Parallel synthesis of an imidazole-4,5-dicarboxamide library bearing amino acid esters and alkanamines

Article abstract of DOI:10.3390/molecules13123149

The imidazole-4,5-dicarboxylic acid scaffold is readily derivatized with amino acid esters and alkanamines to afford compounds with intramolecularly hydrogen bonded conformations that mimic substituted purines and therefore are hypothesized to be potential inhibitors of kinases through competitive binding to the ATP site. In this work, a total of 126 dissymmetrically disubstituted imidazole-4,5-dicarboxamides with amino acid ester and alkanamide substituents were prepared by parallel synthesis. The library members were purified by column chromatography on silica gel and the purified compounds characterized by LC-MS with LC detection at 214 nm. A selection of the final compounds was also analyzed by ¹H-NMR spectroscopy. The analytically pure final products have been submitted to the Molecular Library Small Molecule Repository (MLSMR) for screening in the Molecular Library Screening Center Network (MLSCN) as part of the NIH Roadmap.

Full text of DOI:10.3390/molecules13123149

Molecules 2008, 13, 3149-3170; DOI: 10.3390/molecules13123149
OPEN ACCESS
molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
Parallel Synthesis of an Imidazole-4,5-dicarboxamide Library
Bearing Amino Acid Esters and Alkanamines
Rosanna Solinas, John C. DiCesare and Paul W. Baures *
Department of Chemistry and Biochemistry, The University of Tulsa, 800 South Tucker Drive, Tulsa,
OK 74104, USA; E-mail: rosannasolinas@yahoo.it (R. S.); john-dicesare@utulsa.edu (J-C. D.)
* Author to whom correspondence should be addressed; E-mail: paul-baures@utulsa.edu
Received: 20 November 2008; in revised form: 11 December 2008 / Accepted: 12 December 2008 /
Published: 15 December 2008
Abstract: The imidazole-4,5-dicarboxylic acid scaffold is readily derivatized with amino
acid esters and alkanamines to afford compounds with intramolecularly hydrogen bonded
conformations that mimic substituted purines and therefore are hypothesized to be
potential inhibitors of kinases through competitive binding to the ATP site. In this work, a
total of 126 dissymmetrically disubstituted imidazole-4,5-dicarboxamides with amino acid
ester and alkanamide substituents were prepared by parallel synthesis. The library
members were purified by column chromatography on silica gel and the purified
compounds characterized by LC-MS with LC detection at 214 nm. A selection of the final
1
compounds was also analyzed by H-NMR spectroscopy. The analytically pure final
products have been submitted to the Molecular Library Small Molecule Repository
(MLSMR) for screening in the Molecular Library Screening Center Network (MLSCN) as
part of the NIH Roadmap.
Keywords: Imidazole; NIH Roadmap; Heterocyclic scaffold; Drug discovery.
Introduction
There remains a need for selective small molecule probes of biological processes in order to discern
cellular communication and signaling pathways, as well as for potential application as therapeutic
agents against diseases [1-4]. In general, the most useful biological probes will also meet the

Molecules 2008, 13
3150
parameters commonly found for drugs or drug-like molecules, including Lipinski’s “rule of five” [5]
and the number of rotatable bonds [6], since such parameters are indications of solubility and cellular
permeability [7]. There is nonetheless a growing awareness that biological probes or chemical tools
will often violate one or more of these rules, but that this does not necessarily void the usefulness of
the compounds to medicinal research [8].
Imidazole-4,5-dicarboxylic acid (I45DA) is a scaffold that is readily derivatized with amines to
yield imidazole-4,5-dicarboxamides (I45DCs) [9]. Primary amines and amino acid esters retain an N-H
bond in the final compound that forms a strong intramolecular hydrogen bond [9-12]. The quasi ring,
in combination with the imidazole and substituents, then affords a product that is a reasonable mimic
of a substituted purine [9], an important class of small molecule biological probes [13].
We have previously reported on methods to synthesize dissymmetrically disubstituted imidazole-
4,5-dicarboxamides (dI45DCs) with different primary alkanamides [14], anilines with either
alkanamines or amino acid esters [15], or combinations of amino acid esters and alkanediamines to
create bis-I45DCs [16]. The synthetic strategies to these I45DC derivatives are different (Figure 1).
The dI45DCs with only alkanamine substituents proceed through an imidazole phenyl ester-
carboxamide substituted intermediate [14], while the dI45DCs substituted with an aniline and bis-
I45DCs are synthesized from aniline and amino acid ester substituted pyrazines [15,16], respectively.
Figure 1. The synthetic intermediates to dissymmetrically disubstituted imidazole-4,5-
dicarboxamides, including those bearing a) different primary alkanamines, b) anilines with
alkanamies or amino acid esters, as well as c) amino acids esters and alkanamines leading
to bis-I45DCs.
a
N
R1
O
H
O
O
R2
H
R1
O
N
H
O
N
N
O
N
N
O
O
O
O
N
N
O
N
N
H
N
H
b
c
H
N
R
N
R
H
N
N
O
O
R2
N
O
N
O
O
R1
O
R
N
N
N
N
H
H
H
N
N
O
H
R2
N
R
O
N
O
O
R1
O
N
n
N
N
O
N
R2
R1
O
O
H
R1
O
O
O
O
H
O
R2
N
R1
O
N
N
O
O
R2
R
N
H
N
N
H

Molecules 2008, 13
3151
The library reported herein combines amino acid ester substituents with alkanamines to produce
dI45DCs where no structural examples have been previously reported in the literature. In the process
of completing this library we have also improved on the synthetic methods to yield the amino acid
ester pyrazine intermediates. The final compounds are all of analytical purity and have been submitted
to the Molecular Library Small Molecule Repository (MLSMR) for use in the Molecular Library
Screening Center Network (MLSCN) as part of the NIH Roadmap [2, 17]. We have included tables of
data (formula, molecular weight, clogP values, physical form of the compound, Rf values, and
retention times in the LC-MS) for library members 5{1-126}, LC-MS spectra for all library members,
1
LC-MS data for 18 reactions to crude library members, as well as H-NMR spectra for the crude
reactions and purified library members for 18 representative compounds in a supporting file. The same
information is also available for each compound at the project website [18]. Additional synthetic
efforts that are part of the NIH Roadmap are now being reported [19-31].
Results and Discussion
The building blocks for this library were selected as a minimal set that would maximize chances for
identifying biologically active leads through the screens conducted by the MLSCN. All of the
dI45DCs in this library are expected to favor an intramolecular hydrogen bonded conformation by
analogy to similar compounds, and thereby the presentation of the building blocks in space is
predisposed [9-12]. Thus, the overall shape of the library members is similar and the selected library
building blocks vary the size, electrostatic, and hydrophobic characteristics of the library members
within a range of values that are considered “drug-like” [5,6].
Table 1. Amino acid ester salts, 2{1-9}, used in library synthesis.
R1
O
X H3N
R2
O
2{1-9}
membe
r
R1
R2
X
C(CH3)
2{1}
2{2}
2{3}
2{4}
2{5}
2{6}
2{7}
2{8}
2{9}
H
Cl
H
CH2Ph
C(CH3)
Cl
Cl
Cl
CH3
CH3
CH2Ph
CH2CH(CH3) C(CH3)
Cl
CH2CH(CH3)
CH2Ph
OSO2C6H4CH
C(CH3)
CH2Ph
Cl
Cl
Cl
CH2Ph
CH2Ph
C(CH3)
(CH2)4NH2

