Synthesis and SAR study of novel peptide aldehydes as inhibitors of 20S proteasome

Article abstract of DOI:10.3390/molecules16097551

Based on the analysis of the crystal structure of MG101 (1) and 20S proteasomes, a new series of peptide aldehyde derivatives were designed and synthesized. Their ability to inhibit 20S proteasome was assayed. Among them, Cbz-Glu(OtBu)-Phe-Leucinal (3c), Cbz-Glu(OtBu)-Leu-Leucinal (3d), and Boc-Ser(OBzl)-Leu-Leucinal (3o) exhibited the most activity, which represented an order of magnitude enhancement compared with MG132 (2). The covalent docking protocol was used to explore the binding mode. The structure-activity relationship of the peptide aldehyde inhibitors is discussed.

Full text of DOI:10.3390/molecules16097551

Molecules 2011, 16, 7551-7564; doi:10.3390/molecules16097551
OPEN ACCESS
molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
Synthesis and SAR Study of Novel Peptide Aldehydes as
Inhibitors of 20S Proteasome
Yuheng Ma, Bo Xu, Yuan Fang, Zhenjun Yang, Jingrong Cui, Liangren Zhang * and
Lihe Zhang
State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences,
Peking University, Beijing 100191, China
* Author to whom correspondence should be addressed; E-Mail: liangren@bjmu.edu.cn;
Tel.: +86-10-82802567; Fax: +86-10-82805063.
Received: 1 August 2011; in revised form: 29 August 2011 / Accepted: 30 August 2011 /
Published: 5 September 2011
Abstract: Based on the analysis of the crystal structure of MG101 (1) and 20S
proteasomes, a new series of peptide aldehyde derivatives were designed and synthesized.
Their ability to inhibit 20S proteasome was assayed. Among them, Cbz-Glu(OtBu)-Phe-
Leucinal (3c), Cbz-Glu(OtBu)-Leu-Leucinal (3d), and Boc-Ser(OBzl)-Leu-Leucinal (3o)
exhibited the most activity, which represented an order of magnitude enhancement
compared with MG132 (2). The covalent docking protocol was used to explore the binding
mode. The structure-activity relationship of the peptide aldehyde inhibitors is discussed.
Keywords: 20S proteasome; inhibitor; peptide aldehydes; synthesis; structure-activity
relationship
1. Introduction
Lysosomes and the ubiquitin-proteasome pathway (UPP) are two major routes for cellular protein
degradation [1-3]. The UPP is essential for many cellular regulatory mechanisms and plays a crucial
role in the regulation of many physiological processes. For example, degradation of the p53 tumor
suppressors [4] and inhibition of cyclin-dependent p27 kinases [5] can promote tumorigenesis,
disorders of protein degradation that originated from UPP can cause the development of many human
diseases, such as cancer, Alzheimer’s and Parkinson’s diseases, etc. [6-8]. Recently, the study of

Molecules 2011, 16
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proteasome inhibition has received much attention [9-14]. In UPP, proteolysis takes place in the 26S
proteasome, which consist of one or two 19S regulatory particles (RP) [15] and a central catalytic
particle known as the 20S proteasome (CP). The 20S proteasome is a large cylindrically-shaped
complex composed of two copies of seven distinct α- and seven distinct β-type subunits [16,17]. It
possesses three protease activities, namely the post-glutamyl-peptide hydrolyzing (PGPH), the trypsin-
like (T-L), and the chymotrypsin-like (ChT-L) activity, which are assigned as the active subunits β1,
β2, and β5, respectively [18,19].
Small molecules, have been developed to inhibit the proteasome such as cyclic peptides [10,20-22],
peptide boric acids [23], peptide epoxides [24], peptide vinyl sulfones [25], and nonpeptidic molecules
[26-29]. Among all the proteasome inhibitors ever studied, peptide aldehydes were the first developed
and are still the most widely used in in vitro and in vivo studies [30]. MG101 (1, Ac-Leu-Leu-nLeu-al,
Figure 1), one of calpain inhibitors, is the first well-known 20S proteasome inhibitor [16,17,31]. The
crystal structure of the 20S proteasome in complex with MG101 confirms that the hydroxyl group of
the N-terminal threonine of the β5 subunit reacted with the aldehyde group and formed a reversible
hemiacetal. MG132 (2, Cbz-Leu-Leu-Leu-Al, Figure 1), a more potent and selective analog of
MG101, which bears a benzyloxycarbonyl group instead of an acetyl group, is one of the most
commonly used synthetic proteasome inhibitors [32,33]. Up to now, many peptide aldehydes have
been designed and synthesized [34,35].
Figure 1. Structures of MG101 (1), MG132 (2) and peptide aldehydes (3).
