Synthesis and biological activity of benzamide DNA minor groove binders

Article abstract of DOI:10.1016/j.bmcl.2015.12.090

A range of di- and triaryl benzamides were synthesised to investigate the effect of the presence and nature of a polar sidechain, bonding and substitution patterns and functionalisation of benzylic substituents. These compounds were tested for their antiproliferative activity as well as their DNA binding activity. The most active compounds in all assays were unsymmetrical triaryl benzamides with a bulky or alkylating benzylic substituent and a polar amino sidechain.

Full text of DOI:10.1016/j.bmcl.2015.12.090

Bioorganic & Medicinal Chemistry Letters xxx (2015) xxx–xxx
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and biological activity of benzamide DNA minor groove
binders
⇑
Gul Shahzada Khan, Lisa I. Pilkington, David Barker
School of Chemical Sciences, University of Auckland, 23 Symonds St, Auckland, New Zealand
a r t i c l e i n f o
a b s t r a c t
Article history:
A range of di- and triaryl benzamides were synthesised to investigate the effect of the presence and nat-
ure of a polar sidechain, bonding and substitution patterns and functionalisation of benzylic substituents.
These compounds were tested for their antiproliferative activity as well as their DNA binding activity. The
most active compounds in all assays were unsymmetrical triaryl benzamides with a bulky or alkylating
benzylic substituent and a polar amino sidechain.
Received 4 September 2015
Revised 16 December 2015
Accepted 25 December 2015
Available online xxxx
Ó 2015 Elsevier Ltd. All rights reserved.
Keywords:
DNA binding agents
Minor groove binders
Benzamides
Anti-proliferative
DNA melting analysis
DNA minor groove binders (MGB’s) are a diverse group of com-
pounds, of both natural (e.g., distamycin 1a)1 and synthetic (e.g.,
tallimustine 1b)2 origins (Fig. 1).3 Although wide-ranging in nat-
ure, they all have a concave-shaped aromatic framework that can
fit in to the minor groove of DNA in addition to containing groups
that are capable of hydrogen bonding.4
of non-symmetrical and more complicated symmetrical oligoa-
mides with various additional functionalities. Herein we report
the synthesis and biological evaluation of complex diaryl and sym-
metrical and unsymmetrical triaryl benzamide MGB’s. These struc-
tures have been chosen to explore various structural features that
can be incorporated in to benzamide MGB’s, including the effect of
the presence and nature of a polar sidechain, bonding and substi-
tution patterns and functionalisation of benzylic substituents.
We envisioned that complex symmetric triaryl benzamide
MGB’s could be formed through the coupling of a symmetric dia-
cid chloride 3. To incorporate benzylic substitution into the resul-
tant triaryl oligoamide that could be functionalised or allow for
conjugation to other bioactive molecules, we wished to synthe-
sise an appropriate aniline for the coupling; aniline 4, with an
easily removable TBDMS (tert-butyldimethylsilyl) group was
thought to be suitable for this purpose. To provide 4, dinitroben-
zyl alcohol 5 was mono-reduced using Zinin reduction proce-
dures,8 and then both the resultant amine and alcohol groups
were acetylated to give diacetate 6 (Scheme 1). Diacetate 6 was
then selectively hydrolysed with sodium hydroxide in ethanol
to provide an alcohol which was then protected to give aniline
4 in a very high yield of 97% over two steps.9 With required ani-
line 4 in hand, we next sought to achieve dicoupling of 3 and 4.
After screening various reaction conditions, we found that using
K2CO3 (5.4 equiv) in THF at rt efficiently produced the desired tri-
aryl benzamide in an excellent 96% yield, which was then depro-
tected with TBAF (tetra-n-butylammonium fluoride) to provide
diol 7 in a high yield.
