Theoretical study of tautomeric structures and fluorescence spectra of Hoechst 33258

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.

Deciphering the binding mechanism of an anti-cancer phytochemical plumbagin with calf thymus DNA using biophysical and in silico techniques

Plumbagin (PLM), a plant derivative, is well known for a wide range of therapeutic effects in humans including anti-cancer, anti-inflammatory, anti-oxidant, and anti-microbial. Cytotoxic and genotoxic potential of this phytochemical has been studied which demands further insight. DNA being a major target for several drugs was taken to study against PLM to understand its effects on the cellular system. UV-Vis spectroscopy has indicated the binding of PLM to ctDNA and dye displacement assays have confirmed the formation of PLM-ctDNA complex. The insignificant changes in circular dichroism spectra suggested that PLM is not affecting the structural makeup of the ctDNA, hence the binding could be peripheral and not intercalating. Further, the relative viscosity and minimal change in melting temperature upon the complex formation supported this finding and confirmed the groove binding of PLM. Molecular docking analysis and simulation studies also show PLM as a minor groove binder to DNA and provide details on the interaction dynamics of PLM-DNA complex. Docking followed by a 100 ns simulation reveals the negative Gibbs free energy change (∆G = -6.6 kcal mol-1), and the formation of a stable complex. The PLM- DNA complex with stable dynamics was further supported by different parameters including RMSD, RMSF, SASA, Rg, and the energy profile of interaction. This study provides an insight into the cytotoxic and genotoxic mechanism of PLM which can be a crucial step forward to exploit its therapeutic potential against several diseases including cancer.

Evaluation of DNA damage induced by acesulfame potassium: spectroscopic, molecular modeling simulations and toxicity studies

Acesulfame potassium (Ace-K) is a widely used artificial sweetener that has been reported to interact with DNA and cause important genetic damage. However, the type of interaction mechanism is unknown. This study provides an approach to understanding the in vitro mechanism of Ace-K interaction with Ct-DNA using spectroscopic methods combined with molecular simulations. The hypochromic effect as obtained from UV-Vis spectra indicated the formation of the DNA-Ace-K complex in the minor groove. Further evidence for groove binding mode comes from the decrease in Hoechst-DNA fluorescence caused by increasing Ace-K concentrations, alongside no detectable change in MB-DNA emission band intensity. A negative value of ΔH and ΔS represents the hydrogen bonds and van der Waals forces between Ace-K and DNA. Based on the molecular docking, Ace-K was located between the guanine10 and 16 in DNA minor groove and stabilized by two hydrogen bonds and one π-Sulfur interaction. In vitro cell culture results showed that about 5 mg/mL of Ace-K caused the death of 85% of HUVEC cells after 48 h. Communicated by Ramaswamy H. Sarma.

Synthesis and biological evaluation of 1-phenyl-4,6-dihydrobenzo[b]pyrazolo[3,4-d]azepin-5(1H)-one/thiones as anticancer agents

Cancer is associated with uncontrolled cell proliferation invading adjoining tissues and organs. Despite the availability of several chemotherapeutic agents, the constant search for newer approaches and drugs is necessitated owing to the ever-growing challenge of resistance. Over the years, DNA has emerged as an important druggable therapeutic drug due to its role in critical cellular processes such as cell division and maintenance. Further, evading apoptosis stands out as a hallmark of cancer. Hence, designing new compounds that would target DNA and induce apoptosis plays an important role in cancer therapy. In the current work, we carried out the synthesis and anticancer evaluation of 1-aryl-4,6-dihydrobenzo[b]pyrazolo[3,4-d]azepin-5(1H)-ones/thiones (26 compounds) against selected human cancer cell lines. Among these, compounds 8ae, 8ad, 8cf, 10ad and Kenpaullone have shown good inhibitory properties against HeLa cells (IC₅₀ < 2 µM) with good selectivity over the non-cancerous human embryonic kidney (Hek293T) cells. In cell cycle analysis, the compounds 8ad and 8cf have exhibited G₂/M cell cycle arrest in HeLa cells. In addition, the compounds 8ad and 8cf induced apoptosis in a dose-dependent manner in the Annexin-V FITC staining assay. The DAPI staining clearly demonstrated the condensed and fragmented nuclei in 8ad, 8cf, 8ae and Kenpaullone-treated HeLa cells. In addition, these compounds strongly suppressed the healing after 48 h in in vitro cell migration assay. The DNA binding experiments indicated that compounds 8ae, 8cf, and 8ad as well as Kenpaullone interact with double-stranded DNA by binding in grooves which may interrupt the DNA replication and kill fast-growing cells. Molecular docking studies revealed the binding pose of 8ad and Kenpaullone at HT1 binding pocket of double-stranded DNA. Compounds 8ad and 8cf demonstrated moderate topo II inhibition which could be a possible reason for their anticancer properties. Compounds 8ad and 8cf may cause the topo II and DNA covalent complex, which leads to the inhibition of DNA replication and transcription. This eventually increases the DNA damage in cells and promotes cell apoptosis. With the above interesting biological profile, the new 1-aryl-2,6-dihydrobenzo[b]pyrazolo[3,4-d]azepin-5(4H)-one/thione derivatives have emerged as promising leads for the discovery of new anticancer agents.

Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change (ΔGmo) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (ΔvHHmo) -(50.84 ± 0.19) kJ mol^-1 and entropy change (ΔSmo) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.

A study of structure-activity relationship and anion-controlled quinolinyl Ag(I) complexes as antimicrobial and antioxidant agents as well as their interaction with macromolecules

In this communication, we feature the synthesis and in-depth characterization of a series of silver(I) complexes obtained from the complexation of quinolin-4-yl Schiff base ligands ((E)-2-((quinolin-4-ylmethylene)amino)phenol L_a, 2-(quinolin-4-yl)benzo[d]thiazole L_b, (E)-N-(2-fluorophenyl)-1-(quinolin-4-yl)methanimine L_c, (E)-N-(4-chlorophenyl)-1-(quinolin-4-yl)methanimine L_d, (E)-1-(quinolin-4-yl)-N-(p-tolyl)methanimine L_e, (E)-1-(quinolin-4-yl)-N-(thiophen-2-ylmethyl)methanimine L_f) and three different silver(I) anions (nitrate, perchlorate and triflate). Structurally, the complexes adopted different coordination geometries, which included distorted linear or distorted tetrahedral geometry. The complexes were evaluated in vitro for their potential antibacterial and antioxidant activities. In addition, their interactions with calf thymus-DNA (CT-DNA) and bovine serum albumin (BSA) were evaluated. All the complexes had a wide spectrum of effective antibacterial activity against gram-positive and gram-negative bacterial and good antioxidant properties. The interactions of the complexes with CT-DNA and BSA were observed to occur either through intercalation or through a minor groove binder, while the interaction of the complexes with BSA reveals that some of the complexes can strongly quench the fluorescence of BSA through the static mechanism. The molecular docking studies of the complexes were also done to further elucidate the modes of interaction with CT-DNA and BSA.

Deciphering the sensing of α-amyrin acetate with hs-DNA: a multipronged biological probe

In this study, we focus on the biomimetic development of small molecules and their biological sensing with DNA. The binding of herring sperm deoxyribonucleic acid (hs-DNA) with naturally occurring bioactive small molecule α-amyrin acetate (α-AA), a biomimetic - isolated from the leaves of Ficus (F.) arnottiana is investigated. Collective information from various imaging, spectroscopic and biophysical experiments provides evidence that α-AA is a minor groove sensor of hs-DNA and preferentially binds to the A-T-rich regions. Interactions of different concentrations of small molecule α-AA with hsDNA were evaluated via various analytical techniques such as UV-Vis, circular dichroism (CD) and fluorescence emission spectroscopy. Fluorescence emission spectroscopy results suggest that α-AA decreases the emission level of hsDNA. DNA minor groove sensor Hoechst 33258 and intercalative sensor EB, melting transition analysis (T M) and viscosity analysis clarified that α-AA binds to hs-DNA via a groove site. Biophysical chemistry and molecular docking studies show that hydrophobic interactions play a major role in this binding. The present research deals with a natural product biosynthesis-linked chemical-biology interface sensor as a biological probe for α-AA: hs-DNA.

