Design, synthesis, antitubercular and antibacterial activities of pyrrolo[3,2-b]pyridine-3-carboxamide linked 2-methoxypyridine derivatives and in silico docking studies

Article abstract of DOI:10.1080/00397911.2019.1618874

A novel series pyrrolo[3,2-b]pyridine-3-carboxamide linked 2-methoxypyridine derivatives have been designed, synthesized and confirmed by FT-IR, ¹H NMR, ¹³C NMR, ¹⁹F NMR, MS, and elemental analysis. The synthesized compounds were screened for their antitubercular activity using microplate alamar blue assay method and antibacterial activity. Among the tested compounds, 4- fluorophenyl (8m), 4- chlorophenyl (8n) and 4-methoxyphenyl (8i) showed potent anti-TB activity (3.12 μg/mL) in comparison with reference drug, Pyrazinamide ((3.12 μg/mL). In addition, all compounds were docked into DprE1 (PDB code: 4KW5) to explore their binding interactions at the active site. The compounds exhibited essential key interactions as that of reported DprE1 inhibitors and hence, the synthesized compounds may be considered as molecular scaffolds for antitubercular activity. Compounds, 4-chlorophenyl (8n) and 4-flurophenyl (8m) showed significant antibacterial activity against Escherichia coli and Staphylococcus aureus strains. In silico prediction of toxicities, druglikeness and drug score profiles of the tested compounds are promising.

Full text of DOI:10.1080/00397911.2019.1618874

Synthetic Communications
An International Journal for Rapid Communication of Synthetic Organic
Chemistry
ISSN: 0039-7911 (Print) 1532-2432 (Online) Journal homepage: https://www.tandfonline.com/loi/lsyc20
Design, synthesis, antitubercular and antibacterial
activities of pyrrolo[3,2-b]pyridine-3-carboxamide
linked 2-methoxypyridine derivatives and in silico
docking studies
Srinu Bodige, Parameshwar Ravula, Kali Charan Gulipalli, Srinivas Endoori,
Purna Koteswara Rao Cherukumalli, Narendra Sharath Chandra JN &
Nareshvarma Seelam
To cite this article: Srinu Bodige, Parameshwar Ravula, Kali Charan Gulipalli, Srinivas Endoori,
Purna Koteswara Rao Cherukumalli, Narendra Sharath Chandra JN & Nareshvarma Seelam
(2019): Design, synthesis, antitubercular and antibacterial activities of pyrrolo[3,2-b]pyridine-3-
carboxamide linked 2-methoxypyridine derivatives and inꢀsilico docking studies, Synthetic
Communications, DOI: 10.1080/00397911.2019.1618874
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SYNTHETIC COMMUNICATIONS
https://doi.org/10.1080/00397911.2019.1618874
Design, synthesis, antitubercular and antibacterial activities
of pyrrolo[3,2-b]pyridine-3-carboxamide linked 2-
methoxypyridine derivatives and in silico docking studies
a
b
a
a
Srinu Bodige , Parameshwar Ravula , Kali Charan Gulipalli , Srinivas Endoori ,
a
c
Purna Koteswara Rao Cherukumalli , Narendra Sharath Chandra JN , and
Nareshvarma Seelam
a
a
b
Department of Chemistry, Koneru Lakshmaiah Education Foundation, Guntur, India; Department of
Pharmaceutical Chemistry, School of Pharmacy, Gurunanak Institutions Technical Campus, Hyderabad,
c
India; Department of Pharmaceutical Chemistry, Guruktupa Institute of Pharmacy, Majalgaon,
Maharashtra, India
ABSTRACT
ARTICLE HISTORY
A novel series pyrrolo[3,2-b]pyridine-3-carboxamide linked 2-methoxy-
pyridine derivatives have been designed, synthesized and confirmed
Received 15 March 2019
1
13
19
KEYWORDS
Antitubercular activity;
by FT-IR, H NMR, C NMR, F NMR, MS, and elemental analysis. The
synthesized compounds were screened for their antitubercular activ-
ity using microplate alamar blue assay method and antibacterial
activity. Among the tested compounds, 4- fluorophenyl (8m), 4-
chlorophenyl (8n) and 4-methoxyphenyl (8i) showed potent anti-TB
activity (3.12 mg/mL) in comparison with reference drug, Pyrazinamide
1
,4-azaindoles; docking
studies; synthesis
(
(
(3.12mg/mL). In addition, all compounds were docked into DprE1
PDB code: 4KW5) to explore their binding interactions at the active
site. The compounds exhibited essential key interactions as that of
reported DprE1 inhibitors and hence, the synthesized compounds
may be considered as molecular scaffolds for antitubercular
activity. Compounds, 4-chlorophenyl (8n) and 4-flurophenyl (8m)
showed significant antibacterial activity against Escherichia coli and
Staphylococcus aureus strains. In silico prediction of toxicities, druglike-
ness and drug score profiles of the tested compounds are promising.
GRAPHICAL ABSTRACT
CONTACT Nareshvarma Seelam
nareshvarma.klu@gmail.com
Department of Chemistry, Koneru Lakshmaiah
Education Foundation, Green Fields, Vaddeswaram, Guntur, 522502, India.
Color versions of one or more of the figures in the article can be found online at www.tandfonline.com/lsyc.
Supplemental data for this article is available online at on the publisher’s website
ß 2019 Taylor & Francis Group, LLC