Distamycin 1a is a naturally occurring MGB isolated from Strep-
tomyces distallicus, and despite having little antitumor activity and
low cytotoxicity owing to their reversible binding to DNA, 1a has
been a lead compound in the synthesis of DNA MGB’s,1 with a large
number of polypyrrolic analogues synthesised, a notable of exam-
ple of which is 1b.2,5 Unfortunately, there are significant problems
associated with polypyrrole MGB’s; due to their electron rich nat-
ure there are limited reaction conditions that they can withstand
and that can be used to functionalise them. Also, added sub-
stituents on the nitrogen have been known to undergo unwanted
intramolecular cyclisation, negating the benefits these substituents
could provide to activity.3,6 Additionally, to construct MGB’s with
appropriate curvature, only substitution at the 2- and 4-positions
would provide compounds with the desired curvature. A strategy
to overcome these problems is to synthesise benzamide derived
MGB’s. The synthesis of benzamide derivatives (e.g., 2) is known,7
however these benzamide derivatives are either simple symmetri-
cal diaryl derivatives or triaryl amides, none with alkylating func-
tional groups; there is little literature precedent for the synthesis
⇑
Corresponding author. Tel.: +64 9 373 7599; fax: +64 9 373 7422.
E-mail address: d.barker@auckland.ac.nz (D. Barker).
http://dx.doi.org/10.1016/j.bmcl.2015.12.090
0960-894X/Ó 2015 Elsevier Ltd. All rights reserved.
Please cite this article in press as: Khan, G. S.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.12.090

2
G. S. Khan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
R
N
OTBDMS
O
NH2
HCl
COCl
(i)
NH
4
+
H
N
HN
H
N
AcHN
N
H
O
R
O
N
N
R
O
8
R = H,
R = NO2, 9
10
R = H,
(ii),(iii)
Cl
H
N
11
12
R = NO2,
R = NAc,
1a
R =
=
O
O
Distamycin 1a
Tallimustine 1b
N
OH
Cl
H
N
1b
(iv)
O
N
AcHN
N
H
N
H
N
R
O
O
13
R = H,
O
R = NAc, 14
N
H
N
H
Scheme 2. Reagents, conditions and yields: (i) pyridine, rt, 16 h, 84% 10, 77% 11; (ii)
10% Pd/C, H2, MeOH, rt, 3 h, quant; (iii) Ac2O, Et3N, DMF, rt, 24 h, 89%; (iv) TBAF,
AcOH, THF, rt, 24 h, 84% 13, 93% 14.
2
Figure 1. Distamycin 1a, tallimustine 1b and benzamide 2.
After successfully synthesising simplified benzamides 13 and
14, we wished to adapt our methods to produce diaryl benzamides
with additional sidechains, which as stated above, should aid in
solubility and binding of the resultant MGB’s. Aniline 4 was cou-
pled11 with meta and para regioisomers of various previously pre-
pared10 benzamides 15–18 to provide benzamides 19–22 which
were then deprotected to provide alcohols 23–26. Synthesising
both meta and para substituted benzamides would allow us to
investigate the effect of curvature on the activity.
OH
OAc
(iii)-(v)
(i), (ii)
O2N
NO2
O2N
NHAc
5
6
OTBDMS
Additionally, we sought to investigate the effect of altering the
pattern of amide bonding (from ArNHCOR to ArCONHR); we antic-
ipated that this alteration would have a strong effect on the elec-
tronic character in the molecule which could also play an
important role in the solubility and activity of the compounds.
Once again aniline 4 was used; it was coupled11 to benzoic acids
27 and 2810 to provide benzamides 2912 and 30 in very good yields
of 96% (29) and 80% (30). Silyl group deprotection with TBAF gave
alcohols 31 and 32. Alcohol 31 was further functionalised to the
mesylate which was immediately converted13 to the correspond-
ing chloride 33,14 an alkylating agent, in 96% over two steps (see
Scheme 3).
