Efficient synthesis of novel pyridine-based derivatives via suzuki cross-coupling reaction of commercially available 5-bromo-2-methylpyridin-3-amine: Quantum mechanical investigations and biological activities

Article abstract of DOI:10.3390/molecules22020190

The present study describes palladium-catalyzed one pot Suzuki cross-coupling reaction to synthesize a series of novel pyridine derivatives 2a-2i, 4a-4i. In brief, Suzuki cross-coupling reaction of 5-bromo-2-methylpyridin-3-amine (1) directly or via N-[5-bromo-2-methylpyridine-3-yl]acetamide (3) with several arylboronic acids produced these novel pyridine derivatives in moderate to good yield. Density functional theory (DFT) studies were carried out for the pyridine derivatives 2a-2i and 4a-4i by using B3LYP/6-31G(d,p) basis with the help of GAUSSIAN 09 suite programme. The frontier molecular orbitals analysis, reactivity indices, molecular electrostatic potential and dipole measurements with the help of DFT methods, described the possible reaction pathways and potential candidates as chiral dopants for liquid crystals. The anti-thrombolytic, biofilm inhibition and haemolytic activities of pyridine derivatives were also investigated. In particular, the compound 4b exhibited the highest percentage lysis value (41.32%) against clot formation in human blood among all newly synthesized compounds. In addition, the compound 4f was found to be the most potent against Escherichia coli with an inhibition value of 91.95%. The rest of the pyridine derivatives displayed moderate biological activities.

Full text of DOI:10.3390/molecules22020190

AErfticfleicient Synthesis of Novel Pyridine-Based
Derivatives via Suzuki Cross-Coupling Reaction of
Commercially Available 5-Bromo-2-methylpyridin-3-
amine: Quantum Mechanical Investigations and
Biological Activities
1
1,
1
1
2
Gulraiz Ahmad , Nasir Rasool *, Hafiz Mansoor Ikram , Samreen Gul Khan ,Tariq Mahmood ,
2
1
3
4
Khurshid Ayub , Muhammad Zubair , Eman Al-Zahrani , Usman Ali Rana ,
5
6,
Muhammad Nadeem Akhtar and Noorjahan Banu Alitheen *
1
Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan;
Gulchemist35@gmail.com (G.A.); chemistue@gmail.com (H.M.I.); samreengul@gcuf.edu.pk (S.G.K.);
nr_308@hotmail.com (M.Z.)
Department of Chemistry, COMSATS Institute of Information Technology, University Road, Tobe Camp,
2
22060 Abbottabad, Pakistan; mahmood@ciit.net.pk (T.M.); khurshid@ciit.net.pk (K.A.)
Chemistry Department, Faculty of Science, Taif University, 888-Taif, Saudi Arabia; em-s_z@yahoo.com
Sustainable Energy Technologies Center, College of Engineering, P.O. Box 800, King Saud University,
3
4
Riyadh 11421, Saudi Arabia; ranausmanali4u@gmail.com
Faculty of Industrial Sciences & Technology, University Malaysia Pahang, Lebuhraya Tun, Razak 26300,
5
Kuantan Pahang, Malaysia; nadeemupm@gmail.com
Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, Serdang,
6
Selangor Darul Ehsan 43400, Malaysia
* Correspondence: nasirrasool@gcuf.edu.pk (N.R.); noorjahan@upm.edu.my (N.B.A.);
Tel.: +92-332-7491790 (N.R.); +60-3-8946-7471 (N.B.A.); Fax: +92-41-9201032 (N.R.); +60-3-8946-7510 (N.B.A.)
Academic Editor: Diego Muñoz-Torrero
Received: 20 November 2016; Accepted: 6 January 2017; Published: date
Abstract: The present study describes palladium-catalyzed one pot Suzuki cross-coupling reaction to
synthesize a series of novel pyridine derivatives 2a–2i, 4a–4i. In brief, Suzuki cross-coupling reaction
of 5-bromo-2-methylpyridin-3-amine (1) directly or via N-[5-bromo-2-methylpyridine-3-yl]acetamide
(3) with several arylboronic acids produced these novel pyridine derivatives in moderate to good
yield. Density functional theory (DFT) studies were carried out for the pyridine derivatives 2a–2i
and 4a–4i by using B3LYP/6-31G(d,p) basis with the help of GAUSSIAN 09 suite programme. The
frontier molecular orbitals analysis, reactivity indices, molecular electrostatic potential and dipole
measurements with the help of DFT methods, described the possible reaction pathways and potential
candidates as chiral dopants for liquid crystals. The anti-thrombolytic, biofilm inhibition and haemolytic
activities of pyridine derivatives were also investigated. In particular, the compound 4b exhibited the
highest percentage lysis value (41.32%) against clot formation in human blood among all newly
synthesized compounds. In addition, the compound 4f was found to be the most potent against
Escherichia coli with an inhibition value of 91.95%. The rest of the pyridine derivatives displayed
moderate biological activities.
Keywords: Suzuki cross-coupling reaction; pyridine derivatives; density functional theory (DFT);
anti-thrombolytic; biofilm inhibition; haemolysis
Molecules 2017, 22, 190; doi:10.3390/molecules22020190
www.mdpi.com/journal/molecules

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1. Introduction
It is generally accepted that cross-coupling reactions catalyzed by transition metals offer facile
systematic routes for carbon-carbon bond formation when synthesizing a variety of organic compounds
of interest [1]. Among the various transition metals, palladium (Pd) exhibits the highest activity for
C–C coupling reactions [2]. The Suzuki-Miyaura cross-coupling reaction provides an appropriate and
practical approach for the synthesis of biaryl compounds, due to its ability to tolerate a wide range of
functional groups and good reaction yields [3]. In the past, pyridine and its derivatives have been used
as starting precursors for several useful compounds due to their availability and stability for direct
cross-coupling reactions [4–12]. With this approach, Liu and co-workers have described the Suzuki
cross-coupling reactions between 2-aryl-1,2,3-triazole-N-oxides and pyridine-N-oxide with good
yield of the final products [5]. Pyridine compounds have a number of biological activities, including
anti-tumor [13,14], anti-viral [15–17], anti-microbial [18,19], anti-diabetic [20] anti-leishmanial [21]
and anti-oxidant [22]. Recently, we have reported the efficient synthesis of a series of 5-aryl-2-bromo-3-
hexylthiophene-based compounds and a thorough investigation of their biological activities [23]. The
biological importance of heterocyclic compounds inspired us to now synthesize some pyridine
derivatives and investigate their biological activities. In the present work, we carried out the successful
synthesis of a series of novel pyridine derivatives by making use of Suzuki-Miyaura cross-coupling
reactions. These novel pyridine derivatives were further explored by the computational studies using
DFT methods and their biological activities were also examined in the course of this study.
2. Results and Discussion
2.1. Synthesis
Recently, we have reported the successful synthesis of 5-aryl-2-bromo-3-hexylthiophene derivatives
by employing the Suzuki cross-coupling reaction [23]. Ikram and co-workers have also reported the
application of double Suzuki cross-coupling reactions for the synthesis of 2,5-biaryl-3-hexylthiophene
derivatives [24]. In the present work we have utilized the commercially available 5-bromo-2-
methylpyridin-3-amine (1), which was coupled with a series of arylboronic acids in the presence of
tetrakis(triphenylphosphine)palladium(0) as a catalyst and K3PO4 as a base to produce a series of
novel 5-aryl-2-methylpyridin-3-amine molecules 2a–2i (Scheme 1, Figure 1).
Scheme 1. Synthesis of compounds 2a–2i, 3 and 4a–4i; Reagents and Conditions: (i) 1 (0.2 g, 1.069 mmol),
Pd(PPh3)4 (5 mol %), arylboronic acid (1.1759 mmol), K3PO4 (2.318 mmol), 1,4-dioxane:water (2:0.5 mL),
18 h reflux, 90 °C; (ii) 1 (2.0 g, 12.7 mmol), acetic anhydride (1.95 g, 19.1 mmol) in acetonitrile (20 mL); (iii)
3 (0.1 g, 1 mmol), Pd(PPh3)4 (5 mol %), arylboronic acid (1.1 mmol), K3PO4 (1.5 mmol), 1,4-dioxane:water
(2:0.5 mL), 18 h reflux, 90 °C.

