Open Access Article
Ying
Zhou‡
,
Krzysztof
Bielec‡
,
Pakorn
Pasitsuparoad
and
Robert
Hołyst
*
Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland. E-mail: rholyst@ichf.edu.pl
First published on 20th July 2020
Anthracyclines are one of the most studied anticancer drugs approved for medical treatment. The equilibrium constant (K) of the reaction between these drugs with DNA in both in vitro and in vivo experiments lacks consensus. The K values vary from 104 up to 108 M−1, which suggest a 1000-fold error in determining the effective concentration needed to form the drug–DNA complex. Until 2014, only one study by García [J. Phys. Chem. B, 2014, 118, 1288–1295] showed that the binding of anthracycline representative doxorubicin occurs in two reactions. We support this result by brightness analysis at a single molecular level for the four most common anthracyclines: doxorubicin, daunorubicin, epirubicin, and idarubicin.
Due to the cardio-toxicity and dose resistance of DOX, people prefer to use the less harmful DOX derivatives–daunorubicin (DNR), epirubicin (EPR), and idarubicin (IDR) in cancer treatment.11 However, compared with DOX, there are fewer kinetic studies about these anthracycline–DNA interactions. In addition, the reported K values suggest a similar methodological inaccuracy as that in the case of DOX (see Table 2). Considering the structures of these drugs, they are all tetracenequinone-based chromophore groups and possess the positive nitrogen on the sugar moiety. It was inferred that the small structural differences of the hydroxyl groups (Fig. 1) should not significantly affect the K values of these drugs in their reaction with DNA. However, there is still a lack of systematic kinetic studies to compare the kinetics of these four drugs. Will they share the same reaction mechanism with the corresponding K values?
In our previous work, we developed a sensitive and accurate method to determine the equilibrium constant based on the molecular brightness (MB) of a single fluorophore. We have used this approach previously to determine the strength of the interaction between a pair of complementary oligonucleotides labeled with only one dye, even at 100 pM concentration of DNA strands.19 We define MB as the number of photons emitted by a number of molecules (e.g. anticancer drug) inside the confocal volume. After the formation of a drug–DNA complex, its MB could be enhanced or quenched, and thus the number of emitted photons changes.20K was determined using the ratio of the MB of drug molecules at free and bound states at a given concentration of the second substrate. With this approach, even a slight change in the number of emitted photons can be distinguished.
Here, we report a revised mechanism of DOX–, DNR–, EPR–, and IDR–DNA interactions consisting of two reactions, following with the corresponding K in each one. We observed the MB change of each drug at a single molecular level in the formation of the drug–DNA complexes. We proposed the structural model of interaction in the second reaction by analyzing drug fluorescence anisotropy properties. The determined average K in experiments with DOX binding to the different structures (linear or circular) and lengths of DNA (from 20 bp to 48 kbp) are equal to (6.9 ± 1.4) × 107 M−1 in the first reaction and (1.5 ± 0.6) × 106 M−1 in the second one. By monitoring the MB change of each drug, we proposed the structural binding insights and determined the transition point between each reaction (around 0.4 drug molecules per bp). The determined K values in the first (K1) and the second reaction (K2) show around a 40-time difference among all four anthracyclines.
502 bp) were purchased from Thermo Fisher Scientific, USA; and purified calf thymus DNA (ct DNA, 13
200 bp) was purchased from Merck KGaA, Darmstadt, Germany. All types of DNA were stored in standard Tris-EDTA buffer at −20 °C. In a typical experiment for K determination, the selected DNA was diluted into a series of working concentrations from 800 nM to 80 nM of bp (in terms of bp); there were 16 concentrations in total. No chemicals were further purified unless specifically stated.
The anthracycline working solution was mixed in equal volumes with the DNA. The mixture was incubated over 12 hours at 25 °C before measurement. The final concentration of anthracycline in the experiment was set at 40 nM unless explicitly stated otherwise.
| V0·NA·cdrug·α = Ndrug·α = I0 | (1) |
When DNA is added into the drug solution, the drug molecules intercalate into the bp of DNA.
