WO2021176428A1 - Phenanthroline, carbazole and flavylium based cyanines and compositions and methods of making and using the same - Google Patents

Phenanthroline, carbazole and flavylium based cyanines and compositions and methods of making and using the same Download PDF

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WO2021176428A1
WO2021176428A1 PCT/IB2021/051887 IB2021051887W WO2021176428A1 WO 2021176428 A1 WO2021176428 A1 WO 2021176428A1 IB 2021051887 W IB2021051887 W IB 2021051887W WO 2021176428 A1 WO2021176428 A1 WO 2021176428A1
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formula
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Govindaraju Thimmaiah
Yelisetty VENKATA SUSEELA
Pardhasaradhi SATHA
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Jawaharlal Nehru Centre For Advanced Scientific Research
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    • C07D519/00Heterocyclic compounds containing more than one system of two or more relevant hetero rings condensed among themselves or condensed with a common carbocyclic ring system not provided for in groups C07D453/00 or C07D455/00
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    • C07D311/58Benzo[b]pyrans, not hydrogenated in the carbocyclic ring other than with oxygen or sulphur atoms in position 2 or 4
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    • C09B23/00Methine or polymethine dyes, e.g. cyanine dyes
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    • C09B23/04Methine or polymethine dyes, e.g. cyanine dyes the polymethine chain containing an odd number of >CH- or >C[alkyl]- groups one >CH- group, e.g. cyanines, isocyanines, pseudocyanines
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    • C09B23/02Methine or polymethine dyes, e.g. cyanine dyes the polymethine chain containing an odd number of >CH- or >C[alkyl]- groups
    • C09B23/06Methine or polymethine dyes, e.g. cyanine dyes the polymethine chain containing an odd number of >CH- or >C[alkyl]- groups three >CH- groups, e.g. carbocyanines
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    • C09B23/10The polymethine chain containing an even number of >CH- groups
    • C09B23/105The polymethine chain containing an even number of >CH- groups two >CH- groups

Definitions

  • the present disclosure is in the field of pharmaceutical and chemical sciences, including the synthesis of theranostic agents and processes for preparing such agents.
  • the disclosure relates to important phenanthroline, carbazole and flavylium based cyanine group containing chemical compounds, method of preparing such molecules and compositions thereof, and the use of such molecules and compositions as a probe and diagnostic agent in the diagnosis and treatment of diseases including cancer.
  • Phenanthroline containing cyanines based chemical molecules are useful for GQ detection by near far-red fluorescence turn on mechanism, and have related applications including but not limited to cell imaging. Further, phenanthroline containing cyanines are useful for treating cancer, in particular lung cancer. Carbazole containing cyanines based chemical molecules are employed for GQ DNA detection and have related applications including but not limited to fluorescence spectroscopy, diagnostics, imaging and therapeutic applications. Flavylium containing cyanines based chemical molecules are useful for GQ detection by near infra-red fluorescence switch-on mechanism, and have related applications including but not limited to cell imaging. Organelle sensing is the specialty of the molecule in addition to diagnosis.
  • GQ BACKGROUND G-quadruplex
  • GQ is an important structural element in maintaining the stability of genome and regulation of core cellular processes like replication, transcription, and translation. Putative GQs are overrepresented in proto-oncogenes by 69% as compared to tumor suppressor genes. Small molecules that stabilize GQ structure have provided convincing evidence linking expression levels of protooncogenes and GQ structure. Therefore, controlling the ensuing function of GQ structure using small molecules is viewed as an alternative therapeutic strategy for cancer and age related diseases.
  • BMVC a carbazole diiodide derivative
  • BMVC a carbazole diiodide derivative
  • a carbazole diiodide derivative is one of the first theranostic agents reported which suppressed tumor progression and can be used for visualizing GQ structures with good selectivity.
  • its wider use is hampered by the relatively low wavelength of excitation (a430 nm) which restricts in vivo imaging applications.
  • Availability of small molecules with such dual property (therapeutic and diagnostic) are limited and therefore development of new probes with theranostic capability provides insights into the mechanistic pathways involving G- quadruplexes in progression of cancer.
  • An excellent theranostic probe must exhibit good cell membrane permeability, water solubility, high selectivity for GQs over various nucleic acid structures, turn-on emission at longer wavelength and high photostability.
  • Figure 3 a) Fluorescence lifetime measurements of TGP18 in presence of quadruplex and duplex DNA. b) Non-denaturing PAGE images of GQs and non- GQs stained with SYBR Gold (top) and 1 mM TGP18 (down), respectively. c) Quantified oligonucleotide band intensities of gel stained by SYBR Gold and TGP18 using Image J.
  • Figure 4 a) CD melting profile of free promoter sequence BCL-2 and its complex with TGP18 in the ratio 1:1.
  • Figure 5 a) Fluorescence images of cellular uptake in live and fixed A549 cells stained with 300 nMTGP18 incubated for 1 hour.
  • Figure 7 shows representative immunofluorescence images of NPM1 (green) in A549 cells treated with 1 ⁇ M TGP18 (red) for 1 h. Arrow indicates nucleolus distortion.
  • Figure 8 showsrepresentative immunofluorescence images of ⁇ H2AX (green) in A549 cells treated with or without 1 and 5 ⁇ M TGP18 for 6 and 12 h. UV exposure of A549 cells for 1 h. The nuclei were stained with DAPI (blue).
  • Figure 9 shows representative immunofluorescence images of Nrf2 (green) in A549 cells treated with or without (control) TGP18 (1 and 5 ⁇ M) orpyridostatin (PDS, 10 ⁇ M) for 6 (left) and 24 h (right).
  • FIG. 10 showsa) 3D tumor spheroid growth inhibition in A549 cells upon TGP18 treatment for 24 h.
  • Figure 11 Efficacy of TGP18 in subcutaneous tumor xenografts. a) Tumor growth inhibition in MDA-MB-231 xenograft model.
  • mice compared with treated mice (n 6) injected with TGP18 and doxorubicin at 0.5 mg/kg and 10 mg/kg bodyweight for twice a week.
  • Figure 12 Efficacy of TGP18 in subcutaneous tumor xenografts. a) Kaplan- Meier survival plot for the three groups of mice. b) Tumor growth inhibition in A549 xenograft model.
  • Control mice compared with treated mice (n 6) injected with TGP18 and gemcitabine at 0.5 mg/kg and 100 mg/kg bodyweight for twice a week.
  • Figure 13 shows images (40x) of tumor tissue from vehicle control and TGP18 treated A549 xenografts, showing DAPI-stained and TGP18 fluorescent images together with merged images showing superposition of DAPI and TGP18 staining. The images are of sections close to the tumor surface.
  • Figure 1A shows chemical structures of carbazole-based monocyanine derivatives.
  • Figure 1AA shows absorbance and fluorescence spectra showing solvatochromic effects on 5 ⁇ M carbazole derivatives recorded in solvents of different polarity [dichloromethane (DCM), tetrahydrofuran (THF), dimethyl sulphoxide (DMSO) and PBS buffer (20 mM PBS, 100 mM KCl, pH 7.4)].
  • DCM dichloromethane
  • THF tetrahydrofuran
  • DMSO dimethyl sulphoxide
  • Figure 2A shows Absorption spectra of carbazole derivatives without and with 1 equiv of GQ sequences measured in PBS solution (20 mM PBS, 100 mMKCl, pH 7.4).
  • Figure 3A shows fluorescence response of carbazole derivatives titrated with GQ and duplex forming DNA sequences measured in PBS (20 mM PBS, 100 mM KCl, pH 7.4).
  • Figure 4A shows NMR interactions showing chemical shift of TGS17a/TGS41 protons in presence of c-MYC/BCL-2 GQ titration.
  • Figure 5A a) ITC profiles of TGS17a and TGS41 with BCL-2 and c-MYC promoter GQ sequences. The top panel display the isothermal plot of the TGS17a or TGS41-GQ complex formation, whereas lower panel represent the integrated binding isotherm generated from the integration of peak area as a function of molar ratio.
  • FIG. 1 shows (A) Confocal images showing colocalization of TGS17a and TGS41 (0.5 ⁇ M; green) with GQ selective antibody BG4 (red) and nuclear stain. (B) Confocal images showing nucleolin distortion upon treatment with TGS17a/TGS41 (1 PM) at 12 and 24 h respectively. Scale bar 10 Pm.
  • Figure 1B shows chemical structures of flavylium derivatives and their positioning in the electromagnetic spectrum by respective emission wavelengths.
  • FI fluorescence intensity.
  • Figure 3B shows a) Fluorescence intensity (FI at 695 nm) variation of FLV1 (2 PM) in presence of various GQ (K + and Na + , 2 PM) and duplex DNA (2 PM).
  • Fluorescence images showco-staining of FLV1 (500 nM, 1 h) with mitoorange (250 nM, 30 min) and lysoblue (1 PM, 1 h) in live A549 and HeLa cells. Fluorescent intensity overlay (right side) of FLV1 with mitoorange/lysoblue in a specific region of interest (ROI).
  • Figure 8B a) CD conformational changes of PQF mtDNA (2 PM) sequences in presence and absence of FLV1 (2 PM) and FLV3 (2 PM) in 20 mM PBS, 100 mMKCl, pH 7.4.
  • the present disclosure provides phenanthroline-based monocyanine probes by functionalizing with various electron accepting moieties and demonstrated their in cellulo GQ selectivity at the promoter level besides GQ visualization in live cells and their therapeutic potential.
  • the present disclosure provides a compound comprising the following structure: Formula I wherein, R, R 1 , R 2 are individually selected from a group comprising hydrogen,7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde,straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl,
  • R is either 7-(diethylamino)-2-oxo- 2H-chromene-3-carbaldehyde or8-hydroxy-1,2,3,5,6,7-hexahydropyrido[3,2,1- ij]quinoline-9-carbaldehyde.
  • R 1 is either absent or hydrogen.
  • R 2 is selected from a group comprising hydrogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen.
  • the present disclosure provides a compound selected from: ; and Any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
  • Synthesis of phenanthroline containing cyanine compounds and their photophysical properties Design and synthesis of phenanthroline derivatives where electron deficient phenanthroline derivative (particularly neocuproine) was condensed with electron donors such as coumarin and hydroxy julolidine carboxaldehydes to obtain target molecules (TGP17, TGP18 and TGP21) with extended S-conjugation (Figure 1a).
  • TGP17, TGP18 and TGP21 were subjected to preliminary screening for in vitro selectivity towards various GQ (BCL-2, C-MYC, C-KIT2 and TEL22) structures and duplex conformation using fluorescence spectroscopy.
  • F/F0 overall fluorescence intensity enhancement
  • TGP18 showed fluorescence enhancement specific to parallel conformation of BCL-2 quadruplex gene compared to various other topologies of GQ and duplex DNA.
  • TGP18 (1 PM) showed 200-fold fluorescence enhancement in presence of BCL-2 quadruplex at 640 nm accompanied by a blue shift (10 nm)while the corresponding enhancement was less than 50-fold for other quadruplex forming sequences and almost negligible for duplex DNA (Figure 2b).
  • the dissociation constants (K D ) of TGP18 calculated from the fluorescence spectra shown in Figure 2c were found to be in the low micromolar range (0.5–5 PM) for quadruplex compared to duplex (12.2 PM) DNA.
  • K D 730 nM
  • TGP18 exhibited strong red shift of 40 nm and maximum hyperchromism in the absorbance spectra upon titration with BCL-2 and other quadruplexes (Figure 2d) while no shift in absorbance maxima was observed for duplex DNA.
  • the striking enhancement in fluorescence of TGP18 for BCL-2 quadruplex versus other GQ and duplex forming nucleic acid structures unambiguously establishes the selective recognition of TGP18 towards parallel BCL-2 structure.
  • the lifetime traces were measured in the presence of at least a three-fold excess of nucleic acid compared with the end point of steady-state emission titrations, so that the concentration of free compound is negligible.
  • interesting trends in the fluorescence lifetime decay profiles for TGP18 in presence of nucleic acid topologies were observed.
  • TGP18 showed 3-fold longer fluorescence decay time in presence of BCL-2 quadruplex (2.05 ns) compared to duplex DNA (0.63 ns) which clearly supports the steady state intensity difference between GQ and duplex DNA ( Figure 2a).
  • In presence of c-MYC quadruplex TGP18 showed slightly shorter lifetime of 1.5 ns compared to BCL-2 GQ highlighting the topology selectivity (Figure 3a).
  • TGP18 can be used as an optical probe to visualize G-quadruplexes selectively in live cells using fluorescence lifetime imaging microscopy.
  • the selective recognition of GQs by TGP18 was further established through polyacrylamide gel electrophoresis analysis.
  • SYBR Gold a fluorescent dye that binds to nucleic acids, shows staining of all oligonucleotide sequences including duplex DNA corresponding to its non-selectivity.
  • TGP18 showed selective staining of BCL-2 GQ structure while staining of other nucleic acids is insignificant under the similar conditions (Figure 3b).
  • the quantified band intensities shown in Figure 3c further confirms the potential utility of TGP18 for selective fluorescence identification of BCL-2 quadruplex in vitro.
  • Interaction studies of TGP18 with the BCL2 GQ Circular dichroism (CD) experiments were performed to examine any conformational changes that may be induced as a result of TGP18 binding in the quadruplex structure.
  • Parallel GQ shows positive peak near 260 nm whereas antiparallel GQ shows a positive peak at 290 nm and a negative peak at 260 nm.
  • Hybrid quadruplex structures show a positive peak at 290 nm, a positive hump at 270 nm and a negative peak at 235 nm.
  • a positive peak near 260 nm for BCL-2 sequence clearly indicates formation of parallel GQ structure and we have seen almost no change in CD spectra of BCL-2 in presence of TGP18 (data not shown). This indicates that TGP18 upon binding with BCL-2 does not change its overall parallel conformation. Further investigations were carried out with GQ stabilization induced by TGP18 using thermal melting profiles obtained through CD measurements.
  • BCL2 PDB ID: 2F8U
  • the least energy binding mode is connected to minor groove binding and the corresponding binding free energy is -8.2 kcal/mol (with inhibition constant of 945 nM correlates with K D [730 nM] calculated from the fluorescence data).
  • the other low energy binding modes are associated with binding of the probe to GQ through end-stacking mode.
  • FIG. 5b illustrates the anti-proliferation effects of TGP18 in HeLa, A549, MCF-7 and MDA-MB- 231 cancer cells and HEK293T non-tumorigenic cells through MTT assay following treatment with TGP18 for 24 h.
  • Apoptosis and BCL-2 downregulation Overexpression of BCL-2 gene, which encodes the antiapoptotic Bcl-2 protein, greatly contributes to the resistance for apoptosis cancer cells.
  • Targeting the BCL- 2 gene to inhibit protein expression is an effective way to prevent the evasion of apoptosis in cancer cells and increase chemotherapeutic efficacy.
  • Stabilizing the GQ forming sequence located upstream the P1 promoter using small molecules can regulate the BCl-2 transcription and expression levels. Many small molecules have been shown to bind and stabilize BCL2-GQ with subsequent inhibition of Bcl-2 transcription and expression levels.
  • TGP18 was evaluated for its effect on transcriptional regulation of BCL-2 gene in A549 cells (Figure 6a).
  • Total mRNA was isolated from A549 cells after treatment with varying concentrations (1.0, 5 and 10 PM) of TGP18 for 24 hours.
  • the level of BCL-2 mRNA was quantified using quantitative real-time polymerase chain reaction (qRT-PCR) and the gene expression was normalized relative to the expression of a constitutively expressed house-keeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH).
  • qRT-PCR quantitative real-time polymerase chain reaction
  • TGP18 As the concentration of TGP18 is increased, G1 phase populations were decreased (61.6 % to 47 %) and G2/M phase population increased (4 % to 10 %). Cell cycle analysis suggests arrest of the cell cycle predominantly in S and G2 phase. Thus, it can be concluded that TGP18 could induce cell cycle arrest and cellular apoptosis reasoning the anti- proliferative effect.
  • caspase-3 activation assay was performed as caspases play a central role in many forms of apoptosis.
  • A549 cells were exposed to 5 and 10 ⁇ MTGP18 for 24hours and subjected to a fluorometric caspase-3 activity assay.
  • Significant increase in the caspase-3 activation was observed in the treated cells comparable with the anti- cancer drug camptothecin (10 ⁇ M) as shown in the Figure 6c.
  • Untreated cells did not emit fluorescence, indicating that the substrate was not cleaved and hence caspase-3 activity was absent.
  • An increase in the caspase-3 activity further supports the apoptosis induced by TGP18.
  • Nucleophosmin is one of the most abundant non-ribosomal nucleolar proteins like nucleolin, play a key role in ribosome biogenesis and implicated in ribosome maturation and response to stress stimuli.
  • NPM1 has been characterized as a GQ–binding protein, that binds GQ regions of rDNA genes in vitro and in vivo. Having shown ( Figure 5a) that TGP18 localizes in the nucleolus and binds rDNA GQs with higher affinity in vitro, it was hypothesized that it can effectively compete with NPM1 for GQ binding (Figure 7).
  • NPM1 localization within A549 lung cancer cells.
  • A549 cells were treated with 1 PM TGP18 and endogenous NPM1 localization was visualized at various time points by immunofluorescence technique to monitor the effect of TGP18.
  • Figure 7 shows that after 1hour treatment, NPM1 starts to localize outside the nucleolus and after 24 hours treatment, almost diffused nuclear staining was observed (data not shown).
  • nucleolus distortion has been observed where nucleoli were no longer as phase- dense and compact; they instead appeared distorted and lost round shape.
  • Nrf2 Nuclear factor erythroid 2-related factor 2
  • TGP18 showed time-dependent effect as revealed by the increased Nrf2 in the nucleus at 24 h compared to 6 h of incubation time in A549 cells with TGP18.
  • the oxidative stress induced at 1 and 5 PM treatment at both 6- and 24-hours treatment found to be elevated compared to 0.5 PM treatment.
  • Pyridostatin, GQ stabilizer known to cause DNA damage has been taken as positive control to check for its oxidative stress response and indeed Nrf2 accumulation was observed in the nucleus similar toTGP18.
  • the above immunofluorescence study recapitulates features of oxidative stress accumulation as a possible pathway for DNA damage response, cell cycle arrest and apoptosis stimulated by TGP18 in A549 cancer cells.
  • TGP18 In vitro tumor spheroid inhibition
  • the anti-cancer efficacy of TGP18 that has been characterized in 2D monolayer cells is initially validated in tumor mimicking 3D spheroids formed by A549 cancer cells.
  • the turn-on fluorescence in red region allowed us to monitor the tumor penetration ability of TGP18 in 3D spheroids.
  • 3D spheroids of A549 cells were treated with TGP18 and nuclei were stained with Hoechst. Fluorescence microscopic images reveal uniform distribution of TGP18 all around the spheroid including both the periphery and core of the spheroid.
  • the efficient spheroid penetration ability of TGP18 encouraged us to study its effect on 3D spheroid growth after treatment.
  • the growth delay experiment was performed, and volume of the spheroid quantified for up to 7 days, from the day of the treatment. It has been observed that increase in the volume of spheroid of the untreated group, while significant inhibition of growth was observed in the case of TGP18 (2.5, 5 and 10 PM) treated spheroids.
  • This in vitro tumor spheroid inhibition thus provides another valuable impetus for studying anticancer activity of TGP18 in animal model.
  • the ex vivo red blood cell haemolysis assay of TGP18t0 screen for toxic haemolysis has been performed prior to in vivo study. Different concentrations of TGP18 with collected human red blood cells in PBS and is appropriately We co-incubated.
  • the amount of haemoglobin released during the incubation period is quantified as a measure of red blood cell lysis, which is normalized to the amount of haemoglobin released in positive control samples lysed by a detergent. Haemolysis was not observed at the therapeutic concentrations of TGP18, however higher concentrations above 25 PM induced haemolysis.
  • anticancer efficacy was evaluated in vivo in mouse xenograft models of human breast cancer (MDA-MB-231) and human lung carcinoma (A549) established in Athymic Nude mice ( Figure 11 and 12).
  • the maximum tolerated dosage (MTD) for intravenous administration of TGP18 was found to be ca 0.5 mg/kg with no treatment related adverse effects in terms of body weight and clinical signs (Figure 12a).
  • MDA-MB-231 breast and A549 lung tumor xenograft model conducted at 0.5 mg/kg, each twice weekly, over a period of two weeks.
  • MDA- MB-231) model twice weekly dosing of TGP18 at 0.5 mg/kg resulted in a marginal tumor growth inhibition of 43% (p ⁇ 0.001) compared to the vehicle treated group ( Figure 11).
  • the reference compound doxorubicin showed 90% tumor growth inhibition at 10 mg/kg, which was statistically significant (p ⁇ 0.0001) as shown in Figure 11.
  • TGP18 showed a dose-dependent anti-tumor response with the minimal dose of 0.5 mg/kg producing a significant growth inhibition (p ⁇ 0.0001) in comparison with 100 mg/kg dose of gemcitabine, a reference anticancer drug used for lung cancer treatment (Figure 12).
  • the anti-tumor activity of TGP18 at 0.5 mg/kg dose was comparable with the efficacy achieved by 100 mg/kg dose of gemcitabine.
  • the body weights only slightly changed for TGP18/gemcitabine treated mice ( Figure 12).
  • the ex vivo tumor weight of different treatment groups further confirmed the significant tumor growth inhibition by TGP18 in A549 lung cancer model (Figure 12e).
  • the anti- tumor activity of TGP18 at much lower dosage is evidently more effective in lung cancer (A549) model with significant growth inhibition comparable with very high dosage (100 mg/kg) of conventional anticancer drug used gemcitabine.
  • These results clearly confirmed the greater tumor suppressive efficacy of TGP18 for lung cancer.
  • the images of tumor sections were collected at different depths and reconstructed in three-dimensional box to present the spatial distribution of TGP18 in A549 tumor tissue samples.
  • R 1 , R 2 are individually selected from a group comprising hydrogen, 7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph
  • the phenanthroline derivative or its salt is either 2,9-dimethyl-1,10-phenanthroline or 1,2,9-trimethyl-1,10- phenanthrolin-1-ium halide.
  • the phenanthroline derivative or its salt is either 2,9-dimethyl-1,10-phenanthroline or 1,2,9-trimethyl- 1,10-phenanthrolin-1-ium iodide.
  • the aldehyde derivative is compound of formula III.
  • R is individually selected from a group comprising hydrogen, 7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph,
  • the reagent is a base or acid anhydride.
  • the solvent is alcohol or acid anhydride.
  • the solvent is ethyl alcohol or acetic anhydride.
  • a process for the preparation of compound represented by TGP18 as mentioned above comprising step of reacting 1,2,9-trimethyl-1,10-phenanthrolin-1-ium iodide with 7-(diethylamino)-2- oxo-2H-chromene-3-carbaldehyde in presence of piperidine and ethanol under heating conditions to obtain TGP18.
  • a process for the preparation of compound represented by TGP21 as mentioned above comprising step of reacting 1,2,9-trimethyl-1,10-phenanthrolin-1-ium iodide with 8-hydroxy- 1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde in presence of piperidine and ethanol under heating conditions to obtain TGP21.
  • the process is carried out at a temperature ranging from about 30°C to about 90°C, and for a time period ranging from about 60 minutes to about 24 hours.
  • the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof.
  • the present disclosure further provides a pharmaceutical composition
  • a pharmaceutical composition comprising compound of Formula I Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof; wherein, R, R 1 , R 2 are individually selected from a group comprising hydrogen,7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde,straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryl
  • the present disclosure further provides a pharmaceutical composition comprising compound selected from a group comprising ; and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
  • the present disclosure furthermore provides a method of administration of a pharmaceutical composition comprising compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof a group comprising intravenous administration, intramuscular administration, intraperitoneal administration, hepatoportal administration, intra articular administration and pancreatic duodenal artery administration, or any combination thereof.
  • the present disclosure furthermore provides use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula I for GQ staining in vitro and in cellulo conditions.
  • the present disclosure furthermore provides use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula I as a probe for GQ DNA detection.
  • the present disclosure furthermore provides use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula I along with their conjugates as diagnostic probes.
  • Phenanthroline-based cyanines have potential use as selective GQ staining probes in vitro and in cellulo. Phenanthroline-based cyanines show selective GQ binding and have extensive potential to be used as diagnostic probes owing to their GQ selectivity.
  • the present disclosure also provides a composition or formulation comprising a therapeutically effective amount of compound(s) of Formula I, optionally along with excipient(s).
  • the excipient is selected from a group comprising, but not limited to granulating agent, binding agent, lubricating agent, disintegrating agent, sweetening agent, glidant, anti-adherent, anti-static agent, surfactant, anti-oxidant, gum, coating agent, colouring agent, flavouring agent, coating agent, plasticizer, preservative, suspending agent, emulsifying agent, plant cellulosic material, spheronization agents and combinations thereof.
  • the composition further comprises a compound of Formula I.
  • the composition is administered by mode selected from group comprising intravenous, subcutaneous, transdermal, intrathecal, oral and any other compatible mode, or any combination thereof.
  • the present disclosure further provides an in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula I with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence.
  • the present disclosure further provides an in vitro method of detection or quantification of BCL-2 GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula I with a BCL-2 GQ DNA sequence to allow for hybridization of the probe with the BCL-2 GQ DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to BCL-2 GQ DNA sequence, upon hybridization of the probe to BCL-2 GQ DNA sequence.
  • Compounds of formula I have potential use as selective GQ staining probes in vitro and in cellulo.
  • Compounds of formula I show selective GQ binding and have extensive potential to be used as anti-cancer drugs owing to their GQ targeting therapeutic potential.
  • the significant anti-tumor activity of Compounds of formula I shown in A549 xenograft model envisage its therapeutic application for cancer therapy.
  • the specific interaction or binding is by non-covalent interaction, resulting in the fluorescence.
  • the specific interaction or binding is by non-covalent interaction including hydrophobic, S-stacking and electrostatic interactions, resulting in the fluorescence.
  • the present disclosure provides a method of inhibiting growth of a cell, said method comprising contacting the compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition of compound of Formula I with the cell.
  • the cell is an eukaryotic cell and is either cancerous cells or cells infected with microorganisms.
  • the present disclosure provides a method of managing or treating a disease in a subject, said method comprising step of administering the compound of Formula I as claimed in claim 1 or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula I in said subject to manage and treat the disease.
  • composition/formulations formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • aqueous suspension capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein.
  • the present disclosure provides a method of inhibiting the growth of cancer in xenograft mice model, said method comprising contacting the compound of Formula I with the said animal model.
  • the present disclosure provides a method for treating cancer in a subject, said method comprising administering the compound of Formula I.
  • the present disclosure provides a method for treating cancer in a subject, said method comprising administering the composition comprising compound of Formula I.
  • the present disclosure provides a method of inhibiting the growth of lung cancer in xenograft mice model, said method comprising contacting the compound of Formula I with the said animal model.
  • the present disclosure provides a method for treating lung cancer in a subject, said method comprising administering the compound of Formula I.
  • the present disclosure provides a method for treating lung cancer in a subject, said method comprising administering the composition comprising compound of Formula I.
  • the present disclosure provides carbazole-based monocyanine probes by functionalizing with various electron accepting moieties and demonstrated their in cellulo GQ selectivity at the promoter level besides GQ visualization in live cells and their therapeutic potential.
  • R, R 1 , R 2 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof;
  • R is either hydrogen or formyl group.
  • R 1 is selected from a group comprising methyl, ethyl, propyl, acetyl, phenyl or benzyl.
  • R 2 is selected from a group comprising 4-methylbenzothiazolyl, 4-methyllepidinyl or 4-methylquinolinyl.
  • Carbazole fluorophores were prepared by employing Knoevenagel reaction as the key step for conjugating carbazole di- or mono-aldehyde with methylated benzothiazole (TGS17a andTGS41), lepidine (TGS17b andTGS42) and quinaldine (TGS17c andTGS43) scaffolds as different acceptor moieties to obtain donor–S–acceptor (D–S–A) based molecular systems with extendedS- conjugation.
  • Figure 1A shows the molecular structures of carbazole-based monocyanine fluorophores.
  • Scheme 1A Synthetic route to carbazole-based monocyanine derivatives.
  • POCl3, DMF 100 °C, 30 hours;
  • POCl3, DMF 80 °C, 8 hours;
  • Piperidine CH 2 Cl 2 : MeOH (1:1), reflux, 60 °C, 2 hours.
