Synthesis, crystal structure, molecular docking and antimicrobial evaluation of new pyrrolo[3,2-c]pyridine derivatives

Article abstract of DOI:10.1016/j.molstruc.2014.10.006

New antibacterial agents, pyrrolo[3,2-c]pyridine derivatives have been designed and synthesized. The structural considerations of the designed molecules were further supported by the docking study with GlcN-6-P synthase. The chemical structures of the new compounds were characterized by NMR, mass spectral analysis and elemental analysis. Single crystals of two compounds, C₁₃H₁₅N₂Cl [6a] and C₂₁H₂₄N₃OCl, CH₄O [7c] were obtained allowing for structural analysis. [C₁₃H₁₅N₂Cl] monoclinic, P2₁/c, a = 9.9763(6) A?, b = 9.6777(6) A?, c = 13.3002(9) A?, β = 106.459(7)°, V = 1231.47(14) A?³, Z = 4, T = 173(2) K, μ(Cu Kα) = 2.522 mm^-1, D_calc = 1.266 g/mm³, 7124 reflections, 2404 unique (R_int = 0.0381), R₁ = 0.0420 (I > 2σ(I)) and wR₂ = 0.1254 (all data). [C₂₁H₂₄N₃OCl, CH₄O] triclinic, P-1, a = 10.1478(7) A?, b = 12.0945(8) A?, c = 18.3244(10) A?, α = 104.369(5)°, β = 90.766(5)°, γ = 99.235(6)°, V = 2147.1(2) A?³, Z = 4, T = 173(2) K, μ(Cu Kα) = 1.744 mm^-1, D_calc = 1.243 g/mm³, 14238 reflections, 8297 unique (R_int = 0.0330), R₁ = 0.0578 (I > 2σ(I)) and wR₂ = 0.1773 (all data). The in vitro antimicrobial activities of the compounds were conducted against various Gram-negative, Gram-positive bacteria and fungi. Amongst the tested compounds 7e displayed promising antibacterial activity against Gram-positive bacteria Bacillus flexus compared to antibiotic Amoxicillin.

Full text of DOI:10.1016/j.molstruc.2014.10.006

Journal of Molecular Structure 1081 (2015) 85–95
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Synthesis, crystal structure, molecular docking and antimicrobial
evaluation of new pyrrolo[3,2-c]pyridine derivatives
a
a
b
Gilish Jose a, T.H. Suresha Kumara a,e, , Gopalpur Nagendrappa , H.B.V. Sowmya , Jerry P. Jasinski ,
⇑
Sean P. Millikan b, Sunil S. More c, Bhavya Janardhan c, B.G. Harish d, N. Chandrika a
a Postgraduate Department of Chemistry, Jain University, 52 Bellary Road, Hebbal, Bangalore, Karnataka 560024, India
b Department of Chemistry, Keene State College, Keene, NH 03435-2001, USA
c Department of Biochemistry, Center for Postgraduate Studies, Jain University, Bangalore, Karnataka 560011, India
d Department of Master of Computer Applications, Center for Postgraduate Studies, Visvesvaraya Technological University, Bangalore, Karnataka 560054, India
e Department of Chemistry, University B.D.T. College of Engineering, Davanagere, Karnataka 577004, India
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
ꢀ
ꢀ
ꢀ
A new series of pyrrolo[3,2-c]pyridine
derivatives were designed and
synthesized.
The molecular docking of the GlcN-6-
P synthase with target compounds
was carried out.
X-ray crystal structure determination
and analysis of 6a and 7c were carried
out.
ꢀ
ꢀ
In vitro antibacterial and antifungal
screening was carried out.
Compound 7e showed substantial
antibacterial activity against B. flexus.
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 19 March 2014
Received in revised form 4 October 2014
Accepted 4 October 2014
Available online 12 October 2014
New antibacterial agents, pyrrolo[3,2-c]pyridine derivatives have been designed and synthesized. The
structural considerations of the designed molecules were further supported by the docking study with
GlcN-6-P synthase. The chemical structures of the new compounds were characterized by NMR, mass
spectral analysis and elemental analysis. Single crystals of two compounds, C13H15N2Cl [6a] and
C21H24N3OCl, CH4O [7c] were obtained allowing for structural analysis. [C13H15N2Cl] monoclinic, P21/c,
a = 9.9763(6) Å, b = 9.6777(6) Å, c = 13.3002(9) Å, b = 106.459(7)°, V = 1231.47(14) Å3, Z = 4, T = 173(2) K,
Keywords:
l
(Cu K
(I > 2
(I)) and wR2 = 0.1254 (all data). [C21H24N3OCl, CH4O] triclinic, PÀ1, a = 10.1478(7) Å,
b = 12.0945(8) Å, c = 18.3244(10) Å, = 104.369(5)°, b = 90.766(5)°,
= 99.235(6)°, V = 2147.1(2) Å3,
Z = 4, T = 173(2) K, (Cu
) = 1.744 mmÀ1 Dcalc = 1.243 g/mm3, 14238 reflections, 8297 unique
(Rint = 0.0330), R1 = 0.0578 (I > 2 (I)) and wR2 = 0.1773 (all data). The in vitro antimicrobial activities of
a
) = 2.522 mmÀ1, Dcalc = 1.266 g/mm3, 7124 reflections, 2404 unique (Rint = 0.0381), R1 = 0.0420
Antimicrobial activity
GlcN-6-P synthase
Pyrrolo[3,2-c]pyridine
X-ray crystallography
r
a
c
l
K
a
,
r
the compounds were conducted against various Gram-negative, Gram-positive bacteria and fungi.
Amongst the tested compounds 7e displayed promising antibacterial activity against Gram-positive bac-
teria Bacillus flexus compared to antibiotic Amoxicillin.
Ó 2014 Elsevier B.V. All rights reserved.
⇑
Corresponding author at: Department of Chemistry, University B.D.T. College of
Engineering, Davanagere, Karnataka 577004, India. Tel.: +91 9916588466.
E-mail addresses: suresha.kumara@gmail.com, suresha.kumara@rediffmail.com
(T.H. Suresha Kumara).
http://dx.doi.org/10.1016/j.molstruc.2014.10.006
0022-2860/Ó 2014 Elsevier B.V. All rights reserved.

86
G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
[22]. We report herein, synthesis, X-ray crystal structure analysis,
Introduction
molecular docking and antimicrobial evaluation of new pyrrol-
o[3,2-c]pyridine derivatives.