Protective effect of baicalein on DNA oxidative damage and its binding mechanism with DNA: An in vitro and molecular docking study

In this work, the protective effect of baicalein on DNA oxidative damage and its possible protection mechanisms were investigated. 2-thiobarbituric acid (TBA) colorimetry and agarose gel electrophoresis study found that baicalein protected the deoxyribose residue and double-stranded backbone of DNA from the damage of hydroxyl radicals. Antioxidant analysis results showed that baicalein has excellent radicals scavenging effects and Fe²⁺ chelating ability, which might be the mechanism of baicalein protecting DNA. DNA binding studies indicated that baicalein bound to the minor groove of DNA with moderate binding affinity (K = (7.35 ± 0.91) × 10³ M^-1). Hydrogen bonding and van der Waals forces played a major role in driving the binding process. Molecular docking further confirmed the experimental results. This binding could stabilize DNA double helix structure, thereby protecting DNA from oxidative damage. This study may provide theoretical basis for designing new functional foods of baicalein for DNA damage protection.

Insight into the binding mechanism of macrolide antibiotic; erythromycin to calf thymus DNA by multispectroscopic and computational approaches

In the present study, the interactions between Erythromycin drug and calf thymus deoxyribonucleic acid (ct-DNA) were explored by multi spectroscopic techniques (UV-Visible, fluorescence, circular dichroism spectroscopies), viscosity, molecular docking simulation, and atomic force microscopy (AFM). In addition, the values of binding constant were calculated by the UV-Visible and fluorescence spectroscopy. Competitive fluorescence study with methylene blue (MB), acridine orange (AO), and Hoechst 33258 were indicated that the Erythromycin drug could displace the DNA-bound Hoechst, which displays the strong competition of Erythromycin with Hoechst to interact with the groove binding site of DNA. In addition, the observed complexes in AFM analysis comprise the chains of ct-DNA and Erythromycin with an average size of 314.05 nm. The results of thermodynamic parameter calculations (ΔS° = -332.103 ± 14 J mol^-1 K^-1 and ΔH° = -115.839 ± 0.02 kJ mol^-1) approved the critical role of van der Waals forces and hydrogen bonds in the complexation of Erythromycin-DNA. Fluorescence spectroscopy results demonstrate the existence of a static enhancement mechanism in the interaction of Erythromycin-DNA. According to the obtained results, Erythromycin drug interacts with the major groove of ct-DNA. These consequences were further supported by the molecular docking study, and it could be determined that DNA-Erythromycin docked model was in a rough correlation with our experimental results.Communicated by Ramaswamy H. Sarma.

Evaluation of substituent bioactivity and anion impact of linear and T-shaped silver(i) pyridinyl complexes as potential antiproliferative, antioxidant, antimicrobial agents and DNA- and BSA-binders

The impact of ligand substituents and anion variation on the bio-activity of pyridinyl Ag(I) complexes was evaluated. The complexes showed potential therapeutic ability with notable anticancer, antioxidant, and antimicrobial activities.

In vitro interaction of nucleoside reverse transcriptase inhibitor, didanosine with calf-thymus DNA: Insights from spectroscopic studies

Many antivirals interact with DNA and alter their expression profile. Thus, it is necessary to understand the binding mode. Didanosine, a nucleoside reverse transcriptase inhibitor, is used to treat HIV infection in patients with or without acquired immunodeficiency syndrome. Understanding the mechanism of interaction of this nucleoside reverse transcriptase inhibitor with DNA can prove useful in the development of a rational drug designing system. In vitro studies (UV-vis, fluorescence, and viscometry techniques) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) show that didanosine drug interacts with calf-thymus DNA (ct-DNA) via partial intercalative binding mode. UV-visible spectroscopy confirmed the formation didanosine-DNA complex with a binding strength of about 1.5 × 10⁵ M^-1 thus indicating their biological worth. Dye displace experiments and viscometry confirmed that didanosine partially intercalates toward DNA molecules. Negative value of Gibb's-free energy change revealed that the process is spontaneous. The thermodynamic parameters such as enthalpy change (ΔH) and entropy change (ΔS) showed that the acting forces between didanosine and ct-DNA mainly included hydrophobic interactions.

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.

