Molecular spectroscopy evidence of berberine binding to DNA: comparative binding and thermodynamic profile of intercalation

An aptamer-based fluorometric method for the rapid berberine detection in Kampo medicines

BACKGROUND

Berberine (BBR), a key component in Kampo medicine, is a cationic benzylisoquinoline alkaloid whose detection plays a critical role in the quality control of these traditional remedies. Traditional methods for detecting BBR often involve complex procedures, which can be time-consuming and costly. To address this challenge, our study focuses on developing a simpler, faster, and more efficient detection method for BBR in Kampo medicine formulations.

RESULTS

We successfully developed a rapid fluorometric detection method for BBR using colloidal gold nanoparticle-based systematic evolution of ligands by exponential enrichment (GOLD-SELEX). Initially, specific single-stranded DNA (ssDNA) sequences were selected for their ability to enhance BBR's fluorescence intensity. The optimal ssDNA sequence, identified as BBR38, was further truncated to produce BBR38S, a stem-loop ssDNA that improved fluorescence upon interaction with BBR. To further enhance the fluorescence, the BBR38S aptamer underwent additional modifications, including stem truncation and nucleotide mutations, resulting in the higher fluorescence variant BBR38S-3 A10C. The final product, TetBBR38S, a tetramer version of BBR38S-3 A10C, exhibited a linear detection range of 0.780-50.0 μg mL-1 and a limit of detection of 0.369 μg mL-1. The assay demonstrated sufficient selectivity and was successfully applied to analyze 128 different Kampo medicine formulations, accurately detecting BBR content with high precision.

SIGNIFICANCE

This study represents an advancement in Kampo medicine research, marking the first successful application of an aptamer-based approach for BBR detection in complex matrices. The developed method is not only simple and rapid (with a detection time of 5 min) but also cost-effective, which is crucial for widespread application.

An intratumor bacteria-targeted DNA nanocarrier for multifaceted tumor microenvironment intervention

Intratumor bacteria, which are involved with complex tumor development mechanisms, can compromise the therapeutic efficiencies of cancer chemotherapeutics. Therefore, the development of anti-tumor agents targeting intratumor bacteria is crucial in overcoming the drug inactivation induced by bacteria colonization. In this study, a double-bundle DNA tetrahedron-based nanocarrier is developed for intratumor bacteria-targeted berberine (Ber) delivery. The combination of aptamer modification and high drug loading efficacy endow the DNA nanocarrier TA@B with enhanced delivery performance in anti-tumor therapy without obvious systemic toxicity. The loaded natural isoquinoline alkaloid Ber exhibits enhanced antimicrobial, anticancer, and immune microenvironment regulation effects, ultimately leading to efficient inhibition of tumor proliferation. This intratumor bacteria-targeted DNA nanoplatform provides a promising strategy in intervening the bacteria-related microenvironment and facilitating tumor therapy.

Unique aminothiazolyl coumarins as potential DNA and membrane disruptors towards Enterococcus faecalis

Aminothiazolyl coumarins as potentially new antimicrobial agents were designed and synthesized in an effort to overcome drug resistance. Biological activity assay revealed that some target compounds exhibited significantly inhibitory efficiencies toward bacteria and fungi including drug-resistant pathogens. Especially, aminothiazolyl 7-propyl coumarin 8b and 4-dichlorobenzyl derivative 11b exhibited bactericidal potential (MBC/MIC = 2) toward clinically drug-resistant Enterococcus faecalis with low cytotoxicity to human lung adenocarcinoma A549 cells, rapidly bactericidal effects and no obvious bacterial resistance development against E. faecalis. The preliminary antibacterial action mechanism studies suggested that compound 11b was able to disturb E. faecalis membrane effectively, and interact with bacterial DNA isolated from resistant E. faecalis through noncovalent bonds to cleave DNA, thus inhibiting the growth of E. faecalis strain. Further molecular modeling indicated that compounds 8b and 11b could bind with SER-1084 and ASP-1083 residues of gyrase-DNA complex through hydrogen bonds and hydrophobic interactions. Moreover, compound 11b showed low hemolysis and in vivo toxicity. These findings of aminothiazolyl coumarins as unique structural scaffolds might hold a large promise for the treatments of drug-resistant bacterial infection.

