N-Substituted 5-Amino-6-methylpyrazine-2,3-dicarbonitriles: Microwave-Assisted synthesis and biological properties

Article abstract of DOI:10.3390/molecules19010651

In this work a series of 15 N-benzylamine substituted 5-Amino-6- methylpyrazine- 2,3-dicarbonitriles was prepared by the aminodehalogenation reactions using microwave assisted synthesis with experimentally set and proven conditions. This approach for the aminodehalogenation reaction was chosen due to its higher yields and shorter reaction times. The products of this reaction were characterized by IR, NMR and other analytical data. The compounds were evaluated for their antibacterial, antifungal and herbicidal activity. Compounds 3 (R = 3,4-Cl), 9 (R = 2-Cl) and 11 (R = 4-CF₃) showed good antimycobacterial activity against Mycobacterium tuberculosis (MIC = 6.25 μg/mL). It was found that the lipophilicity is important for antimycobacterial activity and the best substitution on the benzyl moiety of the compounds is a halogen or trifluoromethyl group according to Craig's plot. The activities against bacteria or fungi were insignificant. The presented compounds also inhibited photosynthetic electron transport in spinach chloroplasts and the IC50 values of the active compounds varied in the range from 16.4 to 487.0 μmol/L. The most active substances were 2 (R = 3-CF₃), 3 (R = 3,4-Cl) and 11 (R = 4-CF₃). A linear dependence between lipophilicity and herbicidal activity was observed.

Full text of DOI:10.3390/molecules19010651

Molecules 2014, 19, 651-671; doi:10.3390/molecules19010651
OPEN ACCESS
molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
N-Substituted 5-Amino-6-methylpyrazine-2,3-dicarbonitriles:
Microwave-Assisted Synthesis and Biological Properties
Ondrej Jandourek 1,*, Martin Dolezal 1, Pavla Paterova 2, Vladimir Kubicek 3, Matus Pesko 4,
Jiri Kunes 5, Aidan Coffey 6, Jiahui Guo 6 and Katarina Kralova 7
1
Department of Medicinal Chemistry and Drug Analysis, Faculty of Pharmacy, Charles University in
Prague, Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic; E-Mail: dolezalm@faf.cuni.cz
2
Department of Biological and Medical Sciences, Faculty of Pharmacy, Charles University in Prague,
Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic; E-Mail: pavla.paterova@fnhk.cz
3
Department of Biophysics and Physical Chemistry, Faculty of Pharmacy, Charles University in Prague,
Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic; E-Mail: kubicek@faf.cuni.cz
4
Department of Environmental Ecology, Faculty of Natural Sciences, Comenius University,
Mlynska Dolina CH-2, Bratislava 842 15, Slovakia; E-Mail: matus.pesko@gmail.com
5
Department of Inorganic and Organic Chemistry, Faculty of Pharmacy, Charles University in Prague,
Heyrovskeho 1203, Hradec Kralove 50005, Czech Republic; E-Mail: kunes@faf.cuni.cz
6
Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland;
E-Mails: aidan.coffey@cit.ie (A.C.); gjh0517@yahoo.com (J.G.)
7
Institute of Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-2,
Bratislava 842 15, Slovakia; E-Mail: kata.kralova@gmail.com
* Author to whom correspondence should be addressed; E-Mail: jando6aa@faf.cuni.cz;
Tel.: +420-495-067-275; Fax: +420-495-512-423.
Received: 2 December 2013; in revised form: 29 December 2013 / Accepted: 31 December 2013 /
Published: 7 January 2014
Abstract: In this work a series of 15 N-benzylamine substituted 5-amino-6-methyl-
pyrazine-2,3-dicarbonitriles was prepared by the aminodehalogenation reactions using
microwave assisted synthesis with experimentally set and proven conditions. This
approach for the aminodehalogenation reaction was chosen due to its higher yields and
shorter reaction times. The products of this reaction were characterized by IR, NMR and
other analytical data. The compounds were evaluated for their antibacterial, antifungal and
herbicidal activity. Compounds 3 (R = 3,4-Cl), 9 (R = 2-Cl) and 11 (R = 4-CF3) showed
good antimycobacterial activity against Mycobacterium tuberculosis (MIC = 6.25 µg/mL).
It was found that the lipophilicity is important for antimycobacterial activity and the best

Molecules 2014, 19
substitution on the benzyl moiety of the compounds is a halogen or trifluoromethyl group
652
according to Craig’s plot. The activities against bacteria or fungi were insignificant. The
presented compounds also inhibited photosynthetic electron transport in spinach
chloroplasts and the IC50 values of the active compounds varied in the range from 16.4 to
487.0 µmol/L. The most active substances were 2 (R = 3-CF3), 3 (R = 3,4-Cl) and 11
(R = 4-CF3). A linear dependence between lipophilicity and herbicidal activity
was observed.
Keywords: pyrazinamide derivatives; in vitro biological evaluation; microwave-assisted
synthesis; tuberculosis; lipophilicity
1. Introduction
Mycobacterium tuberculosis is counted with justification among the most dangerous and successful
microorganisms in today’s world, especially in developing countries which have become the reservoir
of resistant strains (the most burdened countries are in South Africa and East Asia) [1]. These strains
are causing the biggest number of problems connected to tuberculosis (TB) treatment [2]. The main
problem is resistance. It can be divided into three groups. The first one is called multidrug-resistant TB
(MDR-TB) and these microbes are resistant to all first-line antituberculotic drugs (pyrazinamide - PZA,
isoniazid - INH, rifampicin - RIF, ethambutol - ETH, streptomycin - STR). The second group is more
treacherous. This type of resistance is called extensively or extremely drug-resistant TB (XDR-TB)
with the resistance to the first-line anti-TB agents isoniazid and rifampicin together with the resistance
to any fluoroquinolone used in the therapy and to at least one of three injectable second-line
antituberculotic drugs (amikacin, kanamycin or capreomycin) [3]. The last and the latest category was
the most dreaded and was called totally drug-resistant TB (TDR-TB) and the first case was recorded in
India [4]. These mycobacterial strains were resistant to all current known therapy. Nowadays, this
group has disappeared with the approval of bedaquiline for therapy of resistant forms of tuberculosis.
Another problem is connected with the HIV pandemic. These two infectious diseases are influencing
each other in a synergic way so this has resulted in efforts to develop new anti-tubercular agents.
This work deals with a microwave-assisted synthesis of pyrazinamide analogues with potential
antimycobacterial activity. It is caused by the fact that pyrazinamide is counted among the first-line
anti-tuberculosis drugs used in current therapy. Its unique ability to kill the dormant forms of
Mycobacterium tuberculosis is crucial in shortening the time needed for the treatment, so PZA has
sterilizing activity especially in combination with rifampicin [5].
PZA itself has multiple mechanisms of action. The first described was the activation of this prodrug
via the enzyme pyrazinamidase (EC 3.5.1.19) to form pyrazinoic acid (POA). This metabolite causes a
lowering of the inner compartment pH in mycobacterial cells. This leads to inhibition of membrane
transport and then to cellular death [6–8]. The gene encoding this enzyme is called pncA gene and its
mutation is responsible for the origin of mycobacterial resistance to PZA [9].
The second mechanism of action is connected with fatty acid synthase I (FAS I) (EC 2.3.1.85). It is
suggested that the disruption of metabolism can be caused by inhibition of the cell membrane