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Figure 1. Structures of the newly synthesized pyridine derivatives viz. 2a–2i, 3, 4a–4i.
These Suzuki cross-coupling reactions were carried out in a solvent mixture of 1,4-dioxane and
water in the volume ratio of 4:1, respectively. As expected, the desired pyridine derivatives were
obtained in moderate to good yields. The labile protons in compounds such as carboxylic acids,
alcohols and primary amines make them a poor choice for Suzuki coupling reactions [25]. It has been
reported that when an amine binds itself with a Pd center, its deprotonation occurs readily with a
base such as K3PO4, which in turn causes a concomitant decrease in the pKa [26,27]. Therefore, instead of
using carboxylic acids, alcohols and primary amines, we have utilized an amide such as N-[5-bromo-2-
methylpyridine-3-yl]acetamide (3) as the starting material for these Suzuki coupling reactions. This
particular amide (N-[5-bromo-2-methylpyridine-3-yl]acetamide (3)) was synthesized by the reaction
of 5-bromo-2-methylpyridin-3-amine (1) with acetic-anhydride following Scheme 1 (conditions ii).
The Suzuki cross-coupling reactions of this newly synthesized compound 3 with several arylboronic
acids in the presence of Pd(PPh3)4 and K3PO4 produced novel pyridine derivatives in moderate to good
yields [28]. These cross-coupling reactions were carried out in a solvent mixture of 1,4-dioxane and
water (volume ratio ~ 4:1), while the temperature was kept between 85 °C to 95 °C [29]. Interestingly,
the N-[5-bromo-2-methylpyridine-3-yl]acetamide (3) reacted efficiently with various functional group

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containing arylboronic acids affording the corresponding pyridine derivatives. The effect of different
arylboronic acids was studied in the same reaction environment. The experimental results reveal that
the electron-donating or electron-withdrawing substituents on the arylboronic acids had no prominent
effect on either the reaction rates or the product yields. The structures of all these newly synthesized
1
13
pyridine based compounds were confirmed by H-NMR and C-NMR studies.
2.2. Density Functional Theory (DFT) Studies
Density functional theory (DFT) studies on all newly synthesized compounds 2a–2i and 4a–4i were
carried out to investigate the structure properties relationships in these systems. First of all, the
geometry optimization of both series 2a–2i and 4a–4i were simulated using the GAUSSIAN 09 software
at B3LYP/6-31G(d,p) level of DFT. Frequency calculations at the same level proved the true optimization,
(no imaginary frequency was observed). Structural analysis like frontier molecular orbitals analysis
(FMOs), electrostatic potential (ESP) and dipole moment were executed with the help of optimized
geometries.
2.2.1. Frontier Molecular Orbital (FMO) Analysis
At present, FMO analysis using DFT methods is becoming vital to explain the reactivity and
molecular excitations, as well as the electronic properties of molecular systems [30]. Frontier orbitals
(HOMO/LUMO) mainly participate in electronic transitions and their energy gap is used to explain
the reactivity and kinetic stability [31]. A low value of HOMO-LUMO energy gap indicates high
reactivity and less kinetic stability [32]. The opposite is true if the value of HOMO-LUMO energy gap
is high. The FMO analysis of all compounds 2a–2i and 4a–4i was performed at the B3LYP/6-31G(d,p)
level of theory, and the respective surfaces are shown in Figure S1 (Supplementary Materials). The
corresponding HOMO/LUMO energy values along with energy gap (ΔE) are provided in Table 1. The
ΔE values for compounds 2a–2i were found in the range ~4.13–4.86 eV, whereas for the compounds 4a–
4i, these values fell in the 4.51–5 eV range. The relatively high values of ΔE for the newly synthesized
biphenyl derivatives 4a–4i indicate that these compounds are kinetically more stable than compounds
2a–2i. Among all the newly synthesized derivatives, the compound 4b showed the value (~5.05 eV),
which indicates its higher stability and less reactivity. In contrast, compound 2g exhibited the lowest ΔE
value (~4.13 eV) among all the newly synthesized pyridine derivatives, indicating its poor stability
and corresponding high reactivity.
The dispersion of iso-density in the HOMO and LUMO orbitals of compounds 2a–2i displayed
similar trends except for 2g. In the HOMO orbitals, the iso-density dispersion was mainly observed on
the biphenyl skeleton, which contained the amino and methyl groups attached to the pyridine ring.
In compounds 2a, 2c, 2d, 2e and 2f, the groups attached to the para position of phenyl ring were involved
with the π-electron cloud on the ring, whereas the groups attached to the meta position showed no
participation with the π-electron cloud, as observed in the case of compounds 2b, 2g, 2h and 2i.
Similarly, in case of the LUMO orbitals, the electronic cloud dispersion in compounds 2a–2i exhibited
similar trends except for compound 2g. The iso-density of the LUMO orbitals reveals that the amino
group in the pyridine ring and the groups attached to the meta position in the phenyl ring showed no
involvement with the π-electron cloud, whereas the groups attached to the para position displayed
direct participation in the electronic transitions. The dispersion of the iso-density in the HOMO orbitals
of compound 2g was mainly restricted around the pyridine ring, along with the groups attached to it,
whereas it was totally shifted to the phenyl ring in the LUMO, indicating a rapid movement of
electrons and more reactivity of compound 2g. The relatively low energy gap between the HOMO
and LUMO orbitals of compound 2g also support this finding.
In the second series of compounds 4a–4i, the iso-density showed a high dependence on the
substituents attached to the biphenyl skeleton. In the HOMO orbitals of all compounds 4a–4i, except
for 4g, the iso-density was dispersed around the main skeleton to which substituents were attached at
the para position. In the HOMO orbitals, a shift in iso-density was observed from the amide group of
the pyridine ring toward the pyridine and phenyl ring. Again, the iso-density dispersion in compound
4g was different. In the HOMO orbitals of compound 4g, the dispersion was concentrated on the