Study on the interactions between B-norcholesteryl benzimidazole compounds with ct-DNA

The study of molecule-DNA interaction is very important for designing an improved therapeutic agent. In previous studies, we synthesized some B-norcholesteryl benzimidazole compounds, and the tests on cancer cells showed that these compounds had good in vitro anti-cancer activities. In order to further investigate mechanism of their actions, three different B-norcholesteryl benzimidazole compounds were selected and interaction of these compounds with the calf thymus DNA (ct-DNA) was monitored by using various methods including UV-Vis and fluorescence spectroscopic techniques, viscosity measurement, and circular dichroism (CD). The results proved a hypochromic effect accompanied with a slight red-shift due to the interaction of the molecules with ct-DNA. According to the UV-Vis and fluorescence spectra, the mentioned compounds were bound to DNA, preferentially through partial intercalation into the DNA helix. Moreover, the ethidium bromide (EB) and Hoechst 33258 competitive binding experiments were also used to confirm the interaction mode of the compounds with ct-DNA. In the Hoechst 33258 displacement experiment, no significant change in the fluorescence intensity was observed. Additional assays such as iodide quenching, viscosity, and CD spectroscopy further confirmed that intercalation should be the major binding mode of the selected compounds with DNA. The cytotoxicity of these three compounds was also evaluated by MTT method, and the results confirmed that binding ability of these compounds to DNA was consistent with their cytotoxicity behavior. The experimental results indicated a higher binding affinity for compound 3 compared to the other compounds. This research provided a better understanding on the molecular mechanism of the interaction between B-norcholesteryl benzimidazole compounds and tumor cells, and offered a beneficial perspective to the designation of novel B-norsteroidal anticancer compounds.

Synthesis, characterization and DNA interaction studies of new copper complex containing pseudoephedrine hydrochloride drug

A new copper(II) complex, [Cu(pse)(phen)Cl₂]; in which phen = 1,10-phenanthroline and pse = pseudoephedrine hydrochloride drug; was synthesized and characterized by FT-IR, Mass and UV-Vis spectroscopy in combination with computational methods. Binding interaction of this complex with calf thymus DNA (ct-DNA) has been investigated by absorption, emission, circular dichroism, molecular docking and viscosity measurements. The complex displays significant binding properties of ct-DNA. The results of fluorescence and UV-Vis absorption spectroscopy indicated that, this complex interacted with ct-DNA in a groove-binding mode, and the binding constant was 8 × 10⁴ L mol^-1. Competitive fluorimetric studies with Hoechst 33258 have shown that Cu(II) complex exhibit the ability to displace the DNA-bound Hoechst 33258 indicating that it binds to DNA in strong competition with Hoechst 33258 for the groove binding. Furthermore, the complex induces detectable changes in the CD spectrum of ct-DNA and does not induce any changes in DNA viscosity which verified the groove-binding mode. The molecular modeling results illustrated that the complex strongly binds to groove of DNA by relative binding energy of docked structure (-27.61 kJ mol^-1).

Protomers of DNA-binding dye fluoresce different colours: intrinsic photophysics of Hoechst 33258

A new form of DNA-binder Hoechst 33258 is stabilised upon desolvation. Altered optical properties include a distinct green fluorescence.

Spectrophotometric study on binding of 2-thioxanthone acetic acid with ct-DNA

Thioxanthone and its derivatives are the most remarkable molecules due to their vast variety of application such as radiation curing that is, until using them as a therapeutic drug. Therefore, in this study it was intended to use 2-Thioxanthone acetic acid with and without NaCl in Tris HCl buffer solution (pH:7.0) to represent the interaction with ct-DNA. The UV-vis absorption spectra of TXCH₂COOH in the presence of ct-DNA showed hypochromism and the intrinstic binding constant (K_b) was determined as 6 × 10³ L mol^-1. The fluoresence intensity of TXCH₂COOH with ct-DNA clearly increased up to 101% which indicated that the fluorescence intensity was very sensitive to ct-DNA concentration. The binding constant (K) and the values of number of binding sites (n) and were calculated as 1.8 × 10³ L mol^-1 and 0.69, respectively. When the quenching constants (K_sv) of free TXCH₂COOH and TXCH₂COOH, which were bonded with ct-DNA were compared, slightly changed values of Ksv were seen. Moreover, displacement assay with Hoechst 33,258 and viscosity measurements in the presence and absence of NaCl salt also confirmed the binding mode which noted the electrostatic interaction following groove binding between TXCH₂COOH and ct-DNA. Last but not least, the salt effect was examined on ct-DNA binding with TXCH₂COOH. The results of the experiments indicated that the groove binding was strengthened by NaCl whereas in the high NaCl concentration, the binding ability of TXCH₂COOH to ct-DNA was inversely affected.

