STYRYL QUINOLINIUM, PROCESS FOR THEIR PREPARATION AND USE THEREOF AS FLUORESCENT PROBES FOR IMAGING

Abstract

The present invention is directed to styryl quinolinium compounds, a process for their synthesis and their use for selective nucleoli staining in cells, preferably in living cells and for imaging rRNA.

Claims

1. A compound of formula (I): ##STR00017## wherein: R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5 are independently selected from H, F, Cl, Br, I, OR, NHR, NR.sub.2, CN, R′SO.sub.3, (R′).sub.4N, (R′).sub.3NH, NO.sub.2. R is independently selected from H or straight or branched C.sub.1-6alkyl; R′ is straight or branched C.sub.1-6 alkyl; and X.sup.− is Cl, Br, I; provided that: in case R.sub.3 is Cl, then one of R.sub.1, R.sub.2, R.sub.4, R.sub.5 is not H; in case R.sub.3 is N(CH.sub.3).sub.2, then one of R.sub.1, R.sub.2, R.sub.4, R.sub.5 is not H; in case R.sub.2 and R.sub.3 are both OCH.sub.3, then one of R.sub.1, R.sub.4, R.sub.5 is not H.

2. The compound of claim 1, wherein R.sub.1 is H, F, Cl, or OR, R.sub.2 is H, F, Cl, OR, NO.sub.2 or CN, R.sub.3 is H, OR, NHR or NR.sub.2, R.sub.4 is H, F, Cl, CN, NO.sub.2, R.sub.5 is H, F, Cl; R being H, or straight or branched C.sub.1-6alkyl and X is I.

3. The compound of claim 1, wherein R.sub.1 is H, F, or OH, R.sub.2 is H, F, OR, NO.sub.2 or CN, R.sub.3 is H, OR, NHR or NR.sub.2, R.sub.4 is H, F, CN or NO.sub.2, R.sub.5 is H or F; R being H, or straight or branched C.sub.1-6alkyl and X is I.

4. A compound according to claim 1, selected from: (E)-2-(4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-a); (E)-2-(4-Methoxystyryl)-1,4-dimethylpyridinium iodide (I-b); (E)-2-(3-Flouro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-c); (E)-2-(3-Flouro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-d); (E)-2-(3, 5-Difluoro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-e); (E)-2-(3, 5-Difluoro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-f); (E)-2-(2,3,5,6-Tetrafluoro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-g); (E)-2-(2,3,5,6-Tetrafluoro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-h); (E)-2-(4-Dimethylaminostyryl)-1,4-dimethylpyridinium iodide (I-i); (E)-2-(3,4-Dihydroxystyryl)-1,4-dimethylpyridinium iodide (I-j); (E)-2-(2-Hydroxy-3-methoxy-5-nitrostyryl)-1,4-dimethylpyridinium iodide (I-k); and (E)-2-(4-Hydroxy-3-nitrostyryl)-1,4-dimethylpyridinium iodide (I-l).

5. A process for the preparation of compound of formula (I) comprising: reacting a compound of formula (II) ##STR00018## with a compound of formula (III) ##STR00019## in the presence of a base and a straight or branched C.sub.1-4alcohol and heating; wherein: R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5 are independently selected from H, F, Cl, Br, I, OR, NHR, NR.sub.2, CN, NO.sub.2; R is independently selected from H or straight or branched C.sub.1-6alkyl; and X.sup.− is Cl, Br, I.

6. The process according to claim 5, wherein the base is a nitrogen base selected from pyridine, piperidine, the C.sub.1-4alcohol is selected from methanol, ethanol, propanol, isopropanol, butanol, sec-butyl alcohol, tert-butyl alcohol and heating is conducted under microwave irradiation.

7. A of formula (I): ##STR00020## wherein: R.sub.1, R.sub.2, R.sub.3, R.sub.4, R.sub.5 are independently selected from H, F, Cl, Br, I, OR, NHR, NR.sub.2, CN, R′SO.sub.3, (R′).sub.4N, (R′).sub.3NH, NO.sub.2. R is independently selected from H or straight or branched C.sub.1-6alkyl; R′ is straight or branched C.sub.1-6 alkyl; and X.sup.− is Cl, Br, I; provided that: in case R.sub.3 is Cl, then one of R.sub.1, R.sub.2, R.sub.4, R.sub.5 is not H; in case R.sub.3 is N(CH.sub.3).sub.2, then one of R.sub.1, R.sub.2, R.sub.4, R.sub.5 is not H; in case R.sub.2 and R.sub.3 are both OCH.sub.3, then one of R.sub.1, R.sub.4, R.sub.5 is not H; for use in staining nucleoli in cells or for use as a fluorescent probe in imaging rRNA.

8. A compound of claim 7 for use as a fluorescent probe in imaging rRNA.

9. A compound of claim 7 for use in imaging rRNA.

10. The compound for the use of claim 7, selected from: (E)-2-(4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-a); (E)-2-(4-Methoxystyryl)-1,4-dimethylpyridinium iodide (I-b); (E)-2-(3-Flouro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-c); (E)-2-(3-Flouro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-d); (E)-2-(3, 5-Difluoro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-e); (E)-2-(3, 5-Difluoro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-f); (E)-2-(2,3,5,6-Tetrafluoro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-g); (E)-2-(2,3,5,6-Tetrafluoro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-h); (E)-2-(4-Dimethylaminostyryl)-1,4-dimethylpyridinium iodide (I-i); (E)-2-(3,4-Dihydroxystyryl)-1,4-dimethylpyridinium iodide (I-j); (E)-2-(2-Hydroxy-3-methoxy-5-nitrostyryl)-1,4-dimethylpyridinium iodide (I-k); and (E)-2-(4-Hydroxy-3-nitrostyryl)-1,4-dimethylpyridinium iodide (I-l).

