Synthesis and antibacterial activity of substituted 1,2,3,4- tetrahydropyrazino [1,2-a] indoles

Article abstract of DOI:10.1016/j.bmcl.2005.09.066

A series of substituted 1,2,3,4-tetrahydropyrazino [1,2-a] indole derivatives have been synthesized and tested against the Gram positive and Gram negative strains of bacteria namely Staphylococcus aureus (MTCCB 737), Salmonella typhi (MTCCB 733), Pseudomonas aeruginosa (MTCCB 741), Streptomyces thermonitrificans (MTCCB 1824) and Escherichia coli (MTCCB 1652). All synthesized compounds showed mild to moderate activity. However, compounds 4d-f were found to have potent activity against pathogenic bacteria used in the study. Their MIC ranged from 3.75 to 60 μg/disc. In vitro toxicity tests demonstrated that toxicity of 4d-f was not significantly different than that of gentamycin. However, at higher concentration (1000-4000 μg/ml) difference was highly significant.

Full text of DOI:10.1016/j.bmcl.2005.09.066

Bioorganic & Medicinal Chemistry Letters 16 (2006) 413–416
Synthesis and antibacterial activity of substituted
1,2,3,4-tetrahydropyrazino [1,2-a] indoles
Rakesh Kumar Tiwari,a Devender Singh,a Jaspal Singh,a Vibha Yadav,b
Ajay K. Pathak,c Rajesh Dabur,c Anil K. Chhillar,b Rambir Singh,c
G. L. Sharma,b Ramesh Chandraa,* and Akhilesh K. Vermaa,*
aSynthetic Organic Chemistry Research Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research,
University of Delhi, Delhi 110007, India
bInstitute of Genomics and Integrative Biology, Mall Road, University Campus, Delhi 110007, India
cInstitute of Biomedical Sciences, Bundelkhand University, Jhansi, UP, India
Received 22 June 2005; revised 12 September 2005; accepted 24 September 2005
Available online 21 October 2005
Abstract—A series of substituted 1,2,3,4-tetrahydropyrazino [1,2-a] indole derivatives have been synthesized and tested against the
Gram positive and Gram negative strains of bacteria namely Staphylococcus aureus (MTCCB 737), Salmonella typhi (MTCCB 733),
Pseudomonas aeruginosa (MTCCB 741), Streptomyces thermonitrificans (MTCCB 1824) and Escherichia coli (MTCCB 1652). All
synthesized compounds showed mild to moderate activity. However, compounds 4d–f were found to have potent activity against
pathogenic bacteria used in the study. Their MIC ranged from 3.75 to 60 lg/disc. In vitro toxicity tests demonstrated that toxicity
of 4d–f was not significantly different than that of gentamycin. However, at higher concentration (1000–4000 lg/ml) difference was
highly significant.
Ó 2005 Elsevier Ltd. All rights reserved.
Since the introduction of penicillin in the 1940s, antibi-
otics have a history of success in controlling morbidity
due to infectious diseases. But, as a consequence of fre-
quent use, bacterial resistance to known classes of anti-
biotics has become a severe global problem in recent
years and presents a continuous clinical challenge.1–3
Resistance can result from modification of an antibacte-
rial target or from functional bypassing of that target, or
it can be contingent on impermeability, efflux or enzy-
matic inactivation of the drug.4 There are serious con-
cerns that untreatable pathogens may develop at an
alarming rate in the near future. Strategies to address
this challenge include the design of improved versions
of antibacterial classes already in clinical use and the
use of drug combinations. The application of these strat-
egies can be quite successful, but a high risk of rapid
resistance development remains. Thus, an urgent need
for new potent classes of antibiotics with novel modes
of action persists.
Pyrazino [1,2-a] indoles have attracted a great deal of
attention due to their therapeutic uses as serotonin
antagonist,5 thrombolytic,6 in cardiovascular diseases,7
antidepressant, anxiolitics,8 central nervous system
depressants,9 anticonvulsants,10 antihistaminic,11 pro-
13
13,14
tein kinase C inhibitors,12 5-HT2A
,
5-HT2C
and
selective imidazoline I2 receptor ligands.15 The antibac-
terial activity of the indole derivatives has not been
much studied. One report shows the activity of pyrazi-
noate towards resistant Mycobacterium tuberculosis.16
Some triazino [5,6-b] indoles have been reported to have
antifungal properties.17
2-(3-Methyl-1H-indol-1-yl) ethylamine 2 was obtained
by the reaction of 3-methylindole 1 with 2-chloroethyl-
amine hydrochloride in CH3CN in the presence of
NaOH and Bu4NHSO4 by reported procedures.18 Key
benzotriazolyl intermediate 2-(1H-1,2,3,4-benzotriazol-
1-ylmethyl)-10-methyl-1,2,3,4-tetrahydropyrazino [1,2-
a] indole 5 and nucleophilic substituted derivative 6a,b
and compounds 7–9 were obtained according to our
Keywords: Synthesis; 1,2,3,4-Tetrahydropyrazino [1,2-a] indole; Anti-
bacterial activity; Toxicity; Haemolytic activity; Gentamycin.
*
Corresponding authors. Tel.: +91 11 55782976, 27666272; fax: +91
11 27666248; e-mail: akvacbr@rediffmail.com
0960-894X/$ - see front matter Ó 2005 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2005.09.066

