Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA

Electrochemical quantification based on the interactions of nucleoside analog cladribine with dsDNA via experimental and in-silico studies

Cladribine is a deoxyadenosine analog prodrug originally developed to treat hairy-cell leukemia and other lymphoproliferative diseases. However, it is now primarily used in the treatment of relapsing types of multiple sclerosis (MS). Understanding how medications interact with dsDNA is crucial for developing more effective and efficient medications. This study aims to examine the binding behavior of cladribine with dsDNA via various analytical methods, such as heat denaturation, UV spectroscopy, fluorescence spectroscopy, electrochemistry, and viscosity tests. The binding constant (Kb) of cladribine with dsDNA has been estimated to be 2.41 × 104 ± 0.20 at 298 K using the Benesi-Hildebrand plot. Molecular docking simulations were employed to explore the dsDNA-cladribine interactions quantitatively at the molecular level. Molecular Dynamic simulations were performed to follow the stability of drug-bound DNA for 50 ns. The simulations revealed that cladribine binds to dsDNA via the minor groove region of DNA by forming hydrogen bonds mainly with Guanine's DNA bases. The post-MD analyses enabled us to follow the stability of DNA and cladribine complex. Additionally, two methods based on the electrochemical approach were developed in this study for low-level cladribine assessment using differential pulse voltammetry (DPV). The first method relies on cladribine oxidation in pH 2 phosphate buffer, while the second method uses deoxyguanosine oxidation signals resulting from cladribine and dsDNA binding in pH 4.80 acetate buffer. The analytical efficacy of the two methods was verified using cladribine concentrations ranging from 2 to 25 μM, with a limit of detection (LOD) of 0.30 and 0.92 μM, respectively. Furthermore, the study conducted percent recovery tests by employing pharmaceutical injection using both established methodologies.

Quantitative study on a simple electrochemical dsDNA-pregabalin biosensor; multi-spectroscopic, molecular docking and modelling studies

Pregabalin (PGB) is a γ-aminobutyric acid (GABA) alkylated analog prescribed to treat neuropathic pain, fibromyalgia, and postherpetic neuralgia. Using analytical, spectroscopic methods and molecular docking and molecular dynamics (MD) simulations, a detailed experimental and theoretical investigation was conducted into the binding process and interactions between PGB and double-stranded fish sperm deoxyribonucleic acid (dsDNA). It was evident from the collected experimental results that PGB binds with ds-DNA. PGB attaches to dsDNA via minor groove binding, as demonstrated by the results of electrochemical studies, UV-Vis absorption spectroscopy, and replacement study with ethidium bromide and Hoechst-32588. PGB's binding constant (Kb) with dsDNA, as determined by the Benesi-Hildebrand plot, is 2.41×104 ± 0.30 at 298 K. The fluorescence investigation indicates that PGB and dsDNA have a binding stoichiometry (n) of 1.21 ± 0.09. Molecular docking simulations were used in the research to computational determination of the interactions between PGB and dsDNA. The findings demonstrated that minor groove binding was the mechanism by which PGB interacted with dsDNA. Based on the electrochemically responsive PGB-dsDNA biosensor, we developed a technique for low-concentration detection of PGB utilizing differential pulse voltammetry (DPV). The voltammetric analysis of the peak current decrease in the deoxyadenosine oxidation signals resulting from the association between PGB and dsDNA enabled a sensitive estimation of PGB in pH 4.80 acetate buffer. The deoxyguanosine oxidation signals exhibited a linear relationship between 2 and 16 μM PGB. The values for the limit of detection (LOD) and limit of quantitation (LOQ) were 0.57 μM and 1.91 μM, respectively.