2
S. BODIGE ET AL.
Introduction
Tuberculosis (TB) is one of the most widespread infectious disease which is caused by
Mycobacterium tuberculosis. It is important to note that despite having an effective
[
1]
treatment, about 1.4 million deaths and 10.9 million clinical cases in 2015. However,
extensive duration of therapy and the emergence of multidrug resistant tuberculosis
(MDR-TB) have created an utmost need to identify more selective new anti-TB drugs
for efficient treatment.
Mycobacterium tuberculosis has a complex cell wall arrangement implicated in mul-
tiple functions related to pathogenesis and cellular physiology. Disruption of its cell wall
synthesis prevents the multiplication and growth of the organism. Targeting the cell
wall synthesis has an important approach in drug design. Decaprenyl phosphoryl-b-D-
ribose 20-epimerase (DprE1) is involved in the conversion of decaprenylphosphoryl-
b-Dribose (DPR) to decaprenylphosphoryl-b-D-arabinofuranose (DPA), an essential
precursor for cell wall synthesis and survival, hence, this enzyme considered as potential
target for tuberculosis.
[
2,3]
In recent years, 1,4-azaindoles reported as DprE1 inhibitors
and in addition, their
derivatives have been paid more attention because of their diverse pharmacological
[
4]
[5]
[6]
[7,8]
activities such as antitubercular, antibacterial, anthelmintic, and anticancer.
On the other hand, pyridine is found to be a core structure in antitubercular
agent, Isonizide.
[
9]
In view of the aforesaid facts, and in continuation of our research on 1,4-azaindoles,
in the present study, it is planned to design target compounds by incorporating pyridine
nucleus in to 1,4-azaindole motif with a view to produce hybrid molecules (Fig. 1).
rd
Further, various alicyclic, aliphatic and aromatic amide linkages are introduced at 3
position of azaindole for structure activity relationship studies. The designed com-
1
13
19
pounds were synthesized and characterized by FT-IR, H NMR, C NMR, F NMR
for 8b, 8c, 8l and, 8m), MS and elemental analysis. In addition, all the synthesized
(
compounds were evaluated for their anti-TB activity against Mycobacterium tuberculosis
using a microplate alamar blue assay (MABA) method and antibacterial activity.
Furthermore, molecular docking study was performed for synthesized compounds
against DprE1 to explore their binding interactions at the active site. Osiris software
was used for prediction of physiochemical properties, which includes bioavailability, lip-
ophilicity, druglikeness, drug score, mutagenicity, tumorigenicity, irritancy and C Log P
of the novel pyrrolo [3,2-b]pyridine-3-carboxamide linked 2-methoxypyridine
derivatives.
Results and discussion
According to Scheme 1, 2-chloro-4-methyl-3-nitropyridine (1) was reacted with ethyl
2
-cyanoacetate (2) in presence of t-BuOK to get the ethyl 2-cyano-2-(4-methyl-3-nitro-
1
pyridin-2-yl) acetate (3). The appearance of a broad singlet at d 14.41 in H NMR
1
6 6
3
(DMSO-d ) and d 168.5, d 138.9 in C NMR (DMSO-d ) showed this to be completely
.[10]
in the vinylogous urethanes form 3a at room temperature
Further, reduction of nitro
group followed by intramolecular cyclization was done in Pd/C in EtOH to afford the 4-
[
11] 1
azaindole ester derivative (4).
H NMR spectrum of compound (4) in (DMSO-d6)

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3
Figure 1. A design strategy of pyrrolo[3,2-b]pyridine-3-carboxamide linked 2-methoxypyridine deriva-
tives from the reference drug isonizide and 1,4-azaindole derivatives.
showed singlet at d 8.26 corresponding to an aromatic pyrrole proton, one broad singlet
at d 12.22 which corresponds to NH proton in pyrrole ring, two doublets at d 8.34 and
13
7
.03 corresponding to pyridine protons which confirmed the structures. C NMR spec-
tra of compound showed aromatic pyrrole carbon peaks in the range of d 118.3–107.1
þ
and in addition m/z 205.1 [M þ H] in the mass spectrum confirmed compound (4).
Compound (4) was reacted with 4-(bromomethyl)-2-methoxypyridine (5) in the pres-
ence of K CO to get compound (6) as major isomer with 65% yield and regioisomer
2
3
(6 A) as minor compound with 24% yield. The crude product was purified by column
chromatography (Combiflash, 0–10% CH OH/CH Cl ) to afford compound (6) which
3
2
2
was confirmed by the disappearance of NH proton at d 12.22 and the appearance of
singlet at d 5.75 which corresponds to CH protons of 2-methoxypyridine group and
2
the aromatic protons appeared doublet at d 8.10, 6.53 and singlet at d 6.17 correspond-
ing to 2-methoxypyridine protons and singlet at d 8.47 corresponding to an aromatic
pyrrole proton. The structures were further confirmed by 2D NOESY. A strong nOe
cross peak between the CH (methyl protons of the pyridine ring) and N–CH and also
3
2

4
S. BODIGE ET AL.
Scheme 1. Synthesis of title compounds. Reagents and conditions (a) 2 (1.7 equiv), t-BuOK (1.6
ꢀ
equiv), IPA, reflux, 6 h, 74% (b) Pd/C, EtOH, 40 C, 24 h, 80% (c) 5 (1.0 equiv), K CO (1.2 equiv), DMF,
2
3
rt, 16 h, 65% (d) LiOH.H O (1.5 equiv), MeOH: THF (1:1), rt, 4 h, 86% (e) R-NH (1.2 equiv), HATU (1.5
2
2
equiv), DIPEA (2.0 equiv), DMF, rt, 16 h.
cross peak between aromatic proton in pyrrole ring and N–CH was clearly observed in
2
13
(
6) confirming the alkylation on pyrrole NH. The C NMR (100 MHz, DMSO-d ) spec-
6
trum of compound (6) showed aromatic carbons in the range of d 113.9–164.0. In add-
þ
ition, the mass spectrum of compound (6) showed [M þ H] peak at m/z 326.2 which
confirmed structure.
Compound (6) was hydrolyzed with LiOH.H O to afford the acid compound (7).
2
The compound (7) was confirmed by the disappearance of ethyl ester protons at d 4.29
1
and 1.32 in the H NMR spectrum. Moreover, the mass spectrum of compound (7)
þ
showed [M þ H] peak at m/z 298.0 clearly indicated the formation compound.
The resultant product (7) was made to react with different amines in HATU/DIPEA
condition to afford the corresponding amide derivatives (8a–p) with good % yield
1
(
Table 1). The appearance of signal around d 8.90 due to NH proton in the H NMR
spectra of compounds (8a–p) clearly indicated the formation of proposed structures.
1
3
Further support of FT-IR, C NMR, mass and elemental analysis also confirmed the
19
structures. Compounds 8b, 8c, 8l and, 8m were also confirmed by F -NMR analysis.
The physical and spectral data of compounds were given under experimental section.
Antitubercular activity
The synthesized compounds (8a–p) were evaluated for anti-TB activity against
Mycobacterium tuberculosis using MABA method and their minimum inhibitory con-
centration (MIC) values in (mg/mL) were presented in Table 2. Among the tested com-
pounds, compounds with aryl moiety (C-4 substitution) showed potent activity against
Mycobacterium tuberculosis in comparison with reference drug, Pyrazinamide (Fig. 2).
Compounds 4-fluorophenyl (8m), 4-chlorophenyl (8n) and 4-methoxyphenyl (8i)
showed potent anti-TB activity (3.12 mg/mL) which is equal to activity of standard drug,
Pyrazinamide (3.12 mg/mL). The aryl ring, when replaced with saturated cyclic rings
(8d, 8e, and 8f), led to the reduction in anti-TB activity while the remaining