The pyrrolopyridine motifs are a growing class of heterocyclic
scaffold present in many natural and unnatural compounds with
significant biological applications. For example, the natural prod-
uct variolin B 1 (Fig. 1) is a promising anticancer agent [1]. Other
examples include the synthetic pyrrolopyridine derivative diazare-
beccamycin 2 is a potent anticancer agent [2], pyrrolo[2,3-c]pyri-
dine 3 which has demonstrated activity as an inhibitor of HIV-1
attachment to CD4+ T cells [3] and pyrrolo[2,3-b]pyridine 4 is a
potent p38 kinase inhibitor [4]. Pyrrolopyridines also posses signif-
icant biological applications such as antimicrobial [5–9], analgesic
[10], antimalarial [11], antiproliferative [12], antihypertensive
[13], cannabinoid activity [14,15] and Factor VIIa inhibitors [16].
As a result of our considerable interest in the synthesis of pyri-
dine-containing compounds and their antimicrobial activity [17],
we initiated a programme directed towards the synthesis of new
pyrrolopyridine compounds.
The emergence of multiple drug resistant microorganisms has
caused major health concern worldwide. Infections caused by bac-
teria and fungi remain a major health concern due to the develop-
ment of resistance to existing antimicrobial agents [18–21].
Therefore, there is an increasing need to design and synthesize
new antimicrobial agents with a broad spectrum of activities. On
the basis of potential antimicrobial properties of pyrrolopyridine
compounds [5–9], we earmarked to design new pyrrolopyridine
derivatives anticipating enhanced antimicrobial activity. The new
pyrrolopyridines were designed based on the assumptions of Lipin-
ski rule to fulfil the drug likeness properties of the molecules. The
structural considerations of the designed molecules were further
supported by the docking study with target enzyme, L-glutamine:
D-fructose-6-phosphate amidotransferase (EC 2.6.1.16), known
under the trivial name of glucosamine-6-phosphatesynthase
(GlcN-6-P synthase), as such new target for antimicrobial studies
Experimental section
General methods: All chemicals and solvents were purchased
from commercial suppliers. All reactions were performed under
an inert atmosphere of dry nitrogen using dry solvents. The pro-
gress of the reactions was monitored by using Si gel 60 F254 thin
layer chromatography plates and spots were detected by UV/
254 nm. Compounds were purified by column chromatography
on silica gel 230–400 using petether/ethyl acetate or dichloro-
methane/methanol solvent mixtures as eluent. All the compounds
were characterized by 1H NMR, 13C NMR, LCMS and elemental
analysis. Melting points of the samples were determined in open
capillary tubes using Buchi Melting point B-540 apparatus and
are uncorrected. 1H and 13C NMR spectra were recorded on a Bru-
ker NMR spectrometer (400 and 100 MHz, respectively) using deu-
terated DMSO as solvent with TMS as internal standard. The mass
recorded in Agilent LCMS 1100 series instrument using API-ES
positive-ion mode and negative-ion mode. The CHN analysis was
recorded in an Elementar vario MICRO cube.
Experimental procedure for the synthesis of 2-chloro-3-iodopyridin-4-
amine (2) [17]
A mixture of 2-chloro-4-amino pyridine 1 (20 g, 0.15 mol),
potassium acetate (22.9 g, 0.23 mol) and ICl (27.7 g, 0.17 mol) in
glacial acetic acid (200 mL) was heated to 70 °C for 4 h. After com-
pletion of the reaction, the solvent was concentrated under
reduced pressure. The residue was neutralized with 10% NaHCO3
solution (250 mL) and extracted with two 300-mL portions of
EtOAc. The combined organic extracts were washed with brine
(200 mL) and dried over anhydrous Na2SO4. The solvent was
removed in vacuum. The crude product showed a mixture of iodo-
pyridines 2, 3 and 4 in the ratio 45:45:10. The required compound
2 (elution 3) was isolated via normal phase preparative HPLC
(mobile phase: 60:40, 0.1% TFA in hexane-IPA; column: SunFire
Silica 19 Â 150 mm, 5
lm; Flow rate: 18.0 mL/min) in 49.7%
yield (19.7 g) as an off white solid; mp 102.9–104.1 °C; 1H NMR
(400 MHz, DMSO-D6): d 7.73 (d, J = 4.0 Hz, 1H), 6.52 (d, J = 4.0 Hz,
1H), 6.50 (s, 2H); MS (m/z): 255.0 [M+H]+. Anal. calcd. for
C5H4ClIN2: C, 23.60; H, 1.58; N, 11.01; found: C, 23.59; H, 1.578;
N, 10.99.
General experimental procedure for the synthesis of 6a–c
In a Schlenk tube, compound 2 (11.79 mmol), Copper (1) iodide
(0.59 mmol), triethylamine (35.37 mmol) and alkyne (14.15 mmol)
were mixed in THF (30 mL). The Schlenk tube was capped with a
rubber septum, evacuated and backfilled with argon (this sequence
was carried out four times). Bis(triphenylphosphine)palladium(II)
dichloride (0.58 mmol) was added and the Schlenk tube was sealed
with a Teflon screw cap. The reaction mixture was refluxed for 1 h.
After completion of the reaction, the reaction mixture was filtered
through a thin pad of celite (eluted with CH2Cl2) and the eluent
was concentrated under reduced pressure. The solvent was
removed under reduced pressure and the crude product was
passed through a small plug of silica (eluted with CH2Cl2) and
the eluent was concentrated under reduced pressure to afford
5a–c. The crude product was as such taken for the next step with-
out purification.
In an oven-dried RB flask, compound 5a–c (8.04 mmol) and
potassium tert-butoxide (16.08 mmol) were mixed in NMP
Fig. 1. Examples of biologically active pyrrolopyridines.

G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
87
(20 mL). The reaction mixture was heated at 100 °C for 1 h. After
completion of the reaction, the reaction mixture was diluted with
DCM (60 mL) and the organic layer was washed with water
(30 mL Â 3) and brine (30 mL). The organic layer was separated,
dried over anhydrous Na2SO4 and concentrated. The crude product
was purified by silica gel column chromatography to provide 6a–c.
J = 7.2 Hz, 2H), 7.52 (t, J = 7.6 Hz, 2H), 7.43 (t, J = 7.6 Hz, 1H), 7.37
(d, J = 5.2 Hz, 1H), 4.46 (d, J = 3.6 Hz, 1H), 3.77 (s, 2H), 3.42–3.41
(m, 1H), 2.71–2.68 (m, 2H), 2.15–2.10 (m, 2H), 1.65–1.63 (m,
2H), 1.34–1.26 (m, 2H); 13C NMR (100 MHz, DMSO-D6): d 142.0,
141.2, 139.5, 139.1, 131.6, 129.1, 128.5, 128.3, 122.3, 108.8,
106.7, 66.4, 50.1, 50.0, 34.6; MS (m/z): 342.2 [M+H]+; Anal. calcd.
for C19H20ClN3O: C, 66.76; H, 5.90; N, 12.29; found: C, 66.74; H,
5.893; N, 12.28.
