Characterization of interaction of calf thymus DNA with gefitinib: Spectroscopic methods and molecular docking

Interfacial interactions between DNA and polysaccharide-coated magnetic nanoparticles: Insight from simulations and experiments

In this work we examine the structural and energetic stability and the interactions between dextran-coated magnetic nanoparticles (MNPs) and a DNA oligonucleotide at ionic strength conditions that are relevant to physiological gene delivery processes. All-atom Molecular Dynamics simulations provided information at the atomic-level regarding the mechanisms responsible for the physical adsorption of Dextran on the magnetic surface and the conditions under which a successful DNA-Dextran complexation can be accomplished. Coulombic interactions were found to play the main role for the formation of the Dextran interfacial layer onto the magnetic surface while hydrogen bonding between the Dextran molecules enhanced the structural integrity of this layer. The Dextran-DNA complexation was also driven by electrostatic interactions between the two moieties. An increase of the salt concentration was found to promote DNA complexation with the DX-coated magnetic nanoparticles, through the modification of the Coulombic interactions between the DX and DNA chains, which worked synergistically with the increase in hydrogen bonding between the two macromolecules. Comparison of the behavior of the coated with the uncoated magnetic nanoparticles, highlighted the significant role of the DX interfacial layer on the DNA association to the magnetic surface. Relevant experimental results provided complementary information for the coated nanoparticle/DNA interactions at different (larger) length scales. A good qualitative agreement was found between the simulation and experimental findings. This study demonstrates that tailoring the nanoparticle coating and ionic strength can optimize the delivery of DNA by fine-tuning the favorable interfacial forces and thus the DNA/MNP binding stability.

Structural investigation of erdafitinib, an anticancer drug, with ctDNA: A spectroscopic and computational study

The interaction of drugs with DNA is crucial for understanding their mechanism of action, particularly in the context of gene expression regulation. Erdafitinib (EDB), a pan-FGFR (fibroblast growth factor receptor) inhibitor approved by the FDA, is a potent anticancer agent used primarily in the treatment of urothelial carcinoma. In this study, the binding interaction between EDB and calf thymus DNA (ctDNA) was assessed using molecular docking, UV-absorption spectroscopy, fluorescence spectroscopy, and circular dichroism (CD) spectroscopy. The absorption spectra indicated a hypochromic effect when EDB was combined with ctDNA. The binding constant (Ka) of EDB-ctDNA complex was calculated as 7.84 × 103 M-1, corresponds to a free energy change (ΔG) value of approximately -5.06 kcal/mol, indicating a moderate binding affinity. Fluorometric analysis revealed a static binding mechanism in the ground state, with a bimolecular enhancement constant (KB) of 7.56 × 1011 M-1. Displacement experiments demonstrated that EDB preferentially binds to the minor groove of ctDNA, with a Ksv value of 5.14 × 104 M-1. Further, KI quenching and CD spectroscopy confirmed the minor groove binding mode, which was associated with a decrease in the Tm from 68.28 °C to 65.84 °C, reflecting a destabilizing effect on DNA helix. Molecular docking supported these findings, showing that EDB exhibits a strong affinity for the minor groove of ctDNA and hydrogen bonding and Vander Waal interactions are the major forces involved in the binding. These results suggest that EDB primarily binds to the minor groove of ctDNA, which may play a role in its anticancer activity.

More than just DNA damage: Pt(ΙΙ)-NHC complexes derived from 4,5-diarylimidazoles augment immunogenic cell death

Platinum-based drugs are a mainstay in chemotherapy, with traditional forms exerting their work directly on DNA. In recent years, it has been observed that platinum complexes had the potential to induce immunogenic cell death (ICD) and effectively trigger antitumor immune responses. Herein, to obtain novel platinum complexes with chemo-immunological properties, a series of Pt(ΙΙ)-N-heterocyclic carbene (Pt(ΙΙ)-NHC) complexes derived from 4,5-diarylimidazoles were synthesized. Among them, the dominant complex 3f was proved to exhibit better anti-liver cancer capacity compared to cisplatin and oxaliplatin. Complex 3f showed the ability to cause DNA damage by binding to DNA. In addition, it triggered intracellular reactive oxygen species (ROS) generation, affected the function of mitochondria, and blocked cells in G0/G1 phase, ultimately induced apoptosis in liver cancer cells. Furthermore, complex 3f activated endoplasmic reticulum stress (ERS) which promoted the release of damage-associated molecular patterns (DAMPs), induced ICD and dendritic cells (DCs) maturation. Interestingly, complex 3f also upregulated PD-L1, consequently converted "cold tumors" into "hot tumors". Overall, complex 3f had the potential to be regarded as a promising chemoimmunotherapy for the treatment of liver cancer.

Dual dye-labeled aptamers for detection of dichlorvos using ratiometric fluorescence resonance energy transfer

BACKGROUND

Dichlorvos (DDVP) is an efficient and highly toxic organophosphorus pesticide. Considering its effects on human health and ecosystems, pesticide residue and pollution monitoring is of great significance. Traditional methods like chromatography with mass spectrometry are not portable or rapid because they use large instruments and complex pre-processing methods. Compared with other optional on-site detection technologies, like enzymatic and antibody methods, aptamers are advantageous because they are stable, readily modified, and inexpensive. Therefore, screening and developing a specific adapter for DDVP detection is necessary and will be of practical value.