Synthesis of novel coumarin nucleus-based DPA drug-like molecular entity: In vitro DNA/Cu(II) binding, DNA cleavage and pro-oxidant mechanism for anticancer action

Despite substantial research on cancer therapeutics, systemic toxicity and drug-resistance limits the clinical application of many drugs like cisplatin. Therefore, new chemotherapeutic strategies against different malignancies are needed. Targeted cancer therapy is a new paradigm for cancer therapeutics which targets pathways or chemical entities specific to cancer cells than normal ones. Unlike normal cells, cancer cells contain elevated copper which plays an integral role in angiogenesis. Copper is an important metal ion associated with chromatin DNA, particularly with guanine. Thus, targeting copper via copper-specific chelators in cancer cells can serve as an effective anticancer strategy. New pharmacophore di(2-picolyl)amine (DPA)-3(bromoacetyl) coumarin (ligand-L) was synthesized and characterized by IR, ESI-MS, 1H- and 13C-NMR. Binding ability of ligand-L to DNA/Cu(II) was evaluated using a plethora of biophysical techniques which revealed ligand-L-DNA and ligand-L-Cu(II) interaction. Competitive displacement assay and docking confirmed non-intercalative binding mode of ligand-L with ctDNA. Cyclic voltammetry confirmed ligand-L causes quasi reversible Cu(II)/Cu(I) conversion. Further, acute toxicity studies revealed no toxic effects of ligand-L on mice. To evaluate the chemotherapeutic potential and anticancer mechanism of ligand-L, DNA damage via pBR322 cleavage assay and reactive oxygen species (ROS) generation were studied. Results demonstrate that ligand-L causes DNA cleavage involving ROS generation in the presence of Cu(II). In conclusion, ligand-L causes redox cycling of Cu(II) to generate ROS which leads to oxidative DNA damage and pro-oxidant cancer cell death. These findings will establish ligand-L as a lead molecule to synthesize new molecules with better copper chelating and pro-oxidant properties against different malignancies.

DNA binding affinity of a macrocyclic copper(II) complex: Spectroscopic and molecular docking studies

The interaction of a novel macrocyclic copper(II) complex, ([CuL(ClO₄)₂] that L is 1,3,6,10,12,15-hexaazatricyclo[13.3.1.1^6,10]eicosane) with calf thymus DNA (ct-DNA) was investigated by various physicochemical techniques and molecular docking at simulated physiological conditions (pH = 7.4). The absorption spectra of the Cu(II) complex with ct-DNA showed a marked hyperchroism with 10 nm blue shift. The intrinsic binding constant (K_b) was determined as 1.25 × 10⁴ M^-1, which is more in keeping with the groove binding with DNA. Furthermore, competitive fluorimetric studies with Hoechst33258 have shown that Cu(II) complex exhibits the ability to displace the ct-DNA-bound Hoechst33258 indicating that it binds to ct-DNA in strong competition with Hoechst33258 for the groove binding. Also, no change in the relative viscosity of ct-DNA and fluorescence intensity of ct-DNA-MB complex in the present of Cu(II) complex is another evidence to groove binding. The thermodynamic parameters are calculated by van't Hoff equation, which demonstrated that hydrogen bonds and van der Waals interactions played major roles in the binding reaction. The experimental results were in agreement with the results obtained via molecular docking study.