4-Chloro-2-(cyclopentylmethyl)-1H-pyrrolo[3,2-c]pyridine (6a)
Pale yellow solid (82%); mp 145.8–148.7 °C; 1H NMR (400 MHz,
DMSO-D6): d 11.73 (s, 1H), 7.87 (d, J = 5.6 Hz, 1H), 7.29–7.28 (m,
1H), 6.24 (s, 1H), 2.72 (d, J = 7.5 Hz, 2H), 2.26–2.22 (m, 1H), 1.72–
1.67 (m, 2H), 1.66–1.54 (m, 2H), 1.53–1.47 (m, 2H), 1.23–1.18
(m, 2H); 13C NMR (100 MHz, DMSO-D6): d 142.4, 140.9, 140.6,
138.5, 123.2, 106.3, 97.2, 38.9, 33.4, 31.9, 24.5; MS (m/z): 235.0
[M+H]+; Anal. calcd. for C13H15ClN2: C, 66.52; H, 6.44; N, 11.93;
found: C, 66.50; H, 6.447; N, 11.92.
1-((4-Chloro-2-phenyl-1H-pyrrolo[3,2-c]pyridin-3-yl)methyl)-3,3-
dimethylpiperidin-4-ol (7c)
White solid (94%); mp 186.7–189.6 °C; 1H NMR (400 MHz,
DMSO-D6): d 12.17 (s, 1H), 7.95 (t, J = 5.2 Hz, 3H), 7.50 (t,
J = 7.6 Hz, 2H), 7.42 (t, J = 7.2 Hz, 1H), 7.37 (d, J = 5.6 Hz, 1H), 4.36
(d, J = 4.8 Hz, 1H), 4.07 (q, J = 5.2 Hz, 1H), 3.77–3.65 (m, 2H), 3.17
(d, J = 5.2 Hz, 1H), 3.09–3.05 (m, 1H), 2.42 (d, J = 10.8 Hz, 1H),
1.90 (d, J = 11.2 Hz, 1H), 1.52–1.48 (m, 1H), 1.43–1.33 (m, 1H),
0.83 (d, J = 7.2 Hz, 6H); 13C NMR (100 MHz, DMSO-D6): d 142.0,
141.1, 139.4, 139.0, 131.5, 129.0, 128.4, 128.3, 122.3, 108.6,
106.8, 73.8, 63.7, 50.1, 48.5, 35.6, 30.7, 25.9; MS (m/z): 375.2
[M+H]+; Anal. calcd. for C21H24ClN3O: C, 68.19; H, 6.54; N, 11.36;
found: C, 68.20; H, 6.546; N, 11.35.
4-Chloro-2-phenyl-1H-pyrrolo[3,2-c]pyridine (6b)
Pale yellow solid (87%); mp 166.8–169.7 °C; 1H NMR (400 MHz,
DMSO-D6): d 12.36 (s, 1H), 7.97–7.93 (m, 3H), 7.50 (q, J = 7.9 Hz,
2H), 7.41–7.37 (m, 2H), 7.03 (s, 1H); 13C NMR (100 MHz, DMSO-
D6): d 142.0, 141.7, 139.8, 139.6, 130.7, 129.0, 128.5, 125.6,
123.7, 106.8, 97.0; MS (m/z): 229.0 [M+H]+; Anal. calcd. for
C
13H9ClN2: C, 68.28; H, 3.97; N, 12.25; found: C, 68.30; H, 3.964;
4-Chloro-2-(cyclohexylmethyl)-3-(morpholinomethyl)-1H-
pyrrolo[3,2-c]pyridine (7d)
N, 12.24.
White solid (89%); mp 105.9–108.7 °C; 1H NMR (400 MHz,
DMSO-D6): d 11.67 (s, 1H), 7.84 (d, J = 5.6 Hz, 1H), 7.26 (d,
J = 5.6 Hz, 1H), 3.69 (s, 2H), 3.56–3.44 (m, 4H), 2.63 (d, J = 6.8 Hz,
2H), 2.45–2.30 (m, 4H), 1.76–1.71 (m, 1H), 1.64–1.56 (m, 4H),
1.16–1.09 (m, 4H), 1.02–0.93 (m, 2H); 13C NMR (100 MHz,
DMSO-D6): d 141.1, 140.7, 140.4, 138.2, 121.7, 106.8, 106.2, 66.3,
52.8, 51.0, 37.6, 33.1, 32.6, 25.8, 25.7; MS (m/z): 348.2 [M+H]+;
Anal. calcd. for C19H26ClN3O: C, 65.60; H, 7.53; N, 12.08; found:
C, 65.61; H, 7.534; N, 12.07.
4-Chloro-2-(cyclohexylmethyl)-1H-pyrrolo[3,2-c]pyridine (6c)
Pale yellow solid (80%); mp 135.8–138.6 °C; 1H NMR (400 MHz,
DMSO-D6): d 11.72 (s, 1H), 7.86 (d, J = 5.5 Hz, 1H), 7.29–7.27 (m,
1H), 6.22 (s, 1H), 2.61 (d, J = 6.8 Hz, 2H), 1.70–1.57 (m, 6H), 1.22–
1.15 (m, 3H), 1.14–0.98 (m, 2H); 13C NMR (100 MHz, DMSO-D6):
d 142.4, 141.4, 140.6, 138.4, 123.1, 106.3, 97.6, 37.3, 35.1, 32.4,
25.8, 25.5; MS (m/z): 249.0 [M+H]+; Anal. calcd. for C14H17ClN2:
C, 67.60; H, 6.89; N, 11.26; found: C, 67.62; H, 6.882; N, 11.28.
General experimental procedure for the synthesis of 7a–f
4-Chloro-2-(cyclohexylmethyl)-3-((4-methylpiperazin-1-yl)methyl)-
1H-pyrrolo[3,2-c]pyridine (7e)
4-Chloro-2-(cyclohexylmethyl)-3-(morpholinomethyl)-1H-pyr-
rolo[3,2-c]pyridine (7d) as an example: In an oven-dried RB flask,
compound 6c (250 mg, 1.01 mmol) and formaldehyde solution,
37–41 wt.% in water (0.15 mL, 2.02 mmol) were mixed in glacial
acetic acid (5 mL). Morpholine (220.4 mg, 2.53 mmol) was added
drop wise at 0 °C. The resulting mixture was stirred at room tem-
perature for 12 h. After completion of the reaction, the excess sol-
vent was evaporated to dryness under reduced pressure. The
residue was neutralized with 10% NaHCO3 solution, the solid
formed was collected by filtration, washed with water and dried.