RESULTS

We screened, modified, and compared two dual-labeled aptamer probes (Cy3-DV55-Cy5 and Cy3-DV65-Cy5). The kinetics studied showed that 5 min was sufficient for the detection reaction. Both aptamers showed selectivity for DDVP but DV55 was superior to DV65. To research the binding stabilities and the mechanism between the aptamers and DDVP, the secondary structures, melting temperatures, fluorescence quenching types, and constants were investigated. Which showed that DV55 was specific for DDVP and showed better binding than DV65. Comparison of the UV absorption and FRET for DV55 and the truncated structures suggested that loop 3 in DV55 might play an important role in the binding of DV55 to DDVP. The Cy3-DV55-Cy5 aptamer had a linear range of 0-100 μM for DDVP detection and the limit of detection was 150 nM. Simulated pesticide residue detection experiments showed that the method was simple, fast, and had acceptable recovery (89.8%-105.2 %).

SIGNIFICANCE

Pesticide detection is important but on-site detection methods are usually not portable or rapid. We developed two dual-labeled aptamer probes that could feasibly be practically applied to rapid on-site DDVP detection of pesticide residues and pollutants. This research provides experimental and theoretical data for the development and design of similar pesticide probes.

Assessing the multi-dimensional impact of lead-induced toxicity on collembola found in maize fields: From oxidative stress to genetic disruptions

The prolonged exposure of agricultural soils to heavy metals from wastewater, particularly in areas near industrial facilities, poses a significant threat to the well-being of living organisms. The World Health Organization (WHO) has established standard permissible limits for heavy metals in agricultural soils to mitigate potential health hazards. Nevertheless, some agricultural fields continue to be irrigated with wastewater containing industrial effluents. This study aimed to assess the concentration of lead in soil samples collected from agricultural fields near industrial areas. Subsequently, we determined the lethal concentration (LC50) of lead (Pb) and other heavy metals for two Collembola species, namely Folsomia candida, a standard organism for soil ecotoxicity tests, and comparing it with Proisotoma minuta. The research further examined the toxic effects of lead exposure on these two species, revealing depletion in the energy reservoirs and alterations in the tissue histology of both organisms. The study revealed that lead can induce genotoxic damage as it evidently has moderate binding affinity with the ct-DNA and hence can cause DNA fragmentation and the formation of micronuclei. Elevated lipid peroxidation (LPO) levels and protein carbonylation levels were observed, alongside a reduction in antioxidant enzymes (CAT, SOD & GPx). These findings suggest that lead disrupts the balance between oxidants and the antioxidant enzyme system, impairing defense mechanisms and consequential derogatory damage within microarthropods. The investigation elucidates a complex network of various signaling pathways compromised as a result of lead toxicity. Hence, it presents a novel perspective that underscores the pressing necessity for implementing an integrated risk assessment framework at the investigated site.

Multispectroscopic and computational techniques to study the interaction of anthraquinone appended sensor with calf thymus DNA

An anthraquinone based derivative (AQ) has been designed and synthesized to find its applications for the interactions with calf thymus DNA (ctDNA) involving various spectroscopic techniques, thermodynamic and computational approaches. The UV-vis studies pointed to interaction of AQ with ctDNA via groove binding mode, which has been further supported well by the ionic strength studies, viscosity measurement, circular dichroism and melting temperature (Tm) curves. These findings have been further validated by dye-displacement assay and molecular docking studies. The analysis of thermodynamic parameters supports that the AQ-ctDNA binding is entropy favoured and enthalpy disfavoured and main acting binding interaction is hydrophobic interaction. The outcomes of the molecular modelling suggested that AQ might have entered the A-T abundant area of the ctDNA.Communicated by Ramaswamy H. Sarma.

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.

Study of the binding interaction of salmon sperm DNA with nintedanib, a tyrosine kinase inhibitor using multi-spectroscopic, thermodynamic, and in silico approaches

The study of the intermolecular binding interaction of small molecules with DNA can guide the rational drug design with greater efficacy and improved or more selective activity. In the current study, nintedanib's binding interaction with salmon sperm DNA (ssDNA) was thoroughly investigated using UV-vis spectrophotometry, spectrofluorimetry, ionic strength measurements, viscosity measurements, thermodynamics, molecular docking, and molecular dynamic simulation techniques under physiologically simulated conditions (pH 7.4). The obtained experimental results showed that nintedanib and ssDNA had an apparent binding interaction. Nintedanib's binding constant (Kb) with ssDNA, as determined using the Benesi-Hildebrand plot, was 7.9 × 104 M-1 at 298 K, indicating a moderate binding affinity. The primary binding contact forces were hydrophobic and hydrogen bonding interactions, as verified by the enthalpy and entropy changes (ΔH0 and ΔS0), which were - 16.25 kJ.mol-1 and 39.30 J mol-1 K-1, respectively. According to the results of UV-vis spectrophotometry, viscosity assays, and competitive binding interactions with ethidium bromide or rhodamine B, the binding mode of nintedanib to ssDNA was minor groove. Molecular docking and molecular dynamic simulation studies showed that nintedanib fitted into the B-DNA minor groove's AT-rich region with high stability. This study can contribute to further understanding of nintedanib's molecular mechanisms and pharmacological effects.

