Alkyl-substituted polyaminohydroxamic acids: A novel class of targeted histone deacetylase inhibitors

Article abstract of DOI:10.1021/jm0505009

The reversible acetylation of histones is critical for regulation of eukaryotic gene expression. The histone deacetylase inhibitors trichostatin (TSA, 1), MS-275 (2) and suberoylanilide hydroxamic acid (SAHA, 3) arrest growth in transformed cells and in h

Full text of DOI:10.1021/jm0505009

6350
J. Med. Chem. 2005, 48, 6350-6365
Alkyl-Substituted Polyaminohydroxamic Acids: A Novel Class of Targeted
Histone Deacetylase Inhibitors
Sheeba Varghese,† Deepak Gupta,† Tiffany Baran,† Anchalee Jiemjit,§ Steven D. Gore,§
Robert A. Casero, Jr.,§ and Patrick M. Woster†,*
Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State
University, Detroit, Michigan 48202, and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University,
Baltimore, Maryland 21231
Received May 27, 2005
The reversible acetylation of histones is critical for regulation of eukaryotic gene expression.
The histone deacetylase inhibitors trichostatin (TSA, 1), MS-275 (2) and suberoylanilide
hydroxamic acid (SAHA, 3) arrest growth in transformed cells and in human tumor xenografts.
However, 1-3 suffer from lack of specificity among the various HDAC isoforms, prompting us
to design and synthesize polyaminohydroxamic acid (PAHA) derivatives 6-21. We felt that
PAHAs would be selectively directed to chromatin and associated histones by the positively
charged polyamine side chain. At 1 µM, compounds 12, 15 and 20 inhibited HDAC by 74.86,
59.99 and 73.85%, respectively. Although 20 was a less potent HDAC inhibitor than 1, it was
more potent than 2, more effective as an initiator of histone hyperacetylation, and significantly
more effective than 2 at re-expressing p21Waf1 in ML-1 leukemia cells. On the basis of these
results, PAHAs 6-21 represent an important new chemical class of HDAC inhibitors.
Introduction
The reversible acetylation of histones, mediated by
histone acetyltransferases (HATs) and histone deacety-
lases (HDACs), plays a critical role in chromatin archi-
tecture and hence in regulation of gene expression.1,2
Acetylation of cationic lysine tails in nucleosome-as-
sociated histones neutralizes charge and promotes
relaxation of chromatin, leading to transcriptional
activation. Conversely, deacetylation of these lysine
residues promotes formation of condensed chromatin,
and transcription is repressed. In some tumor cell types,
excessive hypocetylation of histones results in the
underexpression of growth regulatory factors such as
the cyclin dependent kinase inhibitor p21Waf1 and thus
contributes to the development of cancer.1,2 Histone
hyperacetylation caused by HDAC inhibitors such as
trichostatin (TSA, 1), MS-275 (2) and SAHA (3) (Figure
1) can cause growth arrest in a wide range of trans-
formed cells and can inhibit the growth of human tumor
xenografts.1-4 Cyclic peptide HDAC inhibitors such as
apicidin, depsipeptide, trapoxin and CHAPs have also
shown promising activity in cell culture and in vivo.
Current structure/activity studies involving analogues
of 1-3 have focused largely on modifications to the
aromatic ring moiety and the aliphatic linker region
present in these molecules.4 Although they are effective
both in vitro and in vivo, HDAC inhibitors typified by
1-3 suffer from lack of specificity among the various
forms of HDAC, including deacetylases that target
nonhistone proteins. Further, compounds 1 and 2 (and
to some degree 3) produce side effects through activity
in noncancerous cells. Thus, it would be desirable to
identify potent HDAC inhibitors that restore the ex-
Figure 1. Structures of trichostatin, MS-275, SAHA, sper-
midine and spermine.
pression of normal tumor suppressor factors without
producing significant dose-limiting toxicity.5 To address
these problems, we designed and synthesized a series
of polyaminohydroxamic acid (PAHA) derivatives that
incorporate structural features of the polyamines sper-
midine and spermine (4 and 5, respectively, Figure 1)
and the hydroxamic acid moiety commonly found in
active HDAC inhibitor molecules such as 1 and 3. This
strategy was developed based on the observation that
polyamine analogues can exert antitumor effects by
virtue of their high affinity for DNA.6-9 We postulated
that these compounds could enter cells using the
* To whom correspondence should be addressed. E-mail: pwoster@
wayne.edu.
† Wayne State University.
§ Johns Hopkins University.
10.1021/jm0505009 CCC: $30.25 © 2005 American Chemical Society
Published on Web 09/14/2005

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6351
Scheme 1
polyamine cellular transport system,6,10 and could be
selectively directed to DNA and associated histones, by
virtue of the positively charged polyamine portion of the
structure. In addition, it has been shown that histone
deacetylases differ in primary sequence at specific
residues in the rim region outside the lysine binding
site.3 Therefore, it may be possible to produce isoform
specific inhibitors for individual HDACs by altering the
polyamine chain composition and the terminal alkyl
group on that chain. Using these design criteria, we
successfully identified three lead compounds from a
library consisting of only 16 analogues.
(NaN3, DMF),11 which was immediately reduced to the
corresponding amine 24 by catalytic hydrogenation (10%
Pd/C, 25 psi).12 The desired aralkyl group was then
added by reductive amination13 of the appropriate
aldehyde (NaCNBH3, AcOH) to afford the phthalimide-
protected diamines 25a-c. The secondary amine was
then N-Boc protected (Boc)2O, NaHCO3, NaCl)14 to
provide 26a-c, followed by removal of the phthalimide
(methanolic NH2NH2)15 to give 27a-c. The free primary
amine was then coupled to acid chloride 28a (n)1) or
28b (n ) 3), yielding 29a-e.13,16 The methyl ester in
29a-e was cleaved (1N LiOH),11 resulting in the free
acids 30a-e, and these intermediates were then con-
verted to hydroxamic acids 31a-e in a two step pro-
cess17 involving formation of an activated mixed anhy-
dride (ethylchloroformate, THF) followed by addition of
hydroxylamine (1.76 M NH2OH in MeOH). Removal of
the N-Boc protecting group (20% TFAA in CH2Cl2)14
then afforded compounds 6, 8, 13, 17 and 18 as trifuo-
roacetate salts. During the reductive amination step,
one of the isolated products was tertiary amine 25d,
Chemistry
Depending on structure, one of 5 synthetic routes was
used to produce compounds 6-21, as outlined in Schemes
1-5. The structures and molecular weights of analogues
6-21 are summarized in Table 1. The synthesis of
compounds 6, 8, 11, 13, 17 and 18 is shown in Scheme
1. Commercially available N-(3-bromobutyl)phthalimide
22 was first converted to the corresponding azide 23

6352 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20
Varghese et al.
Scheme 2
which resulted from addition of two equivalents of
2-(phenyl)benzaldehyde. Elaboration of this intermedi-
ate as described above resulted in the formation of
target analogue 11.
22, NaH, DMF)18,19 to give 39, followed by a second
alkylation22 with the appropriate alkyl- or aralky halide
(NaH, DMF) to provide 40a-c. Removal of the phthal-
imide (methanolic NH2NH2)15 followed by coupling to
acid chloride 28a as described above then yielded the
fully protected intermediates 41a-c. Conversion of the
ester in 41a-c was then accomplished in three steps
as described above,11,17 resulting in hydroxamates 42a-
c. Deprotection (30% HBr in AcOH)20,21 then afforded
compounds 7, 9 and 10 as tetrahydrobromide salts.
The synthesis of compound 19 is outlined in Scheme
4. Phthalimide 24 was converted to intermediate 25c
by reductive amination (4-dimethylaminobenzaldehyde,
NaCNBH3, AcOH),13 followed by coupling to acid chlo-
ride 28b as described above13,16 to provide compound
43. Removal of the phthalimide (methanolic NH2NH2)15
followed by N-Boc protection14 afforded 44, and subse-
quent conversion of the ester to the corresponding
hydroxamate as described above11,17 produced 45. Re-
moval of the N-Boc group (20% TFAA in in CH2Cl2)14
then afforded the desired 19 as the trifluoroacetate salt.
The synthesis of analogue 15 is described in Scheme
5. Removal of the phthalimide15 from compound 32 and
The synthetic route used to produce target analogues
12, 16, 20 and 22 is outlined in Scheme 2. The previ-
ously described dimesitylated phthalimide 3218 was
monoalkylated with a suitable aralkyl halide (NaH,
DMF)19 to produce 33a-b. Subsequent removal of the
phthalimide (methanolic NH2NH2)15 provided the free
amines 34a-b. Coupling with 28a or 28b as described
above afforded intermediates 35a-d, followed by ester
cleavage (1 N LiOH)11 to give 36a-d. These intermedi-
ates were then converted to the corresponding hydrox-
amic acids 37a-d as described above,17 and removal of
the mesityl protecting groups (30% HBr in AcOH)20,21
afforded target compounds 12, 16, 20 and 21 as dihy-
drobromide salts. Direct deprotection of carboxylic acid
36a (30% HBr in AcOH)20,21 produced target compound
14.
The synthesis of compounds 7, 9 and 10 is shown in
Scheme 3. Tetramesitylnorspermine 3818,19 was mono-
alkylated (1.1 equiv of N-(3-bromobutyl)phthalimide

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6353
Scheme 3
reductive amination (4-dimethylaminobenzaldehyde,
NaCNBH3, AcOH)13 resulted in 46, which was then
coupled to acid chloride 28a13,16 to afford intermediate
47. The ester was converted to the corresponding
hydroxamic acid 48 as described above,17 and then
removal of the mesityl protecting groups (30% HBr in
AcOH)20,21 resulted in the formation of analogue 15 as
the dihydrobromide salt.
three compounds were subjected to a dose response
analysis using the same commercial assay kit, and
varying the concentration of inhibitor between 0.5 and
1000 nM, with 1 as a positive control. As shown in
Figure 2, compounds 12, 15 and 20 were essentially
equipotent over the concentration range tested (IC50
)
400 nM). Compounds 12, 15 and 20 act as potent
inhibitors of HDAC that are significantly less effective
than 1, but more effective than 24 in this isolated
enzyme assay system.
Biological Evaluation
The most potent inhibitor of isolated HDAC, com-
pound 20, was next evaluated in a series of cell
proliferation studies in the ML-1 human myelocytic
leukemia cell line. The results of these studies are
outlined in Figure 3. Compound 20, as well as the
positive controls 1 and 2, were compared at concentra-
tions between 0.1 and 100 µM, and cell viability was
determined in the ML-1 cultured cell preparation at 3
and 7 days (Figure 3) by direct cell count. Significant
Compounds 6-21 were evaluated for their ability to
inhibit isolated HDAC at 1 µM in a commercially
available assay (Fluor de Lys Assay System, Biomol
International LP, Plymouth Meeting, PA), employing 1
µM 1 and 2 as positive controls. The results of these
studies are summarized in Table 1. Three of these
analogues, compounds 12, 15 and 20, reduced HDAC
activity by 74.86, 59.99 and 73.85%, respectively, and
as such were selected for more extensive studies. These

6354 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20
Varghese et al.
Scheme 4
Scheme 5

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6355
Table 1. Comparison of the in Vitro Inhibitory Activity of 1, 2 and 6-20 at 1 µM Concentration Using an Isolated HDAC Assay Kit

6356 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20
Varghese et al.
Figure 4. Acetylation of histone H3 and H4 and expression
of p21WAF1/CIP1 in ML-1 cells. ML-1 cells were incubated for 24
h with compound 20 prior to Western blot analysis. Compound
2 was used as a positive control.
Figure 2. In vitro dose-response for inhibition of HDAC
caused by trichostatin and PAHAs 12, 15 and 20. The enzyme
preparation was exposed to a concentration range of each
inhibitor as described in the Experimental section. Each data
point is the average of three determinations that in each case
differed by 3% or less.
than 1 and 2, especially at concentrations greater than
10 µM. These effects were similar when cell viability
was monitored at either day 3 or 7. Comparable results
were obtained in a separate set of experiments where
cell proliferation was measured by a standard MTT
assay procedure (data not shown).
Compound 20 was also compared to the HDAC
inhibitor 2 (IC50 ) 4.8 µM)4 for the ability to promote
hyperacetylation of histones H3 and H4 in the ML-1 cell
line, as shown in Figure 4. At 1 µM, compound 20
produced higher levels of acetylated H3 and H4 than 2
after 24 h, as determined by Western blot analysis.
Histone H2a levels were also determined as an internal
standard, and the levels of this protein did not change
in the presence of 2 or 20. Re-expression of the cyclin
dependent kinase inhibitor p21Waf1 was also determined
in the presence of 2 and 20, and 20 was found to be
significantly more effective at promoting the re-expres-
sion of this protein. Taken together, the data shown in
Figures 2-4 suggest that 20 produces more dramatic
effects on ML-1 histone acetylation than 2, even though
it is only a marginally more potent HDAC inhibitor in
the in vitro enzyme assay.
Discussion
Well characterized HDAC inhibitors such as 1-3 and
related analogues typically contain three structural
features that are thought to be required for optimal
activity: an aromatic cap group, an aliphatic chain and
a metal binding functional group (Figure 5). Based on
molecular modeling studies involving the histone deacety-
lase-like protein (HDLP), these molecules are thought
to bind in a pocket in the enzyme active site that
includes a channel region flanked by a zinc ion on one
end, and a region that binds the cap group on the other
end.2 In this model, the aromatic group and aliphatic
chain of the inhibitor are buried in the enzyme pocket
in such a way that the metal binding moiety coordinates
the zinc ion that is required for activity. For these
reasons, compounds such as 1-3 do not inhibit Class
III HDACs, since they do not require zinc for activity.
As was mentioned above, the development of additional
HDAC inhibitors has focused on modifications to the
aliphatic linker group and the aromatic moiety. Some-
what less attention has been paid to the metal binding
group, which is typically a hydroxamic acid. We rea-
Figure 3. Toxicity of 1, 2 and compound 20 to ML-1
myelocytic leukemia cells in culture. Cells were exposed to a
range of concentrations of the inhibitor, and cell viability was
determined by direct cell count. Panel A: 3 days of treatment;
Panel B: 7 days of treatment. Each data point is the result of
three separate determinations that in each case differed by
3% or less.
toxicity was noted in the presence of 1 and 2, with IC50
values less than 10 µM in all cases. By contrast,
compound 20 produced significantly lower cell toxicity

