Pyridine and p-nitrophenyl oxime esters with possible photochemotherapeutic activity: Synthesis, DNA photocleavage and DNA binding studies

Article abstract of DOI:10.3390/molecules21070864

Compared to standard treatments for various diseases, photochemotherapy and photo-dynamic therapy are less invasive approaches, in which DNA photocleavers represent promising tools for novel "on demand" chemotherapeutics. A series of p-nitrobenzoyl and p-

Full text of DOI:10.3390/molecules21070864

molecules
Article
Pyridine and p-Nitrophenyl Oxime Esters with
Possible Photochemotherapeutic Activity: Synthesis,
DNA Photocleavage and DNA Binding Studies
Milena Pasolli 1,†, Konstantinos Dafnopoulos 1,2,†, Nicolaos-Panagiotis Andreou 1,
Panagiotis S. Gritzapis 1, Maria Koffa 3, Alexandros E. Koumbis 4, George Psomas 2 and
Konstantina C. Fylaktakidou 1,
*
1
Laboratory of Organic, Bioorganic and Natural Product Chemistry, Molecular Biology and
Genetics Department, Democritus University of Thrace, University Campus, Dragana,
GR-68100 Alexandroupolis, Greece; milepasolli@gmail.com (M.P.); konsdafn1@mbg.duth.gr (K.D.);
nickpanandreou@hotmail.com (N.-P.A.); psgritzapis@gmail.com (P.S.G.)
Laboratory of Inorganic Chemistry, Chemistry Department, Aristotle University of Thessaloniki,
GR-54124 Thessaloniki, Greece; gepsomas@chem.auth.gr
Laboratory of Cellular Biology and Cell Cycle, Molecular Biology and Genetics Department,
Democritus University of Thrace, University Campus, Dragana, GR-68100 Alexandroupolis, Greece;
mkoffa@mbg.duth.gr
2
3
4
Laboratory of Organic Chemistry, Chemistry Department, Aristotle University of Thessaloniki,
GR-54124 Thessaloniki, Greece; akoumbis@chem.auth.gr
*
Correspondence: kfylakta@mbg.duth.gr; Tel.: +30-25510-30663
†
These authors contributed equally to this work.
Academic Editor: Jean Jacques Vanden Eynde
Received: 30 May 2016; Accepted: 28 June 2016; Published: 30 June 2016
Abstract: Compared to standard treatments for various diseases, photochemotherapy and
photo-dynamic therapy are less invasive approaches, in which DNA photocleavers represent
promising tools for novel “on demand” chemotherapeutics. A series of p-nitrobenzoyl and p-pyridoyl
ester conjugated aldoximes, amidoximes and ethanone oximes were subjected to UV irradiation
at 312 nm with supercoiled circular plasmid DNA. The compounds which possessed appropriate
properties were additionally subjected to UVA irradiation at 365 nm. The ability of most of the
compounds to photocleave DNA was high at 312 nm, whereas higher concentrations were required
at 365 nm as a result of their lower UV absorption. The affinity of selected compounds to calf-thymus
(CT) DNA was studied by UV spectroscopy, viscosity experiments and competitive studies with
ethidium bromide (EB) revealing that all compounds interacted with CT DNA. The fluorescence
emission spectra of the pre-treated EB-DNA exhibited a moderate to significant quenching in the
presence of the compounds indicating the binding of the compounds to CT DNA via intercalation as
concluded also by DNA-viscosity experiments. For the oxime esters the DNA photocleavage and
affinity studies aimed to clarify the role of the oxime nature (aldoxime, ketoxime, amidoxime) and
the role of the pyridine and p-nitrophenyl moieties both as oxime substituents and ester conjugates.
Keywords: photo-cleavage; DNA photo-cleavers; DNA binding; oxime esters; amidoxime;
aldoxime; ketoxime
1. Introduction
Photochemotherapy and photodynamic therapy are, compared to standard treatments for various
types of cancer, less invasive approaches [1–5]. The advantage of light, when used as a co-factor of a
therapeutic process, is that it provides localized photo-activation of the drug at the targeted tumor
cells. In pharmacology, the interaction of drugs with DNA is an important feature which plays a
Molecules 2016, 21, 864; doi:10.3390/molecules21070864
www.mdpi.com/journal/molecules

Molecules 2016, 21, 864
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significant role in the determination of the drug action mechanism as well as in the designing of more
efficient, specifically targeting drugs with less side effects. Thus, DNA is among the cellular targets for
photo-activated drugs, as well as for many cytotoxic anticancer agents [6,7]. Photo-activated “chemical
nucleases”, known also as “photocleavers” [ 14], interact with DNA and cause its cleavage when
8–
exited with light of a proper wavelength. The need for external chemical initiators is eliminated,
due to the fact that the chemical reaction occurs only when the mixture of the photo-cleaver and
DNA is irradiated. The excited photocleaver initiates reactions which via various mechanistic
pathways [2,4,14] may lead to single-strand (ss) DNA damage, repairable by enzymatic processes [15],
and/or double-strand (ds) DNA cleavage [13
trigger self-programmed cell death, making this approach an efficient tool for cancer therapy.
Aldoximes, ketoximes and amidoximes (Figure 1, general structures II and III, respectively)
,16,17]. The latter, which is more difficult to repair, may
I,
retain a complementary position in drug design and discovery since they are individually considered
as pharmacophores. They, additionally, participate as parent compounds in multiple transformations
leading to biologically interesting derivatives [18
Ib IIb and IIIb) have the ability to act as metal free DNA photocleavers, with aroyl conjugates shown
to be the most active ones [24 30]. In this case, homolysis of the weak N-O bond of the oximes
generates active aroyloxyl radicals (ArCOO ) able to attack DNA. On the other hand, aliphatic acyloxyl
radicals may rapidly decarboxylate, producing thus less active radicals [31 33]. Very recently, alkyl
and aryl ketoxime and amidoxime sulfonates (Figure 1, general structures IIc and IIIc, respectively)
were found to be very efficient DNA photocleavers [34 35]. The ability of oximes to cleave phosphate
bonds in nucleic acids and act as metal-free artificial nucleases has also been examined [36].
–23]. Oxime carboxylates (Figure 1, general structures
,
–
¨
–
,
Figure 1. General structures of aldoximes (I), ketoximes (II); amidoximes (III); and their derivatives
(Ib, IIb, IIIb, IIc, IIIc), which exhibit photo-cleaving activity.
Pyridine oxime derivatives exhibit a diverse biological profile, including cytotoxic, antiviral,
analgesic, cardiovascular, anti-inflammatory, antidiabetic and antispasmodic activities [37]. Additionally,
they are widely known as efficient reactivators of nerve agent inhibited acetylcholinesterases, offering a
treatment from poisoning by organophosphorous compounds [38
interest in the chemistry and biology of oximes [23 41 50] as well as in the DNA photocleavage
caused by oxime derivatives [30 34 35]. We have discovered that p-nitro-benzoyl ester conjugates
–40]. Our team has a continuous
,
–
,
,
of pyridine aldoxime and amidoxime [30], as well as p-nitrophenyl sulfonates of pyridine ethanone
oxime [34] and amidoxime [35] exemplified, among other conjugates, the best activities. The facts that
(a) p-nitrophenyl carbamidoxime sulfonates are active derivatives with good affinity to calf-thymus (CT)
DNA [35]; (b) p-nitrobenzoyl groups may exhibit their own photochemistry which could also lead to
DNA cleavage [51–54]; (c) pyridoyl moieties show activity as heterocyclic oxime ester conjugates [28];
and (d) the pyridine moieties in vitamin B6 are endogenous photosensitizers [55] have prompted us
to further investigate the role of pyridine and p-nitrophenyl moieties as oxime substituents and ester
conjugates (Figure 2, Results and Discussion) both with regards to the photocleaving ability of the
compounds, as well as their affinity to DNA.