Biophysical insights on the interaction of anticoagulant drug dicoumarol with calf thymus-DNA: deciphering the binding mode and binding force with thermodynamics

The biological activity of drugs is exhibited due to their interactions with bio-receptors. Dicoumarol (DIC) is a natural hydroxycoumarin and a well-known anticoagulant. DNA is the genetic material and one of the targets of numerous drugs. The interaction of DIC with calf-thymus DNA (ct-DNA) has been studied using different biophysical techniques and docking studies. The binding constant in the order of 103 to 104 M-1 was observed from spectroscopic studies. Thermodynamic studies at 4 different temperatures revealed the spontaneity of the interaction with the entropy-driven process. Marker displacement studies with competitive markers of intercalators (ethidium bromide) and groove binders (Hoechst 33258) confirmed the groove-binding nature of DIC in DNA. The groove-binding mode of DIC was complemented by different studies like viscosity measurements, DNA melting, and the effect of KI on the binding. A minor perturbation in the DNA viscosity and no significant change in the DNA melting temperature (Tm) after binding with DIC further confirms the groove binding mode. The effect of KI on the DIC and DIC-DNA system suggested the absence of DIC intercalation. The absence of significant electrostatic force was revealed from the ionic-strength effect study. Binding-induced conformational variation in ct-DNA was absent in circular dichroism studies. Molecular docking studies suggested the position of DIC within the minor groove of ct-DNA, covering three base pairs long. The outcome of this report may help in understanding the pharmacodynamics and pharmacokinetics of dicoumarol analogs and related molecules.Communicated by Ramaswamy H. Sarma.

Synthesis, crystallographic, DNA binding, and molecular docking/dynamic studies of a privileged chalcone-sulfonamide hybrid scaffold as a promising anticancer agent

In the present study, a drug-like molecular hybrid structure between chalcone and sulfonamide moieties was synthesized and characterized. The structural peculiarities of the synthesized hybrid were further verified by means of single crystal X-ray crystallography. Furthermore, its biological activity as an anticancer agent was evaluated. The synthesized model of chalcone-sulfonamide hybrid 3 was found to have potent anticancer properties against the studied cancer cell lines. Hence, the in vitro binding interaction of hybrid 3 with Calf thymus DNA (CT-DNA) was studied at a simulated physiological pH to confirm its anticancer activity for the first time. This was investigated by applying different spectroscopic techniques, ionic strength measurements, viscosity measurements, thermodynamics, molecular dynamic simulation and molecular docking studies. The obtained results showed a clear binding interaction between hybrid 3 and CT-DNA with a moderate affinity via a minor groove binding mechanism. The binding constant (Kb) at 298 K calculated from the Benesi-Hildebrand equation was found to be 3.49 × 104 M-1. The entropy and enthalpy changes (ΔS0 and ΔH0) were 204.65 J mol-1 K-1 and 35.08 KJ mol-1, respectively, indicating that hydrophobic interactions constituted the major binding forces. The results obtained from molecular docking and dynamic simulation studies confirmed the minor groove binding interaction and the stability of the formed complex. This study can contribute to further understanding of the molecular mechanism of hybrid 3 as a potential antitumor agent and can also guide future clinical and pharmacological studies for rational drug design with enhanced or more selective activity and greater efficacy.[Figure: see text]Communicated by Ramaswamy H. Sarma.

Comparative study of the interaction mechanism of astilbin, isoastilbin, and neoastilbin with CYP3A4

The interactions of human CYP3A4 with three selected isomer flavonoids, such as astilbin, isoastilbin and neoastilbin, were clarified using spectral analysis, molecular docking, and molecular dynamics simulation. During binding with the three flavonoids, the intrinsic fluorescence of CYP3A4 was statically quenched in static mode with nonradiative energy conversion. The fluorescence and ultraviolet/visible (UV/vis) data revealed that the three flavonoids had a moderate and stronger binding affinity with CYP3A4 due to the order of the Ka1 and Ka2 values ranging from 104 to 105  L·mol-1 . In addition, astilbin had the highest affinity with CYP3A4, then isoastilbin and neoastilbin, at the three experimental temperatures. Multispectral analysis confirmed that binding of the three flavonoids resulted in clear changes in the secondary structure of CYP3A4. It was found from fluorescence, UV/vis and molecular docking analyses that these three flavonoids strongly bound to CYP3A4 by means of hydrogen bonds and van der Waals forces. The key amino acids around the binding site were also elucidated. Furthermore, the stabilities of the three CYP3A4 complexes were evaluated using molecular dynamics simulation.

Insight into the binding interactions of fluorenone-pendent Schiff base with calf thymus DNA

A novel fluorenone appended Schiff base (L) has been synthesized and utilized for studying the binding interactions with Calf Thymus DNA (ct-DNA). The mechanism of binding with ct-DNA was explored by employing various spectroscopic techniques viz. UV-Vis absorption spectroscopy, fluorescence emission spectroscopy, gel-electrophoresis, circular dichroism (CD), melting studies, viscosity arrays and molecular modelling methodology. The interpretation of UV-vis absorbance spectra pointed to binding of L within minor groove of ct-DNA with the binding constant of K_b = 0.15 × 10⁴ M^-1. Dye-displacement studies with Rhodamine-B (RhB) and Ethylene Bromide (EB) in fluorescence spectroscopy verified the groove binding mode of interaction between L and ct-DNA. Melting studies, circular dichroism, and viscosity studies further elucidated the binding modes of L with ct-DNA. Thermodynamic variable measurements taken at various temperatures such as ΔG^⁰, ΔH^⁰, and ΔS^⁰ revealed that hydrophobic forces played a significant role in the binding process. The meticulous computational interaction demonstrated by molecular docking confirmed the minor groove binding of L with ct-DNA.

