Design, synthesis and structure of novel para-quinones and their antibacterial activity

Article abstract of DOI:10.1111/j.1747-0285.2011.01187.x

Eight new para-quinones and one known analogue have been synthesized from p-chloranil. Five have been structurally characterized by single crystal diffraction, and a range of ligand folding is observed. All nine have been tested for their potency towards

Full text of DOI:10.1111/j.1747-0285.2011.01187.x

ª 2011 John Wiley & Sons A/S
doi: 10.1111/j.1747-0285.2011.01187.x
Chem Biol Drug Des 2011; 78: 787–799
Research Article
Design, Synthesis and Structure of Novel
Para-Quinones and their Antibacterial Activity
may induce single or double strand breaks in the DNA of carcinoma
cells (18). Many quinones exhibit good lipid solubility, and their low
hydrophilicity may facilitate penetration of the blood brain barrier
making them potentially effective against tumours of the central
nervous system (19). The para-quinonoid moiety of quinones is an
important factor in determining their activity against microorganisms
that cause food poisoning and rheumatic fever (20).
Komala Pandurangan, Kevin D.
Murnaghan, Aurora Walshe,
Helge Mu¨ ller-Bunz, Francesca Paradisi
and Grace G. Morgan*
Centre for Synthesis and Chemical Biology (CSCB), School of
Chemistry and Chemical Biology, University College Dublin, Belfield,
Dublin 4, Ireland
*Corresponding author: Grace G. Morgan, grace.morgan@ucd.ie
Because of this extensive biological activity, design and synthesis of
new quinones continues apace (21,22). Amino-substituted p-benzoqui-
nones have been shown to have good inhibitory activity towards
human colon adenocarcinoma (23) and towards Gram(+) and Gram())
bacteria (24,25). This led to our interest in preparing and testing a
range of new para-quinone analogues with the potentially biologically
active quinonoid structure (20). The inexpensive starting material p-
chloranil was used in the attempted synthesis of a range of quinones
by reaction with amines I–X, Scheme 1, and the activity of the result-
ing quinones towards Gram(+) S. aureus and Gram()) E. coli was
assessed. In this work, nine quinones were successfully prepared by
substitution of chloranil of which five were structurally characterized
by single crystal diffraction. All were tested for their activity towards
Gram(+) S. aureus and Gram()) E. coli using the Kirby–Bauer disc-dif-
fusion method (26) and a range of responses was observed.
Eight new para-quinones and one known analogue
have been synthesized from p-chloranil. Five have
been structurally characterized by single crystal
diffraction, and
a range of ligand folding is
observed. All nine have been tested for their
potency towards Gram(+) S. aureus and Gram(2)
E. coli. Quinones 3, 6, 7 and 8 have shown activity
towards S. aureus and quinones 3 and 8 also show
good activity towards E. coli.
Key words: antibacterial, crystal structure, Escherichia coli, para-
quinone, Staphylococcus aureus
Received 1 February 2011, revised 7 June 2011 and accepted for publi-
cation 9 July 2011
Experimental Section
It is well known that quinones possess a remarkable range of bio-
logical activity. They are essential for many cellular processes
including respiration and photosynthesis (1), and there are many
naturally occurring quinones that possess antioxidant (2), antiinflam-
matory (3) and antitumour properties (4,5). They have the ability to
act as toxic metabolites and are therefore potentially effective anti-
cancer drugs (6). They have long been cited as having a major role
in cellular defence because of their potency in inhibiting bacteria
(7), fungi (8) and parasites (9,10).
General comments
Melting points were determined using a Stuart melting point appa-
ratus (SMP11). Precoated Merck SILICA GEL 60F-254 plates were
used for thin layer chromatography, and the spots were detected
under UV light (254 nm). Column chromatography was performed
using silica gel (0.063–0.200 mm), and the glass column was slurry-
1
packed under gravity. H NMR and 13C NMR spectra were recorded
on a 300, 400 or 500 MHz Varian spectrometer. The samples were
dissolved in DMSO-d6 or CDCl3, and spectra were recorded in a 5-
mm NMR tube. Chemical shifts are reported relative to tetramethyl-
silane, and coupling constants are given in Hertz. The elemental
analysis for C, H and N was performed on an Exeter analytical
CE-450 Elemental analyzer. IR spectra were recorded with a Perkin–
Elmer Paragon 1000 FT-IR Spectrometer as KBr discs. UV ⁄ Vis spec-
tra were recorded with a Unicam UV4 Spectrometer. Electrospray
mass spectrometry (MS) was performed with a Perkin Elmer (Wal-
tham, MA, USA) or Waters Micromass (Milford, MA, USA) quadru-
pole tandem mass spectrometer, using solutions made up in 50%
acetonitrile and 50% methanol. MS spectra were obtained in the
ES+ (electrospray positive ionization) mode for all compounds.
