1,4-Thienodiazepine-2,5-diones via MCR (II): Scaffold Hopping by Gewald and Ugi-Deprotection-Cyclization Strategy

Article abstract of DOI:10.1111/j.1747-0285.2010.00990.x

A second scaffold of 1,4-thienodiazepine-2,5-diones was discovered and is synthetically accessible from Gewald 2-aminothiophenes via Ugi-Deprotection- Cyclization (UDC) strategy. This approach yielded hybrid peptidomimetic diazepine structures with six po

Full text of DOI:10.1111/j.1747-0285.2010.00990.x

ª 2010 John Wiley & Sons A/S
doi: 10.1111/j.1747-0285.2010.00990.x
Chem Biol Drug Des 2010; 76: 130–141
Research Article
1,4-Thienodiazepine-2,5-diones via MCR (II):
Scaffold Hopping by Gewald and
Ugi-Deprotection-Cyclization Strategy
peptide structures with diversely substituted moieties (10–12).
¨
Yijun Huang and Alexander Domling*
Recently, hybrid peptidomimetic BDZs have been investigated during
the lead generation process, such as tripeptide compounds 1-3
(Figure 1) (13–17). Therefore, the development of new synthetic
scaffolds based on 1,4-diazepines has attracted considerable atten-
tion in the design of biologically active compounds (18,19).
Department of Pharmaceutical Sciences, School of Pharmacy,
University of Pittsburgh, Pittsburgh, PA 15261, USA
*Corresponding author: Alexander Dçmling, asd30@pitt.edu
A second scaffold of 1,4-thienodiazepine-2,5-diones
was discovered and is synthetically accessible from
Gewald 2-aminothiophenes via Ugi-Deprotection-
Cyclization (UDC) strategy. This approach yielded
hybrid peptidomimetic diazepine structures with
six points of diversity introduced from readily
available starting materials. A virtual compound
library (N = 50 000) was generated and evaluated
for chemical space distribution and drug-like
properties.
The chemistry developed based on 1,4-benzodiazepine scaffolds has
contributed to the emergence of thiophene as a useful isostere of
a benzene ring (20). Bioisosterism successfully led to the discovery
of a series of 1,4-thienodiazepine drugs (such as olanzapine, clotia-
zepam, and brotizolam), which are heterocyclic compounds contain-
ing a 1,4-diazepine ring fused to a thiophene ring. It is of great
interest to develop the synthesis of new 1,4-thienodiazepine scaf-
folds, which are much less investigated compared to 1,4-benzodia-
zepines. Recently, compound 4 has been identified as an inhibitor
of MAPKAP kinase-2 (MK-2) (21). The cocrystal structure of com-
pound 4 and MK-2 complex reveals the unique properties of a 1,4-
thienodiazepine scaffold (Figure 2) (21). However, chemical space
and the structural biology of 1,4-thienodiazepines are still largely
unexplored. We are particularly interested in the synthesis of new
1,4-thienodiazepine-2,5-dione (TDZ) scaffolds, which have been not
investigated as potential pharmacophore so far.
Key words: 1,4-thienodiazepine-2,5-dione, 2-aminothiophene, Gewald
reaction, multicomponent reaction, peptidomimetic, Ugi reaction
Abbreviations: BDZ, 1,4-benzodiazepine-2,5-dione; G-3CR, Gewald
three-component reaction; MCR, multicomponent reaction; TBD, 1,5,7-
triazabicyclo[4,4,0]dec-5-ene; TDZ, 1,4-thienodiazepine-2,5-dione; UDC,
Ugi-Deprotection-Cyclization; U-4CR, Ugi four-component reaction.
Received 21 January 2010, revised 14 April 2010 and accepted for pub-
lication 18 April 2010
Multicomponent reaction (MCR) chemistry is particularly useful for
the fast and efficient discovery of diverse scaffolds (22). Isocyanide-
based MCRs provide powerful tools for producing diverse arrays of
compounds with high atom economy (23). In search of a novel syn-
thetic route for the construction of TDZ scaffolds, 2-aminothiophene
has been considered as the most appropriate precursor. Gewald
three-component reaction (G-3CR) is a unique method using elemen-
tal sulfur to yield 2-aminothiophenes 5, which builds a platform for
the synthesis of new thiophene scaffolds (24,25). We found that
Gewald 2-aminothiophene is clearly an isostere of anthranilic acids
(26). Ugi four-component reaction (U-4CR) is known to be one of
the most versatile tools for the construction of a-aminoacylcarbona-
mides and related backbones (27). For example, orthogonally pro-
tected anthranilic acids were used as a key synthon for the
synthesis of 1,4-benzodiazepin-2,5-diones via the Ugi-Deprotection-
Cyclization (UDC) approach (28–31). In our recent study, we devel-
oped UDC strategy using 2-aminothiophene derivatives 6 and ethyl
glyoxalate to access TDZ derivatives as potential p53-Mdm2
antagonists (32). Herein, we utilized the UDC strategy (Figure 3) to
synthesize another new scaffold of TDZs starting from 2-aminothio-
phenes, which were prepared by Gewald reactions.
The synthesis and evaluation of new scaffolds based on privileged
structures play an important role in the drug discovery process. Pri-
vileged structures are often preferentially chosen by medicinal che-
mists, as there is the belief that the 'spirit' of an approved and
successful compound based on such a scaffold can be transferred
into a new compound for a different indication (1). Over 40 medica-
tions highlight 1,4-benzodiazepine as a classic privileged structure
with a broad range of therapeutic treatment (2). As the discovery of
benzodiazepine family, many synthetic derivatives with a wide phar-
macological spectrum have been extensively developed (3,4). For
example, farnesyltransferase (FTase) inhibitor BMS-214662 has
undergone evaluation as an anti-cancer drug in phase I and II clini-
cal trials (5). Moreover, 1,4-benzodiazepines may act as mimetics of
peptide secondary structures such as a-helix and b-turn, because of
their unique structural motifs and physicochemical properties (6–9).
It is noteworthy that 1,4-benzodiazepine-2,5-diones (BDZ) as a sub-
family of benzodiazepine scaffolds have been synthesized as cyclic
130

Scaffold Hopping by Gewald and Ugi-Deprotection-Cyclization Strategy
H
N
O
Cl
Me
N
O
H
N
O
O
N
H
O
N
I
O
n
O
Ph
Ph
N
H
N
H
O
N
N
O
CO2H
N
(CH2)4CO2H
N
H
O
H
O
N
H
3
1
Cl
2
Figure 1: Hybrid peptidomimetic 1,4-benzodiazepine-2,5-diones.
MeO
H
N
NH2
S
NH
O
4
Figure 2: X-ray crystal structure of compound 4 bound to MAPKAP kinase-2 (MK-2, PDB code: 3FYK). Compound 4 is shown in sticks. The
receptor binding pocket is shown, and some amino acids are labeled. The hydrogen-bonding network is shown in dash lines.
H
S
R5
N
O
S
R5
NHBoc
O
MeOOC
H2N
R2
UDC
R6
R2
R1 NC
N
+
+
+
O
R3
R4
O
R6
COOH
R4
NHR1
R3
6
Figure 3: Ugi-Deprotection-Cyclization approach for the synthesis of 1,4-thienodiazepine-2,5-dione scaffolds (R1, R2, R3, R4, R5, R6: points
of diversity).