  • the present disclosure also provides a process for the preparation of compound represented by Formula IA as mentioned above, said process comprising step of: a. formylating compound of formula IIA to obtain compound of formula IIIA
  • R and R 1 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted; b.
  • R, R 1 , R 2 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted.
  • the formylation is carried out in present of formylating reagent.
  • the formylation of compound of formula IIA to obtain compound of formula IIIA is carried out in presence of formylating reagent.
  • a process for the preparation of compound represented by TGS17a as mentioned above comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylbenzothiazole to obtain TGS17a.
  • a process for the preparation of compound represented by TGS41 as mentioned above comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylbenzothiazole to obtain TGS41.
  • a process for the preparation of compound represented by TGS17b as mentioned above comprising step of: a.
  • a process for the preparation of compound represented by TGS42 as mentioned above comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b.
  • a process for the preparation of compound represented by TGS17c as mentioned above comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylquinolinium to obtain TGS17c.
  • a process for the preparation of compound represented by TGS43 as mentioned above comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylquinolinium to obtain TGS43.
  • the formylation is carried out in presence of a formylating reagent.
  • the formylating reagent is selected from a group comprising Phosphoryl halide, Phosphoryl chloride, oxalyl chloride, thionyl chloride and combinations thereof.
  • the process is carried out at a temperature ranging from about 30 °C to about 120 °C, and for a time period ranging from about 60 minutes to about 40 hours.
  • the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof.
  • the present disclosure further provides a pharmaceutical composition
  • a pharmaceutical composition comprising compound of Formula IA Formula I wherein, R, R 1 , R 2 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof, optionally along with at least one pharmaceutically acceptable excipient.
  • the present disclosure further provides a pharmaceutical composition comprising compound selected from a group comprising
  • the present disclosure furthermore provides a method of administration of a pharmaceutical composition comprising compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof a group comprising intravenous administration, intramuscular administration, intraperitoneal administration, hepatoportal administration, intra articular administration and pancreatic duodenal artery administration, or any combination thereof.
  • the present disclosure furthermore provides use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IA for GQ staining in vitro and in cellulo conditions.
  • the present disclosure furthermore provides use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IA as a probe for GQ DNA detection.
  • the present disclosure furthermore provides use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula IA along with their conjugates as diagnostic probes.
  • Carbazole-based cyanines have potential use as selective GQ staining probes in vitro and in cellulo. Carbazole-based cyanines show selective GQ binding and have extensive potential to be used as diagnostic probes owing to their GQ selectivity.
  • the present disclosure also provides a composition or formulation comprising a therapeutically effective amount of compound(s) of Formula I, optionally along with excipient(s).
  • the excipient is selected from a group comprising, but not limited to granulating agent, binding agent, lubricating agent, disintegrating agent, sweetening agent, glidant, anti-adherent, anti-static agent, surfactant, anti-oxidant, gum, coating agent, coloring agent, flavouring agent, coating agent, plasticizer, preservative, suspending agent, emulsifying agent, plant cellulosic material, spheronization agents and combinations thereof.
  • the composition further comprises a compound of Formula I.
  • the composition is administered by mode selected from group comprising intravenous, subcutaneous, transdermal, intrathecal, oral and any other compatible mode, or any combination thereof.
  • the composition/formulation is formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • the present disclosure provides as a diagnostic and therapeutic probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein.
  • the present disclosure provides a method of identifying GQ structures in cellulo conditions, said method comprising the step of contacting the compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula I.
  • the present disclosure provides a method of identifying GQ structures in cellulo conditions, said method comprising the step of contacting the compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of Formula IA by turn on fluorescence mechanism.
  • the present disclosure further provides an in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of Formula IA with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b.
  • the present disclosure further provides an in vitro method of detection or quantification of BCL-2 GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of Formula IA with a BCL-2 GQ DNA sequence to allow for hybridization of the probe with the BCL-2 GQ DNA sequence; b.
  • the present disclosure further provides an in vitro method of detection or quantification of c-MYC GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of Formula IA with a c-MYC GQ DNA sequence to allow for hybridization of the probe with the c-MYC GQ DNA sequence; b.
  • detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to c-MYC GQ DNA sequence, upon hybridization of the probe to c-MYC GQ DNA sequence.
  • Compounds of Formula IA have potential use as selective GQ staining probes in vitro and in cellulo.
  • Compounds of Formula IA show selective GQ binding and have extensive potential to be used as anti-cancer drugs owing to their GQ targeting therapeutic potential.
  • the specific interaction or binding is by non-covalent interaction, resulting in the fluorescence.
  • the specific interaction or binding is by non-covalent interaction including hydrophobic, S-stacking and electrostatic interactions, resulting in the fluorescence.
  • the present disclosure provides a method of inhibiting growth of a cell, said method comprising contacting the compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition of compound of Formula IA with the cell.
  • the cell is an eukaryotic cell and is either cancerous cells or cells infected with microorganisms.
  • the present disclosure provides a method of managing or treating a disease in a subject, said method comprising step of administering the compound of Formula IA as claimed in claim 1 or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IA in said subject to manage and treat the disease.
  • composition/formulations formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • aqueous suspension capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein.
  • the present disclosure provides a method for treating cancer in a subject, said method comprising administering the compound of Formula I.
  • the present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the compound of Formula I.
  • the present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the composition comprising compound of Formula I.
  • the present disclosure provides a method for treating cancer in a subject, said method comprising administering the composition comprising compound of Formula I.
  • the present disclosure provides a method for treating breast cancer in a subject, said method comprising administering the compound of Formula I.
  • the present disclosure provides a method for treating breast cancer in a subject, said method comprising administering the composition comprising compound of Formula I.
  • the large bathochromic shift and strong increase in fluorescence response signifies the stronger binding of carbazole-based monocyanine derivatives with quadruplex structure compared to duplex DNA albeit their non-selectivity among various GQ topologies.
  • Table 1A Summary of photophysical measurements of carbazole derivatives in presence of different DNA structures.
  • thermodynamic parameters measured by isothermal titration calorimetry ITC.
  • K D equilibrium binding constant
  • enthalpy 'H
  • 'G Gibbs free energy
  • entropy 'S
  • TGS17a and TGS41 (benzothiazole conjugated) surprisingly showed selective binding interactions with BCL-2 and c-MYC with dissociation constants of 1.15 PM and 932 nM, respectively and showed no interactions with other promoter GQ highlighting their integrity (Figure 5Aa).
  • the implication of simple aldehyde group on carbazole derivatives is found to be remarkable in achieving intracellular GQ selectivity while underscoring their structure-activity relationship.
  • TGS17a showed weaker binding (-9.1 kcal/mol) with c-MYC quadruplex structure compared to BCL-2.
  • TGS41 preferred groove binding interactions (-8.0 kcal/mol) with c-MYC parallel quadruplex conformation through hydrogen bonding and electrostatic interactions.
  • NMR titration experiments were performed on TGS17a/TGS41 in the presence or absence of c-MYC or BCL-2 GQs.
  • NMR data revealed that ligands interact with GQ by stacking of carbazole and benzothiazole aromatic moieties, as confirmed from the chemical shift and splitting of aromatic protons (Figure 4A).
  • the downfield shift in aldehyde group specific to TCA confirmed its role in additional hydrogen bonding with guanine phosphate backbone as shown by the docking studies, rendering its high affinity for BCL-2 GQ.
  • TGS41-43 showed effective inhibition of cancer cell proliferation compared to the TGS17a-17c.
  • MDAMB 231 cells were treated with TGS17a (0.5 and 1 PM) and TGS41 (0.5 and 1 PM) for 30 minutes and colocalized with BG4 antibody.
  • TGS17a and TGS41 foci well co-localized with BG4 staining in the nucleus which was again clearly observed in 3D images (not shown).
  • BG4 colocalization results underline the importance of these derivatives for staining GQ structures in live cells.
  • the sensitivity of our molecular probes to visualize GQs in live cells is endorsed by longer fluorescence decay times observed in vitro for TGS17a and TGS41 in presence of GQ compared to duplex DNA.
  • Time-correlated single photon counting (TCSPC) system was used to measure the fluorescence lifetimes of TGS17a and TGS41 using 480 nm laser in presence of quadruplex (BCL-2 and C-MYC) and duplex DNA sequences (Figure 6A).
  • TGS41 showed 11-fold and 9-fold longer fluorescence decay time in presence of c-MYC (0.79 ns) and BCL-2 (0.63 ns) quadruplex respectively, compared to duplex DNA (0.07 ns) endorsing the fluorescence measurements observed in Figure 3A.
  • TGS17a showed slightly shorter fluorescence decay time in presence of both c-MYC (0.078 ns) and BCL-2 (0.063) GQs compared to TGS41, which signify slightly lower efficiency in detection. Also, lifetime traces of TGS17a in presence of duplex could not be measured due to negligible fluorescence emission. Nonetheless, fluorescence lifetime measurements of TGS17a and TGS41 showed longer decay times which are in corroboration with the photophysical studies ( Figure 3A). The appreciable differences observed in fluorescence lifetime decay further makes TGS41 and TGS17a an enticingly promising probes to visualize GQs selectively in live cells using FLIM technique.
  • the confocal images in addition to their BG4 colocalization also evidently showed nucleolar localization of TGS17a and TGS41.
  • time dependent confocal study was performed to observe their cellular localization and it was evident that TGS17a and TGS41 localized in the nucleolus within 30 min to 1 h time frame (data not shown).
  • Immunofluorescence experiment was again performed to confirm the nucleolar localization by colocalizing with nucleolin, which is a protein marker specific to nucleolus (Figure B of 7A).
  • TGS17a and TGS41 showed clear colocalization with nucleolin, accompanied by prominent nucleolar distortion at 1 hour treatment.
  • Carbazole derivatives showed fluorescence enhancement specific to quadruplex genes compared to duplex DNA attributed to their high binding affinities for GQ structures. Carbazole derivatives exhibited significant anti-proliferative effects in several cancer cells through induction of apoptosis. Benzothiazole appended carbazole derivatives (TGS17a and TGS41) demonstrated enhanced intracellular quadruplex selectivity.
  • TGS17a and TGS41 have also been demonstrated the effectiveness of TGS17a and TGS41 as a possible tool for the visualization of GQ localization in live cells.
  • the present invention demonstrates the dual functionality of visualization and therapeutic potential of small molecules targeting GQ conformation.
  • cyanine-based fluorescence probes shown to selectively stabilize GQ structures with turn-on fluorescence response and potential therapeutic effect highlighting their unique property to be theranostic agents for cancer therapy. Therefore, the dual property of cyanine probes address the current limitations in GQ targeting anti-cancer drugs.
  • TGS17a and TGS41 showed intracellular GQ selectivity and selective anti- proliferative effects in cancer cells demonstrating the therapeutic potential.
  • TGS17a and TGS41 were also shown to visualize GQs in MDAMB 231 cells using BG4 antibody specific to GQ structures highlighting their potential role to visualize GQs in live cells.
  • the carbazole-based cyanine derivatives are potential drugs with diagnostic and therapeutic application for cancer therapy.
  • the present disclosure provides a compound comprising the following structure: Formula IB wherein, ‘X’ is methine unit; and ‘n’ is methine carbons wherein n is 1-6. any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
  • ‘[X] n ’ is either a methine or polymethine. In another embodiment of the present disclosure, ‘[X] n ’ is either .
  • the present disclosure provides a compound selected from: and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
  • the present disclosure also provides a process for the preparation of compound represented by Formula IB as mentioned above, said process comprising step of: c. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N- diethylamino-4-methyl-flavylium; and d.
  • Formula IB The present disclosure also provides a process for the preparation of compound represented by FLV-1 as mentioned above, said process comprising step of: c. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N- diethylamino-4-methyl-flavylium; and d.
  • the present disclosure also provides a process for the preparation of compound represented by FLV-3 as mentioned above, said process comprising step of: a. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N- diethylamino-4-methyl-flavylium; and b.
  • the process is carried out at a temperature ranging from about 30°C to about 90 °C, and for a time period ranging from about 30 minutes to about 24 hours.
  • the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof.
  • Compound of formula IB were studied to demonstrate their cellular uptake and quadruplex selectivity (Figure 1).
  • Compound of formula IB are flavylium-methine fluorophores as analogues to cyanine family of dyes with emission in the NIR region of the electromagnetic spectrum and possible applications in biological imaging.
  • Cyanine dyes are nitrogen containing polymethines with varying methine units and their absorption and emission span visible and NIR wavelength regions, illustrating their possible use in live-cell microscopy.
  • FLV1 showed in vitro selectivity for quadruplex over duplex conformation, especially with enhanced fluorescence for a particular quadruplex sequence of promoter VEGF.
  • the in vitro selectivity of FLV1 was further validated by GQ staining in polyacrylamide gel electrophoresis (PAGE). Interestingly, FLV1 showed strong binding to mtDNA quadruplex forming sequences with significant fluorescence response and selective localization in mitochondria of live cells reflects the potential of flavylium derivative for binding of GQ specific to mitochondria organelle.
  • the present disclosure further provides a pharmaceutical composition comprising compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof, optionally along with at least one pharmaceutically acceptable excipient.
  • the present disclosure further provides a pharmaceutical composition
  • a pharmaceutical composition comprising compound of Formula IB Formula I wherein, ‘X’ is methine unit; and ‘n’ is methine carbons wherein n is 1-6. or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof, optionally along with at least one pharmaceutically acceptable excipient.
  • the present disclosure further provides a pharmaceutical composition comprising compound selected from a group comprising ; and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
  • the present disclosure furthermore provides a method of administration of a pharmaceutical composition comprising compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof a group comprising intravenous administration, intramuscular administration, intraperitoneal administration, hepatoportal administration, intra articular administration and pancreatic duodenal artery administration, or any combination thereof.
  • the present disclosure furthermore provides use of compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IB for GQ staining in vitro and in organelle conditions.
  • the present disclosure furthermore provides use of compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IB as a probe for selective mitochondrial staining and its GQ DNA detection.
  • the present disclosure furthermore provides use of compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula IB along with their conjugates as diagnostic probes.
  • Flavylium-based cyanines have potential use as selective GQ staining probes in vitro and in organelle.
  • Flavylium-based cyanines show selective GQ binding and have extensive potential to be used as diagnostic probes and organelle markers owing to their GQ and organelle selectivity respectively.
  • the present disclosure also provides a composition or formulation comprising a therapeutically effective amount of compound(s) of Formula I, optionally along with excipient(s).
  • the excipient is selected from a group comprising, but not limited diluent, carrier, granulating agent, binding agent, lubricating agent, disintegrating agent, sweetening agent, glidant, anti-adherent, anti-static agent, surfactant, anti-oxidant, gum, coating agent, coloring agent, flavouring agent, coating agent, plasticizer, preservative, suspending agent, emulsifying agent, plant cellulosic material, spheronization agents and combinations thereof.
  • the composition further comprises a compound of Formula I.
  • the composition is administered by mode selected from group comprising intravenous, subcutaneous, transdermal, intrathecal, oral and any other compatible mode, or any combination thereof.
  • the composition/formulation is formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound of formula IB or a composition as described herein.
  • the present disclosure provides a method of identifying GQ sequence particularly present in VEGF gene, said method comprising the step of contacting the compound of formula IB by NIR fluorescence switch-on mechanism.
  • the specific interaction or binding of formula IB to the GQ through non-covalent end-stacking interaction results in fluorescence.
  • Flavylium containing cyanines based chemical molecules are useful for GQ detection by near infra-red fluorescence switch-on mechanism, and have related applications including but not limited to cell imaging.
  • Organelle sensing is the specialty of the molecule in addition to diagnosis.
  • the present disclosure further provides an in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula IB or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula IB with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence.
  • the present disclosure further provides an in vitro method of detection or quantification of VEGF GQDNA sequence, said method comprising a.
  • the present disclosure provides a method of staining organelles of a cell, said method comprising contacting the compound of formula IB with cells.
  • Compounds of formula IB have potential use as selective VEGF GQ staining probes in vitro and in cellulo specific to organelles. Compounds of formula IB show selective VEGF GQ binding and have extensive potential to be used as anti-cancer drugs owing to their VEGF GQ targeting therapeutic potential.
  • the specific interaction or binding is by non-covalent interaction, resulting in the fluorescence. In an embodiment of the present disclosure, the specific interaction or binding is by non-covalent interaction including hydrophobic, S-stacking and electrostatic interactions, resulting in the fluorescence.
  • the present disclosure provides a method of inhibiting growth of a cell, said method comprising contacting the compound of Formula IB or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition of compound of Formula IB with the cell.
  • the cell is an eukaryotic cell and is either cancerous cells or cells infected with microorganisms.
  • the present disclosure provides a method of managing or treating a disease in a subject, said method comprising step of administering the compound of Formula IB as claimed in claim 1 or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IB in said subject to manage and treat the disease.
  • composition/formulations formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • aqueous suspension capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof.
  • the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein.
  • the present disclosure provides a method for treating cancer in a subject, said method comprising administering the compound of Formula I.
  • the present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the compound of Formula I.
  • the present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the composition comprising compound of Formula I.
  • Design and synthesis of flavylium containing cyanine compounds Flavylium-methine fluorophores were prepared by the introduction of an activated flavylium heterocycle 1 to an aldehyde in presence and absence of oxygen following the procedure reported in literature.
  • FLV1 (2 PM) and FLV3 (2 PM) showed strong fluorescence enhancement (monitored at 695 and 780 nm, respectively) in presence of quadruplex compared to duplex DNA ( Figure 2c and 2d).
  • FLV1 showed 400-fold fluorescence enhancement for quadruplex forming sequence of oncogene promoter VEGF.
  • FLV3 showed no selectivity among the topologies of quadruplex but notable difference of 200-300 fold fluorescence enhancement observed for GQ compared to duplex DNA.
  • FLV1 and FLV3 both did not exhibit fluorescence in the absence of any DNA (in 20 mM PBS, 100mMKCl, pH 7.4) due to facile intramolecular twist motion of the C–C bond of the polymethine linker.
  • FLV1 is a selective turnon fluorescence probe for quadruplex DNA, especially VEGF quadruplex ( Figure 3a).
  • the efficiency of probe FLV1 in binding to specific quadruplex sequence as compared to FLV3 may be explained by the precise size of the molecule to fit into a constrained environment available on the GQ structure.
  • the fluorescent response of a probe during optical imaging enables the direct visualization of cellular uptake, localization, distribution and probe-nucleic acid binding interactions in living cells.
  • fluorescence lifetime measurement which is concentration independent has the potential to distinguish between different nucleic acid topologies.
  • TCSPC time-correlated single photon counting
  • the large difference in decay time between quadruplex and duplex DNA is pivotal for cellular imaging using fluorescence lifetime imaging to differentiate GQ from duplex conformation. 5
  • the turn on NIR fluorescence behavior of probe FLV1 in the presence of GQ DNA inspired us to explore the use of FLV1 as a staining agent to detect quadruplex over duplex formation in the gel electrophoresis.
  • the quadruplex and duplex forming (1 PM) sequences were subjected to polyacrylamide gel electrophoresis and the gel was visualized under UV illumination after staining with FLV1 and SYBR Gold (control).
  • UV- illuminated gel image showed strong fluorescence intensity for VEGFGQ sequence compared to other quadruplex sequences while duplex DNA band was not stained by FLV1 ( Figure 4).
  • SYBR Gold an extremely sensitive fluorescent dye that binds to nucleic acids, shows staining of all oligonucleotides including duplex corresponding to its non-selectivity for different nucleic acid conformations. It is clear from gel electrophoresis studies that FLV1 probe selectively detects and discriminates quadruplex from duplex DNA sequences. Moreover, FLV1 detects VEGF quadruplex with relatively high signal intensity compared to other quadruplexes further corroborating with the observation from fluorescence response data.
  • the region of interest evidently indicates the overlay of fluorescence intensities from FLV1 with Mitoorange in A549 and HeLa cells which confirmed the mitochondrial localization.
  • DAPI channel, ⁇ em 460 nm
  • the selectivity of FLV1 to mtDNAin cellulo was validated by performing deoxyribonuclease (DNase) digestion studies ( Figure 6). Upon treatment with DNase, mtDNA was degraded and fluorescence staining of FLV1 in the cytoplasm sharply diminished ( Figure 6b).
  • FLV1 preferentially binds to mtDNA in the complex internal cellular meilieu revealing intracellular selectivity. This was anticipated as FLV1 is positively charged hydrophobic molecule, an essential property of a probe to achieve selective mitochondrial targeting and imaging.
  • Interactions with mtDNA quadruplex The specific fluorescence response to G-quadruplex structures over duplex in vitro and selective localization in mitochondria motivated us to study the source of fluorescence response in cellulo. The fact that there are a200 PQF sequences of mtDNA, emphasize the importance of identifying all G-quadruplexes that may be involved in mitochondrial function. Six quadruplexes forming mtDNA sequences were chosen and characterized their GQ topology using CD.
  • FLV1 In contrast to parallel quadruplex (VEGF promoter) binding in vitro, FLV1 showed maximum fluorescence response for antiparallel and mixed hybrid structures for PQF mtDNA sequences which needs further studies to explain. FLV3 conversely showed slight increase in fluorescence for all mtDNA sequences in vitro implying its non-selective interaction (Figure 8c). CD showed that FLV1 (1:1 ratio) did not induce any conformational changes to mtDNA quadruplexes except for a slight hypochromism in the signal, signifying no overall conformational change in the quadruplex structures (Figure 8a).
  • DMSO Dimethyl sulfoxide
  • MTT 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazoliumbromide
  • Hoechst 33258, DAPI for cell culture and thiazole orange were purchased from Sigma-Aldrich. All other chemicals were of analytical reagent grade and used without further purification.
  • Ultrapure water prepared by Milli-Q Gradient ultrapure water system (Millipore) was used in all experiments. 1 H and 13 C NMR spectra were recorded on a Bruker AV-400 MHz spectrometer with chemical shifts reported as parts per million (ppm) (in DMSO- d6, tetramethylsilane as an internal standard) at 20 °C.
  • DNA stock solutions were prepared by dissolving oligo samples in double- distilled (dd) water in the order of 10 -4 M. All experiments were carried out using 20 mM potassium phosphate buffer containing 100 mM potassium chloride or sodium chloride at pH 7.4. Ligands were dissolved in the same buffer. All oligonucleotides were dissolved in the above mentioned buffer and heated in water bath at 95 °C for 10 minutes. The oligonucleotides were slowly cooled to room temperature and then stored at 4 °C for 48 h. UV absorption and fluorescence spectroscopy. The UV-vis absorption and emission spectra were recorded on Agilent Technologies Cary series UV-vis-NIR absorbance and Cary eclipse fluorescence spectrophotometers, respectively.
  • Spectra were recorded using a 10 mm cuvette. The absorption spectra were scanned from 230 to 800 nm. The excitation wavelength for TGP18 was fixed at 560 nm and the emission wavelength was scanned from 570 nm to 800 nm. 1 ⁇ M of TGP18 were titrated against increasing concentration (0–30 ⁇ M) of different GQ sequences until saturation was almost reached. The changes in fluorescence of TGP18 were measured upon addition of quadruplexes. The fluorescence titration data were also used to calculate the dissociation constant (KD) value by plotting the change in fluorescence ( ⁇ F/ ⁇ F max ) at 645 nm of TGP18 versus increasing concentration of TGP18.
  • KD dissociation constant
  • PAGE was performed in 1 ⁇ TBE buffer solution (90 mM tris-boric acid and 2 mM EDTA) using 15% polyacrylamide gel containing 100 mM KCl. Oligonucleotides (1 ⁇ M) were loaded on the gel, and electrophoresis was run at 90 V for 1 h at 4 °C. After electrophoresis, the gel was stained using either 100 ⁇ M TGP18 in Tris-K + or 1 ⁇ SYBR Gold, under constant agitation for 15 min, then lightly rinsed with water and visualised using Chemidoc MP imaging system (Biorad).
  • Fluorescence images were acquired with excitation wavelength of 532 nm using the emission filters of 575 nm (for SYBR Gold) and 640 nm (for TGP18). The histogram was generated using Image J software.
  • Cell culture Human breast adenocarcinoma cell lines (MCF-7 and MDA-MB- 231) (ATCC), lung adenocarcinoma cell line (A549) (ATCC), and cervical adenocarcinoma cell line (HeLa) (ATCC) and Kidney cells (HEK293T) were separately cultured in complete Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) and supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 50 ⁇ g/mL gentamycin, 1% Pen-Strep in a fully humidified CO2 incubator at 37 0 C and 5% CO 2 .
  • DMEM Dulbecco’s modified Eagle’s medium
  • MTT assay was performed in different cancer cell lines to evaluate the selective anti-proliferative properties of TGP18.
  • MCF-7, MDAMB231, HeLa, A549 and HEK293T cells were sub-cultured into 96- well microtiter plates at a density of 1 ⁇ 10 4 cells/well in 100 ⁇ L of respective culture media treated with an increasing concentration gradient (0–100 ⁇ M) of TGP18 for 24 h.
  • DMSO-treated set was considered as a negative control to nullify the cytotoxic effects of DMSO (as TGP18 was solubilized in DMSO).
  • the percentage cell viability was calculated as the percentage of MTT absorption Treatment, RNA isolation and cDNA preparation.
  • A549 cells were sub- cultured into 6-well microtiter plates at a density of 1 ⁇ 10 6 cells per well until they reached 60% confluence and were then treated with different concentrations (5 and 15 PM) of TGP18.
  • the control set received equivalent amount of DMSO, as the drug was suspended in DMSO.
  • RNA (1 ⁇ g, from both control and treated) was reverse transcribed using 200 U Revert Aid reverse transcriptase (Fermentas) and random hexamer primers (5 ⁇ M) in 20 ⁇ L reaction volume at 42 °C, following manufacturer’s protocol.
  • Real time qPCR was carried out using Maxima SYBR Green/ROX qPCR Master Mix (2X) (Thermo-Scientific) as per manufacturer’s protocol.
  • the housekeeping gene GAPDH was used as an internal control to normalize the variability in expression level.
  • PCR primers were designed using Primer-BLAST, NCBI, and analyzed in OligoAnalyser 3.1-IDT (Table 2). Cell cycle analysis.
  • A549 cells (1 ⁇ 10 6 ) per 60 mm petridish were either untreated (DMSO) or treated with various concentrations of TGP18 (1, 2, 5 and 10 ⁇ M) for 24 h. Cells were then trypsinized and collected by centrifugation at 300g for 5 min, and resuspended in PBS containing 10 ⁇ g/mL DAPI and 10 ⁇ g/mL RNaseA. After incubation for 30 min in dark at 37 °C, cells were analysed for DNA content using a FACS flow cytometer (BD Biosciences). Cell distribution among cell cycle phases and the percentage of apoptotic cells were evaluated using Cell-Quest Pro software (BD). Table 2. Primer sequences used in qPCR Haemolytic assay.
  • TGP18 was assayed on human erythrocytes (O blood group) for hemolytic activity.
  • the human blood samples were obtained from healthy volunteers. The blood was centrifuged at 5,000 rpm for 5 min and subjected to repeated washing with sterile PBS to remove plasma. Suspension of human erythrocytes (2%) in sterile PBS were treated with different concentrations of TGP18. After 30 min incubation at room temperature, cells were centrifuged and the supernatant was used to measure the liberated haemoglobin by monitoring the absorbance at 418 nm. Two controls were prepared without TGP18, negative control received sterile PBS, while positive control received 0.1% Triton X-100. The average value was calculated from triplicate assays.
  • Haemolysis percentage for each sample was calculated by dividing sample absorbance with positive control absorbance (complete hemolysis) multiplied by 100.
  • Caspase-3 activity assay was performed using Enzchek Caspase-3 assay kit following manufacturer's protocol. Lysates prepared from A549 cells were either untreated (DMSO) or treated with TGP18 (5 and 10 ⁇ M) and camptothecin (10 ⁇ M) for 24 h.
  • A549 cells were treated with 4% (wt/vol) paraformaldehyde for 10 min and rinsed twice with PBS before incubation with TGP18. After incubation, cells were washed with PBS three times to remove the excess ligand and bathed in DMEM (2 mL) before imaging. Cell nuclei were stained with Hoechst 33258 (8 ⁇ g/mL) and DAPI (300 nM) for live and fixed cells, respectively. Localisation of TGP18 was viewed under confocal fluorescence microscope (Olympus FV3000). Immunofluorescence. A549 cells were plated in 35 mm glass-bottomed culture dishes (Genetix Biotech) and cultured overnight.