Molecules 2008, 13
3152
Table 2. Alkanamines, 4{1-14}, used in library synthesis.
HNR3R4
membe
R3
R4
r
4{1}‡
H
CH3
(CH2)4NH-Boc
CH2Ph
4{2}
H
4{3}
H
4{4}
H
R-CH(CH3)Ph
S-CH(CH3)Ph
[CH(CH2CH2)2N-Boc
CH2C6H4CH2NH-Boc
CH(Ph)2
4{5}
H
4{6}
4{7}‡
H
H
4{8}
H
4{9}
CH3
CH2CH3
CH2Ph
4{10}
4{11}
4{12}
4{13}
4{14}‡
CH2CH3
(CH2CH2)2N-Boc
(CH2)(CH2CH2)C6H4
(CH2CH2)2CHCH3
(CH2CH2)2N-Ph
‡These alkanamines were used as their hydrochloride salts.
The amino acid ester variations (Table 1) included no side chain (Gly, 2{1,2}), a smaller (Ala,
2{3,4}) and larger (Leu, 2{5,6}) aliphatic side chain, and an aromatic side chain (Phe, 2{7,8}) all with
either a tert-butyl ester or benzyl ester, as well as a Boc protected polar side chain (Lys, 2{9}) with a
tert-butyl ester. Likewise, the alkanamine building blocks (Table 2) include a small and large aliphatic
chain, aromatic amines with or without chirality, cyclic amines, and both primary and secondary
amines. These selected building blocks create dI45DC library members with drug-like properties as
illustrated by their molecular weights that range from 282−612 g/mol and an average value of 450
g/mol, as well as their cLogP values that range from -0.88−4.67 and an average value of 2.62.
The synthetic strategy to the pyrazine intermediates and final dI45DCs is shown in Scheme 1. The
starting pyrazine diacid chloride, 1, was prepared as previously described [8]. Reaction of 1 with two
equivalents of amino acid ester hydrochloride or tosylate salt, 2{1-9}, and four equivalents of N,N-
diethylaniline as a scavenger for the acid in the reaction produced good to excellent yields (76-93%) of
the intermediate amino acid ester substituted pyrazines 3{1-9} (Table 3). The reactions between these
intermediates and amines 4{1-14} were performed in culture tubes in parallel with diisopropylethyl-
amine added to those reactions with an alkanamine hydrochloride salt, 4{1,7,14}. Two equivalents of
alkanamine (or alkanamine hydrochloride with the tertiary amine base) were used except in the case of
methylamine hydrochloride, 4{1}, where a total of four equivalents were used due to the increased
volatility of the free alkanamine. The products, 5{1-126}, were obtained in low to excellent yields (20-
96%) following purification by silica gel chromatography (Table 4).

Molecules 2008, 13
3153
Scheme 1. Synthetic Strategy to Library Members.
N
Cl
R1
N
N
1
O
O
O
O
X H3N
R2
+
O
Cl
O
N
2{1-9}
diethylaniline
CH2Cl2
-78 °C
rt
O
H
R2
N
N
O
N
N
O
R1
O
R1
O
O
N
O
R2
N
H
O
3{1-9}
HNR3R4,
CH2Cl2
4{1-14}
[ EtN(iPr)2 ]
R1
O
O
H
R3
O
R2
N
N
O
R4
N
N
H
5{1-126}
Table 3. Pyrazines Substituted with Amino Acid Esters, 3 {1-9}.
amino
acid ester
yield
(%)
compound
3{1}
3{2}
3{3}
3{4}
3{5}
3{6}
3{7}
3{8}
3{9}
2{1}
2{2}
2{3}
2{4}
2{5}
2{6}
2{7}
2{8}
2{9}
86
91
87
93
83
87
86
87
76

Molecules 2008, 13
Table 4. Amino Acid Ester—Alkanamine Disubstituted I45DCs, 5{1-63}.
3154
yield
(%)
yield
(%)
yield
(%)
cmpd
reactants
3{1}
cmpd
reactants
3{4}
cmpd
reactants
5{1}
5{2}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
36
65
55
90
53
42
91
88
49
39
47
52
49
74
25
37
50
49
50
43
79
75
50
35
43
45
34
67
77
58
53
52
45
41
93
92
5{43}
5{44}
5{45}
5{46}
5{47}
5{48}
5{49}
5{50}
5{51}
5{52}
5{53}
5{54}
5{55}
5{56}
5{57}
5{58}
5{59}
5{60}
5{61}
5{62}
5{63}
5{64}
5{65}
5{66}
5{67}
5{68}
5{69}
5{70}
5{71}
5{72}
5{73}
5{74}
5{75}
5{76}
5{77}
5{78}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
62
50
44
37
38
35
65
70
49
35
48
38
31
73
77
41
42
45
20
23
74
85
29
53
37
55
31
67
71
58
46
46
39
44
83
89
5{85}
5{86}
3{7}
4{1}
78
69
90
76
66
57
93
80
62
73
42
36
54
79
62
57
55
38
40
42
93
80
54
21
52
51
40
82
50
55
56
48
42
32
90
93
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{1}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{2}
3{3}
3{3}
3{3}
3{3}
3{3}
3{3}
3{3}
3{3}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{4}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{5}
3{6}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
4{1}
4{2}
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
3{7}
3{7}
3{7}
3{7}
3{7}
3{7}
3{7}
3{7}
3{7}
3{7}
3{7}
3{7}
5{3}
5{87}
5{4}
5{88}
5{5}
5{89}
5{6}
5{90}
5{7}
5{91}
5{8}
5{92}
5{9}
5{93}
5{10}
5{11}
5{12}
5{13}
5{14}
5{15}
5{16}
5{17}
5{18}
5{19}
5{20}
5{21}
5{22}
5{23}
5{24}
5{25}
5{26}
5{27}
5{28}
5{29}
5{30}
5{31}
5{32}
5{33}
5{34}
5{35}
5{36}
5{94}
5{95}
5{96}
5{97}
5{98}
3{7}
3{8}
5{99}
5{100}
5{101}
5{102}
5{103}
5{104}
5{105}
5{106}
5{107}
5{108}
5{109}
5{110}
5{111}
5{112}
5{113}
5{114}
5{115}
5{116}
5{117}
5{118}
5{119}
5{120}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{8}
3{9}
3{6}
3{6}
3{6}
3{6}
3{6}
3{6}
3{6}
3{9}
3{9}
3{9}
3{9}
3{9}
3{9}
3{9}