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pyridine ring, while in the LUMO, it totally shifted to the phenyl ring. This rapid shifting of electronic
cloud indicates the more reactive nature of compound 4g towards electrophiles when compared to
the other compounds of this series 4a–4i.
Table 1. The values of HOMO and LUMO energies for compounds 2a–2i and 4a–4i along with the
energy gaps (ΔE). All energy values are reported in eV unit.
Compound HOMO LUMO ΔE
2a
2b
2c
2d
2e
2f
2g
2h
2i
4a
4b
4c
4d
4e
4f
4g
4h
4i
−5.51
−5.51
−5.38
−6.03
−5.72
−5.39
−5.66
−5.80
−5.66
−6.08
−6.10
−5.82
−6.30
−6.42
−5.71
−6.28
−6.55
−6.38
−0.67
−0.65
−0.53
−1.40
−0.98
−0.74
−1.52
−1.09
−1.52
−1.07
−1.05
−0.95
−1.37
−1.47
−1.13
−1.75
−1.76
−1.39
4.84
4.86
4.85
4.63
4.74
4.65
4.14
4.71
4.14
5.01
5.05
4.87
4.93
4.95
4.58
4.53
4.79
4.99
2.2.2. Reactivity Indices
Reactivity indices like chemical hardness (η), electrophilicity (ω) and electronic chemical potential
are excellent tools to describe the chemical hardness, reactivity and stability of compounds [33]. Chemical
hardness of any compound can be expressed in terms of the following mathematical equation:
η = (EHOMO − ELUMO)/2
Using the equation above the chemical hardness of all derivatives 2a–2i and 4a–4i was calculated
and given in Table 2, along with reactivity indices (electrophilicity and electronic chemical potential).
From Table 2 it is clear that among all derivatives, 4b has highest value of η i.e., of 2.52 eV and is the
chemically hardest compound among all, whereas 2g has the lowest value and is chemically soft and
more reactive. These findings are consistent with the HOMO-LUMO band gaps of all synthesized
derivatives. The electronic chemical potential (µ) value gives an idea about the charge transfer within
any compound in its ground state. Mathematically it can be defined by the equation below:
µ = (EHOMO + ELUMO)/2
From Table 2, it is clear that 4h has the highest electronic chemical potential value (4.15 eV),
among both series 2a–2i and 4a–4i while 2c has the lowest chemical potential value.
The electrophilicity index (ω) is a thermodynamic property that measures the changes in energy
when a chemical system becomes saturated by adding electrons. It plays an excellent role in describing
the chemical reactivity of a system and is mathematically defined by the following equation:
2
ω = µ /2η
where µ is the electronic chemical potential, η is chemical hardness. The results from Table 2 indicate
that 2b has the lowest electrophilicity index value and is nucleophilic in nature, whereas 4h has the
highest value i.e., of 3.60 eV and is strongly electrophilic in nature.

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Table 2. Reactivity indices of compounds 2a–2i and 4a–4i.
Compound η (eV) µ (eV) ω (eV)
2a
2b
2c
2d
2e
2f
2g
2h
2i
4a
4b
4c
4d
4e
4f
4g
4h
4i
2.42
2.43
2.42
2.31
2.37
2.32
2.07
2.35
2.07
2.5
2.52
2.43
2.46
2.47
2.29
2.26
2.39
2.49
3.09
3.08
2.95
3.71
3.35
3.06
3.59
3.44
3.59
3.57
3.57
3.38
3.83
3.94
3.42
4.01
4.15
3.88
1.97
1.95
1.79
2.97
2.36
2.01
3.11
2.51
3.11
2.54
2.52
2.35
2.98
3.14
2.55
3.55
3.6
3.02
2.2.3. Molecular Electrostatic Potential (MEP) Analysis
MEP analysis with the help of quantum mechanical methods has been used extensively to explain
the reactive sites within a compound [34]. With MEP analysis, the reactive sites can be located by
different color codes, such as the red color in a MEP graphic indicates an electron-rich site, blue color
indicates an electron-deficient site, while the green color is indicative of a neutral region [32]. The MEP
analysis of both series of compounds viz. 2a–2i and 4a–4i was carried out using the B3LYP/6-31G(d,p)
basis set of DFT. Figure 2 displays the MEP surfaces of the newly synthesized pyridine derivatives
viz. 2a–2i, 3, 4a–4i at B3LYP/6-31G(d,p) level of DFT and graphics, while the corresponding +ꢀꢁ and
– ꢀꢁ potential values from the MEP analysis of these compounds are given in Table 3. The MEP
surfaces of compounds 2a–2i exhibited similar electronic density trends. In all these compounds, the
red color appeared on the pyridine ring nitrogen indicating the electron rich site, while the blue color
was concentrated on the amino group, reflecting the electron deficient site.
2a
2b
2c
2f
2d
2e
Figure 2. Cont.

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2g
2h
2i
4a
4d
4g
4b
4e
4h
4c
4f
4i
Figure 2. MEP surfaces of the newly synthesized pyridine derivatives viz. 2a–2i, 3, 4a–4i at B3LYP/
6-31G(d,p) level of DFT
Table 3. The +ꢀꢁ and – ꢀꢁ potential values from the MEP analysis of compounds 2a–2i and 4a–4i.
Compound +ꢂꢃ Potential −ꢂꢃ Potential
2a
2b
2c
2d
2e
2f
2g
2h
2i
4a
4b
4c
4d
4e
4f
4g
4h
4i
−0.05351
−0.05365
−0.05348
−0.05401
−0.05124
−0.05285
−0.05037
−0.05193
−0.05198
−0.05573
−0.05579
−0.05643
−0.05268
−0.05207
−0.05527
−0.05600
−0.05275
−0.05230
0.05351
0.05365
0.05348
0.05401
0.05124
0.05285
0.05037
0.05193
0.05198
0.05573
0.05579
0.05643
0.05268
0.05207
0.05527
0.05600
0.05275
0.05230
From the MEP analysis, it is clear that the lone pair of the nitrogen in the pyridine ring was
available for electrophiles. In contrast, the lone pair of the amino group exhibited delocalization on the

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biphenyl skeleton. Similarly, in the case of the second series of compounds 4a–4i, where a hydrogen
atom of the amino group was replaced by an acetyl group, the electronic density showed a clear shift
toward the acetyl group oxygen, as reflected by red color. The light red color on the nitrogen atom of
pyridine still showed its affinity for electrophiles.
2.2.4. Dipole Moment
Biphenyl compounds having restricted rotation around single bonds and a large dipole moment
exhibit the potential to influence the liquid crystalline properties, therefore, they are frequently used
as chiral dopants for liquid crystals [35]. Biphenyl compounds having greater dipole moments can
effectively act as chiral dopants for liquid crystals [36]. The dipole moment of all newly synthesized
biphenyl derivatives was calculated at the B3LYP/6-31G(d,p) level of theory and are given in Table 4.
Table 4. The values of dipole moment (Debye) for the newly synthesized pyridine derivatives viz.
2a–2i, 3, 4a–4i calculated at B3LYP/6-31G(d,p) level of DFT.
Compounds Dipole moment (Debye)
2a
2b
2c
2d
2e
2f
2g
2h
2i
4a
4b
4c
4d
4e
4f
4g
4h
4i
3.0645
3.0012
2.6799
3.7669
3.6042
3.9239
2.7658
3.7223
3.6598
3.3070
3.3294
4.1817
1.0557
1.1464
3.5552
4.7299
1.4438
2.0915
The dipole moment values for compounds 2a–2i were in the ~2.7658–3.9239 Debye range.
Compound 2d displayed the highest dipole moment ~3.7669 Debye, indicating a high suitability of
this compound to act as a chiral dopant for liquid crystals. For the second series of compounds 4a–4i, the
dipole moment values were recorded in the 1.0557–4.7299 Debye range. Among these compounds,
compound 4g displayed the highest value of dipole moment, indicating its high suitability in terms
of chiral dopant properties.
2.3. Pharmaceutical Studies
2.3.1. Anti-Thrombolytic Activity
It has been reported that the thrombotic component is one of the major causes of sudden
coronary death and myocardial infarction [37,38]. Hence, we have explored the anti-thrombolytic
activity of all newly synthesized compounds. Table 5 displays the anti-thrombolytic activity values for
the newly synthesized pyridine derivatives at a concentration of 50 µM/mL. For comparison,
streptokinase was used as positive control. The results revealed that compound 2i exhibited the highest
anti-thrombolytic activity (31.61%) among the 2a–2i pyridine derivatives. This high activity indicated
that compound 2i might be related to the presence of two different halogen groups (chloro and flouro)
attached at the 3 and 4 positions of the aryl ring, respectively. On the other hand, the compound 2e

