Exploring the mechanism of interaction of glipizide with DNA: Combined in vitro and bioinformatics approach

DNA, vital for biological processes, encodes hereditary data for protein synthesis, shaping cell structure and function. Since revealing its structure, DNA has become a target for various therapeutically vital molecules, spanning antidiabetic to anticancer drugs. These agents engage with DNA-associated proteins, DNA-RNA hybrids, or bind directly to the DNA helix, triggering diverse downstream effects. These interactions disrupt vital enzymes and proteins essential for maintaining cell structure and function. Analysing drug-DNA interactions has significantly advanced our understanding of drug mechanisms. Glipizide, an antidiabetic drug, is known to cause DNA damage in adipocytes. However, its extract mechanism of DNA interaction is unknown. This study delves into the interaction between glipizide and DNA utilizing various biophysical tools and computational technique to gain insights into the interaction mechanism. Analysis of UV-visible and fluorescence data reveals the formation of complex between DNA and glipizide. The binding affinity of glipizide to DNA was of moderate strength. Examination of thermodynamic parameters at different temperatures suggests that the binding was entropically spontaneous and energetically favourable. Various experiments such as thermal melting assays, viscosity measurement, and dye displacement assays confirmed the minor grove nature of binding of glipizide with DNA. Molecular dynamics studies confirmed the glipizide forms stable complex with DNA when simulated by mimicking the physiological conditions. The binding was mainly favoured by hydrogen bonds and glipizide slightly reduced nucleotide fluctuations of DNA. The study deciphers the mechanism of interaction of glipizide with DNA at molecular levels.

Insight into the interaction of isochroman with bovine serum albumin: extensive experimental and computational investigations

The way therapeutic compounds interact with serum protein provides valuable information on their pharmacokinetics, toxicity, effectiveness, and even their structural-related information. Isochroman (IC) is a phytochemical compound obtained from the leaves of Olea europea plant. The derivatives of IC have various pharmacological properties including antidepressants, antihistamines, antiinflammation, anticonvulsants, appetite depressants, etc. The binding of small molecules to bovine serum albumin (BSA) is useful to ensure their efficacy. Thus, in this study, we have found out the binding mode of IC with BSA using several spectroscopic and in silico studies. UV and fluorescence spectroscopy suggested the complex formation between IC and BSA with a binding constant of 103 M-1. IC resulted in fluorescence quenching in BSA through static mechanism. The microenvironmental and conformational changes in BSA were confirmed using synchronous and three-dimensional studies. Site marker experiment revealed the IC binding in site-III of BSA. The influence of vitamins, metals and β-cyclodextrin (β-CD) on binding constant of IC-BSA complex was also examined. Circular dichroism spectra showed that α-helical of BSA decreased upon interaction with IC. Computational and experimental results were complimentary with one another and assisted in determining the binding sites, nature of bonds and amino acids included in the IC-BSA complex formation.Communicated by Ramaswamy H. Sarma.

Nizatidine interacts with ct-DNA causing genotoxicity and cytotoxicity: an assessment by in vitro, in vivo, and in silico studies

H2 receptor antagonists are the medication given for treating stomach ulcers, but lately, reports have shown their role in healing several malignant ulcers. The present work entails the interaction of H2 blocker nizatidine with calf thymus (ct)-DNA for determining the binding mode and energetics of the interaction. Multi-spectroscopic, calorimetric, viscometric and bioinformatic analysis revealed that nizatidine interacted with ct-DNA via groove-binding mode and is characterised by exothermic reaction. Moreover, assessment of genotoxic potential of nizatidine in vitro was carried out in peripheral human lymphocytes by alkaline comet assay. DNA damage occurred at high concentrations of nizatidine. Genotoxicity of nizatidine was also evaluated in vivo by assessing cytogenetic biomarkers viz. micronuclei formation and chromosomal aberration test. Nizatidine was able to induce micronuclei formation and chromosomal damage at high dose. Additionally, cytotoxic activity of nizatidine was determined in cancer cell lines, namely HeLa and HCT-116 and compared with the normal human cell line HEK-293 employing MTT assay. It was observed that nizatidine was more toxic towards HeLa and HCT-116 than HEK-293. Cell morphology analysis by compound inverted microscopy further strengthens the finding obtained through MTT assay.