cRGD-targeted gold-based nanoparticles overcome EGFR-TKI resistance of NSCLC via low-temperature photothermal therapy combined with sonodynamic therapy

Epidermal growth factor receptor tyrosine kinase inhibitor (EGFR-TKI) is a first-line targeted drug for the treatment of advanced non-small cell lung cancer (NSCLC) in clinical practice, but EGFR-TKI-acquired resistance limits its therapeutic effect. To address this challenge, a novel multifunctional gold-based targeted nanoparticle-based drug delivery system is fabricated. The gold-based nanoparticle is loaded with the EGFR-TKI (gefitinib) and IR780, and the surface-modified gold nanoshell layer has a photothermal effect for thermally triggered drug release. Finally, the unique binding of cyclic arginine-glycine-aspartic acid (cRGD) to the α_vβ₃ receptor ensured that the nanoparticle (cRGD-GIPG) targeted transport into drug-resistant NSCLC cells was functional. Due to the sonodynamic properties of IR780, ultrasound (US) irradiation promoted reactive oxygen species (ROS) generation, while low-temperature photothermal therapy (PTT) not only promoted the release of drug, but also further enhanced the cytotoxic effects of ROS. In turn, it blocked the activation of TGF-β/PDLIM5/SMAD resistance pathway and induced apoptosis of drug-resistant cells through mitochondrial apoptosis, enabling the treatment of EGFR-TKI-resistant NSCLC. The low-temperature PTT combined with sonodynamic therapy (SDT) by cRGD-GIPG thus shows potent anticancer activity against EGFR-TKI-resistant NSCLC cells in vitro and in vivo. The present work provides a valuable strategy for highly targeted and EGFR-TKI-resistant reversal therapy in NSCLC.

The interaction mechanism of candidone with calf thymus DNA: A multi-spectroscopic and MD simulation study

In this investigation, the effects of candidone on the structure and conformation of DNA were evaluated by spectroscopic methods, molecular dynamics simulation, and molecular docking studies. Fluorescence emission peaks, ultraviolet-visible spectra, and molecular docking exhibited the complex formation between candidone and DNA in a groove-binding mode. Fluorescence spectroscopy results also showed a static quenching mechanism of DNA in the presence of candidone. Moreover, thermodynamic parameters demonstrated that candidone spontaneously bound to DNA with a high binding affinity. The hydrophobic interactions were the dominant forces over the binding process. Based on the Fourier transform infrared data candidone tended to attach to the A-T base pairs of the minor grooves of DNA. The thermal denaturation and circular dichroism measurements displayed that candidone caused a slight change in the DNA structure, which was confirmed by the molecular dynamics simulation results. According to the obtained findings from the molecular dynamic simulation, the structural flexibility and dynamics of DNA were altered to a more extended structure.

ACW-02 an Acridine Triazolidine Derivative Presents Antileishmanial Activity Mediated by DNA Interaction and Immunomodulation

The present study proposed the synthesis of a novel acridine derivative not yet described in the literature, chemical characterization by NMR, MS, and IR, followed by investigations of its antileishmanial potential. In vitro assays were performed to assess its antileishmanial activity against L. amazonensis strains and cytotoxicity against macrophages through MTT assay and annexin V-FITC/PI, and the ability to perform an immunomodulatory action using CBA. To investigate possible molecular targets, its interaction with DNA in vitro and in silico targets were evaluated. As results, the compound showed good antileishmanial activity, with IC50 of 6.57 (amastigotes) and 94.97 (promastigotes) µg mL-1, associated with non-cytotoxicity to macrophages (CC50 > 256.00 µg mL-1). When assessed by flow cytometry, 99.8% of macrophages remained viable. The compound induced an antileishmanial effect in infected macrophages and altered TNF-α, IL-10 and IL-6 expression, suggesting a slight immunomodulatory activity. DNA assay showed an interaction with the minor grooves due to the hyperchromic effect of 47.53% and Kb 1.17 × 106 M-1, and was sustained by docking studies. Molecular dynamics simulations and MM-PBSA calculations propose cysteine protease B as a possible target. Therefore, this study demonstrates that the new compound is a promising molecule and contributes as a model for future works.

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.

4-Chloro-orthophenylenediamine alters DNA integrity and affects cell survival: inferences from a computational, biophysical/biochemical, microscopic and cell-based study

The deleterious impact of toxic constituents of hair dyes over the human health has gained immense attention in the recent past. Their oncogenicity, mutagenicity, role in protein modification, impact on cellular metabolism has been documented. There is little information on the mechanism of reactivity of hair dye components with the nucleic acids and its implications. This work, therefore, uses computational, biophysical/biochemical, microscopic and cell-based study to analyze the interaction of monocyclic aromatic amine and a hair dye component, 4-chloro-orthophenylenediamine (4-Cl-OPD) with the DNA, its impact on DNA structure and cell survival. The results suggest that 4-Cl-OPD binds with the DNA in minor groove of the duplex involving three base pairs preferentially the G-C residues, induces strand breaks and makes DNA thermally labile through loss of hydrogen bonding/base unstacking. 4-Cl-OPD causes fragmentation of DNA, reduction in size of the molecule, alters B-DNA conformation and disrupts its secondary structure. The modified DNA gives fragmented appearance, shows broken strands and aggregation in ultra-structural analysis. 4-Cl-OPD induces ROS generation in lymphocytes, increases the comet's average tail length and reduces the viability of lymphocytes. This study forms a base for establishing the direct toxicity of 4-Cl-OPD at the molecular and cellular level through direct production of superoxide radicalCommunicated by Ramaswamy H. Sarma.