O
R3
O
O
H
H
H
N
H
R4
N
H
N
H
CbzHN
N
N
N
AcHN
N
H
H
H
H
O
O
O
R2
P2
O
O
O
P4
P3
P1
1 MG101
2 MG132
3
R=substituted groups
P=substituted amino acids
Previous studies have demonstrated that hydrophobic groups around the P1 and P3 positions are
beneficial to enhance the activity of peptide aldehydes 3 [36-38]. Bulky substituents at the P2 position
and aromatic groups at P4 position also contribute to enhance the inhibitory activity [37]. According to
the crystal structure of complexed MG101 and 20S proteasome, the leucine side chain of P3 projects
into the S3 pocket of β5 subunit, which is an open space in the vicinity of the isopropyl groups. Since
the P3-leucine moiety only partially fills the S3 pocket, we supposed that introducing a large group at
P3 to fill the open space might enhance inhibitory activity. Thus, in this study, we mainly focus on the
variation of P3 position to reveal the structure-activity relationships. A series of peptide aldehyde
derivatives are designed which have a bulky P3 moiety aiming to increase the hydrophobic interactions
with S3.

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2. Results and Discussion
2.1. Synthesis of Peptide Aldehydes 3a-r
The synthesis of the peptide aldehydes is shown in Scheme 1. L-Leucine (4) was treated with
NaBH4 and I2 under argon to give L-leucinol (5) in 89% yield [39], which was then coupled with
Boc-protected amino acids to form the dipeptide alcohols 6 in 71%–80% yield. The dipeptide alcohold
were deprotected with 20% trifluoroacetic acid in dichloromethane, followed by reaction with
t-butoxy-carbonyl (Boc)- or benzyloxycarbonyl (Cbz)-protected amino acids to give 8a–r (crude
products were used in the next step without further purification). After Swern oxidation [40],
compounds 3a–r were obtained in 49%–59% yields.
Scheme 1. Synthesis of peptide aldehydes 3.
O
iii
i
ii
OH
BocHN
OH
OH
H2N
N
H2N
H
O
R2
4
5
6a R2=Bn
6b R2=iPr
R3
O
R3
O
v
O
iv
H
H
N
H
N
OH
TFA H2N
OH
R4HN
N
R4HN
N
N
H
H
H
O
R2
3a-r
O
O
R2
8a-r
R2
7a R2=Bn
7b R2=iPr
Reagents and Conditions: (i) NaBH4, I2, 89%; (ii) Boc-Leu-OH or Boc-Phe-OH, DCC, HOBt, 0 °C
to rt, 76%; (iii) TFA/DCM; (iv) Cbz-AA-OH or Boc-AA-OH, DCC, HOBt, DIPEA, 0 °C to rt; (v)
oxalyl chloride, DMSO, TEA, −78 °C, 49%–58%.
2.2. Assays for Proteasome Activities and SAR
Inhibitory activities of peptide aldehydes on the 20S proteasome are assayed in vitro [41]. MG132
was used as the positive control (Table 1). The results indicate that most of the peptide aldehydes
exhibited inhibitory activities against ChT-L, which is closely associated with the substituted amino
acids at P3. Out of 17 synthesized compounds, nine exhibited inhibitory activities with IC50 in the nM
range, and three compounds in particular (3c, 3d, and 3o) demonstrated much higher activities than the
control MG132.
These inhibitors can be classified into Cbz and Boc series, based on the moiety at the P4 position
(R4). Among the Cbz series, a P3 residue with a bulky hydrophobic branch (compounds 3a–3e, 3h)
affords a highly active inhibitor, whereas, the electropositive branches (compounds 3f and 3g) show
dramatically decreased activity. Compounds 3c and 3d exhibited about 10-fold higher activity than the
others, indicating that a relatively long bulky side chain may favor the increase of activity. For the Boc

Molecules 2011, 16
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series, the P3 residue with a hydrophobic bulky side chain generally affords an active ChT-L inhibitor.
The activities of Boc series compounds with different P3 residues go in an order of 3o > 3p > 3i and
3k > 3j > 3l, also showing that a bulky side chain is too long to give higher activity. Both 3m and 3n
show poor activities with IC50 > 50 μM, and the reason for this deceased potency might be derived
from the presence of a proline pyrrolidine moiety at the P3 position, which is consistent with reported
results [37]. Furthermore, in contrast to the Cbz series, in which the activity does not vary obviously
with the side chain of P2, in the Boc series, a benzyl group at P2 (3i and 3k) affords much higher
activity than the corresponding isobutyl branched compound (3j and 3l).
Table 1. Inhibition of peptide aldehydes to ChT-L activity of 20S proteasome.
Compounds
R4
P3
P2
ChT-L（IC50, μM）
0.21 ± 0.014
0.20 ± 0.035
0.028 ± 0.006
0.089 ± 0.02
0.85 ± 0.047
>50
3a
3b
3c
3d
3e
3f
3g
3h
3i
3j
3k
3l
3m
3n
3o
3p
3q
Cbz
Cbz
Cbz
Cbz
Cbz
Cbz
Cbz
Cbz
Boc
Boc
Boc
Boc
Boc
Boc
Boc
Boc
Boc
Cbz
Asp(OtBu)
Asp(OtBu)
Glu(OtBu)
Glu(OtBu)
Phe
Phe
Leu
Phe
Leu
Leu
Leu
Leu
Leu
Phe
Leu
Phe
Leu
Phe
Leu
Leu
Leu
Leu
Leu
Arg(NO2)
Arg(Tos)
Napa
Asp(OBzl)
Asp(OBzl)
Glu(OBzl)
Glu(OBzl)
Pro
>50
0.41 ± 0.082
4.83 ± 2.30
20.3 ± 2.05
7.14 ± 1.93
>50
>50
>50
0.050 ± 0.002
0.29 ± 0.021
>50
Pro
Ser(OBzl)
Thr(OBzl)
Tyr(OBzl)
Leu
MG132 (3r)
0.28 ± 0.06
a (2-naphthyl)-L-alanine.