(vi), (vii)
ClOC
COCl
+
H2N
HO
NHAc
4
3
O
O
OH
NH
HN
AcHN
NHAc
In addition to the symmetrical triaryl benzamide synthesised
earlier, we also sought to construct various unsymmetrical triaryl
compounds to further explore the activity of these larger com-
pounds. The acid coupling partners 34 and 35 were synthesised
through the coupling of amides 3615 and 377b which contain a
polar amino sidechain, with acid chloride 38 followed by
hydrogenolysis to give 34 and 35. Benzoic acids 34 and 35 were
then coupled11 with aniline 4 to provide triaryl benzamides 39
and 4016 which were then deprotected to provide alcohols 41
and 42. Chloride derivatives 43 and 4417 were also synthesised
from alcohols 41 and 42 in very high yields of 91% and 97%, respec-
tively, over two steps (see Scheme 4).
With various classes of benzamide MGB’s synthesised, we next
sought to investigate their biological activities and the effect of
various structural changes on their activity. As part of the National
Cancer Institute’s Developmental Therapeutics Program, 15 of the
synthesised compounds were selected to be tested for their anti-
proliferative activity against 60 human tumour cell lines.18 The
compounds were not toxic to all cell lines and instead generally
showed very high selectivity for certain cell lines, particularly leu-
kaemia lines K-562, CCRF-CEM, MOLT-4 and SR lines (see Support-
7
Scheme 1. Reagents, conditions and yields: (i) (NH4)2S, MeOH, reflux then rt, 6 h
then 20 h, 81%; (ii) Ac2O, Et3N, DMF, rt, 24 h, 99%; (iii) NaOH, EtOH, rt, 3 h, 98%; (iv)
TBDMSCl, imidazole, DMF, rt, 5 h, 99%; (v) 10% Pd/C, H2, MeOH, rt, 3 h, quant; (vi)
K2CO3, THF, rt, 30 min, 96%; (vii) TBAF, THF, rt, 24 h, 97%.
In order to study the effect of an increased number of aryl
groups on the binding of these compounds, we decided to synthe-
sise a range of diaryl benzamides so they could be compared to tri-
aryl benzamides. We first sought to produce simple benzamides
with no additional sidechains (Scheme 2) and then follow this with
exploration into the addition of polar sidechains to the MGB com-
pounds, which should increase the solubility and binding capabil-
ities of these compounds. Synthesising diaryl benzamides that lack
these functionalities would allow the determination of their effect
on the biological activity. Aniline 4 was reacted with benzoyl chlo-
rides 8 and 9 to give benzamides 10 and 11 (Scheme 2). The nitro
group in 11 was then reduced in quantitative yield to provide ben-
zamide 12. Finally, deprotection of the TBDMS groups in 10 and 12
gave diaryl benzamides 13 and 14 in high yields.
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G. S. Khan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
3
OTBDMS
OH
NH
O
R
O
(ii)
(i)
O
O
R
4
O
R
+
HOOC
AcHN
N
H
AcHN
N
H
NH
NH
meta, R = NEt2, 15
meta, R = CH2CH2N(CH2CH2)2O,
19
met a, R = NEt2,23
meta, R = NEt2,
16
met a, R = CH2CH2N(CH2CH2)2O, 24
para, R = NEt2, 25
meta, R = CH2CH2N(CH2CH2)2O, 20
para, R = NEt2, 21
17
para, R = NEt2,
para, R = CH2CH2N(CH2CH2)2O, 18
26
para, R = CH2CH2N(CH2CH2)2O, 22
para, R = CH2CH2N(CH2CH2)2O,
OTBDMS
R'
O
(ii)
O
(i)
N
H
R
O
4
+
HO OC
AcHN
N
H
AcHN
N
H
H
N
H
N
R
R
O
O
R = NMe2, 27
R = N(CH2CH2)2O, 28
R = NMe2, 29
R = N(CH2CH2)2O, 30
R' = OH, R = NMe2, 31
R' = Cl, R = NMe2, 33
R' = OH, R = N(CH2CH2)2O,
(iii)
32
Scheme 3. Reagents, conditions and yields: (i) DIC (N,N0-diisopropylcarbodiimide), HOBt (hydroxybenzotriazole), DMAP (4-dimethylaminopyridine), DMF, rt, 16 h, 92% 19,
26% 20, 73% 21, 47% 22, 96% 29, 80% 30; (ii) TBAF, THF, rt, 24 h, 84% 23, 66% 24, 54% 25, 93% 26, 94% 31, 71% 32; (iii) MsCl, Et3N, DMF, rt, 2 h, then NaCl, 60 °C, 30 min, 96%.