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

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

Deciphering the nature of binding of dexlansoprazole with DNA: Biophysical and docking approaches

Drugs, in general, exhibit their pharmacological activity in binding with intracellular targets. Numerous anticancer and antibacterial drugs target DNA as one of their primary intracellular targets. Dexlansoprazole (DLP) is a heterocyclic compound containing benzimidazole moiety and a proton pump inhibitor used to treat gastroesophageal reflux disease. The interaction of dexlansoprazole with calf thymus DNA (ct-DNA) has been studied using biophysical methods. The UV-Visible studies revealed a binding constant of 2.15 ± 0.3 × 104 M^-1 which is close to the value of 2.44 ± 0.3 × 10⁴ M^-1 obtained from the fluorescence studies. Competitive displacement studies using the fluorescence spectroscopic method with ethidium bromide and Hoechst as DNA markers suggested the groove binding mode of DLP in ct-DNA. The groove binding mode of DLP in ct-DNA was complemented by the results of viscosity and DNA melting studies. Further studies on the effect of ionic strength and potassium iodide on DLP binding with ct-DNA supported the observed binding mode. Circular dichroism studies reflected no significant conformational variation in ct-DNA after the interaction. The binding mode obtained from the experimental studies was corroborated by the molecular docking studies that showed the position of DLP in the minor groove of ct-DNA along with the receptor interface restudies involved in the interaction.

Molecular docking and machine learning affinity prediction of compounds identified upon softwood bark extraction to the main protease of the SARS-CoV-2 virus

Molecular docking of 234 unique compounds identified in the softwood bark (W set) is presented with a focus on their inhibition potential to the main protease of the SARS-CoV-2 virus 3CL^pro (6WQF). The docking results are compared with the docking results of 866 COVID19-related compounds (S set). Furthermore, machine learning (ML) prediction of docking scores of the W set is presented using the S set trained TensorFlow, XGBoost, and SchNetPack ML approaches. Docking scores are evaluated with the Autodock 4.2.6 software. Four compounds in the W set achieve a docking score below −13 kcal/mol, with (+)-lariciresinol 9′-p-coumarate (CID 11497085) achieving the best docking score (−15 kcal/mol) within the W and S sets. In addition, 50% of W set docking scores are found below −8 kcal/mol and 25% below −10 kcal/mol. Therefore, the compounds identified in the softwood bark, show potential for antiviral activity upon extraction or further derivatization. The W set molecular docking studies are validated by means of molecular dynamics (five best compounds). The solubility (Log S, ESOL) and druglikeness of the best docking compounds in S and W sets are compared to evaluate the pharmacological potential of compounds identified in softwood bark.

Biochemical characterization, cytotoxic, antimutagenic, anticancer and molecular docking studies on Tecomella undulata