11. The compound of claim 10 being I-e.

12. A method for imaging rRNA comprising adding a compound of claim 1 to a sample containing rRNA, and imaging the fluorescence.

13. The method according to claim 12, wherein the compound is of formula I-e.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

[0024] In order to better understand the subject matter that is disclosed herein and to exemplify how it may be carried out in practice, embodiments will now be described, by way of non-limiting example only, with reference to the accompanying drawings, in which:

[0025] FIG. 1 provides evidence for variance of color of the solution solubilizing a compound of the present invention (I-e) depending on the solvent and its polarity. The solvents are (left to right): acetic acid, water, methanol, ethanol, isopropanol, DMSO, DMF, acetone and dichloromethane.

[0026] FIG. 2 demonstrates the photostability of dyes I-a-I-l measured by the loss of fluorescence intensity (2 μM dye, in PBS buffer).

[0027] FIG. 3 provides emission spectra of compound I-e with RNA in water. Compound I-e alone (black), RNA solution+compound I-e (blue), compound I-e+RNA solution+RNASE, control, (green), water+RNASE, control, (red).

[0028] FIGS. 4A-D: provides spectrum scan showing peak of excitation/emission.

[0029] FIG. 4A; compound I-e was added to HeLa cells and these were scanned as described in the Methods section. The strongest excitation, at the emission range of 647-667 nm was found to be 570 nm. Bar=10 μm.

[0030] FIG. 4B; images were analyzed as described in the Methods and the image emission intensities were plotted. The excitation that resulted in the strongest emission was found to be at 570 nm.

[0031] FIG. 4C; 2D heat map exported from acquisition software showing the excitation vs. the emission profiles.

[0032] FIG. 4D; compound I-e localizes to nucleoli in treated cells. Nucleoli are identified by staining with an antibody to the nucleolar marker fibrillarin (green). Hoechst DNA stain is in cyan. No 12e signal is detected in untreated cells. Bar=10 μm.

[0033] FIGS. 5A-C: Compound I-e rapidly stains living HeLa cells and does not affect viability.

[0034] FIG. 5A; Cells were imaged every 5 sec for 5 min. The compound entered the cells within 30 sec and stained nucleoli within 150 sec.

[0035] FIG. 5B; Cells were then imaged every 15 min for 26 hours and the compound intensity remained strong and specific to the nucleoli. The cells remained viable. Bar=20 μm.

[0036] FIG. 5C; Signal-to-noise ratio pixel intensity graph of nucleoli/nucleus and nucleoli/outside of the cell derived from ImageJ software.

[0037] FIGS. 6A-B: Compound I-e binds to RNA in cells.

[0038] FIG. 6A; Wide-field fluorescence images of untreated or DNase treated cells stained with the compound I-e. Hoechst DNA stain is in cyan.

[0039] FIG. 6B; Untreated cells or cells treated with RNase or with the actinomycin D transcriptional inhibitor. DIC images are in grey. Bar=10 μm.

[0040] FIGS. 7A-B: demonstrates the binding of compound I-e to rRNA in cells.

[0041] FIG. 7A; transcriptional inhibition of RNA polymerase I by CX-5461 and BMH-21 diminishes the fluorescence signal of compound I-e in cells.

[0042] FIG. 7B; stress granules formed by arsenite treatment and labeled with anti-G3BP1 (green) do not contain compound I-e (white). Hoechst DNA stain is in cyan. DIC is in grey. Bar=10 μm.

[0043] FIG. 8. Provides evidence that compound I-e binds to secondary structures in rRNA. The binding of compound I-e to rRNA and mRNA in solution at room temperature and at 90° C. In the presence of structured rRNA there is an increase in the fluorescent signal; however, when the samples were heated and the secondary structures of the rRNA are dismantled, then no increase in fluorescence was observed.

[0044] FIG. 9. Provides fluorescence spectra evidencing the binding of compound I-e to DNA without histones

DETAILED DESCRIPTION OF EMBODIMENTS

[0045] The present invention is directed to styryl quinolinium compounds of formula (I), their synthesis and use. The unique process of synthesis by employing microwave irradiation provides a much higher yield than refluxing the solvent and a shorter duration of the reaction.

[0046] Straight or branched alkyl groups according to the present application are straight or branched —CH.sub.3, —C.sub.2H.sub.5, C.sub.3H.sub.7, C.sub.4H.sub.9, C.sub.5H.sub.11, C.sub.6H.sub.13 groups.

[0047] Generally, the synthesis of the styryl quinolinium compounds of formula (I), was conducted by the following path (Knoevenagel condensation):

##STR00003##

[0048] Where heating varied from 5-40 minutes in a microwave at a temperature of 65° C.-85° C. or for 5-20 hours under reflux. The former process is superior by its yield and duration. The base may be selected from pyridine, piperidine, the C.sub.1-4alcohol is selected from methanol, ethanol, propanol, isopropanol, butanol, sec-butyl alcohol, tert-butyl alcohol.