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showed the lowest activity (2.82%), which could be due to the presence of only one halogen moiety
(chloro) at the 4 position of the aryl ring. Furthermore, other derivatives among the 2a–2i series
displayed low to moderate anti-thrombolytic activity values, while compound 2g exhibited no
significant activity against clot formation (Figure 3).
Table 5. Anti-thrombolytic assay of compounds 2a–2i, 3 and 4a–4i at a concentration of 50 µM/mL.
Compounds
% Lysis
15.2 ± 0.05
6.43 ± 0.06
15.4 ± 0.19
21.3 ± 0.21
2.82 ± 0.33
3.72 ± 0.03
0.43 ± 0.22
9.04 ± 0.31
31.6 ± 0.86
34.8 ± 0.03
21.5 ± 0.04
41.3 ± 0.43
2.69 ± 0.16
13.6 ± 0.09
6.43 ± 0.21
12.6 ± 0.15
29.2 ± 0.03
6.31 ± 0.41
14.3 ± 0.03
87.45
2a
2b
2c
2d
2e
2f
2g
2h
2i
3
4a
4b
4c
4d
4e
4f
4g
4h
4i
Streptokinase
100
90
80
70
60
50
40
30
20
10
0
% Lysis (anti-thrombolytic)
% inhibition
% Lysis (haemolysis)
Figure 3. Anti-thrombolytic, biofilm inhibition and haemolytic activities of compounds 2a–2i, 3.
Among the derivatives 4a–4i, compound 4b exhibited the highest activity (41.32%) against clot
formation in human blood (Table 5, Figure 4). This high activity displayed by 4b compared to its
analogue 2b, might have its origin in the acyl group attached on the amino group in 4b. Compound 4c
exhibited the lowest activity against clot formation in human blood among all newly synthesized pyridine
derivatives 4a–4i. The results in Table 5 reveal that compounds 4g and 4a displayed moderate activity
values viz. 29.21% and 21.51%, respectively. Overall, it can be seen that the type of substituents and their

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position on the aryl group had a significant influence on the anti-thrombolytic activity of the newly
synthesized compounds. On the basis of these anti-thrombolytic activity results (Table 5), it is suggested
that the pyridine derivatives containing amino groups masked with an acyl group, and substituted
aryl rings displayed moderate to good characteristics to inhibit the formation of clots in human blood.
2.3.2. Biofilm Inhibition Activity
Bacterial biofilms are formed when unicellular organisms form a community that adheres itself to
a solid surface and is encased in an exopolysaccharide matrix [39]. It is generally accepted that biofilms
can limit the effect of medicine to a great extent [40–42]. Hence, the anti-biofilm activity of all newly
synthesized pyridine-based compounds was evaluated against strains of Escherichia coli. Rifampicin
was used as standard positive control. The corresponding values of anti-biofilm activity measured for
all compounds at a concentration of 50 µM/mL are given in Table 6. In comparison with standard drug
rifampicin (97.53%), compound 2f exhibited the highest activity (90.95 %) among derivatives 2a–2i. This
activity displayed by the compound 2f can be attributed to the existence of the bulky –SMe group
attached to the phenyl ring of this compound. Some of the other compounds such as 2g, 2d, 2a, 2c and
2e also exhibited good anti-bacterial activities (83.76%, 82.04%, 80.05%, 79.78%, 79.38%, respectively)
against E. coli. Among all 2a–2i compounds, compound 2i exhibited the lowest inhibition (69.54%)
compared to the positive control rifampicin (Figure 3).
Table 6. Biofilm inhibition assay of the compounds (2a–2i, 3 and 4a–4i) at a concentration of 50 µM/mL.
Compounds % Inhibition
2a
2b
2c
2d
2e
2f
2g
2h
2i
3
4a
4b
4c
4d
4e
4f
80.05 ± 0.001
77.39 ± 0.040
79.78 ± 0.007
82.04 ± 0.360
79.38 ± 0.030
90.95 ± 0.023
83.76 ± 0.051
78.98 ± 0.212
69.54 ± 0.291
89.63 ± 0.213
87.36 ± 0.031
83.90 ± 0.112
82.97 ± 0.023
84.30 ± 0.121
87.09 ± 0.321
91.95 ± 0.291
83.62 ± 0.521
82.52 ± 0.02
86.48 ± 0.032
97.53 ± 0.021
4g
4h
4i
Rifampicin
In the case of pyridine derivatives 4a–4i, the results in Table 6 show that compound 4f exhibited
the highest anti-bacterial activity (91.95%) compared to all other compounds from this series (Figure 4).
Since the anti-bacterial activity of these compounds differ with the functional groups, the superior
activity exhibited by the compound 4f could be due to the presence of the thiomethyl group on the
phenyl ring in this compound. Several other compounds from this series such as compounds 4a, 4e, 4i,
4d, 4b, 4g, 4c also exhibited fairly high anti-bacterial activity, evidenced by bio-film inhibition against
strains of E. coli with values ~87.36%, 87.09%, 86.48%, 84.30%, 83.90%, 83.62 and 82.97%, respectively.
The lowest bio-film inhibition value was displayed by compound 4h and it is plausible that the attached
iodo substituent might be the possible cause of this low anti-bacterial activity. Overall, the results for
anti-bacterial activity measurements reveal that most of the compounds from both pyridine derivative
series 2a–2i and 4a–4i exhibit moderate to good biofilm inhibition values against E. coli. In general, it
is quite evident that the electron-donating and electron-withdrawing groups attached to different sites

