A multi-spectroscopic and molecular docking approach to investigate the interaction of antiviral drug oseltamivir with ct-DNA

Insights into dopaminergic agent cabergoline-induced DNA-destabilisation through spectroscopic, thermodynamic and molecular docking/metadynamics simulation studies

Investigating the interaction of therapeutic drugs with DNA is crucial for assessing the possibility of drugs inducing significant DNA alterations when administered. The dopaminergic drug cabergoline's (CBG) interaction with CT-DNA was investigated using multi-spectroscopic, calorimetric, electrophoresis, and computational approaches. The UV-Vis and fluorescence spectral results certified the complexation of CBG with CT-DNA. Though competitive dye displacement assay, viscosity measurements, 1H NMR, KI, and urea studies strongly evidenced the intercalation-type binding mode of CBG, the molecular docking studies disclosed CBG as a groove binder as well as a partial intercalator in the minor and major grooves of DNA, respectively. The significant distortions in the characteristic CD bands of CT-DNA and the results of GEL electrophoresis evidenced the DNA-destabilizing nature of CBG. The profound decrease of 7.3 °C in the Tm of CT-DNA in the presence of CBG reiterated CBG as a DNA destabiliser. The results of metadynamics simulation and binding studies of CBG with single-strand DNA showed that the high affinity of CBG towards ssDNA compared to the dsDNA triggered CBG to destabilise dsDNA. Interestingly, the three different thermodynamic parameters resulted in the calorimetric titration of CBG with CT-DNA, exposing the sequential binding pattern involved in the CBG/CT-DNA complexation and proposing the plausible mechanism of CBG-induced DNA destabilisation.

DNA binding studies of antifungal drug posaconazole using spectroscopic and molecular docking methods

The binding studies of DNA with small molecules have been an emerging field of research all the time since DNA as the genetic material is a major biological target for various drugs. Interpretation of small molecule-DNA binding helps in understanding their interactions with designing new drugs of greater medicinal activity. Posaconazole is an antifungal drug in the class of triazoles which are known to possess numerous pharmacological properties. In this work, the nature of the binding of posaconazole with calf-thymus DNA has been studied using spectroscopic techniques and molecular docking studies. A binding constant of the order of 10³ M^-1 was observed from UV-visible and fluorescence studies for the interaction between posaconazole and calf-thymus DNA. The fluorescence property of posaconazole was found to be quenched by calf-thymus DNA with a quenching constant of the order of 10³ M^-1. Competitive displacement of ethidium bromide and Hoechst 33258 by posaconazole using fluorescence technique suggested minor groove binding of posaconazole in calf-thymus DNA. Confirmation of the binding mode was further complemented by the viscosity measurement and DNA melting studies followed by KI quenching experiments. The studies on the effect of ionic strength on the binding suggested a possible role of electrostatic force in the interaction. Molecular docking studies reflected a crescent shape of the posaconazole within the minor groove of calf-thymus DNA validating the experimental findings showing the residues involved in the interaction.

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.

Exploring the binding characteristics of febuxostat, an inhibitor of xanthine oxidase with calf thymus DNA: Multi-spectroscopic methodologies and molecular docking

In this paper, the interacting characteristics of febuxostat (FBST), an inhibitor of xanthine oxidase for treating gout patients with hyperuricemia with calf thymus DNA (ctDNA) was investigated through multi-spectroscopic methodologies combined with theoretical calculation for understanding the interacting mode on ctDNA, affinity with ctDNA, interacting forces, as well as the alteration in the conformation of ctDNA after interacting FBST The experimental results demonstrated that interacting FBST with ctDNA formed 1:1 complex, the association constant was 913 M^-1 at 298 K, suggesting the affinity of FBST on ctDNA was very weak, the interacting mode of FBST on ctDNA was groove binding, and it inserted into the minor groove with rich A-T region of ctDNA. Based on the results of the thermodynamic analysis and theoretical calculation, it can be inferred that the dominated interacting forces between FBST and ctDNA were van der Waals forces and hydrogen bond. And, interacting FBST with ctDNA was a spontaneous, enthalpy-driven, and exothermic process because of ΔG⁰ < 0, ΔH⁰ < 0, and |ΔH⁰| > T|ΔS⁰|. The results of the circular dichroism (CD) measurements indicated the conformation of ctDNA was weakly disturbed after interacting with FBST but still maintained B-conform. The studied results offer significant insight into further clarifying whether it has genotoxicity.