Para-quinones such as vitamin K derivatives, ubiquinone or plasto-
quinones play a vital role in energy conversion (photosynthesis and
respiration) and information transfer (11–14). Doxorubicin (15) and
mitomycin C (16) serve as modern arsenal chemotherapeutic quinon-
es. A variety of para-quinone molecules such as Lapachol (17), pix-
antrone and mitoxantrone are used as chemotherapeutic drugs for
cancer treatment. Cytotoxic quinones are postulated to form site-
specific free radicals that bind to DNA by intercalation and cross-
linking, thereby killing the cancer cells and halting the growth of
the tumour (18). The planar structure of quinones enables intercala-
tion with DNA, and the free radical nature of the bound quinone
787

Pandurangan et al.
HN
N
HN
N
O
O
O
OH
H2N
N
I
N
N
Cl
Cl
Cl
Cl
RHN
Cl
Cl
Ethanol
Reflux
O
NH2
+
H2N
2 R-NH2
H2N
HN
III
H2N
II
NHR
IV
V
VI
O
NH2
OH
NH2
OH
,
NH2
H2N
HO
OH
O
VII
VIII
IX
X
Scheme 1: Synthesis of p-quinone analogues from chloranil.
Synthetic procedure
in DMF yielded an amorphous green-coloured powder. UV ⁄ vis
(CH3CN): kmax ⁄ nm (e ⁄ dm3 mol-1 cm-1) = 237 (5870), 357 (4302).
Anal.: calcd. for C12H8Cl2N6O2: C, 42.50; H, 2.38; N, 24.78. Found:
C, 42.06; H, 2.43; N, 24.05. ESI: 339 (M+). IR (KBr, ⁄ cm), 3312,
3138, 2360(d), 1661, 1573, 1522, 1428, 1320, 1220, 1094, 1005,
861, 671(d) and 590. 1H NMR (400MHz, DMSO- d6) 12.6 (s, 2H,
NH-1Py), 9.3 (s, 2H, NH-2), 7.64 (s, 2H, CH) and 6.10 (d, J = 2.3Hz,
2H). 13CNMR (100MHz, DMSO- d6) 173.8, 146.1, 144.3, 129.6,
104.3 and 102.57.
To a well-stirred solution of p-chloranil (4.06 mmol) in ethanol
(50 mL) was added the neat primary amine (8.12 mmol), and the
solution or suspension was heated under reflux at 90 ꢀC for 4–16 h
(Table 1). The reaction mixture was cooled to room temperature
and filtered. Various coloured products were isolated after recrystal-
lization of the filtered solids, in good yields (Table 1).
2,5-Dichloro-3,6-bis(pyridin-2-ylmethylamino)cyclohexa-2,5-diene-1,4-
dione 1: Yield – 1.50 g (94%). Red-coloured crystals (crystallized
from hot acetonitrile). Anal.: calcd. for C18H14Cl2N4O2: C, 55.54; H,
3.63; N, 14.39. Found: C, 55.19; H, 3.62; N, 14.22. ESI: 389 (M+). IR
(KBr, ⁄ cm), 3193, 3068, 2923, 2361(d), 1660, 1583(d), 1480, 1433(d),
1351, 1320, 1080, 996, 757 and 568.
2,5-Dichloro-3,6-bis(5-methyl-1H-pyrazol-3-ylamino)cyclohexa-2,5-
diene-1,4-dione 5: Yield – 1.27 g (85%). The green powder on
recrystallization in DMF yielded green micro crystals. UV ⁄ vis
(CH3CN): kmax ⁄ nm (e ⁄ dm3 mol-1 cm-1) = 237 (2637), 285 (1000),
362 (1782). Anal.: calcd. for C14H12Cl2N6O2: C, 45.79; H, 3.29; N,
22.89. Found: C, 45.98; H, 3.39; N, 22.49. ESI: 368 (M+). IR (KBr,
⁄ cm), 3400, 3262, 1655, 1577(d), 1514, 1440, 1312, 1222, 1007,
867, 796 and 604. 1H NMR (400 MHz, DMSO- d6) 12.3 (s, 2H,
NH-1Py), 9.25 (s, 2H, NH-2), 5.85 (s, 2H, CH) and 2.19 (s, 6H).