Molecules 2008, 13
3155
Table 4. Cont.
5{37}
5{38}
5{39}
5{40}
5{41}
5{42}
3{3}
3{3}
3{3}
3{3}
3{3}
3{3}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
39
46
38
50
37
96
5{79}
5{80}
5{81}
5{82}
5{83}
5{84}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
54
51
50
56
42
93
5{121}
5{122}
5{123}
5{124}
5{125}
5{126}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
43
45
48
44
41
91
3{6}
3{6}
3{6}
3{6}
3{6}
3{6}
3{9}
3{9}
3{9}
3{9}
3{9}
3{9}
There are no obvious patterns evident in the purified yields when analyzed by either amino acid
ester or alkanamine (Table 5). Instead, the yield range, average, and median are largely alike in each
of these comparisons except for three alkanamines, 4{7,8,14}, which gave an 80% or higher average
yield.
The major impurity present in the crude reactions is an imidazole-4,5-dicarboxylic acid substituted
with only the amino acid ester (an imidazole carboxamide−carboxylic acid substituent combination).
The strongest evidence for this side product is from LC-MS analysis, where the crude reactions show
both the desired product and a faster eluting compound with an observed m/z that is expected for this
structure. This impurity is hypothesized to result from an incomplete reaction between alkanamines 4
and the intermediate pyrazines 3 or competitive hydrolysis of the pyrazine due to adventitious water or
both. We see no evidence of this carboxylic acid impurity in the 1H-NMR spectra of the pyrazines, 3,
lending us to think that the impurity forms during the purification process of the final compounds or in
the reactions to yield these compounds, and not during the washing and isolation steps in the pyrazine
synthesis. Indeed, there are many final compounds from the pyrazines that give excellent yields of the
1
final product, supporting the purity of these intermediates. The H-NMR spectrum of purified library
members is comparable to the spectrum for the corresponding crude reaction and further supports the
presence of only the hydrolysis product of the pyrazine, and suggests it forms during the reactions to
the final products. We have not quantified the level of this impurity in these crude reactions, although
the ratio of peaks observed at 214 nm suggests that it is substantial in most reactions.
Table 5. Yields of purified library members based on amino acid esters,
2{1-9}, and alkanamines, 4{1-14}.
membe
low
high
average median
r
2{1}
2{2}
2{3}
2{4}
2{5}
2{6}
2{7}
2{8}
2{9}
36
25
37
31
20
39
36
21
32
91
79
96
73
85
93
93
93
93
59
49
58
48
49
59
68
55
56
53
47
51
46
44
53
71
53
48

Molecules 2008, 13
3156
Table 5. Cont.
4{1}
4{2}
25
37
42
37
20
23
65
70
29
21
37
36
31
67
78
69
90
90
66
57
93
93
62
73
52
56
54
96
60
54
55
53
44
40
85
84
48
44
45
47
40
80
62
57
53
48
42
42
90
85
49
45
47
50
40
79
4{3}
4{4}
4{5}
4{6}
4{7}
4{8}
4{9}
4{10}
4{11}
4{12}
4{13}
4{14}
All of the library members have been submitted to and accepted into the MLSMR for screening by
the MLSCN. At the time of this writing, compounds in this library have shown bioactivity against
calpain II and in cell based assays that measure an arbovirus challenge, Leishmania major
promastigote inhibition, as well as levels of Amyloid Precursor Protein (APP) translation. The current
biological data is best accessed through the PubChem database [32] by searching the SID
identification numbers within “PubChem Substance.” Table 6 provides the compound number in this
report with the corresponding PubChem SID numbers. PubChemSR is software that operates in a
Windows environment and may be useful in helping researchers mine the data found in PubChem [33].
Table 6. Cross reference guide for library members with the PubChem
database (SID identification number).
PubChem
SID‡
PubChem
SID‡
cmpd
cmpd
5{1}
5{2}
5{3}
5{4}
5{5}
5{6}
5{7}
5{8}
5{9}
5{10}
5{11}
49714445
49733433
49714444
49714441
49731971
49714443
49731972
49714442
49731973
49733435
49714448
5{64}
5{65}
5{66}
§,&5{67}
5{68}
5{69}
5{70}
5{71}
5{72}
5{73}
5{74}
24833560
24833894
24833104
24833105
26732529
26732544
26732517
24833022
24833022
24833129
24833126

Molecules 2008, 13
3157
Table 6. Cont.
5{12}
5{13}
5{14}
5{15}
5{16}
5{17}
5{18}
5{19}
5{20}
5{21}
5{22}
5{23}
5{24}
5{25}
5{26}
5{27}
5{28}
5{29}
5{30}
5{31}
5{32}
5{33}
5{34}
5{35}
5{36}
5{37}
5{38}
5{39}
5{40}
5{41}
5{42}
5{43}
5{44}
5{45}
5{46}
5{47}
5{48}
49714446
49714447
49734318
49731969
50096422
49714435
49714431
49714432
49714434
49714436
49714433
49714439
49714438
49714440
49714437
49731970
49733434
24833676
24833109
24833559
24833114
24833781
24833951
24833140
24833558
50091475
24834116
50091476
26732545
26732528
26732527
26724151
24834138
49713841
26724154
50096424
24833780
†5{75}
¶,$5{76}
26724165
24833555
49713839
24833096
24833112
24833110
24833889
26732526
26732522
26732523
24833099
50091477
24833779
24833101
24833100
24833102
49714426
50096423
49733432
49714430
49734317
49714427
49714429
49714428
24833131
24833885
24833127
24833128
24833130
24833095
49714449
24834139
24833125
24833678
49734320
26732513
50096425
5{77}
5{78}
5{79}
5{80}
5{81}
5{82}
5{83}
5{84}
5{85}
5{86}
5{87}
#5{88}
5{89}
5{90}
5{91}
5{92}
5{93}
5{94}
5{95}
5{96}
5{97}
5{98}
5{99}
^,*5{100}
*5{101}
5{102}
5{103}
5{104}
5{105}
5{106}
5{107}
5{108}
5{109}
5{110}
5{111}