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2. Results and Discussion
2.1. Chemistry
All derivatives (Figure 2) have been synthesized by the reaction of the proper parent compound
(amidoxime, ethanone oxime or aldoxime) with the corresponding acid chloride, in CHCl3 or THF as a
solvent, under an argon atmosphere.
Figure 2. Structures of the amidoxime p-nitrobenzoyl conjugates (
conjugates ( 10), ethanone oxime p-nitrobenzoyl conjugate (11) and pyridoyl conjugates (12), aldoxime
p-nitrobenzoyl conjugates (13–16) and aldoxime pyridoyl conjugates (17–21).
1–5), amidoxime pyridoyl
6–
All reactions performed with the various oximes furnished the products in good yields, without
the need, in most cases, of a chromatographic purification. The structure of the new compounds was
fully assigned from their spectral data. Additionally, all compounds were found to absorb UV light at
least partially over 300 nm, as it was deduced from their UV-Vis spectra (see Supplementary Materials
(SM), Figures S1–S3), with some exhibiting absorption at 365 nm, allowing thus their irradiation at this
wavelength as well. The stereochemistry of the synthesized aldoxime derivatives (regarding H) was
found to be syn [30]. Furthermore, all amidoxime derivatives have the Z-conformation, in accordance
to what had previously been reported [22].
2.2. DNA Photo-Cleavage Experiments
DMF solutions of oxime conjugates
1–21 (100 µM or 500 µM) in DMF were mixed with a Tris
buffer solution (25 M, pH = 6.8) containing the supercoiled circular pBluescript KS II DNA or pBR322
µ
(Form I) and this mixture was irradiated with UV light (312 nm for 15 min and/or 365 nm for 120 min)
at room temperature, under aerobic conditions. Plasmid DNA was analyzed by gel electrophoresis on
1% agarose stained with EB. All experiments were performed at least three times. None of the tested
compounds showed any activity towards DNA in the absence of UV irradiation. The results obtained
are shown in Figures 3 and 4 and in Table 1.

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Figure 3. DNA photo-cleavage by various oxime ester conjugates at concentration of 100 µM with
plasmid DNA pBluescript KS II, at 312 nm for 30 min. Top: Gel electrophoresis picture: Lane 1:
DNA without UV irradiation; Lane 2: DNA with UV irradiation; Lanes 3–9: DNA + amidoximes
or ethanone oxime derivatives (
6,
7,
8,
10, 12, 5, and 11, respectively) + UV irradiation; Lanes 10–14:
DNA + aldoxime derivatives (17
,
18, 19, 20, and 21, respectively) + UV irradiation; Bottom: Calculation
of the % conversion to ss (Form II) and ds (Form III) damage.
Figure 4. DNA photo-cleavage by various oxime ester conjugates at concentration of 500 µM with
plasmid DNA pBR322, at 365 nm for 120 min. Top: Gel electrophoresis picture: Lane 1: DNA without
UV irradiation; Lane 2: DNA with UV irradiation; Lanes 3–9: DNA + oxime derivatives ( 10 21,
1,
2,
3,
5,
,
and 19, respectively) + UV irradiation; Bottom: Calculation of the % conversion to ss and ds damage.
Table 1. % (ss + ds) DNA photocleavage of amidoxime, ethanone oxime and aldoxime derivatives at
312 and 365 nm.
312 nm % (ss + ds)
DNA 3 Cleavage
(STDEV)
365 nm % (ss + ds)
DNA 4 Cleavage
(STDEV)
Imine
Substituent
BDE
(kcal/mol)
Compound
Imine Type 1
Conjugate
90 (˘4) 2
90 (˘3) 2
82 (˘8) 2
30 (˘10)
83 (˘9)
7 (˘4)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
AM
AM
AM
AM
AM
AM
AM
AM
AM
AM
EO
EO
AL
AL
AL
AL
AL
AL
AL
o-pyr
m-pyr
p-pyr
p-MeOPh
p-NO2Ph
o-pyr
m-pyr
p-pyr
p-MeOPh
p-NO2Ph
p-pyr
p-pyr
o-pyr
m-pyr
p-pyr
p-MeOPh
o-pyr
m-pyr
p-pyr
p-NO2Ph
p-NO2Ph
p-NO2Ph
p-NO2Ph
p-NO2Ph
p-pyr
p-pyr
p-pyr
p-pyr
p-pyr
43 (˘7)
79 (˘7)
79 (˘8)
NUV
50 (˘9)
NUV
NUV
NUV
NUV
56 (˘4)
NUV
NUV
NUV
NUV
NUV
NUV
NUV
NUV
15 (˘2)
NUV
0
52.81
51.34
50.83
51.13
50.67
52.41
51.05
50.57
50.71
50.51
46.07
45.89
47.18
47.18
47.00
47.60
46.88
46.95
46.81
47.19
46.98
8 (˘4)
15 (˘3)
6 (˘4)
61 (˘5)
90 (˘5)
84 (˘7)
93 (˘4) 2
91 (˘6) 2
98 (˘2) 2
NC
p-NO2Ph
p-pyr
p-NO2Ph
p-NO2Ph
p-NO2Ph
p-NO2Ph
p-pyr
p-pyr
p-pyr
p-pyr
p-pyr
50 (˘10)
5 (˘2)
83 (˘9)
12 (˘6)
92 (˘10)
AL
AL
p-MeOPh
p-NO2Ph
1
AM = Amidoxime, EO = Ethanone Oxime, AL = Aldoxime; 2 Reference. [30]; 3 Plasmid DNA: pBluescipt KS II,
100 µ µM concentration, in DMF; STDEV = Standard
M concentration, in DMF; 4 Plasmid DNA: pBR322, 500
Deviation, NC = No Cleavage, NUV = no UV absorption at 365 nm, BDE = Bond Dissociation Energy.
In the presence of all compounds (with the exception of 16) the supercoiled plasmid DNA (Form I)
sustained at 312 nm single-stranded (ss) nicks of the double helix, generating the relaxed circular DNA
(Form II), whereas in some cases, the linear DNA (Form III), generated by double-stranded (ds) nicks,
was formed as well.
Nitro substituted compounds have been studied for their ability to cleave DNA, thus, the
p-nitrophenyl moiety may also contribute to the observed DNA photocleavage [51–54]. In the case of

Molecules 2016, 21, 864
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the oxime esters it was evidenced, via photo-chemical experiments, that the aroyloxyl or sulfonyloxyl
radicals are the active intermediates for the carboxylic [24 33] or the sulfonic esters [34 35], respectively.
–
,
Mechanistically, these radicals derive upon the homolysis of the N-O bond of the oxime derivatives, as
depicted in Scheme 1.
Scheme 1. Photo-cleavage of the N-O bond of oxime ester conjugates.
However, the much better activity of the p-NO2-benzoyl conjugates, found for the series of
pyridine aldoximes and amidoximes [30], prompted us to further clarify the issue of the active
component by synthesizing and performing DNA photocleavage experiments of additional oxime
derivatives. This approach could provide an initial insight based on the structure-activity relationships.
In order to further support our study, besides photocleavage experiments, we have designed and
performed DNA affinity studies (vide infra) and we have calculated the bond dissociation energies
(BDEs) of the tested compounds.
Thus, regarding the oxime series bearing a p-NO2-benzoyl conjugate (compounds
all compounds almost completely photocleaved DNA at 312 nm, except the p-MeOPh imine-substituted
ones (compounds and 16). A possible excitation of the nitro group would have also contributed to
DNA photocleavage of the latter compounds, nevertheless, this was not observed. The same may be
concluded checking the activity of pyridoyl conjugates 12 17 and 19, which lack the p-NO2-benzoyl
group. The DNA photo-cleavage activity of these compounds was in general comparable to that of the
p-NO2-benzoyl conjugates (12 vs. 11 19 vs. 15). Additionally, in the cases where the p-NO2-phenyl
group was present as the oxime substituent, no substantial enhancement of the DNA photocleavage
was observed ( vs. or or 21 vs. 19). Thus, the above described experimental results indicate
that N-O bond homolysis occurs, as it had been observed by the analysis of the chemically induced
photo-cleavage of compound 30]. However, involvement of other factors, like oxygen or secondary
1–5, 11, 13–16)
4
,
,
5
1
2
3,
1
[
excitation reactions cannot be excluded. Theoretical calculations concerning the excitation states of
such compounds and mechanistic insights are in due course.
In the amidoxime series, the pyridoyl conjugates (compounds 6–10) do not seem to follow the
same trend, at this concentration. However, we cannot explain this lack of activity either by comparing
the energies of the N-O bonds, or the binding affinities (vide infra), or the UV absorption spectra (SM).
The same applies for the p-MeOPh oxime substrates (compounds 4, 9, 16 and 20) as well. A possible
explanation is that under the conditions applied, these compounds do not efficiently saturate DNA,
or that in-cage reactions affect the outcome of the DNA photo-cleavage. Such reactions have been
observed in the photo-cleavage of oximes [24
,56]. Nevertheless, comparing compounds 6–10 with the
respective aldoxime series 17 21, the approximately 5–6 Kcal/mol lower N-O bond energies and/or
–
the better binding constants (Kb) and intercalation (vide infra) of the latter may serve as the reason of
their higher DNA photo-cleaving activity (8 vs. 19, 10 vs. 21).
Pearson was the first to point out the existence of a relation between the ground state bond
strength (D0) and excitation energy in diatomic molecules, in 1988 [57]. Since then this concept was
extended to polyatomic molecules using a variety of quantum chemical methods showing not only
relations between D0 and the bond dissociation energy in an excited state (D0T1: BDE in the first
excited triplet state), but also relations concerning the activation energy in an excited state and the
T1
T1
rate constant (kr) of a photochemical reaction (e.g., D0
=
α1
+
β1¨D0 or Ea
=
α2
+
β2¨D0T1) [58
–60].