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653
synthesis, which is essential for the survival of Mycobacteria, but this mechanism was mainly rejected
for PZA itself by Boshoff because there is only low inhibition [10]. On the other hand, the PZA
analogues such as 5-chloropyrazinamide, esters of pyrazinoic acid and esters of 5-chloropyrazinoic
acid were proven to act in this way [11–13].
Recent research has suggested a novel mechanism of action of PZA - inhibition of trans-translation.
This process is vital for survival and virulence of Mycobacteria and its inhibition leads to blockage of the
proteosynthetic apparatus in ribosomes and to cellular death. These assumptions were proven by
Zhang et al. [14].
Although PZA is the first-line antituberculotic drug, it was found that this molecule has exhibited
other interesting biological activities such as antifungal, antibacterial, antiviral and antineoplastic
effects [15–20].
There is another application of PZA derivatives that can be used in agriculture. The most successful
pyrazine derivative diquat-dibromide (6,7-dihydrodipyrido[1,2-a:2',1'-c]pyrazinediium-dibromide),
a non-selective, contact herbicide, which has been used to control many submerged and floating
aquatic macrophytes, was found to interfere with the photosynthetic process by releasing strong
oxidizers that rapidly disrupt and inactivate cells and cellular functions (at present banned in many EU
countries) [21]. Many structural variations of pyrazine compounds with herbicidal properties can be found
in the patent literature [22–25]. However, several pyrazine derivatives were also described as inhibitors of
Hill reaction which inhibit photosynthetic electron transport (PET) in photosystem (PS) 2 [18,26].
The site of action of these PET inhibitors in the photosynthetic apparatus was situated predominantly
on the donor side of PS2, in the section between oxygen evolving complex and intermediate D,
i.e., tyrosine radical (TyrD•) occurring on the 161st position in D2 protein. Consequently, these
compounds can be considered as PS2 herbicides which could have ultimately adverse effect on plant
growth. In general, the PET-inhibiting effectiveness of pyrazine derivatives depends on compound
lipophilicity and σ Hammett constants of individual substituents. Hosseini et al. studied the electronic
and structural descriptors, which are the main factors for the cytotoxicity in the series of substituted
N-phenylpyrazine-2-carboxamides [27].
This study is focused on preparation of N-substituted structural and functional derivative of PZA
(5-chloro-6-methylpyrazine-2,3-dicarbonitrile) that was treated with ring-substituted benzylamines
using the advantages of a microwave reactor. It should be stressed that this type of syntheses has
become popular due to its higher yields, shorter reaction times or solvent savings in comparison with
conventional organic syntheses [28]. One of the main advantages is the heating. It is uniform through
the volume of the sample and the microwaves usually interact with molecules themselves not vessel
sides. Another benefit is connected with the temperature reached by the solvent used. The final
temperature is usually far higher than the standard boiling point of the solvent when using over-
pressurized systems. It is reached and bypassed in seconds. Improved heating usually leads to higher
yields and shorter reaction times. There is one limitation for choosing the conditions. It is the polarity
of the solvent when the non-polar solvents cannot be used in the way the polar ones can be. If the polar
solvent is used in the reaction, there is a direct coupling of microwaves with molecules. More polar
solvents have greater ability to interact with microwave radiation. Using the solvents with low polarity
(low absorbers) leads to longer times of heating and reaction. On the contrary, if the reagents
themselves are polar it could lower the disadvantages of non-polar solvents. Finally there are new

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approaches to microwave accelerated methods using ionic liquids or solid phase reactions (adsorption
on mineral oxides, phase transfer catalysis, neat reactions) [29]. Microwave assisted condensation in
polar solvent is used in this work to accelerate the aminodehalogenation reaction. The conditions for
the synthesis were proven experimentally. Antimycobacterial activity of the all prepared compounds
was determined and compounds were evaluated also in relation to inhibition of photosynthetic electron
transport (PET) in spinach (Spinacia oleracea L.) chloroplasts. The structure-activity relationships
between the chemical structure and in vitro biological activities of evaluated compounds are discussed.
2. Results and Discussion
2.1. Chemistry
The starting compound 5-chloro-6-methylpyrazine-2,3-dicarbonitrile and the final compounds 1–15
were synthesized according to the general procedure shown in Scheme 1. The aminodehalogenation
reaction of this starting compound and ring-substituted benzylamines yielded a series of 15 secondary
amines of which 14 were novel. 5-(Benzylamino)-6-methylpyrazine-2,3-dicarbonitrile (6) was
previously synthesised by Takematsu et al. and the reported melting point was 118–119 °C [30]. The
compound we obtained melted at 128.7–130.7 °C. This difference can be caused by the mode of
crystallization. All reactions were done using microwave reactor with focused field and yields were in
the range between 17% and 62%. Lower yields were caused by the purification using preparative
chromatography and recrystallization. It is also known that 3-nitro substitution, for which the yield was
the lowest, is counted among the electron-withdrawing groups reducing the basicity of the amine
nitrogen. Obtained analytical data were fully consistent with the proposed structures. Table 1 shows the
substituents and other data of the synthesized compounds.
Scheme 1. Synthesis of starting compound [30] and microwave assisted aminodehalogenation
reaction resulting in a series of compounds 1–15.

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Table 1. Experimentally determined values of lipophilicity log k, calculated values of log P,
655
electronic Hammett’s σ parameters and π parameters, 50% inhibition concentration
IC50 [μmol/L] values related to PET inhibition in spinach chloroplasts in comparison with
3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) standard and in vitro antimycobacterial
activity against M. tuberculosis H37Rv (minimal inhibition concentration (MIC) [μg/mL])
of compounds 1–15 compared to pyrazinamide (PZA) and isoniazid (INH) standards.
IC50
[μmol/L]
114.0
37.7
16.4
104.7
464.6
-
MIC M.tuberculosis
Compound
R
log P
log k
σ
π
H37Rv [μg/mL]
1
2
2-CH3
3-CF3
3,4-Cl
4-CH3
4-OCH3
H
3.41
3.84
4.04
3.41
2.8
0.4668
0.5369
0.7538
0.5157
0.2820
0.2994
−0.17
0.43
0.1674
0.2375
0.4544
0.2163
>100
12.5
6.25
25
3
0.60
4
−0.17
5
−0.27 −0.0174
>100
25
6
2.92
0
0
7
4-NH2
3-Cl
2.12 −0.2014 −0.15 −0.5008
-
25
8
3.48
3.48
3.08
3.84
3.84
0.5172
0.4663
0.3042
0.5626
0.4865
0.3699
0.1808
0.5384
0.37
0.22
0.06
0.51
0.51
−0.55
0.71
0.23
0.2178
0.1669
0.0048
0.2632
0.1871
0.0705
−0.1186
0.2390
57.4
79.0
195.6
39.6
71.6
-
12.5
6.25
12.5
6.25
12.5
25
9
2-Cl
10
11
12
13
14
15
PZA
INH
DCMU
2-F
4-CF3
2-CF3
2,4-OCH3 2.67
3-NO2
4-Cl
2.71
3.48
487.4
86.5
-
12.5
12.5
12.5
1.5625
-
-
1.9
π = log k(substituted) – log k(unsubstituted).
2.2. Calculated and Experimentally Set Lipophilicity
Lipophilicity is one of the most important factors that can affect the biological effect of the
compound. It is connected with the membrane transport and other biological processes and it is also
connected with solubility in the media. This physical-chemical property can be set experimentally. In
this work we have used the Reversed Phase - High Performance Liquid Chromatography (RP-HPLC)
methodology for measuring the capacity factors k with the calculation of log k that can be correlated to
calculated values of lipophilicity log P (resp. Clog P). These calculations were carried out by using PC
program CS ChemBioDraw Ultra 13.0. The results of these measurements are shown in the Table 1.
The lowest lipophilicity was shown by compound 7 (R = 4-NH2) and on the contrary, compound 3
(R = 3,4-Cl) was the most lipophilic compound of this series. Lipophilicity, based on log k values,
increased for substituents in the benzyl part of the molecule as follows: 4-NH2 < 3-NO2 < 4-OCH3 < H
< 2-F < 2,4-OCH3 < 2-Cl < 2-CH3 < 2-CF3 < 4-CH3 < 3-Cl < 3-CF3 < 4-Cl < 4-CF3 < 3,4-Cl
The dependence of the measured log k parameters on the calculated log P values showed an
approximate linearity, which is shown in Figure 1, and the corresponding correlation can be expressed
by the following regression equation:

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log k = −0.810 × (±0.150) + 0.371 × (±0.045) × log P
(1)
r = 0.915, s = 0.092, F = 66.9, n = 15
Figure 1. Plot of experimentally measured log k parameter on calculated log P (CS
ChemBioDraw Ultra version 13.0).
2.3. Biological Assays
2.3.1. Antimycobacterial In Vitro Screening
All prepared compounds were tested against four strains of Mycobacterium. These were
M. tuberculosis and three non-tuberculosis strains. The most active substances against M. tuberculosis
were compounds 3, 9 and 11. Their activity expressed as minimal inhibition concentration (MIC) was
6.25 µg/mL and the activities of standards were 12.5 µg/mL for PZA and 1.5625 µg/mL for INH.
Nearly the whole series showed activity against M. tuberculosis H37Rv, which was in the range from
25 to 6.25 µg/mL, but compounds 11 and 12 were also active against other strains and both of them
were active against M. avium 152. These strains are usually resistant or unsusceptible to pyrazinamide.
This is the reason why INH was chosen as second standard. Obtained results can be compared with
other synthesised compounds and a comparison can be drawn between more mycobacterial strains not
only M. tuberculosis.
As shown in Figure 2, dependence of antimycobacterial activity on lipophilicity expressed by π
constant (log k) as well as on the σ constant of the R substituent was observed. The most active
compounds (MIC = 6.25 µg/mL) were 3 (R = 3,4-Cl), 9 (R = 2-Cl) and 11 (R = 4-CF3) and were
mentioned above. All of these compounds are situated in the right upper quadrant of the Craig’s plot.
Further groups are represented by compounds 2 (R = 3-CF3), 8 (R = 3-Cl), 10 (R = 2-F), 12 (R = 2-CF3),
14 (R = 3-NO2) and 15 (R = 4-Cl) showing moderate activity with MIC = 12.5 µg/mL and compounds
4 (R = 4-CH3), 6 (R = H), 7 (R = 4-NH2) and 13 (R = 2,4-OCH3) with MIC = 25 µg/mL. Low
antimycobacterial activity with MIC >100 µg/mL was exhibited by compounds 1 (R = 2-CH3) and 5
(R = 4-OCH3). It can be stated that the activity is more dependent on π constant than on σ constant.
On the other hand this dependence is not unambiguous. However, it is clear that the lipophilicity is

Molecules 2014, 19
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important for antimycobacterial activity and the most suitable ring substituents are electron-withdrawing
groups such as halogen or trifluoromethyl moieties.
Figure 2. Dependence of antimycobacterial activity of studied compounds on the π
constant (log k) as well as on the σ constant of R substituent.
2.3.2. Antimycobacterial In Vitro Screening Against M. smegmatis
This evaluation was performed against fast-growing Mycobacterium smegmatis using isoniazid and
ciprofloxacin as standards. None of the compounds showed activity against this mycobacterial strain. This
may be caused by the fact that this fast-growing mycobacterium is less susceptible to antibiotic treatment.
2.3.3. Antifungal and Antibacterial In Vitro Screening
This evaluation was performed in order to obtain results for antifungal and antibacterial activity
against eight fungal strains and eight bacterial strains. None of the prepared compounds showed
antibacterial activity against the tested strains. On the contrary, compounds 7 (MIC = 500 µmol/L),
10 (MIC = 500 µmol/L) and 12 (MIC = 125 µmol/L) exhibited activity against Trichophyton
mentagrophytes but in comparison to standards, this activity was negligible. It can be also caused by
the bigger susceptibility of this fungal strain being evaluated.
2.3.4. Herbicidal Activity of Prepared Compounds
The studied compounds inhibited photosynthetic electron transport in spinach chloroplasts (Table 1).
The PET inhibiting activity of studied compounds 1–15 expressed by IC50 value varied from
16.4 μmol/L (3) to 487.0 μmol/L (14). The inhibitory activity of the most active compounds 3 was 8.6
times lower than that of the standard DCMU (IC50 = 1.9 μmol/L), a well-known PS2 herbicide.

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Compounds 6 (R = H), 7 (R = 4-NH2) and 13 (R = 2,4-OCH3) were inactive and IC50 values related to
PET inhibition could not be determined. It can be stated that the inhibitory activity increases linearly
with increasing lipophilicity of the compounds based on the dependence of PET inhibiting activity of
studied dicarbonitriles 1–15 on log P (Figure 3A) and log k (Figure 3B).
Figure 3. Dependence of PET inhibiting activity on the log P (A) or log k (B) of
compounds 1–15.
5.0
B
A
4.5
3
4.0
3.5
3.0
2.5
2.0
2
12
11
15
4
8
1
9
10
5
2.5
3.0
3.5
4.0
log P
4.5
5.0
5.5
Also if compound 14 (R = 3-NO2) was excluded, the dependence of PET inhibiting activity on the
Hammett constant σ of R substituent showed again linear dependence (Figure 4). A linear increase of
PET-inhibiting activity was observed in the range of σ from -0.15 (7; R = 4-NH2) to 0.6 (3; R = 3,4-Cl).
Figure 4. Dependence of PET inhibiting activity of compounds 1–15 on the σ constant of
the R substituent.
The correlation between log (1/IC50) [mol/L] and log P or between log (1/IC50) [mol/L] and σ
constant of R substituent could be expressed by the following equations:
pI50 = 0.577 × (± 0.882) + 1.002 × (± 0.250) log P
(2)
r = 0.950, s = 0.127, F = 82.5, n = 11