Pittsburgh Mass Spectrometry facility. LC-MS analysis was per-
formed on an SHIMADZU instrument, using an analytical C18 col-
umn (Dionex Acclaim 120 ꢀ, 2.1 · 50 mm, 3.0 lm, 0.2 mL ⁄ min).
Acetonitrile ⁄ water mixtures were used as mobile phase for reverse-
phase HPLC coupled to electrospray ionization-mass spectrometry.
Materials and Methods
General
All reagents were purchased from commercial sources and used
without further purification. The reactions were conducted under air
atmosphere unless otherwise indicated. Analytical thin-layer chro-
matography (TLC) was performed on SiO2 plates on Alumina avail-
able from Whatman. Visualization was accomplished by UV
irradiation at 254 nm. Chromatography was conducted using Pre-
parative Silica gel TLC plates (1000 lm, 20 cm·20 cm). Proton and
carbon NMR spectra were determined on Bruker AvanceTM
600 MHz NMR spectrometer. Chemical shifts are reported as d
values in parts per million (ppm) as referenced to residual solvent.
1H NMR spectra are tabulated as follows: chemical shift, number
of protons, multiplicity (s = singlet, br.s = broad singlet, d = doublet,
t = triplet, q = quartet, m = multiplet), and coupling constant.
High-resolution mass spectra were obtained at the University of
N-(tert-butyl)-2-(2,5-dioxo-1,2,3,5,6,7,8,9-octahydro-4H-
[1]benzothieno[2,3-e][1,4] diazepin-4-yl)acetamide (7a,
Method A): The mixture of 6a (59.4 mg, 0.2 mmol), glycine
methyl ester hydrochloride (0.2 mmol, 25.0 mg), triethylamine
(0.2 mmol, 27.9 lL), aqueous formaldehyde (0.2 mmol, 14.9 lL),
tert-butyl isocyanide (0.2 mmol, 22.6 lL) in 0.5 mL of methanol was
stirred under RT for 2 days. The reaction was quenched by water
and extracted with dichloromethane. The organic layer was washed
with saturated potassium carbonate (aq) and dried over anhydrous
sodium sulfate. After the evaporation of the solvent, the residue
was treated with 0.5 mL of TFA, and stirred under RT for 24 h. To
Chem Biol Drug Des 2010; 76: 130–141
131

¨
Huang and Domling
the reaction was added 10 mL of DCM, then neutralized by satu-
rated potassium carbonate (aq). The mixture was extracted with
DCM, the organic layer was combined and dried over anhydrous
sodium sulfate. After the evaporation of the solvent, the residue
was treated with triethylamine (50 lL) and 1,5,7-triazabicyclo[4,4,0]-
dec-5-ene (TBD) (10 mg) in 0.5 mL of THF, and stirred overnight
under 40 ꢀC. 7a was isolated by silica gel chromatography (petro-
leum ether ⁄ ethyl acetate, 2:1) as yellowish solids (32 mg, yield:
46% over three steps). HPLC ⁄ MS: tR = 9.42 min; m ⁄ z = 350.1
[M+H]+ HRMS: 349.145979 (found); C17H23N3O3S, 349.14601 (calcd.).
1H NMR (600 MHz, CDCl3): 1.33 (9H, s), 1.77 (2H, m), 1.83 (2H, m),
2.62 (2H, m), 2.76 (2H, m), 4.08 (2H, s), 4.12 (2H, s), 6.21 (1H, s).
13C NMR (150 MHz, CDCl3): 22.3, 23.0, 24.5, 25.8, 28.7, 51.5, 52.5,
52.7, 121.7, 129.2, 135.0, 141.4, 164.4, 167.4, 169.0.
C22H31N3NaO3S, 440.19783 (calcd.). 1H NMR (600 MHz, CD3OD):
1.34 (9H, s), 1.45–1.51 (3H, m), 1.61–1.65 (2H, m), 1.81–1.92 (6H,
m), 2.03 (2H, m), 2.23 (1H, m), 2.45 (1H, m), 2.67 (2H, m), 2.97 (1H,
m), 4.11 (2H, s), 6.55 (1H, s). 13C NMR (150 MHz, CD3OD): 22.2,
22.8, 23.9, 25.1, 25.7, 27.48, 27.50, 46.8, 50.7, 50.8, 66.69, 66.71,
122.6, 128.4, 134.4, 142.1, 165.4, 170.7, 174.3.
N-(tert-butyl)-2-(4-chlorophenyl)-2-(2,5-dioxo-1,2,3,5,6,7,8,9-
octahydro-4H-[1] benzothieno[2,3-e][1,4]diazepin-4-yl)ace-
tamide (7f, Method B): The mixture of 6a (59.4 mg, 0.2 mmol),
glycine methyl ester hydrochloride (0.2 mmol, 25.0 mg), triethyla-
mine (0.2 mmol, 27.9 lL), o-chloro-benzylaldehyde (0.2 mmol,
28.0 mg), tert-butyl isocyanide (0.2 mmol, 22.6 lL) in 0.5 mL of
methanol was stirred under RT for 2 days. The reaction was
quenched by water and extracted with DCM. The organic layer was
washed with saturated potassium carbonate (aq) and dried over
anhydrous sodium sulfate. After the evaporation of the solvent, the
residue was treated with 0.5 mL of TFA, and stirred under RT for
24 h. To the reaction was added 10 mL of DCM, then neutralized
by saturated potassium carbonate (aq). The mixture was extracted
with DCM, the organic layer was combined and dried over anhy-
drous sodium sulfate. After the evaporation of the solvent, 7f was
isolated by silica gel chromatography (petroleum ether ⁄ ethyl acet-
ate, 2:1) as yellowish solids (34 mg, yield: 37% over two steps).
HPLC ⁄ MS: tR = 11.08 min; m ⁄ z = 460.1 [M+H]+ HRMS: 459.137649
(found); C23H26ClN3O3S, 459.13834 (calcd.). 1H NMR (600 MHz,
CD3OD): 1.31–1.34 (2H, m), 1.38 (9H, s), 1.74–1.90 (4H, m), 2.67
(2H, m), 3.23 (1H, m), 3.87 (1H, m), 6.22 (1H, s), 7.33 (2H, d,
J = 7.8 Hz), 7.43 (2H, d, J = 7.8 Hz), 7.94 (1H, s). 13C NMR
(150 MHz, CD3OD): 7.8, 22.2, 22.8, 23.9, 25.5, 27.4, 46.5, 51.2,
120.7, 128.2, 128.8, 130.8, 134.1, 134.2, 134.4, 142.8, 165.1, 169.3,
169.6.
N-(cyclopropylmethyl)-2-(2,5-dioxo-1,2,3,5,6,7,8,9-octahydro-
4H-[1]benzothieno [2,3-e][1,4]diazepin-4-yl)acetamide
(7b, Method A): The product was isolated by silica gel chroma-
tography (petroleum ether ⁄ ethyl acetate, 2:1) as yellowish solids
(12 mg, yield: 17% over three steps). HPLC ⁄ MS: tR = 9.12 min;
m ⁄ z = 348.1 [M+H]+ HRMS: 347.131963 (found); C17H21N3O3S,
1
347.13036 (calcd.). H NMR (600 MHz, CDCl3): 0.19 (2H, m), 0.48–
0.50 (2H, m), 0.94 (1H, m), 1.77–1.84 (4H, m), 2.64 (2H, m), 2.77
(2H, m), 3.11 (2H, m), 4.10 (2H, s), 4.21 (2H, s), 6.49 (1H, s). 13C
NMR (150 MHz, CDCl3): 3.4, 10.5, 22.3, 23.0, 24.5, 25.8, 44.3, 52.0,
52.5, 121.7, 129.2, 135.1, 141.3, 164.5, 168.0, 168.8.