To fully understand the SAR of inhibitors, we constructed a binding mode of the peptide aldehydes
with the β5 subunit of the 20S proteasome based on the crystal structure of 20S proteasome complexed
with MG101. Though docking and biochemical data are often not easily comparable, the insights
gained into the binding behavior by molecular modeling is meaningful. Given that covalent binding is
a unique feature of peptide aldehyde inhibitors, we adopted a covalent docking approach and then
developed a protocol to investigate the binding mode of peptide aldehydes with the 20S proteasome.
The binding mode of the control MG132 is similar to that of MG101 observed in the crystal structure
(Figure 2a). MG132 adopts a β-conformation and fills the gap between strands S2 and S4 by forming
hydrogen bonds with residues Thr21, Gly47, and Ala49 and generating an anti-parallel β-sheet
structure (Figure 2b) [10]. The P1-leucine side chain of MG132 projects into the S1 pocket and the
P2-leucine side chain is towards outside. The P3-leucine side chain stretches out into the subunit-specific
S3 pocket and is in close contact with residues of the adjacent β6 subunit.

Molecules 2011, 16
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Other peptide aldehydes are also docked into the 20S proteasome using the same protocol. Similar
orientations of P1–P4 residues are found in the docked conformations. For example, the P1–P4
residues of 3c are towards the S1–S4 pockets, respectively, like in MG132 (Figure 2a), and so do the
hydrogen bonds (Figure 2b).
Figure 2. (a) Binding modes of 1 (green), 2 (magenta) and 3c (purple) with 20S
proteasome. β5 and β6 subunits are shown in green and yellow, respectively. (b) The
binding sites of proteasome and 1 (green), 2 (magenta) and 3c (purple). Only backbones
and key residues of active sites are shown. (c) Binding modes of 3a which is shown in
magenta and 3c in purple. The side chains at P3 position project into S3 pocket. (d)
Binding modes of 3j (pink) and 3l (green). The side chains at the P3 position project into
S3 pocket. (e) Chymotryptic-like active site in binding modes with 1 (green) and 3m
(orange). (f) Key contacts between residues of the ligand binding site of the 20S
proteasome core particle and the backbones of 1 (green) and 3m (orange).
Biochemical investigation shows that the size and length of the P3 side chain is crucial to activity
[42,43]. Among the Cbz series compounds, Glu(OtBu) residues at P3 (3c and 3d) give the most active
inhibition. The structure of the 20S proteasome shows that the β5 and β6 subunits constitute the

Molecules 2011, 16
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binding cleft of the S3 pocket, which is able to accommodate long and linear side chains. The docking
results show that the tert-butyl glutamic ester (3c) fits this site better than tert-butyl aspartic ester (3a)
and provides a strong hydrophobic interaction with the β5/β6 interface (Figure 2c). Among the Boc
series of compounds, when a phenyl ester was used to replace a tert-butyl ester at P3, the Asp(OBzl)
residue (3j) exhibited more active inhibition than Glu(OBzl) (3l). According to the docking analysis
(Figure 2d), although the phenyl ester of both Asp(OBzl) and Glu(OBzl) project into the S3 pocket, the
large sized benzene ring makes the conformation rigid and pushes the backbone slightly out of the
original orientation, so the shorter side chain of Asp(OBzl) is more suitable for the cleft. The most
suitable length of side chain in this Boc-series is Ser(OBzl), and it gives most active inhibition to
ChT-L. When the residue at the P3 position is changed to proline (3m and 3n), the results show that
the pyrrolidine moiety projects into the S3 pocket (Figure 2e), which makes the binding model of the
main chain different from that of MG132 (Figure 2f), and resulting in the disappearance of activity.
3. Experimental
3.1. Chemistry
3.1.1. General
Unless specified otherwise, all starting materials and reagents were used as obtained from
commercial suppliers without further purification. Thin layer chromatography was performed using
silica gel GF-254 (Qing-Dao Chemical Company, China) plated with detection by UV, and column
chromatography was performed on silica gel (200–300 mesh, Qing-Dao Chemical Company, China).
1
Optical rotations were recorded on a Perkin-Elmer 243B polarimeter. H-NMR (300 or 500 MHz)
spectra was recorded on Varian VXR-300 and Varian Inova VXR-500 spectrometer. Mass spectra
(ESI-TOF+ MS) was obtained on a MDS SCLEX QSTAR instrument and only the most representative
peaks were reported (m/z).