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6357
Figure 5. Refined structural design model for polyaminohydroxamate HDAC inhibitors.
additional analogues. It is of interest to note that of the
soned that this model could be expanded by the addition
of a polyamine chain to the structural model for active
HDAC inhibitors, as shown in Figure 5. It was hypoth-
esized that the polyamine portion would impart benefi-
cial effects on activity, including cellular import of the
molecule by the polyamine transport system, improved
nuclear localization of the analogue, enhanced affinity
of compounds for chromatin, and the potential to
interfere with the association of HDACs with histone
proteins. These suppositions were in part supported by
data showing that the polyamines spermidine and
spermine are known to inhibit yeast HDAC,23 although
it is unclear whether this is a direct inhibition at the
active site or some other effect such as inhibition of
HDAC binding to chromatin. It has also been shown
that the amino acid residues that interact with 1 in the
binding region of HDLP are highly conserved in the
individual HDAC isoforms. However, the amino acids
in the surrounding rim area are less conserved.3 We
further hypothesized that the polyamine tail shown in
Figure 5 would be available to bind to amino acids in
this rim area, and that variations in charge, carbon
chain length and the nature of the R group could be used
to develop isoform-specific inhibitors. Using these pa-
rameters for the design of novel HDAC inhibitors, we
were able to successfully identify three lead compounds
from a library of only 16 analogues. Preliminary biologi-
cal data suggests that some of our suppositions could
be true, but additional experiments now being con-
ducted (transport studies, DNA binding analysis, cell
cycle studies, determination of activity against indi-
vidual HDAC isoforms and molecular modeling) will be
necessary to demonstrate the precise mechanism of
these analogues. Although 20 is more potent with
respect to inducing p21Waf1 re-expression, it demon-
strates less overt growth inhibition in ML-1 cells in vitro
than either 1 or 2. This feature may be therapeutically
exploitable in that the re-expression of previously
inactivated growth regulatory genes without overt cy-
totoxicity may restore more normal growth control to
transformed cells, thus making them less tumorigenic
and potentially more susceptible to combination treat-
ment with other cytotoxic agents. This possibility is
currently being examined experimentally.
three most active analogues (12, 15 and 20), only
compound 15 has a traditional cap group. Compounds
12 and 20 do contain aromatic groups at the terminal
nitrogens of their polyamine chains, but they are
unlikely to be positioned in the aromatic binding region
of HDAC due to their distance from the hydroxamic acid
moiety. This indicates that the polyamine portion of the
chain may in part be responsible for the activity of these
analogues, since each molecule contains two nitrogens
that are charged at physiological pH. Not surprisingly,
conversion of the hydroxamic acid moiety in 12 to a
carboxyl group (as in 14) essentially abolished inhibitory
activity. When the linker region of 12 was expanded
from four to six carbons to produce 16, inhibitory
activity was reduced by nearly 35%. By contrast,
compound 20, with a six-carbon linker region, was
nearly 4 times as active as an HDAC inhibitor as 21,
which has a four-carbon linker region. Compounds with
either one or four protonated nitrogens in the polyamine
segment were generally only moderately active. These
SAR correlations are preliminary, and additional data
from an expanded series of analogues is required to
generate a more substantive pharmacophore. The syn-
thesis of additional analogues and more extensive
biological evaluation procedures are currently underway
in our laboratories, and will be published in a subse-
quent manuscript.
Experimental Section
All reagents were purchased from Aldrich Chemical Co.
(Milwaukee, WI), Sigma Chemical Co. or Acros Chemical
(Chicago, IL) and were used without further purification except
as noted below. Pyridine was dried by passing it through an
aluminum oxide column and then stored over KOH. Triethy-
lamine was distilled from potassium hydroxide and stored in
a nitrogen atmosphere. Methanol was distilled from magne-
sium and iodine under a nitrogen atmosphere and stored over
molecular sieves. Methylene chloride was distilled fron phos-
phorus pentoxide and chloroform was distilled from calcium
sulfate. Tetrahydrofuran was purified by distillation from
sodium and benzophenone. Dimethylformamide was dried by
distillation from anhydrous calcium sulfate and was stored
under nitrogen. Preparative scale chromatographic procedures
were carried out using E. Merck silica gel 60, 230-440 mesh.
Thin-layer chromatography was conducted on Merck precoated
silica gel 60 F-254. Ion exchange chromatography was con-
ducted on Dowex 1 × 8-200 anion-exchange resin. Compounds
32 (Scheme 2) and 38 (Scheme 3) were synthesized as
previously described.
Preliminary examination of the structure/activity
correlations for compounds 6-21 reveals interesting
trends that will be studied through the synthesis of

6358 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20
Varghese et al.
All 1H and 13C NMR spectra were recorded on a General
Electric QE-300 or a Varian Mercury 400 MHz spectrometer,
and all chemical shifts are reported as δ values referenced to
TMS or DSS. Infrared spectra were recorded on a Nicolet
5DXB FT-IR spectrophotometer and are referenced to poly-
styrene. In all cases, 1H NMR, 13C NMR, and IR spectra were
consistent with assigned structures. Melting points were
recorded on a Thomas-Hoover Capillary melting point ap-
paratus and are uncorrected. Mass spectra were recorded on
a Kratos MS 80 RFA (EI and CI) or Kratos MS 50 TC (FAB)
mass spectrometers. Microanalyses were performed by Gal-
braith Laboratories, Knoxville, TN, and were within 0.4% of
calculated values.
N-[4-(Azido)butyl]phthalimide (23). A 1.0 g portion of
N-[4-(bromo)butyl]phthalimide 22 (0.0035 mol) was dissolved
in 10 mL of DMF, and to this solution was added 0.290 g
(0.0044 mol) of sodium azide. The reaction was then allowed
to stir for 5 h under nitrogen, after which the reaction mixture
was concentrated in vacuo to yield a white semisolid. The
semisolid was dissolved in water and extracted with three 50
mL portions of ethyl acetate, the combined organic layers were
dried over anhydrous magnesium sulfate and filtered, and the
solvent was removed to afford 23 (0.760 g, 88%) as a white
amorphous powder. This preparation was used in the next
reaction without further purification. 1H NMR (400 MHz
CDCl3) δ 1.6-1.68 (m, 2H), 1.74-1.82 (m, 2H), 3.3 (t, J ) 7.2
Hz, 2H), 3.7 (t, J ) 7.2 Hz, 2H), 7.71-7.73 (m, 2H), 7.83-7.86
(m, 2H). 13C NMR(400 MHz CDCl3) δ 26.1, 28.6, 44.02, 53.6,
127.4, 128.0, 132.34, 134.12, 168.52, 171.0.
benzaldehyde according to the procedure used to synthesize
25c in 75% yield. 1H NMR (400 MHz CDCl3) δ 1.42 (q, J ) 7.6
Hz, 2H), 1.59 (q, J ) 7.2 Hz, 2H), 2.54 (t, J ) 7.2 Hz, 2H),
3.59 (t, J ) 7.2 Hz, 2H), 3.84 (s, 2H), 7.19-7.45 (complex m,
9H), 7.77-7.81 (m, 4H). 13C NMR (400 MHz CDCl3) δ 25.52,
26.18, 37.8, 47.15, 48.07, 123.38, 126.98, 127.34, 127.86,
128.461,129.37, 139.06, 132.35, 134.10, 141.0, 146.9, 168.50
1-N-{4-[(N,N-Dimethyl)amino]benzyl}-1-N-[(tert-but-
yloxy)carbonyl]-4-phthalimidobutylamine (26c). A 0.800
g portion of 25c (0.0023 mol) was dissolved in 20 mL of
dichloromethane, and the reaction mixture was cooled to 0 °C.
To this mixture was added an aqueous solution of sodium
bicarbonate (0.220 g, 0.0027 mol) and sodium chloride (0.160
g, 0.0027 mol), and the reaction was allowed to stir at 0 °C for
30 min. Di-tert-butyl dicarbonate (0.596 g, 0.0027 mol) was
dissolved in 5 mL of dichloromethane, and the solution was
slowly added to the reaction. The mixture was allowed to stir
at 0 °C for an additional 10 min and warmed to room
temperature, followed by reflux for 12 h. The reaction mixture
was cooled and extracted with three 25 mL portions of
dichloromethane. The combined organic layers were washed
with 50 mL of saturated sodium bicarbonate and 50 mL of
saturated sodium chloride solution and then dried over
anhydrous magnesium sulfate. The mixture was then filtered,
and the solvent was removed in vacuo to yield crude 26c. The
crude compound was purified on a silica gel column eluted with
hexane:ethyl acetate (4:3) and then ethyl acetate (100%), to
1
yield compound 26c as a clear yellow oil (0.950 g, 91.5%). H
NMR (400 MHz CDCl3) δ 1.4 (s, 9H), 1.51-1.61 (broad m, 4H),
2.89 (s, 6H), 3.1-3.18 (broad m, 2H), 3.65 (t, 2H), 4.3 (s, 2H),
6.65 (d, J ) 6.4 Hz, 2H), 7.09 (broad s, 2H), 7.68-7.71 (m,
2H), 7.81-7.83 (m, 2H). 13C NMR (400 MHz CDCl3) δ 25.52,
26.19, 28.66, 37.85, 46.02, 53.65, 60.61, 79.82 123.41,127.36,
127.95, 129.33, 132.34,134.12, 136.92, 168.59. IR (cm-1) 3410.2,
2942.8, 1651.8, 1555.8, 1532.2, 1460.12, 1105.32.
N-[4-(Amino)butyl]phthalimide (24). Compound 23 (0.760
g, 0.0031 mol) was dissolved in 50 mL of ethanol along with
0.100 g of 10% Pd/C, and the suspension was hydrogenated
at 25psi for 12 h. The reaction mixture was then filtered, and
the filtrate was concentrated in vacuo to yield 24 as an
amorphous white solid (0.620 g, 92%) that was of sufficient
purity to use in the next reaction. 1H NMR (400 MHz CD3OD)
δ 1.6-1.8 (m, 4H), 2.9 (t, J ) 7.2 Hz, 2H), 3.7 (t, J ) 7.6 Hz,
2H), 7.9 (m, 4H). 13C NMR (400 MHz CDCl3) δ 26.1, 33.8, 44.0,
46.4, 127.4, 128.0, 132.23, 134.12, 168.25, 171.0
1-N-[4-(Methyl)benzyl]-1-N-[(tert-butyloxy)carbonyl]-
4-phthalimidobutylamine (26b). Compound 26b was syn-
thesized from 25b according to the procedure used to synthe-
size 25c in 92% yield. 1H NMR (400 MHz CDCl3) δ 1.44 (s,
9H), 1.53-1.63 (m, 4H), 2.30 (s, 3H), 3.14-3.22 (broad d, 2H),
3.66 (t, J ) 7.2 Hz, 2H), 4.36 (s, 2H), 7.09 (s, 2H), 7.71 (m,
2H), 7.84 (m, 2H). 13C NMR (400 MHz CDCl3) δ 24.64, 26.19,
28.71, 39.03, 40.92, 51.77, 60.61, 79.82 112.85, 123.41,127.36,
N-{4-[(N,N-Dimethylamino)benzyl]butyl}phthal-
imide (25c). A 0.589 g portion of 24 (0.0027 mol) was dissolved
in 20 mL of dichloroethane, and to this solution N,N-dimeth-
ylaminobenzaldehyde (0.477 g, 0.0032 mol) was added along
with 0.186 g (0.0031 mol) of acetic acid. The reaction was
allowed to stir at room temperature for 20 min. after which
time sodium cyanoborohydride (0.220 g, 0.0035 mol) was
dissolved in 3 mL of methanol and added to the reaction, which
was then allowed to stir for an additional 12 h. The reaction
mixture was concentrated on a rotary evaporator, and the
resulting yellow oil was dissolved in water and extracted with
three 50 mL portions of chloroform. The organic layers were
combined, washed with brine, and then dried over anhydrous
magnesium sulfate. The solution was filtered and concentrated
in vacuo to give crude 25a as a cloudy yellow oil. The crude
compound was purified using column chromatography (hexane:
ethyl acetate 1:3 followed by ethyl acetate:methanol 2:1), to
127.95, 129.33, 132.34,134.12, 136.92, 150.66, 156.17. IR (cm-1
)
2962.5, 2942.8, 1768.7, 1710.3, 1684.3, 1619.4, 1487.2, 1365.4,
1301.4.
1-N-[2-(Phenyl)benzyl]-1-N-[(tert-butyloxy)carbonyl]-
4-phthalimidobutylamine (26a). Compound 26a was syn-
thesized from 25a according to the procedure used to synthe-
1
size 25c in 90.2% yield. H NMR (400 MHz CDCl3) δ 1.38-
1.42 (m, 11H), 1.52 (m, 2H), 2.96 (broad s 1H), 3.09 (broad s
1H), 3.56 (broad s, 2H), 4.34 (s, 1H), 4.43 (s, 1H), 7.18 (d, J )
7.6 Hz,1H), 7.21-7.4 (m,8H),7.70-7.77 (m, 2H), 7.8-7.83(m,
2H). 13C NMR (400 MHz CDCl3) δ 25.52, 26.18, 27.63, 28.62,
37.8, 47.15, 48.07, 79.83, 85.4123.38, 126.98, 127.34, 127.86,
128.461,129.37, 139.06, 132.35, 134.10, 141.0, 146.9, 168.50.
1
yield 25a as a clear yellow oil (0.810 g, 85.4%). H NMR (400
MHz CDCl3) δ 1.55 (q, J ) 7.2 Hz, 2H), 1.72 (q, J ) 7.2 Hz,
2H), 2.65 (t, J ) 7.6 2H), 2.92 (s, 6H), 3.69 (s, 2H), 3.71 (t, J
)7.2 Hz,2H), 6.7 (d,2H), 7.1 (d, 2H),7.68-7.71 (m, 2H), 7.81-
7.83 (m,2H). 13C NMR (400 MHz, CDCl3) δ 24.35, 25.35, 40.9,
50.06, 112.85, 127.4, 128.0, 128.6, 132.34, 134.12, 150.0,
168.52, 169.0.
N-{4-[4-(Methyl)benzylamino]butyl}phthalimide (25b).
Compound 25b was synthesized from 24 and 4-methylbenzal-
dehyde according to the procedure used to synthesize 25c in
73.2% yield. 1H NMR (400 MHz, CDCl3) δ 1.53 (q, J ) 7.2 Hz,
2H), 1.70 (q, J ) 7.2 Hz, 2H), 2.31(s, 3H), 2.62 (t, J ) 7.6 2H),
6H), 3.68 (s, 2H), 3.70 (t, J ) 7.2 Hz,2H), 6.7 (d,2H), 7.1 (d,
2H),7.68-7.71 (m, 2H), 7.81-7.83 (m,2H). 13C NMR (400 MHz
CDCl3) δ 25.52, 26.19, 37.85, 46.02, 53.65, 60.61, 123.41,
127.36, 127.95, 129.33, 132.34, 134.12, 136.92, 168.59.
1-N-{4-[(N,N-Dimethyl)amino]benzyl}-1-N-[(tert-but-
yloxy)carbonyl]-4-aminobutylamine (27c). A 0.90 g (0.0019
mol) portion of 26c was dissolved in 10 mL of methanol, and
0.191 g (0.0059 mol) of hydrazine was added dropwise with
stirring. The reaction was allowed to reflux under nitrogen
for 12 h, and then the reaction mixture was concentrated in
vacuo to yield a white semisolid. This solid was dissolved in
50 mL of 4.0 N ammonium hydroxide and extracted with three
50 mL portions of chloroform. The combined organic layers
were dried over magnesium sulfate, filtered and concentrated
in vacuo, to yield 27c (0.560 g, 88.3%) as a white amorphous
1
solid. H NMR (400 MHz CDCl3) δ 1.37 (broad m, 2H), 1.45
(s, 9H), 1.47 (m, 2H), 2.6 (t, J ) 7.2 Hz, 2H), 2.92 (s, 6H), 3.09
(broad m, 2H), 4.3 (s, 2H), 6.6 (d, 2H), 7.1 (m, 2H). 13C NMR
(400 MHz CDCl3) δ 26.19, 28.66, 37.85, 46.02, 53.65, 60.61,
79.82 123.41, 112.85, 127.36, 127.95, 168.59. IR (cm-1) 3365.8,
2974.8, 2929.7, 1689.8, 1570.5, 1467.0, 1310.1, 1168.6.
N-{4-[2-(Phenyl)benzylamino]butyl}phthalimide (25a).
Compound 25a was synthesized from 24 and 2-(phenyl)-