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pI50 = 3.881 × (± 0.182) + 1.051 × (±0.503) σ
(3)
r = 0.844, s = 0.217, F = 22.34, n = 11
The use of both the above mentioned descriptors (log P and σ) in a multilinear correlation did not
improve the results of statistical analysis:
pI50 = 0.949 × (± 1.669) + 0.887 × (± 0.504) log P + 0.160 × (± 0.594) σ
(4)
r = 0.952, s = 0.131, F = 38.6, n = 11
Similarly, better results of statistical analysis were obtained for the correlation between log (1/IC50)
[mol/L] and log k than for multilinear correlation using two descriptors (log k and σ).
pI50 = 2.703 (±0.414) + 2.835 (±0.816) log k
(5)
r = 0.934, s = 0.144, F = 61.8, n = 11
pI50 = 2.997 × (± 0.331) + 2.034 × (± 0.738) log k + 0.481 (0.303) 
(6)
r = 0.976 s = 0.093 F = 80.2 n = 11
These results indicate that lipophilicity of the compound is determining for PET-inhibiting activity
of the studied N-substituted 5-amino-6-methylpyrazine-2,3-dicarbonitriles. Lee et al. focused on the
search for the minimum structural requirements for herbicidal evaluation of 5-(R1)-6-(R2)-N-(R3-
phenyl)-pyrazine-2-carboxamide analogues as a new class of potent herbicides in a previous paper [31].
Based on IC50 values of 19 pyrazine derivatives related to PET inhibition in spinach chloroplasts which
were published by Dolezal et al. [15], Lee derived and discussed quantitatively 3D-QSARs models
between the substituents (R1–R3) changes of the analogues and their herbicidal activity using
comparative molecular field analysis (CoMFA) and comparative molecular similarity indice analysis
(CoMSIA) methods. It was predicted that the herbicidal activity increases when large steric
substituents were introduced to one part of the ortho- and meta- positions on the N-phenyl ring as
R3- substituent and small steric substituents on the other part. The same 19 pyrazine derivatives with
herbicidal activity were also subjected to the two dimensional quantitative structure activity
relationships studies using Vlife Molecular Design 3.0 module which contains various combinations of
thermodynamic, electronic, topological and spatial descriptors [32]. It was found that decreasing of
number of hydrogen bond acceptor atoms and reduction the any atoms (single, double or triple
bonded) separated from any oxygen atom by a seven bond distance in a molecule could be helpful for
designing more potent herbicidal agents.
Because the studied N-substituted 5-amino-6-methylpyrazine-2,3-dicarbonitriles were found to
inhibit the Hill reaction, they can be considered as photosystem 2 (PS2) inhibitors, i.e., PS2 herbicides
which ultimately adversely affect growth of weeds as well as agricultural plants. The PS2 inhibitors
can act on the donor and/or the acceptor side of PS2. Using EPR spectroscopy it was found that
N-phenylpyrazine-2-carboxamides interacted with the D intermediate which is situated at 161st
position in D2 protein occurring on the donor side of PS2. Due to interaction of these pyrazine
derivatives with this part of PS2, the photosynthetic electron transport from the oxygen evolving
complex to the reaction centre of PS2 was impaired and consequently, the electron transport between
PS2 and PS1 was inhibited [33]. Use of an artificial electron-donor, 1,5-diphenylcarbazide (DPC),

Molecules 2014, 19
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acting in the Z/D intermediate is suitable to estimate whether the studied PET inhibitor acts only on
the donor or also on the acceptor side of PS2. Complete restoration of PET after DPC addition to
chloroplasts activity of which was inhibited by an inhibitor, indicates that PET between the core of
PS2 (P680) and the secondary quinone acceptor QB was not affected by this inhibitor. Consequently,
its site of inhibitory action is situated on the donor side of PS2. However, upon addition of DPC to the
studied dicarbonitriles only partial restoration of PET was observed (up to 85% of the control) and
therefore it could be assumed that the studied compounds block PET not only by interaction with
proteins occurring in the section between the oxygen evolving complex (OEC) and the Z/D
intermediate but to PET inhibition contributes also their interaction with some constituents of
photosynthetic apparatus on the acceptor side of PS2. Similar results were obtained previously with
5-tert-butyl-N-(3-hydroxy-4-chlorophenyl)pyrazine-2-carboxamide and 5-tert-butyl-6-chloro-N-(3-
fluorophenyl)pyrazine-2-carboxamide [33].
Compounds 1–15 affected the chlorophyll a (Chla) fluorescence in spinach chloroplasts. As shown
in Figure 5, the intensity of the Chla emission band at 686 nm belonging to the pigment–protein
complexes in photosystem 2 decreased in the presence of compound 3 [34]. This finding indicates a
perturbation of the Chla–protein complexes in the thylakoid membrane caused by the tested
compound. Similar Chla fluorescence decrease in spinach chloroplasts was observed previously
with several PET inhibitors, i.e., N-benzylpyrazine-2-carboxamides [35], ring-substituted
3-hydroxynaphthalene-2-carboxanilides [36] and 1-hydroxynaphthalene-2-carboxanilides [37],
2-hydroxynaphthalene-1-carboxanilides [38] and ring-substituted 4-arylamino-7-chloroquinolinium
chlorides [39].
Figure 5. Fluorescence emission spectra of Chla of untreated spinach chloroplasts and
chloroplasts treated with 0, 0.13, 0.25 and 0.51 mmol/L of compound 3 (R = 3,4-Cl) (the curves
from top to bottom); excitation wave length λ = 436 nm; chlorophyll concentration 10 mg/L.
120
100
80
60
40
20
0
650
660
670
680
690
700
710
 [nm]
3. Experimental
3.1. General
All the chemicals used for preparation of starting compound and final products were purchased
from Sigma-Aldrich (Sigma-Aldrich, St. Louis, MO, USA) and were reagent or higher grade of purity.
Starting compound was prepared according to proven methodology of conventional organic synthesis.

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The final aminodehalogenation reactions were performed in CEM Discover microwave reactor with
focused field (CEM Corporation, Matthews, NC, USA) connected to the Explorer 24 autosampler
(CEM Corporation) and this equipment was running under CEM’s Synergy™ software for monitoring
the progress of reactions. The reaction progress was checked by Thin Layer Chromatography (TLC)
(Alugram® Sil G/UV254, Machery-Nagel, Postfach, Germany) using 254 nm wavelength UV
detection. All the obtained products were purified by crystallization or by preparative flash
chromatography (CombiFlash® Rf, Teledyne Isco Inc., Lincoln, NE, USA), using gradient elution with
hexane (LacheNer, Neratovice, Czech Republic) and ethyl acetate (Penta, Prague, Czech Republic) as
mobile phases. Silica gel (0.040–0.063 nm, Merck, Darmstadt, Germany) was used as the stationary
1
phase. NMR spectra were recorded on Varian Mercury–VxBB 300 (299.95 MHz for H and
1
75.43 MHz for 13C) or Varian VNMR S500 (499.87 MHz for H and 125.71 MHz for 13C)
spectrometers (Varian Corporation, Palo Alto, CA, USA). Chemical shifts were reported in ppm (δ)
13
and were applied indirectly to tetramethylsilane as a signal of solvent (2.49 for 1H and 39.7 for C in
DMSO-d6). Infrared spectra were recorded with spectrometer FT-IR Nicolet 6700 (Thermo Scientific,
Waltham, MA, USA) using attenuated total reflectance (ATR) methodology. Melting points were
assessed by SMP3 Stuart Scientific (Bibby Scientific Ltd., Staffordshire, UK) and were uncorrected.
Elemental analyses were measured with EA 1110 CHNS Analyzer (Fisons Instruments S. p. A., Carlo
Erba, Milano, Italy). Calculation of electronic Hammett’s σ parameters was carried out on the software
ACD/Percepta ver. 2012 (Advanced Chemistry Development, Inc., Toronto, ON, Canada).
3.2. Starting Compound and Final Products Synthesis
The starting compound 5-chloro-6-methylpyrazine-2,3-dicarbonitrile was synthesized in a two-step
reaction according to the reported methodology [30]. The first step was a condensation reaction
between diaminomaleonitrile (0.025 mol) and pyruvic acid (0.025 mol), which were dissolved in
methanol (60 mL), and hydrochloric acid (10 mL, 15%) was added dropwise. It takes two hours to
react at room temperature. After the evaporation of two thirds of the solvent, hot water (80 mL) was
added and then the rest of methanol was evaporated in vacuo. The whole mixture was cooled to 5 °C to
initiate the crystallization. The product was collected by suction, dried overnight and subsequently
chlorinated with phosphoryl chloride. Product (0.015 mol) was again dissolved in POCl3 (0.060 mol)
and cooled to 0 °C. Pyridine (0.020 mol) was added dropwise and after the termination of the
exothermic reaction, the mixture was heated to 90 °C for 2 h. Excess POCl3 was evaporated in vacuo
and the rest of product was extracted into toluene three or four times, the toluene was evaporated and
then the crude product was recrystallized from chloroform. The starting compound (1.12 mmol) was
finally treated with 15 variously ring-substituted benzylamines (2.24 mmol) and all these
aminodehalogenation reactions took place in the microwave reactor. The conditions used for
microwave syntheses were as follows—150 °C, 30 min, 120 W, methanol as a solvent, pyridine as a
base and were set experimentally. The reaction was monitored by TLC using hexane/ethyl acetate 2:1
mixture as mobile phase. The final compounds were purified using flash column chromatography with
gradient elution using a hexane/ethyl acetate system and if necessary recrystallization from a mixture
of ethanol and water.

