Spectroscopic studies of DNA binding modes of cation-substituted anthrapyrazoles derived from emodin

Chemical Proteomics with Novel Fully Functionalized Fragments and Stringent Target Prioritization Identifies the Glutathione-Dependent Isomerase GSTZ1 as a Lung Cancer Target

Photoreactive fragment-like probes have been applied to discover target proteins that constitute novel cellular vulnerabilities and to identify viable chemical hits for drug discovery. Through forming covalent bonds, functionalized probes can achieve stronger target engagement and require less effort for on-target mechanism validation. However, the design of probe libraries, which directly affects the biological target space that is interrogated, and effective target prioritization remain critical challenges of such a chemical proteomic platform. In this study, we designed and synthesized a diverse panel of 20 fragment-based probes containing natural product-based privileged structural motifs for small-molecule lead discovery. These probes were fully functionalized with orthogonal diazirine and alkyne moieties and used for protein crosslinking in live lung cancer cells, target enrichment via "click chemistry," and subsequent target identification through label-free quantitative liquid chromatography-tandem mass spectrometry analysis. Pair-wise comparison with a blunted negative control probe and stringent prioritization via individual cross-comparisons against the entire panel identified glutathione S-transferase zeta 1 (GSTZ1) as a specific and unique target candidate. DepMap database query, RNA interference-based gene silencing, and proteome-wide tyrosine reactivity profiling suggested that GSTZ1 cooperated with different oncogenic alterations by supporting survival signaling in refractory non-small cell lung cancer cells. This finding may form the basis for developing novel GSTZ1 inhibitors to improve the therapeutic efficacy of oncogene-directed targeted drugs. In summary, we designed a novel fragment-based probe panel and developed a target prioritization scheme with improved stringency, which allows for the identification of unique target candidates, such as GSTZ1 in refractory lung cancer.

The interaction of proanthocyanidins with DNA molecules studied by atomic force microscopy and spectroscopic method

The interactions of the naturally available botanicals with DNA molecules have received considerable attention owing to the potential to develop for medicinal agents. In this study, the interaction of proanthocyanidins with DNA molecules was studied by atomic force microscopy (AFM) and spectroscopic method. The AFM observation indicated that proanthocyanidins induced DNA molecules from double helix chains to the thick rope and toroids. The heights of the formed DNA structures are more than eight times than that of DNA double helix. Spectroscopic measurement results revealed that proanthocyanidins intercalated between the base pairs of DNA in the intercalative binding mode, which resulted in unwinding the DNA helix, twisting the DNA strands and finally transforming into the supercoiled DNA structures. All these results implied that DNA molecule is an important interaction target of proanthocyanidins, and the formed compact DNA structures have biological significance on the gene expression and regulation.

Concentration-dependent mode of binding of drug oxatomide with DNA: multi-spectroscopic, voltammetric and metadynamics simulation analysis

The interaction between antihistaminic drug oxatomide (OXT) and calf-thymus DNA (CT-DNA) has been investigated in a physiological buffer (pH 7.4) using UV-Vis, fluorescence, ¹H NMR and circular dichroism spectral techniques coupled with viscosity measurements, KI quenching, voltammetry and in silico molecular modeling studies. OXT binds with CT-DNA in a concentration-dependent manner. At a lower [Drug]/[CT-DNA] molar ratio (0.6-0.1), OXT intercalates into the base pairs of CT-DNA, while at a higher [Drug]/[CT-DNA] molar ratio (13-6), the drug binds in the minor grooves of CT-DNA. The binding constants for the interaction are found to be in the order of 10³-10⁵ M^-1, and the groove binding mode of interaction exhibits a slightly higher binding constant than that of intercalative mode. Thermodynamic analysis of binding constants at three different temperatures suggests that both these modes of binding are mainly driven by hydrophobic interactions (ΔH^o > 0 and ΔS^o > 0). Voltammetric investigations indicate that the electro-reduction of OXT is an adsorption controlled process and shifts in reduction peak potentials reiterate the concentration-dependent mode of binding of the drug with CT-DNA. The free energy landscape obtained at the all-atom level, using metadynamics simulation studies, revealed two major binding forces: partial intercalation and minor groove binding, which corroborate well with the experimental results.Communicated by Ramaswamy H. Sarma.