Molecules 2008, 13
3158
Table 6. Cont.
5{49}
5{50}
5{51}
5{52}
5{53}
5{54}
5{55}
5{56}
5{57}
†5{58}
†5{59}
5{60}
5{61}
5{62}
5{63}
50091474
26724153
24833694
24833113
49731978
26732519
26732548
49733437
24833796
24833891
24833103
24833557
24833561
24833108
49713840
†5{112}
26732521
24833107
24833556
24833677
24833106
26732518
26724152
49713842
24833097
24834137
24833692
24833098
26732532
26732530
26732543
5{113}
†5{114}
#5{115}
†5{116}
5{117}
5{118}
5{119}
5{120}
%5{121}
5{122}
5{123}
5{124}
5{125}
5{126}
‡The PubChem information for each library member, along with the current bioassay results, can be
found by inserting the appropriate SID number into the spaces indicated by ######### in the link:
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid=########&loc=ec_rcs. Since each
submission of a compound results in a unique PubChem SID number, it is useful to search for other
samples of the same compound under the link “Related Structures.” Biological data may be listed
†
for one sample of a compound and not for other samples of the same compound; These
compounds have shown activity against calpain II; §These compounds have shown activity against
¶
an arbovirus challenge; These compounds have shown Leishmania major promastigote inhibition;
&These compounds have shown inhibition of Amyloid Precursor Protein (APP) translation; #These
compounds have been “cherry picked” for further biological assessment and the results are pending
at the time of this writing; %This compound is active as a small molecule regulator of Bcl-2 family
$
protein interactions; This compound is active as a potentiator or agonist of neuropeptide Y
^
receptor Y2; This compound is active as a potentiator or agonist of neuropeptide Y receptor Y1;
*This compound actively inhibits the RAM network.
Experimental
General
All apparatus was oven-dried and cooled in a desiccator. All reagents were purchased from
commercial suppliers and used without further purification. Reagent grade CH2Cl2 was distilled from
CaH2 before use. Thin layer chromatography (TLC) was performed on 250 µm glass-backed silica gel
plates and visualized using UV. Column chromatography was performed on silica gel (Merck, grade
9385, 230-400 mesh, 60 Å). The columns were prepared in plastic 20 or 30 mL syringe bodies and
filled to approximately 2/3 of their capacity with silica gel. This column volume was sufficient for
purification of most reaction products because the most substantial impurity is the imidazole-4,5-

Molecules 2008, 13
3159
dicarboxylic acid substituted with a carboxamide and carboxylic acid that absorbs strongly to silica
gel. In select cases, a second column was necessary in order to achieve analytically pure material.
Melting points were determined in glass capillary tubes and are uncorrected. The names of the final
compounds are provided in Table 7 at the end of the experimental section.
LC-MS Analysis
Characterization of the purity and identity of the library members was carried out by liquid
chromatography-mass spectrometry (LC-MS) using a Varian 500-MS LC Ion Trap mass spectrometer.
Solutions of the compounds were prepared at an approximate concentration of 1 mg/mL by first
adding <10% by volume of CH2Cl2 to dissolve the sample and then diluting to the final volume with
HPLC grade methanol. Five microliters of the sample was injected onto a Polaris 5 μm C18-A
(50×2.0 mm) HPLC column and eluted with a gradient of CH3CN/H2O containing 0.1% CH3CO2H at a
0.2 mL/min flow rate. Compounds were detected at 214 nm. The gradient was as follows: 0 min., 4:6
CH3CN/H2O → 1 min., 4:6 CH3CN/H2O → 6 min., 9:1 CH3CN/H2O → 8 min., 9:1 CH3CN/H2O → 9
min., 4:6 CH3CN/H2O → 10 min., 4:6 CH3CN/H2O. The mass spectrum was recorded for the entire
elution time by using ESI detection from 50-800 (m/z) with the following parameters: capillary
voltage at 60.0, Rf loading at 100%, drying gas at 250 °C, spray chamber at 50 °C, nebulizer gas at
50.0 psi, drying gas at 25 psi, and damping gas at 0.8 mL/min.
NMR Spectroscopy
1H-NMR and 13C-NMR spectra were recorded at 10 mM at 400 MHz and 100.5 MHz, respectively,
1
in CDCl3 with CHCl3 as the internal reference for H (δ 7.24) and CDCl3 as the internal reference for
1
13C (δ 77.00) or DMSO-d6 with DMSO as the internal reference for H (δ 2.49) and DMSO-d6 as the
internal reference for 13C (δ 39.50). Coupling constants are expressed in Hertz (Hz). Data are
reported in this sequence: 1) chemical shifts (ppm); 2) spin multiplicities given as, s (singlet), bs
(broad singlet), d (doublet), t (triplet), q (quartet), quintet, sextet and m (multiplet); 3) coupling
constant J (Hz); and 4) integration.
Synthesis
5,10-Dioxo-5H,10H-diimidazo{1,5-a:1´,5´-d}pyrazine-1,6-dicarbonyl Glycyl Esters, 3{1-2}. To a dry
round-bottom flask under argon was added dry CH2Cl2 (25 mL). To this stirred solvent at -78 °C were
added, in order, the pyrazine diacid chloride 1 (1.00 g, 3.19 mmol), the glycine ester hydrochloride salt
2{1-2} (6.38 mmol) and N,N-diethylaniline (1.91 g, 2.05 mL, 12.8 mmol). The resulting solution was
held at -78 °C for 30 minutes before stirring 1 hour at room temperature. The solid precipitate was
collected by vacuum filtration and washed with EtOAc to yield 3{1-2}. The final products were
characterized by melting point as well as 1H- and 13C-NMR spectroscopy.
1
3{1}: The product was a white solid obtained in 86% yield: mp > 250 °C; H-NMR (DMSO-d6)
δ 8.97-8.94 (m, 4 H), 3.97 (d, J = 6.4 Hz, 4 H), 1.43 (s, 18 H); 13C-NMR (DMSO-d6) δ 168.4, 159.2,
149.0, 143.9, 138.3, 120.6, 80.9, 41.7, 27.7.