Molecules 2016, 21, 864
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This linear correlation between D0 and D0T1 prompted us to study whether BDE may be used in our
case as an indication for the cleavage ability, upon dissociation, of the oxime esters. Although the DNA
photo-cleavage is a very complex phenomenon, which does not allow us for the moment to extract any
equation, it seems that, in general, the higher the BDE the lower the % DNA photo-cleavage, Figure 5.
(A)
(B)
(C)
(D)
Figure 5. Graphical correlations between BDE and % DNA photo-cleavage. (
p-pyridine oxime substituent and p-nitro-phenyl ester conjugate in amidoxime, ethanone oxime and
aldoxime ( 11 and 15, respectively); ( ) Compounds bearing p-nitro-phenyl oxime substituent and
p-pyridine ester conjugate in amidoxime and aldoxime (10 and 21, respectively); ( ) Compounds
A) Compounds bearing
3,
B
C
bearing o-pyridine oxime substituent and p-nitro-phenyl ester conjugate in amidoxime and aldoxime
(1 and 13, respectively); (D) All DNA photo-cleaving compounds.
Finally, based on the presented results, we may suggest that p-pyridine and p-NO2Ph oxime
substituents favor the right geometry for H abstraction from DNA, something which was also
evidenced for the sulfonyl amidoxime series [35]. The latter phenomenon has been recently studied
for another sensitizer (benzophenone) [61].
At 365 nm amidoximes 3 and 10 seem to retain most of their efficacy, whereas compounds 1, 2,
5 19 and 21 exhibit less activity. This result could be attributed to the lower UV absorption of the
compounds at this wavelength (SM). Nevertheless the observed DNA photo-cleavage proves that
the homolysis of the N-O bond may also occur upon UVA irradiation, as it was presented in other
cases [24,27,31–33].
The promising DNA photo-cleavage activities observed for the oxime esters bearing p-pyridyl
and p-NO2Ph moieties as both oxime substituents and ester conjugates, prompted us to further study
their behavior towards DNA with CT-DNA binding affinities. These studies (following paragraphs)
were expected to shed light to the interaction mode.
2.3. DNA Affinity Studies
The interaction of compounds 1–16, 19 and 21 with CT DNA was investigated directly by UV
spectroscopy and viscosity measurements and indirectly by the evaluation of the EB-displacing ability
of the compounds as examined by fluorescence emission spectroscopy.

Molecules 2016, 21, 864
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2.3.1. DNA-Binding Studies with UV Spectroscopy
The interaction of compounds with CT DNA was initially studied by UV spectroscopy in order
to obtain preliminary information in regard to the existence of any interaction and its possible mode
and to further calculate the DNA-binding constants of the compounds (Kb). Therefore, the UV spectra
of a CT DNA solution were recorded in the presence of the compounds at increasing amounts (for
different r values) as well as the UV spectra of the compounds in the presence of increasing amounts
of CT DNA. The existence of any interaction may perturb the CT DNA band located at 258–260 nm in
the former study or the transition bands of the compounds in the latter study during the titrations
providing, thus, initial information of such interaction.
The CT DNA band located at
in the presence of the compounds either a slight hyperchromism (as representatively in the presence of
compound , Figure 6A) or a slight hypochromism (as representatively in the presence of compound 3,
λmax = 257–258 nm in the UV spectra of a CT DNA solution exhibited
1
Figure 6B) which was accompanied by a red-shift up to 262 nm in most cases. Quite similar features
were observed in the UV spectra of CT DNA in the presence of the other compounds. Such changes in
the UV spectra of CT DNA may reveal the interaction of the compounds with CT DNA which results
in the formation of a new compound-DNA conjugate [62] with a simultaneous stabilization of the CT
DNA duplex [63].
1.2
1.0
0.8
0.6
0.4
0.2
0.0
1.2
1.0
0.8
0.6
0.4
0.2
0.0
(B)
(A)
240 250 260 270 280 290 300 310
240 250 260 270 280 290 300 310
λ(nm)
λ(nm)
Figure 6. UV spectra of CT DNA in buffer solution (150 mM NaCl and 15 mM trisodium citrate at
pH 7.0) in the absence or presence of increasing amounts of ( ) compound ([DNA] = 0.155 mM)
and ( ) compound ([DNA] = 0.147 mM). The arrows show the changes with increasing amounts of
the compounds.
A
1
B
3
The UV spectra of the compounds were recorded in the presence of increasing amounts of a CT
DNA solution (diverse r’ values) and are shown representatively for compounds 12 15 and 19
5
,
9,
,
in Figure 7 and Figure S4. In the UV spectra of the compounds, one UV band is initially observed
(band I) in the range 263–299 nm which shows in the presence of increasing amounts of CT DNA a
slight hypochromism.
Furthermore, the band shows in some cases a slight blue- or red-shift up to 3 nm. The existing
spectroscopic features observed in the UV spectra of the compounds in the presence of CT DNA are
indicative of the interaction of the compounds with CT DNA. Nevertheless, the extent of the observed
hypochromism in the UV spectra of the compounds is not so pronounced that safe conclusions
concerning the possible complex-DNA interaction mode may be arisen only from the existing UV
spectroscopic data [64]; therefore, DNA-viscosity measurements were carried out in an attempt to
better clarify the interaction mode.

Molecules 2016, 21, 864
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1.45
1.40
1.35
1.30
1.25
1.20
1.0
0.8
0.6
0.4
0.2
0.0
1.5
1.0
0.5
0.0
(A)
(B)
265
270
275
280
285
λ (nm)
260
280
300
λ (nm)
320
260
280
300
320
λ (nm)
Figure 7. UV spectra of DMSO solution of compound (
the presence of increasing amounts of CT DNA (r’ = [DNA]/[compound] = 0–0.8). The arrows show
the changes upon increasing amounts of CT DNA.
A
)
9
(2
ˆ
10´5 M) and (
B
)
19 (1
ˆ
10´4 M) in
The DNA-binding constants (Kb) of the compounds (Table 2) were determined by the
Wolfe-Shimer equation (Equation (3)) [65] and the plots [DNA]/(εA ´ εf) versus [DNA]
(representatively shown in Figure S5). In brief, the Kb constants of the compounds are relatively
high with compound 21 bearing the highest Kb constant (=1.85(
compounds. The Kb constants of most of the compounds are higher than that of the classical intercalator
EB (=1.23( 0.07)
105 M´1) as it was previously calculated [66]. Furthermore, the Kb constants of
˘0.18)
ˆ
106 M´1) among the studied
˘
ˆ
these compounds bear values similar to those recently reported for sulfonyl ketoximes [34] and sulfonyl
amidoximes [35].
Table 2. UV spectral features of the interaction of selected compounds 1– , 19 and 21 with CT DNA;
16
UV
-
band (
(∆λ, nm)) and DNA-binding constants (K , M´1).
λ, nm) (percentage of observed hyper-/hypo-chromism (∆A/A0, %), blue-/red-shift of the
λ
max
b
Compound
Band (nm) (∆A/Ao(%) 1, ∆λ(nm)) 2
Kb (M´1
)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
19
21
272 (´2.0, 0)
266 (´7.0, 0)
267 (´2.5, +2)
265 (´3.0, +3)
273 (´1.5, ´1)
277 (´1.0, 0)
273 (´1.0, 0)
264 (´5.0, +2)
275 (´2.5, 0)
272 (´2.5, 0)
272 (´1.0, 0)
274 (´12.0, ´3)
268 (´5.0, +1)
272 (´2.0, 0)
267 (´2.5, +1)
277 (+1.0, 0)
1.62(˘0.18) ˆ 106
2.06(˘0.04) ˆ 105
3.73(˘0.27) ˆ 104
5.88(˘0.41) ˆ 104
1.25(˘0.29) ˆ 106
3.90(˘0.16) ˆ 105
1.59(˘0.16) ˆ 106
3.60(˘0.17) ˆ 105
7.31(˘0.16) ˆ 105
1.52(˘0.10) ˆ 105
4.79(˘0.08) ˆ 104
6.02(˘0.17) ˆ 105
3.04(˘0.22) ˆ 105
8.50(˘0.27) ˆ 105
3.23(˘0.03) ˆ 105
3.47(˘0.27) ˆ 105
1.29(˘0.09) ˆ 106
1.85(˘0.18) ˆ 106
263 (´10.0, 0)
265 (´6.0, 0)
“+” denotes hyperchromism, “´” denotes hypochromism; 2 “+” denotes red-shift, “´” denotes blue-shift.
1

