Photobehaviour and in vitro binding strategy of natural drug, chlorogenic acid with DNA: A case of groove binding

Effect of geometric isomerism on the anticancer property of new platinum complexes with glycine derivatives as asymmetric N, O donate ligands against human cancer

In this project, to fallow the anticancer ability of new Pt drugs, several new Pt complexes were synthesized with the asymmetric bidentate glycine derivatives, as named propyl- and hexyl glycine (L), in the general formula: [Pt(NH3)2(L)]NO3, and cis- and trans-[Pt(L)2]. The structure of two cis- and trans-[Pt(propylgly)2] complexes was proved by single crystallography analysis. However, all complex structures were characterized by various methods of 1H NMR, 13C NMR, 195Pt NMR, FTIR, LC-Mass, and Raman spectroscopy. To study the passage of water-soluble complexes of [Pt(NH3)2(L)]NO3 via cell membrane, their solubility, and lipophilicity were analyzed. In addition, the cytotoxic properties of these complexes were evaluated against normal and malignant cell lines (skin, breast, and lung cancer cells). The results indicated that they were either comparable to cisplatin or less damaging than carboplatin and oxaliplatin. It was expected that due to less steric effect, and the presence of length aliphatic hydrocarbon chain in the complex structure, trans-[Pt(hexylgly)2] is more toxic on cancerous cell lines than trans-[Pt(propylgly)2]. Cellular accumulation of all complexes was evaluated on A549 and MCF7 cell lines, and the amount of platinum metal (ng) was measured by the ICP method. Results showed that trans-[Pt(hexylgly)2] complex has the highest accumulation inside both mentioned cell lines and [Pt(NH3)2(L)]NO3 complexes behave like clinical Pt-drugs. Ultimately, the interaction patterns of DNA were examined using spectroscopic methods and molecular docking simulations for all substances.

Elucidating the Interaction of Indole-3-Propionic Acid and Calf Thymus DNA: Multispectroscopic and Computational Modeling Approaches

Indole-3-propionic acid (IPA) is a plant growth regulator with good specificity and long action. IPA may be harmful to human health because of its accumulation in vegetables and fruits. Therefore, in this study, the properties of the interaction between calf thymus DNA (ctDNA) and IPA were systematically explored using multispectroscopic and computational modeling approaches. Analysis of fluorescence spectra showed that IPA binding to ctDNA to spontaneously form a complex was mainly driven by hydrogen bonds and hydrophobic interaction. DNA melting analysis, viscosity analysis, DNA cleavage study, and circular dichroism measurement revealed the groove binding of IPA to ctDNA and showed that the binding did not significantly change ctDNA confirmation. Furthermore, molecular docking found that IPA attached in the A-T rich minor groove region of the DNA. Molecular dynamics simulation showed that DNA and IPA formed a stable complex and IPA caused slight fluctuations for the residues at the binding site. Gel electrophoresis experiments showed that IPA did not significantly disrupt the DNA structure. These findings may provide useful information on the potential toxicological effects and environmental risk assessments of IPA residue in food at the molecular level.

Synthesize and multi-spectroscopic studies of zinc-naproxen nanodrug as DNA intercalator agent

The zinc-naproxen complex as a nano-drug (NanoD) was synthesized successfully via fast and effective ultrasound-assisted processes. The chemicophysical properties of the NanoD were determined using FT-IR, XRD, SEM, and EDX mapping analyses. The results confirmed the formation of the 55 nm NanoD laminates. The interaction of the obtained NanoD with calf thymus deoxyribonucleic acid (CT-DNA) was studied as well. Structural and topography changes of DNA in interaction with the NanoD were investigated by atomic force microscopy (AFM). The results of electronic absorption spectroscopy, the DNA-viscosity studies, and competition fluorescence spectroscopy showed that CT-DNA binds to the NanoD through the intercalative binding mode. The data of AFM analysis indicated swollen CT-DNA upon interaction with the NanoD. The in vitro investigation of cytotoxicity of the NanoD on HT-29 and Hep G2 cancer cells demonstrated high cytotoxicity activity of the NanoD than that of cisplatin in HT-29 cell line, especially at lower concentrations.

Spectroscopic Studies on the Interaction of Naphthyridines with DNA and Fluorescent Detection of DNA in Agarose Gel

Four new naphthyridine derivatives (R1-R4) possessing amino acid or boronic acid moieties have been synthesized and characterized using ¹H and ¹³C NMR, FT-IR, and mass spectral techniques. The mechanism of binding of these probes with calf thymus DNA (CT-DNA) has been delineated through UV-Vis, fluorescence, and circular dichroism (CD) spectral techniques along with thermodynamic and molecular docking studies. Small hypochromicity in absorption maximum of the probes without any shift in wavelength of absorption suggests groove binding mode of interaction of these probes with CT-DNA, confirmed by CD and 1H NMR spectral data competitive binding assay with ethidium bromide (EB). CT-DNA quenches the fluorescence of these probes via a static quenching mechanism. In the case of R1 and R4, the observed ΔH^o < 0 and ΔS^o > 0suggest that these probes interact with CT-DNA through H-bonding and hydrophobic interactions, while in the interaction of R2 and R3, van der Walls and H-boding forces are found to be dominant (ΔH^o < 0 and ΔS^o < 0). Results of molecular docking investigations corroborate well with that of spectral studies, and these probes bind in the minor groove of DNA. These probes are found to be effective fluorescent staining agents for DNA in agarose gel in gel electrophoresis experiment with sensitivity comparable to that of EB, and DNA amounts as low as 37.5 ng are visually detectable in the gel.