Multi-spectroscopic and in silico investigation of gambogic acid-calf thymus DNA interactions

Gambogic acid (GA), a xanthanoid compound, is derived from Garcinia Hanbury gamboge resin. Studying GA's DNA binding and targeting processes is crucial to understanding its tumor-targeting potentiality. This study used spectroscopic and in silico methods to investigate the GA-calf thymus DNA-binding interaction. The results of the UV-visible absorbance spectroscopy revealed that GA binds to DNA and forms a complex. Investigation of fluorescence quenching using ethidium bromide-DNA revealed that GA displaced ethidium bromide, and the type of quenching was static in nature, as determined by Stern-Volmer plot data. Thermodynamic analysis of the DNA-GA complex revealed a spontaneous, favorable interaction involving hydrogen bonding and hydrophobic interactions. Quenching experiments with potassium iodide, Acridine orange, and NaCl verified GA's groove-binding nature and the presence of weak electrostatic interactions. The thermal melting temperature of DNA in its native and bound states with GA did not differ significantly (69.27° C to 71.25° C), validating the binding of GA to the groove region. Furthermore, the groove-binding nature of GA was confirmed by studying its interaction with ssDNA and DNA viscosity. The methods of DSC, FT-IR, and CD spectroscopy have not revealed any structural aberrations in DNA bound with GA. Molecular docking and modeling studies revealed that GA has a groove-binding nature with DNA, which is consistent with prior experimental results. Finally, the findings shed information by which GA attaches to DNA and provide insights into its recognized anticancer effects via topoisomerase inhibition causing DNA cleavage, inhibition of cell proliferation and apoptosis.

Spectroscopic studies on noncovalent binding of nicotinamide-modified BRCA1 (856-871) analogs to calf thymus DNA

Various peptide drugs have entered the market with the development of molecular biology. Peptide drugs are used for treat diseases such as diabetes, breast cancer, and HIV infection. In this study, three nicotinamide-modified peptides were synthesized by modifying the N-terminus of BRCA1 (856-871, Y856R, K862Y, R866W) peptide with three nicotinic acid derivatives using solid-phase peptide synthesis. The results of calf thymus DNA (ctDNA) binding activity indicated that binding constants of BRCA1 (856-871, Y856R, K862Y, R866W) (P0) and three nicotinamide-modified peptides (P1, P2, and P3) to ctDNA were 1.89 × 10³, 2.97 × 10⁴, 7.61 × 10⁴, and 8.09 × 10⁴ L·mol^-1, respectively. The binding affinity of the modified peptides was superior to that of BRCA1 (856-871, Y856R, K862Y, R866W). ΔH^θ < 0 and ΔS^θ < 0 indicated that van der Waals force and hydrogen bond contributed most to peptide-ctDNA binding. Results obtained by Circular dichroism (CD) indicated that peptide binding interaction led to conformational changes in ctDNA. Ultraviolet-visible (UV) spectroscopy, ethidium bromide (EB) competition experiments, DNA melting experiments, and viscosity measurements verified that peptides interacted with ctDNA via groove binding. Ionic strength experiments manifested that electrostatic binding was also involved in peptide-ctDNA binding.

Polyamine-Drug Conjugates: Do They Boost Drug Activity?

Over the past two decades, the strategy of conjugating polyamine tails with bioactive molecules such as anticancer and antimicrobial agents, as well as antioxidant and neuroprotective scaffolds, has been widely exploited to enhance their pharmacological profile. Polyamine transport is elevated in many pathological conditions, suggesting that the polyamine portion could improve cellular and subcellular uptake of the conjugate via the polyamine transporter system. In this review, we have presented a glimpse on the polyamine conjugate scenario, classified by therapeutic area, of the last decade with the aim of highlighting achievements and fostering future developments.

2-Phenylquinoline-polyamine conjugate (QPC): Interaction with bovine serum albumin (BSA)

A novel 2-phenylquinoline-polyamine conjugate (QPC) was synthesized and characterized, its interaction with bovine serum albumin (BSA) was evaluated using UV-Vis, fluorescence and circular dichroism (CD) spectroscopy. The results showed that QPC caused a whole train of spectral variation, including enhancement of UV-vis absorption and reduction of fluorescence (FL), indicating QPC-BSA complex formed. FL results showed that the type of FL quenching waslarge static quenching, which was also accompanied with a process of dynamic quenching. Binding constants, thermodynamic parameters and docking results showed that the interaction between QPC and BSA was basically a Van der Waals, hydrogen bond and hydrophobic interaction. Synchronous and 3D-FL analysis revealed that QPC resulted in unapparent conformational alteration of BSA. The docking study suggested QPC was situated at the binding sites II of BSA, and 2-phenylquinoline moiety contributed to the hydrophobic interaction. The results of molecular dynamics revealed QPC altered the conformation of BSA, which showed that the inconsistency between experimental data and theoretical calculation results may be due to the instability of the compound.