In this study bioassay-guided screening of Tecomella undulate was performed for its cytotoxic, antimutagenic and anticancer potential. The ariel parts were extracted on a polarity basis (methanol, dichloromethane and hexane). The in vivo toxicity was assessed on Caenorhabditis elegans, and its locomotion was affected by Tecomella undulata hexane (TUAH) the most. Ames test for antimutagenicity showed Tecomella undulata methanol (TUAM) exhibited against mutagen 2AA showed inhibition of 71.03% and 26.32% 2AA in TA98 while in in vitro MTT assay on carcinoma cell lines TUAM showed 68.1% cytotoxicity. Moreover, In resazurin assay on fibroblast cells African green monkey kidney VERO and on the panel of carcinoma cell lines, the most effective extract was TUAM on liver HepG-2 with CC50 value 117.37 ± 4.73 µg/ml followed by on lungs A549 with 142.01 ± 5.3. Furthermore, for the bioassay-guided screening, the selectivity index was calculated for TUAM CC50 ratio on HepG-2 and VERO which showed a decent 2.77 score. After column chromatography, the fraction TU-63 should remarkable cytotoxic effect in dose-response manner assay as (Hep-G2) CC50 value 11. 67 ± 1.37 µg/ml followed by (A549) CC50 value 17.23 ± 0.58 µg/ml. For qualitative analysis of anticancer potential LC-ESI-MS/MS the potential phytochemicals were identified. In silico molecular modelling against selected carcinogenic proteins. The results suggest Tecomella undulate the substantial anticancer potential which supports potential natural anticancer therapeutic drug candidate development for combating cancer.

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.

Study the interaction between juglone and calf thymus DNA by spectroscopic and molecular docking techniques

Juglone (Jug) is one of the main active substances of Cortex Juglandis Mandshuricae in a folk anti-cancer prescription. Previously, there were few studies on its interaction with DNA and mechanism of action. The present paper studied, the mechanism of action between Jug and calf thymus DNA (ctDNA) by fluorescence spectroscopy, together with ethidium bromide (EB) fluorescence probe, UV-vis absorption spectroscopy, salt effect and ctDNA melting point (T_m) experiment, resonance scattering spectroscopy and molecular docking under the simulated human physiological conditions. The experimental findings indicated that Jug quiescently quenched the fluorescence of EB-ctDNA system, characteristic absorption peak intensity of ctDNA presented a decolorization effect after the interaction of ctDNA and Jug, the interaction with ctDNA enhanced of Jug resonance scattering peak and generated new resonance scattering peak, the salt exerted less effect on the interaction between Jug and ctDNA molecules, and the interaction with Jug increased the T_m value of ctDNA by 5.0 °C The binding constant (K_A) between Jug and ctDNA was 2.12 × 10⁵ L/mol (310 K) and the number of binding sites (n) was about 1. The interaction between Jug and ctDNA was an entropically driven spontaneous and endothermic process. The results of molecular docking further showed that the naphthoquinone plane was embedded in the region between the two TA bases in the ctDNA groove, and the 5'-hydroxyl and 4-naphthoquinone groups extended to the outside of the ctDNA double helix.

Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches

β-resorcylic acid (BR) is a phytochemical which is widely used in the food industry as a flavouring agent and preservative. It has also been found to exhibit antibacterial action against several types of food-borne bacteria. DNA is the main molecular target for many small molecules of therapeutic importance. Hence, the interest is rapidly growing among the researchers to elucidate the interaction between small molecules and DNA. Thus, paving the way to design novel DNA-specific drugs. In this study, an attempt was made to examine the mechanism of binding of BR with calf thymus DNA (ctDNA) with the help of various experiments based on spectroscopy and in silico studies. The spectroscopic studies like UV absorption and fluorescence affirmed the complex formation between BR and ctDNA. The observed binding constant was in the order of 10³ M^-1 which is indicative of the groove binding mechanism. These findings were further verified by dye-displacement assay, potassium iodide quenching, urea denaturation assay, the study of the effect of ssDNA, circular dichroism and DNA thermal denaturing studies. Different temperature-based fluorescence and isothermal titration calorimetry (ITC) experiments were employed to evaluate thermodynamic parameters. The analysis of thermodynamic parameters supports the enthalpically driven, exothermic and spontaneous nature of the reaction between BR and ctDNA. The forces involved in the binding process were mainly found to be hydrogen bonding, van der Waals and hydrophobic interactions. The results obtained from the molecular docking and molecular dynamics (MD) simulation were consistent with the in vitro experiments, which support the groove binding mode of BR with ctDNA.