Molecules 2017, 22, 190
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of the phenyl ring are responsible for the different antibacterial activity against E. coli. The pyridine
derivatives 4a–4i exhibited relatively better anti-bacterial activities compared to the 2a–2i series of
compounds. Moreover, one approach to enhance the anti-bacterial activity is to mask the amino functional
group with an acyl group, as seen earlier in the case of compound 4b. Hence, pyridine derivatives
containing an amino group masked by an acyl group produce potentially useful compounds that can
successfully inhibit the formation of biofilms formed by E. coli.
2.3.3. Haemolytic Activity
The haemolytic activity of the newly synthesized pyridine derivatives 2a–2i and 4a–4i and
compound 3 was also examined. For comparison purposes Triton X-100 was employed as the positive
control. The cytotoxicity values for these novel derivatives at a concentration of 50 µM/mL are
expressed in Table 7. Among derivatives 2a–2i, compound 2i exhibited the highest percentage lysis
(11.72%) against red blood cells (RBCs). This superior haemolytic activity displayed by compound 2i
might be related with the halogen functional groups (–Cl and –F) attached to the aryl ring in this
compound. In contrast, the compound 2g exhibited the lowest cytotoxicity (2.52%) against RBCs, possibly
due to the presence of acyl group attached to the aromatic ring which somehow inhibits the activity of
this compound against red blood cells.
In the case of pyridine 4a–4i derivatives, compound 4g displayed the highest cytotoxicity (19.82%)
when compared with the standard drug. Given the presence of two acyl groups in this compound, this
remarkably high cytotoxic activity displayed by the compound 4g was somewhat surprising. From this
result, it can be established that upon masking the amino group with an acyl group in the pyridine
derivatives, high cytotoxic activity can be achieved against RBCs. The results from Table 7 revealed that
the compound 4e also exhibited good percentage lysis (8.28%) against RBCs. Other pyridine molecules
exhibited low to moderate haemolytic activity when compared to Triton X-100. Overall, the results
reveal that the haemolytic activity of the newly synthesized pyridine derivatives showed significant
variations due to the presence of different substituents at the aromatic ring in these compounds. The
high haemolytic activity displayed by most of the newly synthesized pyridine derivatives make them
potential active anti-tumor agent candidates [43].
Table 7. Heamolytic assay of the compounds (2a–2i, 3 and 4a–4i) at a concentration of 50 µM/mL.
Compounds
% Lysis
5.45 ± 0.02
3.21 ± 0.51
5.40 ± 0.09
7.87 ± 0.21
5.92 ± 0.05
4.82 ± 0.03
2.52 ± 0.03
4.94 ± 0.11
11.7 ± 0.17
13.6 ± 0.57
2.32 ± 0.04
4.82 ± 0.04
3.67 ± 0.06
3.39 ± 0.29
0.14 8.28±
6.55 ± 0.03
19.82 ± 0.37
3.39 ± 0.04
4.48 ± 0.03
99
2a
2b
2c
2d
2e
2f
2g
2h
2i
3
4a
4b
4c
4d
4e
4f
4g
4h
4i
Triton X-100

Molecules 2017, 22, 190
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100
90
80
70
60
50
40
30
20
10
0
% Lysis (anti-thrombolytic)
% inhibition
% Lysis (haemolysis)
Figure 4. Anti-thrombolytic, biofilm inhibition and haemolytic activities of compounds (4a–4i).
3. Experimental Section
3.1. General Information
A Buchi B-540 melting point apparatus (Buchi, New Castle, DE, USA) was used to measure the
melting points of the newly synthesized pyridine derivatives. For qualitative analysis, an AM-400 NMR
13
1
spectrometer (Bruker, Billercia, MA, USA) was applied and the C-NMR and H-NMR spectra were
obtained in CDCl and CD OD at 400/100 MHz, respectively. All chemicals used in the present work
3
3
were acquired from Sigma Aldrich (St. Louis, MO, USA) and Alfa Aesar (Ward Hill, MA, USA). EIMS
spectra were obtained on a JMS-HX-110 spectrometer (JEOL, Peabody, MA, USA).
3.2. General Procedure for the Synthesis of Compounds 2a–2i
All compounds were synthesized following the previously reported method [28]. Briefly 5-
bromo-2-methylpyridin-3-amine (1, 0.2 g with tetrakis(triphenylphosphine)palladium (5 mol %) and
1,4-dioxane (2 mL) were mixed in a Schlenk flask. The reaction mixture was stirred at room temperature
for 30 min and then the arylboronic acid (1.1759 mmol), potassium phosphate (2.318 mmol) and water
(0.5 mL) were added and the mixture again stirred at 85–95 °C for more than 15 h. After lowering the
temperature, the mixture was filtered and diluted with ethyl acetate (50 mL). The excess solvent in the
solution was evaporated by rotary evaporator in order to obtain a concentrated solution. Column
chromatography was applied to get the desired pure product (silica gel, n-hexane and ethyl acetate). The
final products were dried, recrystallized and then characterized using different spectroscopic techniques.
1
2-Methyl-5(4-methylphenyl)pyridin-3-amine (2a). m.p.: 208–209 °C. H-NMR (CDCl
3
) δ 7.99–7.64 (m, 2H-
13
pyridine), 7.41 (m, 2H-Ar), 7.21 (m, 2H-Ar), 2.50 (s, 3H-methyl), 2.41 (s, 3H-methyl); C-NMR (CDCl
3
+ CD
[M − NH
3
OD) δ 16.7, 21.3, 120.5, 126.8, 128.8, 132.5, 133.8, 134.9, 144.2, 145.8. EI-MS m/z (+ion mode): 198,
+
+
+
2
] = 183, [M − NH
2
and CH
3
] = 170, [M − NH
2
and 2CH
3
] = 155. Anal. calcd for C13
H14N
2
(198.26): C, 78.74; H, 7.11. Found: C, 78.69; H, 7.02%.
1
5-(3,5-Dimethylphenyl)-2-methylpyridin-3-amine (2b). m.p.: 232–233 °C. H-NMR (CDCl
3
) δ 8.2 (s, 1H-
pyridine), 7.6 (m, 2H-Ar), 7.3–7.02 (m, 1H-pyridine, 1H-Ar), 2.51 (s, 3H-methyl), 2.41 (s, 3H-methyl);
13
C-NMR (CDCl
3
+ CD
3
OD) δ 15.5, 21.5, 120.5, 125.3, 130.6, 132.0, 134.1, 136.4, 138.3, 144.3, 145.8.
+
+
+
EI-MS m/z (+ion mode): 212, [M − NH
Anal. calcd for C14
2
] = 197, [M − NH
2
and CH
3] = 183, [M − NH
2
and 3CH
3
] = 140.
H
16
N
2
(212.25): C, 79.19; H, 7.59. Found: C, 78.17; H, 7.56%.