  • the cells were then untreated (DMSO) or treated with TGP18 (0.5, 1 and 5 ⁇ M) or Pyridostatin (10 ⁇ M) for 24 h.
  • DMSO untreated
  • TGP18 0.5, 1 and 5 ⁇ M
  • Pyridostatin 10 ⁇ M
  • A549 cells were exposed to UV light for 1 h in DMEM media with low serum percentage.
  • cells were fixed in 4% (wt/vol) paraformaldehyde at room temperature for 10 min and washed thrice with PBS.
  • the cells were then permeabilised with 0.1% Triton X-100 in PBS for 5 min and blocked with 4% BSA in PBS for 30 min.
  • Imaging was performed using a 480 nm and a 560 nm laser connected to a Fluoview confocal microscope (Olympus FV3000) with a 60 ⁇ numerical aperture 1.4 lens and the data was analysed using cellsens software (Olympus).
  • protein databank reference ID is 2F8U. All three ligands were built using molden software and then geometry optimized using Gaussian09 software at B3LYP/6-31+G* level of theory. Blind docking was carried out and subjected the whole quadruplex structure for the identification of the binding sites.
  • the centre of the grid box was chosen as the centre of mass of the quadruplex and the number of grid points were chosen as 130, 130, 110 with a default grid size of 0.375 ⁇ .
  • the Lamarckian genetic algorithm was used to locate various binding sites and binding modes for the ligands within quadruplex. As many as 500 low energy complex configurations were stored for each ligand:quadruplex complex. Molecular dynamic (MD) simulations were also carried out to study the stability of the TGP18 binding to quadruplex. Structure from docking was used as the input configuration for MD.
  • the GAFF force-field was used to describe the dispersion interaction while atomic charges obtained using CHELPG method were used to describe the electrostatic interaction.
  • B3LYP/6-31+G* level of theory was used, and medium has been water solvent described using polarizable continuum.
  • FF99SB force-field was used and water solvent has been described using TIP3P force-field.
  • Suitable number of counter ions added to neutral and as many as 15000 water molecules were added to simulation.
  • the simulations were carried out at 300K and 1atm pressure. 1 fs was used as the time step to integrate equation of motion and an equilibration run of 5 ns.
  • the final production run in isothermal-isobaric ensemble was carried out for 20 ns.
  • the RMSD value for ligand and other properties were computed for the last 5 ns.
  • In vivo pharmacokinetic studies of TGP18 All animal experiments were performed in accordance with the guidelines of the Committee for the Purpose of Control and Supervision of Experiments on Animals (CPCSEA), India and were approved by the Institutional Animal Ethics Committee (IAEC) of Anthem Biosciences.
  • the maximum tolerated dose (MTD) study of TGP18 was performed in female BALB/c mice.
  • the TGP18 of a single dose was determined and repeat dosing was performed twice weekly for a period of two weeks at different concentrations of TGP18 (0.5, 1, 2.5, 10 and 25 mg/kg), administered intravenously (IV).
  • IV intravenously
  • female NCr nude mice (1–2 months old, weighing 18–20 g) were injected subcutaneously with 5 ⁇ 10 6 cells (MDA-MB- 231) or 1 ⁇ 10 6 cells (A549) cells in the right flank region (1x HBSS (Hank’s Balanced Salts Solution) + Matrigel).
  • HBSS Hank’s Balanced Salts Solution
  • mice 14 days, mean size 100-200 mm 3 ), the mice were divided into three therapeutic groups with six mice/group for each xenograft model.
  • the standard-of-care (SOC) drugs gemcitabine and doxorubicin hydrochloride were used as reference control for A549 and MDA-MD-231 xenograft model respectively.
  • the TGP18 samples were dissolved in 5% DMA + 95% saline to the required concentration and gemcitabine/doxorubicin directly dissolved in saline for IV administration.
  • Tumor size was measured weekly twice using a digital Verniercalliper. Tumor volume was calculated as follows: and the mice were also weighed and examined at the same time to determine any signs of toxicity from the drug.
  • Tumor growth inhibition was calculated based on the following formula (TV vehicle Final - TV vehicle Initial)
  • Group 1 6 mice treated with a twice weekly dose of 0.5 mg/kg of TGP18 in 5% DMA+95% saline.
  • Group 2 6 mice treated with a twice weekly dose of 100 mg/kg of gemcitabine (A549 xenograft model) or once weekly dose of 10mg/kg of doxorubicin (MDA- MB-231 xenograft model) in saline.
  • Group 3 6 control mice treated with 5% DMA+95% saline only, twice weekly. Mice were culled if tumors ulcerated or if a weight loss of 10–20% of the initial body weight was observed.
  • Tumor Imaging studies Tumor samples collected after sacrificing the mice were fixed in neutral buffered formalin solution (NBF). Tumors from mice M5 of group 2 (treated with 0.5 mg/kg of TGP18) and mouse M1 from group 1 (control) were snap-frozen and cut in 20 Pm sections. These tissue sections were incubated with DAPI for 10 min and mounted on a glass slide. Images were acquired using a confocal fluorescence microscope (Olympus FV3000). TGP18 observed to be an efficient theranostic probe to target GQ.
  • TGP18 is a structure-specific probe with turn-on emission at 640 nm (O em ) which binds to the BCL-2 quadruplex structure in vitro with good selectivity and shows potential anti-cancer activity in vivo thereby qualifying as a theranostic agent. Effects on BCL-2 mRNA and protein expression is reported together with cellular localization data. TGP18 strongly binds in vitro with BCL-2 quadruplex in the groove region and the binding interactions has been examined using molecular dynamics simulations. Cellular apoptosis induced by TGP18 through BCL-2 downregulation and cell cycle arrest synergized with DNA damage response, NPM1 translocation to nucleoplasm and Nrf2 nuclear accumulation by chemical GQ stabilization.
  • TGP18 shows significant anti-tumor activity in A549 xenograft lung cancer model compared to MDAMB 231 breast cancer model. These findings show that GQ stabilization using fluorescence probe TGP18 is an attractive theranostic strategy for lung cancer.
  • Dulbecco’s modified eagle medium (DMEM), fetal bovine serum (FBS), L-glutamine, penicillin-streptomycin and amphotericin B for molecular biology were procured from Himedia.
  • Annexin V and propidium iodide (PI) apoptosis detection kit was bought from BD Pharminogen.
  • Single-stranded oligonucleotide sequences (Table 1A) are purchased from Eurofins India Pvt. Ltd. Dimethyl sulfoxide (DMSO), Hoechst 33258, DAPI and 3-(4, 5-dimethylthiazol- 2-yl)-2, 5-diphenyltetrazoliumbromide (MTT) for cell culture were purchased from Sigma-Aldrich. All other chemicals were of analytical reagent grade and used without further purification. Ultrapure water, prepared by Milli-Q Gradient ultrapure water system (Millipore), was used in all experiments.
  • DMSO dimethyl sulfoxide
  • Hoechst 33258 Hoechst 33258
  • DAPI 3-(4, 5-dimethylthiazol- 2-yl)-2, 5-diphenyltetrazoliumbromide
  • MTT 5-diphenyltetrazoliumbromide
  • Example 1A Synthesis of 9-ethyl-carbazole-3,6-dicarbaldehyde (1) DMF (22 mL, 0.3 mol) was added slowly to POCl3 (28 mL, 0.3 mol) under stirring, in an ice bath. After 30 min a white precipitate was obtained and a solution of 9-ethylcarbazole (1.5 g, 16 mmol) in 20 mL of DMF was added. The mixture was slowly heated to 100 °C and reacted at this temperature for 30 h and then cooled to room temperature. The brown viscous oily product was poured into a mixture of ice-water and followed by extraction with dichloromethane (100 mL).
  • Example 2A Synthesis of 9-ethyl-carbazole-3-carbaldehyde (2) DMF (15 mL) was added slowly to POCl 3 (15.2 g, 0.1 mol) under stirring in an ice bath at room temperature until the solution became red.
  • TCSPC Horiba Delta Flex time-correlated single photon counting
  • Circular dichroism spectra were recorded on a Jasco 815 spectrometer equipped with a Peltier-type temperature controller (CDF-4265/15) under a nitrogen atmosphere to avoid water condensation. Scans were performed over the range of 220–700 nm with a speed of 100 nm/min, and the spectra represent an average of three scans. The band width was 1 nm. All measurements were carried out using a 10 mm path length cuvette in a reaction volume 500 ⁇ L. 1 ⁇ M of each quadruplex sequences were added with 1 ⁇ M of carbazole derivative at a ratio of 1:1. Readings were taken 5 min after each addition to ensure complete complex formation.
  • MCF-7 and MDAMB 231 were separately cultured in complete Dulbecco’s modified Eagle’s medium (DMEM) (Himedia) supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 50 ⁇ g/mL gentamycin, 1% pen-Strep, and 2.5 ⁇ g/mL amphotericin B in a fully humidified CO 2 incubator (ESCO cell culture CO 2 Incubator, CCL-1708-8-UV) at 37 0 C and 5 % CO 2 .
  • DMEM Dulbecco’s modified Eagle’s medium
  • FBS fetal bovine serum
  • FBS fetal bovine serum
  • 2 mM L-glutamine 50 ⁇ g/mL gentamycin, 1% pen-Strep, and 2.5 ⁇ g/mL amphotericin B in a fully humidified CO 2 incubator
  • ESCO cell culture CO 2 Incubator, CCL-1708-8-UV at 37
  • MTT assay we performed MTT assay in different cancer cell lines to evaluate the selective anti-cancer properties of the carbazole derivatives.
  • MCF-7, MDAMB231, HeLa, A549, PC3 and HEK293T cells were sub-cultured into 96- well microtiter plates at a density of 1 ⁇ 10 4 cells/well in 100 ⁇ L of respective culture media treated with an increasing concentration gradient (0–30 ⁇ M) of all carbazole derivatives (TGS17a-17c and TGS41-43) for 24 h.
  • Annexin V-FITC-PI binding assay MDAMB231 cells were seeded into 6 well microtiter plates at a density of 1 ⁇ 10 6 cells per well. Cells were treated with carbazole derivatives (TGS17a-17c and TGS41-43) at increasing concentration gradient for 24 h. Cells were then trypsinized, washed twice with 1 ⁇ PBS and subjected to flow cytometric assays using BD PharmigenTM Annexin V-FITC Apoptosis detection Kit as per manufacturer's protocol. In brief, cell pellets were resuspended into 1 ⁇ binding buffer.
  • Dulbecco’s modified eagle medium (DMEM), fetal bovine serum (FBS), L-glutamine, penicillin-streptomycin and SYBR Gold for molecular biology were procured from Invitrogen. All oligonucleotide sequences shown in Table 1, obtained from Integrated DNA technologies. Dimethyl sulfoxide (DMSO), Hoechst 33258, DAPI, for cell culture and thiazole orange were purchased from Sigma-Aldrich. All other chemicals were of analytical reagent grade and used without further purification.
  • Ultrapure water prepared by Milli-Q Gradient ultrapure water system (Millipore), was used in all experiments.
  • 1 H and 1 3 C NMR spectra were recorded on a Bruker AV-400 MHz spectrometer with chemical shifts reported as parts per million (ppm) (in DMSO-d 6 , tetramethylsilane as an internal standard) at 20 °C.
  • UV-vis absorption and emission spectra were measured in quartz cuvettes of 1 cm path length.
  • High resolution mass spectra (HRMS) were obtained on Agilent Technologies 6538 UHD Accurate-Mass Q-TOF LC/MS spectrometer.
  • Example 1B Synthesis of 7-N,N-diethylamino-4-methyl-flavylium (1).
  • 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone (1 g, 5.1 mmol, 1 equiv.) was dissolved in acetic acid (60 mL), acetophenone( 0.69 g, 5.6 mmol, 1.1 equiv.) and perchloric acid (30 mL) was added.
  • reaction mixture was refluxed for 15 h, after cooled to room temperature the precipitate was filtered and washed with hexane, diethyl ether yielded compound 1 as a red colour solid (1 g, 3.42 mmol, 67%).
  • DNA stock solutions were prepared by dissolving oligo samples in double-distilled (dd) water in the order of 10 -4 M. All experiments were carried out using 20 mM potassium phosphate buffer containing 100 mM potassium chloride or sodium chloride at pH 7.4. Ligands were dissolved in the same buffer. All oligonucleotides were dissolved in the above mentioned buffer and heated in water bath at 95 °C for 10 minutes. The oligonucleotides were slowly cooled to room temperature and then stored at 4 °C for 48 hours. UV and fluorescence spectroscopy. The UV-vis absorption and emission spectra were recorded on Agilent Technologies Cary series UV-vis-NIR absorbance and Cary eclipsefluorescence spectrophotometers, respectively.
  • Spectra were recorded using a 10 mm cuvette. The absorption spectra were scanned from 230 to 800 nm. The excitation wavelength for FLV1 was fixed at 635 nm and the emission wavelength was scanned from 645 nm to 800 nm. 2 ⁇ M of FLV1 were titrated against increasing concentration (0–30 ⁇ M) of different GQ sequences until saturation was almost reached. The changes in fluorescence of FLV1 were measured upon addition of quadruplexes. The fluorescence titration data were also used to calculate the dissociation constant (K D ) value by plotting the change in fluorescence at 695 nm of FLV1 versus increasing concentration of VEGF. The experimental data points obtained were fitted in one site saturation binding equation.
  • Oligonucleotides (1 ⁇ M) were loaded on the gel, and electrophoresis was run at 90 V for 1 h at room temperature. After electrophoresis, the gel was stained using either 100 ⁇ MFLV1 in Tris-K + or 1 ⁇ SYBR Gold, under constant agitation for 15 min, then lightly rinsed with water and visualized using Chemidoc MP imaging system (Biorad). Fluorescence images with excitation wavelength of 532 nm were recorded using the emission filters of 575 nm (for SYBR Gold) and epi-UV illumination for FLV1. Cell culture.
  • Lung adenocarcinoma cell line (A549) (ATCC) and cervical adenocarcinoma cell line (HeLa) (ATCC) were separately cultured in complete Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) and supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 50 ⁇ g/mL gentamycin, 1% Pen-Strep in a fully humidified CO 2 incubator at 37 0 C and 5% CO 2 . Fluorescence microscopy.
  • Live A549 cells grown on confocal dish were incubated with the FLV1probe (500 nM) for 30 min and cellular nuclei were stained with Hoechst 33258 (8 ⁇ g/mL),rinsed twice with phosphate-buffered saline (PBS) before visualization under a fluorescence microscope (Leica) (Ziess) equipped with an oil immersion 63X objective.
  • FLV1 probe 500 nM
  • nuclei were stained with 4′,6-diamidino-2-phenylindole (DAPI) followed by washing before visualization.
  • DAPI 4′,6-diamidino-2-phenylindole
  • Fluorescence images of DAPI and FLV1 were collected under DAPI and Cy5 channel, respectively. Localization experiment of FLV1 in cells. HeLa and A549 cells were incubated with FLV1 (500 nM) for 4 h, followed by washing three times with Dulbecco's PBS (pH 7.4). The adherent cells were then incubated with MitoTracker orange (250 nM, Invitrogen; product no. M7510) and LysoTracker blue (50 nM, Invitrogen; product no. L7525) for 30 min and 1 h respectively, washed three times with PBS (pH 7.4) to remove the excess. Nuclei were stained with Hoechst.
  • the cells were then imaged under fluorescence microscope (Leica) equipped with an oil immersion 63 ⁇ objective lens.
  • the fluorescence of LysoTracker blue was visualized using DAPI channel (emission: 475 nm); fluorescence of MitoTracker orange was visualized using Rhodamine channel (emission: 590 nm) and FLV1 under Cy5 channel (emission: 680 nm).
  • the structure of FLV1 were energy minimized with the MMFF94 force field using Avogadro, and Gasteiger partial charges were added using AutoDock tools.
  • the NMR structure of VEGF quadruplex was retrieved from the RCSB PDB databank (PDB ID 2M27).
  • Polar hydrogen was added to the GQ using MGT AutoDock tools. Precise docking was carried out on 3' and 5' end-stacking of the quadruplex conformation to ascertain the most probable binding sites. The grid dimension was assigned to 25 ⁇ 30 ⁇ 30 ⁇ . The Lamarckian Genetic Algorithm was used for the process. All other parameters were set as default. Docking results were analyzed using Discovery Studio 3.5. The docking poses were captured using VMD tools. Thus, the present application demonstrates the design and synthesis of flavylium- methine-based probes FLV1 and FLV3 with emission in NIR region.
  • FLV1 fluorescence response and gel electrophoresis studies demonstrated in vitro selectivity of the probe FLV1 for quadruplex over duplex DNA conformation.
  • FLV1 showed 3-fold higher selectivity for promoter VEGF GQ sequence underscoring its conformation selectivity among various GQ forming sequences studied.
  • the large difference in the fluorescence decay life times of FLV1 between the quadruplex and duplex DNA is useful in visualization of GQs in live cells. Fluorescence imaging and colocalization studies using known mito- and lyso-trackers elucidated that FLV1 enters mitochondria and binds with mtDNA, which is further supported by DNase digestion studies.
  • FLV1 probe offers a promising platform to directly monitor mitochondrial GQ DNA in living cells with minimal background interference and photodamage due to its emission in the NIR region. Additional embodiments and features of the present disclosure will be apparent to one of ordinary skill in art based on the description provided herein. The embodiments herein provide various features and advantageous details thereof in the description. Descriptions of well-known/conventional methods and techniques are omitted so as to not unnecessarily obscure the embodiments herein.

Abstract

The present disclosure is in the field of pharmaceutical and chemical sciences, including the synthesis of theranostic agents and processes for preparing such agents. In particular, the disclosure relates to important phenanthroline, carbazole and flavylium based cyanine group containing chemical compounds, method of preparing such molecules and compositions thereof, and the use of such molecules and compositions as a probe and diagnostic agent in the diagnosis and treatment of diseases including cancer.

Description

“PHENANTHROLINE, CARBAZOLE AND FLAVYLIUM BASED CYANINES AND COMPOSITIONS AND METHODS OF MAKING AND USING THE SAME” TECHNICAL FIELD The present disclosure is in the field of pharmaceutical and chemical sciences, including the synthesis of theranostic agents and processes for preparing such agents. In particular, the disclosure relates to important phenanthroline, carbazole and flavylium based cyanine group containing chemical compounds, method of preparing such molecules and compositions thereof, and the use of such molecules and compositions as a probe and diagnostic agent in the diagnosis and treatment of diseases including cancer. Phenanthroline containing cyanines based chemical molecules are useful for GQ detection by near far-red fluorescence turn on mechanism, and have related applications including but not limited to cell imaging. Further, phenanthroline containing cyanines are useful for treating cancer, in particular lung cancer. Carbazole containing cyanines based chemical molecules are employed for GQ DNA detection and have related applications including but not limited to fluorescence spectroscopy, diagnostics, imaging and therapeutic applications. Flavylium containing cyanines based chemical molecules are useful for GQ detection by near infra-red fluorescence switch-on mechanism, and have related applications including but not limited to cell imaging. Organelle sensing is the specialty of the molecule in addition to diagnosis. BACKGROUND G-quadruplex (GQ), a non-canonical secondary nucleic acid structure formed by the guanine-rich genomic sequences has captivated considerable attention during the past two decades because of its biological significance and potential applications. Exploring the structural dynamics of GQ formation and its cellular consequences is of great importance, however limited by the use antibody-based approaches which needs cell fixing and permeabilization. To this end, fluorescence microscopy using cell membrane-permeable GQ selective small molecular probes is a promising technique. Nonetheless, one should bear in mind that putative quadruplex DNA structures in vivo are embedded into a massive excess of the prevailingly double-stranded genome, and their selective detection can be made possible by the probes that have overwhelmingly higher binding affinity for GQ over duplex DNA. Notably, small molecule fluorescence probes that are capable of selectively recognizing GQ structures have opened up the possibility of their direct intracellular visualization and tracking. Besides, it is highly desirable to develop GQ-responsive fluorescence probes with emission in long wavelength (Far- red to near infrared) region for in cellulo and in vivo bioimaging applications. Such probes offer numerous advantages, including minimum photodamage to biological samples, diminishing Rayleigh–Tyndall scattering of light, deep tissue penetration and minimum autofluorescence of endogenous fluorophores. GQ is an important structural element in maintaining the stability of genome and regulation of core cellular processes like replication, transcription, and translation. Putative GQs are overrepresented in proto-oncogenes by 69% as compared to tumor suppressor genes. Small molecules that stabilize GQ structure have provided convincing evidence linking expression levels of protooncogenes and GQ structure. Therefore, controlling the ensuing function of GQ structure using small molecules is viewed as an alternative therapeutic strategy for cancer and age related diseases. The discovery of clinically viable GQ specific small molecules remains a key challenge despite a flurry of interest in this direction mainly due to high degree of structural polymorphism (parallel, antiparallel, hybrid-type, mixed parallel−antiparallel stranded GQ) exhibited by GQs depending on ionic and molecular crowding conditions. One of the quadruplex- binding compounds CX-3543 has entered phase II clinical trial as a first in-class candidate for multiple types of cancers signifying the impeccable scope for designing novel small molecules to target GQ. Small molecule-based fluorescence probes that selectively stabilizes specific GQ structures with potential therapeutic effect would be placed uniquely as theranostic agents for cancer therapy. BMVC, a carbazole diiodide derivative is one of the first theranostic agents reported which suppressed tumor progression and can be used for visualizing GQ structures with good selectivity. However, its wider use is hampered by the relatively low wavelength of excitation (a430 nm) which restricts in vivo imaging applications. Availability of small molecules with such dual property (therapeutic and diagnostic) are limited and therefore development of new probes with theranostic capability provides insights into the mechanistic pathways involving G- quadruplexes in progression of cancer. An excellent theranostic probe must exhibit good cell membrane permeability, water solubility, high selectivity for GQs over various nucleic acid structures, turn-on emission at longer wavelength and high photostability. Therefore, there is a need to develop novel compounds, which have excellent theranostic probe activity and therapeutic activity. The present disclosure aims in developing novel compounds with the aforesaid properties. BRIEF DESCRIPTION OF THE DRAWINGS In order that the invention may be readily understood and put into practical effect, reference will now be made to exemplary embodiments as illustrated with reference to the accompanying figures. The figures together with a detailed description below, are incorporated in and form part of the specification, and serve to further illustrate the embodiments and explain various principles and advantages in accordance with the present invention. Figure 1: a) Chemical structures of phenanthroline based cyanines/neocuproine derivatives TGP17, TGP18 and TGP21. b) Fluorescence response of TGP17 (λex = 460 nm) and TGP21 (λex = 540 nm) in the absence (control) and presence of GQ (BCL-2, C-MYC, C-KIT2, TEL22) and duplex DNA (D2). c) Absorbance and fluorescence spectra of TGP18 in phosphate buffer (20 mM, pH 7.4). FI: fluorescence intensity. Figure 2: Fluorescence response of TGP18. a) NFI of TGP18 at 640 nm on a variety of parallel (K+), antiparallel (Na+) GQ and duplex forming sequences. c) Plot of NFI(F/F0) of increased concentration of TGP18 (0–30 PM) in presence of fixed concentrations (1 PM) of GQ and duplex DNA. F0 and F represent the fluorescence intensity of TGP18 before and after interacting with DNA respectively. b) Fluorescence and d) Absorbance spectra of probe TGP18 (1 PM) in presence and absence of different GQ (K+ and Na+, 1PM) and duplex (1 PM) forming sequences. All experiments were carried out using 20 mM phosphate buffer containing 100 mM potassium chloride or sodium chloride, pH 7.4 at λex = 560 nm. NFI: normalized fluorescence intensity; FI: fluorescence intensity. Figure 3: a) Fluorescence lifetime measurements of TGP18 in presence of quadruplex and duplex DNA. b) Non-denaturing PAGE images of GQs and non- GQs stained with SYBR Gold (top) and 1 mM TGP18 (down), respectively. c) Quantified oligonucleotide band intensities of gel stained by SYBR Gold and TGP18 using Image J. Figure 4: a) CD melting profile of free promoter sequence BCL-2 and its complex with TGP18 in the ratio 1:1. b) The proposed binding model of TGP18 to the parallel BCL-2 G-quadruplex. Figure 5: a) Fluorescence images of cellular uptake in live and fixed A549 cells stained with 300 nMTGP18 incubated for 1 hour. Live and fixed cells nuclei were stained with Hoechst and DAPI respectively. b) Anti-proliferative effect of TGP18 on MCF-7, HeLa, MDA-MB-231 and A549 cell lines treated for 24 hours. Figure 6: a) Real time PCR analysis show TGP18 mediated repression of BCL-2 gene expression in A549 cells. b) The cell cycle analysis of A549 cells after 24 hours treatment with TGP18. The cells were collected and stained with 4′,6- diamidino-2-phenylindole (DAPI). c) Effect of TGP18 (5 and 10 PM) and camptothecin (10 PM) treatment on Caspase-3 activity in A549 cells for 24 hours. Figure 7shows representative immunofluorescence images of NPM1 (green) in A549 cells treated with 1 μM TGP18 (red) for 1 h. Arrow indicates nucleolus distortion. Figure 8 showsrepresentative immunofluorescence images of γH2AX (green) in A549 cells treated with or without 1 and 5 μM TGP18 for 6 and 12 h. UV exposure of A549 cells for 1 h. The nuclei were stained with DAPI (blue). Figure 9 shows representative immunofluorescence images of Nrf2 (green) in A549 cells treated with or without (control) TGP18 (1 and 5 μM) orpyridostatin (PDS, 10 μM) for 6 (left) and 24 h (right). Cells treated with pyridostatin (PDS, 10 μM) for 24 h as positive control. The nuclei were stained with DAPI (blue). Figure 10 showsa) 3D tumor spheroid growth inhibition in A549 cells upon TGP18 treatment for 24 h. b) Fluorescence images of 3D spheroid treated with TGP18. c) Hemolysis percentage of red blood cells in presence of TGP18. Figure 11: Efficacy of TGP18 in subcutaneous tumor xenografts. a) Tumor growth inhibition in MDA-MB-231 xenograft model. Control mice compared with treated mice (n = 6) injected with TGP18 and doxorubicin at 0.5 mg/kg and 10 mg/kg bodyweight for twice a week. b) Tumor inhibition rate, c) tumor weight and d) body weight over time for the three experimental groups of mice. e) Representative image shows reduced tumor size of the mice treated compared to vehicle control. **P<0.001, ***P<0.0001, one way ANOVA followed by Dunnett’s test compared to Control. Figure 12: Efficacy of TGP18 in subcutaneous tumor xenografts. a) Kaplan- Meier survival plot for the three groups of mice. b) Tumor growth inhibition in A549 xenograft model. Control mice compared with treated mice (n = 6) injected with TGP18 and gemcitabine at 0.5 mg/kg and 100 mg/kg bodyweight for twice a week. c) Representative image shows reduced tumor size of the mice treated compared to vehicle control. d) Tumor inhibition rate, e) tumor weight and f) body weight over time for the three experimental groups of mice. **P<0.001, ***P<0.0001, One way ANOVA followed by Dunnett’s test compared to Control. Figure 13 shows images (40x) of tumor tissue from vehicle control and TGP18 treated A549 xenografts, showing DAPI-stained and TGP18 fluorescent images together with merged images showing superposition of DAPI and TGP18 staining. The images are of sections close to the tumor surface. Figure 1A shows chemical structures of carbazole-based monocyanine derivatives. Figure 1AA shows absorbance and fluorescence spectra showing solvatochromic effects on 5 μM carbazole derivatives recorded in solvents of different polarity [dichloromethane (DCM), tetrahydrofuran (THF), dimethyl sulphoxide (DMSO) and PBS buffer (20 mM PBS, 100 mM KCl, pH 7.4)]. Figure 2A shows Absorption spectra of carbazole derivatives without and with 1 equiv of GQ sequences measured in PBS solution (20 mM PBS, 100 mMKCl, pH 7.4). Figure 3A shows fluorescence response of carbazole derivatives titrated with GQ and duplex forming DNA sequences measured in PBS (20 mM PBS, 100 mM KCl, pH 7.4). Figure 4A shows NMR interactions showing chemical shift of TGS17a/TGS41 protons in presence of c-MYC/BCL-2 GQ titration. Figure 5A. a) ITC profiles of TGS17a and TGS41 with BCL-2 and c-MYC promoter GQ sequences. The top panel display the isothermal plot of the TGS17a or TGS41-GQ complex formation, whereas lower panel represent the integrated binding isotherm generated from the integration of peak area as a function of molar ratio. The solid line represents the best fit data using 'one site binding model'. b) Docking binding poses of TGS17a and TGS41 in presence of parallel BCL-2 and c-MYC GQs, respectively. Figure 6A Fluorescence lifetime decay profiles of TGS17a and TGS41 in presence of GQ and duplex DNA at 1: 5 stoichiometric ratio. Figure 7A shows (A) Confocal images showing colocalization of TGS17a and TGS41 (0.5 μM; green) with GQ selective antibody BG4 (red) and nuclear stain. (B) Confocal images showing nucleolin distortion upon treatment with TGS17a/TGS41 (1 PM) at 12 and 24 h respectively. Scale bar 10 Pm. Figure 1B shows chemical structures of flavylium derivatives and their positioning in the electromagnetic spectrum by respective emission wavelengths. Figure 2B shows Absorbance and emission spectra of a) FLV1(λabs = 660 nm; λem = 700 nm) and b) FLV3 (λabs = 750 nm; λem = 795 nm). Fluorescence response of c) FLV1 (λex = 635 nm, λem = 695 nm) and d) FLV3 (λex = 740 nm, λ
Figure imgf000008_0001
