0292 mmol, 43%) as
a white powder, mp 202-203℃. [α]25 +1.0° (c 0.10, MeOH). IR (film) ν cm-1: 3292, 3072,
D
max
1
2924, 2852, 2359, 1734, 1649, 1635, 1558, 1541. H NMR (400 MHz, CDCl3) δ:
1.03-1.91 (11H, m), 3.70-4.81 (1H, m), 4.61-4.68 (1H, m), 4.73-4.81 (1H, m), 5.02 (1H,
13
s), 6.50 (1H, s), 7.33-7.59 (6H, m), 7.81 (2H, d, J=7.3 Hz), 8.01 (2H, d, J=6.9 Hz). C
NMR (100 MHz, CDCl3) δ: 24.8, 25.5, 32.9, 48.7, 53.2, 64.6, 127.3, 128.6, 128.8, 129.2,
129.9, 132.2, 133.5, 166.8, 167.6, 167.7. HR-MS (ESI) m/z: Calcd for C23H25N2O4Na
[M+Na]+ 417.1790, Found 417.1794.
(S)-N-(E)-2’-Methoxy-3-phenylprop-2-enoicserine(benzoyl)cyclohexylamide
(7f)
(16.6 mg, 36.9 mol, 57%) (E:Z=5:2) as a white powder, mp 201-204℃. [α]25 +11° (c
D
0.10, MeOH). IR (film) ν cm-1: 3282, 3072, 2931, 2862, 1726, 1643, 1610, 1542, 1491,
max
1
1462. H NMR (400 MHz, CDCl3) δ: 1.04-1.94 (11H, m), 3.78 (1H, s), 3.87 (1H, s),
4.30 (0.33H, dd, J=11.2, 5.2 Hz), 4.49 (0.33H, dd, J=12.0, 5.6 Hz), 4.59 (0.67H, dd,
J=11.2, 5.2 Hz), 4.70 (0.67H, dd, J=12.0, 6.4 Hz), 4.75-4.81 (0.17H, d, J=16.0 Hz),
4.90-4.98 (0.83H, m), 6.03 (0.29H, d, J=12.4 Hz), 6.60 (0.71H, d, J=16.0 Hz), 6.76
(0.23H, d, J=8.8 Hz), 6.81 (0.23H, t, J=7.2 Hz), 6.81 (0.23H, t, J=7.2 Hz), 6.88-6.98
(0.42H, m), 7.02 (0.15H, d, J=12.4 Hz), 7.15-7.20 (0.21H, m), 7.32 (0.77H, t, J=8.8 Hz),
7.39-7.48 (2.58 H, m), 7.56 (0.79H, t, J=7.2 Hz), 7.86-7.92 (1.79H, m), 8.02 (2H, d,
J=8.0 Hz). 13C NMR (100 MHz, CDCl3) δ: 24.8, 25.5, 32.9, 48.7, 52.8, 55.9, 56.0, 64.6,
109.7, 110.6, 111.1, 117.8, 121.0, 122.3, 123.2, 127.5, 128.5, 129.6, 129.7, 129.8, 133.4,
139.1, 142.0, 149.2, 150.9, 166.4, 166.6, 167.9. HR-MS (ESI) m/z: Calcd for
C26H30N2O5Na [M+Na]+ 473.2052, Found 473.2051.
(S)-N-(E)-3’,4’-Dimethoxy-3-phenylprop-2-enoicserine(benzoyl)cyclohexylamide
(7g) (E:Z=3:1) (9.3 mg, 19.4 mol, 37%) as a white powder, mp 199-202℃. [α]25 +18°
D
(c 0.10, MeOH). IR (film) ν cm-1: 3282, 3080, 3022, 2931, 2846, 1728, 1643, 1614,
max
1516, 1452. 1H NMR (400 MHz, CDCl3) δ: 1.09-1.94 (11H, m), 3.66-3.81 (1H, m), 3.89
(6H, s), 4.46 (0.25H, dd, J=12.0, 5.2 Hz), 4.56-4.63 (1H, m), 4.71 (0.75H, dd, J=11.2,
6.0 Hz), 4.81-4.87 (0.25H, m), 4.93 (0.75H, dd, J=12.8, 6.0 Hz), 5.87 (0.25H, d, J=8.0
28

Hz), 6.07 (0.25H, d, J=9.6 Hz), 6.26 (0.75H, d, J=8.0 Hz), 6.34 (0.75H, d, J=16.0 Hz),
6.53-6.59 (0.25H, m), 6.65 (0.75H, d, J=8.8 Hz), 6.70-6.77 (0.5H, m), 6.84 (0.75H, d,
J=8.0 Hz), 7.02 (0.75H, s), 7.07 (1H, d, J=8.0 Hz), 7.30 (0.25H, s), 7.43 (2H, t, J=8.0
Hz), 7.53-7.61 (1.5H, m), 7.93 (0.5H, d, J=8.0 Hz), 8.02 (1.5H, d, J=8.0 Hz). 13C NMR
(100 MHz, CDCl3) δ: 24.8, 25.5, 32.9, 48.7, 52.8, 55.9, 56.0, 64.6, 109.7, 111.1, 121.1,
122.3, 123.2, 127.6, 128.5, 129.6, 129.7, 129.8, 133.4, 142.0, 149.2, 150.9, 166.4, 166.6,