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5
Table 1. Protocol for the synthesis of the title compounds.
Entry
R
Yield (%)
83
8a
8b
81
8c
74
8
8
d
e
65
89
8f
82
8
8
g
h
85
85
8
8
i
j
83
81
8
8
k
l
83
68
8
8
m
n
76
77
(
continued)

6
S. BODIGE ET AL.
Table 1. Continued.
Entry
R
Yield (%)
82
8o
8p
83
Table 2. Antitubercular activity of synthesized compounds (8a–p).
Compound
MIC (mg/mL)
12.5
6.25
6.25
>25.0
12.5
6.25
12.5
6.25
3.12
12.5
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
12.5
12.5
3.12
3.12
6.25
12.5
3.12
Pyrazinamide
compounds displayed moderate to less activity. Compound (8a) bearing ethyl side chain
showed less anti-TB activity with MIC value of 12.5 mg/mL when compared to com-
pounds (8b) and (8c) with di and trifluoroethyl side chains respectively (MIC ¼
12.5 mg/mL).
Antibacterial activity
Further, the synthesized compounds were evaluated for their antibacterial activity using
Agar well diffusion method against Escherichia coli (Gram-negative) and Staphylococcus
aureus (Gram-positive) strains. The obtained screening data are shown in Table 3

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7
Figure 2. Antitubercular activity of synthesized compounds (8a-p).
Table 3. Antibacterial activity of synthesized compounds (8a–p).
Zone of inhibition (mm)
Escherichia coli
Gram-negative)
Staphylococcus aureus
(Gram-positive)
(Conc. lg/mL)
(Conc. lg/mL)
Compound
100
200
100
200
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
14
15
17
10
12
15
17
15
18
15
14
18
22
25
14
15
27
16
18
19
14
15
18
19
18
20
17
18
19
26
28
18
18
30
15
17
19
12
15
16
14
15
17
15
14
15
20
23
16
16
25
18
20
22
14
18
19
16
18
20
17
16
18
27
28
19
20
29
Chloramphenicol
indicated that the compounds (8n) and (8m) bearing 4-chlorophenyl and 4-flurophenyl
moieties respectively showed significant antibacterial activity. The introduction of satu-
rated cyclic rings (8d, 8e, and 8f) showed less activity than fluorine side chain bearing
compounds (8a, 8b, and 8c). Remaining compounds were found to possess moderate
activity against gram þ ve and gram-ve strains when compared with standard drug
Chloramphenicol.
Assessment of lipophilicity, drug likeness, drug score profiles and toxicity risks
The Osiris Explorer was utilized for anticipating the overall toxicity of the synthesized
compounds. The prediction process depends on a set of predetermined data of

8
S. BODIGE ET AL.
Table 4. Computationally predicted lipophilicity, solubility, druglikeness, drug score profiles, and tox-
icity risks of the synthesized compounds.
[
a]
[b]
[c]
Compound
C Log P
Log S
Druglikeness
Drug score
Molecular weight
Toxicity risks
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
8
a
b
c
d
e
f
g
h
i
j
k
l
m
n
o
p
2.13
1.66
2.61
2.33
2.96
3.28
3.06
2.96
2.96
3.52
3.41
3.34
3.34
3.89
3.59
2.20
ꢁ2.09
ꢁ2.56
ꢁ2.83
ꢁ2.56
ꢁ3.10
ꢁ3.37
ꢁ3.11
ꢁ3.13
ꢁ3.13
ꢁ3.19
ꢁ3.23
ꢁ3.61
ꢁ3.61
ꢁ4.03
ꢁ3.64
ꢁ2.50
2.15
ꢁ1.78
ꢁ5.98
2.42
ꢁ0.29
ꢁ2.61
1.35
1.59
2.50
2.77
2.06
0.80
0.50
0.41
0.84
0.58
0.41
0.71
0.70
0.73
0.72
0.71
0.36
0.59
0.64
0.34
0.62
324
360
378
336
364
378
386
416
416
400
400
390
390
406
386
373
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
Negative
ꢁ1.32
0.40
2.62
0.21
1.48
[
[
[
a]Calculated lipophilicity.
b]solubility parameter.
c]mutagenicity, tumorigenicity, irritancy, and reproductive effects.
structural fragments that offers ascend to toxicity alerts in case they are encountered in
the structure. All the synthesized compounds exhibited low in silico toxicity risks as
given in Table 4. As indicated by the Osiris program, the orally administered molecules
are considered to be drug candidates, if it fulfills the accompanying criteria: (a) C Log P
must not be more than 5; (b) Log S values more than ꢁ5; (c) molecular weight under
500. Compounds violating any one of these rules are expected to have bioavailability
problems. The results showed (Table 4) that the hydrophilicity (C Log P) of all the syn-
thesized compounds was less than 5.0, Log S values were observed more than ꢁ5 with
the molecular weight under 500.
Further, the program also determines compound druglikeness based on topological
descriptors, fingerprints on MDL structure keys, C Log P and molecular weights. The
positive value states that drug molecules contain fragments which are frequently present
in commercial drugs. The drug score combines druglikeness, Log S, C Log P, molecular
weight and toxicity risks that might be utilized to judge the virtual compounds for their
overall potential to qualify as a possible drug. A value around 0.5 makes synthesized
compounds as a promising lead for the development of safe and efficient drug.
Prediction of druglikeness and drug score for the target compounds are given in
Table 4. Interestingly, all the derivatives exhibited good values of druglikeness and drug
score. This information recommends that synthesized molecules could be considered as
drug candidates.
Molecular docking
In the present study, the synthesized compounds were docked into DprE1 (PDB code:
4
KW5) to explore their docking interactions at the active site. Molecular docking
revealed that prepared compounds (8a–p) interacted with amino acid residues such LYS
18, GLY 117, LYS 134 and SER 228 which are also found to interact with reported
4