[0049] More particularly, the reaction was carried in the presence of piperidine in ethanol in a microwave as follows:

##STR00004##

[0050] In particular, specific compounds of formula (I) are: [0051] (E)-2-(4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-a); [0052] (E)-2-(4-Methoxystyryl)-1,4-dimethylpyridinium iodide (I-b); [0053] (E)-2-(3-Flouro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-c); [0054] (E)-2-(3-Flouro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-d); [0055] (E)-2-(3, 5-Difluoro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-e); [0056] (E)-2-(3, 5-Difluoro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-f); [0057] (E)-2-(2,3,5,6-Tetrafluoro-4-hydroxystyryl)-1,4-dimethylpyridinium iodide (I-g); [0058] (E)-2-(2,3,5,6-Tetrafluoro-4-methoxystyryl)-1,4-dimethylpyridinium iodide (I-h); [0059] (E)-2-(4-Dimethylaminostyryl)-1,4-dimethylpyridinium iodide (I-i); [0060] (E)-2-(3,4-Dihydroxystyryl)-1,4-dimethylpyridinium iodide (I-j); [0061] (E)-2-(2-Hydroxy-3-methoxy-5-nitrostyryl)-1,4-dimethylpyridinium iodide (I-k); and [0062] (E)-2-(4-Hydroxy-3-nitrostyryl)-1,4-dimethylpyridinium iodide (I-l).

[0063] The compounds, depending on their substituents vary in their properties such as their solubility, absorbance wavelength, quantum yield and photostability. These properties vary depending on the nature of the solvent as well. The styryl quinolinium compounds of formula (I), were found to be nontoxic to leaving cells and therefore may be used for staining cells, particularly living cells and fluorescent probes for imaging, particularly rRNA. The compounds of the present invention display unique and specific properties when stain and dye living cells. The compounds clearly show preference to binding to secondary structures in the rRNA, wherein under heating when the secondary structure disappears, binding is lost.

[0064] The invention will now be described with reference to the following non-limiting Examples and drawings.

Example 1: Chemical Synthesis

[0065] A mixture of compounds (II) and (III) was irradiated at a temperature of about 65° C.-85° C. To a 10 mL microwave reaction vessel equipped with a magnetic stirring bar were added 1,4-dimethyl quinolinium iodide ((II); 0.5 mmol), absolute ethanol (5 mL), piperidine (cat. amount), and a substituted benzaldehyde ((III); 0.5 mmol). Thus 3,5-Difluoro-4-hydroxybenzaldehyde, or 2,3,5,6-Tetrafluoro-4-hydroxybenzaldehyde (whose .sup.1H NMR, .sup.13C NMR, .sup.19F NMR and High Resolution Mass Spectrum (HRMS) are given below are exemplified. The vessel was sealed, and the mixture was irradiated in a microwave oven (CEM Focused Microwave type Discover) for 5 to 30 min at 70-80° C. (as indicated in Table 1). Then the reaction mixture was cooled to RT, and diethyl ether (10 mL) was added to precipitate the products as black crystals. The latter were vacuum-filtered and washed 3×3 mL with diethyl ether to yield pure products. In a similar manner all compounds I-a-I-l were isolated in a high yield, >95% purity e as determined by .sup.1H NMR, .sup.13C NMR, .sup.19F NMR, DEPT, UV and HRMS.

[0066] Following are the .sup.1H NMR, .sup.13C NMR and/or .sup.19F NMR and HRMS of compounds of two compounds of formula (III) and of the I-a-I-l styryl quinolinium compounds.

3,5-Difluoro-4-hydroxybenzaldehyde

[0067] .sup.1H-NMR (400 MHz, CDCl.sub.3): 9.82 (t, J=1.8 Hz, 1H), 7.49 (d, J=6.4 Hz, 2H). .sup.13C NMR (ppm): 190.93, 152.32, 137.15, 132.74, 111.53. .sup.19F NMR (376 MHz, CDCl.sub.3) δ −135.14 ppm. HRMS Calcd for C.sub.7H.sub.4F.sub.2O.sub.2 m/z 158.03035, Found 158.03024.

2,3,5,6-Tetrafluoro-4-hydroxybenzaldehyde

[0068] .sup.1H NMR (DMSO, 400 MHz): δ 10.22 (s, 1H), 3.36 (bs, 1H). .sup.13C NMR (DMSO 75.45 MHz): δ 91.5, 98.7, 136.1, 139.5, 143.2, 146.5, 182.3. Calcd for C.sub.7H.sub.2F.sub.4O.sub.2 m/z 194.09183, Found 193.09189.

##STR00005##

(E)-2-(4-hydroxystyryl)-1,4-dimethylpyridinium Iodide (I-a)

[0069] .sup.1H-NMR (400 MHz, DMSO (d6)): 8.97 (d, 5.89 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 7.93 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 6.95 (d, 8.72 Hz, 2H, Ar), 4.31 (s, 3H, +NCH.sub.3). .sup.13C NMR (ppm): 157.71, 157.32, 142.85, 132.54, 130.83, 130.52, 129.98, 129.54, 128.14, 126.91, 126.71, 125.02, 123.82, 119.87, 116.16, 115.95, 46.92. HRMS Calcd for C.sub.18H.sub.16NOI m/z 389.23025, Found 389.23024.

##STR00006##

(E)-2-(4-Methoxystyryl)-1,4-dimethylpyridinium Iodide (I-b)

[0070] .sup.1H-NMR (400 MHz, DMSO (d6)): 8.96 (d, 5.89 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 7.93 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 6.95 (d, 8.72 Hz, 2H, Ar), 4.31 (s, 3H, +NCH.sub.3), 3.92 (s, 3H, OCH.sub.3). .sup.13C NMR (ppm): 157.71, 157.32, 142.85, 132.54, 130.83, 130.52, 129.98, 129.54, 128.14, 126.91, 126.71, 125.02, 123.82, 119.87, 116.16, 115.95, 55.52, 46.92. HRMS Calcd for C.sub.19H.sub.18NOI m/z 403.48018, Found 403.48026.