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3.3. Analytical Data of the Prepared Compounds
5-Methyl-6-[(2-methylbenzyl)amino]pyrazine-2,3-dicarbonitrile (1). Light orange crystalline solid.
Yield 47.9%; M.p. 152.1–152.9 °C; IR (ATR-Ge, cm−1): 3381m (-NH-), 2226m (-CN), 1570vs, 1521s,
1
1403vs, 1349m (arom.); H-NMR (500 MHz) δ 8.61 (1H, bs, NH), 7.25–7.10 (4H, m, H3', H4', H5',
13
H6'), 4.56 (2H, s, NCH2), 2.47 (3H, s, CH3), 2.33 (3H, s, CH3); C-NMR (125 MHz) δ 152.9, 147.5,
136.0, 135.6, 130.2, 130.1, 127.5, 127.2, 125.9, 117.4, 115.7, 114.8, 42.5, 21.3, 19.0; Elemental
analysis: calc. for C15H13N5 (MW 263.12): 68.42% C, 4.98% H, 26.60% N; found 68.22% C,
5.17% H, 26.44% N.
5-Methyl-6-{[3-(trifluoromethyl)benzyl]amino}pyrazine-2,3-dicarbonitrile (2). Yellow-orange crystalline
solid. Yield 51.6%; M.p. 158.5–159.7 °C (decomp.); IR (ATR-Ge, cm−1): 3377m (-NH-), 2227m (-CN),
1570vs, 1521s, 1402vs, 1353m, 1324vs (arom.), 1128vs (-C-F); 1H-NMR (300 MHz) δ 8.75 (1H, bs, NH),
7.77–7.60 (1H, m, H2'), 7.68–7.50 (3H, m, H4', H5', H6'), 4.69 (2H, d, J = 4.6 Hz, NCH2), 2.46 (3H, s,
CH3); 13C-NMR (75 MHz) δ 152.9, 147.7, 139.6, 131.8, 130.0, 129.6, 129.2 (q, J = 31.5 Hz), 124.5 (q,
J = 4.0 Hz), 124.4 (q, J = 272.3 Hz), 124.0 (q, J = 4.0 Hz), 117.7, 115.6, 114.8, 44.0, 21.2; Elemental
analysis: calc. for C15H10F3N5 (MW 317.27): 56.78% C, 3.18% H, 22.07% N; found 56.59% C, 3.30%
H, 21.93% N.
5-[(3,4-Dichlorobenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (3). Light yellow crystalline solid.
Yield 60.9%; M.p. 154.4–156.2 °C; IR (ATR-Ge, cm−1): 3329m (-NH-), 2227m (-CN), 1568vs, 1516s,
1
1466m, 1402vs (arom.); H-NMR (300 MHz) δ 8.69 (1H, bs, NH), 7.61 (1H, d, J = 1.9 Hz, H2'), 7.57
(1H, d, J = 8.2 Hz, H5'), 7.33 (1H, dd, J = 8.2 Hz, J = 1.9 Hz, H6'), 4.59 (2H, s, NCH2), 2.46 (3H, s,
CH3); 13C-NMR (75 MHz) δ 152.8, 147.8, 139.4, 131.1, 130.6, 130.0, 129.8, 129.6, 127.9, 117.8,
115.6, 114.8, 43.3, 21.2; Elemental analysis: calc. for C14H9Cl2N5 (MW 318.16): 52.85% C, 2.85% H,
22.01% N; found 52.71% C, 3.05% H, 21.88% N.
5-Methyl-6-[(4-methylbenzyl)amino]pyrazine-2,3-dicarbonitrile (4). Light yellow crystalline solid.
Yield 60.5%; M.p. 140.8–142.3 °C; IR (ATR-Ge, cm−1): 3370s (-NH-), 2223m (-CN), 1576vs, 1519s,
1438m, 1400vs, 1351s (arom.); 1H-NMR (300 MHz) δ 8.68 (1H, bs, NH), 7.24–7.18 (2H, m, AA', BB',
H2', H6'), 7.14–7.09 (2H, m, AA', BB', H3', H5'), 4.55 (2H, bs, NCH2), 2.44 (3H, s, CH3), 2.26 (3H, s,
CH3); 13C-NMR (75 MHz) δ 152.8, 147.5, 136.4, 135.0, 130.1, 128.1, 127.5, 117.3, 115.7, 114.9, 44.1,
21.2, 20.8; Elemental analysis: calc. for C15H13N5 (MW 263.30): 68.42% C, 4.98% H, 26.60% N;
found 68.30% C, 5.17% H, 26.43% N.
5-[(4-Methoxybenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (5). Ochre crystalline solid. Yield
61.3%; M.p. 153.0–154.2 °C (decomp.); IR (ATR-Ge, cm−1): 3345m (-NH-), 2948w (-OCH3), 2223m
1
(-CN), 1585s, 1570vs, 1511vs, 1462m, 1403vs (arom.); H-NMR (300 MHz) δ 8.66 (1H, bs, NH),
7.29–7.23 (2H, m, AA', BB', H2', H6'), 6.90–6.84 (2H, m, AA', BB', H3', H5'), 4.52 (2H, bs, NCH2),
3.71 (3H, s, OCH3), 2.43 (3H, s, CH3); 13C-NMR (75 MHz) δ 158.6, 152.8, 147.4, 130.1, 129.9, 129.0,
117.3, 115.7, 114.9, 113.9, 55.2, 43.8, 21.2; Elemental analysis: calc. for C15H13N5O (MW 279.30):
64.51% C, 4.69% H, 25.07% N; found 64.35% C, 4.81% H, 24.84% N.

