Synthesis, characterization, spectroscopy, cytotoxic activity and molecular dynamic study on the interaction of three palladium complexes of phenanthroline and glycine derivatives with calf thymus DNA

Exploring the interaction of tepotinib with calf thymus DNA using molecular dynamics simulation and multispectroscopic techniques

In recent times, there has been a surge in the discovery of drugs that directly interact with DNA, influencing gene expression. As a result, understanding how biomolecules interact with DNA has become a major area of research. One such drug is Tepotinib (TPT), an FDA-approved anti-cancer medication known as a MET tyrosine kinase inhibitor, used in chemotherapy for metastatic non-small cell lung cancer (NSCLC) with MET exon 14 skipping alterations. In our study, we adopted both biophysical and in-silico methods to investigate the binding relationship of TPT and ctDNA. The absorption spectra of ctDNA exhibited a hypochromic effect when titrated with TPT and the binding constant of TPT-ctDNA complex was calculated, Ka = 9.91 × 104 M-1. By computing bimolecular enhancement constant (KB) and thermodynamic enhancement constant (KD) in fluorometric investigations, it was found that the fluorescence enhancement is a result of a static process involving the ctDNA-TPT complex formation in the ground state, as opposed to a dynamic process. The displacement assay results further supported this finding, showing that TPT exhibits a binding preference for minor groove of ct-DNA and was also demonstrated by KI quenching and CD spectroscopy. The molecular docking and molecular dynamic simulations validated TPT's groove binding nature and binding pattern with ctDNA, respectively. Thus, the results of our present investigation offer valuable insights into the interaction between TPT and ctDNA. It is evident that TPT, as an anti-cancer medication, binds to the minor groove of ctDNA.

Binding of Mammea A/AA (MA) to calf thymus DNA revealed by the ratiometric absorbance of MA in the UV-visible range molecular dynamic simulations and TD-DFT calculations

The in vitro anti-proliferative activity of MA (5,7-dihydroxy-8-(3-methylbut-2-enyl)-6-(3-methyl-1-oxobutyl)-4-phenyl[1]2H-[1]benzopyran-2-one)on a variety of cancer cells was previously demonstrated. This work strives to understand the mechanisms by which MA exerts this biological activity. Thereafter, the binding of MA to calf thymus DNA was studied by monitoring the change in the UV-visible absorbance of MA. It was found that, the response of MA to binding with calf thymus DNA is characterised by an increase in the AS/AL ratio of the absorbance of the longest wavelength absorption band to the shortest one, and the appearance of a new band at about 377 nm assigned to S0→S1 transition, which is red shifted as compared to free MA. From the bands ratio, the binding constant is found to be 4.3x105 M-1, indicating strong binding. The deduced binding free energy, enthalpy and entropy are -7.7 kcal/mol, -10.89 ± 0.28 kcal/mol and -54.46 ± 4 J/K, respectively, indicating that MA binds to DNA by a non-bonding Van der Waals type interactions and hydrogen bonds. Further study with classical molecular dynamics shows that MA binds to DNA by intercalation, where it is positioned between two AT base pairs. Unlike isolated MA, TDDFT calculations on ten images extracted from the MD trajectory show that, the frontier molecular orbitals of the complex are distributed over the DNA and MA. This indicates a strong stacking interaction and then explains the hypochromism and the red shift of the S0→S1 transition. The present work demonstrates the potency of MA as antitumor compound and as absorbance-based molecular probe.Communicated by Ramaswamy H. Sarma.

Spectroscopy and molecular dynamic study of the interaction of calf thymus DNA by anticancer Pt complex with butyl glycine ligand

Despite the past few decades since the discovery of anticancer drugs, there is still no definitive treatment for its treatment. Cisplatin is a chemotherapy medication used to treat some cancers. In this research, the DNA binding affinity of Pt complex with butyl glycine ligand was studied by various spectroscopy methods and simulation studies. Fluorescence and UV-Vis spectroscopic data showed groove binding in ct-DNA-[Pt(NH₃)₂(butylgly)]NO₃ complex formation by the spontaneous process. The results were also confirmed by small changes in CD spectra and thermal study (T_m), as well as the quenching emission of [Pt(NH₃)₂(butylgly)]NO₃ complex on DNA. Finally, thermodynamic and binding parameters displayed that hydrophobic forces are the main forces. Based on docking simulation, [Pt(NH₃)₂(butylgly)]NO₃ could bind to DNA and via minor groove binding on C-G center on DNA, formed a stable DNA complex.