3.1.2. Synthesis
L-Leucinol (5) [39]. Sodium borohydride (1.42 g, 37 mmol, 2.4 eq.) was dissolved in anhydrous THF
(40 mL) and L-leucine (2.00 g, 15 mmol, 1 eq.) was added in one portion. The solution was cooled to
−5 °C in an ice-salt bath, and a solution of iodine (3.87 g, 15 mmol, 1 eq.) in anhydrous THF (10 mL)
was added dropwise over 40 min. After the gas evolution was ceased, the reaction solution was
refluxed for 16 h. The solution was cooled to room temperature and methanol was added cautiously
until the mixture became clear. After stirring 30 min, the solution was evaporated and the residue was
dissolved by addition of 45 mL aqueous NaOH. The solution was stirred for 2.5 h and extracted with
methylene chloride (30 mL × 4). The combined organic extracts were dried over Na2SO4 and
concentrated, affording crude product which was distilled under reduced pressure to yield colorless oil
5 (1.59 g, 89.3%, 80–83 °C/25 mmHg). [α]2D0 +4.0 (c 0.3, MeOH). 1H-NMR (500 MHz, CDCl3): δ 0.91
(d, 6H, J = 6.5 Hz), 1.19–1.14 (m, 2H), 1.70–1.65 (m, 1H), 2.04 (br s, 3H, NH2, OH), 3.23 (dd, 1H,
J = 3.0, 8.0 Hz), 3.57 (dd, 1H, J = 3.0, 8.0 Hz). MS (ESI-TOF+): 118 [M+H]+.

Molecules 2011, 16
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Boc-L-Phenylalanine-L-Leucinol (6a). Boc-L-phenylalanine (0.25 g, 0.95 mmol, 1.0 eq.), L-leucinol
(0.20 g, 1.04 mmol, 1.0 eq.), and HOBt (0.14 g, 1.0 mmol, 1.1 eq.) were mixed in anhydrous THF
(2 mL). N,N`-Dicyclohexylcarbodiimide (DCC, 0.22 g, 1.0 mmol, 1.1 eq.) and 5 (0.11 g, 0.95 mmol,
1 eq.) was added at 0 °C, and the mixture was warmed to room temperature and stirred for 16 h. After
filtration to remove dicyclohexylurea, the solvent was removed and the residue was partitioned
between EtOAc (20 mL) and H2O (10 mL). The organic phase was washed with 10% citric acid
(10 mL × 3), saturated NaHCO3 (10 mL × 3), and then brine (10 mL × 2). The solution was dried over
Na2SO4 and evaporated to an amorphous solid. The crude product was purified by flash
chromatography on silica gel to give compound 6a as white solid (0.25 g, 71.2%). [α]2D0 −19.4 (c 0.3,
1
MeOH). H-NMR (500 MHz, CDCl3): δ 0.87 (d, 6H, J = 7.2 Hz), 1.26–1.23 (m, 2H), 1.42 (s, 9H),
1.50–1.46 (m, 1H), 1.95 (s, 1H), 3.02–2.98 (m, 1H), 3.11–3.07 (m, 1H), 3.35 (m, 1H), 3.48 (d, 1H,
J = 11.0 Hz), 3.95–3.93 (m, 1H), 4.25 (m, 1H), 5.06 (s, 1H), 5.60 (d, 1H), 7.28–7.14 (m, 5H).
MS(ESI-TOF+): 345 [M+H]+.
Boc-L-Leucine-L-Leucinol (6b). Compound 6b was obtained by using similar procedure as 6a. White
solid. [α]2D0 −11.6 (c 0.52, MeOH). 1H-NMR (500 MHz, CDCl3): δ 0.93–0.88 (m, 12H), 1.32–1.27 (m,
1H), 1.40–1.36 (m, 1H), 1.42 (s, 9H), 1.64–1.60 (m, 4H), 2.63 (s, 1H), 3.51–3.46 (m, 1H), 3.69–3.63
(m, 1H), 4.01–3.98 (m, 2H), 4.84 (s, 1H), 6.20 (d, 1H, J = 8.0 Hz). MS (ESI-TOF+): 331 [M+H]+.
TFA L-Phenylalanine-L-Leucinol (7a). To a suspension of 6a (0.50 g, 1.27 mmol) in CH2Cl2 (3 mL)
was added TFA (1 mL) at 0 °C. After stirred at room temperature for 2 h, the solution was evaporated
and the crude product was used in the next step without purification. TFA L-Leucine-L-Leucinol (7b)
was prepared by a similar procedure.
Cbz-L-Asp(OtBu)-L-Phe-L-Leuninol (8a). Cbz-L-Asp(OtBu)-OH (0.20 g, 0.62 mmol, 1 eq.) was
dissolved in anhydrous THF (5 mL), HOBt (92 mg, 0.68 mmol, 1.1 eq.) and DCC (0.14 g, 0.68 mmol,
1.1 eq.) were added after cooling to 0 °C. The mixture was stirred for 60 min then 7a (0.21 g,
0.62 mmol, 1 eq.) and diisopropylethylamine (0.22 mL, 1.24 mmol, 2 eq.) were added. The reaction
mixture was stirred at room temperature overnight. The insoluble material was filtered off and the
solution was washed successively with 10% citric acid, saturated NaHCO3 and brine. After drying with
Na2SO4 the solvents were removed under reduced pressure. The crude products were used in the next
step without further purification. Compounds 8b-r were prepared using similar procedures.