13C NMR (100 MHz, DMSO- d6) 173.8, 146.2, 144.2, 139.0,
104.1, 101.5 and 11.1.
2,5-Dichloro-3,6-bis(2-(pyridin-2-yl)ethylamino)cyclohexa-2,5-diene-1,4-
dione 2: Yield – 1.40 g (83%). Pink crystals (crystallized from hot
acetonitrile). Anal.: calcd. for C20H18Cl2N4O2: C, 57.57; H, 4.50; N,
13.43. Found: C, 57.35; H, 4.36; N, 13.24. ESI: 417 (M+). IR (KBr,
⁄ cm), 3109, 2965, 2361(d) 1658, 1578(d), 1498, 1437, 1322, 1219,
1063, 776 and 573.
2,5-Dichloro-3,6-bis(methyl(2-(pyridin-2-yl)ethyl)amino)cyclohexa-2,5-
diene-1,4-dione 3: Yield – 1.55 g (85%). The reaction mixture was
filtered and a purple-coloured powder was recovered which on
recrystallization from ethanol yielded purple-coloured crystals.
UV ⁄ vis (CH3CN): kmax ⁄ nm (e ⁄ dm3 mol-1 cm-1) = 259 (3372), 303
(1736). Anal.: calcd. for C22H22N4O2Cl2: C, 59.32; H, 4.98; N, 13.43.
Found: C, 59.25; H, 4.96; N, 13.10. ESI: 447 (M+). IR (KBr, ⁄ cm):
3271, 3060, 2923, 2850, 1707, 1647 and 990.
Diethyl 4,4¢-(2,5-dichloro-3,6-dioxocyclohexa-1,4-diene-1,4-diyl)bis(aza-
nediyl)dibutanoate 6: Yield – 1.15 g (65%). The reddish purple pow-
der on recrystallization in hot acetone yielded purple-coloured
crystals. UV⁄ vis (CH3CN): kmax ⁄ nm (e ⁄ dm3 mol-1 cm-1) = 225 (5559),
354 (6793). Anal.: calcd. for C18H24Cl2N2O6: C, 49.67; H, 5.56; N,
6.44. Found: C, 49.59; H, 5.41; N, 6.34. ESI: 379 (M+). 1H NMR
(500 MHz, CDCl3) 7.20 (br.s, 2H, NH-), 4.15 (q, 2H, J = 7.1 Hz), 3.92
(q, 6.9 Hz, 2H) 2.41 (t, J = 7.2 Hz, 2H), 2.02 (p, J = 7.2 Hz, 2H) 1.27
(t, J = 7.1 Hz, 3H). 13C NMR (125MHz, CDCl3) d 172.96, 172.60,
172.33 145.10 (s), 60.70 (s), 43.92 (s), 30.88 (s), 26.00 (s) and 14.17
2,5-Bis(1H-pyrazol-3-ylamino)-3,6-dichlorocyclohexa-2,5-diene-1,4-di-
one 4: Yield – 1.12 g (80%). The green powder on recrystallization
Table 1: Yields and reaction
conditions used in preparation of
Entry
Primary amine
Conditionsa
Colour
Yield %
1–9
1
2
3
4
5
6
7
8b
9
2.0 equiv.
2.0 equiv.
2.0 equiv.
2.0 equiv.
2.0 equiv.
2.0 equiv.
2.0 equiv.
2.0 equiv.
2.0 equiv.
Ethanol (50 mL), reflux, 90 ꢀC, 4 h
Ethanol (50 mL), reflux, 90 ꢀC, 4 h
Ethanol (50 mL), RT, 90 ꢀC, 4 h
Ethanol (50 mL), reflux, 90 ꢀC, 4 h
Ethanol (50 mL), reflux, 90 ꢀC, 4 h
Ethanol (50 mL), reflux, 90 ꢀC, 16 h
Ethanol (50 mL), reflux, 90 ꢀC, 16 h
Ethanol (50 mL), 90 ꢀC, 4 h
Red
95
95
85
80
85
65
70
90
98
Dark pink
Dark purple
Green
Green
Brown
Metallic brown
Purple
Dark green
Ethanol (50 mL), reflux, 90 ꢀC, 4 h
aConventional heating was performed in a thermally preheated oil bath under identical conditions.
bPreviously reported route employed THF as solvent (28).