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1
5-(4-Methoxyphenyl)-2-methylpyridin-3-amine (2c). m.p.: 232 °C. H-NMR (CDCl3) δ 8.12 (s, 1H-pyridine),
13
7.55 (m, 2H-Ar), 7.31 (m, 1H-pyridine), 7.03 (m, 2H-Ar), 3.9 (s, 3H-methyl), 2.45 (s, 3H-methyl); C-NMR
(CDCl3 + CD3OD) δ 17.1, 55.6, 114.7, 120.5, 128.4, 129.8, 132.3, 134.3, 144.3, 145.8, 160.3. EI-MS m/z (+ion
+
+
+
mode): 214, [M − NH2] = 199, [M − NH2 and CH3] = 185, [M − OCH3] = 184. Anal. calcd for C13H14N2O
(214.21): C, 72.79; H, 6.55. Found: C, 72.75; H, 6.53%.
1
5-(4-Iodophenyl)-2-methylpyridin-3-amine (2d). m.p.: 258 °C. H-NMR (CDCl3) δ 8.09 (s, 1H-pyridine),
13
7.71–7.49 (m, 4H-Ar), 7.15 (s, 1H-pyridine), 2.5 (s, 3H-methyl); C-NMR (CDCl3 + CD3OD) δ 15.8, 94.1,
+
120.1, 130, 132.1, 134.5, 135.7, 138.4, 144.2, 145.5. EI-MS m/z (+ion mode): 310, [M − NH2] = 295, [M − NH2
+
+
and CH3] = 281, [M − I] = 184. Anal. calcd for C12H11IN2 (310.13): C, 46.47; H, 3.58. Found: C, 46.41;
H, 3.52%.
1
5-(4-Chlorophenyl)-2-methylpyridin-3-amine (2e). m.p.: 228 °C. H-NMR (CDCl3) δ 8.2 (s, 1H-pyridine),
13
7.71–7.41 (m, 4H-Ar), 7.11 (s, 1H-pyridine), 2.5 (s, 3H, methyl); C-NMR (CDCl3 + CD3OD) δ 15.7, 120.4,
+
128.3, 129.8, 132, 134.3, 135.3, 144.2, 145.6. EI-MS m/z (+ion mode): 310, [M − NH2] = 295, [M − NH2
+
+
and CH3] = 281, [M − I] = 184. Anal. calcd for C12H11ClN2 (218.68): C, 66.01; H, 5.07. Found: C, 66.0;
H, 5.03%.
1
2-Methyl-5-[4-(methylsulfonyl)phenyl]pyridin-3-amine (2f). m.p.: 240 °C. H-NMR (CDCl3) δ 8.23 (s, 1H-
13
pyridine), 7.69–7.11 (m, 4H-Ar, 1H-pyridine), 2.59 (s, 3H, methyl), 2.5 (s, 3H, methyl). C-NMR
(CDCl3 + CD3OD) δ 14.6, 17, 120.1, 127.2, 128.3, 132.2, 133.4, 135, 139.5, 144, 146.1. EI-MS m/z (+ion
+
+
+
mode): 230, [M − NH2] = 215, [M − NH2 and CH3] = 201, [M − SCH3] = 184. Anal. calcd for C13H14N2S
(230.33): C, 66.98; H, 5.99. Found: C, 66.95; H, 5.95%.
1
1-[3-(5-Amino-6-methylpyridin-3-yl)phenyl]ethanone (2g). m.p.: 270 °C. H-NMR (CDCl3) δ 8.24 (d, J =
3.4 Hz, 1H-Ar), 8.17 (s, 1H-pyridine), 7.96–7.49 (m, 3H-Ar), 7.25 (s, 1H-pyridine), 2.7 (s, 3H-COCH3),
13
2.5 (s, 3H-methyl). C-NMR (CDCl3 + CD3OD) δ 16.3, 26.4, 120.5, 126.5, 128.2, 129.7.131.2, 132.8, 134.8,
+
+
136.6, 138, 144.5, 146.1, 195. EI-MS m/z (+ion mode): 226 [M + H] : [M − NH2] = 211: [M − NH2 and
+
+
CH3] = 197: [M − OCH3] = 184. Anal. calcd for C14H14N2O (226.19): C, 74.27; H, 6.18. Found: C, 74.26;
H, 6.17%.
1
5-(3,5-Difluorophenyl)-2-methylpyridin-3-amine (2h). m.p.: 208 °C. H-NMR (CDCl3) δ 7.9 (s, 1H-pyridine),
13
7.57 (m, 1H-pyridine), 7.55–6.82 (m, 3H-Ar), 2.5 (s, 3H, methyl). C-NMR (CDCl3 + CD3OD) δ 16.3,
+
+
104.8, 111.2, 120, 132.4, 134.5, 139.3, 144.3, 145.8. EI-MS m/z (+ion mode): 220 [M + H] : [M − NH2] =
+
+
205: [M − NH2 and CH3] = 191: [M − 2F] = 184. Anal. calcd for C12H10F2N2 (220.22): C, 65.45; H, 4.56.
Found: C, 65.41; H, 4.54%.
1
5-(3-Chloro-4-fluorophenyl)-2-methylpyridin-3-amine (2i). m.p.: 240 °C. H-NMR (CDCl3) δ 8.22 (s, 1H-
13
pyridine), 7.72–7.08 (m, 3H-Ar, 1H-pyridine), 2.5 (s, 3H, methyl). C-NMR (CDCl3 + CD3OD) δ 16.6,
+
117.1, 120.4, 121.1, 128, 129.4, 132.2, 133.1, 134.6, 143.9, 145.2. EI-MS m/z (+ion mode): 236 [M + H] :
+
+
+
+
+
[M − NH2] = 221: [M − NH2 and CH3] = 207: [M − F] = 218: [M − Cl] = 202: [M − F and Cl] = 184.
Anal. calcd for C12H10ClFN2 (236.67): C, 60.90; H, 4.27. Found: C, 60.85; H, 4.22%.
3.3. Synthesis of N-[5-Bromo-2-methylpyridine-3-yl]acetamide (3)
Under a nitrogen atmosphere, a solution of 5-bromo-2-methylpyridine-3-amine (1, 2 g), acetic
anhydride (1.95 g) and acetonitrile (20 mL) was stirred at 60 °C and treated with 96% H2SO4 (a few
drops). Stirring was continued for another half an hour while the reaction was monitored by TLC.
The reaction mixture was evaporated and allowed to cool to room temperature. After cooling, water
was added dropwise to form a precipitate. Then the mixture was stirred near one hour around room
temperature and then filtered. The impure solid was washed with deionized water and later dried in
an oven [44].