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6359
1-N-[4-(Methyl)benzyl]-1-N-[(tert-butyloxy)carbonyl]-
4-aminobutylamine (27b). Compound 27b was synthesized
from 26b according to the procedure used to synthesize 27c
in 82.8% yield. 1H NMR (400 MHz CDCl3) δ 1.38 (m, 2H),
1.44-1.48 (m, 11H), 2.32 (s, 3H), 2.66 (t, J ) 6.8 Hz, 2H), 3.11-
3.19 (broad m, 2H), 4.38 (s, 2H), 7.11 (s, 4H). 13C NMR (400
MHz CDCl3) δ 25.39, 28.67, 31.22, 42.13, 46.36.49.68, 50.13,
3H), 4.33 (s, 2H), 7.12 (s, 4H). 13C NMR (400 MHz CDCl3) δ
25.77, 26.46, 28.99, 29.08, 34.17, 36.85, 39.23, 46.04, 49.85,
50.4, 51.66, 80.01, 127.41,127.94, 129.36, 135.55, 137.00,
156.13, 173.30, 174.41. IR (cm-1) 3338.4, 3318.9, 2936.2,
2858.4, 1736.2, 1690.8, 1651.9, 1548.1, 1509.1.
5-{4-[(tert-Butyloxy)carbonyl]-[2-(phenyl)benzyl]-
amino}butylcarbamoyl}pentanoic Acid Methyl Ester
(29a). Compound 29a was synthesized from 27a and 28a
according to the procedure used to synthesize 29d in 62.4%
yield. 1H NMR (400 MHz CDCl3) δ 1.23-1.48 (m,13H), 1.62-
1.71 (m, 4H), 2.15 (m, 2H), 2.31-2.38 (m, 2H), 2.96 (s, 1H),
3.08 (m, 4H), 3.64 (s, 3H), 4.35 (s, 1H), 4.43 (s, 1H), 6.26 (s,
1H), 7.20-7.42 (m, 9H). 13C NMR (400 MHz CDCl3) δ 24.86,
28.33, 36.502, 39.35, 46.12, 47.14, 48.15, 51.73, 51.78, 60.60,
79.97, 126.76, 126.92, 127.41, 127.59, 127.85, 128.49, 129.31,
130.15, 172.93, 173.48, 174.13, 175.72. IR (cm-1) 3304.9,
2921.0, 1722.3, 1671.4, 1651.9., 1551.6, 1158.9.
79.69, 115.28, 127.33, 127,92, 129.33, 135.67, 138.90. IR (cm-1
)
3360.6, 2975.8, 2929.3, 1690.8, 1514.9, 1410.6, 1365.3, 1245.0.
1-N-[2-(Phenyl)benzyl]-1-N-[(tert-butyloxy)carbonyl]-
4-aminobutylamine (27a). Compound 27a was synthesized
from 26a according to the procedure used to synthesize 27c
in 78.6% yield. 1H NMR (400 MHz CDCl3) δ 1.24-1.31(m, 4H),
1.461(s, 9H), 2.56(m, 2H), 2.95(broad s, 1H), 3.08(bs, 1H), 4.35-
(s, 1H), 4.45(s, 1H), 7.31-7.41(m, 9H) 13C NMR (400 MHz
CDCl3) δ 25.32, 25.38, 28.56, 28.63, 31.08, 42.06, 46.19, 46.63,
48.05, 79.72, 126.97, 127.36, 127.85, 128.45, 129.36, 130.12,
141.06 IR (cm-1) 3372.9, 2929.4, 1683.0, 1569.4, 1514.2, 1473.2,
1198.7.
5-{4-[N-(tert-Butyloxy)carbonyl]-4-[N,N-(dimethylamino)-
benzyl]amino}butylcarbamoylpentanoic Acid (30d). A
0.500 g (0.0011 mol) portion of 29d was dissolved in 6 mL of
tetrahydrofuran:water (4:2) and cooled to 0 °C, and 6 mL of
1.0 N LiOH was added to the mixture by dropwise addition.
The solution was warmed to room temperature and allowed
to stir for 16 h, during which time the reaction was monitored
by TLC. The mixture was again cooled to 0 °C, neutralized by
the dropwise addition of 2.0 N HCl, and extracted with three
50 mL portions of ethyl acetate. The ethyl acetate layers were
combined, washed with brine, and dried over anhydrous
magnesium sulfate. Removal of the solvent in vacuo yielded
compound 30d as a cloudy yellow oil (0.375 g, 75.8%) of
sufficient purity to be used in the next reaction without further
5-{4-[N-(tert-Butyloxy)carbonyl]-4-[N,N-(dimethylamino)-
benzyl]amino}butylcarbamoylpentanoic Acid Methyl
Ester (29d). A 0.500 g (0.0051 mol) portion of 27c was
dissolved in 15 mL of dichloromethane, and the reaction
mixture was cooled to 0 °C. Two to three drops of triethylamine
was then added to the solution, and the reaction was allowed
to stir for 15 min. The acid chloride 28a (0.333 g, 0.0019 mol)
was slowly added to the reaction mixture, which was allowed
to stir at 0 °C for 15 min, then heated to room temperature
and allowed to stir for an additional 8 h. The solvent was
removed in vacuo, and the residue was dissolved in water and
extracted with three 50 mL portions of chloroform. The organic
layers were combined and washed with 50 mL of saturated
sodium bicarbonate and 50 mL of saturated sodium chloride
and then dried over magnesium sulfate. Filtration and removal
of the solvent in vacuo then afforded crude 29d. Purification
on silica gel (hexane:EtOAc 1:3) then gave pure 29d (0.580 g,
1
purification. H NMR (400 MHz CDCl3) δ 1.2 (m, 4H), 1.4 (s,
9H), 1.5 (m, 4H), 2.11 (t, J ) 7.2 Hz, 2H), 2.28 (t, J ) 7.2 Hz,
2H), 2.93 (s, 6H), 3.22 (m, 4H), 4.3 (s, 2H), 6.6 (d, J ) 8.8 Hz,
2H), 7.1 (m, 2H). 13C NMR (400 MHz CDCl3) δ 21.29, 24.57,
25.20, 26.35, 28.72, 29.64, 29.92, 36.19, 39.26, 40.99, 45.76,
50.09, 60.65, 80.01, 113.01, 128.68, 150.09, 171.45, 172.28. IR
(cm-1) 3325.4, 2929.7, 2858.4, 1716.8, 1658.4, 1613. 0, 1554.6,
1486.8, 1006.0.
1
80.2%) as a clear yellow oil. H NMR (CDCl3) δ 1.2 (m, 4H),
1.4 (s, 9H), 1.5 (m, 4H), 2.11 (t, J ) 7.2 Hz, 2H), 2.28 (t, J )
7.6 Hz, 2H), 2.93 (s, 6H), 3.22 (m, 4H), 3.6 (s, 3H), 4.3 (s, 2H),
6.6 (d, J ) 8.4 Hz, 2H), 7.1 (m, 2H).13C NMR (400 MHz CDCl3)
δ 24.64, 25.35, 26.32, 28.71, 33.89, 34.01, 36.41, 39.30, 40.92,
45.57, 50.06, 51.77, 79.72, 112.84, 128.66, 150.06, 156.17,
172.93, 174.21 IR (cm-1) 3416.2, 2942.7, 1736.2, 1651.9, 1554.6,
1522.2, 1256.8.
7-{4-[N-(tert-Butyloxy)carbonyl]-4-[4-(methyl)benzyl]-
amino}butylcarbamoylheptanoic Acid (30e). Compound
30e was synthesized from 29e according to the procedure used
1
to synthesize 30d in 72.7% yield. H NMR (400 MHz CDCl3)
7-{4-[(tert-Butyloxy)carbonyl]-[4-(methyl)benzyl]-
amino}butylcarbamoylheptanoic Acid Methyl Ester (29e).
Compound 29e was synthesized from 27b and 28b according
to the procedure used to synthesize 29d in 64.8% yield. 1H
NMR (400 MHz CDCl3) δ 1.33 (m, 4H), 1.46 (broad s, 13H),
1.62 (m, 4H), 2.14 (m, 2H), 2.29 (m, 2H), 2.39 (s, 3H), 3.22 (m,
4H), 3.66 (s, 3H), 4.37 (s, 2H), 7.12 (s, 4H). 13C NMR (400 MHz
CDCl3) TM 24.94, 25.55, 25.77, 26.46, 28.66, 28.99, 29.08,
34.17, 36.85, 39.23, 46.04, 49.85, 50.4, 51.66, 80.01, 127.41,-
127.94, 129.36, 135.55, 137.00, 156.13, 173.30, 174.41. IR
(cm-1) 3607.4, 3328.7, 2936.2, 2858.4, 1738.6, 1691.8, 1652.0,
1548.6, 1509.1.
7-{4-[(tert-Butyloxy)carbonyl]-4-[N,N-(dimethylamino)-
benzyl]amino}butylcarbamoylheptanoic Acid Methyl
Ester (29c). Compound 29c was synthesized from 27c and
28b according to the procedure used to synthesize 29d in
76.5% yield. 1H NMR (CDCl3) δ 1.40-1.59 (m, 13H), 1.60 (m,
8H), 2.11 (m, 2H), 2.3 (m, 2H), 2.95 (s, 6H), 3.20 (m, 4H), 3.66
(s, 3H), 4.23 (s, 2H), 6.69 (d,J ) 8 Hz, 2H), 7.11(broad s, 2H).
13C NMR (400 MHz CDCl3) δ 24.64, 25.35, 26.32, 28.25, 28.64,
28.71, 29.07, 33.89, 35.98, 36.88, 40.01, 41.13, 46.57, 50.07,
51.92, 80.02, 128.66, 129.50, 150.06, 156.17, 172.93, 174.21.
IR (cm-1) 3437.5, 2956.6, 1739.3, 1651.0, 1550.6, 1522.2,
1256.8.
δ 1.18 (m, 6H), 1.39 (bs, 12H), 1.53 (m, 4H), 2.10 (m, 2H), 2.2
(m, 2H), 2.26 (s, 3H), 3.14 (m, 4H), 4.30 (s, 2H), 7.05 (s, 4H)
13C NMR (400 MHz CDCl3) δ, 21.93, 24.93, 25.70, 26.44, 28.62,
28.87, 29.01, 31.07, 36.6, 39.26, 46.05, 49.73, 50.35, 60.58,
64.53, 80.09, 127.34, 127.85, 129.33, 135.45, 136.93, 156.1,
171.38, 173.91. IR (cm-1) 3326.9, 2932.8, 2863.1, 1730.5,
1691.0, 1644.1, 1661.8, 1555.3, 1464.62, 1366.05, 1244.7,
1168.19, 1036.0, 729.15 (cm-1
)
7-{4-[N-(tert-Butyloxy)carbonyl]-4-[N,N-(dimethylamino)-
benzyl]amino}butylcarbamoylheptanoic Acid (30c). Com-
pound 30c was synthesized from 29c according to the proce-
dure used to synthesize 30d in 72.3% yield. 1HNMR (400 MHz
CDCl3) δ 1.35-1.44 (m, 17H), 1.63 (m, 4H), 2.2 (m, 4H), 2.32
(m, 2H), 2.93 (s, 6H), 3.16 (m, 4H), 4.29 (s, 2H), 6.69 (d, J )
8.8 Hz, 2H), 7.11 (m, 2H). 13C NMR (400 MHz CDCl3) δ 14.34,
21.19, 21.93, 24.93, 25.46, 25.76, 26.43, 28.60, 28.88, 29.01,
31.07, 36.6, 39.26, 46.05, 49.73, 50.35, 60.58, 64.53, 80.09,
127.34, 127.85, 129.33, 135.45, 136.93, 156.1, 171.38, 173.91.
IR (cm-1) 3348.2, 2929.7, 1718.3, 2658.4, 1616.4, 1555.6,
1478.8, 1398.1, 1110.7.
5-{4-[(tert-Butyloxy)carbonyl]-[4-(methyl)benzyl]-
amino}butylcarbamoylpentanoic Acid Methyl Ester (30b).
Compound 30b was synthesized from 29b according to the
procedure used to synthesize 30d in 70.9% yield. 1H NMR (400
MHz CDCl3) δ 1.2(m, 4H), 1.40 (broad s, 9H), 1.53 (m, 4H),
2.10 (m, 2H), 2.2 (m, 2H), 2.30 (s, 3H), 3.20 (m, 4H), 4.32 (s,
2H), 7.05 (s, 4H). 13C NMR (400 MHz CDCl3) δ 25.70, 26.44,
28.62, 28.87, 29.01, 31.07, 36.6, 39.26, 46.05, 49.73, 50.35,
60.58, 64.53, 80.09, 127.34, 127.85, 129.33, 135.45, 136.93,
5-{4-[(tert-Butyloxy)carbonyl]-[4-(methyl)benzyl]-
amino}butylcarbamoylpentanoic Acid Methyl Ester (29b).
Compound 29b was synthesized from 27b and 28a according
to the procedure used to synthesize 29d in 70.7% yield. 1H
NMR (400 MHz CDCl3) δ 1.44 (broad s, 13H), 1.60 (m, 4H),
2.14 (m, 2H), 2.29 (m, 2H), 2.4 (s, 3H), 3.22 (m, 4H), 3.67 (s,