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Novel Para-Quinones and their Antibacterial Activity
(s). IR (KBr, ⁄ cm): 3440, 3254(d), 2989, 2369(d), 1723(d), 1581(d),
1200, 1434(d), 1336(d), 1280, 1190, 1074(d) and 580.
rated on each plate. Stock solutions (DMSO) of all the compounds
were prepared by dissolving 10 mg in 100 lL to test the effect in
different concentrations. Each plate was then tested with 3, 6, 9
and 12 lL of stock solution. The plates were covered and placed in
an incubator at 37 ꢀC for 24 h. The plates were then removed, and
the zone of clearance (defined as the diameter of inhibited bacterial
growth around the filter paper) for each sample was measured in
millimetres.
Diethyl 6,6¢-(2,5-dichloro-3,6-dioxocyclohexa-1,4-diene-1,4-diyl)bis(az
anediyl)dihexanoate 7: Yield – 1.40 g (70%). The hot reaction mix-
ture was filtered, and a purple-coloured product was obtained after
evaporation of solvent. The product was purified by column chroma-
tography using pentane ⁄ chloroform, and the product was isolated
as brown-coloured fibrous needles. The reddish brown powder on
recrystallization in hot acetone yielded purple-coloured fibres.
UV ⁄ vis (CH3CN): kmax ⁄ nm (e ⁄ dm3 mol-1 cm-1) = 224 (5644), 355
(6820). Anal.:calcd. for C22H32Cl2N2O6: C, 53.77; H, 6.56; N, 5.70%.
Results and Discussion
1
Found: C, 53.50; H, 6.42; N, 5.71. H NMR (500 MHz, CDCl3) 7.13
Synthesis
(br.s, 2H, NH-), 4.13 (q, J = 7.1 Hz, 2H), 3.88 (dd, J = 14.2, 6.9 Hz,
2H), 2.33 (dd, J = 15.6 Hz, J = 8.1Hz 2H), 1.76–1.57 (m, 2H), 1.49–
1.34 (m, 2H), 1.26 (t, J = 7.1 Hz, 3H. 13C NMR (125 MHz, CDCl3) d
173.76, 173.33, 172.22, 145.80, 60.29, 44.58, 33.93, 30.53, 26.02,
24.41 and 14.21. ESI: 439 (M+). IR (KBr, ⁄ cm) -3421, 3100, 2940,
2858, 1737, 1567, 1489, 1369, 1337, 1162, 1069, 792 and 580.
Synthesis of ten new quinones (1–7 and 9, Table 2) and one
known example, compound 8 (28), was attempted, by refluxing the
appropriate amine with p-chloranil in ethanol, Scheme 1, of which
nine (1–9) were successful. Compound 10 did not form, instead
the starting amine, 2-aminophenol (X), was observed to dimerise in
the presence of p-chloranil to produce 2-aminophenoxazine-3-one.
Our results on the antibacterial activity of the resulting 2-aminophe-
noxazine-3-one and its silver(I) complex are reported elsewhere (29).
The two carboxylic acids VI and VII reacted with the ethanol solvent
to produce the ethyl esters, 6 and 7, Table 2. Formation of the di-
esters 6 and 7 is confirmed by NMR, IR, elemental analysis and by
a crystal structure of 6. Formation of di-esters rather than the free
acid has been previously observed for several amino acids (30,31).
Addition of the primary amine to the p-chloranil produced intensely
coloured solutions that were filtered after 4 h. In the case of
amines I, II, IV, V and IX, highly coloured powders of products 1, 2,
4, 5 and 9 precipitated immediately and were collected by suction
filtration and recrystallized from acetone or hot acetonitrile yielding
X-ray quality crystals of 1, 2, 6 and 9 (Table 1). Quinones 3, 6, 7
and 8 were recovered as powders that were purified by column
chromatography. The resulting precipitates were recrystallized from
various solvents that yielded X-ray quality crystals in the case of
product 3.
2,5-Dichloro-3,6-bis(2-hydroxyethylamino)cyclohexa-2,5-diene-1,4-
dione 8: Yield – 1.08 g (90%). The purple-coloured product was
obtained after evaporation of solvent. The purple powder on
recrystallization in hot ethanol yielded purple-coloured crystals.
UV ⁄ vis (CH3CN): kmax ⁄ nm (e ⁄ dm3 mol-1 cm-1) = 226 (1202), 290
(681), 357 (385). Anal.: calcd. for C10H12Cl2N2O4: C, 40.70; H,
4.10; N, 9.49. Found: 40.42; H, 3.9; N, 9.26. ESI: 295 (M+). IR
(KBr, ⁄ cm): 3423(s), 3195(s), 2360(d), 1578(d), 1500(s), 1447,
1
1333, 1296, 1212, 1035 and 786. H NMR (400MHz, DMSO- d6)
7.84 (s, 2H), 4.95 (br.s, 2H), 3.8(q, J = 5.9 Hz, 4H) and 3.56 (t,
4H). 13C NMR (100 MHz, DMSO-d6) d 171.77, 145.95, 98.71,
60.52 and 46.68.