O
CO2Bn
alkylating chloro group had a LC50 78.2 lM for CCRF-CEM. The
+
(i), (ii)
(iii)
H2N
N
H
R
results from the anti-proliferative testing enabled analysis of the
effect of altering various structural features in these synthesised
compounds. It was shown from these results that the addition of
a sidechain in the diaryl structures produced no discernible
increase in activity, when comparing 13 and 14 with 23–26, with
all of these compounds having very similar activities (all with a
mean growth percentage between 104.5% and 107%). The only
compound of notable activity in this group was 13 which inhibited
growth of non-small cell lung cancer NCI-H23 line, with inhibition
of 49%. Comparing compounds 23–26 (with an ArCONHR amide
linkage pattern) and 31 and 32 (with ArNHCOR linkage), we can
see that they have very similar activity profiles, with no obvious
differences in activities. As described above, the most promising
candidates from this screen were the triaryl unsymmetrical MGB’s,
the synthesised symmetric triaryl derivative, 7, on the other hand,
had no such notable activity.
ClOC
38
R = Me, 36
R = (CH2)3NMe2, 37
O
O
N
H
N
H
R
4
+
HOOC
R = Me, 34
R = (CH2)3NMe2, 35
R1
O
O
NH
HN
To investigate the binding of these polybenzamides to DNA,
DNA melting analysis was performed on six of the synthesised
compounds (Table 1). Diarylbenzamides 23 and 25 showed slight
increase in the DNA thermomelt value (8.7 and 10.2 °C), indicating
they bound weakly with DNA.19 The similarity in their results indi-
cate that for these compounds, the meta, para bonding pattern
which was the only point of difference between these two com-
pounds, had little effect on the DNA binding of these diaryl deriva-
tives. Diaryl benzamide 33, had a chloro benzyl substituent, as
O
R
AcHN
HN
R = Me, R1 = OTBDMS, 39
R = (CH2)3NMe2, R1 = OTBDMS, 40
(iv)
(v)
1
41
R = Me, R = OH,
R = (CH2)3NMe2, R1 = OH, 42
R = Me, R1 = Cl, 43
R = (CH2)3NMe2, R1 = Cl, 44
Table 1
D
Tm and C50 values of selected ligands bound with poly AT DNA
Scheme 4. Reagents, conditions and yields: (i) K2CO3, THF, rt, 30 min; (ii) 10% Pd/C,
H2, MeOH, rt, 5 h, 79% (2 steps) 34, 94% (2 steps) 35; (iii) DIC, HOBt, DMAP, DMF, rt,
18 h, 95% 39, 26% 40; (iv) TBAF, THF, rt, 24 h, 91% for 41, Et3Nꢀ3HF, THF, rt, 24 h, 61%
for 42; (v) MsCl, Et3N, DMF, rt, 2 h, then NaCl, 60 °C, 30 min, 91% 43, 97% 44.
Compound
D
Tm 1 (°C)
C50 value
23
25
31
33
40
42
44
8.7
10.2
—
21.6
47.2
30.7
38.7
>1 mM
—
>1 mM
506
5.0
117.6
9.9
l
M
ing information for full screen data). Owing to this, the most active
compounds, 40 and 44, both triaryl benzamides, were selected for
5-dose testing. In these tests, 44, the triaryl benzamide with an
lM
lM
lM
Please cite this article in press as: Khan, G. S.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.12.090

4
G. S. Khan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
opposed to a hydroxyl group for the other diaryl benzamides
tested in this assay, as well as an different amide linkage and
longer tether to the amine on the sidechain. Compound 33 did have
an increased thermomelt value compared to 23 and 25 (21.6 °C).