New imino-methoxy derivatives: design, synthesis, characterization, antimicrobial activity, DNA interaction and molecular docking studies

Four new diarylmethylamine imine compounds (5a-5d) were prepared in order to examine their DNA binding properties, antimicrobial activity and molecular docking. The compounds were characterized by the common spectroscopic and analytic methods. Furthermore, solid-state structure of compounds 5a and 5c were determined by single-crystal X-ray diffraction studies. The compounds were then investigated for their DNA binding properties employing UV absorption, fluorescence spectroscopy under the physiological pH condition Tris-HCl buffer at pH 7.4. The compounds 5a-5d showed moderate binding constants with Kb values of 3.56 ± 0.3 × 10⁴, 2.18 ± 0.2 × 10⁵, 1.44 ± 0.3 × 10⁵ and 2.56 ± 0.3 × 10⁴ M^-1, respectively. The molecular dockings were performed to investigate the ligand-DNA interactions. The in-silico DNA-compound interaction studies showed that the compounds interact with DNA in groove binding mode. Antimicrobial activity studies of imine compounds were tested against E. coli as bacteria, S. typhimurium, S. aureus, B. cereus, B. subtilis, and C. albicans as fungi. While all compounds show moderate activity against bacteria, no activity against fungi has been investigated.Communicated by Ramaswamy H. Sarma.

Hantzsch-Like Synthesis, DNA Photocleavage, DNA/BSA Binding, and Molecular Docking Studies of Bis(sulfanediyl)bis(tetrahydro-5-deazaflavin) Analogs Linked to Naphthalene Core

The cyclocondensation reaction of aldehydes with dimedone and bis(6-aminopyrimidin-4-one) in acetic acid led to the formation of the corresponding bis(pyrimido[4,5-b]quinoline-4,6-diones) which are known as bis(sulfanediyl)bis(tetrahydro-5-deazaflavin) analogs in a single step. Also, bis(pyrimido[4,5-b]quinoline-4,6-diones) which are linked to naphthyl core via phenoxymethyl linkage is prepared. The interactions of the synthesized compounds with DNA and bovine serum albumin (BSA) were studied. Gel electrophoresis assay was used to show the capability of the compounds to photocleave the supercoiled pBR322 plasmid DNA in UV-A (365 nm). Besides, the most photocleavable compound, bis(tetrahydropyrimido[4,5-b]quinoline-4,6-dione) linked to pyridin-3-yl at position-5 exhibits good binding affinities toward CT-DNA and BSA as supported by UV/VIS spectral studies. In addition to the experimental findings, a molecular docking simulation was performed to collect detailed binding data for this compound to both biomolecules.

Multi-spectroscopic, thermodynamic, and molecular docking/dynamic approaches for characterization of the binding interaction between calf thymus DNA and palbociclib

Studying the binding interaction between biological macromolecules and small molecules has formed the core of different research aspects. The interaction of palbociclib with calf thymus DNA at simulated physiological conditions (pH 7.4) was studied using different approaches, including spectrophotometry, spectrofluorimetry, FT-IR spectroscopy, viscosity measurements, ionic strength measurements, thermodynamic, molecular dynamic simulation, and docking studies. The obtained findings showed an apparent binding interaction between palbociclib and calf thymus DNA. Groove binding mode was confirmed from the findings of competitive binding studies with ethidium bromide or rhodamine B, UV–Vis spectrophotometry, and viscosity assessment. The binding constant (K_b) at 298 K calculated from the Benesi–Hildebrand equation was found to be 6.42 × 10³ M⁻¹. The enthalpy and entropy changes (∆H⁰ and ∆S⁰) were − 33.09 kJ mol⁻¹ and 61.78 J mol⁻¹ K⁻¹, respectively, showing that hydrophobic and hydrogen bonds constitute the primary binding forces. As indicated by the molecular docking results, palbociclib fits into the AT-rich region of the B-DNA minor groove with four base pairs long binding site. The dynamic performance and stability of the formed complex were also evaluated using molecular dynamic simulation studies. The in vitro study of the intermolecular binding interaction of palbociclib with calf thymus DNA could guide future clinical and pharmacological studies for the rational drug scheming with enhanced or more selective activity and greater efficacy.

Intrinsically Fluorescent Anti-Cancer Drugs

At present, about one-third of the total protein targets in the pharmaceutical research sector are kinase-based. While kinases have been attractive targets to combat many diseases, including cancer, selective kinase inhibition has been challenging, because of the high degree of structural homology in the active site where many kinase inhibitors bind. Despite efficacy as cancer drugs, kinase inhibitors can exhibit limited target specificity and rationalizing their target profiles in the context of precise molecular mechanisms or rearrangements is a major challenge for the field. Spectroscopic approaches such as infrared, Raman, NMR and fluorescence have the potential to provide significant insights into drug-target and drug-non-target interactions because of sensitivity to molecular environment. This review places a spotlight on the significance of fluorescence for extracting information related to structural properties, discovery of hidden conformers in solution and in target-bound state, binding properties (e.g., location of binding sites, hydrogen-bonding, hydrophobicity), kinetics as well as dynamics of kinase inhibitors. It is concluded that the information gleaned from an understanding of the intrinsic fluorescence from these classes of drugs may aid in the development of future drugs with improved side-effects and less disease resistance.