##STR00007##

(E)-2-(3-Flouro-4-hydroxystyryl)-1,4-dimethylpyridinium Iodide (I-c)

[0071] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.06 (d, 5.89 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 8.43 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 6.95 (d, 8.72 Hz, 1H, Ar), 4.31 (s, 3H, +NCH.sub.3). .sup.13C NMR (ppm): 157.81, 153.33, 147.45, 146.94, 139.83, 136.62, 133.44, 129.98, 126.14, 125.14, 124.91, 123.76, 123.09, 122.12, 118.67, 117.46, 112.65, 45.32. .sup.19F NMR −130.94 ppm. HRMS Calcd for C.sub.18H.sub.15FNOI m/z 407.22431, Found 407.21909.

##STR00008##

(E)-2-(3-Flouro-4-methoxystyryl)-1,4-dimethylpyridinium Iodide (I-d)

[0072] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.06 (d, 5.89 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 8.43 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 6.95 (d, 8.72 Hz, 1H, Ar), 4.31 (s, 3H, +NCH.sub.3), 3.82 (s, 3H, OCH.sub.3). .sup.13C NMR (ppm): 157.81, 153.33, 147.45, 146.94, 139.83, 136.62, 133.44, 129.98, 126.14, 125.14, 124.91, 123.76, 123.09, 122.12, 118.67, 117.46, 112.65, 55.23, 45.32. .sup.19F NMR −129.83 ppm. HRMS Calcd for C.sub.19H.sub.17FNOI m/z 421.49363, Found 421.51019.

##STR00009##

(E)-2-(3, 5-Difluoro-4-hydroxystyryl)-1,4-dimethylpyridinium Iodide (I-e)

[0073] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.02 (d, 5.8 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 7.93 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 4.31 (s, 3H, +NCH.sub.3). .sup.13C NMR (ppm): 157.81, 153.33, 147.45, 146.94, 139.83, 136.62, 133.44, 129.98, 126.14, 125.14, 124.91, 123.76, 123.09, 122.12, 118.67, 117.46, 112.65, 45.32. .sup.19F NMR −133.13 ppm. HRMS Calcd for C.sub.18H.sub.14F.sub.2NOI m/z 425.22031, Found 425.21901.

##STR00010##

(E)-2-(3, 5-Difluoro-4-methoxystyryl)-1,4-dimethylpyridinium Iodide (I-f)

[0074] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.02 (d, 5.8 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 7.93 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 4.31 (s, 3H, .sup.+NCH.sub.3), 3.83 (s, 3H, OCH.sub.3). .sup.13C NMR (ppm): 157.81, 153.33, 147.45, 146.94, 139.83, 136.62, 133.44, 129.98, 126.14, 125.14, 124.91, 123.76, 123.09, 122.12, 118.67, 117.46, 112.65, 62.35, 45.32. .sup.19F NMR −133.13 ppm. HRMS Calcd for C.sub.19H.sub.16F.sub.2NOI m/z 439.14021, Found 439.15001.

##STR00011##

(E)-2-(2,3,5,6-Tetrafluoro-4-hydroxystyryl)-1,4-dimethylpyridinium Iodide (12g)

[0075] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.02 (d, 5.8 Hz, 1H, Ar), 8.63 (d, 7.8 Hz, 1H, Ar), 8.41 (d, 5.4 Hz, 1H, Ar), 8.23 (dd, 7.8, 5.4 Hz, 1H, Ar), 8.11 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.84 (d, 5.8 Hz, 1H, Ar), 7.22 (d, 16.1 Hz, 1H, CH═CH), 6.78 (d, 16.1 Hz, 1H, CH═CH), 4.31 (s, 3H, .sup.+NCH.sub.3). .sup.13C NMR (ppm): 157.81, 153.33, 147.45, 146.94, 139.83, 136.62, 133.44, 129.98, 126.14, 125.14, 124.91, 123.76, 123.09, 122.12, 118.67, 117.46, 112.65, 45.32. .sup.19F NMR −156.27, −133.13 ppm. HRMS Calcd for C.sub.18H.sub.12F.sub.4NOI m/z 461.77062, Found 461.77059.

##STR00012##

(E)-2-(2,3,5,6-Tetrafluoro-4-methoxystyryl)-1,4-dimethylpyridinium Iodide (12-h)

[0076] The dye was not sufficiently soluble in any solvent in order to perform NMR tests. HRMS Calcd for C.sub.19H.sub.14F.sub.4NOI m/z 475.26041, Found 475.26039.

##STR00013##

(E)-2-(4-Dimethylaminostyryl)-1,4-dimethylpyridinium Iodide (I-i)

[0077] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.11 (d, 5.89 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 7.93 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 6.95 (d, 8.72 Hz, 2H, Ar), 4.42 (s, 3H, +NCH.sub.3), 3.01 (s, 6H, N(CH.sub.3).sub.2). 157.71, 157.32, 142.85, 132.54, 130.83, 130.52, 129.98, 129.54, 128.14, 126.91, 126.71, 125.02, 123.82, 119.87, 116.16, 115.95, 46.92, 41.39. HRMS Calcd for C.sub.20H.sub.21N.sub.2I m/z 416.71421, Found 416.71409.