Triaryl benzamides (compounds 40, 42 and 44) showed far greater
DNA binding activity than the diaryl compounds, as can be seen by
the increase in DNA thermomelt values (47.2, 30.7 and 38.7 °C for
40, 42 and 44). All tested triaryl benzamides differed only in the
benzyl substituent; it can be seen from the reported results that
40 (with an OTBDMS group) binds strongest to DNA, followed by
44 with a chloro substituent. Of the triaryl benzamides, 42 bound
the weakest, indicating that the hydroxyl group is not as favour-
able for DNA binding activity as the other test substituents.
Owing to the ability of ethidium bromide to bind with DNA,
ethidium displacement assays have been used to study the bind-
ing activities of minor groove binding agents,7,20 whereby ethid-
ium displacement from DNA by the minor groove binder can be
measured through fluorescence. To further quantify the extent of
DNA binding of these synthesised compounds, an ethidium dis-
placement assay was used; we report the C50 (amount of ligand
required to displace ethidium from DNA, with a resultant 50%
drop in fluorescence intensity)21 of six selected compounds. As
with the DNA melt assay, diaryl benzamides (23, 31 and 33) were
the least active in displacing ethidium, diaryl benzamides 23 and
31 had C50 > 1 mM. Diaryl benzamide 33, which differs from 31
only in the chloro substituent (as opposed to a hydroxy group
References and notes
1. (a) Pugliese, A.; Martinetto, P. G. Batteriol. Virol. Immunol. 1978, 71, 198; (b)
Baraldi, P. G.; Preti, D.; Fruttarolo, F.; Tabrizi, M. A.; Romagnoli, R. Bioorg. Med.
Chem. 2007, 15, 17.
2. Arcamone, F. M.; Animati, F.; Barbieri, B.; Configliacchi, E.; D’Alessio, R.; Geroni,
C.; Giuliani, F. C.; Lazzari, E.; Menozzi, M. J. Med. Chem. 1989, 32, 774.
3. (a) Neidle, S. Nat. Prod. Rep. 2001, 18, 291; (b) Khan, G. S.; Shah, A.; Zia-ur-
Rehman, ; Barker, D. J. Photochem. Photobiol., B 2012, 115, 105.
4. Chen, X.; Ramakrishnan, B.; Sundaralingam, M. Nat. Struct. Biol. 1995, 2, 733.
5. Baraldi, P. G.; Cozzi, P.; Geroni, C.; Mongelli, N.; Romagnoli, R.; Spalluto, G.
Bioorg. Med. Chem. 1999, 7, 251.
6. He, G. X.; Browne, K. A.; Groppe, J. C.; Blasko, A.; Mei, H. Y.; Bruice, T. C. J. Am.
Chem. Soc. 1993, 115, 7061.
7. (a) Dasgupta, D.; Rajagopalan, M.; Sasisekharan, V. Biochem. Biophys. Res.
Commun. 1986, 140, 626; (b) Yan, Y.; Liu, M.; Gong, B. Bioorg. Med. Chem. Lett.
1997, 7, 1469; (c) Gong, B.; Yan, Y. Biochem. Biophys. Res. Commun. 1997, 240,
557; (d) Fox, K.; Yan, Y.; Gong, B. Anti-Cancer Drug Des. 1999, 14, 219.
8. (a) Meindl, W. R.; Angerer, E.; Schoenenberger, H.; Ruckdeschel, G. J. Med. Chem.
1984, 27, 1111; (b) Zinin, N. J. Prakt. Chem. 1842, 27, 140; (c) Barker, D.;
Lehmann, A. L.; Mai, A.; Khan, G. S.; Ng, E. Tetrahedron Lett. 2008, 49, 1660.
9. See Supporting information for further experimental details on the synthesis of
aniline 4.
10. Khan, G. S.; Dickson, B. D.; Barker, D. Tetrahedron 2012, 68, 1790.
11. General procedure for the coupling of acid and aniline: To a solution of acid
(1 equiv) in dry DMF (5 mL/mmol), was added aniline (0.5 equiv) and catalytic
amount of DMAP (1–2 mg) and the mixture was stirred for 5–10 min under an
atmosphere of nitrogen. DIC (1 equiv) was then added dropwise and the
resulting solution stirred for 2 min, followed by the addition of HOBt (1 equiv).