The interaction of folate-modified Bletilla striata polysaccharide-based micelle with bovine serum albumin

We fabricated an amphiphilic folate-modified Bletilla striata polysaccharide (FA-BSP-SA) copolymer that exhibited good biocompatibility and superior antitumor effects. This study investigated the affinity between FA-BSP-SA and bovine serum albumin (BSA) via multispetroscopic approaches. Changes in the morphology and particle size showed that FA-BSP-SA formed a blurry "protein corona". Stern-Volmer equation demonstrated that FA-BSP-SA micelles decreased the fluorescence of BSA via static quenching. The measurement results of thermodynamic parameters (entropy change, enthalpy change, and Gibbs free energy) suggested that the binding between FA-BSP-SA and BSA was spontaneous in which Van der Waals forces and hydrogen bonding played major roles. The results from synchronous fluorescence, circular dichroism, and UV spectra also revealed that BSA conformation was slightly altered by decreasing α-helical contents. In addition, the antitumor effects in vitro of Dox@FA-BSP-SA micelles and the cellular uptake behavior of micelles in 4T1 cells were decreased after incubating with BSA.

Interaction of constituents of MDT regimen for leprosy with Mycobacterium leprae HSP18: impact on its structure and function

Mycobacterium leprae, the causative organism of leprosy, harbors many antigenic proteins, and one such protein is the 18-kDa antigen. This protein belongs to the small heat shock protein family and is commonly known as HSP18. Its chaperone function plays an important role in the growth and survival of M. leprae inside infected hosts. HSP18/18-kDa antigen is often used as a diagnostic marker for determining the efficacy of multidrug therapy (MDT) in leprosy. However, whether MDT drugs (dapsone, clofazimine, and rifampicin) do interact with HSP18 and how these interactions affect its structure and chaperone function is still unclear. Here, we report evidence of HSP18-dapsone/clofazimine/rifampicin interaction and its impact on the structure and chaperone function of HSP18. These three drugs interact efficiently with HSP18 (having submicromolar binding affinity) with 1 : 1 stoichiometry. Binding of these MDT drugs to the 'α-crystallin domain' of HSP18 alters its secondary structure and tryptophan micro-environment. Furthermore, surface hydrophobicity, oligomeric size, and thermostability of the protein are reduced upon interaction with these three drugs. Eventually, all these structural alterations synergistically decrease the chaperone function of HSP18. Interestingly, the effect of rifampicin on the structure, stability, and chaperone function of this mycobacterial small heat shock protein is more pronounced than the other two MDT drugs. This reduction in the chaperone function of HSP18 may additionally abate M. leprae survivability during multidrug treatment. Altogether, this study provides a possible foundation for rational designing and development of suitable HSP18 inhibitors in the context of effective treatment of leprosy.

Biophysical and theoretical studies of the interaction between a bioactive compound 3,5-dimethoxy-4-hydroxycinnamic acid with calf thymus DNA

3,5-Dimethoxy-4-hydroxycinnamic acid commonly known as Sinapic acid is a well-known derivative of hydroxycinnamic acids, is commonly present in human diet. Due to its wide variety of pharmacological activities like antioxidant, antimicrobial, anti-inflammatory, anticancer, and anti-anxiety, it has attracted much attention for the researchers. In our previous published work we have already analyzed the interaction between sinapic acid (SA) with a model transport protein. In this work our aim is to demonstrate a detailed investigation of the binding interaction between sinapic acid with another carrier of genetic information in a living cell, the DNA. Here we have used calf thymus DNA (ct-DNA) as a model. The binding characteristic of SA with ct-DNA was investigated by different spectroscopic and theoretical tools. The spectroscopic investigation revealed that quenching of intrinsic fluorescence of SA by ct-DNA occurs through dynamic quenching mechanism. The thermodynamic parameters established the involvement of hydrogen bonding and weak van der Waals forces in the interaction. Further, the circular dichroism, competitive binding experiment with ethidium bromide and potassium iodide quenching experiment suggested that SA possibly binds to the groove position of the ct-DNA. Finally, molecular docking analysis established the SA binds to minor groove position of ct-DNA in G-C rich region through hydrogen bonding interaction. Additionally, gel electrophoresis analysis has been performed to determine the protective efficacy of SA against UVB induced DNA damage and 50 μM of SA was found to protect the DNA from UVB induced damage. We hope that our study could provide the validation of SA on behalf of therapeutics and development of next generation therapeutic drug as well as designing new efficient drug molecule and methodology for the interaction study of the drug with DNA.

