Probing the behavior of calf thymus DNA upon binding to a carboxamide fungicide boscalid: insights from spectroscopic and molecular docking approaches

Quantification of mirtazapine in tablets via DNA binding mechanism; development of a new HPLC method

Atypical antidepressant mirtazapine (MIR) is mostly prescribed for the management of major depressive disorder. The identification of MIR in pharmaceutical dosage forms was made possible by developing a novel, quick, sensitive high-performance liquid chromatography (HPLC) approach that was verified in accordance with ICH recommendations. In the first part of this study, HPLC investigations were optimized with regard to variables including pH, working column, mobile phase, temperature, and flow rate. The limit of detection (LOD) was 0.013 ppm, the limit of quantification (LOQ) was 0.044 ppm, and the linear range was computed as 0.5-15 ppm (R2 = 0.9998). The recovery investigation assessed the method's accuracy, which was shown to range between 98.82 and 100.97 %. In the second part, by using UV-vis spectroscopy, HPLC, thermal denaturation, and viscosity measurements, the mechanism of binding interaction of MIR with double-stranded fish sperm deoxyribonucleic acid (dsDNA) has been thoroughly studied. The DNA binding constants (Kb) were determined using UV-Vis absorption and HPLC methods. To investigate the interactions of MIR with dsDNA, molecular docking calculations and additionally, molecular dynamics simulations were performed. Results showed that MIR is located in the minor groove of dsDNA, and in addition to hydrogen bonding, electrostatic interaction is also formed between the aromatic ring of MIR and phosphate oxygen of dsDNA. Finally, a binding characterization study using MIR tablets was also conducted in order to assess the interaction mechanism of the DNA with the drug using the validated analytical procedure developed for the MIR molecule.

Exploring the Interaction Between the Newly Designed Antitumor Zn(II) Complex and CT-DNA/BSA: Spectroscopic Methods, DFT Computational Analysis, and Docking Simulation

A new zinc(II) complex formulated as [Zn(pipr-ac)2], where pipr-ac stands for piperidineacetate, was synthesized and structurally identified with the help of experimental and DFT methods. Frontier molecular orbital (FMO) analysis demonstrated that the new complex has higher biological activity compared to the free ligand. Molecular electrostatic potential (MEP) showed the nitrogen atoms and oxygen of carbonyl groups are the active sites of Zn(II) compound. Also, natural bond orbital (NBO) analysis confirmed the charge transfer from the ligating atoms to the metal ion and formation of four coordinated Zn(II) complex. MTT assay illustrated a noticeable cytotoxic activity of the new zinc(II) complex compared to cisplatin on K562 cell line. The CT-DNA and serum albumin (SA) binding of the Zn(II) complex were explored individually. In this regard, UV-Vis spectroscopy and florescence titration revealed the occurrences of fluorescence quenching of CT-DNA/SA by metal compound via static mechanism and creation of hydrogen bonds and van der Waals interactions between them. The binding was further confirmed by viscosity measurement and gel electrophoresis assay for CT-DNA and circular dichroism spectroscopy for SA. Moreover, molecular docking simulation demonstrated that the new compound binds mainly through hydrogen bonds to the groove of DNA and hydrogen bonds and van der Waals interactions to site I of SA.

Analytical studies on some pesticides with antifungal effects: Simultaneous determination by HPLC, investigation of interactions with DNA and DNA damages

A simple, and fast method was developed for the simultaneous determination of five fungicides, namely thiram (THR), epoxiconazole (EPO), hexaconazole (HEX), tebuconazole (TEB), and diethofencarb (DIE), in different matrices by HPLC-UV. Parameters influencing the peak shape and resolution, such as the composition of mobile phase, pH and concentration of buffer solution, and column temperature, were examined and optimized. The proposed method was validated in terms of linearity, sensitivity, precision, and accuracy. Forced degradation studies were carried out for all analytes to demonstrate the specificity of the method and to evaluate the stability of analytes under different conditions. DNA interaction and DNA damage studies were conducted by HPLC and comet assay, respectively. All fungicides were found to bind DNA, except for DIE. While the binding coefficients for EPO, HEX, and TEB were of the order of 104, THR was found to interact more strongly with DNA with a binding coefficient of higher than 106. DIE did not induce DNA damage at any concentration tested. On the other hand, TEB, HEX, and EPO induced DNA damage up to 30 µg/mL. THR showed cytotoxic effects at 20 and 30 µg/mL and caused significant DNA damage at lower concentrations.