##STR00014##

(E)-2-(3,4-Dihydroxystyryl)-1,4-dimethylpyridinium Iodide (I-j)

[0078] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.02 (d, 5.89 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 7.93 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.29 (s, 1H, Ar), 7.17 (s, 1H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 6.95 (d, 8.72 Hz, 2H, Ar), 6.64 (s, 1H, Ar), 4.31 (s, 3H, +NCH.sub.3). .sup.13C NMR (ppm): 160.6, 157.42, 146.32, 140.05, 139.51, 136.83, 133.44, 126.08, 125.84, 125.61, 124.91, 124.03, 123.99, 123.82, 122.87, 119.35, 118.95, 111.77, 46.02. HRMS Calcd for C.sub.18H.sub.15BrNOI m/z 405.13662, Found 405.13648.

##STR00015##

(E)-2-(2-Hydroxy-3-methoxy-5-nitrostyryl)-1,4-dimethylpyridinium Iodide (I-k)

[0079] The dye was not sufficiently soluble in any solvent in order to perform NMR tests. HRMS Calcd for C.sub.19H.sub.17N.sub.2O.sub.4I m/z 464.26553, Found 464.25919.

##STR00016##

(E)-2-(4-Hydroxy-3-nitrostyryl)-1,4-dimethylpyridinium Iodide (I-l)

[0080] .sup.1H-NMR (400 MHz, DMSO (d6)): 9.06 (d, 5.89 Hz, 1H, Ar), 8.68 (d, 8.5 Hz, 1H, Ar), 8.43 (d, 16.1 Hz, 1H, CH═CH), 7.91 (d, 16.1 Hz, 1H, CH═CH), 7.8 (d, 7.8 Hz, 1H, Ar), 7.66 (dd, 8.5, 7.8 Hz, 1H, Ar), 7.57 (d, 5.8 Hz, 1H, Ar), 7.31 (d, 8.72 Hz, 2H, Ar), 7.16 (dd, 8.5, 7.8 Hz, 1H, Ar), 6.95 (d, 8.72 Hz, 1H, Ar), 4.31 (s, 3H, +NCH.sub.3). .sup.13C NMR (ppm): 157.81, 153.33, 147.45, 146.94, 139.83, 136.62, 133.44, 129.98, 126.14, 125.14, 124.91, 123.76, 123.09, 122.12, 118.67, 117.46, 112.65, 45.32. HRMS Calcd for C.sub.18H.sub.15N.sub.2O.sub.3I m/z 434.02911, Found 434.028922.

[0081] The process of preparation under microwave irradiation according to the present invention is superior to carrying the reaction of compounds (II) and (III) in the presence of a base and refluxing in a suitable alcohol (prior art) as apparent in Table 1. Yield is higher (90-98% compared to 27-85%) and reaction time shortened significantly to 5-30 minutes compared to 9-20 hours.

TABLE-US-00001 TABLE 1 Methos of synthesis-present invention (microwave) and conventional reflux of solvent Microwave Normal condition condition in EtOH in EtOH Reaction Temper- Reaction Temper- Yield time ature Yield time ature Product (%) (min) (° C.) (%) (h) (° C.) I-a 94 15 70 65 9 Reflux I-b 96 25 80 53 6 Reflux I-c 91 10 75 27 12 Reflux I-d 95 15 75 55 12 Reflux I-e 99 5 75 85 9 Reflux I-f 90 10 75 73 14 Reflux I-g 99 5 75 45 10 Reflux I-h 95 15 80 37 16 Reflux I-i 98 5 80 81 8 Reflux I-j 94 20 80 64 12 Reflux I-k 91 30 80 60 18 Reflux I-l 90 30 80 59 20 Reflux

Physical Properties

Example 2: Solubility in Various Polar Solvents

[0082] The compounds (I-a-I-l) are soluble in nonpolar organic solvents only to a rather limited extent, while they are readily soluble in polar organic solvents. Some are readily soluble in water. In polar solvent such as water, the zwitterion form of the compounds dominates, while in nonpolar solvents such as chloroform, the neutral form prevails. More particularly, styryl quinolinium compounds having a hydroxyl group at the para position of the styryl moiety, are soluble in a wide range of solvents giving colored solutions, the color of which is solvent-dependent. Turning to FIG. 1, color change of the solution depending on the polarity of the solvent dissolving compound I-e is presented where compound I-e is dissolved in (from left to right): acetic acid, water, methanol, ethanol, isopropanol, DMSO, DMF, acetone and dichloromethane.

Example 3: Absorption Wavelength

[0083] The styryl quinolinium compounds of formula (I) are characterized by λ.sub.abs, of 440-658 nm; λ.sub.em, of 485-715 nm; and ϵ− of 12,200-49,000 M.sup.−1cm.sup.−1 at polar solvents having polarity values between 1 to 0.355. The more polar the solvent is, the shorter is the absorption wavelength of the dye. Table 2 provides photophysical properties of the compounds (I-a-I-l) in various solvents at a range of relative polarity values; between 1 (water) to 0.355 (acetone).