Cbz-L-Asp(OtBu)-L-Phe-L-Leucinal (3a) A solution of oxalyl chloride (63 mg, 0.49 mmol, 1.4 eq.) in
CH2Cl2 (0.4 mL) was cooled to −78 °C, DMSO (45 μL, 0.63 mmol, 1.8 eq.) in CH2Cl2 (0.1 mL) was
added dropwise over 10 min. The resulting mixture was stirred for 30 min at −78 °C. A solution of 8a
(0.20 g, 0.35 mmol, 1 eq.) in CH2Cl2 (1.5 mL) was then added dropwise over 30 min affording a
cloudy mixture which was allowed to stir at −78 °C for 2 h. Triethylamine (0.19 mL, 1.41 mmol, 4 eq.)
was then slowly added over 30 min, and the solution was gradually warmed to room temperature. The
reaction mixture was washed with saturated aq NaHCO3, and brine. The organic phase was dried,
filtered and concentrated. The crude product was purified by flash chromatography on silica gel to give
1
compound 3a as white solid (0.10 g, 52.3%). White solid. [α]2D0 −19.1 (c 0.4, CHCl3). H-NMR

Molecules 2011, 16
7558
(300 MHz, CDCl3): δ 0.86 (d, 6H, J = 6.2 Hz), 1.40 (s, 9H), 1.70–1.53 (m, 3H), 2.73–2.68 (m, 2H),
3.10–3.04 (m, 2H), 4.38–4.30 (m, 2H), 4.71 (d, 1H, J = 7.2 Hz), 5.09 (d, 2H, J = 3.6 Hz), 5.72 (m,
1H), 6.58 (d, 1H, J = 7.5 Hz), 6.82 (t, 1H, J = 8.7 Hz), 7.38–7.19 (m, 10H), 9.43 (d, 1H). MS
(ESI-TOF+): 568 [M+H]+. Elemental Anal.Calcd. for C31H41N3O7: C, 65.59; H, 7.28; N, 7.40. found:
C, 65.67; H, 7.48; N, 7.32.
Compounds 3b-3r were obtained using a similar procedure as 3a.
Cbz-L-Asp(OtBu)-L-Leu-L-Leucinal (3b): White solid. [α]2D0 −21.0 (c 0.5, CHCl3). 1H-NMR (300 MHz,
CDCl3): δ 0.97–0.88 (m, 12H), 1.42 (s, 9H), 1.69–1.57 (m, 6H), 4.48–4.43 (m, 3H), 5.13 (d, 2H,
J = 3.6 Hz), 5.88 (s, 1H), 6.67–6.65 (m, 2H), 7.37 (m, 5H), 9.52 (s, 1H). MS (ESI-TOF+): 534 [M+H]+.
Elemental Anal.Calcd. for C28H43N3O7: C, 63.02; H, 8.12; N, 7.87. found: C, 63.09; H, 8.19; N, 7.88.
Cbz-L-Glu(OtBu)-L-Phe-L-Leucinal (3c): White solid. [α]2D0 −28.1 (c 0.6, CHCl3). 1H-NMR (300 MHz,
CDCl3): δ 0.90 (d, 6H, J = 5.4 Hz), 1.44 (s, 9H), 1.56–1.49 (m, 3H), 1.91–1.88 (m, 2H), 2.25 (t, 2H,
J = 6.3 Hz), 3.14 (t, 2H, J = 8.4 Hz), 4.06–3.96 (m, 1H), 4.38–4.33 (m, 1H), 4.75–4.69 (m, 1H), 5.04
(dd, 2H, J = 8.3, 22.2 Hz), 6.02 (s, 1H), 6.70–6.64 (m, 1H), 7.35–7.18 (m, 10H), 9.43 (d, 1H, J = 4.8
Hz). MS (ESI-TOF+): 582 [M+H]+. Elemental Anal.Calcd. for C32H43N3O7: C, 66.07; H, 7.45; N, 7.22.
found: C, 65.99; H, 7.45; N, 7.26.
1
Cbz-L-Glu(OtBu)-L-leu-L-Leucinal (3d): White solid. [α]2D0 −14.4 (c 0.7, CHCl3). H-NMR (300 MHz,
CDCl3): δ 0.97–0.90 (m, 6H), 1.44 (s, 9H), 1.74–1.54 (m, 6H), 2.09–1.96 (m, 2H), 2.40 (t, 2H, J = 5.1
Hz), 4.18 (t, 1H, J = 7.2 Hz), 4.49–4.38 (m, 2H), 5.10 (d, 2H, J = 3.3 Hz), 6.14 (s, 1H), 6.62 (s, 1H),
6.96 (s, 1H), 7.35–7.26 (m, 5H), 9.52 (d, 1H, J = 9.3 Hz). MS (ESI-TOF+): 548 [M+H]+. Elemental
Anal.Calcd. for C29H45N3O7: C, 63.60; H, 8.28; N, 7.67. found: C, 62.54; H, 8.19; N, 7.70.