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.

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.

Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies

Buprofezin (BUP) is an insecticide which belongs to the thiadiazine structural family and known to damage DNA in mice. Though its toxic effect on human is not known clearly, understanding the mechanism of interaction of BUP with DNA can prove useful when required. Multi-spectroscopic experiments such as UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR coupled with viscosity measurements, urea effect and voltametric studies were performed to ascertain the mode of binding of BUP with calf thymus DNA (CT-DNA). Analysis of UV-Vis and fluorescence spectra indicated the formation of a complex between BUP and CT-DNA. Other experiments such as competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, effect of urea, CD, voltammetric studies and ¹H NMR spectral analysis suggested that BUP intercalates into the base pairs of CT-DNA. All these results revealed that the binding mode of BUP with CT-DNA should be intercalation and the binding constant is in the order of 10⁴ M^-1. The ΔH^o < 0 and ΔS^o < 0 suggested that H-bonding or van der Waals force was the main binding force between BUP and CT-DNA. The proposed mode of binding of BUP with CT-DNA has been visualized using in silico molecular docking and metadynamics simulation studies, which showed that the phenyl ring of BUP binds to CT-DNA via π-π stacking interaction in addition to H-bond formation.Communicated by Ramaswamy H. Sarma.

Binding and thermodynamic study of thalidomide with calf thymus DNA: Spectroscopic and computational approaches

The thalidomide-DNA interactions have been investigated in detail by numerous biophysical techniques such as UV-vis, dye displacement assay, viscosity, cyclic voltammetry, circular dichroism, molecular docking, molecular dynamic simulation, FT-IR and ¹H NMR spectroscopy. CD spectroscopy, thermal denaturation and viscosity measurement explained that thalidomide is groove binder. Molecular docking analysis highlighted that thalidomide binds trough minor groove of calf thymus DNA which also confirmed from dye displacement experiment. To our knowledge, this is the first instance thalidomide was shown to binds with calf thymus DNA. Molecular dynamic simulation indicated that the thalidomide-DNA system was stabilized by electrostatic attraction as the main interaction and mode of binding is minor groove. Our study provides a better understanding to the DNA-thalidomide binding affinity and it mechanism. Overall, all these in formations can be used for further understanding the pharmacological effects of thalidomide.

Interaction study of engeletin toward cytochrome P450 3A4 and 2D6 by multi-spectroscopy and molecular docking

The inhibitory effects of engeletin on the activities of human cytochrome P450 3A4 and 2D6 (CYP3A4 and CYP2D6) were investigated by enzyme kinetics, multi-spectroscopy and molecular docking. Engeletin was found to strongly inhibit CYP3A4 and CYP2D6, with the IC₅₀ of 1.32 μM and 2.87 μM, respectively. The inhibition modes of engeletin against CYP3A4 and CYP2D6 were a competitive type and a mixed type, respectively. The fluorescence of the two CYPs was quenched statically by engeletin, which was bound to CYP3A4 stronger than to CYP2D6 at the same temperature. Circular dichroism spectroscopy, three-dimensional fluorescence, ultraviolet-visible spectroscopy and synchronous fluorescence confirmed that the conformation and micro-environment of the two CYPs protein were changed after binding with engeletin. Molecular docking, ultraviolet-visible spectroscopy and the fluorescence data revealed that engeletin had strong binding affinity to the two CYPs through hydrogen and van der Waals forces. The findings here suggested that engeletin may cause the herb-drug interactions for its inhibition of CYP3A4 and CYP2D6 activities.

Conformational Transition-Triggered Disassembly of Therapeutic Peptide Nanomedicine for Tumor Therapy

Cationic therapeutic peptides have received widespread attention due to their excellent antibacterial and antitumor properties. However, most of these peptides have undesirable delivery efficiency and high hemolytic toxicity due to the positively charged α-helix structure containing many lysine and arginine, which may restrict its in vivo applications. Herein, a conformationally transformed therapeutic peptide Pep-HCO₃ modified with bicarbonates on guanidine groups is designed. Such a design allows Pep-HCO₃ ((nap-RAGLQFPVGRLLRRLLRRLLR) nHCO₃ ) to self-assemble into nanoparticles (NP-Pep) due to disrupting helix folding and the formation of intermolecular hydrogen bonding between bicarbonates and guanidine groups. When pH is from 7.4 to 6.5 at the tumor sites, guanidine bicarbonate can be hydrolyzed to form CO₂ and guanidine groups, resulting in the disassembling of the NP-Pep into monomers α-Pep with a positively charged α-helix structure. In vivo, NP-Pep not only inhibits the tumor growth of xenografted mice with a twofold enhanced inhibition rate compared with α-Pep treatment group, but also significantly reduces the hemolytic toxicity by responding to the pH of tumor microenvironment. Therefore, the strategy of conformational transition-triggered disassembly of nanoparticles allows efficient delivery of cationic therapeutic peptides and lowering the hemolytic toxicity, which may provide an avenue for developing high-performance cationic peptide in vivo applications.