Targeting Natural Polymeric DNAs with Harmane: An Insight into Binding and Thermodynamic Interaction Through Biophysical Approach

DNA is one of the major molecular targets for a broad range of anticancer drugs. Hence, interaction studies involving cellular DNA and small molecules can be highly beneficial as they often lead to rational and efficient drug design. In this study, the binding interaction of Harmane (a naturally occurring, bioactive indole alkaloid) with two natural polymeric DNAs, that is, Calf thymus (CT) DNA and Herring testis (HT) DNA has been elucidated using biophysical techniques. A ground state, 1:1 complexation, was revealed by steady-state fluorescence spectroscopy. The thermodynamic profile and energetics of the associated reaction were evaluated by temperature-dependent fluorescence spectroscopy. The spontaneity of the binding was confirmed by the negative ΔG° values in both cases. Negative enthalpy change, along with stronger positive entropic contribution, indicated the dominant electrostatic nature of the interaction and finally the entropy-driven exothermic binding process throughout. Salt-dependent studies further demonstrated the significant contribution of electrostatic interactions in ligand binding toward DNA. Infrared data substantiated the structural information of the said interactions, leading to the exploration of the structure-function relationship.

Probing the Strength and Mechanism of Binding Between Amifampridine and Calf Thymus DNA

In this work, we have investigated the strength and mechanism of amifampridine (3,4-Diaminopyridine/3,4-DAP) interaction with calf thymus DNA (ct-DNA). The existence and the strength of interaction are evaluated using circular dichroism (CD), UV-vis absorption, and differential pulse voltammogram studies. Results from UV-vis absorption technique indicate that amifampridine can significantly interact with DNA through a binding constant of Kb = 1.66 × 105 M-1 at 298 K. The mechanism of the interaction between amifampridine and DNA is also studied using ionic effect investigations, competitive fluorescence experiments, viscosity measurements, and molecular docking studies. The viscosity results indicate that amifampridine can bind to DNA via intercalation binding mode. Competitive fluorescence experiments using Acridine Orange (AO) and Hoechst 33258 (HO) probes also reveal that amifampridine binds to DNA via an intercalation mode of binding. Finally, the molecular docking studies also suggest that amifampridine tends to bind with the G-C rich region of DNA.

Electrochemical, spectroscopic, and molecular docking studies of the interaction between the anti-retroviral drug indinavir and dsDNA

In this study, an electrochemical DNA biosensor was developed using a straightforward methodology to investigate the interaction of indinavir with calf thymus double-stranded deoxyribonucleic acid (ct-dsDNA) for the first time. The decrease in the oxidation signals of deoxyguanosine (dGuo) and deoxyadenosine (dAdo), measured by differential pulse voltammetry, upon incubation with different concentrations of indinavir can be attributed to the binding mode of indinavir to ct-dsDNA. The currents of the dGuo and dAdo peaks decreased linearly with the concentration of indinavir in the range of 1.0–10.0 μg/mL. The limit of detection and limit of quantification for indinavir were 0.29 and 0.98 μg/mL, respectively, based on the dGuo signal, and 0.23 and 0.78 μg/mL, respectively, based on the dAdo signal. To gain further insights into the interaction mechanism between indinavir and ct-dsDNA, spectroscopic measurements and molecular docking simulations were performed. The binding constant (K_b) between indinavir and ct-dsDNA was calculated to be 1.64 × 10⁸ M⁻¹, based on spectrofluorometric measurements. The obtained results can offer insights into the inhibitory activity of indinavir, which could help to broaden its applications. That is, indinavir can be used to inhibit other mechanisms and/or hallmarks of viral diseases.