Molecules 2008, 13
3160
3{2}: The product was a white solid obtained in 91% yield: mp 222-223 °C (dec); 1H-NMR (DMSO-
d6) δ 9.07 (t, J = 6.0 Hz, 2 H), 8.97 (d, J = 6.0 Hz, 2 H), 7.39-7.31 (m, 10 H), 5.18 (s, 4H), 4.15 (d, J =
13
6.0 Hz, 4 H); C-NMR (DMSO-d6) δ 169.3, 159.4, 148.9, 143.7, 138.3, 135.8, 128.4, 128.0, 127.9,
120.7, 66.0, 41.1.
5,10-dioxo-5H,10H-diimidazo{1,5-a:1´,5´-d}pyrazine-1,6-dicarbonyl Amino Acid Esters, 3{3-9}. To a
dry round-bottom flask under argon was added dry CH2Cl2 (25 mL). To this stirred solvent at -78 °C
were added, in order, the pyrazine diacid chloride 1 (1.00 g, 3.19 mmol), the amino acid ester
hydrochloride or tosylate salt 2{3-9} (6.38 mmol) and N,N-diethylaniline (1.91 g, 2.05 mL, 12.8
mmol). The resulting solution was held at -78 °C for 30 minutes before stirring 1 hour at room
temperature. The reaction was washed against water (3×) and the organic fraction was dried over
MgSO4, filtered and concentrated. The residue was suspended in boiling EtOAc, stirred for 15 minutes
and then cooled at 0 °C. The solid product 3{3-9} was collected by vacuum filtration and washed with
1
EtOAc. The final product was characterized by melting point as well as H- and 13C-NMR
spectroscopy.
1
3{3}: The product was a light yellow solid obtained in 87% yield: mp 225 °C (dec); H-NMR
(DMSO-d6) δ 8.68 (d, J = 7.6 Hz, 2 H), 8.64 (s, 2 H), 4.71 (quintet, J = 7.2 Hz, 2 H), 1.51 (d, J = 6.8
Hz, 6 H), 1.48 (s, 18 H); 13C-NMR (DMSO-d6) δ 171.6, 157.2, 149.2, 146.9, 138.3, 118.9, 82.3, 49.2,
27.9, 18.4.
3{4}: The product was a yellow solid obtained in 93% yield: mp 141-143 °C; 1H-NMR (DMSO-d6) δ
8.68 (d, J = 7.2 Hz, 2 H), 8.62 (s, 2 H), 7.35-7.31 (m, 10 H), 5.21 (dd, J = 12 Hz, J = 12 Hz, 4 H), 4.87
13
(quintet, J = 7.2 Hz, 2 H), 1.56 (d, J = 7.2 Hz, 6 H); C-NMR (DMSO-d6) δ 172.2, 157.6, 148.9,
146.7, 138.4, 135.2, 128.6, 128.5, 128.2, 118.9, 67.4, 48.8, 18.3.
3{5}: The product was a white solid obtained in 83% yield: mp 222-223 °C (dec); 1H-NMR (DMSO-
d6) δ 8.63 (s, 2 H), 8.51 (d, J = 8 Hz, 2 H), 4.79-7.74 (m, 2 H), 1.77-1.65 (m, 3.22 6 H), 1.47 (s, 18 H),
13
0.97 (d, J = 6.4 Hz, 12 H); C-NMR (DMSO-d6) δ 171.6, 157.4, 149.0, 147.1, 138.4, 118.8, 82.3,
52.0, 41.9, 28.0, 25.1, 22.8, 22.2.
3{6}: The product was a white solid obtained in 87% yield: mp 176-178 °C (Lit. 140-141 °C, Ref.
[16]); 1H-NMR (DMSO-d6) δ 8.62 (s, 2 H), 8.52 (d, J = 8.4 Hz, 2 H), 7.35-7.29 (m, 10 H), 5.18 (s, 4
H), 4.94-4.88 (m, 2 H), 1.82-1.69 (m, 6 H), 0.95 (d, J = 2.4 Hz, 6 H); 0.94 (d, J = 2.0 Hz, 6 H); 13C-
NMR (DMSO-d6) δ 172.1, 157.6, 149.0, 146.6, 138.4, 135.3, 128.6, 128.4, 128.2, 119.0, 67.2, 51.5,
41.4, 25.0, 22.8, 22.2.
3{7}: The product was a white solid obtained in 87% yield: mp 201-203 °C (dec) (Lit. 179-180 °C
1
(dec) [10]); H-NMR (DMSO-d6) δ 8.59 (d, J = 4 Hz, 2 H), 8.57 (s, 2 H), 7.27-7.19 (m, 10 H), 5.00
13
(dd, J = 6.4 Hz, J = 6.4 Hz, 2 H), 3.22 (d, J = 6.4 Hz, 4 H), 1.41 (s, 18 H); C-NMR (DMSO-d6) δ
170.0, 157.3, 148.9, 146.7, 138.3, 136.0, 129.4, 128.3, 126.9, 118.8, 82.6, 54.3, 38.1, 27.9.