Interaction between phloretin and insulin: a spectroscopic study

Diabetes is among the top ten deadly diseases in the world. It occurs either when the pancreas does not produce enough insulin (INS) or when the body cannot effectively use the insulin it produces. Phloretin (PHL) has a biological effect that can treat diabetes. A spectroscopic study was carried out to explore the interaction between phloretin and insulin. UV/Vis spectroscopy, fluorescence spectroscopy, and circular dichroism spectropolarimeter were used in the study. UV/Vis spectra showed that the interaction between PHL and INS produced strong absorption at a wavelength of 282 nm. The fluorescence analysis results showed that the excitation and emission occurred at 280-nm and 305-nm wavelengths, respectively. Temperature changes did not affect INS emissions. However, the interaction of PHL–INS caused a redshift at 305 to 317 nm. Temperature affected the binding constant (Ka) and the binding site (n). Ka decreased with increasing temperature and increased the binding site. The thermodynamic parameters such as enthalpy (ΔH0) and entropy (ΔS0) each had a value of − 16,514 kJ/mol and 22.65 J/mol·K. PHL and INS interaction formed hydrogen bonds and hydrophobic interaction. The free energy (ΔG0) recorded was negative. PHL and INS interactions took place spontaneously. The quenching effect was dynamic and static. KD values were greater than KS. The higher the temperature, the less was KD and KS. The appearance of two negative signals on circular dichroism (CD) spectropolarimeter implies that phloretin could induce regional configuration changes in insulin. The addition of PHL has revealed that the proportion of α-helix in the insulin stabilizes its structure. Phloretin’s stabilization and enhancement of the α-helix structural configuration in insulin indicate that phloretin can improve insulin resistance.

The Use of Molecular Docking and Spectroscopic Methods for Investigation of The Interaction Between Regorafenib with Human Serum Albumin (HSA) and Calf Thymus DNA (Ct-DNA) In The Presence Of Different Site Markers

BACKGROUND

Interactions of drugs with DNA and proteins may modify their biological activities and conformations, which effect transport and biological metabolism of drugs.

OBJECTIVE

In this study the interaction of anticancer drug regorafenib (REG) with calf thymus-DNA (ct-DNA) and human serum albumin (HSA) has been investigated Methods: Hence, for the first time, it was discovered interaction between REG with DNA and HSA using multi-spectroscopic, zeta potential measurements and molecular docking method.

RESULTS AND DISCUSSION

DNA displacement studies showed that REG does not have any effect on acridine orange and methylene blue bound DNA, though it was substantiated by displacement studies with Hoechst (as groove binder). Furthermore, the different concentrations of REG induce slight changes in the viscosity of ct-DNA. Zeta potential parameters indicated that hydrophobic interaction plays a major role in the DNA-REG complex. Results obtained from molecular docking demonstrate that the REG prefers to bind on the minor groove of DNAs than that of the major groove. Binding properties of HSA reveal that intrinsic fluorescence of HSA could be quenched by REG in a static mode. The competitive experiments in the presence of warfarin and ibuprofen (as site markers) suggested that the binding site of REG to HSA was most probably located in the subdomain IIA. Measurements of the zeta potential indicated that REG bound to HSA mainly by both electrostatic and hydrophobic interactions. It was found on docking procedures that REG could fit well into HSA subdomain IIA, which confirmed the experimental results.

CONCLUSION

In conclusion, REG can be delivered by HSA in a circulatory system and affect DNA as potential target.

Synthesis, comparative in vitro antibacterial, antioxidant and UV fluorescence studies of bis indole Schiff bases and molecular docking with ct-DNA and SARS-CoV-2 Mpro

In this study, synthesis of 15 novel bis indole-based Schiff bases (SBs) 4a-4o was conducted by condensation of 2-(1-aminobenzyl)benzimidazole with symmetrical bis-isatins linked via five alkyl chains (n = 2-6). These were subjected to ADME (absorption, distribution, metabolism and excretion), physiochemical properties, molecular docking, in vitro antibacterial and antioxidant studies. The in silico studies indicated lower toxicity with metabolic stability for nearly all the derivatives proving reliability as drug candidates. The comparative antibacterial study against Staphylococcus aureus and Escherichia coli, also showed a superior inhibition than reference drug and their mono counterparts. The increase in linker alkyl chain length and variation of substituents in indole, further predicted increased inhibition, with maximum value for compound 4o at 50 μg/ml. The in vitro calf thymus DNA (ct-DNA) binding ability of compounds 4c, 4f, 4i, 4l, 4 m, 4n, and 4o was evaluated via ultraviolet-visible and fluorescence spectroscopy techniques. A hyperchromic effect was observed with no apparent wavelength shift which predicted for the groove binding mode. A moderate binding constant for 4o, in fluorescence results, confirms groove binding. The molecular docking of 4o with ct-DNA (PDBID:1BNA) and SARS-CoV-2 M^pro (3CL protease, PDBID:6LU7) prove its efficacy as potential DNA binder and antiviral agent.