Bioactive platinum complex of ligand bearing pyrimidine skeleton: DNA/BSA binding, molecular docking, anticancer, antioxidant and antimicrobial activities

A new octahedral platinum complex [PtLCl₄] of Schiff base ligand containing pyrimidine and morpholine skeleton (where, L is 4,6-dichloropyrimidin-5-yl)methylene)-2-morpholinoethanamine) was isolated and characterized by elemental analysis, ¹H-NMR, FTIR, UV-visible and ESI-MS techniques. DNA interaction of isolated compounds with calf thymus (CT-DNA) was explored by UV-vis absorption, fluorescence, cyclic voltametric and viscometric methods. The result shows that prepared compounds can interact with CT-DNA through electrostatic interactions. Bovine serum album (BSA) binding behavior of isolated compounds was also studied by UV-vis absorption and fluorescence techniques. Both the spectroscopic results suggest that the isolated ligand and its complex bind with BSA through static quenching. The optimized structure of ligand and platinum complex were achieved by the DFT calculations. Moreover, molecular docking of ligand and its complex were studied. These analysis results reveal that ligand has low binding affinity on DNA and BSA molecules in contrast to its complex. In vitro anticancer activity of isolated compounds toward normal cell line (NHDF) as well as cancer cell lines (MCF-7, HepG2, HeLa and A549) was studied by MTT assay. The results supports that isolated platinum complex can control the growth of cancer cells (MCF-7, 20.12 ± 1.00 µg/mL; HepG2, 32.2 ± 1.69 µg/mL; HeLa, 24.68 ± 1.29 µg/mL; A549, 23.46 ± 1.17 µg/mL) without inhibiting the normal cell line (NHDF, 109.26 ± 5.46 µg/mL). Antioxidant and antimicrobial activities of isolated compounds indicate that ligand and Pt complex are found to have good radical scavenging against four different free radicals and antimicrobial abilities on E. coli and C. albicans antimicrobial species. HighlightsPlatinum complex of Schiff base with pyrimidine and morpholine linkage was synthesized.Pt complex has better biomolecular interaction with DNA and BSA.Molecular docking of Pt complex with DNA and BSA has been studiedPt complex has good anticancer activities.Pt complex has better antioxidant and antimicrobial activities.

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.

Complete chemical shift assignment and molecular modeling studies of two chromene derivatives as potential leads for new anticancer drugs

The compounds 7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one (5) and 5-[-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione (7), were synthesized from dimedone and barbituric acid and had their three-dimensional structures and precise chemical shifts assignments obtained by Nuclear Magnetic Resonance (NMR) from ¹H, ¹³C, APT, COSY, HSQC, and HMBC spectra. Additional HOMO-LUMO DFT calculations corroborated the NMR results and pointed to the most stable stereoisomers of each compound. Besides, further docking and molecular dynamic studies suggest that the stereoisomers (9S)-7-chloro-9-(2-hydroxy-4,4-dimethyl-6-oxocyclohex-1-en-1-yl)-3,3-dimethyl-2,3,4,9-tetrahydro-1H-xanthen-1-one, and 5-[(5S)-7-chloro-2,4-dioxo-1H, 2H, 3H, 4H, 5H-chromeno[2,3-d]pyrimidin-5-yl)]-1,3-diazinane-2,4,6-trione of these compounds may act as DNA intercalators and qualify as potential leads for the development of new anticancer drugs.Communicated by Ramaswamy H. Sarma.

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.

DNA/Lysozyme-binding affinity study of novel peptides from TAT (47-57) and BRCA1 (782-786) in vitro by spectroscopic analysis