Hydrazyl hydroxycoumarins as new potential conquerors towards Pseudomonas aeruginosa

A class of unique hydrazyl hydroxycoumarins (HHs) as novel structural scaffold was developed to combat dreadful bacterial infections. Some HHs could effectively suppress bacterial growth at low concentrations, especially, pyridyl HH 7 exhibited a good inhibition against Pseudomonas aeruginosa 27853 with a low MIC value of 0.5 μg/mL, which was 8-fold more active than norfloxacin. Furthermore, pyridyl HH 7 with low hemolytic activity and low cytotoxicity towards NCM460 cells showed much lower trend to induce the drug-resistant development than norfloxacin. Preliminarily mechanism exploration indicated that pyridyl HH 7 could eradicate the integrity of bacterial membrane, result in the leakage of intracellular proteins, and interact with bacterial DNA gyrase via non-covalent binding, and ADME analysis manifested that compound 7 gave good pharmacokinetic properties. These results suggested that the newly developed hydrazyl hydroxycoumarins as potential multitargeting antibacterial agents should be worthy of further investigation for combating bacterial infection.

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.

Analysis of Binding Modes between Three Perfluorosulfonates and GPER Based on Computational Simulation and Multiple Spectral Methods

Perfluorinated compounds (PFCs) belong to a significant category of global environmental pollutants. Investigating the toxicological effects of PFCs within biological systems is of critical significance in various disciplines such as life sciences, environmental science, chemistry, and ecotoxicology. In this study, under simulated human physiological conditions (pH = 7.4), a combination of multiple spectroscopic techniques and computational simulations was employed to investigate the impact of perfluorinated compounds (PFCs) on the G protein-coupled estrogen receptor (GPER). Additionally, the research focused on exploring the binding modes and toxicological mechanisms between PFCs and GPER at the molecular level. All three perfluorinated sulfonic acids (PFSAs) can induce quenching of GPER fluorescence through static quenching and non-radiative energy transfer. Steady-state fluorescence calculations at different temperatures revealed apparent binding constants in the order of 106, confirming a strong binding affinity between the three PFSAs and GPER. Molecular docking studies indicated that the binding sites of PFSAs are located within the largest hydrophobic cavity in the head region of GPER, where they can engage in hydrogen bonding and hydrophobic interactions with amino acid residues within the cavity. Fourier transform infrared spectroscopy, three-dimensional fluorescence, and molecular dynamics simulations collectively indicate that proteins become more stable upon binding with small molecules. There is an overall increase in hydrophobicity, and alterations in the secondary structure of the protein are observed. This study deepens the comprehension of the effects of PFCs on the endocrine system, aiding in evaluating their potential impact on human health. It provides a basis for policy-making and environmental management while also offering insights for developing new pollution monitoring methods and drug therapies.

Conjugated Oligoelectrolyte with DNA Affinity for Enhanced Nuclear Imaging and Precise DNA Quantification

Precise DNA quantification and nuclear imaging are pivotal for clinical testing, pathological diagnosis, and drug development. The detection and localization of mitochondrial DNA serve as crucial indicators of cellular health. We introduce a novel conjugated oligoelectrolyte (COE) molecule, COE-S3, featuring a planar backbone composed of three benzene rings and terminal side chains. This unique amphiphilic structure endows COE-S3 with exceptional water solubility, a high quantum yield of 0.79, and a significant fluorescence Stokes shift (λex = 366 nm, λem = 476 nm), alongside a specific fluorescence response to DNA. The fluorescence intensity correlates proportionally with DNA concentration. COE-S3 interacts with double-stranded DNA (dsDNA) through an intercalation binding mode, exhibiting a binding constant (K) of 1.32 × 106 M-1. Its amphiphilic nature and strong DNA affinity facilitate its localization within mitochondria in living cells and nuclei in apoptotic cells. Remarkably, within 30 min of COE-S3 staining, cell vitality can be discerned through real-time nuclear fluorescence imaging of apoptotic cells. COE-S3's high DNA selectivity enables quantitative intracellular DNA analysis, providing insights into cell proliferation, differentiation, and growth. Our findings underscore COE-S3, with its strategically designed, shortened planar backbone, as a promising intercalative probe for DNA quantification and nuclear imaging.

Emodin Alcohols: Design, Synthesis, Biological Evaluation and Multitargeting Studies with DNA, RNA, and HSA

OBJECTIVE

A series of novel emodin alcohols were designed and prepared in an effort to overcome the increasing microorganism resistance.