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1
N-[5-Bromo-2-methylpyridine-3-yl]acetamide (3). Yield: 85 %; m.p.: 256 °C. H-NMR (CDCl3) δ 7.8 (s, 1H-
13
pyridine), 7.38 (s, 1H-pyridine), 2.6 (s, 3H, methyl), 2.45 (s, 3H, COCH3). C-NMR (CDCl3 + CD3OD) δ
+
+
16.5, 24.1, 112.3, 127.9, 147.2, 150, 169.1. EI-MS m/z (+ion mode): 229 [M + H] : [M − CH3] = 207: [M −
+
Br] = 150. Anal. calcd for C8H9BrN2O (229.07): C, 41.95; H, 4.01. Found: C, 41.93; H, 3.97%.
3.4. General Procedure for the Synthesis of Compounds 4a–4i
All compounds were synthesized by reported method [28]. N-[5-bromo-2-methylpyridine-3-
yl]acetamide (3, 0.1 g), tetrakis(triphenylphosphine)-palladium (5 mol %) and 1,4-dioxane (2 mL) were
placed in the Schlenk flask at room temperature and the mixture was stirred for 30 min . Then the
appropriate arylboronic acid (1.1 mmol), potassium phosphate (1.5 mmol) and H2O (0.5 mL) were added
to the mixture, which was stirred and kept at 85–95 °C for more than 15 h. After reaching room
temperature, the mixture was filtered and then diluted with ethyl acetate (50 mL). The excess solvent was
evaporated by rotary evaporator in order to obtain a concentrated solution. Column chromatography
(silica gel, n-hexane and ethyl acetate?) was applied to obtain the desired pure products. The final
product was dried and recrystallized and further analyzed using different spectroscopic techniques.
1
5-(3-Chloro-4-fluorophenyl)-2-methylpyridin-3-amine (4a). m.p.: 310 °C. H-NMR (CDCl3) δ 8.77 (s, 1H-
pyridine), 8.7 (d, J =2.5 Hz, 1H-pyridine), 7.6 (m, 2H-Ar), 7.4 (m, 2H-Ar), 2.65 (s, 3H, methyl), 2.5 (s,
13
3H, methyl), 2.4 (s, 3H, COCH3). C-NMR (CDCl3 + CD3OD) δ 16.4, 21.5, 24.2, 126.1, 127.6, 129.2, 132.1,
+
+
+
133.2, 134, 136.8, 149.2, 168.2. EI-MS m/z (+ion mode): 240 [M + H] : [M − CH3] = 226: [M − 2CH3] =
212. Anal. calcd for C15H16N2O (240.3): C, 74.89; H, 6.69. Found: C, 74.87; H, 6.65%.
1
N-[5-(3,5-Dimethylphenyl)-2-methylpyridine-3-yl]acetamide (4b). m.p.: 338 °C. H-NMR (CDCl3) δ 8.6 (s,
1H-pyridine), 8.5 (s, 1H-pyridine), 7.49 (d, 2H-Ar), 7.35 (s, 1H-Ar), 2.49 (s, 3H, methyl), 2.32 (s, 6H,
13
methyl), 2.05 (s, 3H, COCH3). C-NMR (CDCl3 + CD3OD) δ 16.5, 21.7, 24, 125.2, 126.6, 130.1, 133.5, 136.4,
+
+
+
138.6, 149.3, 167.9. EI-MS m/z (+ion mode): 254 [M + H] : [M − CH3] = 240: [M − 3CH3] = 212. Anal. calcd
for C16H18N2O (254.33): C, 75.48; H, 7.09. Found: C, 75.45; H, 7.07%.
1
N-[5-(4-Methoxyphenyl)-2-methylpyridine-3-yl]acetamide (4c). m.p.: 337 °C. H-NMR (CDCl3) δ 8.27 (s, 1H-
pyridine), 7.7 (d, J = 2.3 Hz, 1H-pyridine), 7.15–7.05 (m, 4H-Ar), 3.95 (s, 3H, methoxy), 2.6 (s, 3H, methyl),
13
1.75 (s, 3H, COCH3). C-NMR (CDCl3 + CD3OD) δ 16.6, 24, 55.6, 114.7, 126.2, 128.3, 129.9, 133.3, 136.8,
+
+
+
149.4, 160.5, 168.3. EI-MS m/z (+ion mode): 256 [M + H] : [M − CH3] = 242: [M − 2CH3] = 228. Anal.
calcd for C15H16N2O2 (256.30): C, 70.29; H, 6.26. Found: C, 70.27; H, 6.24%.
1
N-[5-(4-Chlorophenyl)-2-methylpyridine-3-yl]acetamide (4d). m.p.: 316 °C. H-NMR (CDCl3) δ 8.48 (s, 1H-
pyridine), 8.22 (s, 1H-pyridine), 7.55 (m, 2H-Ar), 7.45 (m, 2H-Ar), 2.5 (s, 3H, methyl), 2.22 (s, 3H, methyl).
13
C-NMR (CDCl3 + CD3OD) δ 16.1, 24.2, 126.6, 128.7, 129.9, 133.4, 134.7, 136.5, 149.2, 169.1. EI-MS m/z
+
+
+
+
(+ion mode): 260 [M + H] : [M − CH3] = 247: [M − Cl] = 226: [M − Cl and CH3] = 212. Anal. calcd for
C14H13ClN2O (260.72): C, 64.49; H, 5.08. Found: C, 64.44; H, 5.02%.
1
N-[5-(3,5-Difluorophenyl)-2-methylpyridine-3-yl]acetamide (4e). m.p.: 310 °C. H-NMR (CDCl3) δ 8.73 (s,
1H-pyridine), 8.46 (s, 1H-pyridine) 7.29 (m, 2H-Ar), 6.64 (s, 1H-Ar), 2.53 (s, 3H-methyl), 2.04 (s,
13
3H-methyl). C-NMR (CDCl3 + CD3OD) δ 16.6, 24.3, 104.9, 111.2, 126.7, 133.8, 136.5, 139.3, 149.5, 164.8,
+
+
+
168.4. EI-MS m/z (+ion mode): 262 [M + H] : [M − CH3] = 248: [M − 2F] = 226. Anal. calcd for
C14H12F2N2O (262.23): C, 64.12; H, 4.61. Found: C, 64.08; H, 4.54%.
1
N-[2-Methy-5-(4-methylsulfonyl)phenylpyridin-3-yl]acetamide (4f). m.p.: 325 °C. H-NMR (CDCl3) δ 7.69–7.39
13
(m, 4H-Ar, 2H-pyridine), 2.55 (s, 3H-methyl), 1.7 (s, 3H-methyl). C-NMR (CDCl3 + CD3OD) δ 14.7, 16.8,
+
+
24.2, 127.1, 128.2, 132.8, 133.8, 136.2, 139.1, 149.6, 168.5. EI-MS m/z (+ion mode): 272 [M + H] : [M − CH3]
+
= 258: [M − 2CH3] = 244. Anal. calcd for C15H16N2OS (272.37): C, 66.15; H, 5.92. Found: C, 66.10; H, 5.91%.
1
N-[5-(3-Acetylphenyl)-2-methylpyridine-3-yl]acetamide (4g). m.p.: 340 °C. H-NMR (CDCl3) δ 8.33 (s,
1H-pyridine), 8.25 (d, J = 1.9 Hz, 1H-pyridine), 8.0 (m, 1H-Ar), 7.80 (m, 1H-Ar), 7.68 (m, 1H-Ar), 7.4 (m,