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5-(Benzylamino)-6-methylpyrazine-2,3-dicarbonitrile (6) [30]. Yellow-orange crystalline solid. Yield
53.3%; M.p. 128.7–130.7 °C (described in the literature 118–119 °C); IR (ATR-Ge, cm−1): 3404m
1
(-NH-), 2228m (-CN), 1564vs, 1508vs, 1454m, 1400vs, 1357s (arom.); H-NMR (300 MHz) δ 8.72 (1H,
bs, NH), 7.37–7.20 (5H, m, H2', H3', H4', H5', H6'), 4.61 (2H, d, J = 3.3 Hz, NCH2), 2.45 (3H, s,
CH3); 13C-NMR (75 MHz) δ 152.9, 147.5, 138.1, 130.1, 128.5, 127.5, 127.2, 117.4, 115.7, 114.9, 44.3,
21.2; Elemental analysis: calc. for C14H11N5 (MW 249.27): 67.46% C, 4.45% H, 28.10% N; found
67.21% C, 4.63% H, 27.95% N.
5-[(4-Aminobenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (7). Brown crystalline solid. Yield
37.2%; M.p. 154.9–156.5 °C; IR (ATR-Ge, cm−1): 3413m (-NH2), 3376m (-NH-), 2234m (-CN), 1572vs,
1
1519vs, 1440m, 1402vs, 1352s (arom.); H-NMR (300 MHz) δ 8.54 (1H, bs, NH), 7.04–6.94 (2H, m,
AA', BB', H2', H6'), 6.54–6.45 (2H, m, AA', BB', H3', H5'), 4.97 (2H, bs, NH2), 4.41 (2H, d, J = 3.8 Hz,
NCH2), 2.41 (3H, s, CH3); 13C-NMR (75 MHz) δ 152.7, 148.0, 147.3, 130.2, 128.7, 124.7, 117.0,
115.8, 114.9, 113.9, 44.2, 21.2; Elemental analysis: calc. for C14H12N6 (MW 264.29): 63.62% C,
4.58% H, 31.80% N; found 63.48% C, 4.45% H, 31.65% N.
5-[(3-Chlorobenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (8). Yellow crystalline solid. Yield
60.2%; M.p. 151.0–151.8 °C; IR (ATR-Ge, cm−1): 3306m (-NH-), 2248m (-CN), 1567vs, 1513vs, 1468m,
1
1401vs, 1351s (arom.); H-NMR (300 MHz) δ 8.70 (1H, t, J = 5.9 Hz, NH), 7.43–7.39 (1H, m, H2'),
7.38–7.27 (3H, m, H4', H5', H6'), 4.61 (2H, d, J = 5.9 Hz, NCH2), 2.46 (3H, s, CH3); 13C-NMR
(75 MHz) δ 152.9, 147.7, 140.7, 133.2, 130.4, 130.0, 127.4, 127.2, 126.2, 117.7, 115.6, 114.9, 43.8,
21.2; Elemental analysis: calc. for C14H10ClN5 (MW 283.72): 59.27% C, 3.55% H, 24.68% N; found
59.08% C, 3.71% H, 24.57% N.
5-[(2-Chlorobenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (9). Dark orange crystalline solid.
Yield 24.7%; M.p. decomp.; IR (ATR-Ge, cm−1): 3381m (-NH-), 2227m (-CN), 1570vs, 1521s, 1474m,
1
1440m, 1401s, 1351s (arom.); H-NMR (300 MHz) δ 8.68 (1H, bs, NH), 7.51–7.24 (4H, m, H3', H4',
13
H5', H6'), 4.66 (2H, s, NCH2), 2.49 (3H, s, CH3); C-NMR (75 MHz) δ 153.0, 147.7, 134.9, 132.3,
130.0, 129.4, 129.1, 128.9, 127.4, 117.8, 115.6, 114.8, 42.4, 21.2; Elemental analysis: calc. for
C14H10ClN5 (MW 283.72): 59.27% C, 3.55% H, 24.68% N; found 59.08% C, 3.68% H, 24.90% N.
5-[(2-Fluorobenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (10). Dark yellow crystalline solid.
Yield 60.8%; M.p. 134.8–136.3 °C; IR (ATR-Ge, cm−1): 3377m (-NH-), 2231m (-CN), 1573vs, 1523s,
1
1491m, 1402s, 1354s (arom.); H-NMR (300 MHz) δ 8.68 (1H, t, J = 5.3 Hz, NH), 7.42–7.10 (4H, m,
H3', H4', H5', H6'), 4.63 (2H, d, J = 5.3 Hz, NCH2), 2.46 (3H, s, CH3); 13C-NMR (75 MHz) δ 160.0 (d,
J = 244.8 Hz), 152.9, 147.6, 129.8 (d, J = 20.4 Hz), 129.8, 129.4 (d, J = 8.3 Hz), 124.6 (d, J = 17.8
Hz), 124.5 (d, J = 6.6 Hz), 117.7, 115.5 (d, J = 9.2 Hz), 115.2, 114.8, 38.3, 21.2; Elemental analysis:
calc. for C14H10FN5 (MW 267.26): 62.92% C, 3.77% H, 26.20% N; found 62.71% C, 3.59% H,
26.38% N.
5-Methyl-6-{[4-(trifluoromethyl)benzyl]amino}pyrazine-2,3-dicarbonitrile (11). Light yellow crystalline
solid. Yield 38.3%; M.p. 148.4–149.6 °C; IR (ATR-Ge, cm−1): 3397m (-NH-), 2232m (-CN), 1570vs,
1
1520s, 1422m, 1399s, 1324vs (arom.), 1114vs (-C-F); H-NMR (300 MHz) δ 8.54 (1H, t, J = 5.3 Hz,