METHODS

Novel emodin alcohols were prepared from commercial emodin and different nitrogen-containing heterocycles via different synthetic strategies, such as O-alkylation and N-alkylation. The antimicrobial activity of synthesized emodin compounds was evaluated in vitro by a two-fold serial dilution technique. The interaction of emodin compound 3d with biomolecule was researched using UV-vis spectroscopic method and fluorescence spectroscopy.

RESULTS

Emodin compound 3d containing 2-methyl-5-nitro imidazole ring showed relatively good antimicrobial activity. Notably, it exhibited equivalent activity against S. aureus in comparison to the reference drug norfloxacin (MIC = 4 μg/mL). The combination of strong active compound 3d with reference drugs showed better antimicrobial activity with less dosage and a broader antimicrobial spectrum than their separate use. Further research displayed that emodin compound 3d could intercalate into S. aureus DNA to form the 3d-DNA complex, which might correlate with the inhibitory activity. The hydrogen bonds were found between S. aureus DNA gyrase and strong active compound 3d during the docking research, which were in accordance with the spectral experiment results. The interaction with yeast RNA of compound 3d could also form a complex via hydrogen bonds. The hydrogen bonds were found to play a major role in the transportation of emodin compound 3d by human serum albumin (HSA), as confirmed by molecular simulation.

CONCLUSION

This work provides a promising starting point to optimize the structures of emodin derivatives as potent antimicrobial agents.

Benzopyrone-mediated quinolones as potential multitargeting antibacterial agents

A new type of benzopyrone-mediated quinolones (BMQs) was rationally designed and efficiently synthesized as novel potential antibacterial molecules to overcome the global increasingly serious drug resistance. Some synthesized BMQs effectively suppressed the growth of the tested strains, outperforming clinical drugs. Notably, ethylidene-derived BMQ 17a exhibited superior antibacterial potential with low MICs of 0.5-2 μg/mL to clinical drugs norfloxacin, it not only displayed rapid bactericidal performance and inhibited bacterial biofilm formation, but also showed low toxicity toward human red blood cells and normal MDA-kb2 cells. Mechanistic investigation demonstrated that BMQ 17a could effectually induce bacterial metabolic disorders and promote the enhancement of reactive oxygen species to disrupt the bacterial antioxidant defense system. It was found that the active molecule BMQ 17a could not only form supramolecular complex with lactate dehydrogenase, which disturbed the biological functions, but also effectively embed into calf thymus DNA, thus affecting the normal function of DNA and achieving cell death. This work would provide an insight into developing new molecules to reduce drug resistance and expand antibacterial spectrum.

An overview of imidazole and its analogues as potent anticancer agents

The quest for novel, physiologically active imidazoles remains an exciting topic of research among medicinal chemists. The imidazole ring is a five-membered aromatic heterocycle that is found in both natural and synthesized compounds. Multiple anticancer drug classes are currently available on the market, but concerns including toxicity, limited efficacy and solubility have lowered the overall therapeutic index. Therefore, the hunt for new potential chemotherapeutic agents persists. The development of imidazole as a reliable and safer alternative to anticancer treatment is generating much attention among experts. Tubulin or microtubule polymerization inhibition and changes in the structure and function of DNA, VEGF, topoisomerase, kinases, histone deacetylases and certain other proteins that affect gene expression are among the putative targets.

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.

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.

Multi-spectroscopic and molecular simulation methods of analysis to explore the mode of binding of Mebendazole drug with calf-thymus DNA

UV-vis, fluorescence, circular dichroism (CD) and ¹H NMR spectroscopic techniques have been employed to explore the mode of binding of Mebendazole (MBZ) drug with calf thymus DNA (CT-DNA). UV-vis and fluorescence spectral studies suggested a complex formation between the drug and nucleic acid. The fluorescence of MBZ was found to enhance upon binding with CT-DNA through a ground state complex formation with K_b in the order of 10⁴ M^-1. The thermodynamic aspects indicated that the complex formation is a spontaneous process and an entropy-driven one. ΔH⁰ > 0 and ΔS⁰ > 0 revealed that hydrophobic interaction plays a dominant role in the stabilization of the complex. Competitive dye displacement assays with ethidium bromide (EB) and Hoechst 33258 dyes and viscosity measurements pointed out that MBZ binds with CT-DNA via intercalation mode, which is confirmed by CD and ¹H NMR spectral studies as well as denaturation studies. Molecular docking analysis could not match well with the experimental results. However, molecular simulation studies and the resultant free energy surface (FES) analysis clearly showed that the benzimidazole ring of MBZ intercalated between the base pairs of the nucleic acid, which is in excellent agreement with the results of the various biophysical experiments.