The crude product was purified by silica gel column chromatogra-
phy to provide title compound.
Off white solid (91%); mp 115.9–118.6 °C; 1H NMR (400 MHz,
DMSO-D6): d 11.62 (s, 1H), 7.84 (d, J = 5.6 Hz, 1H), 7.25 (d,
J = 5.6 Hz, 1H), 3.66 (s, 2H), 2.62 (d, J = 7.2 Hz, 2H), 2.46–2.33 (m,
4H), 2.29–2.15 (m, 4H), 2.09 (s, 3H), 1.76–1.71 (m, 1H), 1.69–
1.63 (m, 2H), 1.62–1.53 (m, 3H), 1.21–1.09 (m, 3H), 1.02–0.93
(m, 2H); 13C NMR (100 MHz, DMSO-D6): d 141.1, 140.6, 140.3,
138.2, 121.7, 107.3, 106.2, 54.8, 52.1, 50.6, 45.7, 37.6, 33.2, 32.6,
25.9, 25.7; MS (m/z): 361.2 [M+H]+; Anal. calcd. for C20H29ClN4:
C, 66.56; H, 8.10; N, 15.52; found: C, 66.59; H, 8.111; N, 15.53.
N-benzyl-N-((4-chloro-2-(cyclohexylmethyl)-1H-pyrrolo[3,2-
c]pyridin-3-yl)methyl) ethanamine (7f)
Off white solid (88%); mp 155.6–158.5 °C; 1H NMR (400 MHz,
DMSO-D6): d 11.63 (s, 1H), 7.83 (d, J = 5.6 Hz, 1H), 7.25–7.23 (m,
5H), 7.16 (s, 1H), 3.81 (s, 2H), 3.49 (s, 2H), 2.60 (d, J = 7.2 Hz, 2H),
2.45–2.40 (m, 2H), 1.75–1.67 (m, 1H), 1.66–1.55 (m, 3H), 1.54–
1.50 (m, 2H), 1.17–1.05 (m, 3H), 0.99–0.95 (m, 3H), 0.92–0.86
(m, 2H); 13C NMR (100 MHz, DMSO-D6): d 140.9, 140.7, 140.6,
140.1, 138.0, 128.5, 127.9, 126.5, 121.9, 107.9, 106.3, 56.8, 46.6,
46.3, 37.4, 33.1, 32.5, 25.8, 25.6, 11.6; MS (m/z): 396.2 [M+H]+;
Anal. calcd. for C24H30ClN3: C, 72.80; H, 7.64; N, 10.61; found: C,
72.81; H, 7.647; N, 10.60.
4-Chloro-2-(cyclopentylmethyl)-3-((4-isopropylpiperazin-1-
yl)methyl)-1H-pyrrolo[3,2-c]pyridine (7a)
Off white solid (93%); mp 195.8–198.7 °C; 1H NMR (400 MHz,
DMSO-D6): d 11.63 (s, 1H), 7.84 (d, J = 5.6 Hz, 1H), 7.25 (d,
J = 5.6 Hz, 1H), 3.66 (s, 2H), 2.72 (d, J = 7.6 Hz, 2H), 2.56–2.53 (m,
1H), 2.45–2.25 (m, 9H), 1.70–1.57 (m, 4H), 1.53–1.44 (m, 2H),
1.28–1.17 (m, 2H), 0.90 (d, J = 6.4 Hz, 6H); 13C NMR (100 MHz,
DMSO-D6): d 142.4, 141.1, 140.7, 138.1, 121.7, 106.9, 106.2, 53.5,
52.6, 50.6, 48.0, 38.9, 31.7, 31.2, 24.4, 18.1; MS (m/z): 375.2
[M+H]+; Anal. calcd. for C21H31ClN4: C, 67.27; H, 8.33; N, 14.94;
found: C, 67.26; H, 8.324; N, 14.93.
X-ray crystallography
1-((4-Chloro-2-phenyl-1H-pyrrolo[3,2-c]pyridin-3-
yl)methyl)piperidin-4-ol (7b)
The structures of 6a and 7c were unequivocally established by
X-ray crystallographic analysis. A suitable crystal was selected
and analyzed on an Agilent, Eos, Gemini diffractometer. The crystal
was kept at 173(2) K during data collection. Using Olex2 [23], the
White solid (90%); mp 206.8–209.7 °C; 1H NMR (400 MHz,
DMSO-D6): d 12.17 (s, 1H), 7.95 (d, J = 5.6 Hz, 1H), 7.90 (d,

88
G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
structure were solved the Superflip [24] structure solution pro-
gram using Charge Flipping and refined with the ShelXL [25]
refinement package using Least Squares minimization.
c = 13.3002(9) Å,
T = 173(2) K, (Cu K
reflections measured (9.244 6 2
(Rint = 0.0381) which were used in all calculations. The final R1
was 0.0420 (I > 2 (I)) and wR2 was 0.1254 (all data) (Table 1).
b = 106.459(7)°,
) = 2.522 mmÀ1, Dcalc = 1.266 g/mm3, 7124
6 145.144), 2404 unique
V = 1231.47(14) Å3,
Z = 4,
l
a
H
r
Crystal structure determination of [6a]
The X-ray crystallographic analysis of 6a was carried out on an
off white crystal, with dimensions 0.34 mm  0.18 mm Â
0.08 mm, grown from the slow evaporation of methanol at room
temperature. Crystal data for 6a, C13H15N2Cl (M = 234.72): mono-
clinic, space group P21/c, a = 9.9763(6) Å, b = 9.6777(6) Å,
Crystal structure determination of [7c]
The X-ray crystallographic analysis of 7c was carried out on a
white crystal, with dimensions 0.38 mm  0.34 mm  0.22 mm,
grown from the slow evaporation of a dichloromethane and
methanol solvent mixture at room temperature. Crystal data for
7c, C21H24N3OCl, CH4O, (M = 401.92): triclinic, space group PÀ1,
a = 10.1478(7) Å, b = 12.0945(8) Å, c = 18.3244(10) Å, b = 90.766(5)°,
Table 1
Crystal data and structure refinement for 6a and 7c.