Red-Emitting Hybrid Based on Eu3+-dbm Complex Anchored on Silica Nanoparticles Surface by Carboxylic Acid for Biomarker Application

Luminescent organic-inorganic hybrids containing lanthanides (Ln³⁺) have been prominent for applications such as luminescent bio-probes in biological assays. In this sense, a luminescent hybrid based on dense silica (SiO₂) nanospheres decorated with Eu³⁺ β-diketonate complexes using dibenzoylmethane (Hdbm) as a luminescent antenna was developed by using a hierarchical organization in four steps: (i) anchoring of 3-aminopropyltriethoxysilane (APTES) organosilane on the SiO₂ surface, (ii) formation of a carboxylic acid ligand, (iii) coordination of Eu³⁺ to the carboxylate groups and (iv) coordination of dbm^- to Eu³⁺. The hybrid structure was elucidated through the correlation of thermogravimetry, silicon nuclear magnetic resonance and photoluminescence. Results indicate that the carboxylic acid-Eu³⁺-dbm hybrid was formed on the surface of the particles with no detectable changes on their size or shape after all the four steps (average size of 32 ± 7 nm). A surface charge of -27.8 mV was achieved for the hybrid, assuring a stable suspension in aqueous media. The Eu³⁺ complex provides intense red luminescence, characteristic of Eu³⁺⁵D₀→⁷F_J electronic transitions, with an intrinsic emission quantum yield of 38%, even in an aqueous suspension. Therefore, the correlation of luminescence, structure, particle morphology and fluorescence microscopy images make the hybrid promising for application in bioimaging.

A Novel Hybrid of Chloroquine and Primaquine Linked by Gold(I): Multitarget and Multiphase Antiplasmodial Agent

Plasmodium parasites kill 435 000 people around the world every year due to unavailable vaccines, a limited arsenal of antimalarial drugs, delayed treatment, and the reduced clinical effectiveness of current practices caused by drug resistance. Therefore, there is an urgent need to discover and develop new antiplasmodial candidates. In this work, we present a novel strategy to develop a multitarget metallic hybrid antimalarial agent with possible dual efficacy in both sexual and asexual erythrocytic stages. A hybrid of antimalarial drugs (chloroquine and primaquine) linked by gold(I) was synthesized and characterized by spectroscopic and analytical techniques. The CQPQ-gold(I) hybrid molecule affects essential parasite targets, it inhibits β-hematin formation and interacts moderately with the DNA minor groove. Its interaction with PfTrxR was also examined in computational modeling studies. The CQPQ-gold(I) hybrid displayed an excellent in vitro antimalarial activity against the blood-stage of Plasmodium falciparum and liver-stage of Plasmodium berghei and efficacy in vivo against P. berghei, thereby demonstrating its multiple-stage antiplasmodial activity. This metallic hybrid is a promising chemotherapeutic agent that could act in the treatment, prevention, and transmission of malaria.

Synthesis, antimicrobial activity, molecular docking and ADMET study of a caprolactam-glycine cluster

Density functional theory calculations were performed with DFT method using both b3lyp/6-311++G(d,p) and wb97xd/6-311++G(d,p) levels of theory to predict the molecular geometry, to evaluate the molecular electrostatic potential and frontier molecular orbitals of synthesized a new compound: caprolactam-glysine cluster (CL-Gly). Molecular docking study of the CL-Gly was carried out to clarify the interaction and the probable binding modes, between the title compound and DNA. The antibacterial activities of CL-Gly cluster against Gram-positive and Gram-negative bacteria was determined. In silico ADMET study was also performed for predicting pharmacokinetic and toxicity profile of the synthesized cluster which expressed good drug-like behavior and non-toxic nature. It was revealed that the compound has importance in drug discovery process.Communicated by Ramaswamy H. Sarma.

Kinetic and Thermodynamic Investigation of Human Serum Albumin Interaction with Anticancer Glycine Derivative of Platinum Complex by Using Spectroscopic Methods and Molecular Docking

In this paper, a new anticancer Pt (II) complex, cis-[Pt (NH₃)₂(tertpentylgly)]NO₃, was synthesized with glycine-derivative ligand and characterized. Cytotoxicity of this water-soluble Pt complex was studied against human cancer breast cell line of MCF-7. The interaction of human serum albumin (HSA) with Pt complex was studied by using UV-Vis, fluorescence spectroscopy methods, and molecular docking at 27 and 37 °C in the physiological situation (I = 10 mM, pH = 7.4). The negative [Formula: see text] and positive [Formula: see text] indicated that electrostatic force may be a major mode in the binding between Pt complex and HSA. Binding constant values were obtained through UV-Vis and fluorescence spectroscopy that reveal strong interaction. The negative Gibbs free energy that was obtained by using the UV-Vis method offers spontaneous interaction. Fluorescence quenching the intensity of HSA by adding Pt complex confirms the static mode of interaction is effective for this binding process. Hill coefficients, n_H, Hill constant, k_H, complex aggregation number around HSA, <J>, number of binding sites, g, HSA melting temperature, T_m, and Stern-Volmer constant, k_SV, were also obtained. The kinetics of the interaction was studied, which showed a second-order kinetic. The results of molecular docking demonstrate the position of binding of Pt complex on HSA is the site I in the subdomain IIA.

Water-soluble binary and ternary palladium(ıı) complexes containing amino acids and intercalating ligands: synthesis, characterization, biomolecular interactions and cytotoxicities

Novel water soluble palladium(ii) complexes have been synthesized and characterized. Moreover, the cytotoxicities of these complexes against different human tumor and healthy cell lines were investigated by the XTT assay.