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2.3.2. DNA-Binding Study with Viscosity Measurements
The interaction of the selected compounds (i.e.,
1–
16,
19 and 21) with CT DNA was also monitored
through the changes of DNA-viscosity upon addition of the compounds. The measurement of the
DNA-viscosity of DNA is among the most reliable techniques and may provide significant aid to clarify
the interaction mode of a compound with DNA, since it is sensitive to such DNA-length changes [67];
more specifically, the relative DNA-viscosity (
(L/L0) occurring in the presence a DNA-binder and are correlated by the equation L/L0 = (
η
/
η0) is sensitive to the relative DNA-length changes
1/3
η
/
η0
)
[67].
In general, upon binding of a compound to DNA via intercalation, the separation distance of the
DNA-base pairs located at the intercalation sites will exhibit an increase in order to host the compound
inserting in-between the DNA-base pairs and, subsequently, the relative DNA-length will also increase
and lead to an increase of DNA-viscosity, the magnitude of which is usually in accordance to the
strength of the interaction [68]. On the other hand, in the case of non-intercalation (i.e., electrostatic
interaction or external groove-binding), the binding of a compound to DNA grooves will induce a
bend or kink in the DNA helix leading rather to slight shortening of the relative DNA-length which
may be revealed via a slight decrease of the DNA-viscosity [68].
Within this context, the viscosity of a CT DNA solution (0.1 mM) was monitored upon addition
of increasing amounts of the compounds (up to the value of r = 0.35). Initially and up to r value of
0.1, the viscosity of CT DNA exhibit a decrease in the presence of most compounds and for higher
concentrations, the DNA-viscosity presented a noteworthy increase (Figure 8).
1.4
(A)
(B)
1.5
1.4
1.3
1.2
1.1
1.0
0.9
1
3
5
2
4
6
8
10
7
9
1.3
1.2
1.1
1.0
0.9
0.0
0.1
0.2
0.3
0.0
0.1
0.2
0.3
r = [compound]/[DNA]
r = [compound]/[DNA]
(D) 1.5
1.4
1.3
(C)
13
15
14
16
11
19
12
21
1.2
1.1
1.0
0.9
1.3
1.2
1.1
1.0
0.9
0.0
0.1
0.2
0.3
0.0
0.1
0.2
0.3
r = [compound]/[DNA]
r = [compound]/[DNA]
1/3
Figure 8. Relative viscosity (
η
/η
)
of CT DNA (0.1 mM) in buffer solution (150 mM NaCl and
, ( 10, ( 13 16 and
o
15 mM trisodium citrate at pH 7.0) in the presence of compounds (
A
)
1–
5
B
)
6
–
C
)
–
(D) 11, 12, 19 and 21 at increasing amounts (r = [compound]/[DNA]).
Considering the overall changes of the DNA-viscosity in the presence of the compounds tested,
we may suggest that they initially interact to CT DNA probably by non-classical intercalation (i.e., as
groove-binders) so as to closely approach to DNA. Afterwards and as a subsequent step, they may
intercalate within the CT DNA base pairs. Such behaviour may better clarify and justify the findings
from the UV spectroscopic studies.

Molecules 2016, 21, 864
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2.3.3. EB-Displacement Studies with Fluorescence Emission Spectroscopy
The ability of the compounds to displace EB from the EB-DNA complex may further clarify and
verify indirectly their intercalating ability. EB is a known fluorescence dye and is a typical indicator of
DNA-intercalation [69] which takes place via the insertion of its planar phenanthridine ring in-between
the DNA base pairs. The formed EB-DNA conjugate exhibits an intense fluorescence emission band at
592–593 nm, when excited at 540 nm. The addition of another intercalating compound may induce
quenching of this emission band [69,70].
The EB-DNA conjugate was prepared via the pre-treatment of an EB solution ([EB] = 20
CT DNA ([DNA] = 26 M) for ~1 h. The fluorescence emission spectra ( = 540 nm) of this EB-DNA
solution were recorded in the presence of increasing amounts of the compounds (representatively
shown for compound in Figure S6). In brief, the addition of the compounds in the EB-DNA solution
resulted in a moderate-to-significant quenching of the DNA-EB emission band at 592 nm (Figure 9); the
final quenching ( I/Io) is in the range 51.4%–77.4% of the initial EB-DNA fluorescence (Table 3). Thus,
µM) with
µ
λ
ex
1
∆
the extent of the observed quenching may reveal that the compounds have the potential to displace
EB from the EB-DNA conjugate as a result of the competition with EB when binding to the DNA
intercalation sites; thus we may indirectly conclude the existence of intercalation of the complexes to
CT DNA [71].
(B)
100
80
60
40
20
0
(A)
100
80
60
40
20
0
6
8
7
9
1
3
5
2
4
10
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.0
0.1
0.2
0.3
0.4
r = [compound]/[DNA]
r = [compound]/[DNA]
(D)
100
80
60
40
20
0
(C)
100
13
15
14
16
11
19
12
21
80
60
40
20
0
0.0
0.1
0.2
0.3
0.0
0.1
0.2
0.3
0.4
0.5
0.6
r = [compound]/[DNA]
r = [compound]/[DNA]
Figure 9. Plot of EB-DNA relative fluorescence emission intensity (%I/Io) at
λ
em
= 592 nm vs. r
(
r = [compound]/[DNA]) in buffer solution (150 mM NaCl and 15 mM trisodium citrate at pH 7.0) in
the presence of compounds (
, 33.5 for , 30.4% for , 39.8% for
EB-DNA fluorescence for
up to 35.5% of the initial EB-DNA fluorescence for 13, 36.3% for 14, 35.2% for 15 and 42.6% for 16);
11 12 19 and 21 (quenching up to 33.9% of the initial EB-DNA fluorescence for 11, 32.5% for 12
30.0% for 19 and 33.6% for 21).
A
)
1
–
5
4
(quenching up to 22.6% of the initial EB-DNA fluorescence for
and 40.1% for ); ( 10 (quenching up to 48.6% of the initial
, 33.6% for , 33.4% for and 22.6% for 10); ( 13 16 (quenching
1
2
3
5
B) 6–
6
, 41.9% for
7
8
9
C
)
–
(
D)
,
,
,