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9
Table 5. Docking interaction patterns of synthesized compounds (8a-p) with active site amino acids
of DprE1 in molecular docking studies.
Distance between
ligand and active site
amino acid in Å
Active site amino acid
interactions
Compd
Percentage binding (%)
Type of interaction
8
8
8
a
b
c
HIS 132
LYS 418, GLY 117,
VAL 365
LYS 418
Stacking
Hydrophobic
–
–
49.2
–
2.73
–
Hydrogen
Hydrophobic
TYR 314, GLY 117, VAL
365, TRP 230
GLY 117
TRP 230
38.4
–
2.55
–
Hydrogen
Stacking
LYS 418, THR 314,
VAL 365
LYS 134
–
–
Hydrophobic
8
8
d
e
46.9
–
2.67
–
Hydrogen
Hydrophobic
GLY 117, VAL 365, TRP
230, TYR 314, SER 245
SER 228
LYS 418
GLY 117, VAL 365, TRP
83.0
45.0
–
2.53
2.54
–
Hydrogen
Hydrogen
Hydrophobic
230, TYR 314, HIS 132
8
8
8
8
8
f
LYS 418
GLY 117, VAL 365, TRP
52.9
–
2.61
–
Hydrogen
Hydrophobic
230, TYR 314, SER 228
g
h
i
HIS 132
GLY 117, VAL 365, LYS
Stacking
Hydrophobic
–
–
–
–
418, ILE 131
HIS 132
GLY 117, VAL 365, LYS
Stacking
Hydrophobic
418, TYR 60, LEU 363
HIS 132
GLY 117, VAL 365, LYS
39.5
–
2.74
–
Hydrogen
Hydrophobic
418, THR 118, ILE 131
j
SER 228
LYS 134
50.6
–
2.58
–
Hydrogen
Stacking
TRP 230
–
–
Stacking
GLY 117, VAL 365, TYR
–
–
Hydrophobic
3
14, HIS 132
8
8
k
l
SER 228
LYS 418
GLY 117, VAL 365, TYR
30.0
–
–
2.49
–
–
Hydrogen
Stacking
Hydrophobic
314, TRP 230
LYS 418
LYS 418
GLY 117, VAL 365, TYR
10.1
46.8
–
3.39
2.49
–
Hydrogen
Hydrogen
Hydrophobic
3
14, TRP 230
8
8
m
n
LYS 418
GLY 117, VAL 365, TYR
41.5
–
2.46
–
Hydrogen
Hydrophobic
314, TRP 230
SER 228
LYS 418
22.0
–
2.51
–
Hydrogen
Stacking
GLY 117, VAL 365, TYR
–
–
Hydrophobic
314, TRP 230, HIS 132
8
o
p
LYS 418
SER
GLY 117, VAL 365, CYS
34.9
85.0
–
2.64
2.65
–
Hydrogen
Hydrogen
Hydrophobic
387, TRP 230
8
LYS 418
LYS 868
GLY 117, VAL 365, TYR
16.2
51.6
–
3.20
2.56
–
Hydrogen
Hydrogen
Hydrophobic
314, TRP 230

1
0
S. BODIGE ET AL.
Figure 3. (A) Two-dimensional representation of the interacting mode of 8 m with DprE1. (B) Three-
dimensional structural model of compound 8 m into DprE1.
[
12–14]
DprE1 inhibitors.
Compound 8m showed effective hydrogen bond interaction
with LYS 418 of 41.5% binding at a distance of 2.46 Å. Moreover, the compound was
surrounded by GLY 117, VAL 365, TYR 314 and TRP 230. These interactions