N-(2-phenylethyl)-2-(2,5-dioxo-1,2,3,5,6,7,8,9-octahydro-
4H-[1]benzothieno[2,3-e] [1,4]diazepin-4-yl)acetamide (7c,
Method A): The product was isolated by silica gel chromatogra-
phy (petroleum ether ⁄ ethyl acetate, 2:1) as yellowish solids (10 mg,
yield: 13% over three steps). HPLC ⁄ MS: tR = 9.81 min; m ⁄ z = 398.1
[M+H]+ HRMS: 397.145798 (found); C21H23N3O3S, 397.14601 (calcd.).
1H NMR (600 MHz, CDCl3): 1.77–1.83 (4H, m), 2.63 (2H, m), 2.73
(2H, m), 2.80 (2H, m), 3.51 (2H, m), 3.99 (1H, s), 4.15 (2H, s), 6.48
(1H, m), 7.17–7.21 (3H, m), 7.25–7.28 (2H, m). 13C NMR (150 MHz,
CDCl3): 22.3, 23.0, 24.5, 25.8, 35.5, 40.6, 52.1, 52.4, 121.5, 126.5,
128.6, 128.8, 129.1, 135.0, 138.7, 141.6, 164.5, 168.2, 168.7.
N-(tert-butyl)-2-(2,5-dioxo-1,2,3,5,6,7,8,9-octahydro-4H-
[1]benzothieno[2,3-e][1,4] diazepin-4-yl)-3-phenylpro-
panamide (7g, Method B): The product was isolated by silica
gel chromatography (petroleum ether ⁄ ethyl acetate, 2:1) as yellow-
ish solids (18 mg, yield: 21% over two steps). HPLC ⁄ MS:
tR = 11.03 min; m ⁄ z = 440.3 [M+H]+ HRMS: 439.193597 (found);
C24H29N3O3S, 439.19296 (calcd.). 1H NMR (600 MHz, d6-DMSO):
0.86 (1H, s), 1.22 (9H, s), 1.61–1.69 (4H, m), 2.55 (2H, s), 2.88 (1H,
m), 3.14 (1H, m), 3.96 (1H, m), 5.36 (1H, s), 7.22 (1H, m), 7.26 (3H,
m), 7.29 (1H, m), 7.44 (1H, m), 7.51 (1H, s). 13C NMR (150 MHz, d6-
DMSO): 22.4, 23.1, 24.3, 26.0, 28.2, 28.8, 35.8, 48.0, 50.9, 57.6,
120.7, 126.6, 127.1, 128.4, 129.4, 134.6, 137.9, 164.0, 169.7.
N-(tert-butyl)-2-(2,5-dioxo-1,2,3,5,6,7,8,9-octahydro-4H-
[1]benzothieno[2,3-e][1,4] diazepin-4-yl)-3-methylbu-
tanamide (7d, Method A): The product was isolated by silica
gel chromatography (petroleum ether ⁄ ethyl acetate, 2:1) as yellow-
ish solids (12 mg, yield: 15% over three steps). HPLC ⁄ MS:
tR = 10.69 min; m ⁄ z = 392.2 [M+H]+ HRMS: 391.192703 (found);
C20H29N3O3S, 391.19296 (calcd.). 1H NMR (600 MHz, d6-DMSO):
0.72 (3H, d, J = 6.0 Hz), 0.89 (3H, d, J = 6.6 Hz), 1.23 (9H, s), 1.61–
1.78 (5H, m), 2.10 (1H, m), 2.58 (2H, m), 3.16 (1H, m), 3.86 (1H, d,
J = 14.4 Hz), 4.63 (1H, d, J = 10.8 Hz), 7.72 (1H, s). 13C NMR
(150 MHz, d6-DMSO): 19.2, 19.6, 22.5, 23.1, 24.4, 26.1, 28.0, 28.8,
47.2, 50.7, 50.8, 121.0, 127.2, 134.5, 159.9, 164.2, 169.9.
Methyl 2-(2-(tert-butoxycarbonylamino)-N-(2-(tert-butyla-
mino)-2-oxoethyl)-4,5,6,7-tetrahydrobenzo[b]thiophene-
3-carboxamido)-3-methylbutanoate (8): The mixture of 6a
(74.3 mg, 0.25 mmol), valine methyl ester hydrochloride (0.25 mmol,
41.8 mg), triethylamine (0.25 mmol, 34.8 lL), aqueous formaldehyde
(0.25 mmol, 18.6 lL), tert-butyl isocyanide (0.25 mmol, 28.3 lL) in
0.5 mL of methanol was stirred under RT for 1 day. The reaction
was quenched by water and extracted with DCM. The organic layer
was washed with saturated potassium carbonate (aq) and dried
over anhydrous sodium sulfate. After the evaporation of the solvent,
the product was isolated by silica gel chromatography (petroleum
ether ⁄ ethyl acetate, 3:1) as yellowish solids (90 mg, yield: 69%).
N-(tert-butyl)-1-(2,5-dioxo-1,2,3,5,6,7,8,9-octahydro-4H-
[1]benzothieno[2,3-e][1,4] diazepin-4-yl)cyclohexane-
carboxamide (7e, Method A): The product was isolated by
silica gel chromatography (petroleum ether ⁄ ethyl acetate, 2:1) as
yellowish solids (8 mg, yield: 10% over three steps). HPLC ⁄ MS:
tR = 11.00 min; m ⁄ z = 418.3 [M+H]+ HRMS: 440.1981 (found);
132
Chem Biol Drug Des 2010; 76: 130–141

Scaffold Hopping by Gewald and Ugi-Deprotection-Cyclization Strategy
HRMS: 523.272509 (found); C26H41N3O6S, 523.27161 (calcd.). 1H
m ⁄ z = 426.3 [M+H]+ HRMS: 425.177499 (found); C23H27N3O3S,
425.17731 (calcd.). H NMR (600 MHz, CDCl3, major rotamer): 0.79
1
NMR (600 MHz, CDCl3): 0.82 (1H, d, J = 6.0 Hz), 0.85 (1H, d,
J = 6.6 Hz), 1.36 (9H, s), 1.50 (9H, s), 1.74–1.82 (4H, m), 2.05 (1H,
m), 2.24 (1H, m), 2.62–2.65 (3H, m), 3.68 (3H, s), 3.86 (1H, d,
J = 15.0 Hz), 4.02 (1H, d, J = 10.2 Hz), 4.62 (1H, d, J = 15.6 Hz),
5.53 (1H, s), 10.03 (1H, s). 13C NMR (150 MHz, CDCl3): 18.9, 19.4,
22.6, 23.4, 24.0, 28.2, 28.3, 28.6, 29.6, 45.0, 51.8, 52.1, 66.3, 80.3,
126.6, 129.7, 137.5, 153.0, 167.6, 168.8, 170.6.