TABLE-US-00002 TABLE 2 Photophysical properties of derivatives I-a-I-l. λ.sub.Abs ϵ.sub.em λ.sub.Abs ϵ λ.sub.em Dye (nm) (M.sup.−1cm.sup.−1) (nm) Dye (nm) (M.sup.−1cm.sup.−1) (nm) Water MeOH I-a 460 21200 515 12a 475 22100 525 I-b 438 20700 501 12b 440 19900 490 I-c 508 26300 560 12c 560 27200 610 I-d 502 24900 555 12d 508 24900 600 I-e 520 45800 605 12e 535 46100 670 I-f 515 41200 580 12f 520 40900 648 I-g 503 23300 518 12g 505 23800 591 I-h 478 22900 508 12h 490 22900 580 I-i 510 29800 575 12i 530 30300 665 I-j 470 19200 503 12j 478 18600 500 I-k 440 16400 495 12k 445 17400 495 I-l 475 13300 499 12l 480 12200 500 EtOH DMSO I-a 480 21900 525 I-a 490 23500 528 I-b 450 21300 495 I-b 465 20600 501 I-c 565 27100 640 I-c 566 25700 660 I-d 510 28200 605 I-d 520 23600 610 I-e 556 49000 685 I-e 600 44700 715 I-f 548 41200 665 I-f 591 42100 675 I-g 509 23900 625 I-g 499 22950 603 I-h 506 22700 608 I-h 500 20900 595 I-i 544 31000 675 I-i 590 30100 703 I-j 480 17900 495 I-j 480 18400 500 I-k 460 16900 495 I-k 450 17900 501 I-l 485 13900 506 I-l 485 12200 509 DMF Aceton I-a 490 21500 520 I-a 90 19900 520 I-b 460 21100 500 I-b 55 18100 505 I-c 555 28100 660 I-c 10 27600 628 I-d 519 25000 610 I-d 90 26300 605 I-e 599 44900 715 I-e 50 47100 702 I-f 590 41100 675 I-f 90 44500 685 I-g 495 22100 603 I-g 00 23200 590 I-h 500 23400 595 I-h 05 22900 590 I-i 588 29800 705 I-i 80 28300 695 I-j 482 19200 503 I-j 60 18700 495 I-k 450 16400 500 I-k 90 15800 515 I-l 485 11100 505 I-l 80 12200 508

Example 4: pH Dependence of Absorption and Emission

[0084] The absorption and emission wavelengths of the styryl quinolinium compounds of formula (I) containing OH/NMe.sub.2 groups in the para position of the styryl moiety is pH dependent. A red-shift of the wavelengths of absorption and emission is obtained in basic vs. acidic medium. The styryl quinolinium compounds of formula (I) are further characterized by quantum yield that is dependent on the viscosity of the solvent. The more polar the solvent is, the shorter is the absorption wavelength of the dye. Table 3 provides values of absorption and emission wavelengths of compounds I-a-I-l that as evident depend on the pH. A red-shift of the wavelengths of absorption and emission was obtained in basic vs. acidic medium

TABLE-US-00003 TABLE 3 The absorption and emission wavelengths of compounds I-a-I-l depending on the pH. λ.sub.abs (nm) λ.sub.abs (nm) λ.sub.em (nm) λ.sub.em (nm) Dye pH 2 pH 10 pH 2 pH 10 I-a 460 467 515 522 I-b 438 438 501 500 I-c 508 512 560 564 I-d 502 502 555 556 I-e 520 531 605 608 I-f 515 515 580 580 I-g 503 501 518 520 I-h 478 478 508 508 I-i 510 508 575 578 I-j 470 475 503 500 I-k 440 447 495 499 I-l 475 477 499 502

Example 5: Photostability of Compounds

[0085] Turning to FIG. 2, the photostability of compounds of the present invention is provided by demonstrating the measured loss of fluorescence intensity of dyes I-a-I-l. FIG. 2 clearly demonstrates that the styryl quinolinium compounds of formula (I) are photostable, for up to 200 minutes of irradiation (96% remaining). The photostability of dyes I-a-I-l was tested by exposure to a light source of a Cary Eclipse Fluorescence Spectrophotometer (λ.sub.ex 500-650 nm), with the exclusion of ambient light. 2 μM of the Compound in phosphate buffer solution were irradiated for 200 min, with an assessment of their fluorescence intensity at five-minute intervals.

[0086] Results after a 200-minute irradiation in PBS buffer as provided in FIG. 2 demonstrate in a clear manner that the fluorescence intensity of dyes I-a-I-l was not affected by the irradiation. The remaining emission percentages of the dyes after 200 min were: I-a (89%), I-b (93%), I-c (91%), I-d (88%), I-e (96%), I-f (92%), I-g (95%), I-h (93%), I-i (95%), I-j (88%), I-k (94%) and I-l (87%).

Example 6: Quantum Yield

[0087] The quantum yields of compounds of formula (I) of the present invention were found to vary. The fluorescence quantum yields of the compounds (I) were determined relative to rhodamine B in ethanol at 25° C. The quantum yield was calculated according to the following equation:

Φ.sub.F=Φ.sub.RI/I.sub.R*OD.sub.R/OD*η.sup.2/η.sub.R

Here, Φ and Φ.sub.R are the fluorescence quantum yield of the sample and the reference, respectively, I and I.sub.R are areas under the fluorescence spectra of the sample and of the reference, respectively, OD and OD.sub.R are the absorption values of the sample and the reference at the excitation wavelength, and η and η.sub.R are the refractive index for the respective solvents used for the sample and the reference. The photostability of all the dyes was tested by exposure to a light source of a Cary Eclipse Fluorescence Spectrophotometer, with the exclusion of ambient light. 2 μM Dye solutions in PBS were irradiated for 200 min, with an assessment of their fluorescence intensity at five-minute intervals.