Multi-spectroscopic, thermodynamic and molecular simulation studies on binding of pyrroloquinoline quinone with DNA: coexistence of intercalation and groove binding modes

The interaction between enzyme-like pyrroloquinoline quinone (PQQ) and calf-thymus DNA (CT-DNA) has been investigated by means of multi-spectroscopic (UV-Vis, fluorescence and circular dichroism), isothermal titration calorimetric (ITC), viscometry and molecular docking and metadynamics simulation techniques. Absorption spectral data suggested the formation of a PQQ/CT-DNA complex, which quenched the fluorescence of PQQ via the dynamic quenching process. The results of CD spectral studies coupled with viscosity measurements, competitive binding assays with Hoechst 33258 and ethidium bromide (EB), KI quenching experiments, gel electrophoresis and DNA melting studies indicated groove binding mode of interaction of PQQ with CT-DNA. ITC experiment revealed that the complex formation is a spontaneous process (ΔGo < 0) with a binding constant of 1.05 × 104 M-1. The observed ΔHo < 0 and ΔSo < 0 pointed out that the complex is stabilized by van der Waals forces along with H-bonding interactions. The outcomes of molecular docking and simulation studies confirmed the binding of PQQ with DNA. The free energy surface (FES) analysis pointed out the existence of an equilibrium between partial intercalation and groove binding modes, which is in good agreement with the competitive binding assays.Communicated by Ramaswamy H. Sarma.

Bovine serum albumin interaction, molecular docking, anticancer and antimicrobial activities of Co(II) Schiff base complex derived from Nophen ligand

In this report, synthesis, characterization, biological and molecular modeling studies of Nophen Schiff base [N,N-bis(2-hydroxy-1-naphthaldehyde)-o-phenylenediamine] and Co(II)-Nophen complex have been furnished. BSA binding affinities of the ligand and Co(II)-Nophen complex have been appraised by UV-visible, fluorescence and cyclic voltammetric techniques. Spectroscopic measurements indicate strong binding of the complex with BSA protein through static quenching mechanism with binding constant in the order of 10⁴ M^-1. The negative shift of the peak potential in cyclic voltammetry suggested an electrostatic interaction. Molecular docking analysis reveals significant binding affinity (-6.3 kcal/mol) of the complex towards BSA protein. It is amazing that the in vitro cytotoxicity of Co(II)-Nophen complex against A549 cell lines (Human lung carcinoma cells) has remarkable potentials with 29 ± 1.2 µM as IC₅₀ value. Comparing the biological activity towards microorganisms, Co(II)-Nophen complex show substantial response than the Nophen ligand.Communicated by Ramaswamy H. Sarma.

Structural, spectroscopic, in silico, in vitro and DNA binding evaluations of tyrosyl-lysyl-threonine

The main objective of the present study is to investigate the molecular structure and DNA binding interaction of the tyrosyl-lysyl-threonine (YKT) tripeptide, which has anticancer, antioxidant and analgesic properties, using various in silico (MD, QM, molecular docking), spectroscopic (UV, FT-IR, FTIR-ATR, Raman, gel electrophoresis) and in vitro (MCF-7 and HeLa cancer cell lines and BEAS-2B cell line) methods. The optimized geometry, vibrational wavenumbers, molecular electrostatic potential (MEP), natural bond orbital (NBO) and HOMO-LUMO (highest occupied molecular orbital- lowest unoccupied molecular orbital) calculations were carried out with Density Functional Theory (DFT) using B3LYP/6-311++G(d,p) basis set to indicate conformational, vibrational and intramolecular charge transfer characteristics. The assignment of all fundamental theoretical vibration wavenumbers was performed using potential energy distribution analysis (PED). DNA is a significant pharmacological target of drugs in several diseases such as cancer. For this reason, molecular docking calculation was used to elucidate the binding and interaction between YKT tripeptide and DNA at the atomic level. Also, the dynamic behaviors of YKT and DNA was examined using MD simulations. Besides, the interaction of YKT with DNA was experimentally examined by UV titration method and agarose gel electrophoresis method. Experimental results showed that YKT was intercalatively and electrostatically bound to CT-DNA (Calf thymus DNA) and cleavage pBR322 DNA in the presence of H₂O₂. The pharmacokinetic profile of YKT was also obtained. Cytotoxic effect of YKT was evaluated on MCF-7, HeLa and BEAS-2B cell lines. Hence, these studies about YKT tripeptide may pave the way for the development of various cancer drugs. Communicated by Ramaswamy H. Sarma.

Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA

Remdesivir (REM) is an antiviral drug, which exercises its effect by targeting specifically RNA-dependent RNA polymerase. The interaction of REM with calf thymus DNA (CT-DNA) was investigated by multi-spectroscopic techniques (UV-Vis, fluorescence, circular dichroism and ³¹P NMR) in combination with different biophysical experiments and metadynamics simulation studies. UV-Vis and fluorescence spectroscopic analysis indicated formation of a complex between REM and CT-DNA, whose binding constant is in the order of 10⁴ M^-1. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 shown that REM binds to CT-DNA via intercalation mode. Significant alteration in the band due to base stacking pairs at 274 nm in the circular dichroism spectrum, appreciable increase in relative viscosity of the biomolecule upon binding with REM and the results of potassium iodide quenching studies confirmed that REM intercalates into the base pairs of CT-DNA. Thermodynamic parameters revealed that the binding of REM to CT-DNA is a spontaneous process (ΔG⁰ < 0) and the main force which holds them together in the REM/CT-DNA complex is electrostatic interaction (ΔH⁰ < 0 and ΔS⁰ > 0). The up-field shift in the ³¹P NMR signal of REM on interaction with CT-DNA suggested that phenyl ring adjacent to the phosphate moiety of REM may involve in the intercalation process. This is well supported by the analysis of free energy surface landscape derived from metadynamics simulation studies.

Investigation of binding characteristics of ritonavir with calf thymus DNA with the help of spectroscopic techniques and molecular simulation

The binding behavior of ritonavir (RTV), a HIV/AIDS protease inhibitor, with ct-DNA was characterized through multiple testing technologies and theoretical calculation. The findings revealed that the RTV-DNA complex was formed through the noncovalent interaction mainly including conventional hydrogen bonds and carbon hydrogen bonds as well as hydrophobic interactions (pi-alkyl interactions). The stoichiometry and binding constant of the RTV-DNA complex were 1:1 and 1.87 × 10³ M^-1 at 298 K, respectively, indicating that RTV has moderate affinity with ct-DNA. The findings confirmed that RTV binds to the minor groove of DNA. The outcomes of CD experiments showed that the binding with RTV changed the conformation of DNA slightly. However, the conformation of RTV had obvious changes after binding to DNA, meaning that the flexibility of RTV molecule played an important role in stabilizing the RTV-DNA complex. Meanwhile, the results of DFT calculation revealed that the RTV and DNA interaction caused the changes in the frontier molecular orbitals, dipole moment and atomic charge distribution of RTV, altering the chemical properties of RTV when it bound to DNA. Communicated by Ramaswamy H. Sarma.

The research progress in and perspective of potential fungicides: Succinate dehydrogenase inhibitors

Succinate dehydrogenase inhibitors (SDHIs) have become one of the fastest growing classes of new fungicides since entering the market, and have attracted increasing attention as a result of their unique structure, high activity and broad fungicidal spectrum. The mechanism of SDHIs is to inhibit the activity of succinate dehydrogenase, thereby affecting mitochondrial respiration and ultimately killing pathogenic fungi. At present, they have become popular varieties researched and developed by major pesticide companies in the world. In the review, we focused on the mechanism, the history, the representative varieties, structure-activity relationship and resistance of SDHIs. Finally, the potential directions for the development of SDHIs were discussed. It is hoped that this review can strengthen the individuals' understanding of SDHIs and provide some inspiration for the development of new fungicides.

A novel palladium(II) antitumor agent: Synthesis, characterization, DFT perspective, CT-DNA and BSA interaction studies via in-vitro and in-silico approaches

Since numerous people annually pass away due to cancer, research in this field is essential. Thus a newly made and water like palladium(II) complex of formula [Pd(phen)(acac)]NO₃, where phen is 1,10-phenanthroline and acac is acetylacetonato ligand, has been synthesized by the reaction between [Pd(phen)(H₂O)₂](NO₃)₂ and sodium salt of acetylacetone in the molar ratio of 1:1. It has been structurally characterized via the methods such as conductivity measurement, elemental analysis and spectroscopic methods (FT-IR, UV-Vis and ¹H NMR). The geometry optimization of this complex at the DFT level of theory reveals that Pd(II) atom is situated in a square-planar geometry. The complex has been screened for its antitumor activity against K562 cancer cells which demonstrated efficacious activity. The interaction of above palladium(II) complex with CT-DNA as a target molecule for antitumor agents and BSA as a transport protein was studies by a variety of techniques. The results of UV-Vis absorption and fluorescence emission indicated that the Pd(II) complex interacts with EB + CT-DNA through hydrophobic and with BSA by hydrogen bonding and van der Waals forces at very low concentrations. In these processes, the fluorescence quenching mechanism of both the macromolecules seems to be the combined dynamic and static. The interaction was further supported for CT-DNA by carrying out the gel electrophoresis and viscosity measurement and for BSA by the circular dichroism and Förster resonance energy transfer experiments. Furthermore, results of partition coefficient determination showed that the [Pd(phen)(acac)]NO₃ complex is more lipophilic than that of cisplatin. Moreover, molecular docking simulation confirms the obtained results from experimental tests and reveals that the complex tends to be located at the intercalation site of DNA and Sudlow's site I of BSA.