Molecules 2008, 13
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1
3{8}: The product was a white solid obtained in 86% yield: mp 175-177 °C; H-NMR (DMSO-d6) δ
8.56 (d, J = 8 Hz, 2 H), 8.53 (s, 2 H), 7.34-7.04 (m, 20 H), 5.15-5.10 (m, 6 H), 3.27 (dd, J = 6.0 Hz, J =
13
14, 2 H), 3.20 (dd, J = 6.0 Hz, J = 13.6, 2 H); C-NMR (DMSO-d6) δ 170.8, 157.4, 148.7, 146.4,
138.3, 135.5, 135.0, 129.3, 128.5, 127.1, 118.9, 67.4, 53.9, 37.8.
1
3{9}: The product was a white solid obtained in 76% yield: mp 150-152 °C; H-NMR (DMSO-d6) δ
8.71-8.68 (m, 4 H), 4.78-4.73 (m, 2 H), 4.49 (broad, 2 H), 3.08 (bs, 4 H), 2.01-1.94 (m, 2 H), 1.85-1.78
(m, 2 H), 1.53-1.32 (m, 44 H); 13C-NMR (DMSO-d6) δ 170.8, 157.5, 155.9, 149.2, 146.9, 138.6, 118.8,
82.6, 79.2, 53.2, 40.4, 32.1, 29.7, 28.4, 28.02, 28.0, 22.3.
Dissymmetric Imidazole-4,5-dicarboxamides 5{2-6}, 5{8-13}, 5{16-20}, 5{22-27}, 5{30-34}, 5{36-
41}, 5{44-48}, 5{50-55}, 5{58-62}, 5{64-69}, 5{72-76}, 5{78-83}, 5{86-90}, 5{92-97}, 5{100-
104}, 5{106-111}, 5{114-118}, 5{120-125},Disubstituted with Amino Acid Esters 2{1-9} and
Alkanamines 4{2-6}, 4{8-13}. Screw capped culture tubes were dried overnight in an oven. Each of
the nine amino acid ester substituted pyrazine 3{1-9} (0.100 mmol) was transferred to 11 culture tubes
followed by dry CH2Cl2 (3 mL). Solutions of the eleven different amines 4{2-6} and 4{8-13} at 4 M
were prepared in CH2Cl2 and 50 μL (0.200 mmol) of each amine was transferred robotically to the
corresponding tubes for a total of 99 tubes (9×11). The tubes were purged with argon and capped. The
tubes were placed on an orbital shaker for 2 days at room temperature and the solutions gently mixed
by the orbital action. The progress of the reactions was followed with TLC by using a mixture of
EtOAc/hexane (1:1) as the eluant. After 2 days the solvent was evaporated and the residues were
purified by column chromatography on silica gel with EtOAc/hexane (1:1) initially and then just
EtOAc as the eluant. The desired fractions were combined and concentrated to give the final products.
The purity and identity of the final products was tested by LC-MS and 1H-NMR.
Dissymmetric Imidazole-4,5-dicarboxamides 5{1}, 5{15}, 5{29}, 5{43}, 5{57}, 5{71}, 5{85}, 5{99},
5{113} Disubstituted with Amino Acid Esters 2{1-9} and Methylamine Hydrochloride 4{1}. Screw
capped culture tubes were dried overnight in an oven. Each tube was filled with one amino acid ester
substituted pyrazine 3{1-9} (0.100 mmol). Methylamine hydrochloride 4{1} (27.0 mg, 0.400 mmol)
was then weighed and transferred into each tube, followed by dry CH2Cl2 (3 mL) for a total of 9 tubes
(9×1). A 4.0 M solution of diisopropylethylamine (DIEA) in CH2Cl2 was prepared and 100 μL (0.400
mmol) of this solution was added to each tube. The tubes were purged with argon and sealed. The
tubes were placed on an orbital shaker for 2 days at room temperature and the solutions gently mixed
by the orbital action. The progress of the reactions was followed with TLC by using a mixture of
EtOAc/hexane (1:1) as the eluant. After 2 days the solvent was evaporated and the residues were
purified by column chromatography on silica gel with EtOAc/hexane (1:1) initially and then just
EtOAc as the eluant. The desired fractions were combined and concentrated to give the final products.
The purity and identity of the final products was tested by LC-MS and 1H-NMR.
Dissymmetric Imidazole-4,5-dicarboxamides 5{7}, 5{21}, 5{35}, 5{49}, 5{63}, 5{77}, 5{91},
5{105}, 5{119} Disubstituted with Amino Acid Esters 2{1-9} and 1-(N-Boc-aminomethyl)-4-
(aminomethyl)benzene 4{7}. Screw capped culture tubes were dried overnight in an oven. Each tube
was filled with one amino acid ester substituted pyrazine 3{1-9} (0.100 mmol). 1-(N-Boc-

Molecules 2008, 13
3162
aminomethyl)-4-(aminomethyl)benzene 4{7} (47.3 mg, 0.200 mmol) was then weighed and
transferred into each tube, followed by dry CH2Cl2 (3 mL) for a total of 9 tubes (9×1). The tubes were
purged with argon and sealed. The tubes were placed on an orbital shaker for 2 days at room
temperature and the solutions gently mixed by the orbital action. The progress of the reactions was
followed with TLC by using a mixture of EtOAc/hexane (1:1) as the eluant. After 2 days the solvent
was evaporated and the residues were purified by column chromatography on silica gel with
EtOAc/hexane (1:1) initially and then just EtOAc as the eluant. The desired fractions were combined
and concentrated to give the final products. The purity and identity of the final products was tested by
LC-MS and 1H-NMR.
Dissymmetric Imidazole-4,5-dicarboxamides 5{14}, 5{28}, 5{42}, 5{56}, 5{70}, 5{84}, 5{98},
5{112}, 5{126} Disubstituted with Amino Acid Esters 2{1-9} and 1-Phenylpiperazine Hydrochloride
4{14}. Screw capped culture tubes were dried overnight in an oven. Each tube was filled with one
amino acid ester substituted pyrazine 3{1-9} (0.100 mmol). 1-Phenylpiperazine hydrochloride 4{14}
(39.7 mg, 0.200 mmol) was then weighed and transferred into each tube, followed by dry CH2Cl2 (3
mL) for a total of 9 tubes (9×1). A 4.0 M solution of diisopropylethylamine (DIEA) in CH2Cl2 was
prepared and 50 μL (0.200 mmol) of this solution was added to each tube. The tubes were purged with
argon and sealed. The tubes were placed on an orbital shaker for 2 days at room temperature and the
solutions gently mixed by the orbital action. The progress of the reactions was followed with TLC by
using a mixture of EtOAc/hexane (1:1) as the eluant. After 2 days the solvent was evaporated and the
residues were purified by column chromatography on silica gel with EtOAc/hexane (1:1) initially and
then just EtOAc as the eluant. The desired fractions were combined and concentrated to give the final
products. The purity and identity of the final products was tested by LC-MS and 1H-NMR.
Table 7. Final Product Numbers and Nomenclature.
cmpd
5{1}
5{2}
5{3}
5{4}
5{5}
5{6}
5{7}
5{8}
5{9}
Name
4-[(methylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
4-[(benzylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
4-[(R-α-methylbenzylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(tert-butoxyglycyl)carbonyl]-
1H-imidazole
4-[(dibenzylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
4-[(N-methylbenzylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole

Molecules 2008, 13
3163
Table 7. Cont.
5{10} 4-[(N,N-diethylamino)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
5{11} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
5{12} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
5{13} 4-[(4-methylpiperidinyl)carbonyl]-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
5{14} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxyglycyl)carbonyl]-1H-imidazole
5{15} 4-[(methylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{16} 4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{17} 4-[(benzylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{18}
5{19}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{20} 4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(benzyloxyglycyl)carbonyl]-
1H-imidazole
5{21}
5{22} 4-[(dibenzylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{23} 4-[(N-methylbenzylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{24} 4-[(N,N-diethylamino)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{25} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{26} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{27} 4-[(4-methylpiperidinyl)carbonyl]-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{28} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxyglycyl)carbonyl]-1H-imidazole
5{29} 4-[(methylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{30} 4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{31} 4-[(benzylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{32}
5{33}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole

Molecules 2008, 13
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Table 7. Cont.
5{34} 4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(tert-butoxy-S-
alanyl)carbonyl]-1H-imidazole
5{35}
5{36} 4-[(dibenzylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{37} 4-[(N-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{38} 4-[(N,N-diethylamino)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{39} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{40} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{41} 4-[(4-methylpiperidinyl)carbonyl]-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{42} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-alanyl)carbonyl]-1H-imidazole
5{43} 4-[(methylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{44} 4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{45} 4-[(benzylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{46}
5{47}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{48} 4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(benzyloxy-S-
alanyl)carbonyl]-1H-imidazole
5{49}
5{50} 4-[(dibenzylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{51} 4-[(N-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{52} 4-[(N,N-diethylamino)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{53} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{54} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{55} 4-[(4-methylpiperidinyl)carbonyl]-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{56} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxy-S-alanyl)carbonyl]-1H-imidazole
5{57} 4-[(methylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole

Molecules 2008, 13
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Table 7. Cont.
5{58} 4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{59} 4-[(benzylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{60}
5{61}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{62} 4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(tert-butoxy-S-
leucyl)carbonyl]-1H-imidazole
5{63}
5{64} 4-[(dibenzylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{65} 4-[(N-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{66} 4-[(N,N-diethylamino)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{67} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{68} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{69} 4-[(4-methylpiperidinyl)carbonyl]-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{70} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-leucyl)carbonyl]-1H-imidazole
5{71} 4-[(methylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{72} 4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{73} 4-[(benzylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{74}
5{75}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{76} 4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(benzyloxy-S-
leucyl)carbonyl]-1H-imidazole
5{77}
5{78} 4-[(dibenzylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{79} 4-[(N-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{80} 4-[(N,N-diethylamino)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{81} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole

Molecules 2008, 13
3166
Table 7. Cont.
5{82} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{83} 4-[(4-methylpiperidinyl)carbonyl]-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{84} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxy-S-leucyl)carbonyl]-1H-imidazole
5{85} 4-[(methylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-
imidazole
5{86}
5{87} 4-[(benzylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{88}
5{89}
5{90}
5{91}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-
imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(tert-butoxy-S-
phenylalanyl)carbonyl]-1H-imidazole
5{92} 4-[(dibenzylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{93} 4-[(N-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{94} 4-[(N,N-diethylamino)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{95} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{96} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{97} 4-[(4-methylpiperidinyl)carbonyl]-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{98} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{99} 4-[(methylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-
imidazole
5{100}
5{101} 4-[(benzylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{102}
5{103}
5{104}
5{105}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
4-[(S-α-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-
imidazole
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(benzyloxy-S-
phenylalanyl)carbonyl]-1H-imidazole

Molecules 2008, 13
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Table 7. Cont.
5{106} 4-[(dibenzylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{107} 4-[(N-methylbenzylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{108} 4-[(N,N-diethylamino)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{109} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{110} 4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{111} 4-[(4-methylpiperidinyl)carbonyl]-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
5{112} 4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(benzyloxy-S-phenylalanyl)carbonyl]-1H-imidazole
4-[(methylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{113}
4-[5-({[(tert-butoxy)carbonyl]amino}pentylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-
butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{114}
4-[(benzylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{115}
4-[(R-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-
imidazole
5{116}
4-[(S-α-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-
imidazole
5{117}
4-[4-({[(tert-butoxy)carbonyl]piperidinyl}amino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-
butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{118}
4-{[(4-{[(tert-butoxy)carbonyl]aminomethyl}phenyl)methylamino]carbonyl}-5-[(tert-butoxy-S-[Nε-(tert-
butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{119}
4-[(dibenzylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{120}
4-[(N-methylbenzylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{121}
4-[(N,N-diethylamino)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{122}
4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-[Nε-(tert-
butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{123}
4-[(1,2,3,4-tetrahydroisoquinolinyl)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-
imidazole
5{124}
4-[(4-methylpiperidinyl)carbonyl]-5-[(tert-butoxy-S-[Nε-(tert-butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{125}
4-({4-[(tert-butoxy)carbonyl]piperazinyl}carbonyl)-5-[(tert-butoxy-S-[Nε-(tert-
butoxy)carbonyl]lysyl)carbonyl]-1H-imidazole
5{126}

Molecules 2008, 13
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Acknowledgements
The authors thank Jennifer Parker for assistance with the submission of these compounds to the
MLSMR, The University of Tulsa for the purchase of a 400 MHz NMR spectrometer, and The
National Institutes of General Medical Sciences for funding this research (5 P41 GM79589).
References and Notes
1. Kaiser, M.; Wetzel, S.; Kumar, K.; Waldmann, H. Biology-inspired synthesis of compound
libraries. Cell Mol. Life Sci. 2008, 65, 1186-1201.
2. Huryn, D. M.; Cosford, N. D. P. The Molecular Libraries Screening Center Network (MLSCN):
Identifying chemical probes of biological systems. Ann. Rep. Med. Chem. 2007, 42 401-406.
3. Winssinger, N.; Pianowski, Z.; Debaene, F.; Probing biology with Small Molecule Microarrays
(SMM). Top. Curr. Chem. 2007, 278, 311-342.
4. Haggarty, S. J.; Schreiber, S. L. Forward chemical genetics. In Chemical Biology. From Small
Molecules to Systems Biology and Drug Design; Schreiber, S. L., Kapoor, T. M., Weiss, G., Eds.
Wiley-VCH Verlag GmbH & Co.: New York, USA, 2007; Vol. 1, pp. 299-354.
5. Lipinski, C. A. Drug-like properties and the causes of poor solubility and poor permeability. J.
Pharmacol. Toxicol. Methods 2000, 44, 235-249.
6. Veber, D. F.; Johnson, S. R.; Cheng, H. Y.; Smith, B. R.; Ward, K. W.; Kopple, K. D. Molecular
properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 2002, 45,
2615-2623.
7. Lipinski, C.A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational
approaches to estimate solubility and permeability in drug discovery and development settings.
Adv. Drug Deliv. Rev. 2001, 46, 3-26.
8. Lipinski, C. A. Lead- and drug-like compounds: the rule of five revolution. Drug Discov. Today
2004, 1, 337-341.
9. Baures, P. W. Imidazole-4,5-dicarboxylic acid: A versatile scaffold for drug discovery and
materials research. Trends Heterocyc. Chem. 2006, 11, 1-22.
10. Baures, P. W.; Caldwell, A. W.; Cashman, C. R.; Masse, M. T.; Van Arnam, E. B.; Conry, R. R.
The influence by substituents on the intermolecular hydrogen-bonding interactions in imidazole-
4,5-dicarboxylic acid derivatives. Cryst. Growth Des. 2006, 6, 2047-2052.
11. Rush, J. R.; Sandstrom, S. L.; Yang, J.; Davis, R.; Prakash, O.; Baures, P. W.; Intramolecular
hydrogen bond strength and pKa determination of N,N’-disubstituted imidazole-4,5-
dicarboxamides. Org. Lett. 2005, 7, 135-138.
12. Baures, P. W.; Rush, J. R.; Wiznycia, A. V.; Desper, J.; Helfrich, B. A.; Beatty, A. M.
Intramolecular hydrogen bonding and intermolecular dimerization in the crystal structures of
imidazole-4,5-dicarboxylic acid derivatives. Cryst. Growth Des. 2002, 2, 653-664.
13. Legraverend, M.; Grierson, D. S.; The purines: potent and versatile small molecule inhibitors and
modulators of key biological targets. Bioorg. Med. Chem. 2006, 14, 3987-4006.
14. Wiznycia, A. V.; Helfrich, B. A.; Baures, P. W. An improved method for the synthesis of
dissymmetric N,N’-disubstituted imidazole-4,5-dicarboxamides. J. Org. Chem. 2002, 67, 7151-
7154.