1
Cbz-L-Phe-L-leu-L-Leucinal (3e): White solid, [α] 2D0 −16.1 (c 0.3, CHCl3). H-NMR (500 MHz,
CDCl3): δ 0.92 (m, 12H), 1.74–1.32 (m, 6H), 4.36–4.33 (m, 1H), 4.54–4.47 (m, 2H ), 5.04–5.00 (d,
2H, J = 12.5 Hz), 5.45–5.40 (m, 1H), 7.00–6.53 (m, 2H), 7.36–7.16 (m, 10H), 9.50 (s, 1H). MS
(ESI-TOF+): 544 [M+H]+. Elemental Anal.Calcd. for C32H37N3O5: C, 70.70; H, 6.86; N, 7.73. Found:
C, 70.74; H, 6.90; N, 7.65.
1
Cbz-L-Arg(NO2)-L-leu-L-Leucinal (3f): White solid, [α]2D0 −67.2 (c 0.1, CHCl3). H-NMR (500 MHz,
CDCl3): δ 0.88–0.86 (m, 12H), 1.66–1.38 (m, 8H), 1.80–1.75 (m, 2H), 3.28–3.24 (m, 2H), 4.07 (dd,
1H, J = 4.5, 15.5 Hz), 4.20–4.16( m, 1H), 4.39–4.30 (m, 2H), 5.08 (s, 2H), 5.98 (s, 1H), 6.49–6.33 (m,
1H), 7.35–7.30 (m, 6H), 7.47 (s, 1H), 8.45 (s, 1H), 9.52 (s, 1H). MS (ESI-TOF+): 564 [M+H]+.
Elemental Anal.Calcd. for C26H41N7O7, C, 55.40; H, 7.33; N,17.40. Found: C, 55.32; H, 7.42;
N, 17.30.
1
Cbz-L-Arg(Tos)-L-leu-L-Leucinal (3g): White solid. [α]2D0 −12.3 (c 0.2, CHCl3). H-NMR (500 MHz,
CDCl3): δ 1.11–0.86 (m, 12H), 1.74–1.31 (m, 8H), 1.95–1.92 (m, 2H), 2.42 (s, 3H), 2.49–2.47 (m,
2H), 4.20–4.15 (m, 1H), 4.32–4.26 (m, 2H), 5.15 (s, 2H), 5.98 (s, 1H), 6.49–6.43 (m, 1H), 7.38–7.25

Molecules 2011, 16
7559
(m, 6H), 7.81 (d, 1H), 8.11 (s, 1H), 9.47 (s, 1H). MS (ESI-TOF+): 673 [M+H]+. Elemental Anal.Calcd.
for C33H48N6O7S, C, 58.91; H, 7.19; N, 12.49. found: C, 58.99; H, 7.12; N,12.36.
1
Cbz-L-(2-Naphthyl)alanine-L-Leu-L-Leucinal (3h): White solid. [α]2D0 −51.1 (c 0.7, CHCl3). H-NMR
(500 MHz, CDCl3): δ 0.93–0.89 (m, 12H), 1.91–1.46 (m, 6H), 3.22–3.16 (dd, 2H, J = 3.9, 7.5 Hz),
4.48–4.43 (m, H), 4.89–4.75 (m, 2H), 5.12 (d, 2H, J = 4.2 Hz), 6.03 (d, 1H), 6.69–6.58 (m, 2H),
7.38–7.31 (m, 6H), 7.51 (t, 1H, J = 7.5 Hz), 7.58–7.55 (m, 1H), 7.77 (d, 1H, J = 8 Hz), 7.88 (d, 1H,
J = 8.0 Hz), 8.26 (d, 1H, J = 9.0 Hz), 9.51 (d, 1H, J = 6.0 Hz). MS (ESI-TOF+): 560 [M+H]+.
Elemental Anal.Calcd. for C33H41N3O5: C, 70.82; H, 7.38; N, 7.51. found: C, 70.90; H, 7.42; N, 7.61.
Boc-L-Asp(OBzl)-L-Phe-L-Leucinal (3i): White solid. [α]2D0 −19.5 (c 0.65, CHCl3). 1H-NMR (300 MHz,
CDCl3): δ 0.94–0.88 (m, 6H), 1.40 (s, 9H), 1.60–1.54 (m, 1H), 1.72–1.66 (m, 2H), 3.04–2.77 (m, 3H),
3.26–3.23 (m, 1H), 4.18–4.10 (m, 2H), 4.71–4.67 (m, 1H), 5.11–5.04 (m, 2H), 5.44 (m, 1H), 6.59
(s, 1H), 6.80 (s, 1H), 7.35–7.21 (m, 10H), 9.40 (s, 1H). MS (ESI-TOF+): 568 [M+H]+. Elemental
Anal.Calcd. for C31H41N3O7: C, 65.59; H, 7.28; N, 7.40. Found: C, 65.38; H, 7.19; N, 7.47.
1
Boc-L-Asp(OBzl)-L-Leu-L-Leucinal (3j): White solid. [α]2D0 −44.5 (c 0.7, CHCl3). H-NMR (300 MHz,
CDCl3): δ 0.95–0.92 (m, 12H), 1.44 (s, 9H), 1.70–1.59 (m, 6H), 2.92 (t, 2H, J = 5.7 Hz), 4.47–4.40
(m, 3H), 5.22 (s, 2H), 5.48 (d, 1H), 6.70 (d, 1H, J = 6.9 Hz), 6.87 (m, 1H), 7.40–7.36 (m, 5H), 9.50
(s, 1H). MS (ESI-TOF+): 534 [M+H]+. Elemental Anal.Calcd. for C28H43N3O7: C, 63.02; H, 8.12; N,
7.87. found: C, 62.65;H, 7.98;N, 7.95.