The fluorescent components in the system are the drug molecules and drug–DNA complexes. Now, the measured number of photons is I1. The drug–DNA complexes have an intrinsic MB γ1, which is different from that of drug MB (α). Therefore, eqn (1) changes to:
| V0·NA·(α·ceqdrug + γ1·ceqdrug–DNA) = I1 | (2) |
The equilibrium constant in this reaction (K1) is given by:
After transformation, I1 can be re-written as:
![]() | (3) |
Recent works show that besides a simple intercalation of DOX to DNA, there is a second interaction mechanism.3,4,9 The second reaction mechanism is the formation of the external complexes between the DOX molecules and the formed DOX–DNA complexes. The impact of this reaction becomes apparent when all the available binding sites on the DNA chain are occupied by DOX molecules, although they occur at the same time.3 The second reaction can be illustrated as:
The drug–(drug–DNA) complexes formed in the second reaction have an intrinsic MB γ2, which is different from α and γ1. In this case, after the addition of the DNA, three fluorescent components can be present in the reaction system (there is no formation of transition state), but the count rate I1 is still the same. Thus, eqn (2) can be written as:
![]() | (4) |
The equilibrium constant in the second reaction (K2) is given by:
Finally, I1 can be transformed into:
![]() | (5) |
In the ESI,† we have described all of the steps to obtain eqn (3) and (5) in detail. To determine K1 and K2 in eqn (5), we measured the MB of each component (α, γ1, and γ2). More specifically, (1) α is determined in one FCS experiment (see Fig. 2, the details can be seen in our previous work6); (2) γ1 is evaluated in a titration experiment when cDNA ≫ cdrug; (3) γ2 is evaluated by a titration experiment when cDNA ≪ cdrug.
The average bp number per binding site is 3.1.21 We expected to reach the saturation of the available binding sites when R was 0.32. Thus, we focused on the regime where 0 < R ≤ 1 to determine the MB of the formed complexes. To determine the MB of each complex, we set the intercept of the linear fitting as DOX MB in each regime. In the first regime (R < 0.4), DOX lost 8.36 ± 1.92 fold of its initial MB, while in the second regime (R > 0.4), we observed a 2.28 ± 0.01-fold decrease. Our determined cross-over point (R = 0.39 ± 0.05) of the two regimes was in good relation with the previously reported number of 0.35.3
The DOX MB loss in the first regime (R < 0.4) can be explained as follows: when there are enough binding sites on the DNA chain, the aromatic group of DOX molecules will intercalate into the DNA bp through π-stacking interactions.22 Due to the stacking, the motion of the DOX aromatic groups is fully limited, leading to a dramatic fluorescence quenching.20 Meanwhile, two possible mechanisms can explain the smaller DOX MB loss in the second regime (R > 0.4). The first hypothesis is chemical interaction. In the formation of a second complex, the DOX molecules bind to the occupied binding sites with a similar conformation as that in the first reaction,4 although the influence on MB of DNA is lower as the first molecule compensates most of the initial interactions. In the second hypothesis, we infer that the chromophore group of the DOX molecules did not participate in the interaction as actively as that in the first reaction. Previous reports suggest an interaction between the positive N3′ nitrogen on the amino sugar of the DOX molecule and the backbone of the negatively charged DNA.2–4,9 Based on the rotation hypothesis, we assume that in the second mechanism, the aminoglycoside ring of the DOX molecules will interact electrostatically with DNA. In such a model (Fig. 4c), the rotational motion of the chromophore group in the DOX molecules is only partially limited; thus, the DOX molecules can emit more photons (the MB loss is less).9,23
To find out which hypothesis in the second interaction mechanism is more accurate, we performed the brightness analysis with different types of DNA: from the very short 20 bp DNA to the very long 48k bp DNA and from the linear 2500 bp DNA to 2686 bp circular plasmid DNA (see Fig. 5). We calculated the relative DOX MB loss as the ratio of free DOX MB to the formed complex MB in each interaction. The larger the value, the more the MB loss. On average, the DOX molecules lost 16.56 ± 10.70 fold of the initial MB during the formation of the first complex and 2.45 ± 0.50 fold in the second one.
There is a correlation between the length of DNA and MB (the longer the DNA, the more significant the MB loss) in the first reaction, except for circular DNA. The MB loss of the second complex was similar irrespective of the DNA length or structure. The structure of the DOX molecules does not allow to transform it into other quenched conformations such as the case of Cy3 dye (trans- to cis-isomerization). The phenomenon in the first reaction can be explained as follows: when the DOX–DNA complexes are formed, the DOX molecules are trapped in the DNA backbone. With the increase in the number of the negatively charged bps in the DNA backbone, the electron polarization increases, which reduces the number of photons emitted from the chromophore group.24 The exception is the circular plasmid DNA, in which the DOX molecules lost more than 37-fold of the initial MB. The excitation of the DOX molecules depends on the proper orientation of the transition dipole moment (see Fig. 4(a)). The random orientation of the twisted linear DNA backbone makes the DOX MB change independent of fluorescence anisotropy. The DOX molecules that bind with circular DNA have a higher orientation order. As a result, they are more dependent on the dipole vector position of the DNA (see Fig. 4(b)). While in the second reaction, the similar MB loss shows that the rotation of the DOX molecules is not limited by the DNA chain. We infer that during the formation of DOX–(DOX–DNA) complexes, the interaction occurs between the aminoglycoside ring of the DOX molecules and the formed DOX–DNA complexes. Since the tetracenequinone chromophore group of the excess DOX can freely rotate, more photons can be emitted, leading to less and similar DOX MB in all DNA (see Fig. 4(c)).