Identification code 6a
7c
V = 2147.1(2) Å3, Z = 4, T = 173(2) K,
l
(Cu
calc = 1.243 g/mm3, 14238 reflections measured (7.656 6 2
145.27), 8297 unique (Rint = 0.0330) which were used in all calcula-
Ka) = ,
1.744 mmÀ1
Empirical formula
Formula weight
Temperature/K
Crystal system
Space group
a (Å)
C
13H15N2Cl
C21H24N3OCl, CH4O
369.88
173(2)
Triclinic
PÀ1
D
H 6
234.72
173(2)
Monoclinic
P21/c
9.9763(6)
9.6777(6)
13.3002(9)
90
106.459(7)
90
1231.47(14)
4
tions. The final R1 was 0.0578 (I > 2r(I)) and wR2 was 0.1773 (all
data) (Table 1).
10.1478(7)
12.0945(8)
18.3244(10)
104.369(5)
90.766(5)
99.235(6)
2147.1(2)
4
b (Å)
c (Å)
In vitro antimicrobial procedure
a
(°)
b (°)
(°)
All the newly synthesized compounds were evaluated in vitro
for their antimicrobial activity. The antimicrobial activities are car-
ried out against Gram-positive bacteria Bacillus flexus, Gram-nega-
tive bacteria Pseudomonas spp., fungal stains Scopulariopsis spp.
and Aspergillus tereus using the nutrient agar disc diffusion method
[26]. The synthesized compounds were dissolved in DMSO to get
stock solutions. The antimicrobial activity was determined by mea-
suring of the inhibition zone, after 20 h of incubation at 37 °C for
bacterial strains and 4 days at 37 °C for fungal strains. The diame-
ter of inhibition zones (in mm) was determined and the data were
statistically evaluated by Turkey’s fair wise comparison test. Com-
c
Volume (Å3)
Z
qcalc (mg/mm3)
1.266
2.522
496.0
1.243
1.744
856.0
m (mm-1
F(000)
)
Crystal size (mm3) 0.34 Â 0.18 Â 0.08
0.38 Â 0.34 Â 0.22
2H range for data 9.244–145.144°
7.656–145.27°
collection
Index ranges
À12 6 h 6 9, À10 6 k 6 11, À10 6 h 6 12,
À16 6 l 6 16
À14 6 k 6 12, À22 6 l 6 22
Reflections
collected
7124
14238
mercial bactericide Amoxicillin was used as standard (100
100 L of sterilized distilled water) concomitantly with the test
samples.
lg per
Independent
reflections
Data/restraints/
parameters
2404[R(int) = 0.0381]
8297[R(int) = 0.0330]
8297/0/527
l
2404/0/145
MIC values for the synthesized compounds were determined by
using broth microdilution [27]. Standard and isolated strain of B.
flexus was used to determine the antibacterial activity as the com-
pounds showed the activity against the above mentioned organ-
ism. Amoxicillin was used as the reference. The bacterium was
cultivated in Mueller–Hinton agar and was diluted with Mueller–
Hinton broth. The synthesized compounds and references were
Goodness-of-fit on 1.054
1.033
F2
Final R indexes
[I P 2 (I)]
R1 = 0.0420, wR2 = 0.1139 R1 = 0.0578, wR2 = 0.1580
r
Final R indexes [all R1 = 0.0530, wR2 = 0.1254 R1 = 0.0716, wR2 = 0.1773
data]
Largest diff. peak/ 0.25/À0.20
0.50/À0.32
hole (e ÅÀ3
)
dissolved in DMSO at a concentration of 1000 lg/mL. Two fold
l
l
5a R1 = c clo ent lmeth l
5b R1 = hen l
l
l
I
I
i
5c R1 = c clohe lmeth l
6a R1 = c clo ent lmeth l
6b R1 = hen l
H2
H2
H2
H2
I
I
3
6c R1 = c clohe lmeth l
7a R1= c clo ent lmeth l,
R2 = 4-iso ro l i er zin-1- l
7b R1 = hen l, R2 = i eri in-4-ol
7c R1 = hen l,
4
1
2
ii
R2 = 3,3- imeth l i eri in-4-ol
7d R1 = c clohe lmeth l,
R2 = mor holino
R1
l
R2
R1
l
l
iii
i
R1
7e R1 = c clohe lmeth l,
R2 = 4-meth l i er zin-1- l
7f R1 = c clohe lmeth l,
R2 = - enz leth n mino
H2
H
H
5a-c
6a-c
7a-f
Scheme 1. Synthesis of pyrrolo[3,2-c]pyridine derivatives; (i) ICl and KOAc in glacial AcOH at 70 °C, 4 h; (ii) R1-acetylene, CuI, PdCl2(PPh3)2, Et3N in THF, reflux, 1 h; (iii) KOt-
Bu in NMP at 100 °C, 1 h; (iv) HCHO, R2-secondary amine in glacial AcOH, rt, 12 h.

G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
89
Fig. 2. Molecular structure of C13H15N2Cl (6a) showing the atom labeling scheme with two molecules in the asymmetric unit and 30% probability displacement ellipsoids.
dilutions of the synthesized compounds and reference compound
Table 2
were added to the wells (750, 700, 650. . .25 lg/mL). Then a sus-
Selected Crystal Bond lengths (Å), Bond angles (°), and Torsion angles (°) for
C13H15N2Cl (6a).
pension of microorganism was inoculated into the wells. Final
inoculums concentrations in the wells were 100 cfu/mL. The plates
were incubated at 37 °C for 24 h for the antibacterial activity. At
the end of the incubation period, MIC values were recorded as
the lowest concentration of the substances that has no visible
turbidity.
C13H15N2Cl
Cl1---C5
N1---C2
N1---C8
N2---C5
N2---C6
1.7476(19)
1.377(2)
1.358(2)
1.316(3)
1.359(3)
C1---C2
C1---C9
C2---C3
C3---C4
C4---C5
1.501(3)
1.503(3)
1.360(3)
1.425(3)
1.387(2)
C
13H15N2Cl
Molecular docking study procedure
C8---N1---C2
C5---N2---C6
C2---C1---C9
N1---C2---C1
C3---C2---N1
109.44(15)
117.28(16)
116.45(17)
117.90(17)
109.80(16)
C3---C2---C1
C2---C3---C4
C5---C4---C3
C5---C4---C8
C8---C4---C3
132.29(19)
106.56(17)
137.33(18)
115.49(17)
107.17(16)
The protein-drug interaction was studied by automated docking
to determine the orientation of inhibitors bound to the active site
of target protein GlcN-6-P synthase. A genetic algorithm method,
implemented in the program AutoDock 4.2, was employed [28].
The 2D structures (.mol) of all the six compounds are converted
to 3D structure (.pdb) using Openbable software tool. The 3D coor-
dinates (.pdb) of each molecule were loaded on to PRODRG server
[29] and PreADMET server for energy minimization and drug-like-
liness prediction respectively. The protein structure file 1Jxa was
downloaded from Protein Data Bank (www.rcsb.org/pdb) was edi-
ted by removing the heteroatom’s, adding C-terminal oxygen [30].