Molecular Spectroscopy Evidence of 1,3,5-Tris(4-carboxyphenyl)benzene Binding to DNA: Anticancer Potential along with the Comparative Binding Profile of Intercalation via Modeling Studies

One of medicinal chemistry's top priorities is the discovery of new molecules with anticancer potential. Compounds that interact with DNA are an intriguing family of chemotherapeutic medications used to treat cancer. Studies in this area have uncovered a plethora of potential anticancer medicines, such as groove binding, alkylating, and intercalator compounds. The anticancer activity of DNA intercalators (molecules that intercalate between DNA base pairs) has drawn special interest. The current study investigated the promising anticancer drug 1,3,5-Tris(4-carboxyphenyl)benzene (H3BTB) against breast and cervical cancer cell lines. In addition, 1,3,5-Tris(4-carboxyphenyl)benzene binds to DNA by groove binding. The binding of H3BTB to DNA was found to be significant which unwinds the DNA helix. Considerable electrostatic and non-electrostatic contributions were present in the binding's free energy. The cytotoxic potential of H3BTB is effectively demonstrated by the computational study outcomes, which include molecular docking and molecular dynamics (MD) simulations. The minor groove binding for the H3BTB-DNA complex is supported by molecular docking research. This study will promote empirical investigation into the synthesis of metallic and non-metallic H3BTB derivatives and their potential use as bioactive molecules for the treatment of cancer.

A review on medicinally important heterocyclic compounds and importance of biophysical approach of underlying the insight mechanism in biological environment

Heterocyclic derivatives have more interesting biological properties which hold a remarkable place in pharmaceutical industries due to their unique physiochemical properties and ease of adaption in various biological environments. Of many, the above-said derivatives have been recently examined for their promising action against a few malignancies. Specifically, anti-cancer research has benefited from these derivatives' natural flexibility and dynamic core scaffold. In any case, concerning some other promising anti-cancer drugs, heterocyclic derivative doesn't come without deficiencies. To be a successful drug candidate it should poses Absorption, Distribution, Metabolism and Eliminations (ADME) parameter, and must also have good binding interaction towards carrier protein as well as DNA and less in toxic nature, economically feasible. In this review, we described the overview of biologically important heterocyclic derivatives and their main application in medicine. Further, we focus types of biophysical techniques to understand the binding interaction mechanism.Communicated by Ramaswamy H. Sarma.

Highly photoluminescent nitrogen-doped carbon quantum dots as a green fluorescence probe for determination of myricetin

Highly photoluminescent N-doped carbon quantum dots (N-CDs) which the quantum yield reached 63% were prepared through hydrothermal treatment. The obtained N-CDs displayed a uniform distribution of particle size, superior stability in high-salt conditions, and excellent sensitivity. A green fluorescence probe based on N-CDs was constructed for ultrasensitive determination of myricetin in vine tea on account of the static quenching. The N-CDs presented excellent linear fluorescence response in the concentration range of 0.2-40 μM and 56-112 μM and with a low detection limit of 56 nM. Additionally, the practicability of the probe was verified in spiked vine tea sample, and the satisfactory recoveries of myricetin varied from 98.8% to 101.2%, with relative standard deviations in the range of 1.52%-3.48%. It is the first time to employ N-CDs without any material modification as a fluorescence sensor to detect myricetin, which is a promising approach to expand the path for myricetin screening.