= 780 nm) in presence of various quadruplex and duplex forming sequences (20 mM PBS, 100 mM KCl/NaCl, pH 7.4). FI: fluorescence intensity. Figure 3B shows a) Fluorescence intensity (FI at 695 nm) variation of FLV1 (2 PM) in presence of various GQ (K+ and Na+, 2 PM) and duplex DNA (2 PM). b) Plot of fluorescence intensity (FI at 695 nm) of FLV1 (2 PM) in presence of varying concentrations (0-30 PM) of GQ and duplex DNA. c) Absorbance spectra of FLV1 (2 PM) with increase in concentration of VEGF GQ. d) Fluorescence lifetime measurements of FLV1 in presence of VEGF GQ and duplex DNA in 1:3 stoichiometry. Figure 4B shows non-denaturing PAGE images of GQ and non-GQ DNAs (1 PM) stained with SYBR Gold (left) and FLV1 (right). Figure 5B. a) Docking end-stacking binding mode of FLV1 to the parallel VEGF G-quadruplex. c) G4-FID assay of FLV1 in presence thiazole orange (TO, 2 PM) bound to VEGF GQ (2 PM). Figure 6B. a) Fluorescence images show cellular uptake of FLV1 (500 nM) in live and fixed A549 cells incubated for 30 min. Live and fixed cells nuclei were stained with Hoechst and DAPI respectively. b) Live-cell staining and DNase digest experiments with FLV1 in A549 cells. Increase the overall brightness of all the images. Figure 7B. Fluorescence images showco-staining of FLV1 (500 nM, 1 h) with mitoorange (250 nM, 30 min) and lysoblue (1 PM, 1 h) in live A549 and HeLa cells. Fluorescent intensity overlay (right side) of FLV1 with mitoorange/lysoblue in a specific region of interest (ROI). Figure 8B. a) CD conformational changes of PQF mtDNA (2 PM) sequences in presence and absence of FLV1 (2 PM) and FLV3 (2 PM) in 20 mM PBS, 100 mMKCl, pH 7.4. b) Fluorescence response in presence of PQF mtDNA sequences (1:1 stoichiometry) of FLV1 and c) FLV3. DETAILED DESCRIPTION OF THE DISCLOSURE The foregoing has broadly outlined the features and technical advantages of the present disclosure in order that the detailed description of the disclosure that follows may be better understood. Additional features and advantages of the disclosure will be described hereinafter which form the subject of the description of the disclosure. It should also be realized by those skilled in the art that such equivalent methods do not depart from the scope of the disclosure. The novel features which are believed to be characteristic of the disclosure, as to method of operation, together with further objects and advantages will be better understood from the following description when considered in connection with the accompanying figures. It is to be expressly understood, however, that each of the figures is provided for the purpose of illustration and description only and is not intended as a definition of the limits of the present disclosure. Further, for the purposes of the following detailed description, it is to be understood that the invention may assume various alternative variations and step sequences, except where expressly specified to the contrary. Moreover, other than in any operating examples, or where otherwise indicated, all numbers expressing, for example, quantities of ingredients used in the specification are to be understood as being modified in all instances by the term "about". It is noted that, unless otherwise stated, all percentages given in this specification and appended claims refer to percentages by weight of the total composition. Thus, before describing the present invention in detail, it is to be understood that this invention is not limited to particularly exemplified systems or process parameters that may of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments of the invention only and is not intended to limit the scope of the invention in any manner. While the disclosure is susceptible to various modifications and alternative forms, specific embodiment thereof has been shown by way of example in the drawings and will be described in detail below. It should be understood, however, that it is not intended to limit the disclosure to the particular forms disclosed, but on the contrary, the disclosure is to cover all modifications, equivalents, and alternative falling within the spirit and the scope of the disclosure. Thus, the use of examples anywhere in this specification including examples of any terms discussed herein is illustrative only, and in no way limits the scope and meaning of the invention or of any exemplified term. Likewise, the invention is not limited to various embodiments given in this specification. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. In the case of conflict, the present document, including definitions will control. It must be noted that, as used in this specification and the appended claims, the singular forms "a," "an" and "the" include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to a "solvent" may include two or more such solvents. The terms "preferred" and "preferably" refer to embodiments of the invention that may afford certain benefits, under certain circumstances. However, other embodiments may also be preferred, under the same or other circumstances. Furthermore, the recitation of one or more preferred embodiments does not imply that other embodiments are not useful and is not intended to exclude other embodiments from the scope of the invention. As used herein, the terms "comprising" "including," "having," "containing," "involving," and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Further, the terms “comprises”, “comprising”, or any other variations thereof, are intended to cover a non-exclusive inclusion, such that a method that comprises a list of acts does not include only those acts but may include other acts not expressly listed or inherent to such method. In other words, one or more acts in a method proceeded by “comprises… a” does not, without more constraints, preclude the existence of other acts or additional acts in the method. With respect to the use of substantially any plural and/or singular terms herein, those having skill in the art can translate from the plural to the singular and/or from the singular to the plural as is appropriate to the context and/or application. The various singular/plural permutations may be expressly set forth herein for sake of clarity. Any discussion of documents, acts, materials, devices, articles and the like that has been included in this specification is solely for the purpose of providing a context for the disclosure. It is not to be taken as an admission that any or all of these matters form a part of the prior art base or were common general knowledge in the field relevant to the disclosure as it existed anywhere before the priority date of this application. A detailed description for the purpose of illustrating representative embodiments of the present invention is given below, but these embodiments should not be construed as limiting the present invention. Unless otherwise indicated, all numbers expressing feature sizes, amounts, and physical properties used in the specification and claims are to be understood as being modified in all instances by the term "about." Accordingly, unless indicated to the contrary, the numerical parameters set forth in the foregoing specification and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by those skilled in the art utilizing the teachings disclosed herein. The use of numerical ranges by endpoints includes all numbers within that range (e.g. 1 to 5 includes 1, 1.5, 2, 2.80, 3, 3.75, 4, and 5) and any range within that range. The present disclosure provides phenanthroline-based monocyanine probes by functionalizing with various electron accepting moieties and demonstrated their in cellulo GQ selectivity at the promoter level besides GQ visualization in live cells and their therapeutic potential. The present disclosure provides a compound comprising the following structure:
Figure imgf000012_0001
Formula I wherein, R, R1, R2are individually selected from a group comprising hydrogen,7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde,straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. In an embodiment of the present disclosure, R is either 7-(diethylamino)-2-oxo- 2H-chromene-3-carbaldehyde or8-hydroxy-1,2,3,5,6,7-hexahydropyrido[3,2,1- ij]quinoline-9-carbaldehyde. In another embodiment of the present disclosure, R1 is either absent or hydrogen. In yet another embodiment of the present disclosure, R2is selected from a group comprising hydrogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen. The present disclosure provides a compound selected from:
Figure imgf000013_0001
; and Any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. Synthesis of phenanthroline containing cyanine compounds and their photophysical properties: Design and synthesis of phenanthroline derivatives where electron deficient phenanthroline derivative (particularly neocuproine) was condensed with electron donors such as coumarin and hydroxy julolidine carboxaldehydes to obtain target molecules (TGP17, TGP18 and TGP21) with extended S-conjugation (Figure 1a). Knoevenagel condensation of dimethyl phenanthroline (neocuproine) starting precursors 4 and 5, with coumarin carboxaldehyde (3) afforded compound TGP17 and TGP18 respectively, while condensation with julolidine carboxaldehyde (6) afforded TGP21 (Figure 1a). TGP17, TGP18 and TGP21 were subjected to preliminary screening for in vitro selectivity towards various GQ (BCL-2, C-MYC, C-KIT2 and TEL22) structures and duplex conformation using fluorescence spectroscopy. TGP17 (Oex = 460 nm, Oem = 540 nm) showed moderate increase in fluorescence in presence of all GQ sequences indicating no selectivity among various topologies of GQ versus duplex and moreover TGP17 alone exhibits fluorescence in PBS that undermine its cellular applications (Figure 1b). In spite of emission in the longer wavelength region, TGP21 (Oex = 575 nm, Oem = 660 nm) showed no change in fluorescence response in presence of GQ and duplex oligosequences studied (Figure 1b). Interestingly, TGP18 showed basal level fluorescence in the unbound state and turn-on fluorescence at 640 nm (Oex = 560 nm) upon binding to GQ forming oligosequences (Figure 1c). Further studies of TGP18 selectivity and sensitivity of quadruplex stabilization in vitro and in vivo conditions using various biophysical studies. Specific sensing of BCL-2 quadruplex by TGP18 The binding interaction of TGP18 was evaluated by screening with different topologies of GQs and duplex DNA using absorbance and fluorescence emission spectroscopy (Table 1). Figure 2a shows comparison of the overall fluorescence intensity enhancement (F/F0) monitored at 640 nm for different nucleic acid conformations. TGP18 showed fluorescence enhancement specific to parallel conformation of BCL-2 quadruplex gene compared to various other topologies of GQ and duplex DNA. Remarkably, TGP18 (1 PM) showed 200-fold fluorescence enhancement in presence of BCL-2 quadruplex at 640 nm accompanied by a blue shift (10 nm)while the corresponding enhancement was less than 50-fold for other quadruplex forming sequences and almost negligible for duplex DNA (Figure 2b). The dissociation constants (KD) of TGP18 calculated from the fluorescence spectra shown in Figure 2c were found to be in the low micromolar range (0.5–5 PM) for quadruplex compared to duplex (12.2 PM) DNA. TGP18 showed a 7- fold selectivity for BCL-2with a KD value of 730 nM, compared to c-KIT2(KD = 5.5 μM), c-MYC(KD= 1.5μM), VEGF (KD= 2.12 μM) and KRAS (KD = 1.3 μM) quadruplexes (Figure 2c). The low KD value of TGP18 for BCL-2 quadruplex highlight their strong binding affinity and selectivity. It is worth mentioning that TGP18 exhibited strong red shift of 40 nm and maximum hyperchromism in the absorbance spectra upon titration with BCL-2 and other quadruplexes (Figure 2d) while no shift in absorbance maxima was observed for duplex DNA. Clearly, the striking enhancement in fluorescence of TGP18 for BCL-2 quadruplex versus other GQ and duplex forming nucleic acid structures unambiguously establishes the selective recognition of TGP18 towards parallel BCL-2 structure. Further, it has been observed that fluorescence intensity of TGP18 is concurrently enhanced as the solvent polarity decreases from water to DCM which suggest that the observed fluorescence enhancement and blue-shift in the emission spectra of the TGP18 is a consequence of interaction and binding of TGP18 to the non-polar hydrophobic region of the G-quadruplex. Intramolecular twisting between donor- acceptor moieties of molecular probes has been shown to be responsible for efficient quenching of fluorescence in unconstrained environments while their binding to compact packets of DNA results in enhanced fluorescence due to restriction of intramolecular twisting. Similar molecular transformations are anticipated with our neocuproine-based TGP18 probe upon interaction with GQ DNA to exhibit turn on fluorescence response. The observed fluorescence enhancement (steady-state intensity) alone would be insufficient for selective cellular imaging of different DNA conformations, owing to possible differences in cellular uptake and intracellular localization, which alter the effective concentration of the probe and in turn, the intensity. On the other hand, fluorescence lifetimes are concentration independent, and therefore fluorescence lifetime measurements of TGP18 could reveal its potential to image and distinguish GQ from different DNA conformations. In this context, time- correlated single photon counting (TCSPC) system was used to measure the fluorescence lifetime of TGP18 using 560 nm laser in the presence of two different quadruplex (BCL-2 and C-MYC) and duplex DNA sequences (Figure 3a). The lifetime traces were measured in the presence of at least a three-fold excess of nucleic acid compared with the end point of steady-state emission titrations, so that the concentration of free compound is negligible. Interesting trends in the fluorescence lifetime decay profiles for TGP18 in presence of nucleic acid topologies were observed. TGP18 showed 3-fold longer fluorescence decay time in presence of BCL-2 quadruplex (2.05 ns) compared to duplex DNA (0.63 ns) which clearly supports the steady state intensity difference between GQ and duplex DNA (Figure 2a). In presence of c-MYC quadruplex TGP18 showed slightly shorter lifetime of 1.5 ns compared to BCL-2 GQ highlighting the topology selectivity (Figure 3a). The observed difference in fluorescence lifetimes between GQ and duplex DNA conformations suggested that TGP18 can be used as an optical probe to visualize G-quadruplexes selectively in live cells using fluorescence lifetime imaging microscopy. The selective recognition of GQs by TGP18 was further established through polyacrylamide gel electrophoresis analysis. SYBR Gold, a fluorescent dye that binds to nucleic acids, shows staining of all oligonucleotide sequences including duplex DNA corresponding to its non-selectivity. In corroboration with fluorescence data, TGP18 showed selective staining of BCL-2 GQ structure while staining of other nucleic acids is insignificant under the similar conditions (Figure 3b). The quantified band intensities shown in Figure 3c further confirms the potential utility of TGP18 for selective fluorescence identification of BCL-2 quadruplex in vitro. Interaction studies of TGP18 with the BCL2 GQ Circular dichroism (CD) experiments were performed to examine any conformational changes that may be induced as a result of TGP18 binding in the quadruplex structure. Parallel GQ shows positive peak near 260 nm whereas antiparallel GQ shows a positive peak at 290 nm and a negative peak at 260 nm. Hybrid quadruplex structures show a positive peak at 290 nm, a positive hump at 270 nm and a negative peak at 235 nm. A positive peak near 260 nm for BCL-2 sequence clearly indicates formation of parallel GQ structure and we have seen almost no change in CD spectra of BCL-2 in presence of TGP18 (data not shown). This indicates that TGP18 upon binding with BCL-2 does not change its overall parallel conformation. Further investigations were carried out with GQ stabilization induced by TGP18 using thermal melting profiles obtained through CD measurements. The selective and strong binding interaction of TGP18 with BCL-2 quadruplex was confirmed by the high 'Tm (5.5 °C, Figure 4a) value compared to other quadruplex forming c-MYC ('Tm = 4 °C), TEL22 ('Tm = 1.1 °C) and KRAS ('Tm = 3.9 °C) sequences (data not shown). Further, computational analysis was performed to understand the binding interactions of TGP18 with BCL-2 quadruplex. Molecular dynamics (MD) simulation was performed to get insights on the mechanism of binding interaction of TGP18-quadruplex at the atomic level. Blind docking studies were performed with BCL2 (PDB ID: 2F8U) to identify the binding modes for TGP18. The least energy binding mode is connected to minor groove binding and the corresponding binding free energy is -8.2 kcal/mol (with inhibition constant of 945 nM correlates with KD [730 nM] calculated from the fluorescence data). The other low energy binding modes are associated with binding of the probe to GQ through end-stacking mode. To gain more information at atomic level MD simulation was performed for 20 ns with BCL-2 control and BCl-2-TGP18 complex. The MD simulations showed that TGP18 is bound in the groove of BCL-2 GQ as shown in Figure 4b. The reason for this mode of binding is that the residues in the grooves of GQ locks the molecule and the dynamics of TGP18 is more localized. The dispersion, electrostatic and hydrophobic interactions appears to be the main driving force for TGP18 binding to quadruplex and the minor groove binding is associated with greater binding affinity and energetically more favoured ('G = -37.04 kcal/mol)than the end- stacking ('G = -25.82 kcal/mol) mode of binding. Cellular localization and cytotoxicity of TGP18 Cellular uptake of TGP18 was investigated over a wide range of incubation times (0.5, 1 and 2 hours) at concentration of 300nM in the A549 cancer cell line using fluorescence microscopy. Fluorescence imaging in A549 cells illustrated the accumulation of TGP18 primarily in the nucleolus and cytoplasm of both live and fixed cells (Figure 5a). There is adequate literature to support the role of the nucleolus in the regulation of the cell cycle, the stress response, and apoptosis. The cellular toxicity of TGP18 before cellular imaging in various cancer and non- cancer cell lines to establish toxic and non-toxic concentration levels for therapeutic and diagnostic roles, respectively were explored. Figure 5b illustrates the anti-proliferation effects of TGP18 in HeLa, A549, MCF-7 and MDA-MB- 231 cancer cells and HEK293T non-tumorigenic cells through MTT assay following treatment with TGP18 for 24 h. TGP18 showed relatively higher anti- proliferation effect in A549, HeLa and MDA-MB-231 cancer cells with IC50 (50% inhibitory concentration) of 4-10 PM compared to MCF7 (IC50= 20-25 PM) and with minimal effects on normal HEK293T cells (25-50 PM). These data clearly indicate that TGP18 is capable of selectively inhibiting the proliferation of cancer cells without damaging the normal cells. Among the cancer cells (A549, HeLa, MCF-7 and MDA-MB-231), TGP18 is most potent in A549 and MDA-MB-231 cells with low IC50 values. The biophysical analysis suggested that TGP18 shows high specificity for the BCL-2 GQ over duplex DNA. This encouraged us to evaluate the molecular mechanism underlying the anti-proliferative effect of TGP18 through modulation of BCl-2 gene in A549 cells. Apoptosis and BCL-2 downregulation Overexpression of BCL-2 gene, which encodes the antiapoptotic Bcl-2 protein, greatly contributes to the resistance for apoptosis cancer cells. Targeting the BCL- 2 gene to inhibit protein expression is an effective way to prevent the evasion of apoptosis in cancer cells and increase chemotherapeutic efficacy. Stabilizing the GQ forming sequence located upstream the P1 promoter using small molecules can regulate the BCl-2 transcription and expression levels. Many small molecules have been shown to bind and stabilize BCL2-GQ with subsequent inhibition of Bcl-2 transcription and expression levels. However, these molecules rarely exhibit topology selectivity for gene specific G-quadruplex structures. Having shown the in vitro selectivity for BCL-2 GQ, TGP18 was evaluated for its effect on transcriptional regulation of BCL-2 gene in A549 cells (Figure 6a). Total mRNA was isolated from A549 cells after treatment with varying concentrations (1.0, 5 and 10 PM) of TGP18 for 24 hours. The level of BCL-2 mRNA was quantified using quantitative real-time polymerase chain reaction (qRT-PCR) and the gene expression was normalized relative to the expression of a constitutively expressed house-keeping gene, glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Analysis of the qRT-PCR data revealed that TGP18 reduced the level of BCL-2 mRNA in a dose dependent manner (Figure6a). To determine whether TGP18 mediated inhibition of A549 cell proliferation was associated with cell cycle arrest, Cell cycle analysis was performed by 4′,6- diamidino-2- phenylindole (DAPI) staining using flow cytometry analysis (Figure 6b). Treatment with 1, 2, 5 and 10 μMTGP18 significantly changed the cell cycle distribution compared with the untreated group. Following exposure of TGP18 (1.0–10 PM) in A549 cells the percentage of S-phase population of the cell cycle was elevated from approximately 26.5 % in untreated cells to 37 % for cells treated with 10 μMTGP18 for 24 hours. As the concentration of TGP18 is increased, G1 phase populations were decreased (61.6 % to 47 %) and G2/M phase population increased (4 % to 10 %). Cell cycle analysis suggests arrest of the cell cycle predominantly in S and G2 phase. Thus, it can be concluded that TGP18 could induce cell cycle arrest and cellular apoptosis reasoning the anti- proliferative effect. To further confirm the apoptosis induction by TGP18, caspase-3 activation assay was performed as caspases play a central role in many forms of apoptosis. To determine if caspase-3 activation was induced by TGP18 treatment, A549 cells were exposed to 5 and 10 μMTGP18 for 24hours and subjected to a fluorometric caspase-3 activity assay. Significant increase in the caspase-3 activation was observed in the treated cells comparable with the anti- cancer drug camptothecin (10 μM) as shown in the Figure 6c. Untreated cells did not emit fluorescence, indicating that the substrate was not cleaved and hence caspase-3 activity was absent. An increase in the caspase-3 activity further supports the apoptosis induced by TGP18. Interfering with G-quadruplex binding displaces NPM1 from nucleoli and induces DNA damage response Nucleophosmin (NPM1) is one of the most abundant non-ribosomal nucleolar proteins like nucleolin, play a key role in ribosome biogenesis and implicated in ribosome maturation and response to stress stimuli. NPM1 has been characterized as a GQ–binding protein, that binds GQ regions of rDNA genes in vitro and in vivo. Having shown (Figure 5a) that TGP18 localizes in the nucleolus and binds rDNA GQs with higher affinity in vitro, it was hypothesized that it can effectively compete with NPM1 for GQ binding (Figure 7). As consequence further examination was carried out whether TGP18 treatment impacts on NPM1 localization within A549 lung cancer cells. In this respect, A549 cells were treated with 1 PM TGP18 and endogenous NPM1 localization was visualized at various time points by immunofluorescence technique to monitor the effect of TGP18. Figure 7 shows that after 1hour treatment, NPM1 starts to localize outside the nucleolus and after 24 hours treatment, almost diffused nuclear staining was observed (data not shown). In addition to NPM1 translocation to nucleoplasm, nucleolus distortion has been observed where nucleoli were no longer as phase- dense and compact; they instead appeared distorted and lost round shape. Alterations in the nucleolar structure induced by TGP18 can cause nucleolar stress that eventually impairs ribosome biogenesis. The evidence for NPM1 role in multiple aspects of ribosome biogenesis is substantial, however a role in DNA damage response (DDR) has emerged recently. Moreover, an intriguing effect of GQ ligands (for example pyridostatin) is the induction of DNA damage and genome instability. Therefore, assessment of the DNA damage response upon TGP18 treatment through the formation of J-H2AX foci, a marker for double- stranded DNA breakage. Interestingly, TGP18 (1 and 5 PM) treatment increased S139-phosphorylated histone H2AX (γH2AX) foci following 6- and 12-hours treatment, which is hallmark of genomic DDR. Number of γH2AX foci significantly increased upon increase in the incubation time and concentration. UV treatment of A549 cells was performed as a positive control that caused DNA damage extensively as seen from high amounts of γH2AX foci. Similarly, TGP18 exerts an anti-cancer effect by inducing pronounced DNA damage response with the appearance of J-H2AX foci. This clearly indicates that DNA damage response induced is certainly involved in the cell cycle arrest in G2/M and S phase, and apoptosis observed in our study. It is evident that DNA damage and apoptosis can be mediated through oxidative stress, and possible nucleolar stress induced by NPM1 dislocation and further motivated for detecting oxidative stress following TGP18 treatment. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor which mediates antioxidant response, in association with the cytoskeleton associated Kelch-like protein Keap1. Under conditions of oxidative stress, Keap1 is oxidized and modified so that it cannot bind to NRF2, thereby leading to the NRF2 translocation to the nucleus. Therefore, Nrf2 translocation from cytoplasm to the nucleus functions as a sensor for oxidative stress. The immunofluorescence study upon TGP18 treatment at different concentrations (0.5, 1 and 5 PM) clearly showed the Nrf2 signal accumulation in the nucleus. However, the control without treatment showed no Nrf2 accumulation in the nucleus. As shown in Figure 9 TGP18 showed time-dependent effect as revealed by the increased Nrf2 in the nucleus at 24 h compared to 6 h of incubation time in A549 cells with TGP18. The oxidative stress induced at 1 and 5 PM treatment at both 6- and 24-hours treatment found to be elevated compared to 0.5 PM treatment. Pyridostatin, GQ stabilizer known to cause DNA damage has been taken as positive control to check for its oxidative stress response and indeed Nrf2 accumulation was observed in the nucleus similar toTGP18. The above immunofluorescence study recapitulates features of oxidative stress accumulation as a possible pathway for DNA damage response, cell cycle arrest and apoptosis stimulated by TGP18 in A549 cancer cells. In vitro tumor spheroid inhibition The anti-cancer efficacy of TGP18 that has been characterized in 2D monolayer cells is initially validated in tumor mimicking 3D spheroids formed by A549 cancer cells. The turn-on fluorescence in red region allowed us to monitor the tumor penetration ability of TGP18 in 3D spheroids. 3D spheroids of A549 cells were treated with TGP18 and nuclei were stained with Hoechst. Fluorescence microscopic images reveal uniform distribution of TGP18 all around the spheroid including both the periphery and core of the spheroid. The efficient spheroid penetration ability of TGP18 encouraged us to study its effect on 3D spheroid growth after treatment. The growth delay experiment was performed, and volume of the spheroid quantified for up to 7 days, from the day of the treatment. It has been observed that increase in the volume of spheroid of the untreated group, while significant inhibition of growth was observed in the case of TGP18 (2.5, 5 and 10 PM) treated spheroids. This in vitro tumor spheroid inhibition thus provides another valuable impetus for studying anticancer activity of TGP18 in animal model. Initially the ex vivo red blood cell haemolysis assay of TGP18t0 screen for toxic haemolysis has been performed prior to in vivo study. Different concentrations of TGP18 with collected human red blood cells in PBS and is appropriately We co-incubated. The amount of haemoglobin released during the incubation period is quantified as a measure of red blood cell lysis, which is normalized to the amount of haemoglobin released in positive control samples lysed by a detergent. Haemolysis was not observed at the therapeutic concentrations of TGP18, however higher concentrations above 25 PM induced haemolysis. In vivo anticancer activity in breast and lung cancer model As further validation of the potential anticancer activity of GQ binding agent TGP18, anti-tumor efficacy was evaluated in vivo in mouse xenograft models of human breast cancer (MDA-MB-231) and human lung carcinoma (A549) established in Athymic Nude mice (Figure 11 and 12). The maximum tolerated dosage (MTD) for intravenous administration of TGP18 was found to be ca 0.5 mg/kg with no treatment related adverse effects in terms of body weight and clinical signs (Figure 12a). A therapeutic schedule of two doses was explored with MDA-MB-231 breast and A549 lung tumor xenograft model, conducted at 0.5 mg/kg, each twice weekly, over a period of two weeks. In breast cancer (MDA- MB-231) model, twice weekly dosing of TGP18 at 0.5 mg/kg resulted in a marginal tumor growth inhibition of 43% (p<0.001) compared to the vehicle treated group (Figure 11). The reference compound doxorubicin showed 90% tumor growth inhibition at 10 mg/kg, which was statistically significant (p<0.0001) as shown in Figure 11. In lung cancer (A549) model, TGP18 showed a dose-dependent anti-tumor response with the minimal dose of 0.5 mg/kg producing a significant growth inhibition (p<0.0001) in comparison with 100 mg/kg dose of gemcitabine, a reference anticancer drug used for lung cancer treatment (Figure 12). At 14 days of the main therapeutic dosage experiment, an average of ca 56% and 64% decrease in tumor growth for TGP18 and gemcitabine treated mice which was statistically significant compared to vehicle treated (Figure 12). Remarkably, the anti-tumor activity of TGP18 at 0.5 mg/kg dose was comparable with the efficacy achieved by 100 mg/kg dose of gemcitabine. Notably, the body weights only slightly changed for TGP18/gemcitabine treated mice (Figure 12). The ex vivo tumor weight of different treatment groups further confirmed the significant tumor growth inhibition by TGP18 in A549 lung cancer model (Figure 12e). The anti- tumor activity of TGP18 at much lower dosage (0.5 mg/kg) is evidently more effective in lung cancer (A549) model with significant growth inhibition comparable with very high dosage (100 mg/kg) of conventional anticancer drug used gemcitabine. These results clearly confirmed the greater tumor suppressive efficacy of TGP18 for lung cancer. The images of tumor sections were collected at different depths and reconstructed in three-dimensional box to present the spatial distribution of TGP18 in A549 tumor tissue samples. Bright fluorescence detected from tissue sections clearly indicate the deep penetration ability of TGP18 and emission collected in the red channel using 560 nm (excitation wavelength) laser in the confocal microscopy (Figure 13). Thus, TGP18 convincingly meet the criteria of both imaging and therapeutic role validating the rationality of our theranostic probe design for targeting GQ. In an embodiment of the present invention, the compounds of formula I were synthesized as shown in scheme 1 and thoroughly characterized by various spectroscopic techniques.