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SYNTHETIC COMMUNICATIONS
11
underscore the importance of inhibitory capacity against DprE1. Data pertaining to the
docking interaction of compounds (8a–p) with amino acids on DprE1active site was
displayed in Table 5 indicated that all the compounds have shown essential key interac-
tions as that of reported DprE1 inhibitors and hence, the synthesized compounds could
be considered as promising inhibitors for tuberculosis. The two-dimensional and three-
dimensional representations of compound 8m were shown in Figure 3.
Conclusion
A novel series pyrrolo[3,2-b]pyridine-3-carboxamide linked 2-methoxypyridine deriva-
tives have been designed, synthesized and characterized. The synthesized compounds
were screened for their antitubercular and antibacterial activities. Among the tested
compounds, 4-fluorophenyl (8m), 4-chlorophenyl (8n) and 4-methoxyphenyl (8i)
showed potent anti-TB activity (3.12 mg/mL) in comparison with reference drug,
Pyrazinamide (3.12 mg/mL). Moreover, the compounds exhibited essential docking inter-
actions as that of reported DprE1 inhibitors and hence, the synthesized compounds
may be considered as molecular scaffolds for antitubercular activity. Compounds, 4-
chlorophenyl (8n) and 4-flurophenyl (8m) showed significant antibacterial activity
against Escherichia coli and Staphylococcus aureus strains. In silico prediction of toxic-
ities, druglikeness and drug score profiles of the tested compounds are promising.
Experimental section
Chemistry
All chemicals were purchased from Sigma–Aldrich, Merck and Combi blocks, and were
used without further purification. Melting points (m.p.) were uncorrected and deter-
mined in one end open capillary tubes using Guna Digital Melting Point apparatus.
Elemental analyses were performed on a Perkin-Elmer 240 CHN elemental analyzer.
1
19
13
FT-IR spectra were recorded on a Bruker FT-IR spectrometer. H, F and C NMR
spectra were recorded on a Bruker AMX 300 spectrometer operating at 400 MHz for
1
19
13
1
13
H, F and 100 MHz for C NMR. The H and C NMR chemical shifts were
expressed in parts per million (ppm) with reference to tetramethylsilane (TMS). Mass
spectra were recorded on Agilent technologies mass spectrometer.
Ethyl 2-cyano-2-(4-methyl-3-nitropyridin-2-yl)acetate (3)
To a stirred solution of potassium t-butoxide (10.4 g, 93.0 mmol) in t-butanol (90.0 mL)
and isopropanol (150 mL) was added ethyl cyanoacetate (11.1 g, 98.8 mmol). After
5
min, 2-chloro-4-methyl-3-nitropyridine 1 (10.0 g, 58.1 mmol) was added and the mix-
ture heated to reflux for 6 h. The dark red solution was cooled to room temperature
and solvents removed under high vacuum. The residue was washed with 1 M hydro-
chloric acid, water and recrystallized twice from methanol to give the title compound as
orange color solid, Yield, 10.7 g, 74%.
ꢀ
ꢁ1
1
M.p. 135–137 C, FT-IR (neat) v
cm 3054, 2224, 1641, 1562, 1330, 1200. H
max
NMR (400 MHz, DMSO-d ): d 14.41 (br s, 1H), 8.23 (d, 1H, J ¼ 6.4 Hz), 7.00 (d, 1H,
6
13
J ¼ 6.4 Hz), 4.20 (q, 2H, J ¼ 7.2 Hz), 2.30 (s, 3H), 1.25 (t, 3H, J ¼ 7.2 Hz). C NMR

1
2
S. BODIGE ET AL.
(
1
4
100 MHz, DMSO-d ) d 168.8, 146.5, 144.6, 139.6, 138.9, 115.7, 115.4, 60.10, 58.51,
6
þ
7.80, 14.33.MS (MM) m/z 250.0 [M þ H] ; Anal. Calcd. C H N O : C, 53.01; H,
11
11 3 4
.45; N, 16.86; Found: C, 53.10; H, 4.36; N, 16.94.
Ethyl 7-methyl-1H-pyrrolo[3,2-b]pyridine-3-carboxylate (4)
To a solution of ethyl 2-cyano-2-(4-methyl-3-nitropyridin-2-yl) acetate 3 (10.0 g,
4
0.1 mmol) in EtOH (100 mL) was added 5% Pd/C (0.32 g) and the mixture was stirred
ꢀ
under 100 psi hydrogen atmosphere at 40 C for 24 h. The Pd/C was removed by
through celite pad and the filtrate was concentrated to give. The crude was purified by
column chromatography on silica gel (Combiflash, 0 to 5% CH OH/CH Cl ) afford the
3
2
2
desired product as a white solid, Yield, 6.60 g, 80%.
ꢀ
ꢁ1
1
M.p. 241–243 C, FT-IR (neat) v
cm 3423, 3187, 3036, 1677, 1578, 1071. H
max
NMR (400 MHz, DMSO-d ): d 12.22 (br s, 1H), 8.34 (d, 1H, J ¼ 4.4 Hz), 8.26 (s, 1H),
6
7
.03 (d, 1H, J ¼ 4.8 Hz), 4.27 (q, 2H, J ¼ 7.2 Hz), 2.51 (s, 3H), 1.31 (t, 3H, J ¼ 7.2 Hz).
1
3
C NMR (100 MHz, DMSO-d ) d 163.2, 144.4, 142.7, 134.8, 130.2, 129.3, 118.3, 107.1,
6
þ
58.85, 16.07, 14.53.MS (MM) m/z 205.1 [M þ H] ; Anal. Calcd. C H N O : C, 64.69;
11
12 2 2
H, 5.92; N, 15.67; Found: C, 64.60; H, 5.80; N, 15.77.
Ethyl 1-((2-methoxypyridin-4-yl) methyl)-7-methyl-1H-pyrrolo[3,2-b]pyridine-3-carb-
oxylate (6)
To a solution of ethyl 7-methyl-1H-pyrrolo[3,2-b]pyridine-3-carboxylate 4 (6.00 g,
2
9.4 mmol) in DMF (60.0 mL) was added K CO (4.87 g, 35.2 mmol) under nitrogen
2 3
atm. and the reaction mixture was stirred at rt for 5 min. then 4-(bromomethyl)-2-
methoxypyridine 5 (5.90 g, 29.4 mmol) was added in one portion and the reaction was
stirred at rt overnight. The reaction mixture was diluted with water and extracted with
EtOAC (3 ꢂ 40.0 mL). The combined organic layers were washed with H O (50.0 mL),
2
brine solution (50.0 mL), dried over Na SO and concentrated. The crude product was
2
4
purified by column chromatography (Combiflash, 0 to 10% CH OH/CH Cl ) to afford
3
2
2
the title compound, ethyl 1-((2-methoxypyridin-4-yl)methyl)-7-methyl-1H-pyrrolo[3,2-
ꢀ
b]pyridine-3-carboxylate (6), Yield, 6.20 g, 65%. M.p. 120–122 C, FT-IR (neat) v
max
ꢁ1
1
cm 3180, 1654, 1602, 1210. H NMR (400 MHz, DMSO-d ): d 8.47 (s, 1H), 8.36 (d,
6
1
H, J ¼ 4.8 Hz), 8.10 (d, 1H, J ¼ 5.2 Hz), 6.97 (d, 1H, J ¼ 4.4 Hz), 6.54 (d, 1H,
J ¼ 4.8 Hz), 6.17 (s, 1H), 5.75 (s, 2H), 4.29 (q, 2H, J ¼ 7.2 Hz), 3.78 (s, 3H), 2.39 (s, 3H),
1
3
1
1
1
1
.32 (t, 3H, J ¼ 7.2 Hz). C NMR (100 MHz, DMSO-d ) d 164.0, 162.6, 151.1, 147.6,
6
44.9, 143.8, 140.0, 130.4, 128.6, 120.3, 113.9, 106.8, 106.4, 59.11, 53.14, 51.06, 17.74,
þ
4.50.MS (MM) m/z 326.2 [M þ H] ; Anal. Calcd. C H N O : C, 66.45; H, 5.89; N,
18
19 3 3
2.91; Found: C, 66.55; H, 5.78; N, 12.80. And region isomer ethyl 4-((2-methoxypyri-
din-4-yl)methyl)-7-methyl-4H-pyrrolo[3,2-b]pyridine-3-carboxylate (6 A), Yield, 2.28 g,
ꢀ
ꢁ1
1
2
4%. M.p. 121–123 C, FT-IR (neat) vmax cm
3180, 1654, 1602, 1210. H NMR
(
7
400 MHz, DMSO-d ): d 8.95 (s, 1H), 8.59 (d, 1H, J ¼ 6.0 Hz), 8.14 (d, 1H, J ¼ 5.2 Hz),
6
.61 (d, 1H, J ¼ 6.0 Hz), 6.68 (d, 1H, J ¼ 5.2 Hz), 6.37 (s, 1H), 5.95 (s, 2H), 4.29 (q, 2H,
13
J ¼ 7.2 Hz), 3.81 (s, 3H), 2.66 (s, 3 H), 1.31 (t, 3H, J ¼ 7.2 Hz). C NMR (100 MHz,
DMSO-d ) d 164.3, 163.7, 150.9, 147.2, 143.8, 143.3, 138.7, 130.9, 128.1, 119.5, 113.6,
6