(3H, d, J = 6.6 Hz), 0.90 (3H, d, J = 6.0 Hz), 1.65–1.72 (2H, m),
1.83–1.93 (3H, m), 2.35–2.38 (1H, m), 2.57–2.61 (1H, m), 2.62–2.63
(1H, m), 2.98–3.00 (1H, m), 3.68 (1H, d, J = 11.4 Hz), 4.11 (1H, d,
J = 15.0 Hz), 4.33–4.45 (3H, m), 7.22–7.31 (6H, m). 13C NMR
(150 MHz, CDCl3, major rotamer): 19.2, 19.9, 22.3, 22.9, 24.5, 25.8,
26.7, 43.5, 56.2, 74.0, 121.7, 127.3, 127.8, 128.6, 128.8, 134.6,
137.9, 140.8, 163.8, 168.5, 169.8.
N-(tert-butyl)-2-(3-isopropyl-2,5-dioxo-1,2,3,5,6,7,8,9-
octahydro-4H-[1]benzothieno [2,3-e][1,4]diazepin-4-
yl)acetamide (9a, Method C): The mixture of 6a (74.3 mg,
0.25 mmol), valine methyl ester hydrochloride (0.25 mmol, 41.8 mg),
triethylamine (0.25 mmol, 34.8 lL), aqueous formaldehyde
(0.25 mmol, 18.6 lL), tert-butyl isocyanide (0.25 mmol, 28.3 lL) in
0.5 mL of methanol was stirred under RT for 2 days. The reaction
was quenched by water and extracted with DCM. The organic layer
was washed with saturated potassium carbonate (aq) and dried
over anhydrous sodium sulfate. After the evaporation of the solvent,
the residue was treated with 0.5 mL of TFA, stirred under 40 ꢀC
overnight. To the reaction was added 10 mL of DCM, then neutra-
lized by saturated potassium carbonate (aq). The mixture was
extracted with DCM, the organic layer was combined and dried
over anhydrous sodium sulfate. After the evaporation of the solvent,
the residue was treated with triethylamine (50 lL) and TBD (10 mg)
in 0.5 mL of THF, stirred overnight under 40 ꢀC. 9a was isolated by
silica gel chromatography (petroleum ether ⁄ ethyl acetate, 2:1) as
yellowish solids (22 mg, yield: 23% over three steps). HPLC ⁄ MS:
tR = 10.44 min, m ⁄ z = 392.3 [M+H]+ HRMS: 391.192778 (found);
C20H29N3O3S, 391.19296 (calcd.). 1H NMR (600 MHz, CDCl3, major
rotamer): 0.92 (1H, d, J = 6.6 Hz), 0.96 (1H, d, J = 6.6 Hz), 1.32 (9H,
s), 1.69 (1H, m), 1.77 (1H, m), 1.89–1.96 (3H, m), 2.43 (1H, m),
2.60–2.68 (2H, m), 3.07 (1H, m), 3.70 (1H, d, J = Hz), 4.07–4.16
(2H, ABd, J = Hz), 6.66 (1H, s). 13C NMR (150 MHz, CDCl3, major
rotamer): 19.4, 20.0, 23.0, 24.5, 25.8, 26.7, 28.6, 51.3, 57.3, 73.8,
122.0, 128.8, 134.7, 140.1, 163.6, 167.6, 170.0.
N-(tert-butyl)-2-(3-benzyl-2,5-dioxo-1,2,3,5,6,7,8,9-octa-
hydro-4H-[1]benzothieno [2,3-e][1,4]diazepin-4-yl)ace-
tamide (9d, Method A): The product was isolated by silica
gel chromatography (petroleum ether ⁄ ethyl acetate, 1:1) as yellow-
ish solids (18 mg, yield: 21% over three steps). HPLC ⁄ MS:
tR = 10.89 min; m ⁄ z = 440.2 [M+H]+ HRMS: 439.194543 (found);
1
C24H29N3O3S, 439.19296 (calcd.). H NMR (600 MHz, CDCl3, 1:1 mix-
ture of rotamers): 1.30 (9H, s), 1.34 (9H, s), 1.71–1.81 (4H, m),
1.91–1.95 (4H, m), 2.52–2.66 (6H, m), 2.97 (2H, m), 3.10 (2H, m),
3.20 (1H, m), 3.62 (2H, m), 3.88 (1H, m), 4.09 (1H, m), 4.19 (1H, m),
4.35 (1H, m), 4.49 (1H, m), 5.99 (1H, s), 6.47 (1H, s), 7.05–7.06 (2H,
m), 7.21–7.28 (8H, m). 13C NMR (150 MHz, CDCl3, 1:1 mixture of
rotamers): 22.3, 22.4, 22.99, 23.03, 24.58, 24.60, 25.5, 26.2, 28.59,
28.63, 32.6, 34.6, 48.3, 51.3, 51.4, 55.4, 57.7, 68.1, 122.3, 122.5,
126.9, 127.3, 128.5, 128.6, 128.9, 129.0, 129.1, 129.45, 129.50,
134.7, 135.0, 135.6, 136.6, 140.2, 141.4, 163.2, 165.5, 167.4, 168.3,
168.4, 169.6.
N-(cyclopropylmethyl)-2-(3-benzyl-2,5-dioxo-1,2,3,5,6,7,8,9-
octahydro-4H-[1] benzothieno[2,3-e][1,4]diazepin-4-yl)ace-
tamide (9e, Method A): The product was isolated by silica gel
chromatography (petroleum ether ⁄ ethyl acetate, 1:1) as yellowish
solids (32 mg, yield: 37% over three steps). HPLC ⁄ MS:
tR = 10.53 min; m ⁄ z = 438.2 [M+H]+ HRMS: 460.1687 (found);
1
C24H27N3NaO3S, 460.16708 (calcd.). H NMR (600 MHz, CDCl3, 1:1
mixture of rotamers): 0.12 (2H, m), 0.16–0.18 (2H, m), 0.40–0.42
(2H, m), 0.45–0.46 (2H, m), 0.84–0.95 (2H, m), 1.75–1.77 (4H, m),
1.90–1.93 (4H, m), 2.55–2.63 (6H, m), 2.92–2.96 (2H, m), 2.98–3.02
(2H, m), 3.06–3.08 (4H, m), 3.25 (1H, m), 3.56 (1H, m), 3.67–3.75
(2H, m), 4.02 (1H, m), 4.13 (1H, m), 4.22 (1H, m), 4.38 (1H, m), 4.51
(1H, m), 6.44 (1H, m), 6.85 (1H, m), 7.04–7.05 (2H, m), 7.19–7.28
(8H, m). 13C NMR (150 MHz, CDCl3, 1:1 mixture of rotamers): 3.3,
3.4, 10.5, 10.6, 22.3, 22.4, 23.00, 23.04, 24.6, 25.5, 26.2, 32.6, 34.3,
41.0, 44.3, 47.2, 52.1, 54.8, 55.7, 57.8, 68.3, 122.2, 122.3, 126.9,
127.3, 128.57, 128.60, 128.8, 128.9, 129.1, 129.3, 129.4, 129.5,
134.6, 134.8, 135.7, 136.6, 140.7, 141.8, 163.4, 165.7, 168.1, 168.5,
168.8, 169.6.