An insight into DNA binding properties of newly designed cationic δ,δ'‑diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies

Two cationic δ,δ'‑diazacarbazoles, 1‑Methyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (MPDPI) and 1,5‑Dimethyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ'‑diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV-Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ'‑diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV-Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to CH₃ (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5‑NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ'‑diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ'‑diazacarbazoles and DNA were weakened, but δ,δ'‑diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.

Copper-metformin ternary complexes: Thermal, photochemosensitivity and molecular docking studies

The copper(II) complexes [Cu(Cl)₂(met)(o-phen)] (1), [Cu(Cl)₂(met)(en)] (2) and [Cu(Cl)₂(met)(opda)] (3) (met = metformin, o-phen = ortho-phenanthroline, en = ethylenediamine, opda = ortho-phenylenediamine) were synthesized and characterized by LC-MS, elemental analysis, molar conductance, thermal analysis, infrared spectra, magnetic moment, electronic spectra and XRD studies. The metal center was found in an octahedral geometry. The activation thermodynamic properties were calculated using Coats-Redfern method. Thermal decomposition processes of complexes 1, 2, 3 are non-spontaneous, i.e., the complexes are thermally stable. The positive value of Gibbs free energy of decomposition (ΔG^⁎) for the Cu(II) complexes is non-spontaneous processes. UV-Visible absorption, fluorescence, and viscosity measurements have been conducted to assess the interaction of the complexes with CT DNA. The complexes showed absorption hyperchromism in its UV-Vis spectrum with DNA. The binding constants K_b from UV-Vis absorption studies were 4.6 × 10⁵, 1.48 × 10⁵, 2.09 × 10⁵ M^-1 for 1, 2, 3 respectively and Stern-Volmer quenching constants (K_sq) from fluorescence studies were 0.636, 0.293, 0.487 for 1, 2, 3 respectively. Finally, viscosity measurements revealed that the binding of the complexes with CT-DNA could be surface binding, mainly due to groove binding. The activity of complexes towards DNA cleavage decreases in the order of 1 > 3 > 2. The complexes were docked in to B-DNA sequence, 5'(D*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*T)-3' retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software.

Binding studies of guggulsterone-E to calf thymus DNA by multi-spectroscopic, calorimetric and molecular docking studies

Guggulsterone, a sterol found in plants is used as an ayurvedic medicine for many diseases such as obesity, internal tumors, ulcers etc. E and Z are two isoforms of guggulsterone, wherein guggulsterone-E (GUGE) has also been shown to have anticancer potential. Most of the anticancer drugs target nucleic acids. Therefore, we studied the mode of interaction between ctDNA and GUGE using UV-Vis, fluorescence and CD spectroscopy, isothermal calorimetry along with molecular docking studies. Hoechst 3325, ethidium bromide and rhodamine-B displacement experiments confirms that GUGE binds in the minor groove of DNA. ITC results further suggest these interactions to be feasible and spontaneous with hydrogen bond formation and van der waals interactions. Lastly, molecular docking also suggests GUGE to be a minor groove binder interacting through a single hydrogen bond formation between OH group of GUGE and nitrogen (N3) of adenosine (A6).

Synthesis and evaluation of 7-substituted-5,6-dihydrobenzo[c]acridine derivatives as new c-KIT promoter G-quadruplex binding ligands

It has been shown that treatment of cancer cells with c-KIT G-quadruplex binding ligands can reduce their c-KIT expression levels thus inhibiting cell proliferation and inducing cell apoptosis. Herein, a series of new 7-substituted-5,6-dihydrobenzo[c]acridine derivatives were designed and synthesized. Subsequent biophysical evaluation demonstrated that the derivatives could effectively bind to and stabilize c-KIT G-quadruplex with good selectivity against duplex DNA. It was found that 12-N-methylated derivatives with a positive charge introduced at 12-position of 5,6-dihydrobenzo[c]acridine ring had similar binding affinity but lower stabilizing ability to c-KIT G-quadruplex DNA, compared with those of nonmethylated derivatives. Further molecular modeling studies showed possible binding modes of G-quadruplex with the ligands. RT-PCR assay and Western blot showed that compound 2b suppressed transcription and translation of c-KIT gene in K562 cells, which was consistent with the property of an effective G-quadruplex binding ligand targeting c-KIT oncogene promoter. Further biological evaluation showed that compound 2b could induce apoptosis through activation of the caspase-3 cascade pathway.