Boc-L-Glu(OBzl)-L-Phe-L-Leucinal (3k): White solid. [α]2D0 −18.1 (c 0.7, CHCl3). 1H-NMR (300 MHz,
CDCl3): δ 0.90–0.87 (m, 6H), 1.37 (s, 9H), 1.69–1.54 (m, 3H), 2.07–2.03 (m, 2H), 2.44 (t, 2H, J = 4.2
Hz), 3.21 (dd, 2H, J = 7.2, 14.1 Hz), 4.05–4.01 (m, 1H), 4.38–4.29 (m, 1H), 4.77–4.74 (m, 1H), 5.13
(d, 2H, J = 3.3 Hz), 5.57 (s, 1H), 6.68–6.56 (m, 2H), 7.38–7.20 (m, 10H), 9.41 (d, 1H, J = 5.4 Hz). MS
(ESI-TOF+); 582 [M+H]+. Elemental Anal.Calcd. for C32H43N3O7: C, 66.07; H, 7.45; N, 7.22. found:
C, 65.91; H, 7.56; N, 7.29.
1
Boc-L-Glu(OBzl)-L-Leu-L-Leucinal (3l): White solid. [α]2D0 −31.5 (c 0.8, CHCl3). H-NMR (300 MHz,
CDCl3):δ 0.95–0.90 (m, 12H), 1.43 (s, 9H), 1.97–1.62 (m, 6H), 2.17–2.12 (m, 2H), 2.57–2.48 (m, 2H),
4.11 (t, 1H, J = 5.7 Hz), 4.48–4.43 (m, 2H), 5.13 (s, 2H), 5.49 (d, 1H), 6.83 (s, 1H), 7.37–7.27
(m, 5H), 9.52 (s, 1H). MS (ESI-TOF+): 548[M+H]+. Elemental Anal.Calcd. for C29H45N3O7: C, 63.60;
H, 8.28; N, 7.67. found: C, 63.71; H, 8.19; N, 7.68.
1
Boc-L-Pro-L-Phe-L-Leucinal (3m): White solid. [α]2D0 −10.0 (c 0.5, CHCl3). H-NMR (300 MHz,
CDCl3): δ 0.98–0.88 (m, 6H), 1.43 (s, 9H), 2.08–1.46 (m, 7H), 3.17–3.13 (m, 2H), 3.40–3.35 (m, 2H),
4.45–4.38 (m, 2H), 5.00–4.94 (m, 1H), 5.92 (s, 1H), 6.72 (s, 1H,), 7.40–7.20 (m, 5H), 9.45 (s, 1H). MS
(ESI-TOF+): 460 [M+H]+. Elemental Anal.Calcd. for C25H37N3O5: C, 65.34; H, 8.11; N, 9.14. found:
C, 65.44; H, 8.19; N, 9.15.

Molecules 2011, 16
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1
Boc-L-Pro-L-Leu-L-Leucinal (3n): White solid. [α]2D0 −23.3 (c 0.6, CHCl3). H-NMR (300 MHz,
CDCl3): δ 1.01–0.93 (m, 12H), 1.50–1.32 (m, 14H), 1.75–1.68 (m, 6H), 4.16–4.12 (m, 1H), 4.52–4.45
(m, 1H), 4.91 (m, 1H), 6.70 (s, 1H), 9.56 (d, 1H, J = 2.7 Hz). MS (ESI-TOF+): 426 [M+H]+. Elemental
Anal.Calcd. for C22H39N3O5: C, 62.09; H, 9.24; N, 9.87. found: C, 61.18; H, 9.28; N, 9.80.
1
Boc-L-Ser(OBn)-L-Leu-L-Leucinal (3o): White solid. [α]2D0 −35.1 (c 0.4, CHCl3). H-NMR (500 MHz,
CDCl3): δ 0.92–0.88 (m, 12H), 1.80–1.40 (m, 15H), 3.65–3.59 (m, 1H), 3.91–3.86 (m, 1H), 4.52–4.20
(m, 3H), 4.54 (s, 2H), 5.39 (s, 1H), 6.94–6.52 (m, 2H), 7.38–7.25 (m, 5H), 9.52 (brs, 1H). MS
(ESI-TOF+): 506 [M+H]+. Elemental Anal.Calcd. for C27H43N3O6: C, 64.13; H, 8.57; N, 8.31. found:
C, 64.10; H, 8.51; N, 8.40.