414
R. K. Tiwari et al. / Bioorg. Med. Chem. Lett. 16 (2006) 413–416
published procedure.18 1-Substituted 1,2,3,4-tetrahydro-
pyrazino [1,2-a] indoles 4a–i were obtained as a racemic
mixture in high yields by the reaction of 2-(3-methyl-1H-
indol-1-yl) ethylamine 2b with benzotriazole and alde-
hydes 3a–i in the presence of catalytic amount of AlCl3
in CH2Cl2 (Scheme 1).19 The structures of new com-
coccus aureus, Salmonella typhi, Streptomyces
thermonitrificans, Pseudomonas aeruginosa and Esche-
richia coli. The experimental27 result of antibacterial
activity indicated a variable degree of efficacy of the
compounds against different strains of bacteria (Table
1). Compound 4a showed strong activity against P.
aeruginosa (MIC 3.75 lg/disc); however, it did not show
any effect on other strains of bacteria even up to a con-
centration of 60.00 lg/disc. Similarly the 4c was effective
against P. aeruginosa and S. thermonitrificans only, the
MIC being 3.75 and 15.00 lg/disc, respectively. Signifi-
cant activity was observed with 4d–4f against all the bac-
terial strains used in the study and their MIC ranged
from 7.50 to 60.00 lg/disc. Other compounds appeared
to be broad spectrum, as they showed mild to moderate
effect on most of the strains, although the compound
with pyrazinoate moiety was shown earlier to inhibit
the growth of M. tuberculosis at a concentration of
0.5–32 lg/ml. However, pyrazino [1,2-a] indoles have
not been investigated. We, for the first time, synthesized
substituted pyrazino [1,2-a] indoles and tested for the
antimicrobial properties. The activity of the compound
1
pounds 4c and 4g are clearly supported by their H,
1
13C NMR spectra and microanalysis.20 The H NMR
spectra showed NCH-pyrazino singlet signal for 4a–i
at ꢀ5.3 ppm. Presence of exchangeable NH-pyrazino
was confirmed by deuterium exchange. 1,3-Dimethyl-
pyrazino [1,2-a] indole 11a and 3-methyl-1-phenyl-pyr-
azino [1,2-a] indole 11b were prepared by the reaction
of 1-propargyl-2-acetylindole 10a and 1-propargyl-2-
benzoylindole 10b in dry ammonia and methanol
(Scheme 2).21 1-Propargyl-2-acetylindole 10a and 1-
propargyl-2-benzoylindole 10b were synthesized by stan-
dard procedure22 starting from 2-acetyl-1H-indole23 and
2-benzoyl-1H-indole.24
The in vitro antibacterial activity was tested by disc dif-
fusion method25 using pathogenic strains of Staphylo-
CH3
CH3
CH3
R
b
R
a
RCHO
N
N
C6H5
NH
4a
4b
4c
4d
4e
4f
4g
4h
4i
N
NH2
p-BrC6H4
m-ClC6H4
p-FC6H4
p-CH3C6H4
p-NO2C6H4
m-CH3OC6H4
2-pyridyl
2-thienyl
H
4a-i
2
3a-i
1
c
CH3
CH3
g
CH3
d
N
N
N
N
N
CH3
N
R1
Bt
Comp. R1
6a-b
5
9
f
6a
6b
e
N
N
N
C6H5
p-CH3C6H4
BtH =
CH3
H
CH3
N
N
OC2H5
O
N
N
P
8
CN
OC2H5
7
Scheme 1. Synthesis of substituted 1,2,3,4-tetrahydropyrazino [1,2-a] indoles. Reagents and conditions: (a) ClCH2CH2NH2HCl, NaOH, TBAHS,
CH3CN, reflux, 36 h; (b) benzotriazole, dichloromethane, catalytic AlCl3, 25 °C, 85–96%; (c) benzotriazole, HCHO (2 equiv), 25 °C stirring; (d)
R1MgX, THF, reflux; (e) NaCN, DMSO, 25 °C, 36 h; (f) P(OEt)3, ZnBr2, DCM, 25 °C, 24 h; (g) NaBH4, THF, reflux,12 h.
R
R
R
R1
O
R1
O
Br
R1
NH3/CH3OH 2N
N
N
N
N
TBAHBr/Benzene
H
11a-b
R=H, R1=CH3, Ph.
10a-b
Scheme 2. Reaction conditions: molar ratio indole 10a–b, 1/2 M NH3 in MeOH = 1:20, sealed tube.