Molecules 2016, 21, 864
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Table 3. Data of the EB-competitive studies of selected compounds. Percentage of EB-DNA fluorescence
quenching (∆I/Io, %), Stern-Volmer constants (KSV, M´1) and quenching constants (kq, M´1s´1).
Compound
∆I/Io (%)
Ksv (M´1
)
kq (M´1s´1
)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
19
21
77.4
66.5
69.6
60.2
59.9
51.4
58.1
66.4
66.6
77.4
66.1
67.5
64.5
63.4
64.7
57.4
70.0
66.4
1.94(˘0.05) ˆ 105
8.27(˘0.27) ˆ 104
1.80(˘0.05) ˆ 105
1.34(˘0.05) ˆ 105
1.20(˘0.03) ˆ 105
4.46(˘0.15) ˆ 104
6.08(˘0.14) ˆ 104
6.85(˘0.25) ˆ 104
3.23(˘0.11) ˆ 105
1.50(˘0.05) ˆ 105
7.15(˘0.16) ˆ 104
1.06(˘0.03) ˆ 105
1.25(˘0.03) ˆ 105
1.53(˘0.04) ˆ 105
3.11(˘0.06) ˆ 105
1.24(˘0.04) ˆ 105
7.27(˘0.19) ˆ 104
1.33(˘0.02) ˆ 105
8.43(˘0.20) ˆ 1012
3.60(˘0.12) ˆ 1012
7.82(˘0.22) ˆ 1012
5.82(˘0.21) ˆ 1012
5.20(˘0.11) ˆ 1012
1.94(˘0.07) ˆ 1012
2.64(˘0.06) ˆ 1012
2.98(˘0.11) ˆ 1012
1.40(˘0.05) ˆ 1013
6.52(˘0.20) ˆ 1012
3.11(˘0.07) ˆ 1012
4.60(˘0.11) ˆ 1012
5.43(˘0.12) ˆ 1012
6.65(˘0.16) ˆ 1012
1.35(˘0.03) ˆ 1013
5.40(˘0.15) ˆ 1012
3.16(˘0.08) ˆ 1012
5.80(˘0.07) ˆ 1012
The quenching of the EB-DNA fluorescence induced by the compounds was found to be in
good agreement (R = 0.99) with the linear Stern-Volmer equation (Equation (4)) [69] as indicated
in the corresponding Stern-Volmer plots (shown in Figures S7 and S8). The KSV constants of the
compounds (Table 3) are moderate-to-high verifying their binding affinity for DNA, with compounds
9
and 15 bearing the highest KSV constants among the compounds. Based on the value of τo = 23 ns
as the fluorescence lifetime of EB-DNA system [72], the quenching constants of the compounds were
calculated with Equation (4). The kq constants of the compounds (Table 3) are significantly higher
´1
than 1010
M
¨
s
´1 suggesting, thus, the quenching of the EB-DNA fluorescence takes place via a static
mechanism [71].
3. Materials and Methods
3.1. General Information
All commercially available reagent-grade chemicals and solvents were used without further
purification. Dry solvents were prepared by literature methods and stored over molecular sieves.
CT DNA, EB, NaCl and trisodium citrate were purchased from Sigma-Aldrich Co. (Schnelldorf,
Germany). CT DNA stock solution was prepared by dilution of CT DNA to buffer (containing
15 mM trisodium citrate and 150 mM NaCl at pH 7.0) followed by 3 days stirring and kept at 4 ˝C
for no longer than two weeks. The stock solution of CT DNA gave a ratio of UV absorbance at
260 and 280 nm (A260/A280) of 1.85–1.88, indicating that the DNA was sufficiently free of protein
contamination [73]. The CT DNA concentration was determined by the UV absorbance at 260 nm
after 1:20 dilution using
ε [74]. pBluescipt KS II plasmid DNA purification was
= 6600 M´1cm´1
performed using the Nucleospin plasmid kit, according to the protocol provided by the manufacturer
(Macherey-Nagel, Duren, Germany). pBR322 was purchased from New England BioLabs (Ipswich,
MA, USA).UV-visible (UV-vis) spectra were recorded on a U-2001 dual beam spectrophotometer
(Hitachi, Tokyo, Japan). Fluorescence emission spectra were recorded in solution on a Hitachi F-7000
fluorescence spectrophotometer (Hitachi, Tokyo, Japan). Viscosity experiments were carried out using
an ALPHA L Fungilab rotational viscometer (Fungilab, Barcelona, Spain) equipped with an 18 mL
LCP spindle and the measurements were performed at 100 rpm. Samples containing pBluescipt KS II
plasmid DNA were irradiated in a Macrovue 2011 transilluminator (LKB Produkter, Bromma, Sweden)

Molecules 2016, 21, 864
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at 312 nm, T-15.M 90 W, 0.225 W/cm2, 10 cm distance. Samples containing pBR322 plasmid DNA
were irradiated with Actinic BL PL-S 9W/10/2P lamps (2
5 cm distance.
ˆ
9 W, Philips, Pila, Poland) at 365 nm,
Mps were measured on a Kofler hot-stage apparatus or a M5000 melting point meter (KRÜSS,
Hamburg, Germany) and are uncorrected. FT-IR spectra were obtained in a Nicolet FT-IR
6700 spectrophotometer(Thermo Fisher Scientific, Madison, WI, USA) using potassium bromide
1
pellets. NMR spectra (500 MHz and 125 MHz for H and 13C, respectively) were recorded on an
Agilent 500/54 spectrometer (Agilent Technologies, Santa Clara, CA, USA) using CDCl3, and/or
DMSO-d6 as solvent. J values are reported in Hz. High resolution mass spectra (HRMS) were recorded
on micrOTOF GC-MS QP 5050 single-quadrupole mass spectrometer (Shimadzu, LTQ ORBITRAP
XL with ETD- Thermo Fisher Scientific, San Jose, CA, USA and Bremen, Germany). All reactions
were monitored on commercial available pre-coated TLC plates (layer thickness 0.25 mm) of Kieselgel
60 F254. Yields were calculated after recrystallization.
3.2. Synthesis: General Procedure for the Synthesis of Oxime Ester Conjugates
Parent amidoxime, ethanone oxime or aldoxime ˝(2 mmol) was dissolved in THF or CHCl3
(0.15 M) and Et3N or DIPEA (2.2 mmol) was added at 0 C under an Ar atmosphere, followed by the
corresponding acid chloride (2.2 mmol). p-Pyridoyl chloride was commercially available as an HCl
salt, therefore in those cases the amount of the amine used was doubled. The temperature was allowed
˝
to slowly rise to 25 C. The reaction was monitored by TLC and, upon completion, water (100 mL) was
added and the mixture was extracted with dichloromethane (2 100 mL). The organic layers were
ˆ
further washed with water (100 mL), dried with Na2SO4, and the solvents were evaporated to dryness.
The crude residue was then recrystallized, unless otherwise mentioned, to give the desired product,
which was found to be sufficiently pure.
(Z)-N’-((4-Nitrobenzoyl)oxy)picolinimidamide (
(DMSO-d6) 8.69 (d, J = 4.4 Hz, 1H), 8.47 (d, J = 8.7 Hz, 2H), 8.34 (d, J = 8.7 Hz, 2H), 8.02 (d,
J = 7.9 Hz, 1H), 7.96 (t, J = 7.1 Hz, 1H), 7.58 (t, J = 5.3 Hz, 1H), 7.36 (br s, 1H), 7.18 (br s, 1H) ppm.
1
). Prepared according to reference [30]. 1H-NMR
δ
(Z)-N’-((4-Nitrobenzoyl)oxy)nicotinimidamide (
). Prepared according to reference [30]. 1H-NMR
(DMSO-d6) 8.94 (d, J = 1.7 Hz, 1H), 8.72 (dd, J = 4.8, 1.4 Hz, 1H), 8.45 (d, J = 8.8 Hz, 2H), 8.34
(d, J = 8.8 Hz, 2H), 8.14 (dt, J = 8.0, 1.8 Hz, 1H), 7.53 (dd, J = 7.8, 4.8 Hz, 1H), 7.33 (br s, 2H) ppm.
(Z)-N’-((4-Nitrobenzoyl)oxy) isonicotinimidamide (
). Prepared according to reference [30]. 1H-NMR
(DMSO-d6) 8.72 (dd, J = 6.0, 1.4 Hz, 2H), 8.45 (dd, J = 9.0, 2.0 Hz, 2H), 8.35 (dd, J = 9.0, 2.1 Hz, 2H),
7.75 (dd, J = 6.0, 0.4 Hz, 2H), 7.36 (br s, 2H) ppm.
2
δ
3
δ
(Z)-4-Methoxy-N
'
-((4-nitrobenzoyl)oxy)˝benzimidamide (
4). Solvent: THF; R.T.: 12 h; amine: Et3N; light
´1
yellow crystals, yield 85%, mp 190–192 C (ethyl acetate/ethanol); IR (KBr): 3481, 3382, 1724, 1623 cm
;
1H-NMR (CDCl3 + DMSO-d6)
δ 8.36 (d, J = 7.7 Hz, 2H), 8.25 (d, J = 7.7 Hz, 2H), 7.68 (d, J = 7.6 Hz, 2H),
6.88 (d, J = 7.6 Hz, 2H), 6.59 (br s, 2H), 3.78 (s, 3H) ppm; 13C-NMR (CDCl3 + DMSO-d6)
δ 161.0, 160.0,
156.2, 148.8, 134.0, 129.5, 127.2, 122.2, 122.0, 112.2, 53.9 ppm; HRMS (ESI) Calc C15H14N3O5 [M + H]+
316.0928; found 316.0925.
(Z)-4-Nitro-N
crystals, yield 79%, mp 243.8 C (ethyl acetate); IR (KBr): 3490, 3360, 3111, 1725, 1627 cm´1; 1H-NMR
(CDCl3 + DMSO-d6) 8.45 (d, J = 8.8 Hz, 2H), 8.29 (d, J = 8.8 Hz, 2H), 8.27 (d, J = 8.8 Hz, 2H), 8.04 (d,
J = 8.8 Hz, 2H), 7.25 (br s, 2H) ppm; 13C-NMR (CDCl3 + DMSO-d6)
160.2, 154.1, 148.4, 147.0, 136.0,
133.0, 129.3, 126.6, 121.6, 121.5 ppm; HRMS (ESI) Calc C14H11N4O6 [M + H]+ 331.0673; found 331.0675.
'-((4-nitrobenzoyl)oxy)benzimidamide (5). Solvent: THF; R.T.: 4 h; amine: Et3N; light yellow
˝
δ
δ