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.

Cholinergic drugs bind at the minor groove and reverse induced oxidative stress of calf thymus DNA: a new perspective towards an unexplored therapeutic efficacy

Four FDA approved cholinesterase inhibitors reverse the hydrogen peroxide induced oxidative damage of ct-DNA.

Insights into the mechanism of groove binding between 4-octylphenol and calf thymus DNA

4-Octylphenol is an endocrine disruptor, belonging to environmental estrogens. It can be enriched in the human body through the food chain and may harm human health. Herein, we used a variety of spectroscopic techniques, molecular docking, and gel electrophoresis to study the interaction of 4-octylphenol and ctDNA. It was found that the mechanism of ctDNA quenching the endogenous fluorescence of 4-octylphenol was static quenching, and formed a complex. The negative enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy (ΔG°) have shown that 4-octylphenol and ctDNA spontaneously bind together under the action of hydrogen bonds and van der Waal's force. Viscosity, melting temperature and iodide quenching experiments showed that 4-octylphenol acted on the groove of ctDNA. Insignificant change in circular dichromism spectra further confirmed this binding mode. The binding sites and groups for 4-octylphenol and ctDNA interaction were identified by molecular docking. Gel electrophoresis found that 4-octylphenol at high concentrations caused DNA cleavage. Above findings may lay a theoretical foundation for understanding the toxicity mechanism of 4-octylphenol.

Hydrothermal synthesis and characterization of magnetic Fe3O4 and APTS coated Fe3O4 nanoparticles: physicochemical investigations of interaction with DNA

Magnetic nanoparticles (MNPs) especially iron oxide (Fe₃O₄) NPs have quite extensively been used for in vivo delivery of biomolecules and drugs because of their high bioconjugation efficiency. In this study, Fe₃O₄ NPs and (3-Aminopropyl) triethoxysilane (APTS) coated Fe₃O₄ NPs were synthesized and their interaction with Calf thymus (Ct) DNA has been studied in order to understand their usage in biomedical applications. Hydrothermal method was used for the NPs synthesis. Characterization of NPs was done using techniques like UV-Visible spectroscopy, FTIR spectroscopy, FE-SEM, EDAX, Zeta Sizer and powder XRD. Further, interaction studies of NPs with Ct-DNA were investigated using various physicochemical techniques. In UV-Visible studies, hypochromicity with binding constant 3.2 × 10⁵ M^-1 was observed. Binding constants calculated using fluorescence studies were found to be k = 3.2 × 10⁴ M^-1, 2.9 × 10⁴ M^-1 at 293 and 323 K respectively. Results of UV-Visible and fluorescence studies were in correlation with other techniques like UV-T_M and CD. All studies suggested alteration in DNA conformation on interaction with surface engineered Fe₃O₄ NPs, stabilizing DNA-NPs conjugate via partial intercalation and electrostatic interactions. This study may facilitate our understanding regarding the physicochemical properties and DNA-binding ability of APTS-Fe₃O₄ NPs for their further application in magnetosensitive biosensing and drug delivery. Iron oxide based magnetic nanoparticles are well known for their excellent bio-conjugation efficiency and therefore APTS-Fe₃O₄ NPs were synthesized via very simple and benign hydrothermal method. Further, the interaction of APTS-Fe₃O₄ NPs with calf thymus DNA was studied using various physicochemical techniques to explore their potential in biomedical applications.