167.9. HR-MS (ESI) m/z: Calcd for C27H32N2O6Na [M+Na]+ 503.2158, Found 503.2150.
(S)-N-(E)-3’,5’-Dimethoxy-3-phenylprop-2-enoicserine(benzoyl)cyclohexylamide
(7h) (12.9 mg, 0.0194 mmol, 19%) as a white powder, mp 175-177℃. [α]23 +3.0° (c 0.10,
D
MeOH). IR (film) ν cm-1: 3396, 3276, 2924, 2846, 2360, 2333, 1726, 1645, 1614,
max
1
1558; H NMR (400 MHz, CDCl3) δ: 1.08-1.91 (11H, m), 3.96 (6H, s), 4.59 (1H, dd,
J=11.3, 6.4 Hz), 4.69 (1H, dd, J=11.3, 6.0 Hz), 4.95-4.99 (1H, m), 6.43-6.47 (2H, m),
6.62 (2H, s), 6.80 (1H, d, J=7.7 Hz), 7.42 (2H, t, J=8.0 Hz), 7.52-7.57 (2H, m), 8.01
13
(2H, d, J=8.0 Hz). C NMR (100 MHz, CDCl3) δ: 24.8, 25.5, 33.0, 48.7, 52.8, 55.5,
64.6, 102.3, 105.9, 120.5, 128.6, 129.5, 129.9, 133.5, 136.4, 142.2, 161.0, 166.0, 166.6,
167.7. HR-MS (ESI) m/z: Calcd for C27H32N2O6Na [M+Na]+ 503.2158 Found 503.2170.
ent-7h: mp 174-175℃. [α]28 -2.4° (c 0.25, MeOH). HR-MS (ESI) m/z: Calcd for
D
C27H33N2O6 [M+H]+ 481.2338, Found 481.2361.
(S)-N-(E)-3’-Methoxy-3-phenylprop-2-enoicserine(benzoyl)cyclohexylamide
(7i)
(16.6 mg, 0.0369 mmol, 57%) as a white powder, mp 192-194℃. [α]27 +1.8°(c 0.10,
D
MeOH). IR (film) ν cm-1: 3438, 3282, 2933, 2854, 2360, 2326, 1722, 1647, 1558,
max
1541. 1H NMR (400 MHz, CDCl3) δ: 1.06-1.96 (1H, m), 3.82 (3H, s), 4.56-4.62 (1H, m),
4.70 (1H, dd, J=12.0, 6.0 Hz), 4.88-4.94 (1H, m), 6.17 (1H, s), 6.45 (1H, d, J=16.0 Hz),
6.68 (1H, d, J=7.2 Hz), 6.89-6.93 (1H, m), 7.00-7.02 (1H, m), 7.09 (1H, d, J=8.0 Hz),
7.43 (2H, t, J=8.0 Hz), 7.54-7.64 (2H, m), 8.02 (2H, d, J=7.2 Hz). 13C NMR (100 MHz,
CDCl3) δ: 15.4, 24.8, 25.5, 32.9, 48.7, 52.8, 55.3, 64.6, 65.9, 113.0, 115.9, 120.4, 120.6,
128.5, 129.6, 129.8, 129.9, 133.4, 136.0, 142.0, 160.0, 166.1, 166.5, 167.9; HR-MS
(ESI) m/z: Calcd for C26H30N2O5Na [M+Na]+ 473.2052, Found 473.2046. ent-7i: mp
194-196℃. [α]28 -2.4° (c 0.25, MeOH). HR-MS (ESI) m/z: Found 473.2060.
D
(S)-N-(E)-4’-Benzoyloxy-3-phenylprop-2-enoicserine(benzoyl)cyclohexylamine (7j)
(17.0 mg, 0.0314 mmol, 52%) as a white powder, mp 220-222℃. [α]28 -1.0° (c 0.40,
D
CHCl3). IR (film) ν cm-1: 3284, 2929, 2854, 2355, 2326, 1734, 1645, 1616, 1556, 1541.
max
1H NMR (400 MHz, CDCl3) δ: 1.08-1.93 (11H, m), 3.72-3.73 (1H, m), 3.93 (1H, s),
29