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Electrochemical DNA biosensor was fabricated for indinavir-DNA interaction study.

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Indinavir was interacted with ct-dsDNA and made eight hydrogen bonds.

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The Kb was calculated to be 1.64 × 10⁸ M⁻¹ by spectrofluorometry.

Introducing a pyrazolopyrimidine as a multi-tyrosine kinase inhibitor, using multi-QSAR and docking methods

In cancer disease, which is one of the problems of today's human societies, the expression of some tyrosine kinase receptors that are effective in the growth and proliferation of cancerous cells rises. Therefore, it is essential to develop and propose new drugs to target the receptors. Performing modeling calculations such as QSAR and docking makes the drug discovery process more efficient. Thus, backpropagation artificial neural network was used for multidimensional quantitative structure-activity relationship (QSAR) to identify essential features of pyrazolopyrimidine moiety, responsible for anticancer activity. The statistical parameters of the model show that multi-QSAR has sufficient validity and accuracy. According to the QSAR modeling, among 26 compounds, the interaction of eight candidates with EGFR, FGFR4, PDGFRA, and VEGFR2 was analyzed by docking modeling. The results showed that 1u compound binds to proteins in a more appropriate area (except FGFR4) with acceptable energy. The results of docking for VEGFR2 binding showed that 1u binds to the active site and binding site of receptor, and it was in the interaction with ten residues in the sites. Although the binding site of 1u molecule in the FGFR4 was not suitable, the binding free energy was excellent (- 9.22 kcal mol^-1), which was less than those two anticancer drugs of gefitinib and regorafenib. Furthermore, the values of binding free energy were - 8.69, - 9.64, and - 9.19 kcal mol^-1 for EGFR, PDGFRA, and VEGFR2, respectively. Therefore, this study introduces 1u as an anticancer agent that can inhibit the tyrosine kinase receptors.

Multi-spectroscopic and molecular docking studies on the interaction of neotame with calf thymus DNA

In this paper, we have studied the in vitro binding of neotame (NTM), an artificial sweetener, with native calf thymus DNA using different methods including spectrophotometric, spectrofluorometric, competition experiment, circular dichroism (CD), and viscosimetric techniques. From the spectrophotometric studies, the binding constant (K_b) of NTM-DNA was calculated to be 2 × 10³ M^-1. The quenching of the intrinsic fluorescence of NTM in the presence of DNA at different temperatures was also used to calculate binding constants (K_b) as well as corresponding number of binding sites (n). Moreover, the obtained results indicated that the quenching mechanism involves static quenching. By comparing the competitive fluorimetric studies with Hoechst 33258, as a known groove probe, and methylene blue, as a known intercalation probe, and iodide quenching experiments it was revealed that NTM strongly binds in the grooves of the DNA helix, which was further confirmed by CD and viscosimetric studies. In addition, a molecular docking method was employed to further investigate the binding interactions between NTM and DNA, and confirm the obtained results.

Studies on the Interaction of [SnMe2Cl2(bu2bpy)] Complex with ct-DNA Using Multispectroscopic, Atomic Force Microscopy (AFM) and Molecular Docking

The interaction of SnMe₂Cl₂(bu₂bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV-Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe₂Cl₂(bu₂bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859 nm were observed by using AFM for Sn(IV) Complex-DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO₂ group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe₂Cl₂(bu₂bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA-complex mixture confirmed the experimental results.