2,5-Dichloro-3,6-bis(2-(hydroxymethyl)phenylamino)cyclohexa-2,5-
diene-1,4-dione 9: Yield – 1.66 g (98%). Dark green crystals
(recrystallized from ethanol). UV ⁄ vis (CH3CN): kmax ⁄ nm (e ⁄ dm3
mol-1 cm-1) = 270 (3214), 387 (2629). Anal.: calcd. for
C20H16Cl2N2O4: C, 57.30; H, 3.85; N, 6.68. Found C, 57.30; H,
3.75; N, 6.80. ESI: 419 (M+). IR (KBr, ⁄ cm): 3465, 3213 2360 (d),
1605, 1567 (d), 1501, 1469 (d), 1327, 1186 (d), 893, 753 and
576. 1H NMR (400 MHz, DMSO-d6) 9.45 (s, 2H), 7.38 (dd, 1H,
J = 7.1, 1.9 Hz), 7.24 (pd, J = 7.4, 1.7 and 2.8 Hz), 7.08 (dd,
J = 8.9, 7.1 Hz), 5.38 (s, 1H) and 4.68 (s, 2H). 13C NMR
(100 MHz, DMSO-d6) 172.2, 142.1, 135.5, 134.6, 125.9, 125.27,
125.04, 101.8 and 59.3.
Characterization
The synthesized quinones were characterized by 1H NMR, 13C
NMR, elemental analysis and mass spectrometry (see Experimental
section). Compounds 4, 5, 6, 7, 8 and 9 have a characteristic
1H NMR signal at around 7.2–7.35 p.p.m. for the NH proton on
the amine attached to the quinone ring and 4 and 5 also have a
pyrazole ring NH signal at ca. 9.4–9.1 p.p.m.. The 13C NMR spec-
tra typically have aromatic signals at 100–150 p.p.m. and a reso-
nance at ca. 170 p.p.m. for the carbonyl carbon of the p-quinone
1
Antibacterial studies
core. Full assignment of the 13C and H NMR spectra is given in
The antibacterial activity of 1–9 was screened against two bacte-
rial strains: Gram(+) Staphylococcus aureus (NCTC 7447) and
Gram()) Escherichia coli. To assess the biological activity of com-
pounds 1–9, the Kirby–Bauer disc-diffusion method was applied
(26). All bacteria were individually cultured from a single colony in
a sterile LB medium (27) overnight at 37 ꢀC (orbital shaker incuba-
tor). All the work was performed under sterile conditions.
the Experimental section. For compounds 1 and 2, 1H NMR and
13C NMR were not recorded because of the poor solubility of the
compounds in routine solvents including chloroform, methanol and
DMSO. However, it was possible to grow single crystals of these
compounds from hot acetonitrile, and their solid state structures
have been determined by single crystal diffraction. IR spectro-
scopic stretching frequencies for 1–9 have characteristic absorp-
tions between 1600 and 1550 ⁄ cm for the quinone carbonyl group
and between 3000 and 3200 ⁄ cm for the NH group. In addition,
compounds 6 and 7 have a characteristic stretching frequency for
For each strain, 70 lL of culture were spread evenly on an agar-LB
medium. Four 5-mm diameter paper discs were placed evenly sepa-
Chem Biol Drug Des 2011; 78: 787–799
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Pandurangan et al.
Table 2: In vitro antibacterial activity of p-quinones 1–9
MIC (lmol ⁄ mL)
Diameter of clearance (mm)
Compound
SA
NS
EC
1
2
3
4
5
6
7
–
NS
O
O
N
Cl
NH
Cl
HN
N
–
NS
14
NA
NA
9
NS
12
O
Cl
NH
N
N
N
HN
Cl
O
O
2.72
–
Cl
N
N
N
Cl
O
NA
NA
NA
NA
O
H
N
Cl
HN
N
N
NH
N
Cl
H
O
–
O
H
Cl
N
HN
N
N
NH
NH
Cl
O
3.16
2.76
O
O
H
N
Cl
O
O
N
Cl
H
O
O
9
O
O
O
H
N
Cl
N
Cl
H
O
O
O
8
9
4.08
–
6
8
O
H
N
Cl
OH
HO
N
Cl
H
O
HO
NA
NA
O
Cl
NH
Cl
HN
O
OH
NS, not soluble; NA, no activity; SA, S. aureus; EC, E. coli; MIC, minimum inhibitory concentration of the sample used. The assay was performed at 37 ꢀC. Both
bacteria were individually cultured from a single colony in LB medium.