1
Boc-L-Thr(OBn)-L-Leu-L-Leucinal (3p): White solid. [α]2D0 −6.0 (c 0.6, CHCl3). H-NMR (500 MHz,
CDCl3): δ 0.87–0.84 (m, 6H), 0.99–0.91 (m, 6H), 1.22–1.16 (m, 3H), 1.45 (s, 9H), 1.77–1.50 (m, 6H),
4.19–4.16 (m, 1H), 4.24–4.20 (m, 1H), 4.36–4.27 (m, 1H), 4.51–4.48 (m, 1H), 4.65 (dd, 1H, J = 4,
12.0 Hz), 5.45 (s, 1H), 6.87–6.54 (m, 2H), 7.35–7.25 (m, 5H), 9.49 (d, 1H, J = 25.0 Hz). MS
(ESI-TOF+): 520 [M+H]+. Elemental Anal.Calcd. for C28H45N3O6: C, 64.71; H, 8.73; N, 8.09. found:
C, 64.78; H, 8.80; N, 8.01.
1
Boc-L-Tyr(OBn)-L-Leu-L-Leucinal (3q): White solid. [α]2D0 −4.6 (c 0.3, CHCl3). H-NMR (500 MHz,
CDCl3): δ 0.93 (m,12), 1.40 (s, 9H), 1.76–1.45 (m, 6H), 3.03–3.00 (m, 2H), 4.29–4.22 (m, 1H),
4.46–4.40 (m, 1H), 4.89 (d, 1H, J = 4.0 Hz), 5.04 (s, 2H), 6.28 (d, 1H, J = 8.5 Hz, NH), 6.36 (m, 1H),
6.74 (s, 1H), 6.92 (dd, 2H, J = 6.0, 11.5 Hz), 7.11 (d, 2H, J = 8 Hz), 7.43–7.26 (m, 5H), 9.51 (s, 1H).
MS (ESI-TOF+): 582 [M+H]+. Elemental Anal.Calcd. for C33H47N3O6: C, 68.13; H, 8.14; N, 7.22.
found: C, 68.07; H, 8.19; N, 7.16.
1
Cbz-L-Leu-L-Leu-L-Leucinal (MG132, 3r): White solid. [α]2D0 −14.4 (c 0.8, CHCl3). H-NMR (300
MHz, CDCl3): δ 0.93–0.88 (m, 18H), 1.65–1.58 (m, 9H), 4.18–4.14 (t, 1H, J = 5.5 Hz), 4.47–4.40 (m,
2H), 5.09–4.89 (m, 2H), 5.44 (d, 1H, J = 22.5 Hz), 6.66 (d, 1H, J = 8.0 Hz), 6.95 (d, 1H, J = 33.5 Hz),
7.28–7.38 (m, 5H), 9.52 (d, 1H). MS (ESI-TOF+): 476 [M+H]+. Elemental Anal.Calcd. for
C26H41N3O5: C, 65.66; H, 8.69; N, 8.83. found: C, 65.70; H, 8.62; N, 8.79.
3.2. Biological Testing
Assays for proteasome activities. The enzymatic activities of the proteasome were assayed using
fluorogenic peptides: Suc-Leu-Leu-Val-Tyr-AMC (Suc represents succinyl and AMC represents
7-amido-4-methylisocoumarin, obtained from Sigma) for ChT-L activity. 20S proteasome purified
from mouse liver (1 μg) was incubated with various concentrations of compounds and 50 μM
fluorogenic peptides in 20 mM Tris-HCl pH 7.8 (100 μL) at 37 °C for 1 h, respectively. The
fluorescence of released AMC was measured by a spectrofluorimeter (Fluostar OPTIMA, BMG
Germany) at excitation/emission wavelengths of 380/440 nm and 335/410 nm, respectively. 0.1%
DMSO was used as solvent control. Compared with the fluorescence of solvent control, an inhibition
rate was calculated and thereafter the IC50 value was deduced.

Molecules 2011, 16
7561
3.3. Molecular Docking
The covalent docking method with Gold 4.0: A radius of 20 Å from the β5-catalytic N-terminal
threonine was used to direct site location. For each of the genetic algorithm runs, a maximum number
of 100,000 operations were performed on a population of 100 individuals with a selection pressure of
1.1. Operator weights for crossover, mutation, and migration were set to 95, 95, and 10, respectively,
as recommended by the authors of the software. 50 GA runs were performed in each docking
experiment as done in the software validation procedure. The default GOLD fitness function was used
to identify the better binding mode. The distance for hydrogen bonding was set to 2.5 Å and the cut-off
value for van der Waals calculation was set to 4 Å. Covalent docking was applied and the terminal
carbonyl carbon of all the ligands have been bonded to the hydroxyl oxygen of Thr1.
4. Conclusions
Based on the binding analysis of proteasome and its inhibitor, a new series of peptide aldehydes
was designed and synthesized. Their abilities to inhibit the 20S proteasome were assayed and the
results show that some compounds have more potency than the positive control MG132. Covalent
docking was used to simulate the binding of the peptide aldehyde compounds with 20S, and the
docking mode is similar to that of the observed crystal complex and that the P3-postion substitutes are
crucial for inhibitor potency. The suggested binding mode provides a potential way to design more
potent inhibitors of the 20S proteasome.
Acknowledgments
We thank Groll M. for kindly providing us with the crystal structure of yeast proteasome:MG101
complex. This study was supported by the National Natural Science Foundation of China
(No. 20672010).
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Sample Availability: Samples of the compounds 3a-3r are available from the authors.
© 2011 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article
distributed under the terms and conditions of the Creative Commons Attribution license
(http://creativecommons.org/licenses/by/3.0/).