Effect of ancillary ligand on DNA and protein interaction of the two Zn (II) and Co (III) complexes: experimental and theoretical study

In the present work we have developed one mononuclear Zn(II) complex [Zn(L)(H2O)] (Complex 1) by utilizing a tetracoordinated ligand H₂L, formed by simple condensation of 2, 2 dimethyl 1,3 diamino propane and 3- ethoxy salicylaldehyde and one newly designed mononuclear Co (III) complex [Co(L)(L1)] (complex 2) by utilizing (H₂L) and 3- ethoxy salicylaldehyde(HL1) as an ancillary ligand. The newly developed complex 2 have been spectroscopically characterized. An interesting phenomenon has been noticed that in presence of ancillary ligand, the solubility in buffer solution and the thermal stability of complex 2 comparatively increases than 1. To check the effect of ancillary ligand, present in complex 2 towards the DNA and HSA binding efficacy, both the complexes have been taken into consideration to inspect their binding potentiality with the macromolecules. The 'on', 'off' fluorescence changes in presence of DNA and HSA, the binding constant values, obtained from electronic spectral titration, iodide induced quenching, competitive binding assay, circular dichroism (CD) spectral titration, time resolved fluorescence experiment unambiguously assure the better binding efficacy of complex 2 with the signal of minor groove binding mode with DNA along with no significant conformational changes of the macromolecules. The strong and spontaneous binding of complex 2 with CT-DNA is further supported by the Isothermal Titration Calorimetry (ITC) study. Furthermore TDDFT calculation of DNA with and without complex 2 significantly authorize the formation of complex 2-DNA adduct during the association. Finally Molecular Docking study properly verifies the experimental findings and provides justified explanation behinds experimental findings.

Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA

The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in ¹H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.

Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations

In this study, the interaction of 5-fluorouracil (5FU) drug with adenine (A), guanine(G), cytosine(C), uracil (U), and thymine (T) nucleobases of DNA and RNA are surveyed at the ωB97XD/LANL2DZ, M06-2X/6-31G (d, p), MPW1PWQ1/6-31G(d, p), PBEPBE/6-31(d, p) and ωB97XD/6-31G(d, p) levels of density functional theory (DFT). The considered complexes of 5FU drug with nucleobases are optimized at the above level of theories. Max Force and RMS of optimization criteria are 0.00035 (Ha), and 0.0003 respectively. From optimized structures, the adsorption energy, thermodynamic parameters in gas and solvent media, quantum theory atom in molecule (QTAIM), electron localized function (ELF), and reduced density gradient (RDG) are calculated at ωB97XD/LANL2DZ and M06-2X/6-31G (d, p) level of DFT theory. The QTAIM, ELF, and RDG results confirm that the nature of bonding between 5FU drug with A, C, G, U, and T nucleobases is electrostatic or hydrogen bond type. The adsorption and thermodynamic energy results demonstrate that the interaction of the 5FU drug with C and G nucleobases is stronger than other nucleobases. The results of this study can be suggested the mechanism of interaction of the 5FU drug with nucleobases of DNA and RNA.Communicated by Ramaswamy H. Sarma.

Interaction of organoruthenium(II)-polypyridyl complexes with DNA and BSA

The interaction of four arene ruthenium complexes [(η⁶-p-cymene)Ru(Me₂dppz)Cl]PF₆ (1) with Me₂dppz = 11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine, [(η⁶-p-cymene)Ru(aip)Cl]PF₆ (2) with aip = 2-(9-anthryl)-1H-imidazo[4,5-f][1,10] phenanthroline), ([(ƞ⁶-toluene)Ru(ppf)Cl]PF₆) (3) and ([(ƞ⁶-p-cymene)Ru(ppf)Cl]PF₆) (4) with ppf = pyrido[2',3':5,6] pyrazino[2,3-f][1,10]phenanthroline with calf thymus DNA were investigated. All of four complexes exhibit DNA-binding activity. UV-Vis spectroscopic studies revealed the intrinsic binding constants of the order 10⁴ M^-1 of magnitude, indicating non-intercalative mode. Fluorescence quenching analysis showed that all complexes interfere with intercalator ethidium bromide and minor groove binder Hoechst 33258 by a singular non-intercalative mode with extent that differs by two orders of magnitude. Gel electrophoresis results on DNA cleavage assay demonstrated that all complexes produced conformational changes of supercoiled circular plasmid pUC19 in concentration dependent way. The results of fluorescence titration bovine serum albumin by 1, 2, 3 and 4 showed that all complexes significantly quench tryptophan residues fluorescence through a static quenching mechanism. The antimicrobial activity against both Gram-positive and Gram-negative bacteria analyzed. Complex 1 was most active, even on Escherichia coli was more active than positive control compound.