the ester carbonyl at 1723 ⁄ cm, and compounds 8 and 9 have a charac-
teristic peak at 3200–3470 ⁄ cm for the alcohol OH group, Table 3. Ele-
mental analysis of all the compounds is in close agreement with the
calculated values, and mass spectrometry shows the parent molecular
weight in all cases. Electronic absorption spectra of 1–9, Table 3, typi-
cally have kmax around 300–390 nm, which is characteristic for p-ben-
zoquinones (24). Compounds 6 and 7 also have a band at 354 nm
characteristic of the ester group (30,31). In addition to these, data
compounds 1, 2, 3, 6 and 9 were structurally characterized by single
crystal diffraction.
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Novel Para-Quinones and their Antibacterial Activity
Table 4: Quinone ring bond lengths of 1, 2, 3, 6 and 9
O
RHN
Cl
Cl
1
2
3
NHR
O
Bond length (ꢀ)
Entry Bond
1
2
3
6
9
1
2
3
4
5
C1–O1
C1–C2
C2–C3
C2–Cl
1.228 (3) 1.231 (3) 1.218 (15) 1.232 (14) 1.231 (2)
1.424 (3) 1.422 (4) 1.456 (18) 1.426 (16) 1.423 (2)
1.363 (3) 1.367 (4) 1.362 (17) 1.379 (16) 1.370 (2)
1.741 (2) 1.734 (3) 1.731 (12) 1.735 (12) 1.733 (16)
C3–NHR 1.323 (3) 1.330 (4) 1.364 (16) 1.329 (15) 1.326 (2)
X-ray crystal structure analysis
Although crystal structure analysis alone is insufficient to predict
antibacterial activity, it is an important property of any bioactive
molecule, particularly as polymorphism is known to affect solubility
and hence biological action. Attempts were therefore made to crys-
tallize all nine quinones reported here and determine their solid
state structures. Single crystals of compounds 1, 2, 3, 6 and 9
were grown by slow evaporation at room temperature and their
structures determined by single crystal X-ray diffraction at 100 K
(with the exception of 3 which was determined at room tempera-
ture). Structural parameters are listed in Table 4, and the structures
are shown in Figures 1–5. Selected bond lengths including the
internal quinone ring and quinone–heteroatom bond length ranges
are given in Table 4. Complete bond lengths and angles for all are
provided in the Supporting Information.
Analysis of the bond lengths and angles confirms that all exist in
the diamagnetic quinone form with regular carbon–oxygen ketonic
bond lengths and carbon–nitrogen distances expected for a single
bond, Table 4. All five structures have an inversion centre in the
middle of the quinone ring, and a striking aspect of the solid state
structures is the wide variation in local geometry on changing R.
Structure of 1
Compounds 1–3 contain an appended pyridine group linked to the
central quinone by a methylene or ethylene group on a secondary
(compounds 1 and 2) or tertiary (compound 3) amine on the qui-
none. The nature of the bridge between the central quinone and
peripheral pyridine has a profound effect on the packing. Com-
pound 1, where the two heterocyclic rings are linked via a methy-
lene group, Figure 1A, is almost planar, Figure 1B. The planar
molecules pack in a layered structure, Figure 1C, which arises
from the stacking of the pyridine and amine nitrogens above two
of the quinone ring carbons, Figure 1(D) leading to the undulating
sheets.
Chem Biol Drug Des 2011; 78: 787–799
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Pandurangan et al.
A
B
C
D
Figure 1: (A) View of compound 1; (B) side-on view of 1 showing planarity of molecule; (C) packing diagram of 1 showing 2-D layered
structure; (D) View of local stacking.
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Novel Para-Quinones and their Antibacterial Activity
A
B
C
Figure 2: (A) View of compound 2; (B) side-on view of 2 showing stepped arrangement; (C) packing diagram of 2.
Chem Biol Drug Des 2011; 78: 787–799
793

Pandurangan et al.
A
B
C
Figure 3: (A) View of compound 3; (B) side-on view of 3 showing S-shaped arrangement; (C) view of hydrogen bonding in 3.