Molecules 2016, 21, 864
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(Z)-N
'
-(Isonicotinoyloxy)picolinimidamide (
6
). Solvent: CHCl3; R.T.: 5 h; amine: DIPEA; white crystals,
˝
yield 77%, mp 161.1 C (ethyl acetate); IR (KBr): 3493, 3380, 3054, 1732, 1632 cm´1 1H-NMR
;
(
CDCl3 + DMSO-d6
1H), 8.00 (dd, J = 4.5, 1.5 Hz, 2H), 7.76 (dt, J = 7.2, 1.6 Hz, 1H), 7.40 (ddd, J = 7.4, 4.9, 0.9 Hz, 1H), 6.82
(br s, 2H) ppm; 13C-NMR (CDCl3 + DMSO-d6)
161.2, 153.5, 149.1, 147.2, 146.5, 135.6, 135.4, 124.4,
121.7, 119.9 ppm; HRMS (ESI) Calc C12H11N4O2 [M + H]+ 243.0877; found 243.0876.
) δ 8.72 (dd, J = 4.5, 1.5 Hz, 2H), 8.56 (d, J = 4.6 Hz, 1H), 8.07 (d, J = 8.0 Hz,
δ
(Z)-N -(Isonicotinoyloxy)nicotinimidamide ( ). Solvent: CHCl3; R.T.: 3 h; amine: DIPEA; white crystals,
yield 73%, mp 155.9 C (ethyl acetate); IR (KBr): 3445, 3313, 3166, 1726, 1634 cm´1; 1H-NMR (500 MHz,
CDCl3 + DMSO-d6) 8.93 (s, 1H), 8.73 (d, J = 4.7 Hz, 2H), 8.63 (d, J = 3.3 Hz, 1H), 8.08 (d, J = 7.9 Hz,
1H), 8.02 (d, J = 5.5 Hz, 2H), 7.37 (dd, J = 7.6, 4.9 Hz, 1H), 7.00 (br s, 2H) ppm; 13C-NMR (125 MHz,
CDCl3 + DMSO-d6) 161.0, 154.5, 149.8, 148.9, 146.6, 135.2, 133.3, 126.2, 121.7, 121.5 ppm; HRMS (ESI)
Calc C12H11N4O2 [M + H]+ 243.0877; found 243.0872.
(Z)-N -(Isonicotinoyloxy)isonicotinimidamide ( ). Solvent: CHCl3; R.T.: 3 h; amine: Et3N; column
chromatography (10% MeOH in ethyl acetate); Light yellow crystals, yield 70%, mp 155 ˝C (ethyl
acetate); IR (KBr): 3459, 3366, 1731, 1627 cm´1; 1H-NMR (DMSO-d6)
8.82 (dd, J = 4.2, 1.3 Hz, 2H),
8.72 (dd, J = 4.4, 1.3 Hz, 2H), 8.09 (dd, J = 4.4, 1.6 Hz, 2H), 7.74 (dd, J = 4.5, 1.6 Hz, 2H), 7.32 (br s, 2H)
ppm; 13C-NMR (DMSO-d6)
162.4, 155.7, 150.6, 150.1, 139.0, 136.3, 122.9, 121.2 ppm; HRMS (ESI) Calc
C12H11N4O2 [M + H]+ 243.0877; found 243.0872.
(Z)-N -(Isonicotinoyloxy)-4-methoxybenzimidamide (
crystals, yield 87%, mp 165.8 C (ethyl acetate); IR (KBr): 3492, 3366, 1728, 1618 cm´1; H-NMR
CDCl3 + DMSO-d6 8.49 (d, J = 5.9 Hz, 2H), 7.66 (d, J = 6.0 Hz, 2H), 7.45 (d, J = 8.9 Hz, 2H), 6.63 (d,
'
7
˝
δ
δ
'
8
δ
δ
'
9). Solvent: THF; R.T.: 7 h; amine: Et3N; white
˝
1
(
) δ
J = 8.9 Hz, 2H), 5.88 (bs, 2H), 3.55 (s, 3H) ppm; 13C-NMR (CDCl3 + DMSO-d6)
δ 162.1, 161.0, 157.3,
149.8, 136.4, 127.9, 122.7, 122.1, 113.1, 54.7 ppm; HRMS (ESI) Calc C14H14N3O3 [M + H]+ 272.1030;
found 272.1032.
(Z)-N
'
-(Isonicotinoyloxy)-4-nit˝robenzimidamide (10). Solvent: THF; R.T.: 7 h; amine: Et3N; yellow
crystals, yield 85%, mp 176.2 C (ethyl acetate); IR (KBr): 3536, 3420, 3120, 1730, 1649 cm´1; 1H-NMR
(
CDCl3 + DMSO-d6) δ 8.72 (d, J = 5.9 Hz, 2H), 8.19 (d, J = 8.9 Hz, 2H), 8.00 (d, J = 8.9 Hz, 2H), 7.99 (d,
J = 5.8 Hz, 2H), 6.90 (br s, 2H) ppm; 13C-NMR (CDCl3 + DMSO-d6)
δ 161.4, 155.0, 149.2, 147.8, 136.6,
135.5, 127.3, 122.1, 121.8 ppm; HRMS (ESI) Calc C13H11N4O4 [M + H]+ 287.0775; found 287.0773.
(E)-1-(Pyridin-4-yl)ethan-1-one O-(4-nitrobenzoyl) oxime (11). Prepared according to reference [32].
1H-NMR (CDCl3)
δ 8.75 (d, J = 5.8 Hz, 2H), 8.37 (d, J = 8.7 Hz, 2H), 8.30 (d, J = 8.7 Hz, 2H), 7.70 (d,
J = 5.8 Hz, 2H), 2.55 (s, 3H) ppm.
(E)-1-(Pyridin-4-yl)ethan-1-one O-isonicotinoyl oxime (12). Solvent: THF; R.T.: 24 h; amine: DIPEA; white
˝
crystals, yield 89%, mp 162.8 C (ethyl acetate); IR (KBr): 1753, 1618 cm´1; 1H-NMR (500 MHz, CDCl3)
δ
8.83 (dd, J = 4.7, 1.2 Hz, 2H), 8.71 (dd, J = 4.7, 1.2 Hz, 2H), 7.91 (dd, J = 4.7, 1.4 Hz, 2H), 7.67 (dd,
J = 4.7, 1.4 Hz, 2H), 2.52 (s, 3H) ppm; 13C-NMR (125 MHz, CDCl3)
δ 162.4, 161.9, 150.8, 150.4, 141.7,
135.9, 122.7, 121.0, 14.2 ppm; HRMS (ESI) Calc C13H12N3O2 [M + H]+ 242.0924; found 242.0922.
1
(E)-Picolinaldehyde O-4-nitrobenzoyl oxime (13). Prepared according to reference [30]. H-NMR (CDCl3)
δ
8.71 (d, J = 4.3 Hz, 1H), 8.67 (s, 1H), 8.35 (d, J = 8.9 Hz, 2H), 8.31 (d, J = 8.9 Hz, 2H), 8.18 (d, J = 7.9 Hz,
1H), 7.82 (dt, J = 7.8, 1.3 Hz, 1H), 7.42 (dd, J = 6.6, 4.9 Hz, 1H) ppm.
(E)-Nicotinaldehyde O-4-nitrobenzoyl oxime (14). Prepared according to reference [30]. 1H-NMR
(DMSO-d6)
δ 9.07 (s, 1H), 8.95 (d, J = 1.6 Hz, 1H), 8.76 (dd, J = 4.8, 1.6 Hz, 1H), 8.42 (dd, J = 8.9,
1.8 Hz, 2H), 8.31 (dd, J = 8.9, 1.8 Hz, 2H), 8.24 (dt, J = 8.0, 1.8 Hz, 1H), 7.58 (dd, J = 7.9, 4.9 Hz, 1H) ppm.
(E)-Isonicotinaldehyde O-4-nitrobenzoyl oxime (15). Prepared according to reference [30]. 1H-NMR
(DMSO-d6)
δ 9.03 (s, 1H), 8.76 (d, J = 5.1 Hz, 2H), 8.41 (d, J = 8.5 Hz, 2H), 8.29 (d, J = 8.5 Hz, 2H), 7.75
(d, J = 5.1 Hz, 2H) ppm.