[0088] In particular, the quantum yield of compounds I-a-I-l was found to depend on the viscosity of the solvent. The more polar the solvent is, the shorter is the absorption wavelength of the compound. An example of the quantum yields of the compounds I-a-I-l that were measured in water and glycerol is shown in the Table 4 below:

TABLE-US-00004 TABLE 4 Quantum yield in water and glycerol Compound Φ.sup.a (water) %) Φ.sup.a (glycerol) (%) I-a 0.69 2.13 I-b 0.61 1.74 I-c 0.94 2.84 I-d 0.87 3.47 I-e 1.77 5.55 I-f 1.61 4.89 I-g 0.62 1.68 I-h 0.48 1.09 I-i 1.07 3.74 I-j 0.79 2.91 I-k 0.11 0.31 I-l 0.28 0.92

[0089] The toxicity of the compounds on T lymphocytes was evaluated by flow cytometry. Cell death was measured by fluorescence-activated cell sorting (FACS), which is a powerful and precise tool for measurement of a single cell within a population. The cell death was checked before adding the compounds and 3 hours after the addition of the dyes. Compounds I-c, I-i and I-e were not toxic for a period of 3 hours.

[0090] The styryl quinolinium compounds of formula (I) stain the nucleoli and the cytoplasm of fixed and living cells. Preferably, the compounds bind to rRNA in the nucleolus and the cytoplasm. In some embodiments, does not stain nuclear dsDNA and binds histones-free DNA extract. The styryl quinolinium compounds of formula (I) may stain the nucleoli rapidly, in about 150 seconds.

Staining and Probing of Cells.

General

[0091] Cell Culture

[0092] Human U2OS cells were cultured under standard conditions at 37° C., 5% CO.sub.2, in low glucose Dulbecco's modified Eagle's medium (DMEM, Biological Industries, Israel) containing 10% fetal bovine serum (FBS, HyClone), and 4 mM Glutamine, 100 IU/mL Penicillin, and 100 μg/mL Streptomycin (Biological Industries). HeLa, HEK293, and mouse embryonic fibroblasts (MEF) were maintained in high glucose DMEM containing 10% FBS, and 100 IU/mL Penicillin, and 100 μg/mL Streptomycin. For RNase digestion, cells were treated with 5 μg/ml actinomycin D (Sigma) for 3 hrs, then fixed in ice cold methanol for 2 min, and digested with RNase (100 mg/ml in PBS with 3 mM MgCl.sub.2, Sigma) for 45 min at room temperature. For DNase treatment, cells were first fixed in ice cold methanol for 2 min, and then incubated (100 mg/ml, 5 mM MgCl.sub.2) for 2 hrs at room temperature. Nuclei were counterstained with 1 μM Hoechst 33342 (Sigma) and coverslips were mounted in mounting medium.

[0093] Immunofluorescence

[0094] Cells were grown on coverslips, washed with PBS and fixed for 20 min in 4% PFA. Cells were then permeabilized in 0.5% Triton X-100 for 2.5 min. Cells were washed twice with PBS and blocked with 5% BSA for 20 min, and immunostained for 1 hr with a primary antibody. After three washes with PBS, the cells were incubated for 1 hr with secondary fluorescent antibodies. Primary antibodies: mouse anti-G3BP1 (Abcam) and rabbit anti-fibrillarin (Abcam). Secondary antibodies: Alexa Fluor 488 goat anti-mouse (Abcam) Alexa Flour 488 goat anti-rabbit (Abcam). Cells were then stained with compound I-e (10 μg/mL). Nuclei were counterstained with 1 μM Hoechst 33342 (Sigma) and coverslips were mounted in mounting medium.

[0095] Fluorescence Microscopy

[0096] For spectral scanning, an inverted Leica SP8 scanning confocal microscope, driven by the LASX software (Leica Microsystems, Mannheim, Germany) and equipped with a super-continuum white light laser, was used. A lambda-lambda scan was performed with the software, with a PL APO 63x/1.40 OIL objective. After export, images were analysed with Cell Profiler to measure the intensity of the images, and data was exported to Excel and plotted. For live cell imaging, a Leica DMI8 wide-field inverted microscope was used, equipped with a Leica sCMOS camera and CO.sub.2/incubation system. Cells were imaged every 5 seconds for the short time course, and every 15 min for the longer time course. Wide-field fluorescence images of fixed cells were obtained using the Cell{circumflex over ( )}R system based on an Olympus IX81 fully motorized inverted microscope (60× PlanApo objective, 1.42 NA) fitted with an Orca-AG CCD camera (Hamamatsu) driven by the Cell® software. ImageJ software was used when measuring the signal-to-noise ratio graph by acquiring the intensity of several pixels from each time point.

[0097] RNA Extraction

[0098] Total RNA was produced by using Tri-Reagent (Sigma), and DNA was removed using Turbo-DNase free kit (Invitrogen). 2 μg of total RNA extracts from HeLa cells were separated by electrophoresis in a 1% agarose gel. The rRNA 28S and 18S bands were extracted separately from the smeared mRNA in the gel. RNAs were cleaned with a Nucleospin gel and PCR clean up kit (Macherey-Nagel).

[0099] DNA and Chromatin Protein Extraction

[0100] Genomic DNA lacking nucleosomes was purified from HEK293 cells using the TIANamp Genomic kit (TIANGEN, China). Genomic DNA including nucleosomes was purified from HEK293T cells as follows. Cells were washed with PBS and collected at 500×g for 5 min and then lysed in Nonidet P-40 lysis buffer (25 mM Tris-HCl, pH 7.4, 150 mM NaCl, 10% glycerol and 1% Nonidet P-40) with a protease inhibitor cocktail (1:100 dilution) at 4° C. for 5 min. After centrifugation at 15,000×g for 5 min, the pellets were collected and washed with Nonidet P-40 lysis buffer. Then Nonidet P-40 lysis buffer with micrococal nuclease (1:100 BioLabs), 5 mM CaCl.sub.2 and a protease inhibitor cocktail (1:100 dilution) were added to the pellets and incubated at 25° C. for 10 min. 10 mM EGTA was added to stop the reaction. After centrifugation at 15,000×g for 15 min, the supernatant containing the chromatin were collected.