R. K. Tiwari et al. / Bioorg. Med. Chem. Lett. 16 (2006) 413–416
415
Table 1. Minimum inhibitory concentrations of substituted-1,2,3,4-tetrahydropyrazino [1,2-a] indoles by disc diffusion assay
Compound
MIC (lg/disc)
Staphyloccus aureus
Salmonella typhi
Pseudomonas aeruginosa
Streptomyces thermonitrificans
Escherichia coli
4a
4b
—
—
03.75
60.0
15.0
30.0
60.0
30.0
—
—
—
—
15.0
—
60.0
—
15.0
03.75
07.5
30.0
15.0
15.0
—
4c
4d
—
30.0
30.0
30.0
60.0
03.75
60.0
30.0
15.0
15.0
15.0
—
30.0
15.0
30.0
30.0
—
15.0
15.0
30.0
30.0
—
4e
4f
4g
4h
4i
—
—
30.0
60.0
60.0
30.0
30.0
—
—
—
—
—
5
6a
—
60.0
60.0
60.0
60.0
30.0
60.0
60.0
0.5
60.0
60.0
30.0
60.0
30.0
60.0
60.0
1.0
—
—
6b
7
—
—
8
9
11a
30.0
60.0
60.0
1.0
30.0
60.0
60.0
1.0
—
60.0
60.0
1.0
2.0
11b
Gentamycin
Doxycycline HCl
1.0
1.0
1.0
1.0
(—) means no activity.
Figure 1. Cytotoxicity of substituted pyrazino [1,2-a] indoles 4d–f analysed by haemolytic assay.
appeared to be associated with the l or 2 substitution on
the 1,2,3,4-tetrahydropyrazino [1,2-a] indoles. The pres-
ence of NH group with substitution on 1-position of
compound 4a–i showed better activity than compounds
5–9 with substituents present on 2-position. Reactivity
data of all the compounds revealed that the presence
of free NH group might be responsible for the requisite
activity. It was observed that the presence of 4-bromo-
phenyl and 3-chlorophenyl substituents at 1-position in
compounds 4b–c showed significant activity against
S. aureus and S. thermonitrificans, respectively. Howev-
er, compounds 4d–f with the presence of 4-fluorophenyl,
4-methylphenyl and 4-nitrophenyl at 1-positon showed
significant activity against all the bacteria used in the
study (Table 1). Enhanced activity of 1-substituted
1,2,3,4-tetrahydropyrazino [1,2-a] indoles (4a–i) as com-
pared to that of 2-substituted 1,2,3,4-tetrahydropyrazi-
no [1,2-a] indoles (5–9) might be due to the availability
of lone pair on the pyrazino nitrogen atom as well as
structure of the pyrazino ring.18
The in vitro cell cytotoxicity of 4d–f was investigated
using haemolytic assay.26 Results demonstrated that
concentrations up to 500 lg/ml of these compounds
lysed 5–10% of erythrocytes. The percent lysis induced
by concentration up to 500 lg/ml of gentamycin was
not significantly different than that of compounds. How-
ever, at higher doses (1000–4000 lg/ml), the difference in
toxicity was significant (Fig. 1).
Series of substituted pyrazino [1,2-a] indole have been
synthesized and were found to have antibacterial activi-
ty against pathogenic strains of S. aureus (MTCCB 737),
S. typhi (MTCCB 733), P. aeruginosa (MTCCB 741), S.
thermonitrificans (MTCCB 1824) and E. coli (MTCCB
1652) (Table 1). The compounds 4d–f were considered
to be potent antibacterial agents due to significant activ-
ity against all the bacteria used in the study. The com-
pounds 4d–f being less toxic than gentamycin could be
considered as safer drug candidates and can be taken
up for the development of suitable antibacterial drug.