Molecules 2016, 21, 864
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(E)-4-Methoxybenzaldehyde O-(4-nitrobenzoyl) oxime (16), ref mp 171 ˝C [75]. Solvent: THF; R.T.: 12 h;
amine: Et3N; light brown crystals, yield 78%, mp 169–171 ˝C (ethyl acetate/ethanol); IR (KBr): 1754,
1599 cm´1; 1H-NMR (CDCl3 + DMSO-d6)
δ
8.34 (s, 1H), 8.12 (d, J = 9.0 Hz, 2H), 8.08 (d, J = 9.0 Hz, 2H),
7.53 (d, J = 8.8 Hz, 2H), 6.76 (d, J = 8.8 Hz, 2H), 3.65 (s, 3H) ppm; 13C-NMR (CDCl3 + DMSO-d6)
δ
162.1,
161.6, 156.7, 150.0, 133.7, 130.2, 129.8, 123.1, 121.4, 113.9, 54.9 ppm; HRMS (ESI) Calc C15H13N2O5
[M + H]+ 301.0819; found 301.0810.
(E)-Picolinaldehyde ˝O-isonicotinoyl oxime (17). Solvent: THF; R.T.: 24 h; amine: DIPEA; beige crystals,
yield 85%, mp 154 C (hexanes/ethyl acetate); IR (KBr): 1754, 1612 cm´1; 1H-NMR (CDCl3) δ 8.84 (d,
J = 5.7 Hz, 2H), 8.69 (d, J = 4.3 Hz, 1H), 8.64 (s, 1H), 8.16 (d, J = 7.9 Hz, 1H), 7.93 (d, J = 5.7 Hz, 2H),
7.79 (dd, J = 7.4, 6.9 Hz, 1H), 7.39 (dd, J = 6.7, 5.1 1H) ppm; 13C-NMR (CDCl3)
δ 162.3, 158.2, 150.8,
150.0, 149.4, 136.8, 135.6, 125.8, 122.8, 122.3 ppm; HRMS (ESI) Calc C12H10N3O2 [M + H]+ 228.0768;
found 228.0765.
(E)-Nicotinaldehyde O-isonicotinoyl oxime (18). Solvent: THF; R.T.: 24h; amine: DIPEA; off white crystals,
yield 82%, mp 152 ˝C (ethyl acetate); IR (KBr): 1749, 1612 cm´1; 1H-NMR (DMSO-d6)
δ
9.05 (s, 1H),
8.95 (s, 1H), 8.88 (d, J = 5.4 Hz, 2H), 8.75 (d, J = 4.6 Hz, 1H), 8.24 (d, J = 7.9 Hz, 1H), 7.95 (d, J = 5.4 Hz,
2H), 7.58 (dd, J = 7.1, 5.0 Hz, 1H) ppm; 13C-NMR (DMSO-d6)
δ 162.0, 156.7, 152.7, 151.0, 149.7, 135.3,
134.9, 126.0, 124.3, 122.6 ppm; HRMS (ESI) Calc C12H10N3O2 [M + H]+ 228.0768; found 228.0766.
(E)-Isonicotinaldehyde O-isonicotinoyl oxime (19). Solvent: THF; R.T.: 24 h; amine: DIPEA; beige crystals,
˝
yield 77%, mp 138 C (hexanes/ethyl acetate); IR (KBr): 1753, 1596 cm´1; 1H-NMR (CDCl3) δ 8.85 (d,
J = 5.8 Hz, 2H), 8.76 (d, J = 5.7 Hz, 2H), 8.55 (s, 1H), 7.92 (d, J = 5.8 Hz, 2H), 7.67 (d, J = 5.9 Hz, 2H)
ppm; 13C-NMR (CDCl3)
δ 162.0, 155.6, 150.8, 150.8, 137.0, 135.4, 122.8, 121.9 ppm; HRMS (ESI) Calc
C12H10N3O2 [M + H]+ 228.0768; found 228.0764.
(E)-4-Methoxybenzaldehyde O-isonicotinoyl oxime (20). Solvent: CHCl3; R.T.:˝4 h; amine: Et3N; column
chromatography (hexanes/ethyl acetate); beige crystals, yield 83%, mp 141 C (hexanes/ethyl acetate);
1
IR (KBr): 1743, 1605 cm´1; H-NMR (CDCl3)
δ 8.81 (dd, J = 4.5, 1.5 Hz, 2H), 8.48 (s, 1H), 7.90 (dd,
J = 4.5, 1.5 Hz, 2H), 7.73 (d, J = 8.8 Hz, 2H), 6.95 (d, J = 8.8 Hz, 2H), 3.85 (s, 3H) ppm; 13C-NMR (CDCl3)
δ
162.7, 162.6, 157.1, 150.7, 136.1, 130.4, 122.8, 122.0, 114.5, 55.4 ppm; HRMS (ESI) Calc C14H13N2O3
[M + H]+ 257.0921; found 257.0920.
(E)-4-Nitrobenzaldehyde O-isonicotinoyl oxime (21). Solvent: CHCl3; R.T.: 4 h; amine: Et3N; yellow
˝
crystals, yield 79%, mp 164 C (hexanes/ethyl acetate); IR (KBr): 1757, 1594 cm´1; 1H-NMR (CDCl3)
δ
8.86 (d, J = 5.7 Hz, 2H), 8.67 (s, 1H), 8.33 (d, J = 8.7 Hz, 2H), 8.01 (d, J = 8.7 Hz, 2H), 7.94 (d, J = 5.7 Hz,
2H) ppm; 13C-NMR (CDCl3)
δ 162.1, 155.2, 150.9, 149.8, 135.6, 135.4, 129.4, 124.2, 122.8 ppm; HRMS
(ESI) Calc C13H10N3O4 [M + H]+ 272.0666; found 272.0663.
3.3. DNA Photo-Cleavage Experiments
3.3.1. Cleavage of Supercoiled Circular pBluescript KS II DNA and pBR322
The reaction mixtures (20
µL) containing supercoiled circular pBluescipt KS II DNA stock solution
(Form I, 50 M/base pair, ~500 ng), compounds, and Tris buffer (25
µ
µM, pH 6.8) in Pyrex vials were
incubated for 30 min at 37 ˝C, centrifuged, and then irradiated with UV light (312 nm, 90 W) under
aerobic conditions at room temperature for 15 min. For the case of pBR322 plasmid DNA, the above
mentioned procedure has been followed. After centrifugion, the samples were irradiated with UVA
light (365 nm, 18 W) under aerobic conditions at room temperature for 120 min. After addition of
the gel-loading buffer (6X Orange DNA Loading Dye 10 mM Tris-HCl (pH 7.6), 0.15% orange G,
0.03% xylene cyanol FF, 60% glycerol, and 60 mM EDTA, by Fermentas), the reaction mixtures were
loaded on a 1% agarose gel with EB staining. The electrophoresis tank was attached to a power
supply at a constant current (65 V for 1 h). The gel was visualized by 312 nm UV transilluminator
and photographed by an FB-PBC-34 camera vilber lourmat. Quantitation of DNA-cleaving activities