Comparative in vitro cytotoxicity and binding investigation of artemisinin and its biogenetic precursors with ctDNA

Artemisinin (ART) and its biogenetic precursors artemisinic acid (AA) and dihydroartemisinic acid (DHAA) are important traditional medicinal herb compounds with tumor growth inhibition properties. Herein, we have studied the cytotoxicity of ART, AA, and DHAA on different cancer cell lines (H1299, A431, and HCT 116) and investigated in detail their binding mechanisms with ctDNA by using spectroscopy, cyclic voltammetry, and computational methods. The UV absorbance, cyclic voltammetry, DNA helix melting, competition binding, and circular dichroism studies suggested that the complex formation of ART-ctDNA and AA-ctDNA occurs through groove binding. However, in the case of DHAA-ctDNA interaction, electrostatic interaction plays a major role. The thermodynamic parameters, viz., ΔG 0, ΔH 0, and ΔS 0 were calculated, which showed the involvement of hydrogen bonds and van der Waals interactions for drug-ctDNA interaction. FTIR and molecular docking results suggested that ART, AA, and DHAA were bound to the A-T rich region in the minor groove of ctDNA.

Investigating the mechanism of binding of nalidixic acid with deoxyribonucleic acid and serum albumin: a biophysical and molecular docking approaches

Nalidixic acid is a bacterial DNA gyrase inhibitor and the first member of the synthetic quinolone antibiotics. It is used in the treatment of various infectious diseases like urinary tract infections, respiratory infections, sexually transmitted diseases, acute bronchitis, and sinusitis. Interactions studies are of great significance as it will be beneficial for designing new therapeutic molecules with preferable plasma solubility and its efficacy. In this paper, we have aim to ascertain the binding mode of nalidixic acid with calf thymus DNA (ct-DNA) and bovine serum albumin (BSA) through various biophysical and in silico method. UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with ct-DNA. The binding constant is in the range of 10³ M^-1, indicating the groove binding mode between ct-DNA and nalidixic acid. Groove binding mode was also validated by competitive displacement assay, potassium iodide quenching experiment, circular dichroism, DNA melting studies. In the case of BSA, UV-visible absorption and fluorescence spectroscopic experiments confirmed the formation of a complex between nalidixic acid with BSA. The value of a binding constant in the case of BSA was found to be 1.517 × 10⁵ M^-1. The site marker displacement experiment revealed the binding location of nalidixic acid to a site I in BSA. Secondary structural and microenvironmental changes also studied through circular dichroism and three-dimensional fluorescence. Furthermore, the synchronous fluorescence spectra of BSA with nalidixic acid showed that there were changes in the microenvironment around tryptophan residues. In silico molecular docking further confirmed the binding of nalidixic acid to site I in BSA and the minor groove of DNA.Communicated by Ramaswamy H. Sarma.

Synthesis, DFT studies, molecular docking, antimicrobial screening and UV fluorescence studies on ct-DNA for novel Schiff bases of 2-(1-aminobenzyl) benzimidazole

Novel Schiff bases (SBs) were synthesized by condensation of 2-(1-Amino benzyl) benzimidazole with heterocyclic and aromatic carbonyl compounds. The structural characterization was done using ¹H, ¹³C NMR, FTIR and ES-MS spectroscopic techniques. The in silico pharmacokinetics showed that nearly all compounds obeyed Lipinski rule of 5 with low toxicity and metabolic stability. The global reactivity descriptors were calculated using DFT approach. The molecular docking result of SBs with ct-DNA suggested interaction via groove binding mode. The antibacterial activity was tested against S. aureus and E. coli, indicated significant inhibition than reference drug. The compound 4d gave best results at 50 μg ml^-1 concentrations. UV/Vis and Fluorescence spectroscopy tools were used to evaluate ct-DNA binding ability of compounds 4a-e through hypochromic shift. The steady state fluorescence predicted a moderate binding constant of 1.12 × 10⁴ for 4d, indicative of non-intercalative mode.