For docking calculations, Gasteigere Marsili partial charges [31]
were assigned to the inhibitors and non-polar hydrogen atoms
were merged. All torsions were allowed to rotate during docking.
The grid map was centered at the residues of the protein, predicted
from the CASTp server [32]. The Lamarckian genetic algorithm and
the pseudo-Solis and Wets methods were applied for minimization
using default parameters. The number of docking runs was 50, the
population in the genetic algorithm was 250, the number of energy
evaluations was 100,000, and the maximum number of iterations
10,000. The docking results for inhibitors against glucosamine-6-
phosphate synthase [PDB Id: 1jka], showed minimum docking
energy, inhibition constant, with RMS as documented. The com-
puter specification used-Operating system: Microsoft Windows
XP, Processor: Intel Pentium 3.40 GHz, RAM: 2 GB, Hard disk:
500 GB, Python: 2.4.
C13H15N2Cl
N1---C2---C3---C4
N2---C6---C7---C8
C1---C2--–C3---C4
C1---C9---C10---C11
C1---C9---C13---C12
0.0(2)
-0.4(3)
178.76(19)
-159.1(2)
155.9(2)
C2---N1---C8---C4
C2---N1---C8---C7
C2---C1---C9---C10
C2---C1---C9---C13
C2---C3---C4---C5
0.12(19)
-179.36(19)
-176.90(19)
66.6(3)
178.5(2)
Table 3
Hydrogen bond interactions for C13H15N2Cl (6a) [Å and °].
D–H. . .A
d(D–H) (Å)
d(H–A) (Å)
d(D–A) (Å)
D–H–A (°)
N1---H1. . .N2a
C1---H1A. . .N2b
0.88
0.99
2.04
2.81
2.890(2)
3.485(3)
162
126.1
Symmetry transformations used to generate equivalent atoms:
a
+X, 3/2 À Y, À1/2 + Z.
b
1 À X, 1 À Y, 1 À Z.
Results and discussion
Chemistry
We describe here an efficient method for the synthesis of novel
pyrrolo[3,2-c]pyridine derivatives (6a–c, 7a–f) (Scheme 1). The
commercially available 1 (2-Chloro-4-amino pyridine) was iodin-
ated with ICl and KOAc in glacial acetic acid at 70 °C to afford a
mixture of iodopyridines 2 (2-chloro-3-iodopyridin-4-amine), 3
(2-chloro-5-iodopyridin-4-amine) and 4 (2-chloro-3,5-diiodopyri-
din-4-amine) in the ratio 45:45:10 [17]. The iodopyridines were
Fig. 3. Packing diagram of C13H15N2Cl (6a) viewed along the a axis. Dashed lines
indicate N---H. . .N hydrogen bonds, which link the molecules into chains along
[001]. H atoms not involved in hydrogen bonding have been deleted for clarity.

90
G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
Fig. 4. Molecular structure of C21H24N3OCl, CH4O (7c) showing the atom labeling scheme and 30% probability displacement ellipsoids.
Table 4
Selected Crystal Bond lengths (Å), Bond angles (°), and Torsion angles (°) for C21H24N3OCl, CH4O (7c).
C21H24N3OCl, CH4O
Cl1A---C4A
Cl2---C4B
1.749(2)
1.744(3)
1.434(3)
1.427(3)
1.419(3)
1.411(3)
1.382(3)
1.360(3)
N1B---C1B
N1B---C7B
N2A---C4A
N2A---C5A
N2B---C4B
N2B---C5B
N3A---C11
N3A---C14A
1.380(3)
1.353(3)
1.309(3)
1.364(3)
1.314(3)
1.354(3)
1.474(3)
1.455(3)
O1A---C16A
O1B---C16B
O1M---C1M
O2M---C2M
N1A---C1A
N1A---C7A
C21H24N3OCl, CH4O
C7A---N1A---C1A
C7B---N1B---C1B
C4A---N2A---C5A
C4B---N2B---C5B
C14A---N3A---C11
C18A---N3A---C11
C18A---N3A---C14A
C1---N3B---C14B
108.80(19)
109.3(2)
117.9(2)
C18B---N3B---C1
C18B---N3B---C14B
N3B---C1---C15B
N1A---C1A---C8A
C2A---C1A---N1A
C2A---C1A---C8A
N1B---C1B---C8B
C2B---C1B---N1B
110.67(19)
111.82(18)
110.8(2)
119.4(2)
110.0(2)
130.5(2)
120.3(2)
109.9(2)
118.2(2)
110.31(18)
112.59(17)
110.37(19)
109.22(18)
C21H24N3OCl, CH4O
O1A---C16A---C17A---C18A
O1A---C16A---C17A---C19A
O1A---C16A---C17A---C20A
O1B---C16B---C17B---C18B
O1B---C16B---C17B---C19B
O1B---C16B---C17B---C20B
N1A---C1A---C2A---C3A
À178.32(18)
64.7(3)
À57.5(3)
179.98(19)
58.7(3)
N1A---C1A---C8A---C9A
N1A---C1A---C8A---C13A
N1B---C1B---C2B---C3B
N1B---C1B---C2B---C14B
N1B---C1B---C8B---C9B
N1B---C1B---C8B---C13B
N2A---C5A---C6A---C7A
N2B---C5B---C6B---C7B
À145.3(2)
36.1(3)
1.0(3)
177.9(2)
142.1(2)
À39.1(3)
2.7(4)
À63.3(3)
0.0(2)
N1A---C1A---C2A---C11
À179.50(19)
À0.9(4)
Table 5
Hydrogen bond interactions for C21H24N3OCl, CH4O (7c) [Å and °].
isolated by preparative HPLC (normal phase). The structures of iod-
opyridines were assigned on the basis of 1H NMR, mass spectral
analysis and elemental analysis. 1H NMR spectrum of elution 1
(4) showed two singlet peaks at d 8.17 and 6.51 ppm corresponds
to aromatic hydrogen at C6 and NH2 group; elution 2 (3) showed
three singlet peaks at d 8.18, 6.65, 6.50 ppm corresponds to aro-
matic protons at C3, C6 and NH2 group, whereas elution 3 (2)
showed two doublet peaks and a single peak at d 7.73, 6.52 and
6.50 corresponds to aromatic protons at C5, C6 and NH2 group.