Synthesis, cytotoxic evaluation and DNA binding study of 9-fluoro-6H-indolo[2,3-b]quinoxaline derivatives

New quaternary ammonium salts of 9-fluoro-6H-indolo[2,3-b] derivatives were synthesized. These compounds possessed enhanced DNA binding ability and improved antitumor activity.

Synthesis, characterization, DNA binding, cleavage activity, cytotoxicity and molecular docking of new nano water-soluble [M(5-CH₂PPh₃-3,4-salpyr)](ClO₄)₂ (M = Ni, Zn) complexes

Some new water soluble complexes [N,N'-bis{5-[(triphenyl phosphonium chloride)-methyl]salicylidine}-3,4-diaminopyridine] M(ii), which are formulated as nano-[Zn(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), [Zn(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), nano-[Ni(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), [Ni(5-CH2PPh3-3,4-salpyr)](ClO4)2 (), and [N,N'-bis{5-[(triphenyl phosphonium chloride)-methyl]salicylidine}-2,3-diaminopyridine]Ni(ii) [Ni(5-CH2PPh3-2,3-salpyr)](ClO4)2 () have been isolated and characterized by elemental analysis, FT-IR, (1)H NMR, (13)C NMR, (31)P NMR, and UV-vis spectroscopy. The morphology and size of the nano complexes were determined using FE-SEM and TEM. In vitro DNA binding studies were investigated by UV-vis absorption spectroscopy, viscosity measurements, CD spectroscopy, cyclic voltammetry, emission spectra and gel electrophoresis, which suggest that the metal complexes act as efficient DNA binders. The absorption spectroscopy of the compounds with DNA reveals that the DNA binding affinity (Kb) has this order: > > > > > Ligand. The metal complexes show DNA binding stronger than the ligand, which is expected due to the nature of the metal. The nano complexes display DNA binding stronger than the other complexes which is related to the effect of size on binding affinity and the Ni(ii) complexes reveal DNA binding stronger than the corresponding Zn(ii) analogues, which is expected due to their z* effect and geometry. The prominent double strand DNA cleavage abilities of compound are observed in the absence of H2O2 with efficiencies of more than 50% even at 70 μM complex concentration. Surprisingly, Zn(ii) complexes (compounds & ) exhibit a higher cytotoxicity (IC50: 7.3 & 10.9 μM at 24 h; IC50: 4.6 & 8.7 μM at 48 h) against human hepatoma (HepG2) and HeLa cell lines than the Ni(ii) complexes (compounds , & ) and 5-fluorouracil as control in spite of their inability to cleave DNA. Finally, DNA binding interactions were performed by docking studies. Density functional theory (DFT) studies were performed using the GAUSSIAN 03 program. The DFT method with B3LYP functional, LANL2DZ basis set for metal centers and 6-311g* for other atoms was used. The synthesized compounds and DNA were simulated by molecular docking to explore more details of the ligands conformation and their orientations in the active site of the receptor.

Bis((1,4-dimethyl-9H-carbazol-3-yl)methyl)amine-mediated anticancer effect triggered by sequence-specific cleavage of DNA leading to programmed cell death in the human U87 cell line

Bis((1,4-dimethyl-9H-carbazol-3-yl)methyl)amine (DMCM) has been designed as a novel anti-cancer agent which is believed to have a sequence-specific groove binding interaction with DNA, leading to anticancer effects.

Two half-sandwiched ruthenium (II) compounds containing 5-fluorouracil derivatives: synthesis and study of DNA intercalation

Two novel coordination compounds of half-sandwiched ruthenium(II) containing 2-(5-fluorouracil)-yl-N-(pyridyl)-acetamide were synthesized, and their intercalation binding modes with calf thymus DNA were revealed by hyperchromism of ultraviolet-visible spectroscopy; the binding constants were determined according to a Langmuir adsorption equation that was deduced on the base of careful cyclic voltammetry measurements. The two compounds exhibited DNA intercalation binding activities with the binding constants of 1.13×10⁶ M^-1 and 5.35 ×10⁵ M^-1, respectively.