Spectroscopic investigations on DNA binding profile of two new naphthyridine carboxamides and their application as turn-on fluorescent DNA staining probes

Two new 10-methoxydibenzo[b,h][1,6]naphthyridine-2-carboxamide derivatives (R1 and R2) have been synthesized and characterized using different spectral techniques. The binding of these probes with DNA was investigated using spectral (Electronic, fluorescence, ¹H NMR and circular dichroism) and molecular docking studies. These probes exhibited a strong fluorescence around 440 nm upon excitation around 380 nm. Electronic and competitive fluorescence titration studies, in HEPES [(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)] buffer/dimethyl sulfoxide (pH 7.4) medium, suggest that these probes bind strongly to DNA, which is substantiated by ¹H NMR study. The binding constants are calculated to be 5.3 × 10⁷ and 6.8 × 10⁶ M^-1 for R1 and R2, respectively. From the results of spectral studies, it is proposed that the mechanism of binding of these probes with DNA is through minor groove binding mode, which is further confirmed by circular dichroism and molecular docking studies. Initial cell viability screening using MTT (3-[4,5-methylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay shows that normal Vero cells are viable towards these probes at nano molar concentration, which is the concentration range employed in the present study for DNA staining (IC₅₀ in the order of 0.023 mM). The enhancement in fluorescence intensity of these probes upon binding with DNA enables the staining of DNA in agarose gel in gel electrophoresis experiment. The sensitivity of these probes is comparable with that of ethidium bromide and DNA amounts as low as 4 nano gram are detectable.Communicated by Ramaswamy H. Sarma.

DNA minor groove binding of a well known anti-mycobacterial drug dapsone: A spectroscopic, viscometric and molecular docking study

Dapsone is a sulfone drug mainly used as anti-microbial and anti-inflammatory agent for the treatment of various diseases including leprosy. Recently, its interaction with protein (bovine serum albumin) is evidenced. But, the binding propensity of this anti-mycobacterial drug towards DNA is still unknown. Also, the mode of dapsone-DNA interaction (if any) is still an unknown quantity. In this study, we have taken a thorough attempt to understand these two unknown aspects using various biophysical and in silico molecular docking techniques. Both UV-visible and fluorescence titrimetric studies indicated that dapsone binds to CT-DNA with a binding constant in order of 10⁴ M^-1. Circular dichroism, thermal denaturation and viscosity experiments revealed that dapsone binds to the grooves of CT-DNA. Competitive DNA binding studies clearly indicated the minor groove binding property of this anti-mycobacterial drug. Molecular docking provided detailed information about the formation of hydrogen bonding in the dapsone-DNA complex. This in silico study further revealed that dapsone binds to the AT-rich region of the minor groove of DNA having a relative binding energy of -6.22 kcal mol^-1. Overall, all these findings evolved from this study can be used for better understanding the medicinal importance of dapsone.

Interactions of Self-Assembled Bletilla Striata Polysaccharide Nanoparticles with Bovine Serum Albumin and Biodistribution of Its Docetaxel-Loaded Nanoparticles