and
as a ratio of the initial DOX MB loss in the first and second complex formations, respectively. Along with either eqn (3) or (5), we determined the value of K1 and K2. We kept a constant DOX concentration (40 nM) and varied the DNA concentration. In each titration point, we measured the count rate and plotted it as a function of initial DNA concentration cbp (see Fig. 6(a)). Instead of fitting the function to the obtained data points with all released variables, we divided the series into previously specified regimes (R1 < 0.4 < R2). We determined K1 by fitting eqn (3) only to the points corresponding to the regime R1 < 0.4. After getting K1, we obtained K2 by fitting all data points with eqn (5). We performed the titration experiments on all DNA strands along with the corresponding MB and the results are shown in Fig. 6b. The average equilibrium constant is (8.3 ± 1.2) × 107 M−1 in the first reaction and (2.0 ± 0.5) × 106 M−1 in the second one. The difference in the equilibrium constant values between those reactions is around 40 times, whereas in Gracia's report, this difference is 200 times.3 This discrepancy could be caused by the ionic strengths we used in our measuring conditions. In the previous reports of DOX–DNA interaction, when the sodium concentration increases from 2.5 mM to 63 mM, the K value decreases from 108 M−1 to 107 M−1.2,3 The weaker the ionic strength, the larger the K value. Since the ionic strength in our measurement was four times stronger than that in Garcia's report,3 it is reasonable for us to have a five times smaller K than them.
The length or the structure of DNA does not affect the K values, except for the K2 obtained with 20 bp DNA (see statistical analysis in Fig. 6(b)). Our method is based on collecting the direct signal from the reaction pool, so that even a single photon change can be monitored. In comparison, the determination of K by the FCS method is not based on observing the MB change in each reaction (even for long DNA). The FCS experiment is based on an analysis of the fluctuation of the fluorescence signal. Thus, the signal from the components with different MB would be averaged by the correlation function.
To ensure that the brightness analysis is observed only by the reaction between the DOX molecules and DNA, we tested the self-aggregation of DOX at our working concentration (40 nM). We checked the possibility of DOX aggregation with UV-vis spectroscopy. From the results of the absorption and emission spectra, we did not observe dimers or higher aggregates of DOX molecules at our working concentration (the details are shown in ESI†).
All three anthracyclines show a similar trend in MB change as DOX. Firstly, a strong MB loss (on average, 8.74 ± 3.10 fold) in the first reaction and then a slight MB loss (averagely, 2.08 ± 0.32 fold) in the second reaction. We determined the cross-over points of the DNR–, EPR– and IDR–DNA interactions with values equal to 0.33 ± 0.04, 0.43 ± 0.04, and 0.30 ± 0.00, respectively. The results prove that the two reaction mechanisms are also present for DOX analogs.
Next, we determined K1 and K2 for those DOX analogs in the reaction with 69 bp DNA. Each measurement was repeated twice to exclude the random error. No self-aggregation of the drugs was observed under UV-vis spectroscopy measurements within the working range (the details can be seen in the ESI†). The obtained K values for all four drugs are presented in Fig. 8.
The formation of the first complex of DOX, DNR, EPR, and IDR with DNA have K1 equal to (7.8 ± 0.2) × 107 M−1, (7.7 ± 1.1) × 107 M−1, (7.5 ± 0.9) × 107 M−1, and (4.8 ± 0.2) × 107 M−1, respectively. In the second reaction, DOX, DNR, EPR, and IDR have K2 equal to (2.1 ± 0.4) × 106 M−1, (9.8 ± 1.0) × 105 M−1, (1.6 ± 0.0) × 106 M−1, and (1.5 ± 0.1) × 106 M−1, respectively.
Determination of the reaction mechanism using the brightness analysis method was possible due to the significant difference in the strength of the interaction and brightness between the formed complexes of the individual reactions. The observation of the inflection point during the determination of the complex MB was a crucial part of the research. We expect no significant differences in the association/disassociation kinetics among those drugs in the binding with DNA based on the collected data during the analysis of the four most popular anthracyclines.
Footnotes |
| † Electronic supplementary information (ESI) available. See DOI: 10.1039/D0AN01108H |
| ‡ These authors contributed equally to this work. |
| This journal is © The Royal Society of Chemistry 2020 |