N-(cyclopropylmethyl)-2-(3-isopropyl-2,5-dioxo-1,2,3,5,6,
7,8,9-octahydro-4H-[1] benzothieno[2,3-e][1,4]diazepin-
4-yl)acetamide (9b, Method C): The product was isolated by
silica gel chromatography (petroleum ether ⁄ ethyl acetate, 1:1) as
yellowish solids (16 mg, yield: 21% over three steps). HPLC ⁄ MS:
tR = 10.10 min; m ⁄ z = 490.3 [M+H]+ HRMS: 389.176195 (found);
C20H27N3O3S, 389.17731 (calcd.). 1H NMR (600 MHz, CDCl3, major
rotamer): 0.16–0.19 (2H, m), 0.46- 0.48 (2H, m), 0.88 (3H, d,
J = 6.6 Hz), 0.92–0.94 (1H, m), 0.95 (3H, d, J = 6.6 Hz), 1.66–1.76
(2H, m), 1.88–1.96 (3H, m), 2.43–2.46 (1H, m), 2.59–2.66 (2H, m),
3.02–3.08 (2H, m), 3.11–3.14 (1H, m), 3.71 (1H, d, J = 11.4 Hz), 4.17
(1H, ABd, J = 15.0 Hz), 4.25 (1H, ABd, J = 15.0 Hz), 6.91 (1H, s).
13C NMR (150 MHz, CDCl3, major rotamer): 3.4, 3.5, 10.6, 19.1,
20.0, 22.3, 23.0, 24.5, 25.9, 26.7, 44.3, 56.1, 73.8, 121.8, 128.6,
134.7, 140.7, 163.7, 168.4, 169.9.
N-(tert-butyl)-2-(3-isobutyl-2,5-dioxo-1,2,3,5,6,7,8,9-octa-
hydro-4H-[1]benzothieno [2,3-e][1,4]diazepin-4-yl)ace-
tamide (9f, Method A): The product was isolated by silica gel
chromatography (petroleum ether ⁄ ethyl acetate, 1:1) as yellowish
solids (11 mg, yield: 14% over three steps). HPLC ⁄ MS:
tR = 10.87 min; m ⁄ z = 406.2 [M+H]+ HRMS: 405.209380 (found);
N-benzyl-2-(3-isopropyl-2,5-dioxo-1,2,3,5,6,7,8,9-octahy-
dro-4H-[1]benzothieno[2,3-e][1,4]diazepin-4-yl)acetamide
(9c, Method C): The product was isolated by silica gel chromato-
graphy (petroleum ether ⁄ ethyl acetate, 1:1) as yellowish solids
(20 mg, yield: 24% over three steps). HPLC ⁄ MS: tR = 10.50 min;
1
C21H31N3O3S, 405.20861 (calcd.). H NMR (600 MHz, CDCl3, a mix-
ture of rotamers): 0.88–0.91 (6H, m), 0.93–0.98 (6H, m), 1.34 (9H,
s), 1.37 (5H, s), 1.47–1.50 (2H, m), 1.57–1.65 (3H, m), 1.71–1.75
(3H, m), 1.80–1.82 (2H, m), 1.90–1.93 (4H, m), 2.09 (1H, m), 2.45–
Chem Biol Drug Des 2010; 76: 130–141
133

¨
Huang and Domling
2.54 (2H, m), 2.63–2.71 (3H, m), 2.92 (1H, m), 3.07–3.11 (2H, m),
3.22 (1H, m), 3.32 (1H, m), 3.79 (1H, d, J = 15.6 Hz), 3.94 (1H, d,
J = 15.0 Hz), 4.12 (1H, d, J = 15.6 Hz), 4.18 (1H, m), 4.22 (1H, m),
4.31 (1H, d, J = 15.0 Hz), 6.35 (1H, s), 6.46 (1H, s). 13C NMR
(150 MHz, CDCl3, a mixture of rotamers): 22.0, 22.26, 22.28, 22.32,
22.4, 22.7, 22.8, 22.96, 23.02, 24.55, 24.59, 25.0, 25.1, 25.5, 25.7,
26.0, 28.6, 28.7, 35.0, 37.9, 42.7, 48.3, 50.5, 51.2, 51.3, 51.7, 52.0,
54.8, 56.1, 60.1, 65.1, 122.4, 122.7, 128.7, 129.5, 134.8, 135.0,
139.7, 141.0, 163.5, 165.9, 167.6, 168.2, 168.8, 170.4.
ide (0.2 mmol, 33.5 mg), triethylamine (0.2 mmol, 27.9 lL), aqueous
formaldehyde (0.2 mmol, 14.9 lL), tert-butyl isocyanide (0.2 mmol,
22.6 lL) in 0.5 mL of methanol was stirred under RT for 2 days.
The Ugi product was isolated by silica gel chromatography (petro-
leum ether ⁄ ethyl acetate, 5:1), then treated with 0.5 mL of DCM
(10% TFA). The reaction mixture was stirred under RT for 24 h.
After the evaporation of the solvent, the residue was treated with
triethylamine (100 lL) and TBD (10 mg) in 0.5 mL of THF, stirred
overnight under 40 ꢀC. The product was isolated by silica gel chro-
matography (petroleum ether ⁄ ethyl acetate, 1:1) as yellowish solids
(5 mg, yield: 7% over three steps). HPLC ⁄ MS: tR = 8.99 min;
m ⁄ z = 338.3 [M+H]+ HRMS: 337.145879 (found); C16H23N3O3S,
N-(tert-butyl)-2-[3-(4-hydroxyphenyl)-2,5-dioxo-1,2,3,5,6,
7,8,9-octahydro-4H-[1] benzothieno[2,3-e][1,4]diazepin-
4-yl]acetamide (9g, Method A): Sodium bicarbonate was
used for the workup instead of saturated potassium carbonate (aq).
The product was isolated by silica gel chromatography (petroleum
ether ⁄ ethyl acetate, 1:1) as yellowish solids (20 mg, yield: 23%
over three steps). HPLC ⁄ MS: tR = 9.53 min; m ⁄ z = 442.2 [M+H]+
HRMS: 441.173542 (found); C23H27N3O4S, 441.17223 (calcd.). 1H
NMR (600 MHz, CD3OD): 1.36 (9H, s), 1.50 (1H, m), 1.67–1.77 (3H,
m), 2.22 (1H, m), 2.46 (2H, m), 2.70 (1H, m), 2.85 (1H, m), 3.22 (1H,
m), 4.13 (1H, m), 4.64 (1H, m), 5.22 (1H, m), 6.62 (2H, m), 6.97 (2H,
m), 7.62 (1H, m). 13C NMR (150 MHz, CD3OD): 22.0, 22.7, 23.7,
25.2, 27.6, 34.1, 43.3, 51.0, 53.3, 63.5, 68.5, 114.8, 123.2, 124.2,
125.2, 128.2, 133.4, 140.3, 156.8, 164.7, 167.7, 170.6.
1
337.14601 (calcd.). H NMR (600 MHz, CDCl3, major rotamer): 0.94
(1H, d, J = 6.6 Hz), 0.98 (1H, d, J = 6.6 Hz), 1.34 (9H, s), 1.95 (1H,
m), 3.75 (1H, d, J = 9.6 Hz), 4.03 (1H, d, J = 15.0 Hz), 4.27 (1H, d,
J = 15.0 Hz), 6.44 (1H, m), 6.87 (1H, d, J = 6.0 Hz), 8.60 (1H, br.s).