Low-Molecular Pyrazine-Based DNA Binders: Physicochemical and Antimicrobial Properties

Pyrazine and its derivatives are a large group of compounds that exhibit broad biological activity, the changes of which can be easily detected by a substituent effect or a change in the functional group. The present studies combined theoretical research with the density functional theory (DFT) approach (B3LYP/6-311+G**) and experimental (potentiometric and spectrophotometric) analysis for a thorough understanding of the structure of chlorohydrazinopyrazine, its physicochemical and cytotoxic properties, and the site and nature of interaction with DNA. The obtained results indicated that 2-chloro-3-hydrazinopyrazine (2Cl3HP) displayed the highest affinity to DNA. Cytotoxicity studies revealed that the compound did not exhibit toxicity toward human dermal keratinocytes, which supported the potential application of 2Cl3HP in clinical use. The study also attempted to establish the possible equilibria occurring in the aqueous solution and, using both theoretical and experimental methods, clearly showed the hydrophilic nature of the compound. The experimental and theoretical results of the study confirmed the quality of the compound, as well as the appropriateness of the selected set of methods for similar research.

Exploring the interaction between Cry1Ac protein and Zn2+, Cd2+ metal ions by fluorescence quenching and molecular docking approaches

Bacillus Thuringiensis (Bt) protein has a strong ability to complex with metal ions, which may increase the transport of metal ions in the soil multi-media system. In this study, the interactions between Cry1Ac protein and metal ions (Zn²⁺ and Cd²⁺) were investigated through spectroscopies and molecular docking methods. The spectra results showed that both Zn²⁺ and Cd²⁺ quenched the fluorescence intensity of Cry1Ac protein through the static quenching. The binding constants with 4-5 orders of magnitude also indicated the interactions between the ions and the Cry1Ac protein. The thermodynamic analysis showed that hydrogen bonds and van der Waals forces were predominant during the processes. In terms of the Förster non-radiation energy transfer theory, the binding distances between metal ions and Cry1Ac protein were approximately 0.21-0.24 nm, indicating the existence of a non-radiative energy transfer between them. Furthermore, molecular docking revealed that the metal ions participated in ligand binding with the Cry1Ac at the locations Asp569, Thr560, Asn564 and Gln566. The present work provided reasonable models helping us further understand the transport effect of heavy metals in the presence of Cry1Ac. The results could provide mechanistic insights into the nature of metal ions-Cry1Ac interactions and offer important information on the toxicity risk of metal ions-Cry1Ac binding interactions.

Phenolic Compound Ethyl 3,4-Dihydroxybenzoate Retards Drug Efflux and Potentiates Antibiotic Activity

The World Health Organization indicated that antibiotic resistance is one of the greatest threats to health, food security, and development in the world. Drug resistance efflux pumps are essential for antibiotic resistance in bacteria. Here, we evaluated the plant phenolic compound ethyl 3,4-dihydroxybenzoate (EDHB) for its efflux pump inhibitory (EPI) activity against drug-resistant Escherichia coli. The half-maximal inhibitory concentration, modulation assays, and time-kill studies indicated that EDHB has limited antibacterial activity but can potentiate the activity of antibiotics for drug-resistant E. coli. Dye accumulation/efflux and MALDI-TOF studies showed that EDHB not only significantly increases dye accumulation and reduces dye efflux but also increases the extracellular amount of antibiotics in the drug-resistant E. coli, indicating its interference with substrate translocation via a bacterial efflux pump. Molecular docking analysis using AutoDock Vina indicated that EDHB putatively posed within the distal binding pocket of AcrB and in close interaction with the residues by H-bonds and hydrophobic contacts. Additionally, EDHB showed an elevated postantibiotic effect on drug-resistant E. coli. Our toxicity assays showed that EDHB did not change the bacterial membrane permeability and exhibited mild human cell toxicity. In summary, these findings indicate that EDHB could serve as a potential EPI for drug-resistant E. coli.

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.