The mixture was then stirred for 18 h at room temperature, before the DMF
was removed in vacuo. The residue was diluted with methanol (10 mL), water
(2 mL) and potassium carbonate (1 equiv). Silica gel was added to form a
slurry. The solvent was then removed in vacuo to give the crude product
adhered to silica. This silica was then loaded and purified by flash
chromatography. In some cases repeated chromatography was needed to
purify the product.
in 31) had a C50 506 lM; this indicates that the chloro sub-
stituent has a marked effect on the ethidium displacement activ-
ity. Once again, 40—a triaryl benzamide with a bulky OTBDPS
benzylic substituent was the most active (C50 5.0 lM). Also corre-
lating to the DNA melt assay, triaryl benzamide with a chloro
substituent, 44, was the second most active compound tested
12. Data for 29: Rf (MeOH/NH3 9:1) = 0.13; IR m
max(NaCl)/cmꢁ1: 3429, 2952, 1670,
1620, 1551, 1459, 1374, 1287; 1H NMR (400 MHz, CD3OD): d 0.10 (6H, s, OSi
(CH3)2), 0.94 (9H, s, OSiC(CH3)3), 1.81 (2H, p, J = 7.3 Hz, CH2CH2CH2), 2.10 (3H, s,
NHCOCH3), 2.26 (6H, s, N(CH3)2), 2.43 (2H, t, J = 7.6 Hz, NCH2), 3.41 (2H, t,
J = 7.0 Hz, CONHCH2), 4.69 (2H, s, ArCH2O), 7.36 (1H, s, Ar-H), 7.42 (1H, s, Ar-H),
7.86–90 (3H, m, Ar-H), 7.96 (2H, d, J = 8.3 Hz, Ar-H); 13C NMR (100 MHz,
CD3OD): d ꢁ5.5 (OSi(CH3)2), 18.2 (OSiC(CH3)3), 23.8 (NHCOCH3), 25.3 (OSiC
(CH3)3), 25.7 (CH2CH2CH2), 38.3 (CONHCH2), 44.2 (N(CH3)2), 56.8 (NCH2), 66.7
(ArCH2O), 110.8 (Ar-C), 113.8 (Ar-C), 114.0 (Ar-C), 127.0 (Ar-C), 127.4 (Ar-C),
136.7 (Ar-C), 137.3 (Ar-C), 138.3 (Ar-C), 138.6 (Ar-C), 142.7 (Ar-C), 165.9, 167.2
and 169.6 (NHCOAr, CONHCH2 and NHCOCH3); m/z (FAB+) 527 (MH+, 72%), 469
(MH+-C4H9, 7%), 450 (100%), 265 (20%); HRMS found (FAB+); MH+ 527.3058,
(C50 9.9
lM). These two compounds were far more active than
42 (C50 117.6
l
M), which differs only from 40 and 44 by the ben-
zylic substituent (hydroxyl for 42). These results once again indi-
cate that triaryl benzamides have an increased activity over their
diaryl counterparts and chloro and the bulky OTBDMS benzylic
substituents are desirable for greater activity over compounds
with an alcohol group.
C28H43N4O4Si requires 527.3054.
13. General procedure for the conversion of benzylic alcohol to chloride: To a solution
of alcohol (1 equiv) and triethylamine (1.5 equiv) in dry DMF (4 mL/mmol
alcohol) at 0 °C was added methanesulfonyl chloride (1.5 equiv) in dry DMF
(3 mL/mmol alcohol) and the resulting solution stirred at room temperature
for 2 h. Sodium chloride (10 equiv) was added and the mixture was heated at
60 °C for 30 min. The solvent was then removed in vacuo. The crude product
was then purified by flash chromatography to furnish the pure product.