Hybrid pharmacophore approach for bio-relevant di-imines based homobimetallic complexes incorporating functionalized dicarboxylates as co-ligands: Synthesis, spectral and structural activity dependent biological insights (in-vitro DNA and HSA binding, antioxidant and cytotoxicity)

Synthesis of bio-efficient homobimetallic complexes, [Cu₂(L¹)₂(dipic)](NO₃)₂.3H₂O (1), [Zn₂(L¹)₂(dipic)](NO₃)₂.4H₂O (2), [Cu₂(L²)₂(oxa)](NO₃)₂.4H₂O (3) and [Zn₂(L²)₂(oxa)] (NO₃)₂.5H₂O (4) was carried out using Schiff bases [(N¹E,N²E)-N¹,N²-bis(5-chlorothiophen-2-ylmethylene)-4-chlorobenzene-1,2-diamine; L¹] and [(N¹E,N²E)-N¹,N²-bis(5-chlorofuran-2-ylmethylene)-4-chlorobenzene-1,2-diamine; L²] as main ligands and dicarboxylate moieties of 2,6-pyridine dicarboxylic acid (H₂-dipic) and oxalic acid (H₂-oxa) as co-ligands, respectively in order to apprehend their structure activity relationships on the basis of pharmacophore hybrid approach. The stoichiometry, geometry, thermal stability, morphology and crystallite size of the compounds were inferred by analytical, spectral (FT-IR, ¹H NMR and ¹³C NMR and Mass), thermal (TGA/DTA), SEM and XRD studies. In-vitro DNA and HSA binding profiles of complexes were analysed by different biophysical measurements. The absorption study divulged that the observed alterations in the physico-chemical properties of complexes upon binding with DNA connoted their intercalative binding mode while fluorescence quenching mechanism was quantified by using Stern Volmer constant (K_SV)_; 1.73×10⁴ (1), 1.47×10⁴ (2), 5.65×10³ (3) and 3.60×10³M^-1 (4) which discerned that hybrid pharmacophore active metal complexes (1 and 2) exhibited efficient quenching effect with Ct-DNA in comparison to complexes (3 and 4) due to greater planarity and extent of conjugation (π-π interactions). The intercalative binding mode of complexes is further supported by competitive displacement assay by using fluorogenic dyes (EtBr and Hoechst 33258). The results of HSA fluorescence study divulged static quenching of the complexes (1-4) with K_SV values of 7.24×10⁴ (1), 6.03×10⁴ (2), 5.06×10⁴ (3) and 2.85×10⁴ (4) while K_b values; 1.16×10⁵ (1), 2.01×10⁴ (2), 5.84×10³ (3) and 8.60×10² (4) suggested them potent avid binder of HSA. Additionally, comparative estimation of scavenging properties using DPPH, superoxide(O₂^.-), hydroxyl (OH^-) and ABTS method and in-vitro cytotoxicity against different cell lines (MCF-7, HeLa and Hep G2) brought out distinct biopotency of complexes due to diverse structural features and chelation effect.

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.

Interaction of capsaicin with calf thymus DNA: A multi-spectroscopic and molecular modelling study

Studying the mode of interaction between small molecules and DNA has received much attention in recent years, as many drugs have been reported to directly interact with DNA thereby regulating the expression of many genes. Capsaicin is a capsaiciniods family phytocompound having many therapeutic applications including diabetic neuropathy, rheumatoid arthritis, prevention of DNA strand breaks and chromosomal aberrations. In this study, we have investigated the interaction of capsaicin with calf thymus DNA using a number of biophysical techniques to get an insight and better understanding of the interaction mechanism. Analysis of UV-vis absorbance spectra and fluorescence spectra indicates the formation of complex between capsaicin and Ct-DNA. Thermodynamic parameters ΔG, ΔH, and ΔS measurements were taken at different temperatures indicated that hydrogen bonding and van der Waal's forces played major role in the binding process. Additional experiments such as iodide quenching, CD spectroscopy suggested that capsaicin possibly binds to the minor groove of the Ct-DNA. These observations were further confirmed by DNA melting studies, viscosity measurements. Molecular docking provided detailed computational interaction of capsaicin with Ct-DNA which proved that capsaicin binds to Ct-DNA at minor groove. Computational molecular docking also revealed the exact sites and groups to which capsaicin interacted.

Elucidating the interaction of sulindac with calf thymus DNA: biophysical and in silico molecular modelling approach

Sulindac is one of the most effective NSAIDs and belongs to the arylalkanoic acid class.