Molecular complexes of calf thymus DNA with various bioactive compounds: Formation and characterization

The interaction between biomacromolecules and ligands has attracted great interest because of their biological properties. Calf thymus DNA (ctDNA) can interact with bioactive compounds to form complexes. Here, ctDNA-ligand complexes were studied using fluorescence, absorption, and infrared spectroscopy, circular dichroism, ABTS assay and competitive displacement. The binding constants of bioactive compounds at the intercalative site of ctDNA ranked in order kaempferol > apigenin > quercetin > curcumin > riboflavin, while the binding constants at minor groove sites ranked quercetin > kaempferol > naringenin ~ apigenin > hesperetin > curcumin ~ resveratrol ~ riboflavin > caffeic acid. CtDNA maintained stable B-form with an enhancement of base stacking and a decrease of right-handed helicity in the presence of these bioactive compounds, except for hesperetin and caffeic acid. Bioactive compounds preferentially bound to guanine bases and tended to transfer into a more hydrophobic environment upon complexation with ctDNA. The DNA complexation did not affect the ABTS·⁺ scavenging capacity of quercetin, kaempferol, resveratrol and apigenin but increased the ones of naringenin, caffeic acid, curcumin, hesperetin and riboflavin. The data gathered here should be useful to understand the binding modes of DNA with ligands for their potential application in pharmaceutical and food industries.

Comprehensive study of the interaction between Puerariae Radix flavonoids and DNA: From theoretical simulation to structural analysis to functional analysis

Puerariae Radix (PR) is a natural herb whose active ingredient is mainly flavonoids. To explore the interaction between PR flavonoids and DNA not only has important biological implications for understanding the mechanism of action, but also helps develop PR products for the design of appropriate dietary interventions to aid cancer treatment. In this work, we comprehensively studied the interaction between six kinds of PR flavonoids and DNA from four different and progressive levels, including molecular docking, multi-spectral analysis, and functional analysis in vitro and in cell. Results show that the DNA binding affinity of six flavonoids is in an order of quercetin > formononetin > daidzein > puerarin > 4'-methoxy puerarin > puerarin 6″-O-xyloside (POS), in which quercetin can significantly inhibit DNA amplification owing to its strongest binding affinity. The binding between quercetin and DNA is further revealed to be intercalated binding, which can cause conformational changes in DNA, thereby exhibiting an activity of cell cycle arrest and anti-proliferative. This property of quercetin can be utilized for the further development of flavonoids with anticancer activity. In addition to the potential application, this work also provides a platform for the comprehensive study of the interaction between micromolecules and DNA.

Photophysical and thermodynamic evaluation on the in vitro and in silico binding profile of Camptothecin with DNA

Camptothecin (CMT) is an anti-tumour alkaloid drug exhibiting selective topoisomerase-I inhibitory activity by eventually hindering dynamic functions of DNA duplex via initiating apoptosis. Unravelling the binding mechanism of CMT with bio macromolecular systems can offer fundamental information regarding the mechanism of actions which can lead to the design of rational proactive drugs. This study endeavoured the binding interactions of CMT with calf thymus DNA (ct-DNA) along with the structural alterations attained by the DNA duplex owing to CMT interactions through multi-spectroscopic, calorimetric and molecular docking studies. The UV-visible absorbance and fluorescence quenching studies revealed the binding strength of CMT with ct-DNA, evident from the binding constants K₁ = 3.79 × 10³ M^-1 and Kq = 2 × 10³ M^-1. The time-resolved lifetime measurements inferred that the quenching was static due to the non-fluorescent ground state complex formation. The dye displacement study, temperature melting and viscosity measurements established a typical non-intercalative binding mode of CMT with ct-DNA. The binding isotherm deduced from ITC was found to be spontaneous and exothermic exerting a promising ΔG value of -6.2 kcal mol^-1. The thermal kinetic parameters implied that the forces primarily involved in the CMT-ct-DNA complexation are hydrogen bonding and van der Waals interactions. Moreover, the structural alterations of DNA duplex reflected in the CD and FTIR spectra could undeniably confirm the groove binding manner of CMT. The in silico extra precision docking study explored more accurate molecular illustrations of sequence specific minor groove binding mechanism evolved between CMT and DNA corroborating well with the experimental results. These innovative findings may shorten the path towards the development of novel and more effective CMT drug derivatives.