Figure imgf000024_0001
Scheme 1. Synthetic route to phenanthroline-based monocyanines compounds (TGP17, TGP18 and TGP21) The present disclosure also provides a process for the preparation of compound represented by Formula I as mentioned above, said process comprising the step of reacting phenanthroline derivative or its salt with aldehyde derivative to obtain compound of formula I. In an embodiment of the present disclosure phenanthroline derivative or its salt is compound of formula II.
Figure imgf000024_0002
Compound of formula II. wherein wherein, R1, R2 are individually selected from a group comprising hydrogen, 7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof; In another embodiment of the present disclosure phenanthroline derivative or its salt with aldehyde derivative in presence of a reagent optionally in present solvent under heating conditions. In yet another embodiment of the present disclosure, the phenanthroline derivative or its salt is either 2,9-dimethyl-1,10-phenanthroline or 1,2,9-trimethyl-1,10- phenanthrolin-1-ium halide. In still another embodiment of the present disclosure, the phenanthroline derivative or its salt is either 2,9-dimethyl-1,10-phenanthroline or 1,2,9-trimethyl- 1,10-phenanthrolin-1-ium iodide. In still another embodiment of the present disclosure, the aldehyde derivative is compound of formula III.
Figure imgf000025_0001
Compound of formula III wherein, R is individually selected from a group comprising hydrogen, 7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof; In still another embodiment of the present disclosure, the aldehyde derivative is either 7-(diethylamino)-2-oxo-2H-chromene-3-carbaldehyde or 8-hydroxy- 1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde. In still another embodiment of the present disclosure, the reagent is a base or acid anhydride. In still another embodiment of the present disclosure, the solvent is alcohol or acid anhydride. In still another embodiment of the present disclosure, the solvent is ethyl alcohol or acetic anhydride. In an embodiment of the present disclosure, a process for the preparation of compound represented by TGP17 as mentioned above, said process comprising step of reacting 2,9-dimethyl-1,10-phenanthroline with 7-(diethylamino)-2-oxo-2H- chromene-3-carbaldehyde in presence of acetic anhydride under heating conditions to obtain TGP17. In another embodiment of the present disclosure, a process for the preparation of compound represented by TGP18 as mentioned above, said process comprising step of reacting 1,2,9-trimethyl-1,10-phenanthrolin-1-ium iodide with 7-(diethylamino)-2- oxo-2H-chromene-3-carbaldehyde in presence of piperidine and ethanol under heating conditions to obtain TGP18. In yet another embodiment of the present disclosure, a process for the preparation of compound represented by TGP21 as mentioned above, said process comprising step of reacting 1,2,9-trimethyl-1,10-phenanthrolin-1-ium iodide with 8-hydroxy- 1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde in presence of piperidine and ethanol under heating conditions to obtain TGP21. In an embodiment of the present disclosure, the process is carried out at a temperature ranging from about 30°C to about 90°C, and for a time period ranging from about 60 minutes to about 24 hours. In still another embodiment of the present disclosure, the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof. The present disclosure further provides a pharmaceutical composition comprising compound of Formula I
Figure imgf000027_0001
Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof; wherein, R, R1, R2are individually selected from a group comprising hydrogen,7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde,straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, optionally along with at least one pharmaceutically acceptable excipient. The present disclosure further provides a pharmaceutical composition comprising compound selected from a group comprising
Figure imgf000028_0001
; and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. The present disclosure furthermore provides a method of administration of a pharmaceutical composition comprising compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof a group comprising intravenous administration, intramuscular administration, intraperitoneal administration, hepatoportal administration, intra articular administration and pancreatic duodenal artery administration, or any combination thereof. The present disclosure furthermore provides use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula I for GQ staining in vitro and in cellulo conditions. The present disclosure furthermore provides use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula I as a probe for GQ DNA detection. The present disclosure furthermore provides use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula I along with their conjugates as diagnostic probes. Phenanthroline-based cyanines have potential use as selective GQ staining probes in vitro and in cellulo. Phenanthroline-based cyanines show selective GQ binding and have extensive potential to be used as diagnostic probes owing to their GQ selectivity. The present disclosure also provides a composition or formulation comprising a therapeutically effective amount of compound(s) of Formula I, optionally along with excipient(s). In an embodiment of the present disclosure, the excipient is selected from a group comprising, but not limited to granulating agent, binding agent, lubricating agent, disintegrating agent, sweetening agent, glidant, anti-adherent, anti-static agent, surfactant, anti-oxidant, gum, coating agent, colouring agent, flavouring agent, coating agent, plasticizer, preservative, suspending agent, emulsifying agent, plant cellulosic material, spheronization agents and combinations thereof. In a non-limiting embodiment of the present disclosure, the composition further comprises a compound of Formula I. In a non-limiting embodiment of the present disclosure, the composition is administered by mode selected from group comprising intravenous, subcutaneous, transdermal, intrathecal, oral and any other compatible mode, or any combination thereof. The present disclosure further provides an in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula I with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence. The present disclosure further provides an in vitro method of detection or quantification of BCL-2 GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula I with a BCL-2 GQ DNA sequence to allow for hybridization of the probe with the BCL-2 GQ DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to BCL-2 GQ DNA sequence, upon hybridization of the probe to BCL-2 GQ DNA sequence. Compounds of formula I have potential use as selective GQ staining probes in vitro and in cellulo. Compounds of formula I show selective GQ binding and have extensive potential to be used as anti-cancer drugs owing to their GQ targeting therapeutic potential. The significant anti-tumor activity of Compounds of formula I shown in A549 xenograft model envisage its therapeutic application for cancer therapy. In an embodiment of the present disclosure, the specific interaction or binding is by non-covalent interaction, resulting in the fluorescence. In an embodiment of the present disclosure, the specific interaction or binding is by non-covalent interaction including hydrophobic, S-stacking and electrostatic interactions, resulting in the fluorescence. The present disclosure provides a method of inhibiting growth of a cell, said method comprising contacting the compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition of compound of Formula I with the cell. In an embodiment of the present disclosure, the cell is an eukaryotic cell and is either cancerous cells or cells infected with microorganisms. The present disclosure provides a method of managing or treating a disease in a subject, said method comprising step of administering the compound of Formula I as claimed in claim 1 or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula I in said subject to manage and treat the disease. In another embodiment of the present disclosure, the composition/formulations formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof. Use of compound of Formula I or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula I in the manufacture of a medicament for treatment of cancer. Use of compound of Formula I or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition comprising compound of Formula I in the manufacture of probes. In another embodiment, the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein. The present disclosure provides a method of inhibiting the growth of cancer in xenograft mice model, said method comprising contacting the compound of Formula I with the said animal model. The present disclosure provides a method for treating cancer in a subject, said method comprising administering the compound of Formula I. The present disclosure provides a method for treating cancer in a subject, said method comprising administering the composition comprising compound of Formula I. The present disclosure provides a method of inhibiting the growth of lung cancer in xenograft mice model, said method comprising contacting the compound of Formula I with the said animal model. The present disclosure provides a method for treating lung cancer in a subject, said method comprising administering the compound of Formula I. The present disclosure provides a method for treating lung cancer in a subject, said method comprising administering the composition comprising compound of Formula I. The present disclosure provides carbazole-based monocyanine probes by functionalizing with various electron accepting moieties and demonstrated their in cellulo GQ selectivity at the promoter level besides GQ visualization in live cells and their therapeutic potential. The present disclosure provides a compound comprising the following structure:
Figure imgf000033_0001
Formula IA wherein, R, R1, R2are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof; In an embodiment of the present disclosure, R is either hydrogen or formyl group. In another embodiment of the present disclosure, R1 is selected from a group comprising methyl, ethyl, propyl, acetyl, phenyl or benzyl. In yet another embodiment of the present disclosure, R2 is selected from a group comprising 4-methylbenzothiazolyl, 4-methyllepidinyl or 4-methylquinolinyl. The present disclosure provides a compound selected from:
Figure imgf000034_0001
Figure imgf000035_0001
; and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. Synthesis of carbazole containing cyanine compounds: Carbazole fluorophores were prepared by employing Knoevenagel reaction as the key step for conjugating carbazole di- or mono-aldehyde with methylated benzothiazole (TGS17a andTGS41), lepidine (TGS17b andTGS42) and quinaldine (TGS17c andTGS43) scaffolds as different acceptor moieties to obtain donor–S–acceptor (D–S–A) based molecular systems with extendedS- conjugation. Figure 1A shows the molecular structures of carbazole-based monocyanine fluorophores. The structure activity of small molecules has been extended to study the role of aldehyde group presence on the carbazole (TGS17a, TGS17b and TGS17c) derivatives for their in vitro and in cellulo selectivity (or optical response) towards nucleic acids. All these derivatives were synthesized as shown in scheme 1 and thoroughly characterized by various spectroscopic techniques.
Figure imgf000036_0001
Scheme 1A. Synthetic route to carbazole-based monocyanine derivatives. (i) POCl3, DMF, 100 °C, 30 hours; (ii) POCl3, DMF, 80 °C, 8 hours; (iii) Piperidine, CH2Cl2 : MeOH (1:1), reflux, 60 °C, 2 hours. The present disclosure also provides a process for the preparation of compound represented by Formula IA as mentioned above, said process comprising step of: a. formylating compound of formula IIA to obtain compound of formula IIIA
Figure imgf000037_0001
Formula IIA Formula IIIA wherein, R and R1 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted; b. reacting compound of formula IIA with R2 moiety to obtain compound of formula I
Figure imgf000037_0002
Formula IA wherein, R, R1, R2 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted. In an embodiment of the present disclosure, the formylation is carried out in present of formylating reagent. In an embodiment of the present disclosure, the formylation of compound of formula IIA to obtain compound of formula IIIA is carried out in presence of formylating reagent. In an embodiment of the present disclosure, a process for the preparation of compound represented by TGS17a as mentioned above, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylbenzothiazole to obtain TGS17a. In another embodiment of the present disclosure, a process for the preparation of compound represented by TGS41 as mentioned above, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylbenzothiazole to obtain TGS41. In yet another embodiment of the present disclosure, a process for the preparation of compound represented by TGS17b as mentioned above, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methyllepidinium to obtain TGS17b. In still another embodiment of the present disclosure, a process for the preparation of compound represented by TGS42 as mentioned above, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methyllepidinium to obtain TGS42. In still another embodiment of the present disclosure, a process for the preparation of compound represented by TGS17c as mentioned above, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylquinolinium to obtain TGS17c. In still another embodiment of the present disclosure, a process for the preparation of compound represented by TGS43 as mentioned above, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylquinolinium to obtain TGS43. In an embodiment of the present disclosure, the formylation is carried out in presence of a formylating reagent. In another embodiment of the present disclosure, the formylating reagent is selected from a group comprising Phosphoryl halide, Phosphoryl chloride, oxalyl chloride, thionyl chloride and combinations thereof. In yet another embodiment of the present disclosure, the process is carried out at a temperature ranging from about 30 °C to about 120 °C, and for a time period ranging from about 60 minutes to about 40 hours. In still another embodiment of the present disclosure, the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof. The present disclosure further provides a pharmaceutical composition comprising compound of Formula IA
Figure imgf000040_0001
Formula I wherein, R, R1, R2 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof, optionally along with at least one pharmaceutically acceptable excipient. The present disclosure further provides a pharmaceutical composition comprising compound selected from a group comprising
Figure imgf000041_0001
; and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. The present disclosure furthermore provides a method of administration of a pharmaceutical composition comprising compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof a group comprising intravenous administration, intramuscular administration, intraperitoneal administration, hepatoportal administration, intra articular administration and pancreatic duodenal artery administration, or any combination thereof. The present disclosure furthermore provides use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IA for GQ staining in vitro and in cellulo conditions. The present disclosure furthermore provides use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IA as a probe for GQ DNA detection. The present disclosure furthermore provides use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula IA along with their conjugates as diagnostic probes. Carbazole-based cyanines have potential use as selective GQ staining probes in vitro and in cellulo. Carbazole-based cyanines show selective GQ binding and have extensive potential to be used as diagnostic probes owing to their GQ selectivity. The present disclosure also provides a composition or formulation comprising a therapeutically effective amount of compound(s) of Formula I, optionally along with excipient(s). In an embodiment of the present disclosure, the excipient is selected from a group comprising, but not limited to granulating agent, binding agent, lubricating agent, disintegrating agent, sweetening agent, glidant, anti-adherent, anti-static agent, surfactant, anti-oxidant, gum, coating agent, coloring agent, flavouring agent, coating agent, plasticizer, preservative, suspending agent, emulsifying agent, plant cellulosic material, spheronization agents and combinations thereof. In a non-limiting embodiment of the present disclosure, the composition further comprises a compound of Formula I. In a non-limiting embodiment of the present disclosure, the composition is administered by mode selected from group comprising intravenous, subcutaneous, transdermal, intrathecal, oral and any other compatible mode, or any combination thereof. In another embodiment of the present disclosure, the composition/formulation is formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof. In another embodiment, the present disclosure provides as a diagnostic and therapeutic probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein. The present disclosure provides a method of identifying GQ structures in cellulo conditions, said method comprising the step of contacting the compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula I. The present disclosure provides a method of identifying GQ structures in cellulo conditions, said method comprising the step of contacting the compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of Formula IA by turn on fluorescence mechanism. The present disclosure further provides an in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of Formula IA with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence. The present disclosure further provides an in vitro method of detection or quantification of BCL-2 GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of Formula IA with a BCL-2 GQ DNA sequence to allow for hybridization of the probe with the BCL-2 GQ DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to BCL-2 GQ DNA sequence, upon hybridization of the probe to BCL-2 GQ DNA sequence. The present disclosure further provides an in vitro method of detection or quantification of c-MYC GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of Formula IA with a c-MYC GQ DNA sequence to allow for hybridization of the probe with the c-MYC GQ DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to c-MYC GQ DNA sequence, upon hybridization of the probe to c-MYC GQ DNA sequence. Compounds of Formula IA have potential use as selective GQ staining probes in vitro and in cellulo. Compounds of Formula IA show selective GQ binding and have extensive potential to be used as anti-cancer drugs owing to their GQ targeting therapeutic potential. In an embodiment of the present disclosure, the specific interaction or binding is by non-covalent interaction, resulting in the fluorescence. In an embodiment of the present disclosure, the specific interaction or binding is by non-covalent interaction including hydrophobic, S-stacking and electrostatic interactions, resulting in the fluorescence. The present disclosure provides a method of inhibiting growth of a cell, said method comprising contacting the compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition of compound of Formula IA with the cell. In an embodiment of the present disclosure, the cell is an eukaryotic cell and is either cancerous cells or cells infected with microorganisms. The present disclosure provides a method of managing or treating a disease in a subject, said method comprising step of administering the compound of Formula IA as claimed in claim 1 or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IA in said subject to manage and treat the disease. In another embodiment of the present disclosure, the composition/formulations formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof. Use of compound of Formula IA or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IA in the manufacture of a medicament for treatment of cancer. Use of compound of Formula IA or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IA in the manufacture of a medicament for inhibiting the growth of cancer cells. Use of compound of Formula IA or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition comprising compound of Formula IA in the manufacture of probes. In another embodiment, the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein. The present disclosure provides a method for treating cancer in a subject, said method comprising administering the compound of Formula I. The present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the compound of Formula I. The present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the composition comprising compound of Formula I. The present disclosure provides a method for treating cancer in a subject, said method comprising administering the composition comprising compound of Formula I. The present disclosure provides a method for treating breast cancer in a subject, said method comprising administering the compound of Formula I. The present disclosure provides a method for treating breast cancer in a subject, said method comprising administering the composition comprising compound of Formula I. In vitro GQ selectivity of carbazole-based monocyanine derivatives The presence of electron-rich carbazole moiety in the probes provides high emission intensity profiles and offer appropriate planar core size to fit on the G- tetrad. The photophysical properties of carbazole derivatives showed broad and featureless absorption band at around 435-450 nm (Omax abs) in PBS (20 mM PBS, 100 mM KCl, pH 7.4, Table 1A, Figure 2A). Upon excitation at their Omax abs these probes exhibited very weak emission (Omax em) at 550-610 nm in PBS buffer (Table 1A). Classic cyanine dyes suffer from a narrow Stokes shift (Δλ< 25 nm) which may result in self-quenching and measurement error, that can decrease the detection sensitivity. Interestingly, carbazole derivatives exhibited large Stokes shifts between the absorption and emission spectra (Δλ = 130-160 nm) due to excited-state intramolecular charge transfer (Table 1A). When these carbazole‐based monocyanines were titrated with the different promoter GQs (TEL22, c-MYC, BCL-2, VEGF, c-KIT, KRAS) and duplex forming DNA sequences in PBS, a strong and progressively increasing (upto 5-10‐fold for TGS17a-17c and 15-80-fold for TGS41-43) in fluorescence intensity was observed in presence of all GQ sequences (Figure 3A). Negligible fluorescence increase was observed in presence of duplex DNA (Figure 3A). The fluorescence enhancement in presence of GQ is attributed to the large reduction in the non- radiative decay of the photoexcited monocyanines due to the restricted rotation of the central C−C bond of the probes upon GQ binding. This is consistent with the observed increase in the fluorescence lifetimes of these monocyanines upon addition of GQ DNA. It is noteworthy to mention the significant red-shift (bathochromic shift) of the absorption spectra in presence of GQ compared to duplex DNA was observed (Figure 2A). TGS17a-17c derivatives showed large bathochromic shift ('Omax abs = 20-45 nm) in presence of GQ DNA compared to duplex DNA ('Omax abs = 2-10 nm) (Table 1A). TGS41-43 derivatives showed similar increase in bathochromic shift ('Omax abs = 15-30 nm) for GQ DNA compared to duplex DNA ('Omax abs = 10-15 nm) with a concomitant decrease in their absorptivities (Figure 2A). The large bathochromic shift and strong increase in fluorescence response signifies the stronger binding of carbazole-based monocyanine derivatives with quadruplex structure compared to duplex DNA albeit their non-selectivity among various GQ topologies. Table 1A. Summary of photophysical measurements of carbazole derivatives in presence of different DNA structures.
Figure imgf000048_0001
Binding interactions with GQ The implicit selectivity of benzothiazole appended carbazole derivatives, TGS17a and TG41 towards BCL-2 and c-MYC promoter GQs, respectively was further investigated using thermodynamic parameters measured by isothermal titration calorimetry (ITC). The equilibrium binding constant (KD) and changes in thermodynamic parameters such as enthalpy ('H), Gibbs free energy ('G) and entropy ('S) were measured by ITC for all carbazole derivatives interacting with different promoter sequences (c-MYC, BCL-2, VEGF-A, and KRAS) (Figure 5Aa). It has been witnessed a series of enthalpy-dominated exothermic binding spontaneous reactions (negative free energy, 'G) between carbazole derivatives and the quadruplexes. In corroboration with luciferase results, lepidine (TGS17b and TGS42) and quinaldine (TGS17c and TGS43) conjugated carbazole derivatives showed almost no binding or weak binding with VEGF GQ, and non- selective binding with c-MYC, BCL-2 and KRAS promoter GQs (Table 3A). However, TGS17a and TGS41 (benzothiazole conjugated) surprisingly showed selective binding interactions with BCL-2 and c-MYC with dissociation constants of 1.15 PM and 932 nM, respectively and showed no interactions with other promoter GQ highlighting their impeccable selectivity (Figure 5Aa). The implication of simple aldehyde group on carbazole derivatives is found to be remarkable in achieving intracellular GQ selectivity while underscoring their structure-activity relationship. The selective recognition of BCL-2 and c-MYC GQs by TGS17a and TGS41, respectively, was further reasoned by employing molecular docking studies. Docking of TGS17a and TGS41 were performed against wild type c-MYC and BCL-2 GQ forming sequence, which showed insights on mode of quadruplex binding interactions (Figure 5Ab). These studies revealed the predominant end-stacking mode of binding for TGS17a with BCL-2 parallel quadruplex conformation with high binding affinity (-9.6 kcal/mol). The carbazole (donor) and benzothiazole (acceptor) moieties together are involved in S-stacking (hydrophobic) interactions with G-quartet at 5'-end of BCL-2 in addition to electrostatic interactions. In corroboration with ITC and luciferase studies, TGS17a showed weaker binding (-9.1 kcal/mol) with c-MYC quadruplex structure compared to BCL-2. In contrary, TGS41 preferred groove binding interactions (-8.0 kcal/mol) with c-MYC parallel quadruplex conformation through hydrogen bonding and electrostatic interactions. To further support these results, NMR titration experiments were performed on TGS17a/TGS41 in the presence or absence of c-MYC or BCL-2 GQs. In support of docking studies, NMR data revealed that ligands interact with GQ by stacking of carbazole and benzothiazole aromatic moieties, as confirmed from the chemical shift and splitting of aromatic protons (Figure 4A). Besides, the downfield shift in aldehyde group specific to TCA confirmed its role in additional hydrogen bonding with guanine phosphate backbone as shown by the docking studies, rendering its high affinity for BCL-2 GQ. The change is chemical shift of protons of ethyl substituent clearly indicates its contribution towards non-polar interactions with GQ. The two distinct binding modes favoured by TGS17a and TG41 with BCL-2 and c-MYC parallel quadruplex structures, respectively, provides a rational explanation for their discriminating potential towards different promoter GQ conformations. Table 3A. GQ and duplex forming oligonucleotide sequences used for photophysical studies.
Figure imgf000050_0001
Anti-cancer activity of carbazole derivatives The anti-proliferative effects of the carbazole derivatives were evaluated in cellulo on different human cancer cell lines (MCF-7, MDAMB 231, A549, PC3, and HeLa) and non-transformed (HEK293T) cells by MTT assay (TABLE 1AA). After 24 hours of treatment, TGS41-43 showed effective inhibition of cancer cell proliferation compared to the TGS17a-17c. The carbazole derivatives with benzothiazolium (TGS17a and TGS41) as an acceptor moiety exhibited profound anti-cancer activities at lower micromolar concentrations (IC50 of TGS17a=10 ± 3.5 μM and IC50 of TGS41 =3 ± 0.98 μM) compared to the lepidine and quinaldine derivatives. They showed negligible cytotoxic effects in the normal cells having 20-30 fold higher IC50 values (IC50a 50 μM) compared to the cancer cells. Intriguingly, their cytotoxic effects were found to be significantly higher in MDAMB 231, A549, and MCF-7 cells, where overexpression of c-MYC and BCL-2 contributes to the cancer cell survival and tumorigenicity (PMID: 22011203, PMID: 22581054). The lepidine (IC50 of TGS17b =19.1 ± 4.9 μM) and quindaline (IC50 of TGS17c = 25.6 ± 2.4 μM) derivatives with aldehyde group exerted moderate cytotoxic effects in cancer cells compared to that of the derivatives without aldehyde group(IC50 of TGS42 = 6 ± 1.9 μM; IC50 of TGS43 =5.4 ± 4.6 μM). Unlike the benzothiazolium compounds, lepidine and quinaldine derivatives manifested a certain degree of toxicity in normal cells (IC50> 20-50 μM). This result is in agreement with photophysical studies which showed their high affinity for G-quadruplex structures, coupled with the lack of selectivity for a specific G-quadruplex structure leading to a strong but indiscriminate cytotoxicity. GQ visualization To explore whether carbazole derivatives (TGS17a and TGS41) binds to GQs in MDAMB 231 cells, immunofluorescence experiment was performed by employing highly specific GQ antibody BG4 to compare the localization of BG4 with TGS17a and TGS41. MDAMB 231 cells were treated with TGS17a (0.5 and 1 PM) and TGS41 (0.5 and 1 PM) for 30 minutes and colocalized with BG4 antibody. As shown in Figure 7A, TGS17a and TGS41 foci well co-localized with BG4 staining in the nucleus which was again clearly observed in 3D images (not shown). BG4 colocalization results underline the importance of these derivatives for staining GQ structures in live cells. The sensitivity of our molecular probes to visualize GQs in live cells is endorsed by longer fluorescence decay times observed in vitro for TGS17a and TGS41 in presence of GQ compared to duplex DNA. Time-correlated single photon counting (TCSPC) system was used to measure the fluorescence lifetimes of TGS17a and TGS41 using 480 nm laser in presence of quadruplex (BCL-2 and C-MYC) and duplex DNA sequences (Figure 6A). TGS41 showed 11-fold and 9-fold longer fluorescence decay time in presence of c-MYC (0.79 ns) and BCL-2 (0.63 ns) quadruplex respectively, compared to duplex DNA (0.07 ns) endorsing the fluorescence measurements observed in Figure 3A. The lifetime traces of TGS17a showed slightly shorter fluorescence decay time in presence of both c-MYC (0.078 ns) and BCL-2 (0.063) GQs compared to TGS41, which signify slightly lower efficiency in detection. Also, lifetime traces of TGS17a in presence of duplex could not be measured due to negligible fluorescence emission. Nonetheless, fluorescence lifetime measurements of TGS17a and TGS41 showed longer decay times which are in corroboration with the photophysical studies (Figure 3A). The appreciable differences observed in fluorescence lifetime decay further makes TGS41 and TGS17a an enticingly promising probes to visualize GQs selectively in live cells using FLIM technique. The confocal images in addition to their BG4 colocalization also evidently showed nucleolar localization of TGS17a and TGS41. To validate this, time dependent confocal study was performed to observe their cellular localization and it was evident that TGS17a and TGS41 localized in the nucleolus within 30 min to 1 h time frame (data not shown). Immunofluorescence experiment was again performed to confirm the nucleolar localization by colocalizing with nucleolin, which is a protein marker specific to nucleolus (Figure B of 7A). TGS17a and TGS41 showed clear colocalization with nucleolin, accompanied by prominent nucleolar distortion at 1 hour treatment. Having shown high quadruplex binding affinity of TGS17a and TGS41 and their localization in nucleolus, it was anticipated that their influence on ribosome biogenesis, possibly to disrupt the interaction of rDNA GQs with the nucleolin protein. Carbazole derivatives showed fluorescence enhancement specific to quadruplex genes compared to duplex DNA attributed to their high binding affinities for GQ structures. Carbazole derivatives exhibited significant anti-proliferative effects in several cancer cells through induction of apoptosis. Benzothiazole appended carbazole derivatives (TGS17a and TGS41) demonstrated enhanced intracellular quadruplex selectivity. From BG4 colocalization and lifetime decay profiles, it has also been demonstrated the effectiveness of TGS17a and TGS41 as a possible tool for the visualization of GQ localization in live cells. The GQ visualization, selective oncogene modulation and anti-proliferation effects together emphasize the diagnostic and therapeutic potential of TGS17a and TGS41. Thus, the present invention demonstrates the dual functionality of visualization and therapeutic potential of small molecules targeting GQ conformation. Thus, cyanine-based fluorescence probes shown to selectively stabilize GQ structures with turn-on fluorescence response and potential therapeutic effect highlighting their unique property to be theranostic agents for cancer therapy. Therefore, the dual property of cyanine probes address the current limitations in GQ targeting anti-cancer drugs. TGS17a and TGS41 showed intracellular GQ selectivity and selective anti- proliferative effects in cancer cells demonstrating the therapeutic potential. TGS17a and TGS41 were also shown to visualize GQs in MDAMB 231 cells using BG4 antibody specific to GQ structures highlighting their potential role to visualize GQs in live cells. Thus, the carbazole-based cyanine derivatives are potential drugs with diagnostic and therapeutic application for cancer therapy. The present disclosure provides a compound comprising the following structure:
Figure imgf000053_0001
Formula IB wherein, ‘X’ is methine unit; and ‘n’ is methine carbons wherein n is 1-6. any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. In an embodiment of the present disclosure, ‘[X]n’ is either a methine or polymethine. In another embodiment of the present disclosure, ‘[X]n’ is either
Figure imgf000054_0001
. The present disclosure provides a compound selected from:
Figure imgf000054_0002
and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. The present disclosure also provides a process for the preparation of compound represented by Formula IB as mentioned above, said process comprising step of: c. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N- diethylamino-4-methyl-flavylium; and d. reacting 7-N,N-diethylamino-4-methyl-flavylium with either ethanol or acetic anhydride and paraformaldehyde in presence of anhydrous sodium acetate to obtain Formula IB .