Design and synthesis of a novel trinuclear palladium(ii) complex containing an oxime chelate ligand: determining the interaction mechanism with the DNA groove and BSA site I by spectroscopic and molecular dynamics simulation approaches

The trinuclear Pd(II) complex containing an oxime ligand showed significant interaction with both CT-DNA and BSA.

Structural and thermodynamic basis of interaction of the putative anticancer agent chelerythrine with single, double and triple-stranded RNAs

Interaction of chl with poly(uau), poly(au) and poly(u).

Characterizations of cationic γ-carbolines binding with double-stranded DNA by spectroscopic methods and AFM imaging

Two cationic γ-carbolines, 2-methyl-5H-pyrido[4,3-b]indolium iodide (MPII) and 2,5-dimethyl-5H-pyrido[4,3-b]indolium iodide (DPII), were synthesized, and the DNA-binding properties of the cationic γ-carbolines were elucidated. Through a series of experiments, we proved that the two cationic γ-carbolines could strongly interact with DNA by intercalative binding. However, DPII, with a methyl group substituting H atom of 5-NH, has shown a stronger intercalative interaction with DNA compared to MPII. The dissociation of H from the 5-NH of MPII resulted in better water solubility and less binding affinity to DNA. Atomic force microscopy (AFM) images of pBR322 showed that both MPII and DPII strongly interacted with DNA and induced conformational changes in DNA. Moreover, the CT-DNA circular dichroism (CD) spectra changes and the statistics of the node numbers of pBR322 in AFM images indicated that MPII had more profound effects on DNA conformations compared to DPII. Furthermore, our studies have shown that the interactions between cationic γ-carbolines and DNA were sensitive to ionic strength. Increased ionic strength in the buffer caused the DNA helix to shrink, and the base stacking would be more compact, which resulted in minimal intercalation of cationic γ-carbolines into DNA.

The role of positive charges on G-quadruplex binding small molecules: learning from bisaryldiketene derivatives

BACKGROUND

G-quadruplexes are promising therapeutic targets for small molecules. In general, the introduction of steady positive charges through the in situ alkylation of nitrogen atoms within potential G-quadruplex ligands can significantly improve their quadruplex binding and stabilization abilities. However, our previous studies on bisaryldiketene derivatives showed that the derivative M4, whose central piperidone moiety is quaternized, exhibits a poor G-quadruplex stabilization ability.

METHODS

To clarify this unusual finding, CD, ITC, UV and NMR analyses were performed to determine the binding behaviors of M4 and its non-quaternized analog M2 to G-quadruplex DNA [d(TGGGT)]4. Molecular modeling approaches were also employed to help illustrate ligand-quadruplex DNA interactions.

RESULTS

The CD melting and ITC analyses revealed that M2 exhibited much stronger stabilization and binding abilities to [d(TGGGT)]4 compared to M4. Moreover, the CD and ITC analyses in combination with UV, NMR and MD simulations revealed that M2 tended to be end-stacked on the G-quartet, whereas M4 tended to be bound in the groove region. Analysis of the electrostatic potential showed that the charged surface of M4 was more positive than that of M2 and other reported ligands that bind to the G-quadruplex via end-stacking interactions.

CONCLUSIONS

The results indicated that the different positively charged surfaces of M2 and M4 might be the key reason for their different binding modes. These different binding modes also lead to different binding affinities and stabilization abilities for [d(TGGGT)]4.

GENERAL SIGNIFICANCE

These results provide new clues for the rational design of G-quadruplex-binding small molecules with steady positive charges.

Synthesis and biological activity evaluation of emodin quaternary ammonium salt derivatives as potential anticancer agents

Twenty-six emodin derivatives (17 novel) which attach quaternary ammonium salt were synthesized and evaluated for their anticancer activities in vitro and in vivo. Compounds 11g + 12g and 11h + 12h had more significant antiproliferative ability against three cancer cell lines and low cytotoxicity to HELF. 11g + 12g and 11h + 12h induced AGS cell apoptosis and arrested cell cycle at the G(0)/G(1) phase in a dose-dependent manner. Furthermore, the activities of the caspase-3, -9 enzymes were increased in the treated cells. In vivo studies revealed that compounds 11g + 12g and 11h + 12h showed significant anti-tumor activity compared with controlled group.