6360 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20
Varghese et al.
156.1, 171.38, 173.91. IR (cm-1) 3326.4, 2934.4, 2863.1, 1729.7,
1691.7, 1645.4, 1664.8, 1555.3, 1464.6, 1421.1, 1168.2, 1136.0,
732.4.
127.47, 127.88, 128.55, 129.3, 130.2, 135.74, 140.95, 141.58,
156.18, 174.09. IR (cm-1) 3260.5, 2975.1, 2929.7, 1664.9,
1651.9, 1554.6.
5-{4-[(tert-Butyloxy)carbonyl]-[2-(phenyl)benzyl]-
amino}butylcarbamoyl}pentanoic Acid Methyl Ester
(30a). Compound 30a was synthesized from 29a according to
the procedure used to synthesize 30d in 86.1% yield. 1H NMR
(400 MHz CDCl3) δ 1.30-1.43 (m,13H),1.54 (m,4H), 2.11-2.27
(m,4H), 2.93-3.05 (m,4H), 4.36(d, J ) 32 Hz, 2H), 7.20-7.38
(m,9H). 13C NMR (400 MHz CDCl3) δ 21.29, 25.58, 26.54,
28.56, 29.68, 29.92, 30.54, 30.85, 36.26, 39.32, 46.38, 47.24,
48.27, 60.64, 64.60, 80.10, 125.75, 126.77, 127.05, 127.44,
127.85, 128.53, 129.3, 130.18, 135.51, 135.83, 140.97, 141.56,
156.03, 173.62. IR (cm-1) 3304.9, 2921.0, 1730.0, 1671.4,
1651.9, 1551.6, 1158.9.
5-{4-[4-N,N-(Dimethyl)aminobenzyl]amino}butyl-
carbamoylpentanohydroxamic Acid (17). Compound 31d
(0.140 g, 0.0003 mol) was dissolved in 5 mL of 20% trifluoro-
acetic acid in dichloromethane, and the reaction was allowed
to stir at room temperature for 8 h. The solvent was then
removed in vacuo, and the residue was taken up in 25 mL of
chloroform and dried over anhydrous magnesium sulfate.
Filtration and removal of the solvent afforded crude 17 (0.110
g, 76.7%) as a buff colored solid. An analytical sample of 17
was prepared by recrystallization from aqueous ethanol. 1H
NMR (400 MHz CD3OD) δ 1.2 (m, 4H), 1.5 (m, 4H), 2.15 (t, J
) 7.2 Hz, 2H), 2.19 (t, J ) 7.2 Hz, 2H), 2.93 (s, 6H), 3.22 (m,
4H), 4.03 (s, 2H), 6.7(d, J ) 8.0 Hz, 2H), 7.3 (m, 2H). 13C NMR
(400 MHz CD3OD) δ 23.28, 24.35, 26.31, 131.63, 161.58. IR
(cm-1) 2988.1, 1671.4, 1554.6, 1444.3, 1203.8, 1165.9. Anal.
for C21H33F3N4O5: C, H, N.
5-{4-[N-(tert-Butyloxy)carbonyl]-4-[N,N-(dimethylamino)-
benzyl]amino}butylcarbamoyl-pentanohydroxamic Acid
(31d). Ethyl chlorformate (0.086 g, 0.0008 mol) and triethy-
lamine (0.08 g, 0.0008 mmol) were added to the solution of
30d (0.300 g, 0.0007 mol) in 5 mL of THF, and the mixture
was cooled to 0 °C. The reaction was allowed to stir for 20 min,
after which time it was filtered and added to 20 mL of freshly
prepared 1.76 M hydroxylamine in methanol. The reaction was
stirred at room temperature for 30 min, filtered and concen-
trated in vacuo to yield the crude 31d. Purification on silica
gel (ethyl acetate:methanol 4:2) then afforded pure 31d (0.252
7-{4-[4-(Methyl)benzyl]aminobutyl}carbamoylheptano-
hydroxamic Acid (18). Compound 18 was synthesized from
31e according to the procedure used to synthesize 17 in 71.6%
yield. An analytical sample of 18 was prepared by recrystal-
1
lization from aqueous ethanol. H NMR (400 MHz CD3OD) δ
1.23-1.43 (m, 4H), 1.59-1.6 (m, 8H), 2.07-2.17 (m, 4H), 2.35
(s, 3H), 2.86 (t, J ) 7.2 Hz, 2H), 3.03 (m, 2H), 3.19 (m, 2H),
4.14 (s, 2H), 7.26 (d, J ) 6.4, 2H), 7.37 (d, J ) 6.8 Hz, 2H),
8.06 (broad s, NHCO), 9.93(broad s, NHOH). 13C NMR (400
MHz CD3OD) δ 23.3, 25.4, 25.7, 26.44, 28.54, 28.62, 32.43,
35.68, 38.27, 50.82, 117.70, 128.33, 129.64, 129.8, 139.7,
160.41, 175.21 IR (cm-1) 3226.6, 2929.7, 2853.4, 1671.4, 1640.3,
1551.0, 1444.7, 1209.8, 1163.8. Anal. for C22H34F3N3O5: C, H,
N.
1
g, 77.5%) as a dark yellow oil. H NMR (400 MHz CDCl3) δ
1.2 (m, 4H), 1.4 (s, 9H), 1.5 (m, 4H), 2.15 (broad s, 4H), 2.93
(s, 6H), 3.22 (m, 4H), 3.6 (s, 3H), 4.3 (s, 2H), 6.6 (d, J ) 8.0
Hz, 2H), 7.1 (m, 2H), 7.8 (broad s, NHOH). 13C NMR (400 MHz
CDCl3) δ 21.2, 23.11, 25.71, 28.72, 31.51, 39.45, 40.91, 41.08,
45.79, 112.86, 1125.73, 126.25, 128.37, 128.62, 132.28, 150.12,
156.13. IR (cm-1) 3396.8, 2929.7, 1638.9, 1610.2,1554.6, 1450.8,
1405.4.
7-{4-[4-N,N-(Dimethylamino)benzyl]aminobutyl}-
carbamoylheptanohydroxamic Acid (13). Compound 13
was synthesized from 31c according to the procedure used to
synthesize 17 in 72.1% yield. An analytical sample of 13 was
prepared by recrystallization from aqueous ethanol. 1H NMR
(400 MHz CD3OD) δ 1.62 (m, 8H), 1.74 (m, 2H), 2.12 (t, J )
6.8 Hz, 2H), 2.21 (t, J ) 6.8 Hz, 2H), 3.06 (m, 2H), 3.15 (s,
6H), 3.21 (m, 2H), 4.20 (s, 2H), 7.36 (broad s, 2H), 7.58 (broad
s, 2H). 13C NMR (400 MHz CD3OD) δ 26.86, 26.9,28.12, 29.01,
29.2, 29.47, 30.13, 30.35, 36.19, 43.09, 46.58, 44.4, 57.0, 112.8,
112.9, 129.32, 129.4, 168.56, 174.23 IR (cm-1) 2982.2, 1671.4,
1556.1, 1445.3, 1203.8, 1168.4. Anal. for C23H37F3N4O5: C, H,
N.
7-{4-[N-(tert-Butyloxy)carbonyl]-4-[4-(methyl)benzyl]-
amino}butylcarbamoylheptanohydroxamic Acid (31e).
Compound 31e was synthesized from 30e according to the
procedure used to synthesize 31d in 78.0% yield. 1H NMR (400
MHz CDCl3) δ 1.24-1.31 (m, 4H), 1.43-1.6 (m, 13H), 2.16 (m,
2H), 2.32 (s, 3H), 3.18 (m, 4H), 4.35 (s, 2H), 7.11 (s, 4H). 13C
NMR (400 MHz CDCl3) δ 20.07, 23.29, 25.29, 25.46, 25.57,
26.38, 28.53, 28.61, 32.45, 35.71, 38.24, 46.88, 50.92, 80.01,
117,7, 128.33, 129.64, 129.74, 139.67, 156.22, 174.0.38. IR
(cm-1) 3221.6, 2929.7, 2858.4, 1671.4, 1638.9, 1554.6, 1450.8,
1190.1, 1150.8, 1110.9.
7-{4-[N-(tert-Butyloxy)carbonyl]-4-[N,N-(dimethylamino)-
benzyl]amino}butylcarbamoyl-heptanohydroxamic Acid
(31c). Compound 31c was synthesized from 30c according to
the procedure used to synthesize 31d in 75.7% yield. 1H NMR
(400 MHz CDCl3) δ 1.24 (m, 4H), 1.44(m, 15H), 1.52 (m, 2H),
2.1 (m, 4H), 2.90 (s, 6H), 3.14 (m, 4H), 4.26 (s, 2H), 6.65 (d, J
) 7.6 Hz, 2H), 7.08 (broad s, 1H). 13C NMR (400 MHz CDCl3)
δ 21.34, 22.43, 23.11, 25.71, 28.72, 31.51, 39.45, 40.91, 41.08,
45.79, 112.86, 1125.73, 126.25, 128.37, 128.62, 132.28, 150.12,
156.13. IR (cm-1) 3385.7, 2932.4, 1632.4, 1622.0.0, 1554.6,
1460.7, 1425.1, 1304.2.
5-{4-[N-(tert-Butyloxy)carbonyl]-4-[4-(methyl)benzyl]-
amino}butylcarbamoylpentanohydroxamic Acid (31b).
Compound 31b was synthesized from 30b according to the
procedure used to synthesize 31d in 80.9% yield. 1H NMR (400
MHz CDCl3) δ 1.24-1.31 (m, 4H), 1.43 (m, 9H), 2.18 (m, 4H),
2.32 (s, 3H), 3.18 (m, 4H), 4.32 (s, 2H), 7.11 (s, 4H). 13C NMR
(400 MHz CDCl3) δ 25.31, 25.06, 26.38, 28.53, 28.61, 32.45,
35.71, 38.24, 46.88, 50.92, 80.24, 127.37, 127.9, 129.64, 129.74,
137.67, 156.33, 174.21. IR (cm-1) 3267.0, 2929.7, 2858.4,
1651.9, 1548.1, 1463.8, 1418.4.
5-{4-[(tert-Butyloxy)carbonyl]-4-[2-(phenyl)benzyl]-
amino}butylcarbamoyl}pentanohydroxamic Acid (31a).
Compound 31a was synthesized from 30a according to the
procedure used to synthesize 31d in 80.6% yield. 1H NMR (400
MHz CDCl3) δ 1.25-1.42(m,15H), 1.56 (m,2H),1.99-2.26 (m,-
4H),2.94-3.05(m,4H), 4.36(d, J ) 31.2 Hz, 2H),7.21-7.40(m,-
9H) 13C NMR (400 MHz CDCl3) δ 25.04, 25.49, 26.47, 28.57,
29.92, 32.24, 35.91, 39.98, 46.5, 48.32, 80.24, 126.8, 125.08,
5-{4-[4-(Methyl)benzyl]aminobutyl}carbamoylpentano-
hydroxamic Acid (8). Compound 8 was synthesized from 31b
according to the procedure used to synthesize 17 in 72.9%
yield. An analytical sample of 8 was prepared by recrystalli-
1
zation from aqueous ethanol. H NMR (400 MHz CD3OD) δ
1.23-1.43 (m, 4H), 1.6 (m, 4H), 2.0-2.1 (m, 4H), 2.35 (s, 3H),
2.86 (t, J ) 7.2 Hz, 2H), 3.02 (m, 2H), 3.20 (m, 2H), 4.23 (s,
2H), 7.24 (d, J ) 6.4, 2H), 7.35 (d, J ) 6.8 Hz, 2H). 13C NMR
(400 MHz CD3OD) δ 26.04, 28.63, 28.54, 34.86, 36.12, 38,99,
51.32, 118.48, 128.33, 129.64, 129.8, 139.7, 160.14, 175.21. IR
(cm-1) 3221.6, 2929.7, 2858.4, 1781.6, 1671.4, 1638,9, 1554.6,
1450.8, 1190.1, 1150.8, 1110.9. Anal. for C20H30F3N3O5: C, H,
N.
5-{4-[2-(Phenyl)benzyl]aminobutyl}carbamoylpentano-
hydroxamic Acid (6). Compound 6 was synthesized from 31a
according to the procedure used to synthesize 17 in 87% yield.
An analytical sample of 6 was prepared by recrystallization
from aqueous ethanol. 1H NMR (400 MHz CD3OD) δ 1.53(m,-
4H),1.60(m,4H),2.10(m,2H),2.18(m,2H),2.82(t, J ) 8 Hz,
2H),3.11 (t, J ) 6.4 Hz, 2H),4.22 (s,2H),7.35(d, J ) 7.2 Hz,
3H), 7.36-7.50(m,5H), 7.66(d, J ) 2.8 Hz, 1H) 13C NMR (400
MHz CD3OD) δ 22.92, 24.9, 25.25, 25.47, 26.2, 32.11, 35.45,
38.10, 47.02, 127.82, 128.31, 1128.70, 128.96, 129.29, 129.47,
130.73, 139.95, 143.27, 155.38, 171.12, 174.79. IR (cm-1
)
3723.51, 2923.24, 2851.89, 1671.35, 1561.08, 1431.35, 1176.6,
1112.7. Anal. for C25H32F3N3O5: C, H, N.
1-Phthalimido-4-{N-[2,4,6-(trimethyl)benzenesulfon-
yl]}-8-{N-[4-(tert-butyl)benzyl]-N-[2,4,6-(trimethyl)-