Molecules 2017, 22, 190
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13
1H-Ar), 2.71 (s, 3H, methyl), 2.51 (s, 3H, COCH3), 2.09 (s, 3H, methyl). C-NMR (CDCl3 + CD3OD) δ
16.5, 24.6, 26.3, 125.8, 126.9, 127.7, 128.6, 129.5, 132, 133.7, 136.2, 137.3, 148.6, 167.8, 196.6. EI-MS m/z
+
+
+
(+ion mode): 268 [M + H] : [M − CH3] = 254: [M − OCH3] = 226. Anal. calcd for C16H16N2O2 (268.29):
C, 71.59; H, 5.99. Found: C, 71.55; H, 5.96%.
1
N-[5-(4-iodophenyl)-2-methylpyridine-3-yl]acetamide (4h). m.p.: 333 °C. H-NMR (CDCl3) δ 8.73 (s, 1H-
pyridine), 8.46 (d, J = 2.5 Hz, 1H-pyridine), 7.99 (m, 2H-Ar), 7.56 (m, 2H-Ar), 2.53 (s, 3H, methyl), 2.04
13
(s, 3H, COCH3). C-NMR (CDCl3 + CD3OD) δ 16.7, 23.9, 94.5, 126.3, 128.2, 130.5, 133.6, 135.7, 136.9,
+
+
+
138.4, 149.1, 168.8. EI-MS m/z (+ion mode): 352 [M + H] : [M − CH3] = 338: [M − F] = 226: [M − F and
+
CH3] = 212. Anal. calcd for C14H13IN2O (352.17): C, 47.75; H, 3.72. Found: C, 47.71; H, 3.67%.
1
N-[5-(3-chloro-4-fluorophenyl)-2-methylpyridine-3-yl]acetamide (4i). m.p.: 325 °C. H-NMR (CDCl3) δ 8.2
(s, 1H-pyridine) 7.71 (m, 1H-pyridine), 7.5 (m, 1H-Ar), 7.35 (d, J = 8.2 Hz, 1H-Ar), 7.09 (d, J = 8.1, 1H-Ar),
13
2.45 (s, 3H, methyl), 1.7 (s, 3H, COCH3). C-NMR (CDCl3 + CD3OD) δ 15.9, 24.4, 117.8, 126.3, 127.9, 129.5,
+
+
+
132.9, 135.5, 136.9, 150, 158.1, 167.5. EI-MS m/z (+ion mode): 279 [M + H] : [M − CH3] = 265: [M − F] =
+
+
261: [M − Cl] = 244: [M − Cl and F] = 226. Anal. calcd for C14H12ClFN2O (278.71): C, 60.33; H, 4.34.
Found: C, 60.27; H, 4.29%.
3.5. Computational Methods
Density functional theory calculations were executed with the help of the GAUSSIAN 09 software
[45] and results/graphics were analyzed with the help of Gauss view 05 [46]. Energy minima geometries
of compounds 2a–2i and 4a–4i were optimized without any symmetry constraints at hybrid B3LYP
(Becke 3-Parameter, Lee, Yang and Parr) method using 6-31G(d,p) basis set. Frequency analysis was
performed at the same level of theory, in order to confirm true optimization. Frontier molecular
orbitals (FMOs) analysis, molecular electrostatic potential (MEP) analysis and dipole measurements
were executed by using the B3LYP/6-31G(d,p) basis set and at DFT level of theory.
3.6. Anti-Thrombolytic Assay
The anti-thrombolytic activity of the novel pyridine derivatives was determined by applying a
previously reported method [26]. Human blood was taken from volunteers and kept in sterile
microcentrifuge tubes. The clot formation in blood was done, when microcentrifuge tubes having
500 μL blood were incubated for the time of 45 min at optimum temperature (37 °C). After clot
formation, the serum was separated and 100 µL test sample solution from the compound (2a–2i, 3,
4a–4i) at a concentration of 50 µM/mL were transferred in microcentrifuge tubes. After adding the
samples, the tubes were incubated again for the duration of more than 90 min at 37 °C. To act as a
positive control, streptokinase was used in this assay, while water was used as a negative control.
The final results, shown by test samples against clot formation, were measured in percentage. This
study was approved by the Board of studies Department of Chemistry and Director advanced
studies, Govt. College University, Faisalabad (DAS600).
3.7. Biofilm Inhibition Assay by Microliter-Plate Method
The anti-bacterial activity of new pyridine molecules was determined by applying a reported method
[25]. Test sample solutions (100 µL) from the compounds 2a–2i, 3, 4a–4i at a concentration of 50 µM/mL
along with bacterial suspension (20 µL) were placed in sterile 96-well plastic tissue culture plates,
which were later incubated for one day at 37 °C. After incubation, phosphate buffer (220 µL) was
applied to treat the content of each plate thrice. The plates were shaken vigorously to eliminate non-
adherent bacteria and the remaining bacteria were fixed with methanol solution (220 µL, 99%). After
drying, the plates were stained by using Crystal Violet solution (220 mL, 50%) for 5 min. Tap water
was used to remove the excess stain from plates. Glacial acetic acid (220 µL, 33%) was then applied
in order to resolubilise the dye attached to adherent cells. The OD value was determined for each
well at 630 nm by a micro-plate reader (BioTek, Winooski, VT, USA).

Molecules 2017, 22, 190
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3.8. Haemolytic Assay
The synthesized molecules were evaluated for their haemolytic activity following a previously
reported method [47]. In brief, heparinized human blood (3 mL) was taken in sterile Falcon tubes.
The tubes were centrifuged at 850 rpm for 5 min. The upper blood layer was taken out and the pellet
was washed three times. With the help of ice cold phosphate buffered saline (PBS, 20 mL), the red blood
cells were counted via a haemocytometer. The red blood cells were kept on ice and diluted using the
8
pure phosphate buffer saline to 7.068 × 10 cells per mL. Next each compound 2a–2i, 3, 4a–4i (20 µL)
was placed in a 2 mL microfuge tube. Triton X-100 with 100% lysis was used as positive control. For the
negative control, phosphate buffered saline with 0.07% lysis was used. The contents of the microfuge
tubes were diluted after adding the suspension of blood cells (180 µL). At a temperature of 37 °C, the
tubes were incubated for 40 min. After that, the tubes were kept on ice for 5–7 min and then centrifuged
at 1315 rpm for 6 min. From this incubated tube, 100 µL of the upper layer was separated, diluted by
using ice cold phosphate buffered saline (900 µL). All the test sample solutions (200 µL) were placed
into 96-well plates. The absorption of each sample was measured by a µ-Quant instrument at 576 nm.
This study was approved by the Board of studies Department of Chemistry and Director advanced
studies, Govt. College University, Faisalabad (DAS600).
4. Conclusions
The present study describes the efficient synthesis in moderate to good yield of a series of novel
pyridine derivatives by the application of palladium catalyzed Suzuki cross-coupling reactions of
5-bromo-2-methylpyridin-3-amine (1) and N-[5-bromo-2-methylpyridine-3-yl]acetamide (3) with
several arylboronic acids. Frontier molecular orbitals (FMO) analysis reveals that the spread of
isodensity was mainly concentrated on the aromatic and pyridine rings. The HOMO/LUMO band
gap studies for all the newly synthesized systems reveal that compound 2g exhibited the lowest band
gap (~4.14 eV), while compound 4b displayed the highest band gap (~5.05 eV), indicating that
compound 2g is the most reactive and 4b the least reactive among all the newly synthesized
compounds. The chemical hardness of 4b has the highest value (2.52 eV), whereas 2g displayed the
lowest value, chemically softness and reactivity. Among all derivatives 4h has the highest value of
electronic chemical potential (4.15 eV). The electrophilicity index described the electrophilicity and
nucleophilicity quantitatively (2b is more nucleophilic and 4b is more electrophilic). The MEP
analysis showed that the negative potential was mainly concentrated on the pyridine ring nitrogen
and the positive potential in the compounds 2a–i was mostly concentrated on the amino group. The
highest dipole moment value was exhibited by 4g (4.7299 Debye), indicating its strong potential to act
as a chiral dopant for liquid crystals. Further studies on the biological activities of these compounds
such as anti-thrombolytic, biofilm inhibition and haemolytic activities revealed the moderate to good
biological activities of these newly synthesized pyridine derivatives. Compound 4b exhibited the highest
anti-thrombolytic activity (~41.32%) against clot formation among all the newly synthesized
compounds. In addition, compound 4f exhibited the highest antibacterial activity (~91.95%) against
bacterial biofilm formation. In this study, the biological screening results established the effect of
different functional groups present at the aromatic ring. In summary, the biological activity studies
suggest the potential use of these novel pyridine derivatives as useful compounds for several applications.
Supplementary Materials: Supplementary materials can be accessed at: http://www.mdpi.com/1420-3049/
22/2/190/s1.
Acknowledgments: The present data is the part of M. Phil thesis research work of Gulraiz Ahmad. The authors
also gratefully acknowledge the financial support by Higher Education Commission of Pakistan (HEC Project
No. 20-1465/R&D/09/5458). U. A. Rana would like to extend his sincere appreciation to the Deanship of Scientific
Research at the King Saud University for its funding of this research through the Prolific Research Group, Project
No. PRG-1436-18. One of us (M.N.A) is also thankful to University of Malaysia Pahang for the grant number
RDU150349 and 150109.

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Author Contributions: N.R and S.G.K conceived and designed the experiments; G.A. and H.M.I. performed the
experiments; M.Z., T.M. and K.A. analyzed the data; E.A., U.A.R. and N.B.A. contributed reagents/materials/
analysis tools; H.M.I and M.N.A. wrote the paper.
Conflicts of Interest: The authors declare no conflict of interest.
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Sample Availability: Samples of the compounds are not available from the authors.
© 2017 by the authors. Submitted for possible open access publication under the
terms and conditions of the Creative Commons Attribution (CC-BY) license
(http://creativecommons.org/licenses/by/4.0/).