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NH), 7.71–7.64 (2H, m, AA', BB', H2', H6'), 7.38–7.52 (2H, m, AA', BB', H3', H5'), 4.69 (2H, d,
J = 5.3 Hz, NCH2), 2.51 (3H, s, CH3); 13C-NMR (75 MHz) δ 152.9, 147.7, 143.1, 130.0, 128.2, 127.9
(q, J = 31.5 Hz), 125.4 (q, J = 3.7 Hz), 124.5 (q, J = 272.0 Hz), 117.8, 115.6, 114.8, 44.0, 21.2;
Elemental analysis: calc. for C15H10F3N5 (MW 317.27): 56.78% C, 3.18% H, 22.07% N; found 56.59%
C, 2.99% H, 21.91% N.
5-Methyl-6-{[2-(trifluoromethyl)benzyl]amino}pyrazine-2,3-dicarbonitrile (12). Yellow-orange crystalline
solid. Yield 49.1%; M.p. 157.8–159.4 °C (decomp.); IR (ATR-Ge, cm−1): 3408m (-NH-), 2230m (-CN),
1
1569vs, 1522s, 1430m, 1409s, 1398s, 1368s, 1314vs (arom.), 1114vs (-C-F); H-NMR (300 MHz) δ 8.76
(1H, bs, NH), 7.77–7.71 (1H, m, H3'), 7.64–7.43 (3H, m, H4', H5', H6'), 4.77 (2H, bs, NCH2),
13
2.51 (3H, s, CH3); C-NMR (75 MHz) δ 153.0, 147.7, 136.3, 132.9, 130.0, 128.3, 127.8, 126.4 (q,
J = 30.3 Hz), 126.1 (q, J = 6.0 Hz), 124.7 (q, J = 274.0 Hz), 118.0, 115.5, 114.7, 41.1, 21.2; Elemental
analysis: calc. for C15H10F3N5 (MW 317.27): 56.78% C, 3.18% H, 22.07% N; found 56.62% C, 3.08%
H, 22.00% N.
5-[(2,4-Dimethoxybenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (13). Ochre crystalline solid.
Yield 62.3%; M.p. 151.6–152.9 °C; IR (ATR-Ge, cm−1): 3336m (-NH-), 2924w (-OCH3), 2224m (-CN),
1
1609s, 1574vs, 1509vs, 1467m, 1440s, 1405vs (arom.); H-NMR (300 MHz) δ 8.45 (1H, t, J = 5.7 Hz,
NH), 7.07 (1H, d, J = 8.2 Hz, H6'), 6.55 (1H, d, J = 2.5 Hz, H3'), 6.43 (1H, dd, J = 8.2 Hz, J = 2.5 Hz,
H5'), 4.47 (2H, d, J = 5.7 Hz, NCH2), 3.80 (3H, s, OCH3), 3.72 (3H, s, OCH3), 2.44 (3H, s, CH3);
13C-NMR (75 MHz) δ 160.1, 158.1, 153.0, 147.4, 130.2, 128.8, 117.3, 117.2, 115.8, 114.9, 104.6,
98.5, 55.7, 55.4, 39.5, 21.3; Elemental analysis: calc. for C16H15N5O2 (MW 309.32): 62.13% C, 4.89%
H, 22.64% N; found 62.36% C, 5.01% H, 22.52% N.
5-Methyl-6-[(3-nitrobenzyl)amino]pyrazine-2,3-dicarbonitrile (14). Orange-red crystalline solid. Yield
17.2%; M.p. decomp.; IR (ATR-Ge, cm−1): 3394m (-NH-), 2231m (-CN), 1571vs, 1547m, 1524vs, 1478m,
1430m, 1396s, 1366s, 1348vs (arom.); 1H-NMR (300 MHz) δ 8.79 (1H, t, J = 5.8 Hz, NH), 8.23 (1H, s,
H2'), 8.11 (1H, d, J = 7.8 Hz, H4'), 7.81 (1H, d, J = 7.8 Hz, H6'), 7.62 (1H, t, J = 7.8 Hz, H5'), 4.73
(2H, d, J = 5.8 Hz, NCH2), 2.47 (3H, s, CH3); 13C-NMR (75 MHz) δ 152.9, 148.0, 147.8, 140.6, 134.4,
130.0, 130.0, 122.5, 122.3, 117.9, 115.6, 114.8, 43.8, 21.2; Elemental analysis: calc. for C14H10N6O2
(MW 294.27): 57.14% C, 3.43% H, 28.56% N; found 56.93% C, 3.64% H, 28.56% N.
5-[(4-Chlorobenzyl)amino]-6-methylpyrazine-2,3-dicarbonitrile (15). Brown crystalline solid. Yield
30.8%; M.p. 152.8–154.8 °C (decomp.); IR (ATR-Ge, cm−1): 3378m (-NH-), 2230m (-CN), 1570vs,
1
1521s, 1487m, 1441m, 1403s, 1347s (arom.), 804s (-C-Cl); H-NMR (500 MHz) δ 8.42 (1H, bs, NH),
7.39–7.33 (4H, m, H2', H3', H5', H6'), 4.59 (2H, s, NCH2), 2.45 (3H, s, CH3); 13C-NMR (125 MHz) δ
152.8, 147.6, 137.2, 131.8, 130.0, 129.4, 128.5, 117.6, 115.6, 114.8, 43.7, 21.2; Elemental analysis:
calc. for C14H10ClN5 (MW 283.72): 59.27% C, 3.55% H, 24.68% N; found 59.16% C, 3.65% H,
24.62% N.

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3.4. Lipophilicity HPLC Determination and Calculations
Experimental lipophilicity parameter log k was ascertained using an Agilent Technologies 1200 SL
HPLC system with a SL G1315C Diode-Array Detector, ZORBAX XDB-C18 5 μm, 4 × 4 mm, Part
No. 7995118-504 chromatographic pre-column and ZORBAX Eclipse XDB-C18 5 μm, 4.6 × 250 mm,
Part No. 7995118-585 column (Agilent Technologies Inc., Colorado Springs, CO, USA). The
separation process was controlled by Agilent ChemStation, version B.04.02 extended by spectral
module (Agilent Technologies Inc.). A solution of MeOH (HPLC grade, 70%) and H2O (HPLC-Milli-
Q Grade, 30%) was used as mobile phase. The total flow of the column was 1.0 mL/min, injection
20 μL, column temperature 30 °C. Detection wavelength λ= 210 nm and monitor wavelength
λ= 270 nm were chosen for this measurement. The KI methanol solution was used for the dead time
(TD) determination. Retention times (TR) of synthesized compounds were measured in minutes. The
capacity factors k were calculated using Microsoft Excel according to formula k = (TR − TD)/TD,
where TR is the retention time of the solute and TD denotes the dead time obtained via an unretained
analyte. Log k, calculated from the capacity factor k, is used as the lipophilicity index converted to
log P scale. Values of log P and Clog P were calculated with the PC programme CS ChemBioDraw
Ultra 13.0 (CambridgeSoft, Cambridge, MA, USA).
3.5. Biological Assays
3.5.1. Antimycobacterial In Vitro Screening
Mycobacterial screening was performed against four mycobacterial stems (M. tuberculosis H37Rv
CNCTC My 331/88, M. kansasii CNCTC My 235/80, M. avium ssp. avium CNCTC My 80/72,
M. avium CNCTC My 152/73 (Czech National Collection of Type Cultures, National Institute of
Public Health, Prague, Czech Republic)) using isoniazid and pyrazinamide (Sigma-Aldrich) as
standards. Culturing medium was Sula’s semisynthetic medium (Trios, Prague, Czech Republic) with
pH 6.0. Tested compounds were dissolved in dimethylsulfoxide (DMSO) and diluted with medium to
final concentrations 100, 50, 25, 12.5, 6.25, 3.125 and 1.5625 μg/mL. The method used for this assay
was microdilution broth panel method. The final concentration of DMSO did not exceed 1% (v/v) and
did not affect the growth of Mycobacteria. The cultures were grown in Sula’s medium at 37 °C in
humid dark atmosphere. The antimycobacterial activity was determined using Alamar Blue colouring
after 14 days, resp. 6 days against M. kansasii, of incubation as MIC (µg/mL). This evaluation was
done in cooperation with Department of Clinical Microbiology, University Hospital in Hradec
Kralove, Hradec Kralove, Czech Republic.
3.5.2. Antimycobacterial In Vitro Screening Against M. smegmatis
This assay was focused on the activity against fast growing Mycobacterium smegmatis MC2155
(CIT Collection, Cork Institute of Technology, Cork, Ireland). The method used there was also
microdilution broth panel method and as the medium was used Middlebrook 7H9 Broth with 10% of
OADC supplement (Sigma-Aldrich). Tested compounds were dissolved in DMSO and medium and
the final concentrations were set as 1000, 500, 250, 125, 62.5, 31.25, 15.625 and 7.8125 µg/mL. The