SISLL-TAT and TAT-SISLL were synthesized by modifying the N- or C-termini of cell-penetrating peptides as transacting activator of transcription TAT (47-57) by attaching BRCA1 (782-786) (SISLL). The novel peptides were synthesized through Fmoc solid-phase synthesis procedures and characterized by LCQ Fleet MS, ¹H NMR and ¹³C NMR. SISLL-TAT and TAT-SISLL displayed forceful antibacterial activities against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, and Salmonella typhimurium with low hemolysis. SISLL-TAT showed better antibacterial activity than TAT-SISLL, with the minimum inhibitory concentration (MIC) values of 10-33 μg·mL^-1. The results of the DNA-binding activities showed that both SISLL-TAT and TAT-SISLL could interact with DNA via the minor groove mode, and the binding constants were 4.97 × 10⁵ L·mol^-1 and 4.42 × 10⁵ L·mol^-1 at 310 K, respectively. Circular dichroism analysis showed slight transformation of the lysozyme secondary structure caused by SISLL-TAT and TAT-SISLL. We also found that the novel peptides SISLL-TAT and TAT-SISLL targeted bacterial DNA resulting in cell death. This explains the antibacterial mechanism of SISLL-TAT and TAT-SISLL, and is a solid theoretical basis for further designing novel and highly effective antibiotics for clinical application.

l,8-Naphthalimide based DNA intercalators and anticancer agents. A systematic review from 2007 to 2017

In this review, we describe a detailed investigation about the structural variations and relative activity of 1,8-naphthalimide based intercalators and anticancer agents. The 1,8-naphthalimides binds to the DNA via intercalation, and exert their antitumor activities through Topoisomerase I/II inhibition, photoinduced DNA damage or related mechanism. Here, our discussion focused on works published over the last ten years (2007-2017) related to therapeutic applications, in the order of cancer treatment followed by other properties of 1,8-naphthalimides. In preparing for this review, we considered that several seminal reviews have appeared over the last fifteen years and focused on closely related subjects, however, none of them is exhaustive.

Molecular spectroscopic and thermodynamic studies on the interaction of anti-platelet drug ticlopidine with calf thymus DNA

Ticlopidine is an anti-platelet drug which belongs to the thienopyridine structural family and exerts its effect by functioning as an ADP receptor inhibitor. Ticlopidine inhibits the expression of TarO gene in S. aureus and may provide protection against MRSA. Groove binding agents are known to disrupt the transcription factor DNA complex and consequently inhibit gene expression. Understanding the mechanism of interaction of ticlopidine with DNA can prove useful in the development of a rational drug designing system. At present, there is no such study on the interaction of anti-platelet drugs with nucleic acids. A series of biophysical experiments were performed to ascertain the binding mode between ticlopidine and calf thymus DNA. UV-visible and fluorescence spectroscopic experiments confirmed the formation of a complex between ticlopidine and calf thymus DNA. Moreover, the values of binding constant were found to be in the range of 10³M^-1, which is indicative of groove binding between ticlopidine and calf thymus DNA. These results were further confirmed by studying the effect of denaturation on double stranded DNA, iodide quenching, viscometric studies, thermal melting profile as well as CD spectral analysis. The thermodynamic profile of the interaction was also determined using isothermal titration calorimetric studies. The reaction was found to be endothermic and the parameters obtained were found to be consistent with those of known groove binders. In silico molecular docking studies further corroborated well with the experimental results.

Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking

The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.

Ultrasonic irradiation enhanced the ability of Fluorescein-DA-Fe(III) on sonodynamic and sonocatalytic damages of DNA molecules

The interaction of DNA with Bis [N,N-bis (carboxymethyl) aminomethyl] fluorescein-Ferrous(III) (Fluorescein-DA-Fe(III)) with dual functional (sonodynamic and sonocatalytic) activity was studied by UV-vis spectroscopy, fluorescence spectroscopy, FT-IR spectroscopy, circular dichroism (CD) spectroscopy and viscosity measurements. And then, the damage of DNA caused by Fluorescein-DA-Fe(III) under ultrasonic irradiation (US) was researched by agarose gel electrophoresis and cytotoxicity assay. Meanwhile, some influenced factors such as ultrasonic irradiation time and Fluorescein-DA-Fe(III) concentration on the damage degree of DNA molecules were also examined. As a control, for Bis [N,N-bis (carboxymethyl) aminomethyl] fluorescein (Fluorescein-DA), the same experiments were carried out. The results showed that both Fluorescein-DA-Fe(III) and Fluorescein-DA can interact with DNA molecules. Under ultrasonic irradiation, Fluorescein-DA shows sonodynamic activity, which can damage DNA molecules. While, in the presence of Fe(III) ion, the Fluorescein-DA-Fe(III) displays not only sonodynamic activity but also sonocatalytic activity under ultrasonic irradiation, which injures DNA more serious than Fluorescein-DA. The researches confirmed the dual function (sonodynamic activity and sonocatalytic activity) of Fluorescein-DA-Fe(III) and expanded the usage of Fluorescein-DA-Fe(III) as a sonosensitizer in sonodynamic therapy (SDT).