Figure imgf000055_0001
Formula IB The present disclosure also provides a process for the preparation of compound represented by FLV-1 as mentioned above, said process comprising step of: c. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N- diethylamino-4-methyl-flavylium; and d. reacting 7-N,N-diethylamino-4-methyl-flavylium with ethanol in presence of anhydrous sodium acetate to obtain FLV-1.
Figure imgf000055_0002
The present disclosure also provides a process for the preparation of compound represented by FLV-3 as mentioned above, said process comprising step of: a. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N- diethylamino-4-methyl-flavylium; and b. reacting 7-N,N-diethylamino-4-methyl-flavylium with acetic anhydride in presence of anhydrous sodium acetate and paraformaldehyde to obtain FLV-3.
Figure imgf000056_0001
In another embodiment of the present disclosure, the process is carried out at a temperature ranging from about 30℃ to about 90 ℃, and for a time period ranging from about 30 minutes to about 24 hours. In yet another embodiment of the present disclosure, the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof. Compound of formula IB were studied to demonstrate their cellular uptake and quadruplex selectivity (Figure 1). Compound of formula IB are flavylium-methine fluorophores as analogues to cyanine family of dyes with emission in the NIR region of the electromagnetic spectrum and possible applications in biological imaging. Cyanine dyes are nitrogen containing polymethines with varying methine units and their absorption and emission span visible and NIR wavelength regions, illustrating their possible use in live-cell microscopy. FLV1 showed in vitro selectivity for quadruplex over duplex conformation, especially with enhanced fluorescence for a particular quadruplex sequence of promoter VEGF. The in vitro selectivity of FLV1 was further validated by GQ staining in polyacrylamide gel electrophoresis (PAGE). Interestingly, FLV1 showed strong binding to mtDNA quadruplex forming sequences with significant fluorescence response and selective localization in mitochondria of live cells reflects the potential of flavylium derivative for binding of GQ specific to mitochondria organelle. The present disclosure further provides a pharmaceutical composition comprising compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof, optionally along with at least one pharmaceutically acceptable excipient. The present disclosure further provides a pharmaceutical composition comprising compound of Formula IB
Figure imgf000057_0001
Formula I wherein, ‘X’ is methine unit; and ‘n’ is methine carbons wherein n is 1-6. or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof, optionally along with at least one pharmaceutically acceptable excipient. The present disclosure further provides a pharmaceutical composition comprising compound selected from a group comprising
Figure imgf000058_0001
; and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. The present disclosure furthermore provides a method of administration of a pharmaceutical composition comprising compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof a group comprising intravenous administration, intramuscular administration, intraperitoneal administration, hepatoportal administration, intra articular administration and pancreatic duodenal artery administration, or any combination thereof. The present disclosure furthermore provides use of compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IB for GQ staining in vitro and in organelle conditions. The present disclosure furthermore provides use of compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IB as a probe for selective mitochondrial staining and its GQ DNA detection. The present disclosure furthermore provides use of compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula IB along with their conjugates as diagnostic probes. Flavylium-based cyanines have potential use as selective GQ staining probes in vitro and in organelle. Flavylium-based cyanines show selective GQ binding and have extensive potential to be used as diagnostic probes and organelle markers owing to their GQ and organelle selectivity respectively. The present disclosure also provides a composition or formulation comprising a therapeutically effective amount of compound(s) of Formula I, optionally along with excipient(s). In an embodiment of the present disclosure, the excipient is selected from a group comprising, but not limited diluent, carrier, granulating agent, binding agent, lubricating agent, disintegrating agent, sweetening agent, glidant, anti-adherent, anti-static agent, surfactant, anti-oxidant, gum, coating agent, coloring agent, flavouring agent, coating agent, plasticizer, preservative, suspending agent, emulsifying agent, plant cellulosic material, spheronization agents and combinations thereof. In a non-limiting embodiment of the present disclosure, the composition further comprises a compound of Formula I. In a non-limiting embodiment of the present disclosure, the composition is administered by mode selected from group comprising intravenous, subcutaneous, transdermal, intrathecal, oral and any other compatible mode, or any combination thereof. In an embodiment of the present disclosure, the composition/formulation is formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof. In another embodiment of the present disclosure, the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound of formula IB or a composition as described herein. The present disclosure provides a method of identifying GQ sequence particularly present in VEGF gene, said method comprising the step of contacting the compound of formula IB by NIR fluorescence switch-on mechanism. The specific interaction or binding of formula IB to the GQ through non-covalent end-stacking interaction, results in fluorescence. Thus, Flavylium containing cyanines based chemical molecules are useful for GQ detection by near infra-red fluorescence switch-on mechanism, and have related applications including but not limited to cell imaging. Organelle sensing is the specialty of the molecule in addition to diagnosis. The present disclosure further provides an in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula IB or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula IB with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence. The present disclosure further provides an in vitro method of detection or quantification of VEGF GQDNA sequence, said method comprising a. contacting the probe of compound of Formula IB or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula IB with a VEGF GQDNA sequence to allow for hybridization of the probe with the VEGF GQDNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to VEGF GQDNA sequence, upon hybridization of the probe to VEGF GQ DNA sequence. The present disclosure provides a method of staining organelles of a cell, said method comprising contacting the compound of formula IB with cells. Compounds of formula IB have potential use as selective VEGF GQ staining probes in vitro and in cellulo specific to organelles. Compounds of formula IB show selective VEGF GQ binding and have extensive potential to be used as anti-cancer drugs owing to their VEGF GQ targeting therapeutic potential. In an embodiment of the present disclosure, the specific interaction or binding is by non-covalent interaction, resulting in the fluorescence. In an embodiment of the present disclosure, the specific interaction or binding is by non-covalent interaction including hydrophobic, S-stacking and electrostatic interactions, resulting in the fluorescence. The present disclosure provides a method of inhibiting growth of a cell, said method comprising contacting the compound of Formula IB or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition of compound of Formula IB with the cell. In an embodiment of the present disclosure, the cell is an eukaryotic cell and is either cancerous cells or cells infected with microorganisms. The present disclosure provides a method of managing or treating a disease in a subject, said method comprising step of administering the compound of Formula IB as claimed in claim 1 or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IB in said subject to manage and treat the disease. In another embodiment of the present disclosure, the composition/formulations formulated into forms selected from a group comprising, but not limited to, solution, aqueous suspension, capsule, tablet, injection, cream, gel, ointment, lotion, emulsion, foam, troche, lozenge, oily suspension, patch, dentifrice, spray, drops, dispersible powder or granule, syrup, elixir, food stuff, and any combination of forms thereof. Use of compound of Formula IB or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IB in the manufacture of a medicament for treatment of cancer. Use of compound of Formula IB or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula IB in the manufacture of a medicament for inhibiting the growth of cancer cells. Use of compound of Formula IB or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition comprising compound of Formula IB in the manufacture of probes. In another embodiment, the present disclosure provides as a probe in the diagnosis and the treatment of a disease or a condition associated with cancer, comprising administering to a subject in need thereof a compound or a composition as described herein. The present disclosure provides a method for treating cancer in a subject, said method comprising administering the compound of Formula I. The present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the compound of Formula I. The present disclosure provides a method for inhibiting growth of cancer cells in a subject, said method comprising administering the composition comprising compound of Formula I. Design and synthesis of flavylium containing cyanine compounds: Flavylium-methine fluorophores were prepared by the introduction of an activated flavylium heterocycle 1 to an aldehyde in presence and absence of oxygen following the procedure reported in literature. 7-N,N-diethylamino-4-methyl- flavylium (1) was prepared which was further transformed in presence of oxygen to monomethine flavylium FLV1 wherein flavylium peroxide generated through radical addition of oxygen, combined with the deprotonated flavylium 1 (scheme 1). Compound FLV3 (Figure 1) was obtained by combining with the paraformaldehyde under basic conditions in the absence of oxygen (scheme 1). The resulted diethylamino flavylium heterocycles FLV1 and FLV3 were studied for their cellular uptake and binding interactions with nucleic acids.
Figure imgf000064_0001
Scheme 1. Synthesis route to flavylium-methine derivatives FLV1 and FLV3. Photophysical properties of FLV1 and FLV3 Flavylium derivatives have interesting photophysical properties which can be used for sensing and imaging applications. The photophysical (absorption and emission) measurements of FLV1 (Oabs = 660 nm, Oem = 700 nm) and FLV3 (Oabs = 750 nm, Oem = 795 nm) displayed excitation and emission in the longer wavelength region owing to extended conjugation, an essential prerequisite to avoid autofluorescence and DNA photo-damage during cellular imaging (Figure 2a and 2b). Preliminary screening of FLV1 and FLV3 was performed for the nucleic acid conformation selectivity using various quadruplex and duplex forming sequences (Table 1, Figure 2). FLV1 (2 PM) and FLV3 (2 PM) showed strong fluorescence enhancement (monitored at 695 and 780 nm, respectively) in presence of quadruplex compared to duplex DNA (Figure 2c and 2d). Interestingly, FLV1 showed 400-fold fluorescence enhancement for quadruplex forming sequence of oncogene promoter VEGF. However, FLV3 showed no selectivity among the topologies of quadruplex but notable difference of 200-300 fold fluorescence enhancement observed for GQ compared to duplex DNA. Interestingly, FLV1 and FLV3 both did not exhibit fluorescence in the absence of any DNA (in 20 mM PBS, 100mMKCl, pH 7.4) due to facile intramolecular twist motion of the C–C bond of the polymethine linker. In vitro GQ selectivity of FLV1 The fluorescence emission study in the presence of various GQ and duplex forming DNA sequences revealed that FLV1 is a selective turnon fluorescence probe for quadruplex DNA, especially VEGF quadruplex (Figure 3a). The efficiency of probe FLV1 in binding to specific quadruplex sequence as compared to FLV3 may be explained by the precise size of the molecule to fit into a constrained environment available on the GQ structure. Fluorescence titration was carried out to measure the binding affinities of FLV1 for quadruplex and duplex DNA. The dissociation constants (KD) calculated were found to be in the micromolar range for VEGF quadruplex (18 PM) and other GQ (25-40 PM) compared to duplex DNA which exhibited KD of >100 PM (Figure 3b). The lower KD concentrations of FLV1 for VEGF quadruplex among various other GQ topologies highlights conformation selectivity. It is worth mentioning that FLV1 exhibited strong red shift of 60 nm and maximum hyperchromism in the absorbance spectra with increase in concentration of VEGF GQ (Figure 3c). The fluorescent response of a probe during optical imaging enables the direct visualization of cellular uptake, localization, distribution and probe-nucleic acid binding interactions in living cells. Besides, fluorescence lifetime measurement which is concentration independent has the potential to distinguish between different nucleic acid topologies. Hence, time-correlated single photon counting (TCSPC) system was used to measure the fluorescence lifetimes of FLV1 in presence of duplex and quadruplex (VEGF) DNA (Figure 3d). The key finding of fluorescence lifetime measurements is that the fluorescence decay time of FLV1 in presence of VEGF quadruplex is much longer (2.58 ns) than that of duplex DNA (0.28 ns). The large difference in decay time between quadruplex and duplex DNA is pivotal for cellular imaging using fluorescence lifetime imaging to differentiate GQ from duplex conformation.5 The turn on NIR fluorescence behavior of probe FLV1 in the presence of GQ DNA inspired us to explore the use of FLV1 as a staining agent to detect quadruplex over duplex formation in the gel electrophoresis. The quadruplex and duplex forming (1 PM) sequences were subjected to polyacrylamide gel electrophoresis and the gel was visualized under UV illumination after staining with FLV1 and SYBR Gold (control). UV- illuminated gel image showed strong fluorescence intensity for VEGFGQ sequence compared to other quadruplex sequences while duplex DNA band was not stained by FLV1 (Figure 4). However, SYBR Gold an extremely sensitive fluorescent dye that binds to nucleic acids, shows staining of all oligonucleotides including duplex corresponding to its non-selectivity for different nucleic acid conformations. It is clear from gel electrophoresis studies that FLV1 probe selectively detects and discriminates quadruplex from duplex DNA sequences. Moreover, FLV1 detects VEGF quadruplex with relatively high signal intensity compared to other quadruplexes further corroborating with the observation from fluorescence response data. Binding interactions of FLV1 Circular dichroism (CD) studies were performed to examine any conformational changes induced by FLV1 binding in the VEGF quadruplex structure. The CD spectra of VEGF GQ shows positive peak around 260 nm and negative peak at 240 nm confirming its parallel GQ confirmation. FLV1 binding showed no changes in the CD spectra of VEGF indicating that overall parallel conformation was not affected. The mode of binding of FLV1 using fluorescent intercalator displacement assay (G4-FID assay) was investigated with thiazole orange (TO) which shows increase in fluorescence upon binding with quadruplex in end- stacking interactions. The complete displacement of TO from VEGF quadruplex with increase in concentration of FLV1 suggest similar binding modes shared by FLV1 and TO. Further, this result indicates end-stacking mode of binding for FLV1 with VEGF GQ. This was supported by molecular docking studies carried out in presence of VEGF quadruplex (PDB ID: 2M27). Remarkably, FLV1 showed higher binding affinity (−8.5 kcal/mol) in the 3'-end stacking mode compared with groove binding (−7.8 kcal/mol) of VEGF parallel GQ. These studies revealed that FLV1 predominantly binds in the 3'-end stacking mode where guanines present in the G-quartet of 3'-end involved in S-S stacking and S- alkyl interactions with aromatic flavylium moiety of the probe. These results are in good agreement with the experimental results obtained from displacement assay and reveal the end-stacking mode of binding of FLV1 with VEGF GQ. The end-stacking interaction of FLV1 on the G-quartet of parallel VEGF quadruplex restricts the intramolecular rotation of flavylium units around the methine linker causing the enhancement in fluorescence. In cellulo organelle selectivity of FLV1 The cellular uptake studies of FLV1 in live and fixed HeLa cell lines were first performed. The fluorescence imaging of FLV1 (500 nM) in Cy5 channel (Oex = 650 nm, Oem = 670 nm) displayed localization mainly in the cytoplasm (Figure 6a). Interestingly, cellular uptake of FLV1 was observed in both live and fixed A549 cells with similar cytoplasmic accumulation after 1 h incubation time. The observed specific staining pattern encouraged us to verify the organelle selectivity of FLV1. To determine the organelle selectivity, co-staining and imaging was performed in living HeLa and A549 cells co-incubated FLV1 with lysotracker blue (lysosome probe) and mitotracker orange (mitochondria probe) as shown in Figure 7. The fluorescence imaging of FLV1 clearly shows the overlay of FLV1 fluorescence (collected in Cy5 channel, Oem = 690 nm) with the mitotracker orange (Rhodamine channel, Oem = 620 nm). The co-staining with nuclear specific hoechst further excluded the localization of FLV1 in the nuclear region. The region of interest evidently indicates the overlay of fluorescence intensities from FLV1 with Mitoorange in A549 and HeLa cells which confirmed the mitochondrial localization. In contrast, FLV1 did not stain lysosomes, as there was no overlay of fluorescence between lysotracker blue (DAPI channel, λem = 460 nm) and FLV1 (Figure 7). In addition, the selectivity of FLV1 to mtDNAin cellulowas validated by performing deoxyribonuclease (DNase) digestion studies (Figure 6). Upon treatment with DNase, mtDNA was degraded and fluorescence staining of FLV1 in the cytoplasm sharply diminished (Figure 6b). These results reveal that FLV1 preferentially binds to mtDNA in the complex internal cellular meilieu revealing intracellular selectivity. This was anticipated as FLV1 is positively charged hydrophobic molecule, an essential property of a probe to achieve selective mitochondrial targeting and imaging. Interactions with mtDNA quadruplex The specific fluorescence response to G-quadruplex structures over duplex in vitro and selective localization in mitochondria motivated us to study the source of fluorescence response in cellulo. The fact that there are a200 PQF sequences of mtDNA, emphasize the importance of identifying all G-quadruplexes that may be involved in mitochondrial function. Six quadruplexes forming mtDNA sequences were chosen and characterized their GQ topology using CD. The CD data suggest that all six PQF sequences of mtDNA form GQs in vitro under physiological conditions with different topologies including parallel (mt8095, mt10252 and mt16250), antiparallel (mt9438) and mixed hybrid (mt1015 and mt10286) structures (Figure 8a). FLV1 showed a300-fold fluorescence enhancement for PQF mtDNA (mt9438, mt1015 and mt10286) sequences illustrating the mitochondrial uptake and mtDNA quadruplex binding (Figure 8b). In contrast to parallel quadruplex (VEGF promoter) binding in vitro, FLV1 showed maximum fluorescence response for antiparallel and mixed hybrid structures for PQF mtDNA sequences which needs further studies to explain. FLV3 conversely showed slight increase in fluorescence for all mtDNA sequences in vitro implying its non-selective interaction (Figure 8c). CD showed that FLV1 (1:1 ratio) did not induce any conformational changes to mtDNA quadruplexes except for a slight hypochromism in the signal, signifying no overall conformational change in the quadruplex structures (Figure 8a). The strong fluorescence enhancement of FLV1 in presence of PQF mtDNA sequences in vitro and selective mitochondrial staining in live HeLa cells provides credible evidence for the intracellular selectivity towards quadruplex DNA specific to mitochondria. Additional embodiments and features of the present disclosure will be apparent to one of ordinary skill in art based upon description provided herein. The embodiments herein provide various features and advantageous details thereof in the description. Descriptions of well-known/conventional methods/steps and techniques are omitted so as to not unnecessarily obscure the embodiments herein. Further, the disclosure herein provides for examples illustrating the above described embodiments, and in order to illustrate the embodiments of the present disclosure certain aspects have been employed. The examples used herein for such illustration are intended merely to facilitate an understanding of ways in which the embodiments herein may be practiced and to further enable those of skill in the art to practice the embodiments herein. Accordingly, the following examples should not be construed as limiting the scope of the embodiments herein. Experimental section General information. Dulbecco’s modified eagle medium (DMEM), fetal bovine serum (FBS), L- glutamine, penicillin-streptomycin and SYBR Gold for molecular biology were procured from Invitrogen. Caspase-3 assay kit was bought from BD Pharminogen. All oligonucleotide sequences (Table 1), purchased from Integrated DNA technologies. Dimethyl sulfoxide (DMSO), 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyltetrazoliumbromide (MTT), Hoechst 33258, DAPI, for cell culture and thiazole orange were purchased from Sigma-Aldrich. All other chemicals were of analytical reagent grade and used without further purification. Ultrapure water prepared by Milli-Q Gradient ultrapure water system (Millipore) was used in all experiments. 1H and 13C NMR spectra were recorded on a Bruker AV-400 MHz spectrometer with chemical shifts reported as parts per million (ppm) (in DMSO- d6, tetramethylsilane as an internal standard) at 20 °C. UV-vis absorption and emission spectra were measured in quartz cuvettes of 1 cm path length. High resolution mass spectra (HRMS) were obtained on Agilent Technologies 6538 UHD Accurate-Mass Q-TOF LC/MS spectrometer. Table 1. GQ and duplex forming sequences studied
Figure imgf000070_0002
Example 1:
Figure imgf000070_0001
Synthesis of TGP17. In a 25 mL round bottom flask 2,9-dimethyl-1,10- phenanthroline 4 (56 mg, 0.27 mmol) was added in acetic anhydride (5 mL). To the solution 7-(diethylamino)-2-oxo-2H-chromene-3-carbaldehyde 3 (72 mg, 0.29mmol) was added and refluxed the reaction mixture for 2 hours under nitrogen atmosphere. After completion of the reaction solvent was evaporated under reduced pressure. The crude product mixture was purified by column chromatography using DCM:MeOH (100:0 to 99:1) as eluant. The product obtained as orange coloured solid. Isolated yield 30 mg (25 %); 1H NMR (400 MHz, CDCl3): δH (ppm) 8.57 (dt, J = 8.2, 5.5 Hz, 2H), 8.29 (d, J = 9.7 Hz, 2H), 8.17 (s, 1H), 8.13 (s, 2H), 7.93 (d, J = 8.2 Hz, 1H), 7.74 (d, J = 8.8 Hz, 1H), 7.71 (d, J = 5.6 Hz, 1H), 7.00 (dd, J = 8.8, 2.5 Hz, 1H), 6.92 (d, J = 2.3 Hz, 1H), 3.86 (q, J = 7.1 Hz, 4H), 3.36 (s, 3H), 1.66 (t, J = 7.1 Hz, 6H).13C NMR (100 MHz, CDCl3): δC (ppm) 161.5, 159.3, 156.3, 155.9, 150.8, 150.0, 145.5, 145.4, 139.4, 136.3, 130.1, 129.4, 128.6, 125.7, 125.5, 123.6, 116.5, 109.2, 97.1, 44.9, 25.6, 12.5. HRMS (ESI-TOF, {M + H}+): calcd.435.1947 for C28H25N3O2, found 436.19801. Synthesis of TGP18. In a 25 mL round bottom flask 1,2,9-trimethyl-1,10- phenanthrolin-1-ium 5 (0.1 g, 0.44 mmol) was added in ethanol (5mL). To the solution 7-(diethylamino)-2-oxo-2H-chromene-3-carbaldehyde 3 (0.12 g, 0.49mmol), 2PL piperidine was added and refluxed for 2 h under nitrogen atmosphere. Progress of the reaction mixture was monitored by TLC after completion of the reaction the solvent was evaporated under reduced pressure. The crude product was purified by column chromatography using DCM: MeOH (98:2) as eluant. The product was obtained as greenish black coloured solid. The compound was further purified by reverse phase, HPLC using CH3CN:Water as solvent system. Isolated yield 60 mg (30 %); 1H NMR (400 MHz, CDCl3): δH (ppm) 9.29 (d, J = 8.9 Hz, 1H), 8.92 (s, 1H), 8.88 (d, J = 8.8 Hz, 1H), 8.78 (d, J = 15.3 Hz, 1H), 8.43 (d, J = 15.3 Hz, 1H), 8.29 (d, J = 8.3 Hz, 1H), 8.00 (d, J = 8.6 Hz, 1H), 7.93 (d, J = 8.6 Hz, 1H), 7.65 (d, J = 1.6 Hz, 1H), 7.63 (s, 1H), 6.67 (dd, J = 9.0, 2.4 Hz, 1H), 6.49 (d, J = 2.2 Hz, 1H), 5.08 (s, 3H), 3.49 (q, J = 7.1 Hz, 4H), 2.89 (s, 3H), 1.26 (d, J = 6.4 Hz, 6H).13C NMR (100MHz, CDCl3): δC (ppm) 160.6, 158.9, 158.6, 157.2, 152.9, 150.0, 145.3, 143.5, 140.1, 138.4,137.2, 131.9, 130.0, 129.9, 129.2, 125.4, 125.0, 124.1, 117.6, 113.8, 110.2, 109.6, 96.6, 49.1, 45.2, 29.6, 25.4, 12.5. HRMS (ESI-TOF, {M} +): calcd.450.2182 for C29H28N3O2 + , found 450.2217. Synthesis of TGP21.In a 50 mL round bottom flask 1,2,9-trimethyl-1,10- phenanthrolin-1-ium 5 (0.15 g, 0.67 mmol) was added in EtOH (10 mL). To the solution, 8-hydroxy-1,2,3,5,6,7-hexahydropyrido[3,2,1-ij]quinoline-9- carbaldehyde 6 (0.160 g, 0.74 mmol), catalytic amount of piperidine (10 PL) was added. The above reaction mixture was refluxed for 3 h. After completion of the reaction, solvent was evaporated under reduced pressure. The crude product was purified by column chromatography using DCM:MeOH (100:0 to 97.5:2.5) as eluant, product obtained as blue coloured solid. Isolated yield 50 mg (17 %); 1H NMR (400 MHz, DMSO-d6): δH (ppm) 9.38 (s, 1H), 8.52 (ddd, J = 44.8, 35.9, 12.0 Hz, 4H), 8.12 (d, J = 8.5 Hz, 1H), 8.03 (d, J = 8.5 Hz, 1H), 7.77 (d, J = 8.3 Hz, 1H), 7.52 (s, 1H), 7.34 (d, J = 15.0 Hz, 1H), 4.76 (s, 3H), 3.31 – 3.26 (m, 4H), 2.82 (s, 3H), 2.65 (dt, J = 25.8, 6.0 Hz, 4H), 1.87 (dd, J = 11.0, 5.7 Hz, 4H). 13C NMR (100 MHz, DMSO-d6): δC (ppm) 163.4, 162.8, 160.5, 153.7, 144.6, 143.1, 134.4, 133.3, 131.7, 130.2, 120.7, 116.7, 114.0, 111.7, 54.9, 54.2, 53.5, 31.9, 30.2, 26.4, 26.0, 25.5. HRMS (ESI-TOF, {M} +): calcd. 422.2232 for C28H25N3O2 , found 422.2214. Sample preparation. Stock solutions of TGP17, TGP18 and TGP21 were prepared in dimethyl sulfoxide (DMSO) in the order of 10-3 M and stored at 4 ◦C. DNA stock solutions were prepared by dissolving oligo samples in double- distilled (dd) water in the order of 10-4 M. All experiments were carried out using 20 mM potassium phosphate buffer containing 100 mM potassium chloride or sodium chloride at pH 7.4. Ligands were dissolved in the same buffer. All oligonucleotides were dissolved in the above mentioned buffer and heated in water bath at 95 °C for 10 minutes. The oligonucleotides were slowly cooled to room temperature and then stored at 4 °C for 48 h. UV absorption and fluorescence spectroscopy. The UV-vis absorption and emission spectra were recorded on Agilent Technologies Cary series UV-vis-NIR absorbance and Cary eclipse fluorescence spectrophotometers, respectively. Spectra were recorded using a 10 mm cuvette. The absorption spectra were scanned from 230 to 800 nm. The excitation wavelength for TGP18 was fixed at 560 nm and the emission wavelength was scanned from 570 nm to 800 nm. 1μM of TGP18 were titrated against increasing concentration (0–30 μM) of different GQ sequences until saturation was almost reached. The changes in fluorescence of TGP18 were measured upon addition of quadruplexes. The fluorescence titration data were also used to calculate the dissociation constant (KD) value by plotting the change in fluorescence (∆F/∆Fmax) at 645 nm of TGP18 versus increasing concentration of TGP18. The experimental data points obtained were fitted in one site saturation binding equation.