Salmon sperm DNA binding study to cabozantinib, a tyrosine kinase inhibitor: Multi-spectroscopic and molecular docking approaches

In the current work, the binding interaction of cabozantinib with salmon sperm DNA (SS-DNA) was studied under simulated physiological conditions (pH 7.4) using fluorescence emission spectroscopy, UV-Vis absorption spectroscopy, viscosity measurement, ionic strength measurement, FT-IR spectroscopy, and molecular modeling methods. The obtained experimental data demonstrated an apparent binding interaction of cabozantinib with SS-DNA. The binding constant (K_b) of cabozantinib with SS-DNA evaluated from the Benesi-Hildebrand plot was equal to 5.79 × 10⁵ at 298 K. The entropy and enthalpy changes (∆S⁰ and ∆H⁰) in the binding interaction of SS-DNA with cabozantinib were 44.13 J mol^-1 K^-1 and -19.72 KJ mol^-1, respectively, demonstrating that the basic binding interaction forces are hydrophobic and hydrogen bonding interactions. Results from UV-Vis absorption spectroscopy, competitive binding interaction with rhodamine B or ethidium bromide, and viscosity measurements revealed that cabozantinib binds to SS-DNA via minor groove binding. The molecular docking results revealed that cabozantinib fits into the AT-rich region of the B-DNA minor groove and the binding site of cabozantinib was 4 base pairs long. Moreover, cabozantinib has eight active torsions, implying a high degree of flexibility in its structure, which played a significant role in the formation of a stable cabozantinib-DNA complex.

Mono- and bis-pyrazolophthalazines: Design, synthesis, cytotoxic activity, DNA/HSA binding and molecular docking studies

In an attempt to find new potent cytotoxic compounds, several mono- and bis-pyrazolophthalazines 4a-m and 6a-h were synthesized through an efficient, one-pot, three- and pseudo five-component synthetic approach. All derivatives were evaluated for their in vitro cytotoxic activities against four human cancer cell lines of A549, HepG2, MCF-7, and HT29. Compound 4e showed low toxicity against normal cell lines (MRC-5 and MCF 10A, IC₅₀ > 200 µM) and excellent cytotoxic activity against A549 cell line with IC₅₀ value of 1.25 ± 0.19 µM, which was 1.8 times more potent than doxorubicin (IC₅₀ = 2.31 ± 0.13 µM). In addition, compound 6c exhibited remarkable cytotoxic activity against A549 and MCF-7 cell lines (IC₅₀ = 1.35 ± 0.12 and 0.49 ± 0.01 µM, respectively), more than two-fold higher than that of doxorubicin. The binding properties of the best active mono- and bis-pyrazolophthalazine (4e and 6c) with HSA and DNA were fully evaluated by various techniques including UV-Vis absorption, circular dichroism (CD), Zeta potential and dynamic light scattering analyses indicating interaction of the compounds with the secondary structure of HSA and significant change of DNA conformation, presumably via a groove binding mechanism. Additionally, molecular docking and site-selective binding studies confirmed the fundamental interaction of compounds 4e and 6c with base pairs of DNA. Compounds 4e and 6c showed promising features to be considered as potential lead structures for further studies in cancer therapy.

Novel indole-thiazole and indole-thiazolidinone derivatives as DNA groove binders

In this study, we report the synthesis of eight novel indole-thiazole and indole-thiazolidinone derivatives, as well as their ability to interact with DNA, analysed through the UV-vis absorption, fluorescence, circular dichroism (CD), viscosity techniques and molecular docking. The ctDNA interaction analysis demonstrated different spectroscopic effects and the affinity constants (Kb) calculated by the UV-vis absorption method were between 2.08 × 10⁵ and 6.99 × 10⁶ M^-1, whereas in the fluorescence suppression constants (Ksv) ranged between 0.38 and 0.77 × 10⁴ M^-1 and 0.60-7.59 × 10⁴ M^-1 using Ethidium Bromide (EB) and 4',6-Diamidino-2-phenylindole (DAPI) as fluorescent probes, respectively. Most derivatives did not alter significantly the secondary structure of the ctDNA according to the CD results. None of the compounds was able to change the relative viscosity of the ctDNA. These results prove that compounds interact with ctDNA via groove binding, which was confirmed by A-T rich oligonucleotide sequence assay with compound JF-252, suggesting the importance of both the phenyl ring coupled to C-4 thiazole ring and the bromo-unsubstituted indole nucleus.

Spectroscopic, computational and molecular docking study of Cu(ii) complexes with flavonoids: from cupric ion binding to DNA intercalation

Copper(ii) complexes with flavonoids as perspective therapeutic agents with DNA as a target molecule.

Exploring the binding mode of donepezil with calf thymus DNA using spectroscopic and molecular docking methods

Donepezil (DNP) is one of approved drugs to treat Alzheimer's disease (AD). However, the potential effect of DNP on DNA is still unclear. Therefore, the interaction of DNP with calf thymus DNA (DNA) was studied in vitro using spectroscopic and molecular docking methods. Steady-state and transient fluorescence experiments showed that there was a clear binding interaction between DNP and DNA, resulting from DNP fluorescence being quenched using DNA. DNP and DNA have one binding site between them, and the binding constant (K_b ) was 0.78 × 10⁴ L·mol^-1 at 298 K. In this binding process, hydrophobic force was the main interaction force, because enthalpy change (ΔH) and entropy change (ΔS) of DNP-DNA were 67.92 kJ·mol^-1 and 302.96 J·mol^-1 ·K^-1 , respectively. DNP bound to DNA in a groove-binding mode, which was verified using a competition displacement study and other typical spectroscopic methods. Fourier transform infrared (FTIR) spectrum results showed that DNP interacted with guanine (G) and cytosine (C) bases of DNA. The molecular docking results further supported the results of spectroscopic experiments, and suggested that both Pi-Sigma force and Pi-Alkyl force were the major hydrophobic force functioning between DNP and DNA.