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final concentration of DMSO did not exceed 2% (v/v) and did not affect the growth of M. smegmatis.
The standards used for determination of activity were isoniazid and ciprofloxacin. MIC was read after
48 h of incubation at 37 °C, addition of Alamar Blue stain was followed by 12 h of additional
incubation with this reagent. This screening was performed under the patronage of the Department of
Biological Sciences, Cork Institute of Technology, Cork, Ireland.
3.5.3. Antifungal and Antibacterial In Vitro Screenings
Antibacterial evaluation was made using the microdilution broth method in plates M27A-M1
(200+10) against eight bacterial stems from the Czech Collection of Microorganisms (Brno, Czech
Republic) or clinical isolates from Department of Clinical Microbiology, University Hospital in
Hradec Kralove (Hradec Kralove, Czech Republic) (Staphylococcus aureus CCM 4516/08,
Staphylococcus aureus H 5996/08 methicillin resistant, Staphylococcus epidermidis H 6966/08,
Enterococcus sp. J14365/08, Escherichia coli CCM 4517, Klebsiella pneumoniae D 11750/08,
Klebsiella pneumoniae J 14368/05 ESBL positive, Pseudomonas aeruginosa CCM 1961). Mueller
Hinton broth was used for the cultivation that was done in humid atmosphere at 35 °C. The readings
were made after 24 and 48 h and MIC was set as 80% inhibition of control. The standards were
neomycin, bacitracin, penicillin G, ciprofloxacin and phenoxymethylpenicillin and tested products
were dissolved in DMSO (final concentration of DMSO did not exceed 1% (v/v)) [40].
Antifungal evaluation was also accomplished with microdilution broth method. On the contrary,
there was used RPMI 1640 broth with glutamine as medium and conditions were humid and dark
atmosphere, pH 7.0 (buffered with 3-morpholinopropane-1-sulfonic acid) and 35 °C. Eight fungal
strains were used (Candida albicans ATCC 44859, Candida tropicalis 156, Candida krusei E28,
Candida glabrata 20/I, Trichosporon asahii 1188, Aspergillus fumigatus 231, Absidia corymbifera
272, Trichophyton mentagrophytes 445) together with 4 antimycotic standards amphotericin B,
voriconazole, nystatin and fluconazole. The MIC was set as 80% inhibition of control and readings were
made after 24 and 48 h (50% IC, 72 and 120 h for fibrous fungi) and tested compounds were also dissolved
in DMSO (final concentration of DMSO in medium did not exceed 2.5% (v/v)) [41].
3.5.4. Study of the Inhibition of Oxygen Evolution Rate in Spinach Chloroplasts
Chloroplasts were prepared from spinach (Spinacia oleracea L.) according to Masarovicova and
Kralova [42]. The inhibition of photosynthetic electron transport (PET) in spinach chloroplasts was
determined spectrophotometrically (Genesys 6, Thermo Scientific, Madison, WI, USA) using an
artificial electron acceptor 2,6-dichlorophenol-indophenol (DCPIP) according to Kralova et al. [43]
and the rate of photosynthetic electron transport (PET) was monitored as a photo-reduction of DCPIP.
The measurements were carried out in a phosphate buffer (0.02 mol/L, pH 7.2) containing sucrose
(0.4 mol/L), MgCl2 (0.005 mol/L) and NaCl (0.015 mol/L). The chlorophyll content was 30 mg/L in
these experiments and the samples were irradiated (~100 W/m2) from a 10 cm distance with halogen
lamp (250 W) using a 4 cm water filter to prevent warming of the samples (suspension temperature 4 °C).
The studied compounds were dissolved in DMSO due to their limited water solubility. The applied
DMSO concentration (up to 4% (v/v)) did not affect the photochemical activity in spinach chloroplasts
(PET). The inhibitory efficiency of the studied compounds was expressed as the IC50 values, i.e., molar

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concentration of the compounds causing 50% decrease in the oxygen evolution relative to the
untreated control. The comparable IC50 value for a selective herbicide 3-(3,4-dichlorophenyl)-1,1-
dimethylurea (Diurone®, DCMU) was about 1.9 μmol/L [44].
3.5.5. Study of Fluorescence of Chlorophyll a in Spinach Chloroplasts
The fluorescence emission spectra of chlorophyll a (Chla) in spinach chloroplasts were recorded on
fluorescence spectrophotometer F-2000 (Hitachi, Tokyo, Japan) using excitation wavelength λex = 436 nm
for monitoring fluorescence of Chla, excitation slit 20 nm and emission slit 10 nm. The samples were
kept in the dark 2 min before measuring. The phosphate buffer used for dilution of the chloroplast
suspension was the same as described above. Due to low aqueous solubility the compounds were
added to a chloroplast suspension in DMSO solution. The DMSO concentration in all samples was the
same as in the control (10% (v/v)). The chlorophyll concentration in chloroplast suspension
was 10 mg/L.
4. Conclusions
A series of 15 pyrazinamide derivatives (14 of them novel) was synthesized by aminodehalogenation
reactions focusing on microwave assisted synthesis. All the final compounds were characterized with
IR, NMR and other analytical data and then subjected to in vitro evaluation in order to discover their
potential antimycobacterial, antifungal, antibacterial and herbicidal activities.
The lipophilicity was measured using RP-HPLC methodology and also calculated or predicted with
the PC program CS ChemBioDraw Ultra 13.0. These values were compared and the dependence
between log k and log P was linear.
In antimycobacterial screening compounds 3 (R = 3,4-Cl), 9 (R = 2-Cl) and 11 (R = 4-CF3) showed
good activity against wild strain M. tuberculosis H37Rv (MIC = 6.25 µg/mL) compared to the standards
pyrazinamide (MIC = 12.5 µg/mL) and isoniazid (MIC = 1.56 µg/mL). Compounds 11 (R = 4-CF3) and 12
(R = 2-CF3) were active against the non-tuberculosis strains M. kansasii and M. avium as well.
Although the majority of synthesized compounds were active, there is no clear dependence between
lipophilicity and antimycobacterial activity, but it can be stated that the most potent substances were
also from the group of most lipophilic compounds and the most favourable substitutions are the
electron-withdrawing groups such as chlorine or trifluoromethyl. Activity against fast growing
Mycobacteria was also determined but no active substances were identified.
No interesting results were observed in antibacterial and antifungal screenings. Three compounds
(7 (R = 4-NH2), 10 (R = 2-F), and 15 (R = 4-Cl)) showed insignificant activity against the fungus
Trichophyton mentagrophytes, which was found to be worse compared to the standards. The rest of
substances showed no in vitro antibacterial or antifungal activity.
On the contrary, N-substituted 5-amino-6-methylpyrazine-2,3-dicarbonitriles were found to inhibit
the Hill reaction in spinach chloroplasts which indicated that these compounds act as PS2 inhibitors.
The IC50 values related to PET inhibition varied in the investigated set in the range from 16.4 μmol/L
(3; R = 3,4-Cl) to 487.0 μmol/L (14; R = 3-NO2). The lipophilicity of the compounds was determinant
for PET-inhibiting activity. The site of inhibitory action of studied compounds in the photosynthetic
apparatus is situated both on the donor and on the acceptor side of PS2. Perturbation of the

Molecules 2014, 19
668
Chla-protein complexes in the thylakoid membranes caused by the tested compounds was documented
by a decrease of the Chla emission band intensity at 686 nm belonging to the pigment-protein
complexes in photosystem 2.
Based on the obtained results it can be assumed that the antifungal and antibacterial activities of
studied compounds are not directly dependent on lipophilicity. This conclusion cannot be applied for
the herbicidal activity because there is a linear dependence between activity and lipophilicity.
Dependence between antimycobacterial activity and the benzyl substituents was found. This reliance
was expressed by the lipophilicity parameter log k resp. π constant and showed the importance of the
ring-substituted benzyl moiety.
Acknowledgments
The publication is co-financed by the European Social Fund and the state budget of the Czech
Republic. Project No. CZ.1.07/2.3.00/20.0235, the title of the project: TEAB. This study was also
supported by the Ministry of Health of Czech Republic (IGA NZ 13346), Grant Agency of Charles
University B-CH/710312, the Slovak Grant Agency VEGA, Grant No. 1/0612/11, by the Project
APVV-0061-11 and by Sanofi-Aventis Pharma Slovakia. The authors also wish to thank Ida Dufkova
for performing and evaluating the antifungal and antibacterial assays and Barbora Servusova and Jan
Zitko for English revisions.
Conflicts of Interest
The authors declare no conflict of interest.
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