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6361
using the method described for the synthesis of 29c in 72.3%
benzenesulfonyl]}amino-4-azaoctane (33a). Sodium hy-
dride 60% oil dispersion (equivalent to 0.027 g, 0.0011 mol of
NaH was dissolved in 1 mL of dimethylformamide under
nitrogen, and the reaction was cooled to 0 °C. Compound 32
(0.500 g, 0.0010 mol) was dissolved in 4 mL of dimethyl-
formamide and added dropwise to the reaction mixture, which
was allowed to stir for 30 min. A 0.250 g portion (0.0011 mol)
of 4-tert-butylbenzyl bromide was dissolved in 2 mL of dim-
ethylformamide and added to the reaction slowly via syringe.
The reaction was stirred for 12 h, the solvent was removed in
vacuo and the residue was dissolved in water and extracted
with three 50 mL portions of ethyl acetate. The combined
organic layers were dried over anhydrous magnesium sulfate
and filtered, and the solvent was removed to yield crude 33a.
Purification of the crude material on silica gel (hexane:ethyl
acetate 4: 3) then afforded pure 33a as a fluffy white solid
(0.619 g, 71.6%). 1H NMR (400 mHz CDCl3) δ 1.25 (s, 9H) 1.4
(m, 2H), 1.61 (m,2H), 1.72 (m, 2H), 2.24 (s, 6H), 2.62 (s, 6H),
2.62 (s, 6H), 3.04-3.06 (t, J ) 6.4 Hz, 4H), 3.18 (t, J ) 7.2 Hz,
2H), 4.17 (s,2H), 6.95 (s, 2H), 7.23 (d, J ) 6.8 Hz, 2H), 7.73
(m, 2H), 7.83-7.85 (m, 2H). 13C NMR (400 MHz CDCl3) δ
21.19, 23.06, 24.32, 24.49, 24.66, 25.29, 25.39, 25.95, 27.11,
28.70, 31.52, 33.78, 33.87, 36.28, 36.40, 36.47, 43.52, 43.64,
51.76, 51.89, 132.15, 132.30, 132.34, 133.18, 140.15, 140.27,
142.92, 173.24, 174.02, 174.17, 178.84.
1
yield. H NMR (CDCl3) δ 1.28 (s, 9H) 1.34 (m, 4H), 1.61 (m,
4H), 1.72 (m, 2H), 2.11 (t, J ) 7.2 Hz, 2H), 2.24 (m, 8H), 2.51
(s, 6H), 2.62 (s, 8H), 3.08 (m, 2H), 3.24 (m, 2H), 3.6 (t, 3H),
4.13 (s,2H), 6.90 (broad s, 2H), 7.22 (broad s, 2H), 7.28 (d, 2H).
13C NMR (400 MHz CDCl3) δ 14.35, 14.41, 21.19, 21.27, 22.87,
23.11, 23.12, 24.17, 24.46, 24.68, 25.29, 27.12, 31.50, 31.8,
33.91, 34.72, 36.34, 36.38, 43.29, 44.57, 45.12, 48.93, 51.75,
60.61, 125.74, 128.38, 132.28, 132.30, 132.56, 133.36, 133.39,
140.25, 140.29, 142.80, 151.11, 172.95, 174.11 IR (cm-1) 3387.9,
2952.2, 1738.3, 1655.3, 1603.5, 1541.2, 1458.2.
17-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[(4-tert-
butyl)benzyl]}amino-13-[N-2,4,6-(trimethyl)benzene-
sulfonyl]-8-oxo-7,11-diazaheptadecanoic Acid Methyl Es-
ter (35b). Compound 35b was synthesized from 34a and 27b
using the method described for the synthesis of 29c in 78.3%
yield. 1H NMR (400 MHz CDCl3) δ 1.28 (s, 9H), 1.32-1.36 (m,
8H), 1.58-1.7 (m, 8H), 2.09 (t,J ) 2.8 Hz, 2H), 2.30 (m, 8H),
2.58 (d, J ) 9.2 Hz, 12H), 3.03 (m, 4H), 3.20 (q, J ) 6.8 Hz,
6H), 3.6 (s, 3H), 4.12 (s, 2H), 5.979 (t, J ) 5.6 Hz, 1H), 6.90 (d,
J ) 8.4 Hz, 2H), 6.96 (s, 4H), 7.27 (d, J ) 1.2 Hz, 2H). 13C
NMR (400 MHz CDCl3) δ 21.19, 23.12, 24.17, 24.46, 24.74,
24.93, 24.97, 25.74, 27.09, 28.89, 28.95, 29.02, 29.10, 31.51,
34.06, 34.2, 34.73, 36.36, 36.76, 43.29, 44.58, 45.13, 48.95,
21.70, 51.72, 125.74, 128.37, 132.28, 132.55, 133.36, 133.39,
140.25, 140.31, 142.81, 151.13, 173.66, 174.45, 178.43. IR
(cm-1) 2929.7, 2864.9, 1736.2, 1645.4, 1600.0, 1554.6, 1314.6,
1139.5.
1-Phthalimido-4-{N-[2,4,6-(trimethyl)benzenesulfon-
yl]}-8-{N-[3,3-(diphenyl)propyl]-N-[2,4,6-(trimethyl)-
benzenesulfonyl]}amino-4-azaoctane (33b). Compound
33b was synthesized from 32 and 3,3-diphenylpropyl chloride
using the procedure described for the synthesis of 33a in 60.3%
17-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[3,3-
(diphenyl)propyl]}amino-13-[N-2,4,6-(trimethyl)-
benzenesulfonyl]-8-oxo-7,11-diazaheptadecanoic Acid
Methyl Ester (35c). Compound 35c was synthesized from
34b and 27b using the method described for the synthesis of
29c in 75.1% yield. 1H NMR (400 MHz CDCl3) δ 1.25-1.39
(m, 8H), 1.55-1.69 (m, 6H), 2.05 (q, J ) 8 Hz, 2H), 2.07 (m,
2H), 2.28 (m, 2H), 2.32 (m, J ) 8 Hz, 8H), 2.45 (s, 6H), 2.57 (s,
6H), 2.93 (t, J ) 7.6 Hz, 2H), 3.10 (t, J ) 7.6 Hz, 2H), 3.15-
3.22 (m, 6H), 3.65 (s, 3H), 3.69 (t, J ) 8 Hz, 1H), 5.84 (t, 1H),
6.91 (d, J ) 9.6 Hz, 2H), 6.98 (d, J ) 7.2 Hz, 4H), 7.14-7.20
(m, 5H). 13C NMR (400 MHz CDCl3) δ 14.42, 21.17, 21.20,
21.29, 22.93, 23.10, 24.47, 24.72, 24.98, 25.73, 27.13, 29.04,
29.12, 32.75, 34.20, 36.35, 36.74, 43.32, 44.09, 45.14, 45.29,
48.87, 51.69, 60.29, 126.65, 127.65, 128.79, 132.24, 132.31,
1
yield. H NMR (400 MHz CDCl3) δ 1.40 (m, 4H), 1.69 (q, J )
7.2 Hz, 2H), 2.08 (q, J ) 8 Hz, 2H), 2.3 (s, 3H), 2.44 (s, 3H),
2.51 (d, J ) 11.2 Hz, 12H), 3.03 (t, J ) 8 Hz, 2H), 3.09 (t, J )
8 Hz, 1H), 3.16 (m, 4H), 3.46 (t, J ) 6.8 Hz, 2H), 3.73 (t, J )
8 Hz, 1H), 6.76 (s, 2H), 6.90 (s, 2H), 7.03 (d, J ) 7.6 Hz, 2H),
7.12-7.27 (m, 7H), 7.68 (m, 2H), 7.8 (m, 2H). 13C NMR (400
MHz CDCl3) δ 14.43, 21.18, 21.20, 21.29, 22.96, 22.99, 24.85,
24.90, 26.74, 32.98, 35.43, 44.37, 44.42, 45.40, 45.44, 48.96,
60.62, 123.40, 126.59, 127.76, 128.78, 132.13, 132.18, 132.19,
133.09, 133.4, 134.23, 140.18, 140.35, 142.49, 142.66, 143.99,
168.25. IR (cm-1) 3059.5, 3020.5, 2936.2, 1768.7, 1716.8,
1600.0, 1561.1, 1450.8, 1139.5.
1-Amino-4-{N-[2,4,6-(trimethyl)benzenesulfonyl]}-8-
{N-[4-(tert-butyl)benzyl]-N-[2,4,6-(trimethyl)benzenesulfon-
yl]}amino-4-azaoctane (34a). Compound 34a was prepared
from 33a using the procedure described for the synthesis of
27c in 70.8% yield. 1H NMR (CDCl3) δ 1.28(s,9H) 1.4 (m, 2H),
1.61 (m,2H), 1.56 (m, 2H), 2.24 (s, 6H), 2.51 (s, 6H), 2.57 (s,-
6H), 2.62 (q, J ) 6.8 Hz, 2H), 3.08 (t, J ) 7.2 2H), 3.24 (t, J )
7.6 Hz, 2H), 3.49 (t, J ) 7.2 Hz, 2H), 4.2 (s,2H), 6.81 (s, 2H),
6.95 (m, 6H), 7.23 (d, J ) 6.8 Hz, 2H). 13C NMR (400 MHz
CDCl3) δ 21.11, 21.48, 21.79, 22.5, 22.8, 25.42, 26.87, 28.43,
28.48, 31.74, 32.59, 40.08, 46.77, 46.81, 125.12, 128.2, 136.44,
145.1, 145.64.
1-Amino-4-{N-[2,4,6-(trimethyl)benzenesulfonyl]}-8-
{N-[3,3-(diphenyl)propyl]-N-[2,4,6-(trimethyl)benzenesulfon-
yl]}amino-4-azaoctane (34b). Compound 34b was prepared
from 33b using the procedure described for the synthesis of
27c in 78.5% yield. 1H NMR (400 MHz CDCl3) δ 1.37 (m, 4H),
1.58 (q, J ) 7.2 Hz, 2H), 2.04 (m, 2H), 2.28 (s, 3H), 2.31 (s,
3H), 2.46 (s, 6H), 2.57 (s, 6H), 2.97 (t, J ) 8 Hz, 2H), 3.10 (t,
J ) 4.8 Hz, 2H), 3.17 (m, 4H), 3.48 (t, J ) 7.2 Hz, 1H), 3.7 (q,
J ) 5.6 Hz, 2H), 6.9 (d, J ) 3.2 Hz, 4H), 7.01 (d, J ) 6.8 Hz,
4H), 7.12-7.23 (m, 5H). 13C NMR (400 MHz CDCl3) δ 14.40,
14.99, 15.84, 21.14, 21.19, 21.26, 22.91, 23.05, 24.66, 25.33,
25.44, 29.90, 31.02, 39.31, 41.28, 42.45, 43.20, 44.63, 45.14,
45.46, 48.90, 52.04, 55.64, 60.06, 64.29, 126.60, 127.67, 128.76,
129.46, 132.18, 133.35, 133.40, 140.22, 140.29, 142.51, 142.60,
143.89, 149.41 IR (cm-1) 3364.3, 3027.0, 2936.2, 2871.4, 1600.0,
1561.1, 1314.6, 1139.5.
133.36, 140.25, 142.61, 142.79, 143.82, 173.42, 174.42 IR (cm-1
2936.2, 2851.9, 1736.2, 1671.4, 1638.9, 1593.5, 1146.0.
)
15-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[3,3-
(diphenyl)propyl]}amino-11-[N-2,4,6-(trimethyl)-
benzenesulfonyl]-6-oxo-7,11-diazapentadecanoic Acid
Methyl Ester (35d). Compound 35d was synthesized from
34b and 27a using the method described for the synthesis of
29c in 72.6% yield. 1H NMR (400 MHz CDCl3) δ 1.32-1.39
(m, 4H), 1.58-1.60 (m, 4H), 1.68 (q, J ) 6.8 Hz, 4H), 1.99 (q,
J ) 8 Hz, 2H), 2.10 (t, J ) 6.8 Hz, 2H), 2.28-2.35 (d, J ) 9.2
Hz, 8H), 2.45 (s, 6H), 2.57 (s, 6H), 2.93 (t, J ) 8 Hz, 2H), 3.09
(t, J ) 9.6 Hz, 2H), 3.15-3.22 (m, 6H), 3.65 (m, 4H), 5.94 (s.
1H), 6.91 (d, J ) 9.6 Hz, 4H), 6.93 (d, J ) 6.8 Hz, 4H), 7.12-
7.22 (m, 5H). 13C NMR (400 MHz CDCl3) δ 14.41, 21.16, 21.19,
21.83, 22.92, 23.09, 24.46, 24.66, 24.71, 25.28, 27.14, 32.74,
33.91, 36.31, 36.42, 43.34, 44.08, 45.14, 45.28, 48.86, 51.75,
60.62, 126.64, 127.64, 128.79, 132.25, 132.31, 133.36, 140.23,
142.62, 142.81, 143.82, 172.96, 174.12. IR (cm-1) 3370.8,
2929.7, 1736.2, 1671.4, 1651.9, 1600.0, 1541.6.
15-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[(4-tert-
butyl)benzyl]}amino-11-[N-2,4,6-(trimethyl)benzene-
sulfonyl]-6-oxo-7,11-diazapentadecanoic Acid (36a). Com-
pound 36a was synthesized from 35a using the method
described for the synthesis of 30d in 70.6% yield. 1H NMR
(CDCl3) δ 1.28 (s,9H) 1.34 (m, 4H), 1.61 (m,4H), 1.72 (m, 2H),
2.11 (t, J ) 8.0 Hz, 2H), 2.24 (m, 8H), 2.51 (s, 6H), 2.62 (s,-
8H), 3.08 (m, 2H), 3.24 (m, 2H), 4.13 (s, 2H), 6.90 (broad s,
2H), 7.22 (broad s, 2H), 7.28 (d, J ) 6.8 Hz, 2H). 13C NMR
(400 MHz CDCl3) δ 14.41, 21.27, 23.11, 14.71, 24.46, 24.11,
27.09, 28.97, 29.11, 30.89, 31.50, 34.35, 34.67, 36.54, 36.26,
43.22, 44.05, 45.61, 48.69, 60.46, 64.76, 125.17, 128.53, 132.72,
15-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[(4-tert-
butyl)benzyl]}amino-11-[N-2,4,6-(trimethyl)benzene-
sulfonyl]-6-oxo-7,11-diazapentadecanoic Acid Methyl Es-
ter (35a). Compound 35a was synthesized from 34a and 27a