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R
SYNTHETIC COMMUNICATIONS
13
þ
1
06.1, 59.26, 52.78, 50.56, 17.41, 14.78.MS (MM) m/z 326.2 [M þ H] ; Anal. Calcd.
C H N O : C, 66.45; H, 5.89; N, 12.91; Found: C, 66.56; H, 5.80; N, 12.81.
1
8
19 3 3
1-((2-methoxypyridin-4-yl)methyl)-7-methyl-1H-pyrrolo[3,2-b]pyridine-3-carboxylic
acid (7)
To a solution of ethyl 1-((2-methoxypyridin-4-yl)methyl)-7-methyl-1H-pyrrolo[3,2-
b]pyridine-3-carboxylate 6 (6.00 g, 18.4 mmol) in MeOH:THF (1:1, 50.0 mL) was added
LiOH.H O (1.16 g, 27.6 mmol) in H O (5.00 mL) and the reaction was stirred at rt for
2
2
4
h. The reaction mixture was concentrated and the crude mixture was washed with
H
EtOAc (2 ꢂ 20.0 mL). Aqueous layer P was adjusted to 3 with 2 N HCl and extracted
with EtOAC (3 ꢂ 40.0 mL). The combined organic layers were washed with H O
2
(50.0 mL), brine solution (50.0 mL), dried over Na SO and concentrated to afford the
2 4
title compound as white solid, Yield, 4.70 g, 86%.
ꢀ
ꢁ1
1
M.p. 258–260 C, FT-IR (neat) v
cm 3450, 3052, 1713, 1597, 1504, 1205. H
max
NMR (400 MHz, DMSO-d ): d 8.31 (s, 1H), 8.26 (d, 1H, J ¼ 4.4 Hz), 8.11 (d, 1H,
6
J ¼ 5.2 Hz), 6.98 (d, 1H, J ¼ 4.8 Hz), 6.56 (d, 1H, J ¼ 5.2 Hz), 6.18 (s, 1H), 5.73 (s, 2H),
1
3
3
.78 (s, 3H), 2.41 (s, 3H). C NMR (100 MHz, DMSO-d ) d 164.6, 164.0, 151.3, 147.6,
6
1
44.1, 143.7, 139.0, 131.3, 128.5, 119.9, 113.9, 106.5, 53.15, 50.93, 17.77.MS (MM) m/z
þ
298.0 [M þ H] ; Anal. Calcd. C H N O : C, 64.64; H, 5.09; N, 14.13; Found: C, 64.74;
1
6
15 3 3
H, 5.18; N, 14.04.
General procedure for the synthesis of title compounds (8a–8p)
To a solution of 7 (0.84 mmol) in DMF (2.00 mL), HATU (1.26 mmol) and DIPEA
(1.68 mmol) were added at room temperature and stirred for 15 min. Then, appropriate
amine (1.00 mmol) was added and stirred at room temperature for 16 h. The reaction
mixture was diluted with water (20 mL) and extracted with EtOAC (2 ꢂ 15.0 mL). The
combined organic layers were washed with H O (15 mL), brine solution (15 mL), dried
2
over Na SO and concentrated. The crude product was purified by column chromatog-
2
4
raphy (methanol/dichloromethane) to afford the title compounds (8a–p).
Antitubercular activity
The antitubercular activity of compounds was assessed against Mycobacterium tubercu-
losis using MABA method. This methodology is nontoxic, uses a thermally stable
reagent and shows good correlation with proportional and BACTEC radiometric
method. Briefly, 200 ll of sterile deionzed water was added to all outer perimeter wells
of sterile 96 wells plate to minimized evaporation of medium in the test wells during
incubation. The 96 wells plate received 100 ll of the Middlebrook 7H9 broth and serial
dilution of compounds were made directly on plate. The final drug concentrations
tested were 100–0.2 lg/ml. Plates were covered and sealed with parafilm and incubated
ꢀ
at 37 C for five days. After this time, 25 ll of freshly prepared 1:1 mixture of Almar
Blue reagent and 10% tween 80 was added to the plate and incubated for 24 hrs. A blue