Molecules 2016, 21, 864
15 of 21
was performed by integration of the optical density as a function of the band area using the program
“Image J” version 1.50.I [76].
3.3.2. Calculation of Single-Strand Damage (ss)% and Double-Strand Damage (ds)%
ss% and ds% damages were calculated according to the following Equations (1) and (2):
Form II
Form I ` Form II ` Form III
Form III
Form I ` Form II ` Form III
ss% “
ds% “
ˆ 100
ˆ 100
(1)
(2)
As Form II we consider Form II of each series minus Form II of the irradiated control DNA.
As Form I we consider Form I of each series. The amount of supercoiled DNA was multiplied by factor
of 1.43 to account for reduced ethidium bromide intercalation into supercoiled DNA.
3.4. Calculation of the N-O Bond Dissociation Energies
All ground state calculation were carried out using the unrestricted B3PW91/6-31g(d) method
without any symmetry constraint. The optimized structures were characterized as minima by frequency
calculation at the same level of theory. Bond dissociation energies (D0) calculated according the general
equation: D0 = E0(radical1) + E0(radical2)
corrected with zero point vibrational energy (ZPE) [77].
´
E0(molecule), where E0 is the calculated electronic energy
3.5. Interaction with CT DNA
In order to evaluate the biological behavior of selected compounds (1–3, 5, 8–15, 19 and 21) with
CT DNA, the compounds were initially dissolved in DMSO (1 mM). Mixing of such solutions with
the aqueous buffer DNA solutions used in the studies never exceeded 5% DMSO (v/v) in the final
solution. All studies were performed at room temperature. Control experiments with DMSO were
performed and no changes in the spectra were observed.
3.5.1. Study with UV Spectroscopy
The interaction of compounds 1–16, 19 and 21 with CT DNA was studied by UV spectroscopy
as a means to investigate the possible binding modes to CT DNA and to calculate the binding
constants to CT DNA (Kb). The UV spectra of a CT DNA solution (0.14–0.16 mM) were recorded in
the presence of the compounds at diverse [compound]/[DNA] mixing ratios (=r) as well as the
UV spectra of the compounds (10–100
µM) in the presence of increasing amounts of CT DNA
(r’ = 1/r = [DNA]/[compound] mixing ratios). Control experiments with DMSO were performed
and no changes in the spectra of CT DNA were observed.
The Kb constants (in M´1) were obtained by monitoring the absorbance changes at the
corresponding
λ
max
with increasing concentrations of CT DNA and were calculated by the ratio
of slope to the y intercept in plots [DNA]/(εA ´ εf) versus [DNA], according to the Wolfe-Shimer
equation [65]:
[DNA]
pεA ´ εfq
[DNA]
pεb ´ εfq Kb pεb ´ εfq
1
“
`
(3)
where [DNA] = is the concentration of CT DNA in base pairs, εA = Aobsd/[compound], εf = the
extinction coefficient for the free compound and εb = the extinction coefficient for the compound in the
fully bound form.
3.5.2. Viscometry
The viscosity of CT DNA ([DNA] = 0.1 mM) in buffer solution (150 mM NaCl and 15 mM
trisodium citrate at pH 7.0) was measured in the presence of increasing amounts of the compounds

Molecules 2016, 21, 864
16 of 21
(up to the value of r = 0.35). All measurements were performed at room temperature. The obtained
1/3
data are presented as (
η
/η0
)
versus r, where η is the viscosity of CT DNA in the presence of the
compound, and η0 is the viscosity of DNA alone in buffer solution.
3.5.3. Competitive Studies with EB
The competitive studies of each compound with EB were investigated with fluorescence emission
spectroscopy in order to examine the potential of the compound to displace EB from its DNA-EB
conjugate. The DNA-EB conjugate was prepared by the pre-treatment of 20 µM EB with 26 µM CT
DNA in buffer (150 mM NaCl and 15 mM trisodium citrate at pH 7.0) for 1 h. The possible intercalating
effect of the compounds was monitored by recording the variation of fluorescence emission spectra
(excitation wavelength at 540 nm) of the DNA-EB system upon stepwise addition of a solution of
the compound.
The Stern-Volmer constant (KSV, in M´1) is used to evaluate the quenching efficiency for each
compound according to the Stern-Volmer equation [69]:
Io
I
“ 1 ` kqτ0rQs “ 1 ` KSVrQs
(4)
where Io and I are the emission intensities in the absence and the presence of the quencher (i.e.,
compounds 16 19 and 21, respectively), [Q] is the concentration of the quencher, o = the average
lifetime of the emitting system without the quencher and kq = the quenching constant. KSV was
1
–
,
τ
obtained from the Stern–Volmer plots by the slope of the diagram Io/I versus [Q]. Taking
τ = 23 ns as
o
the fluorescence lifetime of the EB-DNA system [72], the quenching constants (kq, in M´1s´1) of the
compounds was determined.
4. Conclusions
Oxime esters are easily accessible on a large scale and can be stored for prolonged periods of time.
Aldoxime, ketoxime and amidoxime esters bearing the pyridine and p-nitrophenyl moieties as both
oxime substituents and/or ester conjugates were examined as DNA photocleavers. Both moieties
were found to be important for the activity. Those compounds exhibited good to excellent binding
to DNA and efficient DNA photocleavage, at 312 nm at a concentration of 100
17 19 and 21). Some selected compounds were able to photocleave DNA at 365 nm (
concentration of 500 M). Their mode of action seems to follow the N-O bond homolytic cleavage with
µM (1–
3,
5,
10,
11–15,
,
1–3, 5, 10 at a
µ
the generation of active p-nitrobenzoyl or p-pyridine carbonyloxyl radicals which attack DNA. Since
however, DNA photo-cleavage is a rather complicated phenomenon, some observed differences could
be attributed to other factors such as the presence of oxygen (which may produce reactive oxygen
species), the mode of DNA affinity or the existence of specific structures facilitating H-abstraction.
In general, for compounds with comparable structures, it seems that the lower the BDE the higher the
% DNA photocleavage. Compounds 4, 9 and 16, as well as 6–8, although they possessed adequate
to sufficient DNA binding activities, were found to lack DNA photocleavage activity, at the studied
conditions. Nevertheless, their affinity to DNA may also lead to other cancer therapeutic approaches
than photocleavage. Thus, the studied oxime esters emerge as lead compounds for the investigation of
cancer therapeutics, in general, and in the field of photo-chemotherapy and photo-dynamic therapy,
in particular.
Supplementary Materials: The following are available online at www.mdpi.com/1420-3049/21/7/864/s1.
Supplementary Information contains UV absorption spectra, UV spectra of representative compounds in the
[DNA]
presence of CT DNA, plots of
versus [DNA], EB-DNA fluorescence emission spectra in the presence of
pεA´εfq
compound 1, and Stern-Volmer quenching plot of EB-DNA fluorescence for the compounds.

Molecules 2016, 21, 864
17 of 21
Acknowledgments: We are obliged to the editors who totally waived the publishing fees for the manuscript.
We thank Assoc. A. K. Zarkadis (Univ. of Ioannina, Chemistry Department) for access to Gaussian 09, Revision
B.01 program for support on the calculation of the N-O bond energies of the compounds. We are thankful to the
ProFI (Proteomics Facility at IMBB-FORTH) for performing all the HRMS analyses.
Author Contributions: M.P. and N.-P.A. performed chemical synthesis and DNA photo-cleavage experiments;
P.S.G. performed DNA photo-cleavage experiments and calculations of N-O bond energies; M.K. contributed
reagents, materials and consulting for biology; A.E.K. contributed to NMR spectrometry, analyzed data and
consulted overall; K.D. performed the DNA affinity experiments; G.P. supervised the DNA affinity experiments
and wrote the corresponding part of the manuscript; K.C.F. conceived and designed the whole project, contributed
reagents and materials, supervised the chemical synthesis and DNA photo-cleavage experiments and prepared
the manuscript.
Conflicts of Interest: The authors declare no conflict of interest.
Abbreviations
The following abbreviations are used in this manuscript:
CT
calf-thymus
EB
ethidium bromide
Bond Dissociation Energy
tetrahydrofuran
BDE
THF
DMF
DMSO
DIPEA
Dimethyl formamide
Dimethyl sulfoxide
Diisopropyl ethyl amine
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