6362 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20
Varghese et al.
132.73, 132.15, 133.73, 140.12, 140.43, 142.43, 142.88, 151.81,
171.34, 173.28 IR (cm-1) 3377.3, 2929.7, 1723.2, 1645.4, 1600.0,
1548.1.
J 7.6 Hz, 2H), 6.96 (s, 4H), 7.24 (s, 2H). 13C NMR (400 MHz
CDCl3) δ 20.97, 21.21, 23.12, 24.18, 24.46, 31.51, 34.74, 44.59,
45.21, 48.91, 125.71, 128.31, 132.34, 132.4, 132.5, 133.3,
140.26, 140.21, 142.88, 151.15, 174.12. IR (cm-1) 3247.6,
2936.2, 2858.4, 1716.8, 1646.4, 1606.5, 1541.6, 1457.3.
17-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[(4-tert-
butyl)benzyl]}amino-13-[N-2,4,6-(trimethyl)benzene-
sulfonyl]-8-oxo-7,11-diazaheptadecanoic Acid (36b). Com-
pound 36b was synthesized from 35b using the method
described for the synthesis of 30d in 80.0% yield. 1H NMR (400
MHz CDCl3) δ 1.27 (s,9H), 1.32 (m, 8H), 1.56-1.62 (m, 4H),
1.68 (t, J ) 7.6 Hz, 2H), 2.30 (d, J ) 5.6 Hz, 8H), 2.57 (d, J )
10 Hz, 2H), 3.01 (m, 4H), 3.02-3.23 (m, 4H), 4.12 (s, 2H), 6.05
(s,1H), 6.90 (d, J ) 8 Hz, 2H), 6.95 (d, J ) 3.2 Hz, 4H), 7.25
(d, J ) 8.4 Hz, 2H).13C NMR (400 MHz CDCl3) δ 13.92, 14.41,
19.34, 21.19, 21.27, 23.11, 23.12, 24.17, 24.46, 24.81, 25.68,
27.09, 28.91, 28.99, 29.67, 29.91, 30.83, 31.51, 34.37, 34.72,
36.42, 36.69, 43.32, 44.58, 45.13, 48.94, 60.64, 64.60, 125.74,
128.38, 132.28, 132.31, 132.56, 133.37, 140.25, 140.34, 142.81,
151.11, 171.45, 173.81 IR (cm-1) 3370.9, 2929.7, 1723.2, 1645.4,
1600.0, 1549.2.
17-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[3,3-
(diphenyl)propyl]}amino-13-[N-2,4,6-(trimethyl)-
benzenesulfonyl]-8-oxo-7,11-diazaheptadecanohydrox-
amic Acid (37c). Compound 37c was synthesized from 36c
using the method described for the synthesis of 31d in 75.8%
1
yield. H NMR (400 MHz CDCl3) δ 1.24-1.39 (m, 8H), 1.54-
1.68 (m, 6H), 2.10 (m, 4H), 2.24 (s, 4H), 2.30 (s, 4H), 2.43 (s,
6H), 2.54 (s, 6H), 2.9 (m, 2H), 3.03 (m, 2H), 3.21 (m, 6H), 3.66
(t, 1H), 6.90 (s, 4H), 6.97 (d, J ) 6.4 Hz, 4H), 7.13-7.19 (m,
6H). 13C NMR (400 MHz CDCl3) δ 14.42, 21.21, 22.92, 23.10,
24.37, 24.70, 32.74, 43.42, 44.11, 45.31, 48.83, 60.65, 126.62,
127.66, 128.78, 132.26, 132.34, 133.33, 140.19, 140.24, 142.62,
142.81, 143.86, 171.45, 174.80. IR (cm-1) 3254.1, 2929.7,
2858.4, 1651.9, 1632.4, 1606.5, 1554.6.
17-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[3,3-
(diphenyl)propyl]}amino-13-[N-2,4,6-(trimethyl)-
benzenesulfonyl]-8-oxo-7,11-diazaheptadecanoic Acid
(36c). Compound 36c was synthesized from 35c using the
15-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[3,3-
(diphenyl)propyl]}amino-11-[N-2,4,6-(trimethyl)-
benzenesulfonyl]-6-oxo-7,11-diazapentadecanohydrox-
amic Acid (37d). Compound 37d was synthesized from 36d
using the method described for the synthesis of 31d in 70.2%
yield. 1H NMR (400 MHz CDCl3) δ 1.39 (m, 4H), 1.59-1.68
(m, 6H), 2.01 (m, 4H), 2.20 (s, 3H), 2.25 (s, 3H), 2.43 (s, 6H),
2.54 (s, 6H), 2.91 (m, 2H), 3.05 (m, 2H), 3.17 (m, 6H), 3.64 (t,
J ) 7.6 Hz, 1H), 6.90 (s, 4H), 6.98 (d, J ) 7.2 Hz, 2H), 7.12-
7.26 (m, 5H). 13C NMR (400 MHz CDCl3) δ 14.42, 21.20, 21.29,
22.97, 23.08, 24.68, 29.93, 32.71, 44.08, 45.30, 48.83, 52.55,
60.64, 126.64, 127.65, 128.79, 132.27, 133.31, 140.23, 142.67,
143.83, 162.23, 171.44. IR (cm-1) 3340.5, 1638.9, 1606.6,
1535.1, 1444.3, 1308.1.
15-N-[(4-tert-Butyl)benzyl]amino-6-oxo-7,11-diazapen-
tadecanohydroxamic Acid dihydrobromide (12). A 4.71
g portion of phenol (0.050 mol) was dissolved in 50 mL of 30%
HBr in acetic acid in a stoppered flask, and to this mixture
was added a solution of 37a (0.300 g, 0.0004 mol) in 20 mL of
ethyl acetate in three portions over a period of 3 h After the
addition was complete, the reaction mixture was stirred for
an additional 15 h at room temperature, then cooled to 0 °C,
and diluted with 100 mL of water. The aqueous phase was
washed with two 100 mL portions of ethyl acetate before being
lyophylized to give the crude product as yellow solid. This
crude product was washed with methanol and filtered to yield
the tetrahydrobromide salt of 12 (0.186 g, 77.8%) as an off
white solid. An analytical sample of 12 was prepared by
recrystallization from aqueous ethanol. 1H NMR (D2O) δ 1.20
(s, 9H), 1.42 (m, 4H) 1.61 (m, 4H), 2.01 (m,2H), 2.13 (m, 2H),
2.99 (m, 9H), 3.12 (m, 2H), 4.06 (s, 2H), 7.26 (d, J ) 6.4 Hz,
2H), 7.24 (d, J ) 6.4 Hz 2H). 13C NMR (400 MHz D2O) δ 22.85,
22.92, 22.98, 23.81, 24.06, 24.52, 24.78, 25.77, 30.55, 32.13,
34.26, 35.42, 36.06, 38.93, 45.21, 46.20, 47.00, 47.08, 50.73,
126.44, 127.83, 129.94, 130.13, 153.57, 173.06, 177.18. IR
(cm-1) 3419.0, 2952.2, 1696.8, 1686.5, 1634.6, 1603.5, 1551.6.
Anal. for C24H44Br2N4O3: C, H, N.
1
method described for the synthesis of 30d in 72.8% yield. H
NMR (400 MHz CDCl3) δ 1.25-1.43 (m, 8H), 1.58-1.67 (m,
6H), 1.97-2.08 (m, 4H), 2.27 (d, J ) 14 Hz, 8H), 2.44 (s, 6H),
2.56 (s, 6H), 2.93 (t, J ) 8 Hz, 2H), 3.08 (t, J ) 7.6 Hz, 2H),
3.19 (m, 6H), 3.66 (t, J ) 7.6 Hz, 1H), 6.00 (t, 1H), 6.92 (d, J
) 7.6 Hz, 4H), 6.98 (d, J 7.2 Hz, 4H), 7.12-7.20 (m, 5H). 13C
NMR (400 MHz CDCl3) δ 14.42, 21.17, 21.20, 21.29, 22.93,
23.01, 24.46, 24.72, 24.82, 25.68, 27.10, 28.91, 28.98, 29.65,
29.92, 30.53, 32.74, 34.45, 36.46, 36.66, 38.74, 43.35, 44.09,
45.13, 45.29, 45.78, 48.86, 60.66, 125.74, 126.65, 127.65,
128.80, 132.32, 133.33, 133.36, 140.24, 142.63, 142.82, 143.83,
171.48, 173.85. IR (cm-1) 3367.2, 2931.4, 172.0, 1645.0, 1593.1,
1541.0.
15-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[3,3-
(diphenyl)propyl]}amino-11-[N-2,4,6-(trimethyl)-
benzenesulfonyl]-6-oxo-7,11-diazapentadecanoic Acid
(36d). Compound 36d was synthesized from 35d using the
method described for the synthesis of 30d in 80% yield. 1H
NMR (400 MHz CDCl3) δ 1.41 (m, 4H), 1.43-1.68 (m, 6H),
1.99 (m, 2H), 2.11 (t, J ) 6.8 Hz, 2H), 2.27 (d, J ) 17.2 Hz,
6H), 2.44 (s, 6H), 2.58 (s, 6H), 2.93 (t, J ) 8 Hz, 2H), 3.09 (t,
J ) 6.8 Hz, 2H), 3.20 (m, 6H), 3.66 (t, J ) 7.6 Hz, 1H), 6.08 (s,
1H), 6.93 (d, J ) 8 Hz, 4H), 6.98 (d, J ) 6.8 Hz, 4H), 7.12-
7.21 (m, 5H). 13C NMR (400 MHz CDCl3) δ 14.40, 21.16, 21.19,
21.27, 22.92, 23.08, 24.45, 24.71, 25.14, 27.098, 29.91, 32.72,
33.78, 36.22, 36.54, 43.42, 44.06, 45.18, 45.28, 48.84, 60.64,
126.64, 127.63, 128.78, 132.26, 132.31, 133.30, 140.24, 142.65,
142.81, 143.81, 171.45, 173.37, 177.76. IR (cm-1) 3364.3,
2936.2, 1723.2, 1710.3, 1632.4, 1600.0, 1314.6, 1152.4.
15-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[(4-tert-
butyl)benzyl]}amino-11-[N-2,4,6-(trimethyl)benzene-
sulfonyl]-6-oxo-7,11-diazapentadecanohydroxamic Acid
(37a). Compound 37a was synthesized from 36a according to
the method described for the synthesis of 31d in 76.6% yield.
1H NMR (CDCl3) δ 1.27 (broad s, 13H), 1.61 (m, 4H), 2.16
(broad s, 2H), 2.3 (m, 8H), 2.54 (s, 6H), 2.62 (s, 8H), 2.99 (m,
4H), 3.24 (m, 4H), 4.11 (s, 2H), 6.87 (d, J ) 6.8 Hz,2H), 6.95
(s, 4H) 7.28 (d, J ) 7.2 Hz, 2H). 13C NMR (400 MHz CDCl3) δ
21.18, 23.10, 24.14, 24.40, 24.88, 27.28, 31.50, 34.71, 35.88,
36.83, 43.52, 44.58, 45.15, 48.89, 50.89, 125.72, 128.37, 132.30,
132.52, 133.23, 133.30, 140.23, 140.28, 142.85, 151.09, 174.16.
IR (cm-1) 3340.5, 2936.2, 2858.4, 1716.8, 1644.5, 1600.0,
1544.2, 1457.3.
17-N-[(4-tert-Butyl)benzyl]amino-8-oxo-7,11-diazahep-
tadecanohydroxamic Acid dihydrobromide (16). Com-
pound 16 was synthesized from 37b using the method de-
scribed for the synthesis of 12 in 78.4% yield. An analytical
sample of 16 was prepared by recrystallization from aqueous
ethanol. 1H NMR (400 MHz D2O) 1.15-1.28 (m, 13H), 1.62
(m, 4H), 1.74 (m, 2H), 1.99 (m, 2H), 2.10 (m, 2H), 2.91 (m,
8H), 3.14 (m, 2H), 4.07 (d, J ) 10.08 Hz, 2H), 7.29 (t, J ) 8
Hz, 2H), 7.42 (t, J ) 9.6 Hz, 2H). 13C NMR (400 MHz D2O) δ
22.84, 24.48, 25.23, 25.77, 27.76, 27.91, 30.54, 32.38, 35.70,
36.00, 45.19, 46.16, 47.00, 50.71, 126.44, 127.83,129.94, 130.13,
153.44, 173.41, 177.85. IR (cm-1) 3240.5, 2936.2, 1682.2,
1645.4, 1603.2, 1541.6, 1457.3. Anal. for C26H48Br2N4O3: C,
H, N.
17-{N-[2,4,6-(Trimethyl)benzenesulfonyl-N-[(4-tert-
butyl)benzyl]}amino-13-[N-2,4,6-(trimethyl)benzene-
sulfonyl]-8-oxo-7,11-diazaheptadecanohydroxamic Acid
(37b). Compound 37b was synthesized from 36b using the
1
method described for the synthesis of 31d in 65.9% yield. H
17-N-[4-(3,3-Diphenyl)propyl]amino-8-oxo-7,11-diaza-
heptadecanohydroxamic Acid dihydrobromide (20). Com-
pound 20 was synthesized from 37c using the method de-
scribed for the synthesis of 12 in 75.7% yield. An analytical
NMR (400 MHz CDCl3) δ 1.27 (s, 9H), 1.31 (m, 8H), 1.61-
1.69 (m, 4H), 2.1 (m, 3H), 2.29-2.31 (m, s, 7H), 2.58 (d, J )
7.6 Hz, 12H), 3.02 (m, 4H), 3.23 (m, 4H), 4.10 (s, 2H), 6.88 (d,