In summary, a range of di- and triaryl benzamide MGB’s were
synthesised. These compounds differed from each other in the
presence and nature of a polar sidechain, bonding and substitution
patterns and functionalisation of benzylic substituents. These com-
pounds were tested for their antiproliferative activity as well as
their DNA binding activity. The most active compounds in all
assays were triaryl benzamides 40 and 44, with a bulky and alky-
lating chloro benzylic substituent, respectively, and a polar amino
sidechain. The alcohol that is formed from the deprotection of 40
can be used as an additional site of modification, as shown be
the subsequent of chloride 44. Based on these results, we aim to
further explore compounds similar to 40 and 44, and will report
our results in due course.
14. Data for 33: IR m H
max(NaCl)/cmꢁ1: 3266, 3067, 1642, 1616, 1544, 1455, 1286; 1
NMR (400 MHz, CD3OD): d 2.08 (2H, p, J = 7.3 Hz, CH2CH2CH2), 2.15 (3H, s,
NHCOCH3), 2.94 (6H, s, N(CH3)2), 3.25 (2H, t, J = 7.6 Hz, NCH2), 3.53 (2H, t,
J = 6.9 Hz, CONHCH2), 4.62 (2H, s, ArCH2Cl), 7.47 (1H, t, J = 1.6 Hz, Ar-H), 7.54
(1H, t, J = 1.6 Hz, s, Ar-H), 7.99–8.02 (5H, m, Ar-H); 13C NMR (100 MHz,
CD3OD):
d 24.0 (NHCOCH3), 26.1 (CH2CH2CH2), 37.7 (CONHCH2), 43.6 (N
(CH3)2), 46.8 (ArCH2Cl), 56.8 (NCH2), 113.8 (Ar-C), 117.5 (Ar-C), 118.0 (Ar-C),
128.6 (Ar-C), 128.7 (Ar-C), 138.1 (Ar-C), 139.0 (Ar-C), 140.3 (Ar-C), 140.4 (Ar-C),
144.0 (Ar-C), 167.8, 169.6 and 171.8 (NHCOAr, CONHCH2 and NHCOCH3); m/z
(ESI+): 431 (MH+, 100%), 413 (29%), 381 (20%), 251 (5%), 292 (21%); HRMS
found (ESI+): MH+ 431.1829 C22H28N4O3 requires 431.1839.
15. Sidgwick, N. V.; Neill, J. A. J. Chem. Soc., Trans. 1923, 123, 2813.
16. Data for 40: Rf (MeOH/NH3 9:1) = 0.81; IR m
max(solid)/cmꢁ1: 3287, 2929, 1652,
1606, 1540, 1417, 1254; 1H NMR (400 MHz, CD3OD): d 0.09 (6H, s, OSi(CH3)2),
0.92 (9H, s, OSiC(CH3)3), 1.83 (2H, p, J = 7.6 Hz, CH2CH2CH2), 2.09 (3H, s,
NHCOCH3), 2.24 (6H, s, N(CH3)2), 2.34–2.39 (4H, m, NCH2, NHCOCH2), 4.66 (2H,
s, ArCH2O), 7.24 (1H, t, J = 8.2 Hz, Ar-H), 7.32 (1H, br s, Ar-H), 7.34 (1H, br s, Ar-
H), 7.39 (1H, d, J = 8.0 Hz, Ar-H), 7.42 (1H, s, Ar-H). 7.90 (1H, br s, Ar-H), 7.91
(1H, t, J = 1.8 Hz, Ar-H), 7.95 (4H, m, Ar-H); 13C NMR (100 MHz, CD3OD): d ꢁ5.0
(OSi(CH3)2), 19.3 (OSiC(CH3)3), 24.0 (CH2CH2CH2), 24.1 (NHCOCH3), 26.5 (OSiC
(CH3)3), 35.7 (NHCOCH2), 45.3 (N(CH3)2), 59.9 (NCH2), 66.0 (ArCH2O), 112.8
(Ar-C), 114.2 (Ar-C), 115.4 (Ar-C), 115.8 (Ar-C), 117.6 (Ar-C), 118.0 (Ar-C), 128.9
(Ar-C), 129.0 (Ar-C), 130.1 (Ar-C), 139.0 (Ar-C), 139.1 (Ar-C), 140.0 (Ar-C), 140.2
(Ar-C), 140.3 (Ar-C), 140.4 (Ar-C), 144.1 (Ar-C), 167.8, 167.9, 172.7 and 173.9
(NHCOAr, NHCO, CONH and NHCOCH2); m/z (ESI+): 646 (MH+, 100%), 532 (6%),
384 (22%); HRMS found (ESI+): MH+ 646.3428, C35H48N5O5Si requires
646.3425.