Studies of the binding properties of the food preservative thiabendazole to DNA by computer simulations and NMR relaxation

Thiabendazole (TBZ) is a commonly used food preservative and has a wide range of anthelmintic properties. In this study, computer simulations and experiments were conducted to investigate the interaction mechanism of TBZ and herring sperm DNA (hsDNA) at the molecular level. Molecular docking showed that TBZ interacted with DNA in groove mode and bound in A-T and C-G base pair regions. Molecular dynamics (MD) was used to evaluate the stability of the TBZ–DNA complex and found that the three phases in MD and the hydrogen bonds helped maintain the combination. NMR relaxation indicated that TBZ had a certain affinity to hsDNA with a binding constant of 462.43 L mol⁻¹, and the thiazole ring was the main group bound with DNA. Results obtained from fluorescence experiments showed that the binding of TBZ and hsDNA was predominantly driven by enthalpy through a static quenching mechanism. Circular dichroism and viscosity measurements proved the groove binding mode. The FTIR results clarified the conformational changes of DNA, that the DNA helix became shorter and compact, and the DNA structure transformed from B-form to A-form.

The groove binding of thiabendazole and hsDNA was studied by computer simulation and experimental methods.

Highly functionalized piperidines: Free radical scavenging, anticancer activity, DNA interaction and correlation with biological activity

Twenty-five piperidines were studied as potential radical scavengers and antitumor agents. Quantitative interaction of compounds with ctDNA using spectroscopic techniques was also evaluated. Our results demonstrate that the evaluated piperidines possesses different abilities to scavenge the radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the anion radical superoxide (^•O₂⁻). The piperidine 19 was the most potent radical DPPH scavenger, while the most effective to ^•O₂⁻ scavenger was piperidine 10. In general, U251, MCF7, NCI/ADR-RES, NCI-H460 and HT29 cells were least sensitive to the tested compounds and all compounds were considerably more toxic to the studied cancer cell lines than to the normal cell line HaCaT. The binding mode of the compounds and ctDNA was preferably via intercalation. In addition, these results were confirmed based on theoretical studies. Finally, a linear and exponential correlation between interaction constant (K_b) and GI₅₀ for several human cancer cell was observed.

A (salicylaldiminato)Pt(II) complex with dimethylpropylene linkage: Synthesis, structural characterization and antineoplastic activity

A novel (salicylaldiminato)Pt(II) complex with two different molecular structures, one solventless ((salicylaldiminato)Pt(II)) 1 and another one solvated ((salicylaldiminato)Pt(II). C₂H₅OH), 1·C₂H₅OH, has been obtained by the reaction of a salen ligand with [PtCl₂(DMSO)₂] in ethanol at room temperature. The asymmetric unit of solventless 1 contains 9 such complex molecules whereas 1·C₂H₅OH contains 2 complex molecules and one ethanol molecule. To get insights into the structure and bonding, DFT and TDFT calculation have been carried out. The electronic transition band at 408.0nm (calc. 424.3nm) is assigned to HOMO→LUMO (96%) excitation. The calculated NMR chemical shifts are interrelated with the experimental results, and a very slight effect of solvent was noticed on NMR chemical shifts. A MTT assay and the real-time cell monitoring xCELLigence system revealed that the 1 has significant potential to suppress cell viability and cell proliferation in human HT-29 and SW620 colorectal cancer cell lines.

Anticancer activity of novel amino acid derivative of palladium complex with phendione ligand against of human colon cancer cell line

The aim of this work is the identification of the structural effect of amino acid-Pd complex on DNA as an intracellular target which was studied using various spectroscopic techniques such as fluorescence, UV-visible and circular dichroism in combination with a molecular docking study. Hence, a novel water-soluble palladium complex, [Pd(phendione)(isopentylglycine)]NO₃, has been synthesized and characterized by spectroscopic method. The anticancer activity of complex was investigated against human colon cancer cell line of HCT116 after 24 h of incubation using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. In addition, this complex was interacted with calf thymus DNA (ct-DNA) via positive cooperative interaction. The fluorescence data indicate that Pd complex is intercalated in DNA. These results were confirmed by circular dichroism spectra. The molecular docking results indicate that docking may be an appropriate method for the prediction and confirmation of experimental results. Complementary molecular docking results may be useful for the determination of the binding mechanism of DNA in pharmaceutical and biophysical studies providing new insight into the novel pharmacology and new solutions in the formulation of advanced oral drug delivery systems. Docking and spectroscopic studies show that new water-soluble Pd complex has anticancer activity and it can bind to DNA via intercalation and groove binding.

Design, synthesis, characterization, cytotoxicity, molecular docking and analysis of binding interactions of novel acetylacetonatopalladium(ii) alanine and valine complexes with CT-DNA and BSA

The neutral, water soluble palladium(ii) amino acid complexes, interact with CT-DNA (groove binding) and BSA (H-binding in main pocket). Molecular docking supports the interactions.

Evaluation of bishexadecyltrimethyl ammonium palladium tetrachloride based dual functional colloidal carrier as an antimicrobial and anticancer agent

A dual function carrier with antimicrobial and anticancer activity represents a simple and effective system with future application in drug delivery.