1
4
S. BODIGE ET AL.
color in the well was interpreted as no bacterial growth, and pink color was scored
[
15]
as growth.
Antibacterial activity
Antibacterial activity of all the synthesized compounds was screened by Agar well diffu-
sion method, as recommended by the national committee for clinical laboratory stand-
ards against Gram-positive bacteria such as Staphylococcus aureus (NCIM 2079) and
Gram-negative bacteria Escherichia coli (NCIM 2068) at two concentrations 100 lg/mL
and 200 lg/mL. The obtained results were compared with standard drug
Chloramphenicol. The fresh culture of bacteria is obtained by inoculating bacteria into
ꢀ
nutrient broth media and incubated at 37 C for 24 hr. This culture mixed with nutrient
agar media was poured into petridishes under aseptic conditions. After solidification of
media, bores are made by using sterile cork borer (8 mm diameter). Into these cups,
standard drug and synthesized drugs are introduced; the plates were placed in the
ꢀ
refrigerator at 100 C for proper diffusion of drugs into the media. After 2 hr, the Petri
ꢀ
plates were transferred to an incubator and maintained at 37 ± 2 C for 24 hr. After the
incubation period, the Petri plates were observed for the zone of inhibition. The results
are evaluated by comparing the zone of inhibition shown by the synthesized compounds
[
16,17]
with standard drug.
Docking studies
Docking was performed on windows 2007 using MOE 2008.10 version. DprE1 enzyme
was imported from the protein data bank (PDB ID: 4KW5) and the receptor was visual-
ized using sequence option and non interacting water molecules were deleted along
with the previously bound ligand. The partial charge of protein was adjusted, using the
force field method AMBER 99. Later, the protein was subjected to 3 D protonation at
cut off 12.0, and further hydrogen was added according to standard geometry and the
enzyme was energy minimized using force field MMFF94x at 0.01 KJ mole gradients.
The ligand preparation was done by drawing the structure of ligands by using a builder
module and adjusting the partial charges using Hamilton MMFF94 force field method
and subsequently 3 D protonation and hydrogen addition was performed according to
standard geometry. Ligands were energy minimized at cut off 12 using MMFF94x force
field at 0.01KJ mole gradient. Docking was performed using the option simulation fol-
lowed by dock on selected active site amino acids using sequence option, and further
docked with setting options such as receptor and solvent, selected residues, alpha tri-
angle, affinity DG, force field refinement and best 10 poses. After obtaining docking
results out of the 10 best posed resulted for each chemical structure, the best pose was
retained. The resultant best pose score values in the series were used for analysis of
[
18,19]
docking and interaction.
Assessment of lipophilicity, druglikeness, drug score profiles and toxicity risks
Shredding of each molecule at every rotatable bond gave rise to a set of core fragments.
These in turn were used to reform all possible bigger fragments which could be the

V
R
SYNTHETIC COMMUNICATIONS
15
substructure of the original molecule. Afterward, a search process of substructure deter-
mined the occurrence frequency of every one of the fragment (core and constructed
fragments) within all traded drugs of 3300 as well as 15,000 commercially available
chemicals (Fluka) to predict lipophilicity, druglikeness, drug score profiles and tox-
[
20,21]
icity risks.
Acknowledgments
The authors would like to thank the management of AMRI, Hyderabad research center for giving
an opportunity to carry out this research. The authors are also thankful to Sai Innotech Labs Pvt.
Ltd. for providing synthesis facility.
Disclosure statement
No potential conflict of interest was reported by the authors.
References
[
1] World Health Organisation. Global Tuberculosis Report, to be found under, 2016. http://
apps.who.int/iris/bitstream/10665/250441/1/9789241565394-eng.pdf?ua¼1 (accessed Dec
12, 2016).
[
2] Shirude, P. S.; Shandil, R.; Sadler, C.; Naik, M.; Hosagrahara, V.; Hameed, S.; Shinde, V.;
Bathula, C.; Humnabadkar, V.; Kumar, N.; et al. Azaindoles: Noncovalent DprE1
Inhibitors from Scaffold Morphing Efforts, Kill Mycobacterium Tuberculosis and Are
Efficacious in vivo. J. Med. Chem. 2013, 56, 9701–9708. DOI: 10.1021/jm401382v.
[
3] Shirude, P. S.; Shandil, R. K.; Manjunatha, M. R.; Sadler, C.; Panda, M.; Panduga, V.;
Reddy, J.; Saralaya, R.; Nanduri, R.; Ambady, A.; et al. Lead Optimization of 1,4-
Azaindoles as Antimycobacterial Agents. J. Med. Chem. 2014, 57, 5728–5737. DOI:
10.1021/jm500571f.
[
4] Chatterji, M.; Shandil, R.; Manjunatha, M. R.; Solapure, S.; Ramachandran, V.; Kumar, N.;
Saralaya, R.; Panduga, V.; Reddy, J.; Prabhakar, K. R.; et al. 1, 4-azaindole: potential drug
candidate for the treatment of tuberculosis. Antimicrobl. Agents and Chemother. 2014, 58,
5325–5331. DOI: 10.1128/AAC.03233-14.
[5] Bayomi, S. M.; Price, K. E.; Sowell, J. W., Sr. Synthesis of 7-Oxopyrrolo[3,2-B]Pyridine-6-
Carboxylic Acid Derivatives as Potential Antimicrobial Agents. J. Heterocycl. Chem. 1985,
2
2, 83–88. DOI: 10.1002/jhet.5570220122.
[
6] Jeschke, P.; Harder, A.; Etzel, W.; Gau, w.; G o€ hrt, A.; Buchholz, J. B.; Thielking, G.
Synthesis and Anthelmintic Activity of 7-Substituted 3,4a-Dimethyl-4a,5a,8a,8b-
0
0
Tetrahydro-6H-Pyrrolo[3 ,4 :4,5]Furo[3,2-b]Pyridine-6,8(7H)-Diones. Bioorg. Med. Chem.
Lett. 2005, 15, 2375–2379. DOI: 10.1016/j.bmcl.2005.02.089.
[
7] Carbone, A.; Pennati, M.; Barraja, P.; Montalbano, A.; Parrino, B.; Spano, V.; Lopergolo,
A.; Sbarra, S.; Doldi, V.; Zaffaroni, N.; et al. Synthesis and Antiproliferative Activity of
Substituted 3[2-(1H-Indol-3-yl)- 1,3-Thiazol-4-yl]-1H-Pyrrolo[3,2-b]Pyridines, Marine
Alkaloid Nortopsentin Analogues. CMC. 2014, 21, 1654–1666. DOI: 10.2174/
09298673113206660307.
[
8] Carbone, A.; Pennati, M.; Parrino, B.; Lopergolo, A.; Barraja, P.; Montalbano, A.; Span oꢀ ,
V.; Sbarra, S.; Doldi, V.; De Cesare, M.; et al. Novel 1 H -Pyrrolo[2,3- b ]Pyridine
Derivative Nortopsentin Analogues: Synthesis and Antitumor Activity in Peritoneal
Mesothelioma Experimental Models. J. Med. Chem. 2013, 56, 7060–7072. DOI: 10.1021/
jm400842x.