Figure imgf000072_0001
where ΔF/ΔFmax=Change in fluorescence, L=quadruplex concentration and KD=dissociation constant. Similar experiment was performed with duplex DNA where 2 μMTGP18 was titrated with increasing concentrations of duplex DNA (0–30 μM) under similar experimental condition. Fluorescence lifetime study. Fluorescence lifetimes were performed on a Horiba Delta Flex time-correlated single photon counting (TCSPC) instrument. A 560nm nano-LED with a pulse repetition rate of 1 MHz was used as the light source. The instrument response function (IRF) was collected by using a scatterer (Ludox AS40 colloidal silica, Sigma-Aldrich). Fluorescence lifetime (λexc = 560 nm) and gated emission was measured on FLSP920 spectrometer, Edinburgh Instruments equipped with a micro flash lamp (μF2) set-up. From the measured decay traces, the data were fitted with a multi-exponential decay, and χ2 was less than 1.1. CD spectroscopy. CD spectra were recorded on a Jasco 815 spectrometer equipped with a Peltier-type temperature controller (CDF-4265/15) under a nitrogen atmosphere to avoid water condensation. Scans were performed over the range of 220–700 nm with a speed of 100 nm/min, and the spectra represent an average of three scans. The band width was 1 nm. All measurements were carried out using a 10 mm path length cuvette in a reaction volume 500 μL.1μM of each quadruplex sequences were added with 1 μM of TGP18 at a ratio of 1:1. Readings were taken 5 minutes after each addition to ensure complete complex formation. DNA melting experiments were performed using the same cuvette and reaction mixture with the temperature being varied from 20°C to 90 °C at an interval of 5 °C. All the CD melting experiments were repeated thrice. A blank sample containing 20 mM PBS solution (100 mM KCl, pH = 7.4) was treated in the same manner and subtracted from the collected data. Polyacrylamide gel electrophoresis (PAGE). PAGE was performed in 1× TBE buffer solution (90 mM tris-boric acid and 2 mM EDTA) using 15% polyacrylamide gel containing 100 mM KCl. Oligonucleotides (1 μM) were loaded on the gel, and electrophoresis was run at 90 V for 1 h at 4 °C. After electrophoresis, the gel was stained using either 100 μM TGP18 in Tris-K+ or 1× SYBR Gold, under constant agitation for 15 min, then lightly rinsed with water and visualised using Chemidoc MP imaging system (Biorad). Fluorescence images were acquired with excitation wavelength of 532 nm using the emission filters of 575 nm (for SYBR Gold) and 640 nm (for TGP18). The histogram was generated using Image J software. Cell culture. Human breast adenocarcinoma cell lines (MCF-7 and MDA-MB- 231) (ATCC), lung adenocarcinoma cell line (A549) (ATCC), and cervical adenocarcinoma cell line (HeLa) (ATCC) and Kidney cells (HEK293T) were separately cultured in complete Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) and supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 50 μg/mL gentamycin, 1% Pen-Strep in a fully humidified CO2 incubator at 370C and 5% CO2. Anti-proliferative assay. MTT assay was performed in different cancer cell lines to evaluate the selective anti-proliferative properties of TGP18. MCF-7, MDAMB231, HeLa, A549 and HEK293T cells were sub-cultured into 96- well microtiter plates at a density of 1×104 cells/well in 100 μL of respective culture media treated with an increasing concentration gradient (0–100 μM) of TGP18 for 24 h. 15 μL of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) tetrazolium substrate (in 5 mg/ml of PBS) was added to each well and incubated for 3 h at 37℃ in CO2 incubator. The violet formazan precipitate was solubilized into 100 μL DMSO. Absorbance for each sample was recorded at 570 nm in 96-well microtiter plate reader (Spectramax i3x, molecular devices) having a reference wavelength of 690 nm. All the assays were performed in three replicates, and the DMSO-treated set was considered as a negative control to nullify the cytotoxic effects of DMSO (as TGP18 was solubilized in DMSO). The percentage cell viability was calculated as the percentage of MTT absorption
Figure imgf000074_0001
Treatment, RNA isolation and cDNA preparation. A549 cells were sub- cultured into 6-well microtiter plates at a density of 1 × 106 cells per well until they reached 60% confluence and were then treated with different concentrations (5 and 15 PM) of TGP18. The control set received equivalent amount of DMSO, as the drug was suspended in DMSO. Treated cells were maintained for 24 hours, after which they were observed under microscope to ensure that the cells were still alive, and live cells were taken for RNA isolation. RNA was isolated from control and treated cell cultures using TRIzol® reagent (Invitrogen) following manufacturer’s protocol. The concentration of isolated RNA was determined by measuring absorbance at 260 nm in a spectrophotometer and the quality and integrity of RNA was checked by electrophoresis of denatured RNA in a 1% Agarose gel which showed distinct 28 S and 18 S bands (2:1 intensity ratio) in the gel. Total RNA (1 μg, from both control and treated) was reverse transcribed using 200 U Revert Aid reverse transcriptase (Fermentas) and random hexamer primers (5 μM) in 20μL reaction volume at 42 °C, following manufacturer’s protocol. Real time qPCR was carried out using Maxima SYBR Green/ROX qPCR Master Mix (2X) (Thermo-Scientific) as per manufacturer’s protocol. The housekeeping gene GAPDHwas used as an internal control to normalize the variability in expression level. PCR primers were designed using Primer-BLAST, NCBI, and analyzed in OligoAnalyser 3.1-IDT (Table 2). Cell cycle analysis. A549 cells (1 × 106) per 60 mm petridish were either untreated (DMSO) or treated with various concentrations of TGP18 (1, 2, 5 and 10 μM) for 24 h. Cells were then trypsinized and collected by centrifugation at 300g for 5 min, and resuspended in PBS containing 10 μg/mL DAPI and 10 μg/mL RNaseA. After incubation for 30 min in dark at 37 °C, cells were analysed for DNA content using a FACS flow cytometer (BD Biosciences). Cell distribution among cell cycle phases and the percentage of apoptotic cells were evaluated using Cell-Quest Pro software (BD). Table 2. Primer sequences used in qPCR
Figure imgf000076_0001
Haemolytic assay. TGP18 was assayed on human erythrocytes (O blood group) for hemolytic activity. The human blood samples were obtained from healthy volunteers. The blood was centrifuged at 5,000 rpm for 5 min and subjected to repeated washing with sterile PBS to remove plasma. Suspension of human erythrocytes (2%) in sterile PBS were treated with different concentrations of TGP18. After 30 min incubation at room temperature, cells were centrifuged and the supernatant was used to measure the liberated haemoglobin by monitoring the absorbance at 418 nm. Two controls were prepared without TGP18, negative control received sterile PBS, while positive control received 0.1% Triton X-100. The average value was calculated from triplicate assays. Haemolysis percentage for each sample was calculated by dividing sample absorbance with positive control absorbance (complete hemolysis) multiplied by 100. Caspase-3 activity assay. Caspase-3 assay was performed using Enzchek Caspase-3 assay kit following manufacturer's protocol. Lysates prepared from A549 cells were either untreated (DMSO) or treated with TGP18 (5 and 10 μM) and camptothecin (10 μM) for 24 h. Cell lysates were incubated with the Z- DEVD-R110, caspase-3 substrate alone or with the substrate and Z-DEVD-R110 inhibitor (right panel) and analysed by spectrofluorometry (excitation and emission wavelengths of 496 nm and 520 nm, respectively). Fluorescence response measured was quantified to analyse caspase-3 activity in apoptotic cell lysates. Confocal microscopy. Cellular localisation of TGP18 was monitored by live and fixed cell imaging. A549 cells grown on confocal dish were incubated with TGP18 (300 nM) for 1 h at 37 °C. For fixed cells, A549 cells were treated with 4% (wt/vol) paraformaldehyde for 10 min and rinsed twice with PBS before incubation with TGP18. After incubation, cells were washed with PBS three times to remove the excess ligand and bathed in DMEM (2 mL) before imaging. Cell nuclei were stained with Hoechst 33258 (8 μg/mL) and DAPI (300 nM) for live and fixed cells, respectively. Localisation of TGP18 was viewed under confocal fluorescence microscope (Olympus FV3000). Immunofluorescence. A549 cells were plated in 35 mm glass-bottomed culture dishes (Genetix Biotech) and cultured overnight. The cells were then untreated (DMSO) or treated with TGP18 (0.5, 1 and 5 μM) or Pyridostatin (10 μM) for 24 h. As a control, A549 cells were exposed to UV light for 1 h in DMEM media with low serum percentage. After the respective treatment, cells were fixed in 4% (wt/vol) paraformaldehyde at room temperature for 10 min and washed thrice with PBS. The cells were then permeabilised with 0.1% Triton X-100 in PBS for 5 min and blocked with 4% BSA in PBS for 30 min. Fixed cells were then incubated overnight at 4 °C with primary antibodies: rabbit anti-NPM1 antibody (1:50 dilution, Cell Signalling Technology); rabbit anti-Nrf2 antibody (1:500, Invitrogen); mouse anti-JH2AX antibody (1:100, Invitrogen) in blocking solution. Cells were washed three times in PBS and incubated for 1 h with secondary antibodies: goat anti-rabbit-Alexa 488; goat anti-mouse-Alexa 488 (1:1000) (Molecular Probes, Invitrogen) in blocking solution. Cells were then washed twice in PBS and stained with DAPI for 2 min. Imaging was performed using a 480 nm and a 560 nm laser connected to a Fluoview confocal microscope (Olympus FV3000) with a 60× numerical aperture 1.4 lens and the data was analysed using cellsens software (Olympus). protein databank (reference ID is 2F8U). All three ligands were built using molden software and then geometry optimized using Gaussian09 software at B3LYP/6-31+G* level of theory. Blind docking was carried out and subjected the whole quadruplex structure for the identification of the binding sites. The centre of the grid box was chosen as the centre of mass of the quadruplex and the number of grid points were chosen as 130, 130, 110 with a default grid size of 0.375 Å. The Lamarckian genetic algorithm was used to locate various binding sites and binding modes for the ligands within quadruplex. As many as 500 low energy complex configurations were stored for each ligand:quadruplex complex. Molecular dynamic (MD) simulations were also carried out to study the stability of the TGP18 binding to quadruplex. Structure from docking was used as the input configuration for MD. The GAFF force-field was used to describe the dispersion interaction while atomic charges obtained using CHELPG method were used to describe the electrostatic interaction. In particular, B3LYP/6-31+G* level of theory was used, and medium has been water solvent described using polarizable continuum. For the quadruplex, FF99SB force-field was used and water solvent has been described using TIP3P force-field. Suitable number of counter ions added to neutral and as many as 15000 water molecules were added to simulation. The simulations were carried out at 300K and 1atm pressure. 1 fs was used as the time step to integrate equation of motion and an equilibration run of 5 ns. The final production run in isothermal-isobaric ensemble was carried out for 20 ns. The RMSD value for ligand and other properties were computed for the last 5 ns. In vivo pharmacokinetic studies of TGP18. All animal experiments were performed in accordance with the guidelines of the Committee for the Purpose of Control and Supervision of Experiments on Animals (CPCSEA), India and were approved by the Institutional Animal Ethics Committee (IAEC) of Anthem Biosciences. The maximum tolerated dose (MTD) study of TGP18 was performed in female BALB/c mice. The TGP18 of a single dose was determined and repeat dosing was performed twice weekly for a period of two weeks at different concentrations of TGP18 (0.5, 1, 2.5, 10 and 25 mg/kg), administered intravenously (IV). For therapy studies, female NCr nude mice (1–2 months old, weighing 18–20 g) were injected subcutaneously with 5×106 cells (MDA-MB- 231) or 1×106 cells (A549) cells in the right flank region (1x HBSS (Hank’s Balanced Salts Solution) + Matrigel). When the tumors were established (approx. 14 days, mean size 100-200 mm3), the mice were divided into three therapeutic groups with six mice/group for each xenograft model. The standard-of-care (SOC) drugs gemcitabine and doxorubicin hydrochloride were used as reference control for A549 and MDA-MD-231 xenograft model respectively. The TGP18 samples were dissolved in 5% DMA + 95% saline to the required concentration and gemcitabine/doxorubicin directly dissolved in saline for IV administration. Tumor size was measured weekly twice using a digital Verniercalliper. Tumor volume was calculated as follows:
Figure imgf000079_0002
and the mice were also weighed and examined at the same time to determine any signs of toxicity from the drug. Tumor growth inhibition (TGI) was calculated based on the following formula
Figure imgf000079_0001
(TVvehicle Final - TVvehicle Initial) Group 1: 6 mice treated with a twice weekly dose of 0.5 mg/kg of TGP18 in 5% DMA+95% saline. Group 2: 6 mice treated with a twice weekly dose of 100 mg/kg of gemcitabine (A549 xenograft model) or once weekly dose of 10mg/kg of doxorubicin (MDA- MB-231 xenograft model) in saline. Group 3: 6 control mice treated with 5% DMA+95% saline only, twice weekly. Mice were culled if tumors ulcerated or if a weight loss of 10–20% of the initial body weight was observed. Our study has been limited till two weeks due to the consequence of the tumors in some animals reaching the maximum permitted size. Tumor Imaging studies. Tumor samples collected after sacrificing the mice were fixed in neutral buffered formalin solution (NBF). Tumors from mice M5 of group 2 (treated with 0.5 mg/kg of TGP18) and mouse M1 from group 1 (control) were snap-frozen and cut in 20 Pm sections. These tissue sections were incubated with DAPI for 10 min and mounted on a glass slide. Images were acquired using a confocal fluorescence microscope (Olympus FV3000). TGP18 observed to be an efficient theranostic probe to target GQ. TGP18 is a structure-specific probe with turn-on emission at 640 nm (Oem) which binds to the BCL-2 quadruplex structure in vitro with good selectivity and shows potential anti-cancer activity in vivo thereby qualifying as a theranostic agent. Effects on BCL-2 mRNA and protein expression is reported together with cellular localization data. TGP18 strongly binds in vitro with BCL-2 quadruplex in the groove region and the binding interactions has been examined using molecular dynamics simulations. Cellular apoptosis induced by TGP18 through BCL-2 downregulation and cell cycle arrest synergized with DNA damage response, NPM1 translocation to nucleoplasm and Nrf2 nuclear accumulation by chemical GQ stabilization. TGP18 shows significant anti-tumor activity in A549 xenograft lung cancer model compared to MDAMB 231 breast cancer model. These findings show that GQ stabilization using fluorescence probe TGP18 is an attractive theranostic strategy for lung cancer. General information. Dulbecco’s modified eagle medium (DMEM), fetal bovine serum (FBS), L-glutamine, penicillin-streptomycin and amphotericin B for molecular biology were procured from Himedia. Annexin V and propidium iodide (PI) apoptosis detection kit was bought from BD Pharminogen. Single-stranded oligonucleotide sequences (Table 1A) are purchased from Eurofins India Pvt. Ltd. Dimethyl sulfoxide (DMSO), Hoechst 33258, DAPI and 3-(4, 5-dimethylthiazol- 2-yl)-2, 5-diphenyltetrazoliumbromide (MTT) for cell culture were purchased from Sigma-Aldrich. All other chemicals were of analytical reagent grade and used without further purification. Ultrapure water, prepared by Milli-Q Gradient ultrapure water system (Millipore), was used in all experiments.1H and 13C NMR spectra were recorded on a Bruker AV-400 MHz spectrometer with chemical shifts reported as parts per million (ppm) (in DMSO-d6, tetramethylsilane as an internal standard) at 20 °C. UV-vis absorption and emission spectra were measured in quartz cuvettes of 1 cm path length. High resolution mass spectra (HRMS) were obtained on Agilent Technologies 6538 UHD Accurate-Mass Q- TOF LC/MS spectrometer. Example 1A: Synthesis of 9-ethyl-carbazole-3,6-dicarbaldehyde (1) DMF (22 mL, 0.3 mol) was added slowly to POCl3 (28 mL, 0.3 mol) under stirring, in an ice bath. After 30 min a white precipitate was obtained and a solution of 9-ethylcarbazole (1.5 g, 16 mmol) in 20 mL of DMF was added. The mixture was slowly heated to 100 °C and reacted at this temperature for 30 h and then cooled to room temperature. The brown viscous oily product was poured into a mixture of ice-water and followed by extraction with dichloromethane (100 mL). The resultant dichloromethane solution was washed three times with water (100mL) and dried over anhydrous magnesium sulfate. After extraction the solvent was evaporated under reduced pressure and the crude product was purified by silica-gel column chromatography using DCM:MeOH (100:0 to 99:1) as eluant to obtain compound 1 with 50% yield. Example 2A: Synthesis of 9-ethyl-carbazole-3-carbaldehyde (2) DMF (15 mL) was added slowly to POCl3 (15.2 g, 0.1 mol) under stirring in an ice bath at room temperature until the solution became red. Then 9-ethylcarbazole (1.5 g, 16 mmol) dissolved in 1,2-dichloroethane (25 mL) were added. The mixture was heated to 80 °C and kept at this temperature for 8 h and then cooled to room temperature. The resultant was poured into a mixture of ice-water and followed by extraction with dichloromethane (100 mL). The dichloromethane solution was washed three times with water (100 mL) and dried over anhydrous magnesium sulfate. After extraction the solvent was evaporated under reduced pressure and the crude product was purified by silica-gel column chromatography to obtain compound 2 with 50% yield. Example 3A: Synthesis of carbazole-based cyanine molecules. Synthesis of various carbazole-based monocyanines was achieved through Knoevenagel reaction of 9- ethyl-carbazole-3,6-dicarbaldehyde (1) and 9-ethyl-carbazole-3-carbaldehyde (2) with corresponding 4-methylbenzothiazole, 4-methyllepidinium or 4- methylquinolinium halide. Alkylation of benzothiazole, lepidine and quinaldine was carried out in a sealed tube in toluene with methyl iodide affording the corresponding iodide salt, 3-5 in high yield. The Knoevenagel reaction of aldehydes 1 and 2 with the corresponding 4-methylbenzothiazole (3), 4- methyllepidinium (4) or 4-ethylquinolinium (5) iodide were carried out in the presence of catalytic amount of piperidine in 1:1 mixture of dichloromethane and methanol afforded carbazole-based cyanine molecules (TGS17a, TGS17b, TGS17c, TGS41, TGS42 andTGS43) in a moderate yield (56-62 %) and were fully characterized using 1H-NMR, 13C-NMR and HRMS techniques. Characterization data TGS17a 1H NMR (400 MHz, DMSO-d6): δH (ppm) 10.13 (s, 1H), 9.11 (s, 1H), 8.80 (s, 1H), 8.44-8.40 (t, J = 8.0, 2H), 8.26-8.23 (t, J = 8.4, 2H), 8.12-8.08 (m, 2H), 7.93-7.80 (m, 3H), 7.78-7.77 (d, J = 7.2, 1H), 4.63-4.57 (q, J = 7.2, 2H), 4.39 (s, 3H), 1.41-1.38 (t, J = 7.0, 3H); 13C NMR (DMSO-d6): δC (ppm) 191.9, 171.9, 149.9, 143.9, 142.9, 141.9, 129.3, 129.2, 128.4, 128.2, 127.5, 126.4, 124.1, 123.3, 123.1, 123.0, 122.5, 116.6, 111.1, 110.8, 110.5, 37.9, 36.2, 13.8. HRMS: Found m/z = 397.1366 [M]+,Calcd = 397.1369 [M]+. TGS17b 1H NMR (400 MHz, DMSO-d6): δH (ppm) 10.1 (s, 1H), 9.29 (d, J = 6.4, 1H), 9.09 (d, J = 8.4, 1H), 9.03 (s, 1H), 8.81 (s, 1H), 8.48 (d, J = 8.0, 1H), 8.4 (d, J = 8.0, 1H), 8.37 (s, 3H), 8.26 (t, J = 8, 1H), 8.12 (d, J = 8, 1H), 8.05 (d, J = 8, 1H), 7.83 (q, J = 5.3, 2H), 4.55 (t, J = 7.2, 2H), 4.513 (s, 3H), 1.38 (t, J = 7.0, 3H); 13C NMR (DMSO-d6): δC (ppm) 191.9, 152.8, 147.7, 144.1, 143.8, 142.0 138.8, 134.9, 129.1, 128.9, 128.8, 127.9, 126.4, 126.2, 123.5, 123.1, 122.6, 121.7, 119.3, 117.1, 115.4, 110.5, 110.3, 44.6, 37.8, 13.8. HRMS: Found m/z = 391.1792 [M]+,Calcd = 391.1798 [M]+. TGS17c 1H NMR (400 MHz, DMSO-d6): δH (ppm) 10.15 (s, 1H), 9.02 (s, 1H), 8.99 (d, J = 8.4, 1H), 8.82 (s, 1H), 8.62 (d, J = 9.2, 1H), 8.54 (d, J = 9.2, 1H), 8.46 (d, J = 15.6, 1H), 8.31 (d, J = 8, 1H), 8.18-8.12 (m, 2H), 8.08 (d, J = 8.4, 1H), 8.00 (d, J = 15.6, 1H), 7.92 (t, J = 7.6, 1H), 7.87 (d, J = 8.4, 2H), 4.6 (s, 3H), 4.57 (q, J = 8, 1H), 1.39 (t, J = 7.2, 3H); 13C NMR (DMSO-d6): δC (ppm) 191.9, 156.3, 148.4, 143.9, 143.4, 142.4139.2, 134.7, 129.9, 129.1, 128.7, 128.1, 127.5, 127.3, 123.3, 123.1, 122.5, 122.2, 120.7, 119.2, 116.5, 110.6, 110.3, 37.8, 13.8. HRMS: Found m/z = 391.1810 [M]+,Calcd = 391.1798 [M]+. TGS411H NMR (400 MHz, DMSO-d6): δH (ppm) 8.9 (s, 1H), 8.31 (dd, J = 4, 2H), 8.19-8.23 (m, 3H), 8.03 (d, J = 15.6, 1H), 7.71-7.87 (m, 4H), 7.56 (t, J = 7.4, 1H), 7.35 (t, J = 7.4, 1H), 4.54(q, J = 7.2, 2H),4.37 (s, 3H),1.37 (t, J = 7.2, 3H); 13C NMR (DMSO-d6): δC (ppm) 171.9, 150.6, 142.2, 141.9, 140.3, 129.1, 128.1, 127.9, 127.3, 126.8, 125.2, 124.0, 123.7, 122.9, 122.2, 120.6, 120.3, 116.5, 110.1, 37.4, 36.1, 13.8; HRMS:Found m/z = 369.1426 [M]+; Calcd = 369.1425 [M]+. TGS421H NMR (400 MHz, DMSO-d6): δH (ppm) 8.9 (d, J = 8, 1H), 8.8 (s, 1H), 8.6 (d, J = 8.0, 1H), 8.50 (t, J = 14, 2H), 8.28 (dd, J = 8.0, 2H), 8.17-8.11 (m, 2H), 7.96 (s, 1H), 7.92 (t, J = 7.4, 1H), 7.78 (d, J = 8.0, 1H), 7.70 (d, J = 8.0, 1H), 7.55 (t, J = 7.6, 1H), 7.33 (t, J = 7.4, 1H), 4.5 (s, 3H), 4.51 (q, J = 8, 2H), 1.37 (t, J = 8, 3H); 13C NMR (DMSO-d6): δC (ppm) 156.4, 149.1, 143.1, 141.7, 140.2, 139.2, 134.5, 129.9, 128.5, 127.8, 127.3, 126.7, 126.0, 122.9, 122.5, 120.6, 119.9, 119.1, 115.4, 109.9, 37.3, 13.8; HRMS:Found m/z = 363.1861 [M]+,Calcd = 363.1854 [M]+. TGS431H NMR (400 MHz, DMSO-d6): δH (ppm) 8.6 (d, J = 8, 1H), 8.56 (s, 1H), 8.52 (d, J = 8.0, 1H), 8.34 (t, J = 14, 2H), 8.26 (dd, J = 8.0, 2H), 8.17-8.11 (m, 2H), 7.98 (s, 1H), 7.91 (t, J = 7.4, 1H), 7.79 (d, J = 8.0, 1H), 7.72 (d, J = 8.0, 1H), 7.55 (t, J = 7.6, 1H), 7.33 (t, J = 7.4, 1H), 4.56 (s, 3H), 4.52 (q, J = 8, 2H), 1.37 (t, J = 8, 3H); 13C NMR (DMSO-d6): δC (ppm) 143.1, 140.2, 134.5, 129.9, 127.3, 120.6, 119.9, 115.4, 109.9, 37.3, 13.7; HRMS:Found m/z = 363.1861 [M]+,Calcd = 363.1854 [M]+. Example 4A: Characterization studies: Fluorescence lifetime study. Fluorescence lifetimes were performed on a Horiba Delta Flex time-correlated single photon counting (TCSPC) instrument. A 480nm nano-LED with a pulse repetition rate of 1 MHz was used as the light source. The instrument response function (IRF) was collected by using a scatterer (Ludox AS40 colloidal silica, Sigma-Aldrich). Fluorescence lifetime (λexc = 480 nm) and gated emission was measured on FLSP920 spectrometer, Edinburgh Instruments equipped with a micro flash lamp (μF2) set-up. From the measured decay traces, the data were fitted with a multi-exponential decay, and χ2 was less than 1.1. CD spectroscopy. Circular dichroism spectra were recorded on a Jasco 815 spectrometer equipped with a Peltier-type temperature controller (CDF-4265/15) under a nitrogen atmosphere to avoid water condensation. Scans were performed over the range of 220–700 nm with a speed of 100 nm/min, and the spectra represent an average of three scans. The band width was 1 nm. All measurements were carried out using a 10 mm path length cuvette in a reaction volume 500 μL. 1μM of each quadruplex sequences were added with 1 μM of carbazole derivative at a ratio of 1:1. Readings were taken 5 min after each addition to ensure complete complex formation. DNA melting experiments were performed using the same cuvette and reaction mixture with the temperature being varied from 20 °C to 90 °C at an interval of 5 °C. All the CD melting experiments were repeated twice. A blank sample containing 20mM PBS solution (100 mM KCl, pH = 7.4) was treated in the same manner and subtracted from the collected data. Cell culture. Breast adenocarcinoma cell lines (MCF-7 and MDAMB 231) (ATCC), lung adenocarcinoma cell line (A549) (ATCC), prostate cancer cell line (PC3) (ATCC) and cervical adenocarcinoma cell line (HeLa) (ATCC) and human embryonic kidney cells (HEK293T) were separately cultured in complete Dulbecco’s modified Eagle’s medium (DMEM) (Himedia) supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 50 μg/mL gentamycin, 1% pen-Strep, and 2.5 μg/mL amphotericin B in a fully humidified CO2 incubator (ESCO cell culture CO2 Incubator, CCL-1708-8-UV) at 370C and 5 % CO2. MTT assay. We performed MTT assay in different cancer cell lines to evaluate the selective anti-cancer properties of the carbazole derivatives. MCF-7, MDAMB231, HeLa, A549, PC3 and HEK293T cells were sub-cultured into 96- well microtiter plates at a density of 1×104 cells/well in 100 μL of respective culture media treated with an increasing concentration gradient (0–30 μM) of all carbazole derivatives (TGS17a-17c and TGS41-43) for 24 h. 10 μL of 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) tetrazolium substrate (in 5 mg/ml of phenol-free media) was added to each well and incubated for 4 h at 370C in CO2 incubator. The violet formazan precipitate was solubilized into 100 μL DMSO. Absorbance for each sample was recorded at 570 nm in 96- well microtiter plate reader (Spectramax i3x, molecular devices) having a reference wavelength of 650 nm. All the assays were performed in three replicates, and the DMSO-treated set was considered as a negative control to nullify the cytotoxic effects of DMSO (as carbazole derivatives were solubilized in DMSO). The percentage cell viability was calculated as the percentage of MTT absorption:
Figure imgf000085_0001
Table 1AA. MTT Assay. Anti-proliferative effects of Carbazole ligands (TGS17a, TGS17b, TGS17c, TGS41, TGS42, and TGS43) in different cancer cell lines (MCF-7, MDAMB-231, HeLa and A549), human embryonic kidney cells (HEK293T).
Figure imgf000085_0002
Figure imgf000086_0001
Annexin V-FITC-PI binding assay. MDAMB231 cells were seeded into 6 well microtiter plates at a density of 1×106 cells per well. Cells were treated with carbazole derivatives (TGS17a-17c and TGS41-43) at increasing concentration gradient for 24 h. Cells were then trypsinized, washed twice with 1× PBS and subjected to flow cytometric assays using BD Pharmigen™ Annexin V-FITC Apoptosis detection Kit as per manufacturer's protocol. In brief, cell pellets were resuspended into 1×binding buffer. 100 μL of cell suspension was incubated in 5 μL Annexin V-FITC and 2 μL PI (propidium iodide) for 30 min and 15 min respectively at room temperature. Finally, the mixture was diluted into 500 μL of 1×binding buffer immediately prior to flow cytometric analyses in BD FACS Verse™ Flow cytometer. All the measurements were carried out with three replicates having 1000 number of events and medium flow rate. Table 2A. Thermodynamic parameters of interaction between carbazole derivatives (TGS17b, TGS17c, TGS42 and TGS43) and promoter GQ (c-MYC, BCL-2, KRAS and VEGF-A) sequences calculated from isothermal titration calorimetry. Binding enthalpy ('H), entropy ('S), binding energy ('G), dissociation constant (KD).