Acknowledgements
The authors acknowledge financial support from the Higher
Education Commission of Pakistan and The University of Auckland,
New Zealand. We also acknowledge Assoc. Prof. Lawrence Wakelin
for helpful discussions on this work.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.bmcl.2015.12.
090.
17. Data for 44: Rf (MeOH/NH3 9:1) = 0.74; IR
1606, 1544, 1450, 1416, 1287; 1H NMR (400 MHz, CD3OD): d 2.10 (3H, s,
m
max(solid)/cmꢁ1: 3260, 2930, 1649,
Please cite this article in press as: Khan, G. S.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.12.090

G. S. Khan et al. / Bioorg. Med. Chem. Lett. xxx (2015) xxx–xxx
5
NHCOCH3), 2.10 (2H, pentet, J = 8.0 Hz, CH2CH2CH2), 2.59 (2H, t, J = 8.0 Hz,
NHCOCH2), 2.74 (6H, s, N(CH3)2), 3.24 (2H, t, J = 8.0 Hz, NHCOCH2), 4.61 (2H, s,
ArCH2Cl), 7.30 (1H, t, J = 8.0 Hz, Ar-H), 7.39 (1H, d, J = 8.0 Hz, Ar-H), 7.44 (1H, d,
J = 8.0 Hz, Ar-H), 7.47 (1H, br s, Ar-H), 7.55 (1H, br s, Ar-H), 8.03–8.04 (5H, m,
171.8 and 172.7 (NHCOAr, NHCO, CONH and NHCOCH2); m/z (ESI+): 550 (MH+,
35
100%), 546 (4%); HRMS found (ESI+): MH+ 550.2213, 552.2199, C29
H ClN5O4
33
37
and C29
H ClN5O4 requires 550.2221, 552.2192.
33
18. See Supporting information for full NCI report sheets.
19. (a) Kaushik, M.; Kukreti, S. Spectrochim. Acta A 2003, 59, 3123; (b) Mergny, J. L.;
Lacroix, L. Oligonucleotides 2003, 13, 515.
20. Johnson, H. A.; Thomas, N. R. Bioorg. Med. Chem. Lett. 2002, 12, 237.
21. Pavlov, V.; Lin, P. K. T.; Rodilla, V. Chem. Biol. Interact. 2001, 137, 15.
Ar-H), 8.13 (1H, t, J = 4.0 Hz, Ar-H); 13C NMR (100 MHz, CD3OD):
d
21.4
(CH2CH2CH2), 24.1 (NHCOCH3), 35.4 (NHCOCH2), 43.6 (N(CH3)2), 46.9
(ArCH2Cl), 58.6 (NCH2), 113.8 (Ar-C), 114.4 (Ar-C), 117.5 (Ar-C), 117.6 (Ar-C),
118.0 (Ar-C), 118.2 (Ar-C), 128.9 (Ar-C), 129.0 (Ar-C), 130.1 (Ar-C), 138.9 (Ar-C),
139.0 (Ar-C), 140.1 (Ar-C), 140.2 (Ar-C), 140.4 (Ar-C), 140.6 (Ar-C), 167.8, 167.8,
Please cite this article in press as: Khan, G. S.; et al. Bioorg. Med. Chem. Lett. (2015), http://dx.doi.org/10.1016/j.bmcl.2015.12.090