The 2-amino-3-iodo pyridine (2) were refluxed in THF with a cat-
alytic amount of Bis(triphenylphosphine)palladium(II) dichloride,
copper (I) iodide, triethylamine as a base and acetylenes to afford
desired compounds (5a–c) [33]. The formation of pyrrole ring
was accomplished by treatment of 5 with potassium tert butoxide
and NMP at 100 °C [34] afford compounds (6a–c). The final
D–H. . .A
d(D–H) (Å)
d(H–A) (Å)
d(D–A) (Å)
D–H–A (°)
O1A---H1A. . .N2B
O1B---H1B. . .N2Aa
O1M---H1M. . .O1B
O2M---H2M. . .O1Ab
N1A---H1AA. . .O1Mc
N1B---H1BA. . .O2Md
C9A---H9A. . .N3A
C9B---H9B. . .N3B
0.87(3)
0.80(3)
0.81(3)
0.79(4)
0.88
0.88
0.95
0.95
1.92(3)
1.98(3)
1.88(3)
1.91(4)
1.94
1.92
2.39
2.51
2.774(3)
2.775(3)
2.678(3)
2.702(3)
2.778(3)
2.749(3)
3.217(3)
3.293(3)
171(3)
176(3)
170(3)
176(4)
159.8
155.7
144.8
140.1
Symmetry transformations used to generate equivalent atoms:
a
X, +Y, À1 + Z.
b
1 À X, 1 À Y, 1 À Z.
c
1 + X, +Y, 1 + Z.
ÀX, 1 À Y, 1 À Z.
d

G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
91
Fig. 5. Packing diagram of C21H24N3OCl, CH4O (7c) viewed along the b axis. Dashed lines indicate O---H. . .N, O---H. . .O, N---H. . .O hydrogen bonds and weak C---H. . .N
intermolecular interactions, which link the molecules into a two-dimensional network along (010). H atoms not involved in hydrogen bonding have been deleted for clarity.
Table 6
Antibacterial and antifungal activity of 6a–c, 7a–f.
R2
Cl
N
R1
N
H
Compound
R1
R2
Bacteria
Fungus
Pseudomonas spp.
Bacillus flexus
Scopulariopsis spp.
Aspergillus tereus
6a
–
–
–
–
H
H
6b
–
–
–
–
6c
7a
7b
–
–
–
–
–
–
–
–
–
–
H
+++
++
N
N
N
OH
OH
7c
–
++
–
–
N
N
7d
7e
–
–
++++
–
–
–
–
O
N
+++++
N
(continued on next page)

92
G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
Table 6 (continued)
R2
Cl
N
R1
N
H
Compound
R1
R2
Bacteria
Fungus
Pseudomonas spp.
Bacillus flexus
Scopulariopsis spp.
Aspergillus tereus
7f
–
++++
–
–
N
Amoxycillin
Nystatin
–
–
–
–
+++++
–
+++++
–
–
–
+++++
+++++
Zone of inhibition in mm; +++++ = 32 mm, ++++ = 20 mm, +++ = 15 mm, ++ = 10 mm, hyphen denotes no activity.
compounds (7a–f) were synthesized in 88–94% yield via Mannich
reaction of 6, a secondary amine, and formaldehyde in glacial ace-
tic acid. All the final products, except 7c are achiral and the struc-
tures were assigned on the basis of their 1H NMR, 13C NMR and
mass (LCMS or HRMS) spectral analysis as well as elemental
analysis.
X-ray crystal structure analysis
4-Chloro-2-(cyclopentylmethyl)-1H-pyrrolo[3,2-c]pyridine (6a)
In C13H15N2Cl, one independent molecule crystallizes in the
asymmetric unit (Fig. 2). The five-membered cyclopentane ring
adopts a slightly distorted envelope conformation (q = 0.358(3) Å,
/ = 3.0(5)°) [35] with the carbon atom attached to the methylene
group. The nine-membered pyrrolo[3,2-c]pyridine ring is planar
with the maximum deviation of À0.0026(17) Å and
À0.0034(18) Å from the mean plane by N1 and N2, respectively.
Bond angles and distances are in normal ranges [36] (Table 2). In
the crystal, N1---H1. . .N1 hydrogen bonds are observed (Table 3)
which link the molecules into one-dimensional chains along
[001] (Fig. 3).
Table 7
Antibacterial activity MIC (lg/mL) of compounds 7a–f.
Compound
Structure
MIC (l
g/mL)
LogP
Bacillus flexus
7a
300
4.363
N
Cl
N
N
N
1-((4-Chloro-2-phenyl-1H-pyrrolo[3,2-c]pyridin-3-yl)methyl)-3,3-
dimethylpiperidin-4-ol compound with methanol (7c)
N
The compound 7c is racemic mixture and crystallizes in a cen-
trosymmentric space group PÀ1. In C21H24N3OCl, CH4O, two inde-
pendent compound molecules (A & B) and two independent
methanol solvent molecules crystallize in the asymmetric unit
(Fig. 4). In the compound the 6-membered piperidine ring adopts
a slightly distorted chair conformation (puckering parameters (A)
q, h, and / = 0.578 (3) Å, 177.6 (2)° and 154 (2)°; (B) q, h, and /
= 0.584 (3) Å, 0.0 (3)° and 291 (2)°) [35]. Bond angles and distances
are in normal ranges [36] (Table 4). The dihedral angles between
the mean planes of the nine-membered pyrrolo[3,2-c]pyridin-3-
yl and six-membered phenyl rings are 39.5(8)° (A) and 42.28°
(B), respectively. In the asymmetric unit hydrogen bonds between
the hydroxy group and pyridine ring of the compound (O1A---
H1A. . .N2B) and methanol solvent group with the hydroxyl group
of the compound (O1M---H1M. . .O1B) are observed. Also, O---
H. . .N intermolecular hydrogen bonds involving the compound
and N---H. . .O, O---H. . .O hydrogen bonds between the compound
and methanol solvent molecule are present (Table 5). These inter-
molecular interactions in addition to weak C---H. . .N intermolecu-
lar interactions generate an infinite two-dimensional network
along the (010) plane (Fig. 5).
H
7b
7c
700
650
2.297
3.551
OH
OH
Cl
N
N
H
Cl
Cl
N
N
N
N
N
H
7d
200
4.151
4.196
6.079
À1.352
O
N
N
H
7e
50
Cl
Cl
N
N
N
N
H
Antimicrobial activity
7f
150
The title compounds were tested for their antimicrobial activity
against Gram-positive bacteria B. flexus, Gram-negative bacteria
Pseudomonas spp., fungal stains Scopulariopsis spp. and A. tereus.
Amoxicillin and Nystatin were used as antibacterial and antifungal
references, respectively. As shown in Table 6, six compounds (7a–
f) showed antibacterial activity against B. flexus (Gram-positive
bacteria) and no activity against Gram-negative bacteria. The com-
N
N
H
Amoxicillin
–
25

G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
93
pounds showed no antifungal activity against both Scopulariopsis
spp. and A. tereus.