Structure elucidation, DNA binding specificity and antiproliferative proficiency of isolated compounds from Garcinia nervosa

Garcinia nervosa is an abundant source of bioactive phytochemicals. The present paper deals with the isolation of a novel isoflavone 5,7-dihydroxy-3-(3'-hydroxy-4',5'-dimethoxyphenyl)-6-methoxy-4H-chromen-4-one (1) along with a known compound DL-Allantoin (2) from the ethanolic extract of the leaves of Garcinia nervosa (Family: Guttiferae). Their structures were elucidated on the basis of chemical and physical evidences viz. elemental analysis, UV, FT-IR, ¹H NMR, ¹³C NMR and mass spectral analysis. Single-crystal X-ray analysis was further used for the authentication of structure of both compounds (1 and 2). Interaction studies of compound (1) and (2) with ctDNA were studied by UV-Visible spectroscopy, fluorescence, KI quenching studies, competitive displacement assay and circular dichroism studies, which showed groove binding interaction (non-intercalation) of both the compounds 1 and 2 with ctDNA. However, compound 1 (K=3.9×10⁴M^-1) shows higher binding affinity to the ctDNA than compound 2 (K=1.44×10⁴M^-1). The molecular modeling results also illustrated that compound 1 strongly binds to groove of DNA by relative binding energy of docked structure -6.82kcal/mol. In addition the antiproliferative activity also showed high potential of compound 1 against MCF-7 and MDA-MB 231 cell line with IC₅₀ value 8.44±3.5μM and 6.94±2.6μM, respectively.

DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques

The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 10⁴ L mol^-1 and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure -20.61 KJ mol^-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.

Copper(II) oxide nanoparticles augment antifilarial activity of Albendazole: In vitro synergistic apoptotic impact against filarial parasite Setaria cervi

Mass treatment of lymphatic filariasis with Albendazole (ABZ), a therapeutic benzimidazole, is fraught with serious limitations such as possible drug resistance and poor macrofilaricidal activity. Therefore, we need to develop new ABZ-based formulations to improve its antifilarial effectiveness. CuO nanoparticles were used as an adjuvant with ABZ to form ABZ-CuO nanocomposite, which was characterized by UV-vis spectroscopy, FT-IR, AFM and SEM. Antifilarial activity of nanocomposite was evaluated using relative motility assay and dye exclusion test in dark and under UV light. ROS generation, antioxidant levels, lipid peroxidation and DNA fragmentation in nanocomposite treated parasites were estimated. Biophysical techniques were employed to ascertain the mode of binding of nanocomposite to parasitic DNA. Nanocomposite increases parasite mortality as compared to ABZ in dark, and its antifilarial effect was increased further under UV light. Elevated ROS production and decline of parasitic-GST and GSH levels were observed in nanocomposite treated worms in dark, and these effects were pronounced further under UV light. Nanocomposite leads to higher DNA fragmentation as compared to ABZ alone. Further, we found that nanocomposite binds parasitic DNA in an intercalative manner where it generates ROS to induce DNA damage. Thus, oxidative stress production due to ROS generation and consequent DNA fragmentation leads to apoptosis in worms. This is the first report supporting CuO nanoparticles as a potential adjuvant with ABZ against filariasis along with enhanced antifilarial activity of nanocomposite under UV light. These findings, thus, indicate that development of ABZ-loaded nanoparticle compounds may serve as promising leads for filariasis treatment.

Spectral, electrochemical, and molecular docking evaluation of the interaction of the anti-hyperthyroid drug methimazole with DNA

The interaction of native calf thymus DNA with the anti-hyperthyroid drug methimazole was investigated by different spectroscopic (UV-Vis spectrophotometry, spectroflourimetry, and circular dichroism), electrochemical (cyclic voltammetry and chronoamperometry) methods, and molecular docking calculations. The binding constant (Kb) obtained from the spectrophotometric method was 9.67 × 103 L mol−1, comparable with that of groove binding molecules. The binding mode was further investigated by following the competition between Hoechst 33258 and methimazole for DNA grooves by spectrofluorimetry. Consistent results were obtained from all experimental methods used in this study. Finally, theoretical calculations using the molecular docking method confirmed the experimental results.