Synthesis, Characterization, Biological Evaluation and DNA Interaction Studies of 4-Aminophenol Derivatives: Theoretical and Experimental Approach

In the present study, five 4-aminophenol derivatives (4-chloro-2-(((4-hydroxyphenyl)imino)methyl)phenol(S-1), 4-((4-(dimethylamino)benzylidene)amino)phenol(S-2), 4-((3-nitrobenzylidene)amino)phenol(S-3), 4-((thiophen-2-ylmethylene)amino)phenol(S-4) and 4-(((E)-3-phenylallylidene)amino)phenol(S-5)) were synthesized and characterized by FT-IR, ¹H-NMR, ¹³C-NMR and elemental analyses. The synthesized compounds were tested for their antimicrobial (Gram-positive and Gram-negative bacteria and Saccharomyces cervesea fungus) and antidiabetic (α-amylase and α-glucosidase inhibitory) activities. All the compounds showed broad-spectrum activities against the Staphylococcus aureus (ATCC 6538), Micrococcus luteus (ATCC 4698), Staphylococcus epidermidis (ATCC 12228), Bacillus subtilis sub. sp spizizenii (ATCC 6633), Bordetella bronchiseptica (ATCC 4617) and Saccharomyces cerevisiae (ATCC 9763) strains. The newly synthesized compounds showed a significant inhibition of amylase (93.2%) and glucosidase (73.7%) in a concentration-dependent manner. Interaction studies of Human DNA with the synthesized Schiff bases were also performed. The spectral bands of S-1, S-2, S-3 and S-5 all showed hyperchromism, whereas the spectral band of S-4 showed a hypochromic effect. Moreover, the spectral bands of the S-2, S-3 and S-4 compounds were also found to exhibit a bathochromic shift (red shift). The present studies delineate broad-spectrum antimicrobial and antidiabetic activities of the synthesized compounds. Additionally, DNA interaction studies highlight the potential of synthetic compounds as anticancer agents. The DNA interaction studies, as well as the antidiabetic activities articulated by the molecular docking methods, showed the promising aspects of synthetic compounds.

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

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

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.

Comparison on binding interactions of quercetin and its metal complexes with calf thymus DNA by spectroscopic techniques and viscosity measurement

Quercetin (Qu) and its metal complexes have received great attention during the last years, due to their good antioxidant, antibacterial, and anticancer activities. In this contribution, binding interactions of Qu and Qu-metal complexes with calf thymus DNA (ctDNA) were investigated and compared systematically by using spectroscopic techniques and viscosity measurement. UV-vis absorption spectra of ctDNA-compound systems showed obvious hypochromic effect. Relative viscosity and melting temperature of ctDNA increased after the addition of Qu and Qu-metal complexes, and the change tendency is Qu-Cr(III) > Qu-Mn(II) > Qu-Zn(II) > Qu-Cu(II) > Qu. Fluorescence competition experiments show that hydrogen bonds and van der Waals interaction play an important role in the intercalative binding of Qu and Qu-metal complexes with ctDNA. Qu and Qu-metal complexes could unwind the right-handed B-form helicity of ctDNA and further affect its base pair stacking. Space steric hindrance might be responsible for the differences in the intercalative binding between ctDNA and different Qu-metal complexes. These results provide new information for the molecular understanding of binding interactions of Qu-metal complexes with DNA and the strategy for research of structural influences.

Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity

Non-coding RNAs are regarded as promising targets for the discovery of innovative drugs due to their abundance in the genome and their involvement in many biological processes. Phytochemicals (PCs) are the primary source of ligand-based drugs due to their broad spectrum of biological activities. Since many PCs are heterocyclic and have chemical groups potentially involved in the interaction with nucleic acids, detailed interaction analysis between PCs and RNA is crucial to explore the effect of PCs on RNA functions. In this study, an integrated approach for investigating interactions between PCs and RNAs were demonstrated to verify the RNA-mediated PCs functions by using berberine (BRB) as a model PC. RNA screening of a transcriptome library followed by sequence refinement found minimal RNA motif consisting of a cytosine bulge with U-A and G-U neighbouring base pairs for interaction with BRB. NMR-based structure determination and physicochemical analyses using chemical analogues of BRB demonstrated the importance of electrostatic and stacking interactions for sequence selective interaction and RNA stabilization. The selective interaction with a relatively small RNA motif based on a chemical structure of a planer heterocyclic highlights the biological activities of various PCs mediated by the interactions with particular functional RNAs. In addition, the systematic and quantitative investigations demonstrated in this study could be useful for the development of therapeutic chemicals targeting functional RNAs, based on the PCs, in the future.