Example 7: Compound I-e Binds RNA in Solution

[0101] Binding of dye I-e to RNA was tested by adding this dye to an RNA solution extracted from human cells (as described above) and evaluating the increase in fluorescence intensity. Notably, a significant, 3.1-fold increase in fluorescence intensity was observed once compound I-e interacted with total RNA extract. FIG. 3 shows the Emission spectra of probe I-e with RNA in water. Compound I-e alone, RNA solution+Compound I-e, Compound I-e+RNA solution+RNASE, control, water+RNASE, control.

[0102] Compound I-e Stains Fixed Cells

[0103] The fluorescent properties of the compound I-e in cells were analyzed. Compound I-e was applied to fixed HeLa cells. A lambda-lambda scan, using a scanning confocal microscope equipped with a supercontinuum laser and tunable detection, was done to determine the excitation-emission spectrum of the compound. The peak fluorescent intensity was at the emission range of 647-667 nm and optimal excitation at 570 nm. This clearly showed the detection of the cells as shown in FIGS. 4A-4B. Spectrum scan shows peak of excitation/emission. FIG. 4A shows that following the addition of Compound I-e to HeLa cells these were scanned as described in the Methods section (above). The strongest excitation, at the emission range of 647-667 nm was found to be 570 nm. Bar=10 μm. FIG. 4B demonstrates the analysis of images as described in the Methods (above) and the image emission intensities were plotted. The excitation that resulted in the strongest emission was found to be at 570 nm. FIG. 4C provides a 2D heat map exported from acquisition software showing the excitation vs. the emission profiles. FIG. 4D demonstrates that Compound I-e localizes to nucleoli in treated cells. Nucleoli are identified by staining with an antibody to the nucleolar marker fibrillarin (green). Hoechst DNA stain is in cyan. No I-e signal is detected in untreated cells. Bar=10 μm.

Example 8: Staining of Cells

[0104] Staining Living Cells with Compound I-e

[0105] Compound I-e is highly cell permeable. Within 30 seconds the compound was detected in the cytoplasm, and within 150 seconds the compound stained nucleoli (FIG. 5A). Additionally, compound I-e could be applied to living cells for over 24 hours without affecting viability, cell morphology, or proliferation as cell divisions continuously occurred indicating that compound I-e is not toxic to cells (FIG. 5B). Notably, compound I-e remained fluorescently stable, bright and specifically bound to nucleoli (FIG. 5B), with a high signal-to-noise ratio (FIG. 5C).

Example 9: Staining Fixed Living Cells

[0106] Staining Fixed and Living Cells with Compound I-e

[0107] The binding of compound I-e to nucleic acids within cells was investigated. To this end, fixed and stained cells were treated with either deoxyribonuclease (DNase) or ribonuclease (RNase) to remove DNA or RNA from cells, respectively (FIG. 6). While with the treatment with DNase no considerable loss of fluorescence signal was observed (FIG. 6A), after RNase treatment, cytoplasmic and nucleolar fluorescence signal disappeared in comparison to untreated cells (FIG. 6B). These digestion experiments validated the preference of compound I-e to attach to RNA since cells in which the RNA was removed by RNase, did not stain anymore. When the cells were treated with actinomycin D, an inhibitor of RNA polymerase II that transcribes mRNA (and not rRNA), there was not much change in the intensity of the dye in the cells, suggesting that the dye preferably binds to rRNA in the nucleolus and the cytoplasm.

[0108] The interaction of compound I-e with rRNA was tested, nucleolar rRNA transcription was inhibited by inhibiting RNA polymerase I activity with two specific inhibitors (FIG. 7A). Following these treatments, the fluorescent signal throughout the nucleoli and the cytoplasm was significantly reduced. Further the assembly of cytoplasmic stress granules that contain mRNAs but not rRNAs was induced. This way foci containing mRNAs were formed in the cytoplasm, which might be detectable by the compound if it binds mRNA. Stress granules were formed by the addition of arsenite to the cells. However, the compound did not localize with stress granules, implying that compound I-e is not binding to cytoplasmic mRNA (FIG. 7B).

Example 10: Preference to Secondary Structures in the rRNA

[0109] Compound I-e was found to have preference to secondary structures in the rRNA:

[0110] rRNA and mRNA were purified from total cell RNA extracts. The binding of the compound to these RNAs under two conditions was examined. At room temperature the secondary structures are preserved, and strong binding to rRNA was observed (FIG. 8) as measured by fluoresce (increase of fluorescence). Once the secondary structures of the RNA were destroyed by heating the RNAs to 90° C., the binding to the rRNA was lost (no increase in fluorescence was observed), indicating that indeed compound I-e binds the complex secondary structures of rRNA.

Example 11: Binding of Compound I-e to Histones-Free DNA Extract

[0111] Compound I-e binds secondary structures in the rRNA that are probably double stranded (ds) however nuclear dsDNA was not stained as well since histones forming the nucleosomes on the DNA in cells might mask the binding of the dye. DNA from cells, with or without histones, was extracted. Compound I-e did not bind to DNA with histones and could bind only to DNA extract in which the histones were removed (FIG. 9).