Six compounds from the above result were tested for antibacte-
rial activity (MIC) against B. flexus. The synthesized compounds
(7a–f) exhibited a broad spectrum activity with MIC values of
online http://www.molinspiration.com/cgi-bin/properties site, as
shown in Table 7. At this stage, some structure–activity relation-
ships could be concluded from the data described in Table 7. As a
result, pyrrolo[3,2-c]pyridines that carry aliphatic substituent’s
such as cyclohexylmethyl and cyclopentylmethyl at position 2,
were found to be more potent as antimicrobial agents compared
to compounds carrying phenyl substituent at position 2.
50–700
lg/mL against the gram-positive bacteria B. flexus (Table 7).
The compound 7e gave the best inhibitory activity with MIC 50
lg/
mL. The compounds 7b and 7c were required in higher amounts to
inhibit the activity of the organism in the study. Compound 7c is a
mixture of enantiomers gave the modest inhibitory activity with
Molecular docking studies
MIC 650
l
g/mL. Lipophilicities of the compounds 7a-f, which were
The new pyrrolopyridines were predicted for drug-likeliness
property using PreADMET server [37,38]. To explain the
expressed as logP, was determined using the logP method through
Table 8
Molecular docking of pyrrolo[3,2-c]pyridine motifs with GlcN-6-P synthase.
Compound Docking energy
(kcal/mol)
Binding energy
(kcal/mol)
Intermolecular energy
(kcal/mol)
Inhibition
constant (M)
RMSD
(Å)
Hydrogen
bonds
Bonding
Bond
length (Å)
7a
À12.22
À10.98
À12.30
1.52 Â 10À8
0.71
2
7a:NH:::OH:Pro377
7a:NH:::OH:Gly378
2.92
2.60
7b
7c
À11.48
À10.76
À10.18
À10.39
À11.60
À10.91
1.87 Â 10À8
6.31 Â 10À8
0.80
0.99
0
2
–
–
7c:HO:::HOOC:Pro377 2.86
7c:NH:::OH:Tyr25
2.56
7d
7e
7f
À11.30
À10.40
À10.89
À10.22
À8.81
À8.89
À11.42
À10.49
À10.99
4.25 Â 10À8
1.41 Â 10À7
4.10 Â 10À7
0.82
1.02
0.96
0
0
1
–
–
–
–
2.87
7f:NH:::OH:Tyr25
Fig. 6. Ligplot of GlcN-6-P showing the binding of glucosamine-6-phosphate in an active site of enzyme.

94
G. Jose et al. / Journal of Molecular Structure 1081 (2015) 85–95
Fig. 7. Ligplot images of protein ligand interactions of 7a–f with GlcN-6-P synthase.
antibacterial activity of new pyrrolopyridines, we explore the
binding affinity of the compounds against Glucosamine-6-phosphate
synthase, the target enzyme for the antimicrobial agents. The
molecular docking of the GlcN-6-P synthase with 7a–f and the
standard drug fluconazole yielded best possible conformations
with parameters including the docking energy, binding energy,
intermolecular energy, inhibition constant and RMSD (Table 8).
The topology of the active site of GlcN-6-P synthase was similar in
both pyrrolopyridines and fluconazole, which is lined by interacting
amino acids as predicted from the ligplot. The binding pocket of
GlcN-6-P synthase contains the following amino acid residues,
Cys300, Gly301, Thr302, Ser303, Ser347, Gln348, Ser349, Thr352,
Val399, Ser401, Ala602 and Lys603 (Fig. 6). Fig. 7 illustrates the
protein ligand interactions of pyrrolopyridines with GlcN-6-P
synthase. Theoretically, all the six compounds (7a–f) showed
very good docking energy ranging from À10.40 kcal/mol to
À12.22 kcal/mol. Compounds 7a, 7c and 7f have formed hydrogen
bonds with the active site of the GlcN-6-P synthase. All target com-
pounds (7a–f) containing chlorine as halogen atom have formed
intermolecular bonds with the active site of the GlcN-6-P synthase
in a fashion that resembles the H bonds [39–41]. Compounds con-
taining the halogen atoms will also improve the oral absorption,
skin penetration and also increase membrane permeability [42].
The minimum docking energy was found in the analogue 7a
(À12.22 kcal/mol) with an estimated inhibition constant of
1.52 Â 10À8 M, binding energy À10.98 kcal/mol, intermolecular
energy À12.3 kcal/mol and RMSD (root-mean square deviation)
0.71 Å. Whereas, the docked energy of the standard drug fluconaz-
ole was À5.67 kcal/mol with an inhibition constant of
5.53 Â 10À5 M and RMSD 1.97 Å. The NH group of 7a has formed
two hydrogen bonds with a hydroxy group of amino acid residues
at the active site of the GlcN-6-P synthase, Pro377 (2.92 Å) and
Gly378 (2.6 Å), respectively. In in vitro antimicrobial study com-
pound 7a emerged as active against B. flexus, so it can be predicted
as the activity may be due to inhibition of enzyme GlcN-6-Psynth-
ase, which catalyses a complex reaction involving ammonia trans-
fer from L-glutamine to Fru-6-P followed by isomerisation of the
formed fructosamine-6-phosphate to glucosamine-6-phosphate.
The accuracy of dockings was evaluated by the RMSD of the docked
ligand from original crystal structure. RMSD less than 1.0 Å was
considered as excellent. Compound 7c forms two hydrogen bonds
with amino acid residues in the active site of the GlcN-6-P syn-
thase. The hydroxy group of 7c forms a hydrogen bond with COOH
of Pro377 (2.86 Å) and the NH of 7c also forms a hydrogen bond
with the OH of Tyr25 (2.56 Å). In solid state of 7c, O---H. . .N inter-
molecular hydrogen bonds between the hydroxy group and pyri-
dine ring of the compound, N---H. . .O, O---H. . .O hydrogen
bonds between the compound and methanol solvent molecule
and weak C---H. . .N intermolecular interactions were observed
(Table 5). This intermolecular hydrogen bonding interaction
observed in solid state was further strengthened the binding capa-
bility of the compound 7c and the active sites were NH, OH groups
and pyridine ring. The docking study reveals that the high affinity
of pyrrolopyridine derivatives (7a–f) within the binding pocket of
GlcN-6-P synthase strongly enhanced the determined activities of
these derivatives as potent antimicrobial agents.
Conclusions
In summary, we have synthesized new antibacterial leads (7a,
7d, 7e and 7f) with moderate to good activity against Gram-posi-

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