Molecules 2008, 13
3169
15. Perchellet, E. M.; Perchellet, J. P.; Baures, P. W. Imidazole-4,5-dicarboxamides with
antiproliferative activity against HL-60 cells. J. Med. Chem. 2005, 48, 5955-5965.
16. Wiznycia, A. V.; Rush, J. R.; Baures, P. W. Synthesis of symmetric bis-imidazole-4,5-
dicarboxamides bearing amino acids. J. Org. Chem. 2004, 69, 8489-8491.
17. Zerhouni, E. Medicine: The NIH Roadmap. Science 2003, 302, 63-72.
18. A website with data for these compounds and background information for the overall project is
found at the following link: http://www.imidazole.utulsa.edu.
19. Angell, Y.; Chen, D.; Brahimi, F.; Saragovi, H. U.; Burgess, K. A combinatorial method for
solution-phase synthesis of labeled bivalent beta-turn mimics. J. Am. Chem. Soc. 2008, 130, 556-
565.
20. Fenster, E.; Rayabarapu, D. K.; Zhang, M.; Mukherjee, S.; Hill, D.; Neuenswander, B.; Schoenen,
F.; Hanson, P. R.; Aube, J. Three-component synthesis of 1,4-diazepin-5-ones and the
construction of gamma-turn-like peptidomimetic libraries. J. Comb. Chem. 2008, 10, 230-234.
21. Vedantham, P.; Zhang, M.; Gor, P. J.; Huang, M.; Georg, G. I.; Lushington, G. H.; Mitscher, L.
A.; Ye, Q.-Z.; Hanson, P. R. Studies towards the synthesis of methionine aminopeptidase
inhibitors: diversification utilizing a ROMP-derived coupling reagent. J. Comb. Chem. 2008, 10,
195-203.
22. Carpenter, R. D.; DeBerdt, P. B.; Holden, J. B.; Milinkevich, K. A.; Min, T.; Willenbring, D.;
Fettinger, J. C.; Tantillo, D. J.; Kurth, M. J. Design and synthesis of propeller-shaped
dispiroisoxazolinopiperidinochromanones. J. Comb. Chem. 2008, 10, 225-229.
23. Butler, J. D.; Solano, D. M.; Robins, L. I.; Haddadin, M. J.; Kurth, M J. A facile synthesis of new
5H-indazolo[3,2-b]benzo[d]-1,3-oxazines via one-pot intramolecular Bis-heterocyclizations. J.
Org. Chem. 2008, 73, 234-240.
24. Jeddeloh, M. R.; Holden, J. B.; Nouri, D. H.; Kurth, M. J. A library of 3-aryl-4,5-
dihydroisoxazole-5-carboxamides. J. Comb. Chem. 2007, 9, 1041-1045.
25. Comer, E.; Rohan, E.; Deng, L.; Porco, J. A., Jr. An approach to skeletal diversity using
functional group pairing of multifunctional scaffolds. Org. Lett. 2007, 9, 2123-2126.
26. Nielsen, T. E.; Schreiber, S. L. Towards the optimal screening collection: a synthesis strategy.
Angew. Chem. Int. Ed. 2008, 47, 48-56.
27. Shang, S.; Iwadare, H.; Macks, D. E.; Ambrosini, L. M.; Tan, D. S. A unified synthetic approach
to polyketides having both skeletal and stereochemical diversity. Org. Lett. 2007, 9, 1895-1898.
28. Houghten, R. A.; Pinilla, C.; Giulianotti, M. A.; Appel, J. R.; Dooley, C. T.; Nefzi, A.; Ostresh, J.
M.; Yu, Y.; Maggiora, G. M.; Medina-Franco, J. L.; Brunner, D.; Schneider, J. Strategies for the
use of mixture-based synthetic combinatorial libraries: scaffold ranking, direct testing in vivo, and
enhanced deconvolution by computational methods. J. Comb. Chem. 2008, 10, 3-19.
29. Krchnák, V.; Moellmann, U.; Dahse, H. M.; Miller, M. J. Solid-supported nitroso hetero Diels-
Alder reactions. 1. Acylnitroso dienophiles: scope and limitations. J. Comb. Chem. 2008, 10, 94-
103.
30. Bouillon, I.; Krchnák, V. Efficient solid-phase synthesis of 3-substituted-5-oxo-5H-thiazolo[2,3-
b]-quinazoline-8-carboxamides under mild conditions with two diversity positions. J. Comb.
Chem. 2007, 9, 912-915.

Molecules 2008, 13
3170
31. Just, Z. W.; Larock, R. C. Synthesis of 2(3H)-furanones via electrophilic cyclization. J. Org.
Chem. 2008, 73, 2662-2667.
32. The
PubChem
database
can
be
accessed
at
the
following
link:
http://www.ncbi.nlm.nih.gov/PubMed
33. Hur, J.; Wild, D. J. PubChemSR: A search and retrieval tool for PubChem. Chem. Cent. J. 2008,
2, 11.
Sample Availability: Please contact the corresponding author in regards to sample availability.
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This article is an open-access article distributed under the terms and conditions of the Creative
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