13C NMR (150 MHz, CDCl3, major rotamer): 19.4, 19.9, 27.2, 28.6,
57.2, 73.7, 117.0, 123.8, 128.1, 142.3, 163.2, 167.0, 169.0.
N-(tert-butyl)-2-(2,5-dioxo-7-phenyl-1,2,3,5-tetrahydro-4H-
thieno[2,3-e][1,4] diazepin-4-yl)acetamide (10b): The mix-
ture of 6c (63.8 mg, 0.2 mmol), glycine methyl ester hydrochloride
(0.2 mmol, 25.0 mg), triethylamine (0.2 mmol, 27.9 lL), aqueous for-
maldehyde (0.2 mmol, 14.9 lL), tert-butyl isocyanide (0.2 mmol,
22.6 lL) in 0.5 mL of methanol was stirred under RT for 2 days.
The reaction was quenched by water, and extracted with DCM. The
organic layer was washed with saturated potassium carbonate (aq)
and dried over anhydrous sodium sulfate. After the evaporation of
the solvent, the residue was treated with 1.0 mL of DCM (10%
TFA), and stirred under RT for 24 h. After the evaporation of the
solvent, the residue was treated with triethylamine (200 lL) and
TBD (10 mg) in 0.5 mL of THF, stirred overnight under 40 ꢀC. The
product was isolated by silica gel chromatography (petroleum
ether ⁄ ethyl acetate, 2:1) as yellowish solids (8 mg, yield: 11% over
three steps). HPLC ⁄ MS: tR = 9.66 min; m ⁄ z = 372.1 [M+H]+ HRMS:
371.128759 (found); C19H21N3O3S, 371.13036 (calcd.). 1H NMR
(600 MHz, CD3OD): 1.37 (9H, s), 4.09 (2H, s), 4.21 (2H, s), 7.31–7.33
(1H, m), 7.40–7.42 (2H, m), 7.47 (1H, s), 7.58–7.59 (2H, m). 13C
NMR (150 MHz, CD3OD): 27.5, 50.9, 51.1, 52.9, 122.3, 123.3, 124.9,
127.7, 128.8, 133.0, 135.3, 165.0, 167.7, 168.7.
N-(tert-butyl)-2-[3-(1H-indol-3-ylmethyl)-2,5-dioxo-1,2,3,5,6,
7,8,9-octahydro-4H-[1] benzothieno [2,3-e][1,4]diazepin-4-
yl]acetamide (9h, Method A): The product was isolated by
silica gel chromatography (petroleum ether ⁄ ethyl acetate, 1:1) as
yellowish solids (15 mg, yield: 16% over three steps). HPLC ⁄ MS:
tR = 10.68 min; m ⁄ z = 479.3 [M+H]+ HRMS: 478.203784 (found);
1
C26H30N4O3S, 478.20386 (calcd.). H NMR (600 MHz, CDCl3, 1:1 mix-
ture of rotamers): 1.32 (9H, s), 1.38 (9H, s), 1.68–1.96 (8H, m),
2.53–2.65 (6H, m), 3.11–3.20 (4H, m), 3.36 (1H, m), 3.68 (1H, m),
3.86 (1H, m), 3.99–4.03 (2H, m), 4.18 (1H, m), 4.48–4.50 (2H, m),
6.01 (1H, s), 6.38 (1H, s), 6.89 (1H, s), 7.05 (1H, s), 7.09–7.13 (3H,
m), 7.18 (1H, m), 7.25 (1H, d, J = 7.8 Hz), 7.34 (1H, d, J = 7.8 Hz),
7.53 (1H, d, J = 7.8 Hz), 7.58 (1H, d, J = 7.8 Hz), 8.27 (1H, s), 8.52
(1H, s). 13C NMR (150 MHz, CDCl3, 1:1 mixture of rotamers): 22.2,
22.3, 22.4, 23.0, 24.3, 24.5, 24.6, 25.6, 26.3, 28.6, 28.7, 48.0, 51.36,
51.44, 55.6, 56.9, 67.1, 109.3, 110.2, 111.3, 111.4, 118.17, 118.23,
119.6, 122.00, 122.04, 122.1, 122.5, 123.4, 123.8, 126.8, 127.0,
128.8, 129.5, 134.6, 135.1, 135.9, 136.1, 140.0, 141.1, 163.3, 165.7,
167.6, 168.2, 168.7, 170.0.
Results and Discussion
Synthesis of 1,4-thienodiazepine-2,5-dione
scaffold
As 2-aminothiophenes are optimal starting materials for the synth-
esis of thienodiazepine backbone, we utilized the versatile Gewald
N-(tert-butyl)-2-(3-isopropyl-2,5-dioxo-1,2,3,5-tetrahydro-
4H-thieno[2,3-e][1,4] diazepin-4-yl)acetamide (10a): The
mixture of 6b (48.6 mg, 0.2 mmol), valine methyl ester hydrochlor-
S
R5
S
NH2
R5
R6
NHBoc
COOH
Boc O, DMAP (10 mol%)
(i)
2
(ii) KOH, EtOH, H2O
R6
CO2Me
6a, R5, R6 = (-CH2-)4; 48%
6b, R5, R6 = H; 31%
6c
5a, R5, R6 = (-CH2-)4
5
, R , R6 = H
5b
5c
, R5 = Ph, R6 = H; 47%
, R5 = Ph, R6 = H
Scheme 1: Synthesis of 6a-c.
134
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Scaffold Hopping by Gewald and Ugi-Deprotection-Cyclization Strategy
Table 1: Ugi-Deprotection-Cyclization approach for the synthesis of 1,4-thienodiazepine-2,5-diones from glycine methyl ester
Entry
R1
Oxo component
Formaldehyde
Product
Yield (%)
46a
7a
t-Bu
cyclopropyl
methyl
7b
7c
Formaldehyde
Formaldehyde
17a
phenyl ethyl
13a
7d
7e
t-Bu
t-Bu
Isobutylaldehyde
Cyclohexanone
15a
10a
7f
t-Bu
t-Bu
o-chloro-benzaldehyde
37b
7g
Benzylaldehyde
21
aMethod A, isolated yields (over three steps).
bMethod B, isolated yields (over two steps).
Chem Biol Drug Des 2010; 76: 130–141
135

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Huang and Domling
MCRs to prepare compounds 5a-c. We recently developed a gen-
eral synthetic protocol to synthesize Boc protected thiophene car-
boxylic acids 6a-c (Scheme 1) (32). In the first step, 2-
aminothiophenes 5a-c were obtained by the Gewald reaction of
cyclohexanone, 1,4-dithiane-2,5-diol, and phenylacetaldehyde,
respectively. In the second step, N-Boc thiophene carboxylic acids 6
were prepared by Boc protection of 5 and following hydrolysis
transformation. Hence, we intended to employ the bifunctional
orthogonally protected intermediates 6 and amino acid-derived
methyl esters for the synthesis of new TDZ scaffold via UDC
approach.
leucine, 4-hydroxy phenylglycine, tryptophan methyl esters as well
as several isocyanides are tolerant to this procedure. Compounds
9a–h were isolated by chromatography in 14–37% yield over three
steps. As TBD serves as the catalyst, racemization of chiral center
at amino acid nucleus is unclear (33).