Figure imgf000087_0001
General information. Dulbecco’s modified eagle medium (DMEM), fetal bovine serum (FBS), L-glutamine, penicillin-streptomycin and SYBR Gold for molecular biology were procured from Invitrogen. All oligonucleotide sequences shown in Table 1, obtained from Integrated DNA technologies. Dimethyl sulfoxide (DMSO), Hoechst 33258, DAPI, for cell culture and thiazole orange were purchased from Sigma-Aldrich. All other chemicals were of analytical reagent grade and used without further purification. Ultrapure water, prepared by Milli-Q Gradient ultrapure water system (Millipore), was used in all experiments. 1H and 13C NMR spectra were recorded on a Bruker AV-400 MHz spectrometer with chemical shifts reported as parts per million (ppm) (in DMSO-d6, tetramethylsilane as an internal standard) at 20 °C. UV-vis absorption and emission spectra were measured in quartz cuvettes of 1 cm path length. High resolution mass spectra (HRMS) were obtained on Agilent Technologies 6538 UHD Accurate-Mass Q-TOF LC/MS spectrometer. Example 1B: Synthesis of 7-N,N-diethylamino-4-methyl-flavylium (1). In a 250 mL round bottom flask 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone (1 g, 5.1 mmol, 1 equiv.) was dissolved in acetic acid (60 mL), acetophenone( 0.69 g, 5.6 mmol, 1.1 equiv.) and perchloric acid (30 mL) was added. The reaction mixture was refluxed for 15 h, after cooled to room temperature the precipitate was filtered and washed with hexane, diethyl ether yielded compound 1 as a red colour solid (1 g, 3.42 mmol, 67%).1H NMR (600 MHz, DMSO-d6): δH (ppm) 8.38 (d, J = 7.4 Hz, 2H), 8.19 (d, J = 7.5 Hz, 2H), 7.78 – 7.68 (m, 3H), 7.51 (dd, J = 9.6, 2.2 Hz, 1H), 7.38 (d, J = 2.2 Hz, 1H), 3.73 (dd, J = 13.8, 6.8 Hz, 4H), 2.87 (s, 3H), 1.26 (t, J = 7.0 Hz, 6H).13C NMR (151 MHz, DMSO-d6):δC (ppm) 164.1, 163.4, 158.6, 155.8, 134.0, 129.6, 129.2, 127.7, 121.9, 118.1, 117.6, 111.9, 95.8, 64.9, 48.5, 45.4, 19.5, 15.1.HRMS (ESI-TOF): Calcd. for C20H22NO+ [M]+: 292.1701; found: 292.1691. Table 1B. GQ and duplex forming oligonucleotide sequences used in the study
Figure imgf000088_0001
Example 2B: Synthesis of FLV1. 7-N,N-Diethylamino-4-methyl-flavylium (1) (49.8 mg, 0.17 mmol, 1 equiv.) and anhydrous sodium acetate (30.7 mg, 0.37 mmol, 2.2 equiv.) were dissolved in 10 mL EtOH and refluxed at 90 °C under air for 3 h. The solvent was evaporated and crude product was purified by silicagel and reverse- phase HPLC chromatography. FLV1 was purified via silica gel chromatography, eluting with a DCM/MeOH (99:1) solvent system. The compound was further purified by reverse phase HPLC (water/MeCN with 0.1% TFA) to yield pure FLV1 (11 mg, 0.019, 11%).1H NMR (600 MHz, DMSO-d6): δH (ppm) 8.38 (d, J = 9.5 Hz, 2H), 8.21 – 8.18 (m, 4H), 7.96 (s, 2H), 7.63 (t, J = 7.4 Hz, 6H), 7.44 (s, 1H), 7.10 (dd, J = 9.4, 2.4 Hz, 2H), 7.02 (d, J = 2.4 Hz, 2H), 3.60 (q, J = 7.0 Hz, 8H), 1.23 (t, J = 7.1 Hz, 12H).13C NMR (151 MHz, DMSO-d6):δC (ppm) 158.9, 158.6, 158.3, 158.1, 157.9, 156.3, 155.1, 150.6, 132.6, 131.5, 129.7, 127.6, 126.9, 121.4, 119.0, 116.6, 115.0, 114.0, 112.0, 105.4, 103.6, 97.7. HRMS (ESI-TOF): Calcd. for C39H39N2O2 + [M]+: 567.2971; found: 567.3012. Example 3B: Synthesis of FLV3. 7-N,N-diethylamino-4-methyl-flavylium (1) (49.8 mg, 0.17 mmol, 1.5 equiv.), paraformaldehyde(3.5 mg, 0.11 mmol, 1.0 equiv.), and anhydrous sodium acetate (27.89 mg, 0.34 mmol, 2.0 equiv) were combined in acetic anhydride (1.0 mL). The solution was freezed and degassed with N2, heated at 70°C for 30 min under N2 atmosphere. The solution was cooled to room temperature and evaporated onto silica gel. The crude product was purified via silica gel chromatography, eluting with DCM/MeOH (99:1) solvent system. The compound was further purified by reverse phase HPLC (water/MeCN with 0.1% TFA) to yield pure FLV3 (13.5 mg, 0.022 mmol, 20%). 1H NMR (600 MHz, DMSO-d6): δH (ppm)8.95 (s, 1H), 8.28 (dd, J = 6.7, 2.9 Hz, 4H), 8.13 (d, J = 12.8 Hz, 2H), 8.04 (s, 2H), 7.70 – 7.64 (m, 6H), 7.30 (d, J = 13.0 Hz, 2H), 7.07 (dd, J = 9.4, 2.4 Hz, 2H), 6.91 (d, J = 2.4 Hz, 2H), 3.57 (q, J = 7.0 Hz, 8H), 1.21 (t, J = 7.1 Hz, 12H). 13C NMR (151 MHz, DMSO-d6): δC (ppm) 161.8, 155.6, 154.8, 151.2, 146.1, 130.5, 130.0, 127.9, 125.3, 124.9, 114.2, 112.2, 109.2, 100.9, 95.7, 43.2, 42.7, 30.1, 27.8, 11.3. HRMS (ESI-TOF): Calcd. for C41H41N2O2 + [M]+: 593.3168; found: 593.3071. Example 4B: Characterization studies: Sample preparation. Stock solutions of FLV1 and FLV3 were prepared in dimethyl sulfoxide (DMSO) in the order of 10-3 M and stored at 4 ◦C. DNA stock solutions were prepared by dissolving oligo samples in double-distilled (dd) water in the order of 10-4 M. All experiments were carried out using 20 mM potassium phosphate buffer containing 100 mM potassium chloride or sodium chloride at pH 7.4. Ligands were dissolved in the same buffer. All oligonucleotides were dissolved in the above mentioned buffer and heated in water bath at 95 °C for 10 minutes. The oligonucleotides were slowly cooled to room temperature and then stored at 4 °C for 48 hours. UV and fluorescence spectroscopy. The UV-vis absorption and emission spectra were recorded on Agilent Technologies Cary series UV-vis-NIR absorbance and Cary eclipsefluorescence spectrophotometers, respectively. Spectra were recorded using a 10 mm cuvette. The absorption spectra were scanned from 230 to 800 nm. The excitation wavelength for FLV1 was fixed at 635 nm and the emission wavelength was scanned from 645 nm to 800 nm. 2 μM of FLV1 were titrated against increasing concentration (0–30 μM) of different GQ sequences until saturation was almost reached. The changes in fluorescence of FLV1 were measured upon addition of quadruplexes. The fluorescence titration data were also used to calculate the dissociation constant (KD) value by plotting the change in fluorescence
Figure imgf000090_0003
at 695 nm of FLV1 versus increasing concentration of VEGF. The experimental data points obtained were fitted in one site saturation binding equation. (1)
Figure imgf000090_0001
where
Figure imgf000090_0002
/ Change in fluorescence, L=quadruplex concentration and KD=dissociation constant. Similar experiment was performed with duplex DNA and other quadruplex forming sequences under similar experimental conditions. Fluorescence lifetime study. Fluorescence lifetimes were performed on a Horiba Delta Flex time-correlated single photon counting (TCSPC) instrument. A 634 nm nano-LED with a pulse repetition rate of 1 MHz was used as the light source. The instrument response function (IRF) was collected by using a scatterer (Ludox AS40 colloidal silica, Sigma-Aldrich). Fluorescence lifetime (λexc = 632 nm) and gated emission was measured on FLSP920 spectrometer, Edinburgh Instruments equipped with a micro flash lamp (μF2) set-up. From the measured decay traces, the data were fitted with a multi-exponential decay, and χ2 was less than 1.1. Circular dichroism (CD) spectroscopy. CD spectra were recorded on a Jasco 815 spectrometer equipped with a Peltier-type temperature controller (CDF- 4265/15) under a nitrogen atmosphere to avoid water condensation. Scans were performed over the range of 220–700 nm with a speed of 100 nm/min, and the spectra represent an average of three scans. The band width was 1 nm. All measurements were carried out using a 10 mm path length cuvette in a reaction volume 500 μL. 2 μM of each quadruplex sequences were added with 2 μM of FLV1at a ratio of 1:1. Readings were taken 10 min after each addition to ensure complete complex formation. DNA melting experiments were performed using the same cuvette and reaction mixture with the temperature being varied from 20 °C to 90 °C at an interval of 5 °C. All the CD melting experiments were repeated twice. A blank sample containing 10mM PBS solution (100 mM KCl, pH = 7.4) was treated in the same manner and subtracted from the collected data. Polyacrylamide gel electrophoresis. PAGE was performed in 1× TBE buffer solution (0.09 M Tris-boric acid and 0.002 M EDTA) with 15 % native gels. Oligonucleotides (1 μM) were loaded on the gel, and electrophoresis was run at 90 V for 1 h at room temperature. After electrophoresis, the gel was stained using either 100 μMFLV1 in Tris-K+ or 1× SYBR Gold, under constant agitation for 15 min, then lightly rinsed with water and visualized using Chemidoc MP imaging system (Biorad). Fluorescence images with excitation wavelength of 532 nm were recorded using the emission filters of 575 nm (for SYBR Gold) and epi-UV illumination for FLV1. Cell culture. Lung adenocarcinoma cell line (A549) (ATCC) and cervical adenocarcinoma cell line (HeLa) (ATCC) were separately cultured in complete Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen) and supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 50 μg/mL gentamycin, 1% Pen-Strep in a fully humidified CO2 incubator at 370C and 5% CO2. Fluorescence microscopy. Live A549 cells grown on confocal dish were incubated with the FLV1probe (500 nM) for 30 min and cellular nuclei were stained with Hoechst 33258 (8 μg/mL),rinsed twice with phosphate-buffered saline (PBS) before visualization under a fluorescence microscope (Leica) (Ziess) equipped with an oil immersion 63X objective. For fixed cell treatment, cells were fixed for 10 min in 4% formaldehyde and incubated with FLV1 probe (500 nM) for 30 min and nuclei were stained with 4′,6-diamidino-2-phenylindole (DAPI) followed by washing before visualization. Fluorescence images of DAPI and FLV1 were collected under DAPI and Cy5 channel, respectively. Localization experiment of FLV1 in cells. HeLa and A549 cells were incubated with FLV1 (500 nM) for 4 h, followed by washing three times with Dulbecco's PBS (pH 7.4). The adherent cells were then incubated with MitoTracker orange (250 nM, Invitrogen; product no. M7510) and LysoTracker blue (50 nM, Invitrogen; product no. L7525) for 30 min and 1 h respectively, washed three times with PBS (pH 7.4) to remove the excess. Nuclei were stained with Hoechst. The cells were then imaged under fluorescence microscope (Leica) equipped with an oil immersion 63× objective lens. The fluorescence of LysoTracker blue was visualized using DAPI channel (emission: 475 nm); fluorescence of MitoTracker orange was visualized using Rhodamine channel (emission: 590 nm) and FLV1 under Cy5 channel (emission: 680 nm). Molecular docking. Docking study was carried out using AutoDockVina. The structure of FLV1 were energy minimized with the MMFF94 force field using Avogadro, and Gasteiger partial charges were added using AutoDock tools. The NMR structure of VEGF quadruplex was retrieved from the RCSB PDB databank (PDB ID 2M27). Polar hydrogen was added to the GQ using MGT AutoDock tools. Precise docking was carried out on 3' and 5' end-stacking of the quadruplex conformation to ascertain the most probable binding sites. The grid dimension was assigned to 25 × 30 × 30 Å. The Lamarckian Genetic Algorithm was used for the process. All other parameters were set as default. Docking results were analyzed using Discovery Studio 3.5. The docking poses were captured using VMD tools. Thus, the present application demonstrates the design and synthesis of flavylium- methine-based probes FLV1 and FLV3 with emission in NIR region. The fluorescence response and gel electrophoresis studies demonstrated in vitro selectivity of the probe FLV1 for quadruplex over duplex DNA conformation. FLV1 showed 3-fold higher selectivity for promoter VEGF GQ sequence underscoring its conformation selectivity among various GQ forming sequences studied. The large difference in the fluorescence decay life times of FLV1 between the quadruplex and duplex DNA is useful in visualization of GQs in live cells. Fluorescence imaging and colocalization studies using known mito- and lyso-trackers elucidated that FLV1 enters mitochondria and binds with mtDNA, which is further supported by DNase digestion studies. The significant enhancement in fluorescence of FLV1 in presence of PQF mtDNA sequences provided convincing evidence to support the hypothesis that mtDNA quadruplex is the major target of FLV1. Overall, FLV1 probe offers a promising platform to directly monitor mitochondrial GQ DNA in living cells with minimal background interference and photodamage due to its emission in the NIR region. Additional embodiments and features of the present disclosure will be apparent to one of ordinary skill in art based on the description provided herein. The embodiments herein provide various features and advantageous details thereof in the description. Descriptions of well-known/conventional methods and techniques are omitted so as to not unnecessarily obscure the embodiments herein. The foregoing description of the specific embodiments fully reveals the general nature of the embodiments herein that others can, by applying current knowledge, readily modify and/or adapt for various applications such specific embodiments without departing from the generic concept, and, therefore, such adaptations and modifications should and are intended to be comprehended within the meaning and range of equivalents of the disclosed embodiments. It is to be understood that the phraseology or terminology employed herein is for the purpose of description and not of limitation. Therefore, while the embodiments in this disclosure have been described in terms of preferred embodiments, those skilled in the art will recognize that the embodiments herein can be practiced with modification within the spirit and scope of the embodiments as described herein. While considerable emphasis has been placed herein on the particular features of this disclosure, it will be appreciated that various modifications can be made, and that many changes can be made in the preferred embodiments without departing from the principles of the disclosure. These and other modifications in the nature of the disclosure or the preferred embodiments will be apparent to those skilled in the art from the disclosure herein, whereby it is to be distinctly understood that the foregoing descriptive matter is to be interpreted merely as illustrative of the disclosure and not as a limitation.

Claims

We claim: 1. A compound of formula I comprising the following structure:
Figure imgf000095_0001
wherein, wherein, R, R1, R2are individually selected from a group comprising hydrogen,7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde,straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof. 2. The compound as claimed in claim 1, wherein , R is either 7-(diethylamino)- 2-oxo-2H-chromene-3-carbaldehyde or8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,
2,1-ij]quinoline-9-carbaldehyde; wherein R1 is either absent or hydrogen; R2 is selected from a group comprising hydrogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen.
3. The compound of Formula I as claimed in claim 1 selected from:
Figure imgf000096_0001
and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
4. A process for the preparation of compound of Formula I as claimed in claim 1, said process comprising step of reacting phenanthroline derivative or its salt with aldehyde derivative in presence of a reagent optionally in present solvent under heating conditions to obtain compound of formula I, wherein phenanthroline derivative or its salt is compound of formula II.
Figure imgf000096_0002
Compound of formula II. wherein wherein, R1, R2 are individually selected from a group comprising hydrogen, 7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof; the aldehyde derivative is compound of formula III.
Figure imgf000097_0001
Compound of formula III wherein, R is individually selected from a group comprising hydrogen, 7- (diethylamino)-2-oxo-2H-chromene-3-carbaldehyde, 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, heteroaryl carbaldehyde, chromene-3-carbaldehyde, quinoline-9-carbaldehyde, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, formyl, acetyl, halogen, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, wherein preferably the aldehyde derivative is either 7-(diethylamino)- 2-oxo-2H-chromene-3-carbaldehyde or 8-hydroxy-1,2,3,5,6,7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde, ‘n’ is either 0 or 1, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof; the reagent is a base or acid anhydride; the solvent is alcohol such as ethyl alcohol or acid anhydride such as acetic anhydride.
5. A process for the preparation of compound represented by TGP17 as claimed in claim 3, said process comprising step of reacting 2,9-dimethyl-1,10- phenanthroline with 7-(diethylamino)-2-oxo-2H-chromene-3-carbaldehyde in presence of acetic anhydride under heating conditions to obtain TGP17.
6. A process for the preparation of compound represented by TGP18 as claimed in claim 3, said process comprising step of reacting 1,2,9-trimethyl-1,10- phenanthrolin-1-ium iodide with 7-(diethylamino)-2-oxo-2H-chromene-3- carbaldehyde in presence of piperidine and ethanol under heating conditions to obtain TGP18. 7. A process for the preparation of compound represented by TGP21 as mentioned above, said process comprising step of reacting 1,2,9-trimethyl- 1,10-phenanthrolin-1-ium iodide with 8-hydroxy-1,2,3,5,6,
7- hexahydropyrido[3,2,1-ij]quinoline-9-carbaldehyde in presence of piperidine and ethanol under heating conditions to obtain TGP21.
8. The process as claimed in claims 4 to 7, wherein said process is carried out at a temperature ranging from about 30 °C to about 90°C, and for a time period ranging from about 60 minutes to about 40 hours.
9. The process as claimed in claims 4 to 7, wherein the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof.
10. A compound of formula IA comprising the following structure:
Figure imgf000098_0001
Formula IA wherein, wherein, R, R1, R2are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted, any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
11. The compound as claimed in claim 10, wherein R is either hydrogen or formyl group; R1 is selected from a group comprising methyl, ethyl, propyl, acetyl, phenyl or benzyl; and R2 is selected from a group comprising 4- methylbenzothiazolyl, 4-methyllepidinyl or 4-methylquinolinyl.
12. The compound of Formula IA as claimed in claim 10 selected from:
Figure imgf000099_0001
and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
13. A process for the preparation of compound of Formula IA as claimed in claim 10, said process comprising step of: e. formylating compound of formula IIA in presence of formylating reagent to obtain compound of formula IIIA
Figure imgf000100_0001
Formula IIA Formula IIIA wherein, R and R1 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted; f. reacting compound of formula IIA with R2 moiety to obtain compound of formula IA
Figure imgf000100_0002
Formula IA wherein, R, R1, R2 are individually selected from a group comprising hydrogen, formyl, acetyl, halogen, straight or branched chain alkyl, straight or branched chain alkenyl, straight or branched chain alkynyl, aryl, alkaryl, aralkyl, heteroaryl, heteroaralkyl, alkyloxy, aryloxy, aralkyl oxy, heteroaryloxy and wherein each of them is optionally substituted; wherein the formylating reagent is selected from a group comprising Phosphoryl halide, Phosphoryl chloride, oxalyl chloride, thionyl chloride and combinations thereof.
14. A process for the preparation of compound represented by TGS17a as claimed in claim 12, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylbenzothiazole to obtain TGS17a.
15. A process for the preparation of compound represented by TGS41 as claimed in claim 12, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylbenzothiazole to obtain TGS41.
16. A process for the preparation of compound represented by TGS17b as claimed in claim 12, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methyllepidinium to obtain TGS17b.
17. A process for the preparation of compound represented by TGS42 as claimed in claim 12, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methyllepidinium to obtain TGS42.
18. A process for the preparation of compound represented by TGS17c as claimed in claim 12, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3,6-dicarbaldehyde (1); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylquinolinium to obtain TGS17c
19. A process for the preparation of compound represented by TGS43 as claimed in claim 12, said process comprising step of: a. formylating 9-ethylcarbazole using formylating reagent to obtain 9-ethyl- carbazole-3-carbaldehyde (2); and b. reacting 9-ethyl-carbazole-3,6-dicarbaldehyde (1) with 4- methylquinolinium to obtain TGS43.
20. The process as claimed in claims 13 to 19, wherein said process is carried out at a temperature ranging from about 30 °C to about 120°C, and for a time period ranging from about 60 minutes to about 40 hours.
21. The process as claimed in claims 13 to 19, wherein the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof.
22. A compound of formula IB comprising the following structure:
Figure imgf000103_0001
Formula IB wherein, ‘X’ is methine unit; and ‘n’ is methine carbons wherein n is 1-6. any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
23. The compound as claimed in claim 1, wherein ‘[X]n’ is either a methine or polymethine.
24. The compound as claimed in claim 1, wherein ‘[
Figure imgf000103_0002
’ is either
Figure imgf000103_0003
25. The compound of Formula I as claimed in claim 22 selected from:
Figure imgf000103_0004
and any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof.
26. A process for the preparation of compound of Formula IB as claimed in claim 22, said process comprising step of: g. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7- N,N-diethylamino-4-methyl-flavylium; and h. reacting 7-N,N-diethylamino-4-methyl-flavylium with either ethanol or acetic anhydride and paraformaldehyde in presence of anhydrous sodium acetate to obtain Formula I.
27. A process for the preparation of compound FLV-1 as claimed in claim 25, said process comprising step of: a. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N-diethylamino-4-methyl-flavylium; and b. reacting 7-N,N-diethylamino-4-methyl-flavylium with ethanol in presence of anhydrous sodium acetate to obtain FLV-1.
28. A process for the preparation of compound FLV-3 as claimed in claim 25, said process comprising step of: a. reacting 1-(4-(diethylamino)-2-hydroxyphenyl)ethanone with acetophenone in presence of perchloric acid and acetic acid to obtain 7-N,N-diethylamino-4-methyl-flavylium; and b. reacting 7-N,N-diethylamino-4-methyl-flavylium with acetic anhydride in presence of anhydrous sodium acetate and paraformaldehyde to obtain FLV-3.
29. The process as claimed in claims 26 to 28, wherein said process is carried out at a temperature ranging from about 30 °C to about 90°C, and for a time period ranging from about 30 minutes to about 24 hours.
30. The process as claimed in claims 26 to 28, wherein the process further comprise isolation and/or purification of the corresponding product; wherein said isolation and purification is carried out by acts selected from a group comprising addition of solvent, washing with solvent, cooling, quenching, filtration, extraction, chromatography and combination of acts thereof.
31. A pharmaceutical composition comprising compound of Formula I or Formula IA or Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof, optionally along with at least one pharmaceutically acceptable excipient.
32. The pharmaceutical composition as claimed in claim 31, wherein the pharmaceutically acceptable excipient is selected from a group comprising diluent, carrier, granulating agent, binding agent, lubricating agent, disintegrating agent, sweetening agent, glidant, anti-adherent, anti-static agent, surfactant, anti-oxidant, gum, coating agent, coloring agent, flavouring agent, coating agent, plasticizer, preservative, suspending agent, emulsifying agent, plant cellulosic material, spheronization agents, other conventionally known pharmaceutically acceptable excipient or any combination of excipients thereof.
33. The pharmaceutical composition as claimed in claim 31, wherein the composition is administered to a subject through modes selected from a group comprising intravenous administration, intramuscular administration, intraperitoneal administration, hepatoportal administration, intra articular administration and pancreatic duodenal artery administration, or any combination thereof.
34. The composition as claimed in claim 31, wherein said composition is in a form selected from a group comprising capsule, tablet, injectable, cream, gel, ointment, lotion, solution, emulsion, foam, troche, lozenge, aqueous suspension, oily suspension, patch, dentifrice, spray, drops, powder, granule, syrup, elixir, food stuff and combinations thereof.
35. Compound of Formula I or Formula IA or Formula IB or derivative, tautomeric form, isomer, polymorph, solvate, or intermediates thereof as claimed in claim 1 or the composition as claimed in claim 31, Compound of Formula IA or derivative, tautomeric form, isomer, polymorph, solvate, or intermediates thereof as claimed in claim 10 or the composition as claimed in claim 31 Compound of Formula IB or derivative, tautomeric form, isomer, polymorph, solvate, or intermediates thereof as claimed in claim 22 or the composition as claimed in claim 31.
36. Use of compound of Formula I or Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula I or formula IA for GQ staining in vitro and in cellulo conditions.
37. Use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as claimed in claim 1 or the composition comprising compound of formula I as a probe for GQ DNA detection.
38. Use of compound of Formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as claimed in claim 1 along with their conjugates or composition comprising compound of formula I along with their conjugates as diagnostic probes.
39. An in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula I with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence.
40. An in vitro method of detection or quantification of BCL-2 GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula I or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula I with a BCL-2 GQ DNA sequence to allow for hybridization of the probe with the BCL-2 GQ DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to BCL-2 GQ DNA sequence, upon hybridization of the probe to BCL-2 GQ DNA sequence.
41. A method of inhibiting the growth of cancer in xenograft mice model, said method comprising contacting the compound of Formula I with the said animal model.
42. A method for treating cancer in a subject, wherein the method comprising administering to the subject in need thereof a compound I or compound IA or compound IB or a composition comprising compound I or compound IA or compound IB.
43. A method for treating lung cancer in a subject, wherein the method comprising administering to the subject in need thereof a compound I or compound IA or compound IB or a composition comprising compound I or compound IA or compound IB.
44. Use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IA for GQ staining in vitro and in cellulo conditions.
45. Use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IA as a probe for GQ DNA detection.
46. Use of compound of Formula IA or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula IA along with their conjugates as diagnostic probes.
47. A method of identifying GQ structures in cellulo conditions, said method comprising the step of contacting the compound of formula I or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above along with their conjugates or composition comprising compound of formula I.
48. An in vitro method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula IA with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence.
49. An in vitro method of detection or quantification of BCL-2 GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula IA with a BCL-2 GQ DNA sequence to allow for hybridization of the probe with the BCL-2 GQ DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to BCL-2 GQ DNA sequence, upon hybridization of the probe to BCL-2 GQ DNA sequence.
50. An in vitro method of detection or quantification of c-MYC GQ DNA sequence, said method comprising a. contacting the probe of compound of Formula IA or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula IA with a c-MYC GQ DNA sequence to allow for hybridization of the probe with the c-MYC GQ DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to c-MYC GQ DNA sequence, upon hybridization of the probe to c-MYC GQ DNA sequence.
51. A method for treating breast cancer in a subject, wherein the method comprising administering to the subject in need thereof a compound IA or a composition comprising compound IA.
52. Compound of Formula IB or derivative, tautomeric form, isomer, polymorph, solvate, or intermediates thereof as claimed in claim 22 or the composition as claimed in claim 31 for imaging of biological cells, for GQ staining in vitro and in organelle conditions, as a probe for selective mitochondrial staining and its GQ DNA detection, as selective VEGF GQ staining probes in vitro and in cellulo specific to organelles.
53. Compound of Formula I or Formula IA or Formula IB or derivative, tautomeric form, isomer, polymorph, solvate, or intermediates thereof as claimed in claims 1, 8 and 22 respectively or the composition as claimed in claim 31 for the management and treatment of cancer.
54. Use of compound of Formula I or Formula IA or Formula IB or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition comprising compound of Formula I in the manufacture of probes.
55. Use of compound of Formula I or Formula IA or Formula IB or any derivative, tautomer, isomer, polymorph, solvate or its intermediates thereof, or the composition of compound of Formula I in the manufacture of a medicament for treatment of cancer.
56. A method of detection or quantification of DNA sequence, said method comprising: a. contacting the probe of compound of Formula IB or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula IB with a DNA sequence to allow for hybridization of the probe with the DNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to DNA sequence, upon hybridization of the probe to DNA sequence.
57. A method of detection or quantification of VEGF GQDNA sequence, said method comprising a. contacting the probe of compound of Formula IB or its derivative, tautomer, isomer, polymorph, solvate or intermediates thereof, or the composition comprising compound of formula I with a VEGF GQDNA sequence to allow for hybridization of the probe with the VEGF GQDNA sequence; b. detecting or quantifying the binding intensity by measuring the change in fluorescence of the probe resulting from the specific interaction or binding of the probe to VEGF GQDNA sequence, upon hybridization of the probe to VEGF GQ DNA sequence.
58. Use of compound of Formula IB or any derivative, tautomeric form, isomer, polymorph, solvate and intermediates thereof as described above or composition comprising compound of formula IB for VEGF GQ staining in vitro and in cellulo specific to organelles.
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