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6363
sample of 20 was prepared by recrystallization from aqueous
ethanol. 1H NMR (400 MHz D2O) δ 1.07 (m, 4H), 1.39 (m, 4H),
1.53 (m, 4H), 1.68 (m, 2H), 1.96 (m, 2H), 2.06 (m, 2H), 2.30
(m, 2H), 2.83 (m, 8H), 3.09 (m, 2H), 3.94 (m, 1H), 7.11 (m,-
1H), 7.22 (m, 8H). 13C NMR (400 MHz D2O) δ 20.61, 22.76,
22.86, 24.84, 22.86, 24.84, 25.20, 25.75, 27.73, 27.89, 30.85,
32.33, 35.65, 35.93, 45.12, 45.43, 46.75, 46.94, 48.08, 61.82,
11,15,19-Tris{N-[2,4,6-(trimethyl)benzenesulfonyl]}-22-
{N-[2,4,6-trimethylbenzenesulfonyl)]-N-[2-(cycloheptyl)-
methyl]amino}-6-oxo-7,11,15,19-tetraazadocosanoic Acid
Methyl Ester (41c).
Compounds 41a-c were synthesized from 40a-c and 28a
in two steps using the methods described for the synthesis of
27a and 29a.
63.38, 127.15, 127.58, 129.18, 143.64, 173.58, 177.85 IR (cm-1
)
Compound 41a (70% yield). 1H NMR (CDCl3) δ 1.08 (m, 2H),
1.48 (m, 2H), 1.43-1.79 (m, 8H), 2.05 (m, 2H), 2.21-2.39 (m,
14H), 2.53 (m, 28H), 2.77 (t, J ) 7.2 Hz, 2H), 2.98 (m, 8H),
3.12 (m, 4H), 3.61 (s, 3H), 4.19 (s, 2H), 6.91 (s, 2H), 6.94 (m,
6H), 7.13 (m, 4H), 7.24 (m, 3H), 7.35 (m, 2H). 13C NMR (400
MHz CDCl3) δ 21.18, 22.98, 23.02, 23.05, 23.08, 24.26, 24.68,
25.11, 25.28, 25.41, 25.78, 27.13, 33.91, 34.02, 36.25, 42.75,
43.25, 43.28, 46.18, 51.75, 109.99, 127.69, 127.78, 128.98,
128.65, 129.19, 129.46, 130.29, 132.18, 132.29, 132.34, 132.85,
133.06, 140.06, 140.26, 140.44, 142.46, 142.80, 142.89, 142.95,
172.45, 174.32. IR (cm-1) 3336.0, 2931.4, 1740.5, 1655.3,
1582.7.
3390.3, 2923.2, 2845.4, 1658.4, 1632.4, 1554.6, 1444.3. Anal.
for C30H48Br2N4O3: C, H, N.
15-N-[4-(3,3-diphenyl)propyl]amino-6-oxo-7,11-diaza-
pentadecanohydroxamic Acid dihydrobromide (21). Com-
pound 21 was synthesized from 37d using the method de-
scribed for the synthesis of 12 in 70.1% yield. An analytical
sample of 21 was prepared by recrystallization from aqueous
ethanol. 1H NMR (400 MHz D2O) δ 1.07 (m, 4H), 1.39 (m, 4H),
1.53 (m, 4H), 1.68 (m, 2H), 1.97 (m, 2H), 2.06 (m, 2H), 2.30
(m, 2H), 2.83 (m, 8H), 3.01 (m, 2H), 3.94 (m, 2H), 7.11 (m,
1H), 7.22 (m, 8H). 13C NMR (400 MHz D2O) δ 22.8, 22.89,
24.51, 24.78, 25.79, 30.89, 35.42, 36.02, 45.12, 45.18, 46.49,
46.72, 46.81, 46.97, 48.13, 127.18, 127.18, 127.62, 129.22,
143.68, 177.23. IR (cm-1) 3383.8, 2903.8, 1658.4, 1632.4,
1561.1, 1444.3. Anal. for C28H44Br2N4O3: C, H, N.
Compound 41b (74% yield). 1H NMR (CDCl3) δ 0.01 (m, 2H),
0.46 (m, 2H), 0.75 (m, 1H), 1.58 (m, 12H), 2.01 (m, 2H), 2.32
(s, 12H), 2.43 (m, 2H), 2.68 (s, 24H), 2.92 (d, J ) 6.8 Hz, 2H),
3.06 (m, 10H), 3.18 (m, 4H), 3.78 (s, 3H), 6.98 (m, 8H). IR
(cm-1) 3383.7, 1742.7, 1664.8, 1606.4, 1561.0.
1-(Phthalimido)-4,8,12-tris{N-[2,4,6-(trimethyl)ben-
zenesulfonyl]}-15-N-[2,4,6-trimethylbenzenesulfonyl)-
amino]-4,8,12-triazapentadecane (39). Compound 39 was
synthesized from 38 using the procedure described for the
1
Compound 41c (70.2% yield). H NMR (CDCl3) δ 0.77 (m,
2H), 1.22 (m, 2H), 1.33-1.44 (m, 8H), 1.61-1.78 (m, 12H), 2.1
(t, 2H), 2.22 (m, 14H), 2.53 (s, 12H), 2.58 (s, 14H), 2.75 (d, J )
6.8 Hz, 2H), 2.9-3.01 (m, 12H), 3.14-3.18 (m, 4H), 3.67 (s,-
3H), 6.88-6.94 (m, 8H). 13C NMR (400 MHz CDCl3) δ 21.19,
23.06, 24.32, 24.49, 24.66, 25.29, 25.39, 25.95, 27.11, 28.70,
31.52, 33.78, 33.87, 36.28, 36.40, 36.47, 43.45, 43.52, 43.64,
51.76, 51.89, 132.15, 132.30, 132.34, 133.18, 140.15, 140.27,
142.95, 173.24, 174.02, 174.17, 178.84.
1
synthesis of 33a in 65.7% yield. H NMR (CDCl3) δ 1.22 (m,
4H), 1.33-1.44 (m, 2H), 1.61-1.72 (m, 2H), 2.22 (s, 12H), 2.53
(s, 12H), 2.58 (s, 12H), 2.8 (q, 2H), 2.95 (m, 8H), 3.2 (t, J ) 7.2
Hz, 2H), 6.99 (d, J ) 6.8 Hz, 8H), 7.73 (m, 2H), 7.83-7.85 (m,
2H).
1-(Phthalimido)-4,8,12-tris{N-[2,4,6-(trimethyl)ben-
zenesulfonyl]}- 15-{N-[2,4,6-(trimethyl)benzenesulfonyl]-
N-[2-(phenyl)benzyl]}amino-4,8,12-triazapentadecane
(40a).
1-(Phthalimido)-4,8,12-tris{N-[2,4,6-(trimethyl)ben-
zenesulfonyl]}- 15-{N-[2,4,6-(trimethyl)benzenesulfon-
yl]-N-[(cyclopropyl)methyl]}amino-4,8,12-triazapenta-
decane (40b).
1-(Phthalimido)-4,8,12-tris{N-[2,4,6-(trimethyl)ben-
zenesulfonyl]}-15-{N-[2,4,6-(trimethyl)benzenesulfonyl]-
N-[(cycloheptyl)methyl]}amino-4,8,12-triazapentade-
cane (40c).
Compounds 40a-c were synthesized from 39 and the
appropriate alkyl halide using the method described for the
synthesis of 33a.
11,15,19-Tris{N-[2,4,6-(trimethyl)benzenesulfonyl]}-22-
{N-[2,4,6-trimethylbenzenesulfonyl)]-N-[2-(phenyl)benz-
yl]amino}-6-oxo-7,11,15,19-tetraazadocosanohydroxamic
Acid (42a).
11,15,19-Tris{N-[2,4,6-(trimethyl)benzenesulfonyl]}-22-
{N-[2,4,6-trimethylbenzenesulfonyl)]-N-[(cyclopropyl)-
methyl]amino}-6-oxo-7,11,15,19-tetraazadocosanohydrox-
amic Acid (42b).
11,15,19-Tris{N-[2,4,6-(trimethyl)benzenesulfonyl]}-22-
{N-[2,4,6-trimethylbenzenesulfonyl)]-N-[2-(cycloheptyl)-
methyl]amino}-6-oxo-7,11,15,19-tetraazadocosanohydrox-
amic Acid (42c).
Compounds 42a-c were synthesized from 41a-c in two
steps using the methods described for the synthesis of 30a and
31a.
Compound 40a (65% yield). 1H NMR (400 MHz CDCl3) δ
1.08 (m, 2H), 1.48(m, 2H), 1.62(m, 4H), 2.21(m, 12H), 2.43(s,
6H), 2.46(s, 6H), 2.52(m, 14H), 2.64(t, J ) 6.8 Hz, 2H), 2.75(t,
J ) 7.2 Hz, 2H), 2.91-3.07(m, 8H), 3.42(t, J ) 6.8 Hz, 2H),
4.27(s, 2H), 6.77(s, 2H), 6.85(s, 2H), 6.91(s, 2H), 6.94(s, 2H),
7.16(m, 3H), 7.26(m, 3H), 7.38(m, 3H), 7.72(m, 2H), 7.80(m,
2H).
Compound 42a (62.6% yield). 1H NMR (CDCl3) δ 1.41-1.79
(m, 12H), 2.13 (m, 2H), 2.21-2.38 (m, 14H), 2.40-2.59 (m,
28H), 2.78(t, J ) 7.2 Hz, 2H), 2.98(m, 6H), 3.18(m, 2H), 4.20-
(s, 2H), 6.88(s, 2H),6.96(m, 6H), 7.15-7.43(m, 9H) 13C NMR
(400 MHz CDCl3) δ 14.42, 21.13, 21.18, 21.21, 21.28, 23.02,
23.09, 24.15, 24.40, 27.61, 31.61, 39.57, 42.39, 43.25, 43.82,
45.24, 46.15, 51.71, 60.61, 110.12, 127.66, 127.77, 127.99,
128.64, 129.19, 129.48, 130.27, 132.14, 132.33, 133.08, 133.31,
134.19, 139.11, 140.03, 140.17, 140.29, 140.45, 142.12, 142.46,
142.62, 142.83, 142.93, 168.21, 174.13 IR (cm-1) 3407.6, 2910.1,
2765.4, 1664.7, 1644.9, 1603.6, 1447.84.
Compound 40b (73% yield). 1H NMR (CDCl3) δ 0.02 (m, 2H),
0.45 (dd, J ) 8 Hz, 5.2 Hz, 2H), 0.75 (m, 1H), 1.66 (m, 8H),
2.18 (s, 2H), 2.25 (s, 2H), 2.30 (s, 8H), 2.48 (s, 6H), 2.56 (s,
18H), 2.91 (d, J ) 6.8 Hz, 2H), 3.01 (m, 12H), 3.15 (t, J ) 7.2
Hz, 2H), 3.44(t, J ) 6.8 Hz, 2H), 6.79 (s, 2H), 6.94 (s, 6H),
7.76 (m, 2H), 7.82 (m, 2H).
1
Compound 42b (60.9% yield). H NMR (CDCl3) δ 0.01 (m,
1
Compound 40c (72.2% yield). H NMR (400 MHz CDCl3) δ
2H), 0.5 (m, 2H), 0.72 (m, 1H), 1.73 (m, 12H), 2.29 (m, 2H),
2.30 (m, 2H), 2.41 (s, 12H), 2.65 (s, 24H), 2.88 (d, J ) 6.8 Hz,
2H), 3.04 (t, J ) 7.6 Hz, 2H), 3.10 (m, 8H), 3.21 (t, J ) 7.2 Hz,
2H), 3.28 (m, 4H), 7.06 (s, 8H). 13C NMR (400 MHz CDCl3) δ
5.05, 11.08, 17.20, 18.02, 18.96, 19.05, 19.09, 20.71, 21.30,
21.55, 25.94, 31.74, 32.63, 46.13, 128.21, 128.31, 128.35,
128.96, 129.07, 129.21, 136.29, 138.75, 139.0, 150.92, 169.62,
172.23. IR (cm-1) 3312.0, 2904.4, 1658.2, 1645.4, 1605.8,
1540.9.
0.77 (m,2H),1.22 (m, 8H), 1.33-1.44(m, 6H), 1.61-1.72 (m,
6H), 2.22 (s, 12H), 2.53 (s, 12H), 2.58 (s,12H),2.7 (d, J ) 6.8
Hz, 2H) 2.8 (q, J ) 6.6 Hz, 2H),2.95 (m, 12H), 3.2 (t, J ) 7.2
Hz, 2H), 6.99 (d, J ) 7.6 Hz, 8H), 7.73 (m, 2H), 7.83-7.85 (m,
2H).
11,15,19-Tris{N-[2,4,6-(trimethyl)benzenesulfonyl]}-22-
{N-[2,4,6-trimethylbenzenesulfonyl)]-N-[2-(phenyl)-
benzyl]amino}-6-oxo-7,11,15,19-tetraazadocosanoic Acid
Methyl Ester (41a).
1
Compound 42c (75.9% yield). H NMR (CDCl3) δ 0.77 (m,
11,15,19-Tris{N-[2,4,6-(trimethyl)benzenesulfonyl]}-22-
{N-[2,4,6-trimethylbenzenesulfonyl)]-N-[(cyclopropyl)-
methyl]amino}-6-oxo-7,11,15,19-tetraazadocosanoic Acid
Methyl Ester (41b).
4H), 1.33-1.44 (m, 8H), 1.61-1.78 (m, 12H), 2.15-2.27 (m,
4H), 2.22 (s, 12H), 2.53 (s, 12H), 2.58 (s,12H), 2.66 (d, J ) 7.2
Hz, 2H), 2.9-3.01 (m, 12H), 3.14-3.18 (m, 4H), 6.92-6.98 (m,
8H).13C NMR (400 MHz CDCl3) δ 14.42, 21.19, 21.29, 23.02,