We also investigated other aminothiophene backbones 6b and 6c
for the synthesis of TDZs (Table 3). The corresponding Ugi product
of 6b was isolated by chromatography in 46% yield. Compound
10a was obtained in 16% yield by the further transformation of
the Ugi product. A 10% solution of TFA in dichloromethane was
used for the deprotection step under a mild condition. Similarly,
compound 10b was isolated by chromatography in 11% yield over
three steps.
The synthetic method was designed to allow rapid access to TDZs
in just three steps from the variable precursor building blocks. Initi-
ally, we tried the Ugi reaction of 6a, tert-butyl isocyanide, formal-
dehyde, with glycine methyl ester hydrochloride in the presence of
triethylamine under room temperature for 48 h. After simple extrac-
tion workup, the intermediate Ugi product was subjected to depro-
tection with TFA and subsequent cyclization using a catalytic
amount of TBD (1,5,7-triazabicyclo[4.4.0]dec-5-ene). The product 7a
was isolated by chromatography in 46% yield over three steps. The
'three-step, one-separation' procedure was applied for the synthesis
of 7a-e with variable isocyanides and oxo components (Table 1).
Interestingly, compounds 7f and 7g were obtained in two steps
after the treatment with TFA. It's possible that the intramolecular
cyclization is favorable even without the treatment of TBD (29).
Conformation analysis of TDZ scaffold
NMR spectra of some compounds substituted with amino acid side
chains show clearly the presence of two rotamers, which are not
chromatographically separable. For instance, compounds 9d, 9e,
and 9h show two rotamers at a ratio of 1:1 in CDCl3. The popula-
tion of rotamers was found related to the deuterium solvent used.
For example, the ratio of 9d shows roughly 2:3 in CD3OD (Fig-
ure S1 in Supporting Information). This observation suggests that
seven-membered diazepine nucleus of thienodiazepinedione is quite
rigid, similar to the scaffold of benzodiazepinediones (34,35). The
energy barrier for the interconversion of benzodiazepinedione con-
formers (pseudo-axial and pseudo-equatorial conformers) was calcu-
lated up to 14.8 kcal ⁄ mol (11). We also speculate that 1,4-
thienodiazepine ring inversion is slow enough, therefore conformers
can be detected by NMR under room temperature.
Next, we investigated a series of amino acid methyl esters for the
synthesis of new TDZ scaffolds. We tried the Ugi reaction of 6a,
tert-butyl isocyanide, formaldehyde with valine methyl ester hydro-
chloride in the presence of triethylamine under room temperature
for 24 h (Scheme 2). The Ugi product 8 was isolated by chromato-
graphy in 69% yield. The deprotection of 8 and the following cycli-
zation afford 9a in 59% yield over two steps (41% over three
steps). Running the sequence without any isolation yielded com-
pound 9a 23%. Although the overall yield is lower, the 'three-step,
one-separation' procedure avoids the additional separation step.
Recently, we used MCR methods to develop a-helix mimetics,
which could become very important lead structures to (ant-)ago-
nize protein–protein interactions (36). In our ongoing interest for
the application of peptidomimetic structures generated from
MCRs, the design and synthesis of peptide b-turn mimetic scaf-
folds and libraries are also desirable (37). A b-turn is most often
defined as any tetrapeptide unit occurring in a non-helical region
that causes a reversal of the direction of the peptide chain
Hence, 6a was applied to UDC approach for the synthesis of TDZs
with variable amino acid derivatives (Table 2). Valine, phenylalanine,
S
NHBoc
COOMe
S
NC
NHBoc
N
MeOH, Et3N
RT, 24 h
+
COOMe
HCHO
+
+
O
O
H2N
HCl
COOH
69%
NH
8
H
S
N
O
O
TFA, 40 oC, overnight
(i)
N
TBD, Et N, THF
3
(ii)
O
40 oC, overnight
59%
NH
9a
Scheme 2: Synthesis of 9a.
136
Chem Biol Drug Des 2010; 76: 130–141

Scaffold Hopping by Gewald and Ugi-Deprotection-Cyclization Strategy
Table 2: 1,4-Thienodiazepine-2,5-diones from the variation of amino acids
Entry
R1
Amino acid
Valine
Product
Yield (%)
23b
9a
t-Bu
9b
9c
cyclopropyl methyl
Valine
Valine
21b
benzyl
24b
9d
9e
9f
t-Bu
cyclopropyl methyl
t-Bu
Phenylalanine
Phenylalanine
Leucine
21a
37a
14a
9g
9h
t-Bu
t-Bu
4-hydroxy phenylglycine
23a
Trptophan
16a
aMethod A, isolated yields (over three steps).
bMethod C, isolated yields (over three steps).
Chem Biol Drug Des 2010; 76: 130–141
137

¨
Huang and Domling
Table 3: 1,4-Thienodiazepine-2,5-diones from the variation of aminothiophenes
Entry
10a
R5
H
R6
H
Amino acid
Valine
Product
Yielda (%)
7
10b
Ph
H
Glycine
11
aisolated yields, over three steps.
A
B
C
Figure 4: (A) Structure of a typical b-turn. The PDB code for the protein is 1H2C (chain A, turn region Ile142-Pro146). (B) The core scaffold
was chosen as a model of the investigated b-turn mimetic. (C) Minimized conformation of core scaffold as a b-turn mimetic superimposed
onto a type II b-turn. For clarity, only the backbone and a atoms are shown.
(Figure 4A) (38). As 1,4-benzodiazepines were found to act as b-
turn mimetics (7–9), we speculate that our TDZ scaffold could
also have b-turn mimetic moiety. Thus, the tripeptide fragment
of TDZ scaffold was compared with known protein b-turns (Fig-
ure 4). The core scaffold was investigated as a model superim-
posed onto a type II b-turn backbone (PDB code: 1H2C, turn
region Ile142-Pro146).
These compounds generated from the virtual library were intro-
duced into Instant JChem (Instant JChem 2.5.1, 2009, www.chemax-
on.com) for calculating their physical properties. The distributions of
this random virtual library (N = 50 000) and commercial available
benzodiazepines (N = 2498) were presented in Figure 5. This new
scaffold covers unexplored chemical space of benzodiazepine family.
Owing to the diversity of chemical space, this scaffold is potentially
useful for virtual screening and lead discovery.
Cheminformatics study of TDZ scaffold
To evaluate the potential of combinatorial library design, the physi-
cochemical properties of the virtual compound library (N = 50 000)
were calculated (40). The data were analyzed statistically by fre-
quency distributions in PASW Statistics 18 (Figure S2 in Supplemen-
tal Information). Because of the diversity of reactant components,
the range of molecular weight is between 267.3 Da. and 580.7 Da.
Owing to in silico and computational advances, chemoinformatics
would help to identify promising scaffolds of greater importance in
lead discovery (39). We generated a virtual compound library
(N = 50 000) from a random sample of starting materials to evalu-
ate the chemical space of the TDZs (Supplemental Information).
138
Chem Biol Drug Des 2010; 76: 130–141

Scaffold Hopping by Gewald and Ugi-Deprotection-Cyclization Strategy
A
B
Figure 5: Comparison of chemical space distribution: (A) benzodiazepine library of a substructure search from eMolecules (N = 2498); (B)
a random virtual library of 1,4-thienodiazepine-2,5-diones (N = 50 000).