DNA binding and cytotoxicity studies of magnetic nanofluid containing antiviral drug oseltamivir

In this work, the possibility of preparing a nanoparticle with improved treatment properties was investigated. In this regard, synthesis, characterization, in vitro cytotoxicity and DNA binding of Fe₃O₄@oleate/oseltamivir magnetic nanoparticles (MNPs) were investigated. Fe₃O₄ nanoparticles were synthesized via chemical co-precipitation and coated by oleate bilayers. Then, Fe₃O₄@OA MNPs were functionalized with an antiviral drug (oseltamivir), for better biological applications. The MNPs were subsequently characterized by zeta sizer and Zeta potential measurements, Fourier transform infrared (FT-IR) spectroscopy, vibrating sample magnetometer (VSM) and transmission electron microscopy (TEM) analyses. The TEM image demonstrated that average sizes of Fe₃O₄@OA/oseltamivir MNPs were about 8 nm. The in vitro cytotoxicity of Fe₃O₄@OA/oseltamivir MNPs was studied against cancer cell lines (MCF-7 and MDA-MB-231) and compared with oseltamivir drug. The results illustrated that Fe₃O₄@OA/oseltamivir magnetic nanoparticles have better antiproliferative effects on the mentioned cell lines as compared with oseltamivir. Also, in vitro DNA binding studies were done by UV-Vis, circular dichroism, and Fluorescence spectroscopy. The results indicated that Fe₃O₄@OA/oseltamivir MNPs bound to DNA via groove binding. Moreover, this magnetic nanofluid has potential for magnetic hyperthermia therapy due to magnetic core of its nanoparticles. Communicated by Ramaswamy H. Sarma.

In vitro cytotoxicity and DNA/HSA interaction study of triamterene using molecular modelling and multi-spectroscopic methods

The anticancer activity of triamterene on HCT116 and CT26 colon cancer cells lines was investigated. Furthermore, the mechanism of interaction between triamterene and calf thymus DNA (ct-DNA) and also human serum albumin (HSA) was conducted using spectroscopic and molecular docking techniques. In vitro cytotoxicity of triamterene against HCT116 and CT26 cells showed promising anticancer effects with IC50 values of 31.30 and 24.45 μM, respectively. Competitive studies of the triamterene with NR (neutral red) and MB (methylene blue) as intercalator probes showed that triamterene can be replaced by these probes. The viscosity data also confirmed that triamterene binds to calf-thymus DNA through intercalation binding mode. Binding properties of triamterene with HSA in the presence of warfarin and ibuprofen showed that triamterene competes with warfarin for the site I of human serum albumin (HSA). In addition, the binding modes of triamterene with DNA and HSA were verified by molecular docking technique. Abbreviations ct-DNA calf thymus DNA CV cyclic voltammetry DNA deoxyribonucleic acid DPV differential pulse voltammetry FBS fetal bovine serum HSA human serum albumin NR neutral red MB methylene blue MTT 3-(4,5-dimethylthiazol-2yl)-2,5-diphenyltetrazoliumbromide Communicated by Ramaswamy H. Sarma.

Superstructure-Dependent Loading of DNA Origami Nanostructures with a Groove-Binding Drug

DNA origami nanostructures are regarded as powerful and versatile vehicles for targeted drug delivery. So far, DNA origami-based drug delivery strategies mostly use intercalation of the therapeutic molecules between the base pairs of the DNA origami's double helices for drug loading. The binding of nonintercalating drugs to DNA origami nanostructures, however, is less studied. Therefore, in this work, we investigate the interaction of the drug methylene blue (MB) with different DNA origami nanostructures under conditions that result in minor groove binding. We observe a noticeable effect of DNA origami superstructure on the binding affinity of MB. In particular, non-B topologies as for instance found in designs using the square lattice with 10.67 bp/turn may result in reduced binding affinity because groove binding efficiency depends on groove dimensions. Also, mechanically flexible DNA origami shapes that are prone to structural fluctuations may exhibit reduced groove binding, even though they are based on the honeycomb lattice with 10.5 bp/turn. This can be attributed to the induction of transient over- and underwound DNA topologies by thermal fluctuations. These issues should thus be considered when designing DNA origami nanostructures for drug delivery applications that employ groove-binding drugs.