Probing the Characterization of the Interaction of Aflatoxins B1 and G1 with Calf Thymus DNA In Vitro

The binding characterization of aflatoxins with calf thymus DNA (ctDNA) under physiological conditions was investigated. Multispectroscopic techniques, ctDNA melting, viscosity measurements, and molecular docking techniques were employed to elucidate the binding mechanism of the aflatoxins with DNA. The fluorescence results indicated that both aflatoxin B1 (AFB1) and aflatoxin G1 (AFG1) bound to the ctDNA, forming complexes through hydrogen bonding. The binding constants of AFB1 and AFG1 with ctDNA reached up to 10³ L·mol-1 and 10⁴ L·mol-1, respectively, and AFG1 exhibited a higher binding propensity than that of AFB1. Furthermore, both AFB1 and AFG1 bound to the ctDNA through groove binding, as evidenced by the results of the spectroscopic, iodide quenching effect, viscosity, and ctDNA melting measurements. Changes in the circular dichroism signal manifested that both AFB1 and AFG1 induced an increase in the right-handed helicity, but only minimally influenced the base stacking of the DNA. A molecular docking study of the aflatoxin's binding with the DNA revealed a groove binding mode, which was driven mainly by hydrogen bonding. This study of aflatoxin-ctDNA interaction may provide novel insights into the toxicological effect of the mycotoxins.

Interaction of indomethacin with calf thymus DNA: a multi-spectroscopic, thermodynamic and molecular modelling approach

Indomethacin belongs to the acetic acid derivative class of non-steroidal anti-inflammatory drugs with diverse pharmacological and biological activities. Understanding the mechanism of interaction of drugs with possible target and off-target biomolecules can prove useful in the development of a rational drug designing system. In this paper, we have attempted to ascertain the mode of binding of indomethacin with calf thymus DNA (Ct-DNA) through various biophysical techniques and in silico molecular docking. Analysis of the UV-visible absorbance spectra and fluorescence emission profile of indomethacin upon addition of Ct-DNA indicates the formation of a drug-DNA complex. UV-visible absorbance and steady state fluorescence experiments revealed a binding constant on the order of 103 L mol-1, which is consistent with those of well-known groove binders. Competitive displacement studies with ethidium bromide, acridine orange and Hoechst 33258 further suggested that indomethacin binds to the minor groove of the Ct-DNA. The above observations were further confirmed by KI induced quenching experiments, DNA melting studies, CD spectral analysis and viscosity measurements. The thermodynamic parameters like spontaneous free energy (ΔG < 0) and large favourable enthalpy (ΔH < 0) obtained from isothermal calorimetry indicated the involvement of hydrogen bonding and van der Waals forces in the binding process. Molecular docking further corroborated the experimental results.

1,8-Naphthalimide: A Potent DNA Intercalator and Target for Cancer Therapy

The poor pharmacokinetics, side effects and particularly the rapid emergence of drug resistance compromise the efficiency of clinically used anticancer drugs. Therefore, the discovery of novel and effective drugs is still an extremely primary mission. Naphthalimide family is one of the highly active anticancer drug based upon effective intercalator with DNA. In this article, we review the discovery and development of 1,8-naphthalimide moiety, and, especially, pay much attention to the structural modifications and structure activity relationships. The review demonstrates how modulation of the moiety affecting naphthalimide compound for DNA binding that is achieved to afford a profile of antitumor activity. The DNA binding of imide and ring substitution at naphthalimide, bisnaphthalimide, naphthalimide-metal complexes is achieved by molecular recognition through intercalation mode. Thus, this synthetic/natural small molecule can act as a drug when activation or inhibition of DNA function, is required to cure or control the cancer disease. The present study is a review of the advances in 1,8-naphthalimide-related research, with a focus on how such derivatives are intercalated into DNA for their anticancer activities.