Table 4: Physicochemical properties of synthesized compounds (N = 17) and a random virtual library (N = 50 000)a
Total polar
Number of
rotatable bonds
Hydrogen
bond acceptors
Hydrogen
bond donors
Mean
MW (Da)
LogP
surface area (ꢀ2)
Synthesized compounds
Virtual library
407.1 € 40.7
453.7 € 44.1
3.73 € 0.94
2.46 € 1.84
108.9 € 6.0
149.6 € 27.3
4 € 1
7 € 2
4 € 0
6 € 1
2 € 0
3 € 1
aAll values listed are mean value € standard deviation.
A
B
O
O
H
N
H
N
S
R4
R3
R4
R3
R1
R1
N
N
O
O
O
O
NH
NH
R2
R2
O
H
N
O
H
N
HN R3
O
HN R3
O
S
R1
N
R1
N
R2
O
R2
O
R4
C
R2
O
R2
R1
R3
R3
O
HN
O
O
O
HN R3
X
Y
N
N
O2N
N
O
R4
N
R1
N
R1
R2
N
N
O
N
R2
R3
R1
O
Figure 6: (A) Known structures; (B) multicomponent reaction (MCR) accessible isosteric azepine scaffolds; (C) Other MCR accessible benzo-
diazepines. The scaffold space of benzodiazepines accessible by MCR is very rich. Six different scaffolds can be synthesized using different
isocyanide-based MCR strategies. Of the bioisosteric thienodiazepines currently only two scaffolds are generally amenable by MCR. Armstrong
et al. (28,42), Hulme et al. (43), Tempest et al. (44), Marcaccini et al. (45) and Zhu et al. (46).
The mean of LogP is 2.46 with standard deviation of 1.84, which
indicates acceptable permeability of most compounds. Total polar
surface area of the majority of compounds is between 122.3 ꢀ2
and 176.9 ꢀ2. The mean number of rotatable bonds (NRB), hydrogen
bond acceptors (HBA), and hydrogen bond donors (HBD) are shown
in Table 4. In terms of drug likeness, 79.7% of 50 000 compounds
obey Lipinski's rule. And 93.7% of them are predicted to be bioa-
vailable (mass £ 500, LogP £ 5, HBD £ 5, HBA £ 10, polar surface
Chem Biol Drug Des 2010; 76: 130–141
139

¨
Huang and Domling
area £ 200, NRB £ 10, fused aromatic rings £ 5). For comparison,
the physicochemical properties of synthesized compounds (N = 17)
and a random virtual library (N = 50 000) were summarized in
Table 4. The structure-property relationship indicates the rationale
of diversity-oriented library design with drug-like properties. More-
over, 3D structures of a random virtual library were generated by
the software Omega (Supplemental Information). The compound
library of this new thienodiazepine scaffold (N = 5000) could be
used for docking program and other virtual analysis software to dis-
cover possible hits of suitable receptors.
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clinical candidates R1 15777 (Tipifarnib) and BMS-214662 com-
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Scaffold Hopping
Isofunctional molecules based on different chemical scaffolds are
key to the early drug development process. Leads based on differ-
ent scaffolds can be found by a process called scaffold hopping
(41). This process can rely on known or intuitive bioisosteres or on
advanced chemoinformatic strategies. Early development of several
leads based on different scaffolds has the advantage of reducing
the very high attrition rate in preclinical and early clinical develop-
ment. Additionally, scaffold hopping has great implications for the
maintenance of intellectual property. For example, for the benzodia-
zepine scaffold 4672 structures are registered in SciFinder, whereas
only 381 thienodiazepines are known (Figure 6A). We described
here two thienodiazepine scaffolds with different 2D and 3D distri-
bution of HBD and acceptors. They are clearly related to their ben-
zodiazepine scaffolds amenable by the UDC method (Figure 6B,C).
The chemical space behind the four related scaffolds is, however,
very much different, as the thiophene building block allows for
many more simple variations based on the versatile Gewald MCR.
9. Rosenstrom U., Skold C., Lindeberg G., Botros M., Nyberg F.,
Karlen A., Hallberg A. (2006) Design, synthesis, and incorporation
of a beta-turn mimetic in angiotensin II forming novel pseudo-
peptides with affinity for AT1 and AT2 receptors. J Med
Chem;49:6133–6137.
Conclusions and Future Directions
10. McDowell R.S., Blackburn B.K., Gadek T.R., McGee L.R., Rawson
T., Reynolds M.E., Robarge K.D., Somers T.C., Thorsett E.D.,
Tischler M., Webb R.R., Venuti M.C. (2002) From peptide to non-
peptide. 2. The de novo design of potent, non-peptidal inhibitors
of platelet aggregation based on a benzodiazepinedione scaf-
fold. J Am Chem Soc;116:5077–5083.
11. Loudni L., Roche J., Potiron V., Clarhaut J., Bachmann C., Gesson
J.-P., Tranoy-Opalinski I. (2007) Design, synthesis and biological
evaluation of 1,4-benzodiazepine-2,5-dione-based HDAC inhibi-
tors. Bioorg Med Chem Lett;17:4819–4823.
In summary, we have synthesized a series of TDZs by using the
union of Gewald reaction and UDC strategy. This approach pos-
sesses novel hybrid peptidomimetic 1,4-diazepines with well-defined
diversity, which can be achieved from readily available starting
materials. UDC strategy allows convenient preparation of TDZs
without using the traditional peptide coupling methods. Similar to
the compound libraries of benzodiazepines, the TDZ scaffold could
also be suitable for high-dimensional combinatorial synthesis to
meet the screening purpose. The conformation analysis and
chemical space of this novel scaffold was studied. Based on the
commonly accepted descriptors, it is potentially useful to obtain
lead-like compounds based on this scaffold.
12. Carlier P.R., Zhao H., MacQuarrie-Hunter S.L., DeGuzman J.C.,
Hsu D.C. (2006) Enantioselective synthesis of diversely substi-
tuted quaternary 1,4-benzodiazepin-2-ones and 1,4-benzodiaze-
pine-2,5-diones. J Am Chem Soc;128:15215–15220.
13. Goff D.A., Zuckermann R.N. (1995) Solid-phase synthesis of
Acknowledgment
defined 1,4-benzodiazepine-2,5-dione mixtures.
Chem;60:5744–5745.
J
Org
This work was supported by the NIH grant 1R21GM087617-01 (to
AD) and is part of a NCI-RAND program.
14. Alig L., Chucholowski A., Weller T. (2001) Benzazepinone and
quinazoline derivatives inhibiting the binding of adhesive pro-
teins to vitronectin receptors. WO2001004103.
15. Parks D.J., LaFrance L.V., Calvo R.R., Milkiewicz K.L., Marugan
J.J., Raboisson P., Schubert C., et al. (2006) Enhanced pharma-
cokinetic properties of 1,4-benzodiazepine-2,5-dione antagonists
of the HDM2-p53 protein-protein interaction through structure-
based drug design. Bioorg Med Chem Lett;16:3310–3314.
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Appendix S1. Supplemental information.
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Figure S1. NMR spectra of compound 9d in CDCl3 and CD3OD.
Figure S2. Statistical distributions of physical properties of a ran-
dom virtual library (N = 50 000).
Please note: Wiley-Blackwell is not responsible for the content or
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Any queries (other than missing material) should be directed to the
corresponding author for the article.
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