6364 Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20
Varghese et al.
23.06, 24.72, 24.88, 25.36, 25.94, 28.71, 36.44, 43.38,43.56,
60.64, 64.60, 132.15, 132.34, 132.98, 133.10, 133.33, 133.97,
140.14, 140.26, 142.70, 142.97, 171.44, 173.82.
(m, 4h), 2.29-2.36 (m, 4H), 2.94 (d, J ) 8.4 Hz, 6H), 3.09 (m,
2H), 3.27 (t, J ) 7.2 Hz, 1H), 3.32 (t, J ) 8.6 Hz, 1H), 4.41 (s,
1H), 4.48 (s, 1H), 6.66 (d, J ) 8.4 Hz, 1H), 6.72 (d, J ) 8.8 Hz,
1H), 7.02 (d, J ) 8.8 Hz, 1H), 7.1 (d, J ) 8.8 Hz, 1H), 8.22 (d,
J ) 8.8 Hz, NH). 13C NMR (400 MHz CDCl3) δ 25.00, 25.26,
25.35, 25.88, 27.60, 28.37, 28.64, 28.92, 29.90, 33.00, 33.27,
34.01, 40.28, 40.44, 40.87, 40.91, 45.58, 46.47, 47.65, 50.79,
81.63, 112.89, 113.10, 124.55, 127.50, 129.44, 150.12, 150.27,
155.91, 156.27, 173.19, 173.67, 174.97. IR (cm-1) 3267.0,
2975.1, 2936.2, 2864.9, 1684.3, 1677.8, 1619.5, 1509.2, 1450.8.
22-{N-[2-(Phenyl)benzyl]amino}-6-oxo-7,11,15,19-tetra-
azadocosanohydroxamic Acid (7). Compound 7 was syn-
thesized from 42a using the method described for the synthesis
of 12 in 68% yield. 1H NMR (D2O) δ 1.48 (m, 4H), 1.79 (m,
4H), 1.98 (m, 4H), 2.15 (m, 2H), 2.23 (m, 2H), 2.75 (t, J ) 8.0
Hz, 2H), 2.8-3.05 (m, 12H), 3.12 (t, J ) 6.4 Hz, 2H), 4.16 (s,
2H), 7.24-7.44 (m, 9H). 13C NMR (400 MHz D2O) δ 22.42,
22.76, 22.83, 23.75, 23.81, 24.83, 25.77, 33.42, 33.51, 35.47,
36.06, 43.92, 44.62, 44.67, 45.44, 48.23, 115.47, 120.78, 128.05,
128.21, 128.67, 129.10, 129.56, 129.90, 130.08, 130.12, 130.97,
139.53, 142.81, 177.23, 178.65. IR (cm-1) 3419.0, 3045.5,
2910.6, 1688.5, 1651.3, 1603.4. Anal. for C31H54Br4N6O3: C,
H, N.
7-{[4-(Amino)butyl]-N-[4-(dimethylaminobenzyl)-
carbamoyl]}heptanohydroxamic Acid (19). synthesized
from 32 according to the procedure mentioned for 13 in 90.9%
1
yield. H NMR (400 MHz CD3OD) δ 1.31-1.40 (m, 4H), 1.64
(m, 8H), 2.26-2.36 (m, 2H), 2.38 (t, J ) 4.8 Hz, 1H), 2.49 (t,
J ) 4.8 Hz, 1H), 2.94 (m, 2H), 3.29 (s, 6H), 3.39 (m, 2H), 4.65
(s, 1H), 4.73 (s, 1H), 7.45 (t, J ) 7.2 Hz, 2H), 7.62 (d, J ) 6
Hz, 1H), 7.67 (d, J ) 5.6 Hz, 1H). 13C NMR (400 MHz CD3-
OD) δ 24.14, 24.59, 24.72, 24.77, 24.97, 25.13, 25.42, 28.62,
28.68, 28.78, 32.52, 32.86, 39.11, 50.33, 114.58, 117.45, 120.59,
120.94, 128.400, 129.46, 139.73, 140.57, 141.98, 160.22, 173.05,
174.63, 175.03. IR (cm-1) 2936.2, 1671.4, 1626.0, 1515.7,
1463.8, 1424.8. Anal. for C23H37F3N4O5: C, H, N.
22-{N-[(Cyclopropyl)methyl]amino}-6-oxo-7,11,15,19-
tetraazadocosanohydroxamic Acid (9). Compound 9 was
synthesized from 42b using the method described for the
1
synthesis of 12 in 65% yield. H NMR (D2O) δ 0.22 (m, 2H),
0.54 (m, 2H), 0.91 (m, 1H), 1.45(m, 5H), 1.75 (q, J ) 6.8 Hz,
3H), 1.98 (m, 4H), 2.13 (t, J ) 6.8 Hz, 2H) 2.25(t, J ) 7.2 Hz,
2H), 2.83 (d, J ) 7.6 Hz, 2H), 2.93 (t, J ) 7.6 Hz, 2H), 3.05
(m, 12H), 3.14 (t, J ) 7.2 Hz, 2H). IR (cm-1) 3312.1, 2931.4,
1655.3, 1645.4, 1593.0. Anal. for C22H50Br4N6O3: C, H, N.
22-{N-[2-(Cycloheptyl)methyl]amino}-6-oxo-7,11,15,19-
tetraazadocosanohydroxamic Acid (10). Compound 10
was synthesized from 42c using the method described for the
synthesis of 12
1-N-[2,4,6-(Trimethyl)benzenesulfonyl]amino-4-N-[2,4,6-
(trimethyl)benzenesulfonyl]-8-N-{4-[N,N-(dimethyl)-
benzyl]amino}-4-azaoctane (46). Compound 46 was syn-
thesized in two steps from 32 using the procedure described
for the syntheses of 27c and 25c in 77.3% overall yield. 1H
NMR (400 MHz CDCl3) δ 1.35 (q, J ) 7.6 Hz, 2H), 1.47 (q, J
) 6.8 Hz, 2H), 1.57 (q, J ) 6.8 Hz, 2H), 2.28 (d, J ) 2.8 Hz,
6H), 2.51-2.59 (m, 14H), 2.78 (t, J ) 6.8 Hz, 2H), 3.13 (t, J )
7.6 Hz, 2H), 3.17 (t, J ) 7.6 Hz, 2H), 6.93 (d, J ) 10 Hz, 4H).
13C NMR (400 MHz CDCl3) δ 14.21,19.08, 22.47, 25.6, 26.22,
27.46, 32.41, 40.12, 40.1, 43.88, 46.18, 127.44, 128.14, 136.25,
137.49, 141.58, 142.33.
5-[(4-N,N-(Dimethylamino)benzyl)-(4-{(2,4,6-trimeth-
yl-benzenesulfonyl)-[3-(2,4,6-trimethyl-benzenesulfonyl-
amino)propyl]amino}butyl)carbamoyl]pentanoic Acid
Methyl Ester (47). Compound 47 was synthesized from 46
and 28a using the procedure described for the synthesis of 29d
in 81.6% yield. 1H NMR (400 MHz CDCl3) δ 1.26 (m, 2H), 1.63
(m, 2H), 1.68 (m, 6H), 2.29 (m, 2H), 2.32 (m, 6H), 2.36 (m,
2H), 2.52 (m, 6H), 2.62 (m, 6H), 2.79 (m, 2H), 2.92 (s, 6H),
3.01-3.13 (m, 6H), 3.67 (s, 3H), 4.29 (s, 1H), 4.35 (s, 1H), 6.68
(d, J ) 8.4 Hz, 2H), 6.88-6.95 (m, 6H). IR (cm-1) 3409.7,
2923.2, 1736.8, 1664.8, 1619.4, 1528.6.
5-[(4-N,N-(Dimethylamino)benzyl)-(4-{(2,4,6-trimeth-
yl-benzenesulfonyl)-[3-(2,4,6-trimethyl-benzenesulfon-
ylamino)propyl]amino}butyl)carbamoyl]pentano-
hydroxamic Acid (48). Compound 48 was synthesized in two
steps from 47 using the procedures described for the syntheses
of 30d and 31d in 66.2% overall yield. 1H NMR (400 MHz D2O)
δ 1.40 (m, 4H), 1.50 (m, 2H) 1.63 (m, 4H) 1.80 (m, 1H), 1.98
(m, 1H), 2.07 (m, 1H), 2.31 (m, 1H), 2.71 (m, 1H), 2.90-2.93
(m, 8H), 3.14 (d, J ) 4.4 Hz, 6H), 3.38 (m, 2H), 7.31 (d, J )
8.4 Hz, 2H), 7.44 (d, J ) 8.8 Hz, 1H), 7.49 (d, J ) 8.8 Hz, 1H).
IR (cm-1) 3398.3, 2941.8, 2683.2, 1613.0, 1522.2, 1470.3,
1184.9, 990.3.
1
in 70.4% yield H NMR (D2O) δ 1.08-1.16 (m, 4H), 1.28-
1.58(m, 14H), 1.73-1.78 (m, 2H), 1.93-2.07 (m, 6H), 2.78 (d,
J ) 8.8 Hz, 2H), 2.93 (t, J ) 7.2 Hz, 2H) 2.96-3.01 (m, 12H),
3.12-3.16 (t, J ) 6.8 Hz, 2H).13C NMR (400 MHz D2O) δ 22.66,
22.79, 24.52, 24.76, 25.42, 25.81, 27.95, 31.25, 32.12, 35.42,
36.01, 36.30, 173.11, 177.26 IR (cm-1) 3408.7, 2910.7, 2848.4,
1665.7, 1644.0, 1447.8. Anal. for C26H58Br4N6O3: C, H, N.
7-{4-[(Phthalimido)amino]butyl}-{N-[4-N,N-(dimethyl)-
aminobenzyl]carbamoyl}heptanoic Acid Methyl Ester
(43). Compound 43 was synthesized from 25c and 28b using
the procedure described for the synthesis of 29c in 72.6% yield.
1H NMR (400 MHz CDCl3) δ 1.24-1.35 (m, 4H), 1.61-1.64
(m, 8H), 2.26-2.36 (m, 4H), 2.92 (d, J ) 8.8 Hz, 6H), 3.20 (t,
J ) 7.2 Hz, 1H), 3.36 (t, J ) 6.8 Hz, 1H), 3.65-3.71 (m, 5H),
4.42 (s, 1H), 4.48 (s, 1H), 6.65 (d, J ) 8.8 Hz, 1H), 6.69 (d, J
) 8.4 Hz, 1H), 7.01 (d, J ) 7.6 Hz, 1H), 7.11 (d, J ) 8.4 Hz,
1H), 7.69-7.75 (m, 2H), 7.80-7.86 (m, 2H). 13C NMR (400 MHz
CDCl3) δ 24.82, 24.99, 25.56, 26.21, 28.92, 28.97, 29.20, 29.29,
33.24, 33.40, 34.19, 37.57, 37.86, 40.81, 40.86, 45.39, 46.23,
47.62, 50.79, 51.65, 112.84, 113.00, 123.37, 123.50, 124.50,
125.84, 127.47, 129.46, 132.19, 134.08, 134.26, 150.11, 150.21,
168.57, 173.08, 174.45 IR (cm-1) 3461.6, 2936.2, 2858.4, 1742.7,
1768.7, 1710.3, 1638.9, 1613.0, 1515.7.
7-{4-[N-(tert-Butyloxycarbonyl)amino]butyl}-{N-[4-N,N-
(dimethyl)aminobenzyl]carbamoyl}heptanoic Acid (44).
Compound 44 was synthesized from 43 in three steps using
the procedures described for the synthesis of 27b (phthalimide
cleavage) and 26c (N-Boc protection) and 31c in 70.2% overall
yield. 1H NMR (400 MHz CDCl3) δ 1.25 (m, 2H), 1.30 (m, 2H),
1.39 (s, 12H), 1.47 (m, 2H), 1.58 (m, 4H), 2.15 (m, 2H), 2.29
(m, 2H), 2.86 (d, J ) 7.2, 6H), 3.03 (m, 2H), 3.11 (t, J ) 7.6,
1H), 3.26 (t, J ) 7.2 Hz, 1H), 4.35 (s, 1H), 4.42 (s, 1H), 4.85 (s,
1H), 6.60 (d, J ) 8.8 Hz, 1H), 6.64 (d, J ) 8.8 Hz, 1H), 6.96 (d,
J ) 8.4 Hz, 1H), 7.04 (d, J ) 8.8 Hz, 1H). 13C NMR (400 MHz
CDCl3) δ 14.32, 21.24, 24.24, 25.28, 25.36, 25.86, 27.54, 28.36,
28.62, 28.95, 33.30, 33.94, 40.25, 40.39, 40.84, 40.89, 45.56,
46.47, 47.63, 50.77, 60.60, 81.44, 112.90, 113.09, 124.51,
127.49, 129.38, 150.08, 150.25, 156.30, 171.42, 173.24, 173.32,
173.70. IR (cm-1) 3280.0, 2975.1, 2929.7, 2864.9, 1690.8,
1619.5, 1522.2.
5-[(4-N,N-(Dimethylamino)benzyl)-(4-{(2,4,6-trimeth-
yl-benzenesulfonyl)-[3-(2,4,6-trimethyl-benzenesulfon-
ylamino)propyl]amino}butyl)carbamoyl]pentano-
hydroxamic Acid (15). Compound 15 was synthesized in two
steps from 48 using the procedure described for the synthesis
1
of 12 in 82.2% yield. H NMR (400 MHz D2O) δ 1.14 (s, 9H),
1.43 (m, 4H), 1.59 (m, 4H), 1.72 (q, J ) 7.6 Hz, 2H), 2.11 (t, J
) 6.4 Hz, 2H), 2.32 (t, J ) 7.2 Hz, 2H), 2.85-2.94 (m, 6H),
3.12 (t, J ) 6.4 Hz, 2H), 4.05 (s, 2H), 7.27 (d, J ) 8.4 Hz, 2H),
7.41 (d, J ) 1.6 Hz, 2H). 13C NMR (400 MHz D2O) δ 22.83,
22.96, 23.80, 24.05, 24.84, 25.77, 30.53, 33.49, 34.26, 35.43,
36.02, 45.17, 46.15, 46.97, 50.17, 126.44, 127.81, 129.92,
153.57, 177.28, 178.68. IR (cm-1) 3396.8, 2929.7, 1677.8,
1606.5, 1424.9.
7-{4-[N-(tert-Butyloxycarbonyl)amino]butyl}-{N-[4-N,N-
(dimethyl)aminobenzyl]carbamoyl}heptano-hydroxam-
ic Acid (45). Compound 45 was synthesized from 44 using
the procedure described for the synthesis of 31c in 74.4% yield.
1H NMR (400 MHz CDCl3) δ 1.31 (m, 4H), 1.37 (m, 4H), 1.64
Histone Deacetylase Activity Assay. Compounds 6-21
were evaluated for their ability to inhibit isolated HDAC in a

Alkyl-Substituted Polyaminohydroxamic Acids
Journal of Medicinal Chemistry, 2005, Vol. 48, No. 20 6365
Curr. Med. Chem. 2004, 11, 1629-1643; b. Ryan, Q. C.; Headlee,
D.; Acharya, M.; Sparreboom, A.; Trepel, J. B.; Ye, J.; Figg, W.
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and Pharmacokinetic Study of MS-275, a Histone Deacetylase
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commercially available assay (Fluor de Lys Assay System,
Biomol International LP, Plymouth Meeting, PA), employing
1 and 2 as positive controls. The reaction mixture contains a
HeLa cell nuclear extract and a commercial substrate contain-
ing acetylated lysine side chains. The substrate and extract
are incubated in the presence of the appropriate concentration
of the inhibitor. Deacetylation of the substrate followed by
mixing with mixing with the provided developer generates a
fluorophore, and comparison of inhibited vs control relative
fluorescence using a standard plate reader was employed to
determine percent HDAC activity remaining. All determina-
tions were carried out in triplicate, and reported values are
the average of these determinations, which in no case varied
by more than 3%.
Cell Lines and Drug Treatment. ML-1 cells were main-
tained in RPMI medium supplemented with 10% fetal calf
serum, 0.1 mg/mL gentamicin, and 2 mM L-glutamine. 3 ×
105 cells/ml were treated with 1 (Wako Pure Chemicals,
Richmond, VA), 2 (Mitsui Pharmaceuticals, Chiba, Japan) and
the desired test compound for the concentration and time
indicated in the figure legend.
Histone Preparation. Histones were prepared by a modi-
fication of a previously described method.24 Cells were washed
in 2 mL of HBSS and disrupted by 1 mL of ice-cold lysis buffer
A (10 mM Tris pH 7.6, 5 mM butyric acid, 1% Triton X-100, 1
mM MgCl2, and 1 mM PMSF). Nuclei were collected by
centrifugation at 14 000 rpm for 15 min. The pellet was
resuspended once with 250 µL of ice-cold lysis buffer B (10
mM Tris pH 7.6, 0.25 M Sucrose, 3 mM CaCl2, and 5 mM
butyric acid). Sulfuric acid was added to a concentration of
0.4 N, and the tubes were incubated at 4 °C for overnight.
Debris was pelleted by centrifugation, and the supernatant
was collected. Histones were precipitated by addition of 10 vol
of acetone and incubated at -20 °C overnight. Pellets were
collected by centrifugation, briefly dried under vacuum, and
resuspended in ddH2O.
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an albumin standard curve.
The proteins (10 µg for histone or 30 µg for p21Waf1) were
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analysis using the following antibodies against interesting
proteins: antibodies for acetylhistone H3 (06-599) (diluted
1:1000), acetylhistone H4 (06-866) (diluted 1:500), and histone
H2A (07-146) (diluted 1:1000) were from Upstate Biotechnolo-
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JM0505009