Structure of 2
The solubility of 3 in DMSO is good in contrast to that of the
other two pyridine substituted quinones 1 and 2 and is attrib-
uted to the methyl group on the amine. It is interesting to
note that 3 is the most active compound in the series suggest-
ing that the combination of pyridine and 1,4-benzoquinone rings
is highly effective but the compound must be soluble to be
active.
When the methylene linkage is replaced with ethylene in compound
2, the planarity is lost and the molecule adopts a stepped
arrangement, Figures 2A,B. As for compound 1, both pyridine rings
point away from the central quinone. There are no intermolecular
interactions, and the packing of the stepped molecule, Figure 2C, is
presumably governed solely by packing efficiency.
Structure of 3
Structure of 6
Compound 3 is very similar to compound 2; the only change is that
the secondary amine hydrogen has been replaced by a methyl
group, but the local geometry is very different, Figure 3A, and the
molecule now adopts a distinct S-shape (Figure 3B). Strong intermo-
lecular interactions between the quinone oxygen and the CH2 group
on an adjacent molecule leads to an in-plane ordering of the S-
shaped molecules, Figure 3C, and this extends into a 2-D lattice by
an interaction between the pyridine nitrogen and a pyridine CH on
an adjacent molecule.
Compound 6 differs from 1–3 as it has linear ester groups
appended, rather than pyridine rings (Figure 4A). The conforma-
tion is clearly chair shaped, Figure 4B, and adjacent molecules
are linked by a double donor-acceptor hydrogen bonding motif
where each quinone oxygen and secondary amine hydrogen on
one molecule hydrogen bond to the NH and quinone oxygen on
their nearest neighbour, thus keeping the rings in plane (Fig-
ure 4C). This leads to an efficient herringbone packing pattern
(Figure 4D).
794
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Novel Para-Quinones and their Antibacterial Activity
A
B
C
D
Figure 4: (A) View of compound 6; (B) side-on view of 6 showing stepped arrangement; (C) hydrogen bonding in 6; (D) Packing diagram
of 6.
Chem Biol Drug Des 2011; 78: 787–799
795

Pandurangan et al.
A
B
C
Figure 5: (A) View of compound 9; (B) side-on view of 9 showing out-of-plane twist of appended rings; (C) packing diagram for 9.
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Novel Para-Quinones and their Antibacterial Activity
Structure of 9
Unlike 1–3 and 6, compound 9 does not contain a spacer between
the appended R group and the secondary amine of the quinone,
Figure 5A. The appended benzyl alcohol groups both twist out of
the plane of the central quinone ring, Figure 5B, presumably to min-
imize packing energy, and the resulting packing is less efficient
than the herringbone pattern of 6.
Bond lengths of quinones
The C–O distances of 1.21–1.23 ꢀ are in close agreement with
those observed for the p-quinone compounds (22,32). The C–C bond
lengths of 1.36–1.46 ꢀ in the quinone rings are also in close agree-
ment with those observed for the p-quinone ligands, as are the C–
Cl bond lengths of 1.73–1.74 ꢀ (33,34).
Figure 6: Zone of clearance for active compounds 3, 6, 7 and
8 towards Gram(+) S. aureus. Inactive compounds 1, 2, 4, 5 and 9
had zero zone of clearance and are not shown.
Antibacterial testing
Antibacterial activity of compounds 1–9 towards Gram(+) S. aureus
and Gram()) E. coli were compared using the Kirby–Bauer disc-dif-
fusion method and results are shown in Table 2. For comparative
purposes, compounds 1–9 can be broadly classified according to
the nature of the R group. Using this classification, the compounds
can be grouped into five N-heterocyclic ligands with pyridine (1–3)
or pyrazole (4 and 5) substituents. The remaining four fall into two
categories: two long chain ethoxy esters (6 and 7) and two alco-
hols (8 and 9). The activity of all towards S. aureus and E. coli will
be discussed. Pyridine-containing quinones 1 and 2 were measured
as solid samples applied as spots on the Petri dishes. All other
compounds were loaded as solutions in DMSO.
pounds 1, 2, 4, 5, 6, 7 and 9 were inactive whilst 3 and 8
showed reasonable activity (Figure 7). Again the solubility problems
of pyridine ligands 1 and 2 may affect the measurement, so it is
not possible to absolutely conclude whether they are inactive or if
solid spotting explains the lack of response. In contrast to these,
pyridine ligand 3 shows most activity of the whole series 1–9, as
was the case in the S. aureus investigation. However, the pyrazole
derivatives 4 and 5 are again inactive in the antibacterial test. As
was the case for the N-heterocyclic ligands, the activity of the two
alcohols 8 and 9 towards E. coli mirrors that of their activity
towards S. aureus in that the ethyl alcohol 8 is observed to be
active whilst the benzyl alcohol 9 is inactive. The only functional
group to show a difference in the behaviour towards the two bac-
terial types is the ester, as it is now observed that esters 6 and 7
are inactive towards E. coli in contrast to their good activity
towards S. aureus. The sample solvent (DMSO) was also inactive
towards both bacteria as previously reported (35).