416
R. K. Tiwari et al. / Bioorg. Med. Chem. Lett. 16 (2006) 413–416
18. (a) Katritzky, A. R.; Verma, A. K.; He, H.-Y.; Chandra,
Acknowledgments
R. J. Org. Chem. 2003, 68, 4938; (b) Katritzky, A. R.;
Akhmedov, N. G.; Myshakin, E. M.; Verma, A. K.; Hall,
C. D. Magn. Reson. Chem. 2005, 43, 351.
We gratefully acknowledge financial support from
Department of Science and Technology, New Delhi,
for this work. R.K.T. thanks J. A. Ganguly for JRF;
J.S. and V.Y. are thankful to CSIR for JRF and SRF.
19. Tiwari, R. K.; Singh, J.; Singh, D.; Verma, A. K.;
Chandra, R. Tetrahedron 2005, 61, 9513.
20. Analytical data for 1-(3-methoxyphenyl)-10-methyl-
12,3,4-tetrahydropyrazino [1,2-a] indole 4g: white needles
from EtOAc/hexanes; mp 124–126 °C; 1H NMR d 1.60 (s,
1H, NH), 1.84 (s, 3H, CH3), 3.12–3.30 (m, 2H, H-3), 3.76
(s, 3H, OMe), 3.94–4.12 (m, 2H, H-4), 5.30 (s, 1H, H-1),
6.80–7.50 (m, 8H, Ar); 13C NMR d 8.2 (CH3), 38.5 (C3),
41.5(C1), 54.2 (C4), 57.2 (C30-OMe), 105.6 (C6), 107.8
(C40), 108.3 (C10), 109.2 (C20), 118.7 (C7), 119.1 (C60),
119.5 (C9), 121.7 (C8), 122.4 (C50), 131.1 (C9a), 139.5
(C10), 142.1 (C5a), 143.2 (C10a), 154.4 (C30); LCMS m/z,
293 (5%, M+1), 292 (30%, M), 291 (100%, Mꢁ1). Anal.
Calcd for C19H20N2O: C, 78.00; H, 9.58; N, 9.58. Found:
C, 77.72; H, 9.51; N, 9.54. 1-(3-Chlorophenyl)-10-methyl-
1,2,3,4-tetrahydropyrazino [1,2-a] indole 4c: white needles
from EtOAc/hexanes; mp 101–102 °C; 1H NMR d 1.84 (s,
4H, NH, CH3), 3.12–3.24 (m, 2H, H-3), 3.84–4.12 (m, 2H,
H-4), 5.31 (s, 1H, H-1), 7.04–7.42 (m, 8H, aromatic); 13C
NMR d 8.2 (CH3), 38.2 (C3), 44.6 (C1), 56.7 (C4), 108.5
(C6), 118.3 (C10), 118.9 (C7), 121.0 (C9), 125.1 (C8), 128.6
(C60), 129.2 (C40), 131.2 (C20), 132.4 (C50), 133.1 (C9a),
135.5 (C30), 138.4 (C10), 140.6 (C5a), 142.3 (C10a); LCMS
m/z 297.1 (50%, M+1), 295 (100%, Mꢁ1), 280.1 (7%,
Mꢁ15), 186.2 (12%, Mꢁ110). Anal. Calcd for
C18H17N2Cl: C, 72.80; H, 5.70; N, 9.40. Found: C,
72.52; H, 5.40; N, 9.21.
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