: Amphiphilic copolymers of stearic acid (SA)-modified Bletilla striata polysaccharides (BSPs-SA) with three different degrees of substitution (DSs) were synthesized. The effects of DS values on the properties of BSPs-SA nanoparticles were evaluated. Drug state, cytotoxicity, and histological studies were carried out. The affinity ability of bovine serum albumin (BSA) and the BSPs-SA nanoparticles was also characterized utilizing ultraviolet and fluorescence spectroscopy. Besides, the bioavailability and tissue distribution of docetaxel (DTX)-loaded BSPs-SA nanoparticles were also assessed. The results demonstrated that the DS increase of the hydrophobic stearic acid segment increased the negative charge, encapsulation efficiency, and drug-loading capacity while decreasing the critical aggregation concentration value as well as the release rate of docetaxel from the nanoparticles. Docetaxel was encapsulated in nanoparticles at the small molecules or had an amorphous status. The inhibitory capability of DTX-loaded BSPs-SA nanoparticles against 4T1 tumor cells was superior to that of Duopafei^®. The ultraviolet and fluorescence results exhibited a strong binding affinity between BSPs-SA nanoparticles and bovine serum albumin, but the conformation of bovine serum albumin was not altered. Additionally, the area under the concentration⁻time curve (AUC₀_⁻∞) of DTX-loaded BSPs-SA nanoparticles was about 1.42-fold higher compared with Duopafei^® in tumor-bearing mice. Docetaxel levels of DTX-loaded BSPs-SA nanoparticles in some organs changed, and more docetaxel accumulated in the liver, spleen, and the tumor compared with Duopafei^®. The experimental results provided a theoretical guidance for further applications of BSPs-SA conjugates as nanocarriers for delivering anticancer drugs.

In-vitro evaluation of apoptotic effect of OEO and thymol in 2D and 3D cell cultures and the study of their interaction mode with DNA

Oliveria decumbens is an Iranian endemic plant used extensively in traditional medicine. Recently, some studies have been performed on biological effects of Oliveria essential oil (OEO). However, to our knowledge, the anticancer activity of OEO has not been reported. Based on our GC/MS analysis, the basic ingredients of OEO are thymol, carvacrol, p-cymene and γ-terpinene. Therefore, we used OEO and its main component, thymol, to explore their effects on cell growth inhibition and anticancer activity. Despite having a limited effect on L929 normal cells, OEO/thymol induced cytotoxicity in MDA-MB231 breast cancer monolayers (2D) and to a lesser extent in MDA-MB231 spheroids (3D). Flow cytometry, caspase-3 activity assay in treated monolayers/spheroids and also fluorescence staining and DNA fragmentation in treated monolayers demonstrated apoptotic death mode. Indeed, OEO/thymol increased the Reactive Oxygen Species (ROS) level leading to mitochondrial membrane potential (MMP, ΔΨm) loss, caspase-3 activation and DNA damage caused S-phase cell cycle arrest. Furthermore, immunoblotting studies revealed the activation of intrinsic and maybe extrinsic apoptosis pathways by OEO/thymol. Additionally, in-vitro experiments, indicated that OEO/thymol interacts with DNA via minor grooves confirmed by docking method. Altogether, our reports underlined the potential of OEO to be considered as a new candidate for cancer therapy.

Capecitabine as a minor groove binder of DNA: molecular docking, molecular dynamics, and multi-spectroscopic studies

The interaction mechanism and binding mode of capecitabine with ctDNA was extensively investigated using docking and molecular dynamics simulations, fluorescence and circular dichroism (CD) spectroscopy, DNA thermal denaturation studies, and viscosity measurements. The possible binding mode and acting forces on the combination between capecitabine and DNA had been predicted through molecular simulation. Results indicated that capecitabine could relatively locate stably in the G-C base-pairs-rich DNA minor groove by hydrogen bond and several weaker nonbonding forces. Fluorescence spectroscopy and fluorescence lifetime measurements confirmed that the quenching was static caused by ground state complex formation. This phenomenon indicated the formation of a complex between capecitabine and ctDNA. Fluorescence data showed that the binding constants of the complex were approximately 2 × 10⁴ M^-1. Calculated thermodynamic parameters suggested that hydrogen bond was the main force during binding, which were consistent with theoretical results. Moreover, CD spectroscopy, DNA melting studies, and viscosity measurements corroborated a groove binding mode of capecitabine with ctDNA. This binding had no effect on B-DNA conformation.