Activity towards Gram(+) S. aureus
Compounds 1, 2, 4, 5 and 9 were inactive whilst 3, 6, 7 and 8
showed varying degrees of activity. Pyridine ligand 3 showed the
greatest activity, Figure 6. Therefore, it might be reasonable to
expect that the other pyridine ligands 1 and 2 would also be
active. The absence of any activity may then be due to solubility
differences rather than inherent inactivity as 1 and 2 were the only
compounds to be spotted as solid samples. However, this alone
does not definitively explain the inactivity as compound 9 was also
inactive towards both bacteria despite being applied in solution. In
contrast to pyridine ligand 3, the N-heterocyclic pyrazoles 4 and 5
were totally inactive towards S. aureus.
Given the redox lability of quinones, the antibacterial activity of
some members of the series is likely because of their ability to
When ester groups are appended, some activity is observable, Fig-
ure 6, and 6 and 7 show similar activity to each other but not so
much as for pyridine derivative 3. Finally, the alcohols 8 and 9
show very different activity with no activity for benzyl alcohol deriv-
ative 9 in contrast to the good activity of 8 that is the second most
active of the set towards S. aureus. The major difference between
these is the presence of the benzene ring in 9 suggesting that
decreasing the polarity reduces the activity.
Figure 7: Zone of clearance for active compounds 3 and 8
towards Gram()) E. coli. Inactive compounds 1, 2, 4, 5, 6, 7 and
9 had zero zone of clearance and are not shown.
Activity towards Gram()) E. coli
The pattern of activity of the N-heterocyclic quinones towards the
E. coli is the same as for the activity towards S. aureus. Com-
Chem Biol Drug Des 2011; 78: 787–799
797

Pandurangan et al.
form the toxic semiquinone radical, which is a potent reactive oxy-
gen species (ROS) (36). Production of ROS causes oxidative stress
as the radicals react readily with most bio-molecules to initiate a
chain reaction of free radical formation that can be terminated only
after reaction with another free radical or free radical scavengers
such as antioxidants. These ROS can react with all the macromolec-
ular machinery of cells particularly lipids proteins and DNA (36,37).
This most probably accounts for the reactivity of certain quinones
in the series towards Gram(+) and Gram()) bacteria. Whilst a
significant number of quinones 1–9 showed activity towards S. aur-
eus, fewer were active towards E. coli, and in general, the activity
was not so potent as that observed in a related set of p-quinone
derivatives where the Kirby–Bauer method was also used to assess
antibacterial efficacy (24). In this series, described by Batra et al., a
pair of substituted phenyl rings is appended onto the 3-6-dichloro-
1,4-benzoquinone core and zonal clearance ranges from 8.5–
12.5 mm for S. aureus and 8.6–14.1 mm for E. coli. In comparison
with these values, only compound 3 in our series shows strong
activity suggesting that the nature of the appended aromatic group
is significant in determining activity.
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In our work, we have shown the synthesis of p-quinone analogues
with different functionalities in good yields. Substitution of ana-
logue 2 with a methyl group yields 3 that exhibits good antibacte-
rial activity. All synthesized quinones have been chemically
characterized, and five were characterized by single crystal diffrac-
tion. Structural analysis reveals a variety of ligand conformations in
the solid state including S-, Z- and planar-arrangements. The S-
shaped pyridine substituted quinone 3 was most active and was
also the only soluble member of the pyridine quinone set 1–3.
Antimicrobial activity towards Gram(+) and Gram()) bacteria was
assessed showing that some members of the series had good anti-
microbial activity. Studies are underway to assess the anticancer
activity of these quinones and to synthesize their metal complexes
to test these for their antimicrobial activity.
Acknowledgments
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The award of a Government of Ireland Postgraduate Scholarship to
(K.P.) by the Irish Research Council for Science, Engineering and
Technology (IRCSET) is gratefully acknowledged as is the award of
an Enterprise Ireland Postgraduate Scholarship to (K.D.M.) Financial
support from the UCD School of Chemistry and Chemical Biology is
also gratefully acknowledged.
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