1
6
S. BODIGE ET AL.
[9] Timmins, G. S.; Deretic, V. Mechanisms of Action of Isoniazid. Mol. Microbiol. 2006, 62,
1
220–1227. DOI: 10.1111/j.1365-2958.2006.05467.x.
10] Katz, R. B.; Voyle, M. Synthesis of Some Nitropyridylacetonitriles. Synthesis. 1989, 1989,
14–316. DOI: 10.1055/s-1989-27239.
11] Shanshan, G.; Qi, S. A practical synthesis of 4-azaindole. Adv. Mater. Res. 2014, 859,
53–356.
12] Chikhale, R.; Menghani, S.; Babu, R.; Bansode, R.; Bhargavi, G.; Karodia, N.;
Rajasekharan, M. V.; Paradkar, A.; Khedekar, P. P. Development of Selective DprE1
Inhibitors: Design, Synthesis, Crystal Structure and Antitubercular Activity of
Benzothiazolylpyrimidine-5-Carboxamides. Eur. J. Med. Chem. 2015, 96, 30–46. DOI:
[
[
[
3
3
10.1016/j.ejmech.2015.04.011.
[
13] Chitre, T. S.; Asgaonkar, K. D.; Miniyar, P. B.; Dharme, A. B.; Arkile, M. A.; Yeware, A.;
Sarkar, D.; Khedkar, V. M.; Jha, P. C. Synthesis and Docking Studies of Pyrazine-
Thiazolidinone Hybrid Scaffold Targeting Dormant Tuberculosis. Bioorg. Med. Chem. Lett.
2
016, 26, 2224–2228. DOI: 10.1016/j.bmcl.2016.03.055.
[
[
[
14] Piton, J.; Foo, C. S. Y.; Cole, S. T. Structural Studies of Mycobacterium Tuberculosis
DprE1 Interacting with Its Inhibitors. Drug Discov. Today. 2017, 22, 526–533. DOI:
10.1016/j.drudis.2016.09.014.
15] Achutha, L.; Parameshwar, R.; Reddy, B. M.; Babu, V. H. Microwave-Assisted Synthesis of
Some Quinoxaline-Incorporated Schiff Bases and Their Biological Evaluation. J. Chem.
2
013, 2013, 1–5. DOI: 10.1155/2013/578438.
16] Gulipalli, K. C.; Bodige, S.; Ravula, P.; Bolla, R. S.; Endoori, S.; Cherukumalli, P. K. R.;
Seelam, N. V. A Mild and Efficient Copper-Mediated N-Arylation of 6-Azauracil with
Corresponding Boronic Acids and Their Antibacterial Activity. Asian J. Chem. 2018, 30,
2495–2501. DOI: 10.14233/ajchem.2018.21491.
[
17] Ravula, P.; Babu, H.; Manichandrika, P.; Ramanachary, N.; Narendra Sharath Chandra,
J. N. Microwave assisted synthesis, biological evaluation and docking studies of novel pyr-
azoline derivatives as potent antiinflammatory and antibacterial agents. Int. J. Chem. Sci.
2
016, 14, 769–782.
[
18] Bodige, S.; Ravula, P.; Gulipalli, K. C.; Endoori, S.; Narendra Sharath Chandra, J. N.;
Cherukumalli, P. K. R.; Vanaja, G. R.; Seelam, N. V. Design, Synthesis and Biological
Evaluation of Novel Urea and Thiourea Bearing thieno[3,2-d]-pyrimidines as PI3 Kinase
Inhibitors. Anticancer Agents Med. Chem. 2018, 18, 891–902. DOI: 10.2174/
1871520618666180209151018.
[
19] Gulipalli, K. C.; Bodige, S.; Ravula, P.; Endoori, S.; Vanaja, G. R.; Suresh Babu, G.;
Narendra Sharath Chandra, J. N.; Seelam, N. V. Design, Synthesis, in Silico and in Vitro
Evaluation of Thiophene Derivatives: A Potent Tyrosine Phosphatase 1B Inhibitor and
Anticancer Activity. Bioorg. Med. Chem. Lett. 2017, 27, 3558–3564. DOI: 10.1016/
j.bmcl.2017.05.047.
[
20] Ravula, P.; Vamaraju, H. B.; Paturi, M.; Bodige, S.; Gulipalli, K. C.; Narendra Sharath
Chandra, J. N. Design, Synthesis, and Docking Studies of Novel Dimethyl Triazene
Incorporated Thiazolyl Pyrazolines for Anticancer Activity. J. Heterocycl. Chem. 2018, 55,
1313–1323. DOI: 10.1002/jhet.3163.
[
21] Ravula, P.; Vamaraju, H. B.; Paturi, M.; Narendra Sharath Chandra, J. N. Design, synthe-
sis, in silico and antiproliferative evaluation of novel pyrazole derivatives as VEGFR-2
inhibitors. Archiv. Der Pharmazie. 2017, 1–12.