Multi-spectroscopic, voltammetric and molecular docking studies on binding of anti-diabetic drug rosigiltazone with DNA

The binding of an anti-diabetic drug rosiglitazone (RG) with calf-thymus DNA (CT-DNA) in physiological buffer (pH 7.4) has been investigated using various spectral techniques such as UV-Vis, fluorescence, ¹H NMR and circular dichroism (CD) coupled with viscosity measurement and molecular docking studies. The binding of RG with CT-DNA results in small hypochromism without any change in absorption maximum and fluorescence quenching with hardly any shifts in emission maximum suggesting groove binding mode of interaction. The binding constant is found to be 4.2 × 10² M^-1 at 298 K. Thermodynamic analysis reveal that the binding is spontaneous and H-bonding and van der Waals forces play predominant role in the binding of RG with CT-DNA. Competitive interaction between RG and ethidium bromide with CT-DNA, viscosity measurements, KI quenching, ¹H NMR and CD studies substantiate the prosed mode of binding. Voltammetric investigations suggest that the electro-reduction of RG is an adsorption controlled process and shift of reduction peak to more negative potential, with a binding constant of 3.4 × 10³ M^-1, validates the groove binding mode of interaction between RG and CT-DNA. Molecular docking reveals that RG binds in the minor groove of DNA and the dominating interaction forces are H-bonding and hydrophobic interactions.

Characteristics, Cryoprotection Evaluation and In Vitro Release of BSA-Loaded Chitosan Nanoparticles

Chitosan nanoparticles (CS-NPs) are under increasing investigation for the delivery of therapeutic proteins, such as vaccines, interferons, and biologics. A large number of studies have been taken on the characteristics of CS-NPs, and very few of these studies have focused on the microstructure of protein-loaded NPs. In this study, we prepared the CS-NPs by an ionic gelation method, and bovine serum albumin (BSA) was used as a model protein. Dynamic high pressure microfluidization (DHPM) was utilized to post-treat the nanoparticles so as to improve the uniformity, repeatability and controllability. The BSA-loaded NPs were then characterized for particle size, Zeta potential, morphology, encapsulation efficiency (EE), loading capacity (LC), and subsequent release kinetics. To improve the long-term stability of NPs, trehalose, glucose, sucrose, and mannitol were selected respectively to investigate the performance as a cryoprotectant. Furthermore, trehalose was used to obtain re-dispersible lyophilized NPs that can significantly reduce the dosage of cryoprotectants. Multiple spectroscopic techniques were used to characterize BSA-loaded NPs, in order to explain the release process of the NPs in vitro. The experimental results indicated that CS and Tripolyphosphate pentasodium (TPP) spontaneously formed the basic skeleton of the NPs through electrostatic interactions. BSA was incorporated in the basic skeleton, adsorbed on the surface of the NPs (some of which were inlaid on the NPs), without any change in structure and function. The release profiles of the NPs showed high consistency with the multispectral results.

Assessment on the binding characteristics of dasatinib, a tyrosine kinase inhibitor to calf thymus DNA: insights from multi-spectroscopic methodologies and molecular docking as well as DFT calculation

The binding characteristics of calf thymus DNA (ct-DNA) with dasatinib (DSTN), a tyrosine kinase inhibitor was assessed through multi-spectroscopic methodologies and viscosity measurement combined with molecular docking as well as DFT calculation to understand the binding mechanism, affinity of DSTN onto ct-DNA, effect of DSTN on ct-DNA conformation, and among others. The results confirmed DSTN bound onto ct-DNA, leading to forming the DSTN-ct-DNA complex with the binding constant of 4.82 × 10³ M^-1 at 310 K. DSTN preferentially inserted to the minor groove of ct-DNA with rich A-T region, that was the binding mode of DSTN onto ct-DNA was groove binding. The enthalpic change (ΔH⁰) and entropic change (ΔS⁰) during the binding process of DSTN with ct-DNA were 128.9 kJ mol^-1 and 489.2 J mol^-1 K^-1, respectively, confirming clearly that the association of DSTN with ct-DNA was an endothermic process and the dominative driven-force was hydrophobic interaction. Meanwhile, the results also indicated that there was a certain extent of electrostatic force and hydrogen bonding, but they maybe play an auxiliary role. The CD measurement results confirmed the alteration in the helical configuration of ct-DNA but almost no change in the base stacking after binding DSTN. The results revealed that there was the obvious change in the conformation, the dipole moment, and the atomic charge distribution of DSTN in the B-DNA complexes, compared with free DSTN, to satisfy the conformational adaptation. From the obtained fronitier molecular orbitals of DSTN, it can be inferred that the nature of DSTN alters with the change of the environment around DSTN. Communicated by Ramaswamy H. Sarma.