Synthesis, characterization, antimicrobial and cytotoxic activity and DNA-binding properties of d-metal complexes with hydrazones of Girard's T and P reagents

In this work synthesis, characterization and crystal structures of 1, Zn(II) complex ([ZnL¹(NCS)₂]), with (E)-1-(2-oxo-2-(2-(quinolin-2-ylmethylene)hydrazinyl)ethyl)pyridin-1-ium chloride (HL¹Cl) and 2, Bi(III) complex ([BiHL²Cl₄] × 1/2CH₃OH), with (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(thiazol-2-yl)ethylidene)hydrazinyl)ethan-1-aminium chloride (HL²Cl), have been reported. Zn(II) complex possesses a distorted trigonal bipyramidal geometry while surroundings around Bi(III) ion are extended pentagonal bipyramidal. Antimicrobial activity, brine shrimp assay and DPPH radical scavenging activity of both complexes, including previously synthesized complexes with HL²Cl ligand (Zn(II) and Ni(II)) and complexes with (E)-N,N,N-trimethyl-2-oxo-2-(2-(1-(pyridin-2-yl)ethylidene)hydrazinyl)ethan-1-aminium chloride (HL³Cl) (Zn(II), Cu(II), Cd(II), Co(II), Fe(III), Ni(II)), were evaluated. For the most active complexes, cytotoxic activity against five malignant cancer cell lines (HeLa, A375, MCF7, PC-3 and A549) and normal cell line HaCaT, as well as generation of reactive oxygen species (ROS), was tested.

Anticoccidial Activity of Berberine against Eimeria-Infected Chickens

Avian coccidiosis has a major economic impact on the poultry industry, it is caused by 7 species of Eimeria, and has been primarily controlled using chemotherapeutic agents. Due to the emergence of drug-resistant strains, alternative control strategies are needed. We assessed anticoccidial effects of berberine-based diets in broiler chickens following oral infection with 5 Eimeria species (E. acervulina, E. maxima, E. tenella, E. mitis, and E. praecox). When 0.2% berberine, a concentration that does not affect weight gain, was added to the diet, the 4 groups infected with E. acervulina, E. tenella, E. mitis, or E. praecox showed significant reductions in fecal oocyst shedding (P<0.05) compared to their respective infected and untreated controls. In chickens treated 0.5% berberine instead of 0.2% and infected with E. maxima, fecal oocyst production was significantly reduced, but body weight deceased, indicating that berberine treatment was not useful for E. maxima infection. Taken together, these results illustrate the applicability of berberine for prophylactic use to control most Eimeria infections except E. maxima. Further studies on the mechanisms underlying the differences in anticoccidial susceptibility to berberine, particularly E. maxima, are remained.

Design, Synthesis and Antimicrobial Evaluation of Novel Benzimidazole-incorporated Naphthalimide Derivatives As Salmonella typhimurium DNA Intercalators, and Combination Researches

OBJECTIVE

A series of novel benzimidazole-incorporated naphthalimide derivatives were designed and prepared to overcome the increasing antibiotic resistance.

METHOD

The target novel benzimidazole-incorporated naphthalimide derivatives were synthesized from commercial 4-bromo-1,8-naphthalic anhydride and o-phenylene diamine by aminolysis, N-alkylation, and so on. The antimicrobial activity of the synthesized compounds was evaluated in vitro by a two-fold serial dilution technique. The interaction of compound 10g with Salmonella typhimurium DNA was studied using UV-vis spectroscopic methods.

RESULTS

Compound 10g bearing a 2,4-dichlorobenzyl moiety exhibited the best antimicrobial activities in this series relatively, especially it gave the comparable action against Salmonella typhimurium compared to the reference drug Norfloxacin (MIC = 4 mg/mL). Further research showed that compound 10g could effectively intercalate into the Salmonella typhimurium DNA to form the 10g-DNA complex, which might correlate with the inhibitory activity. Molecular docking results demonstrated that naphthalimide compound 10g could interact with base-pairs of DNA hexamer duplex by p-p stacking. Additionally, the combinations of the solid active combination with clinical drugs gave better antimicrobial efficiency with less dosage and broader antimicrobial spectrum than the separated use alone. Notably, these combined systems were more sensitive to Fluconazole-insensitive M. ruber.

CONCLUSION

This work opened up a good starting point to optimize the structures of benzimidazole-incorporated naphthalimide derivatives as potent antimicrobial agents.

Berberine: A Promising Natural Isoquinoline Alkaloid for the Development of Hypolipidemic Drugs

Berberine, as a representative isoquinoline alkaloid, exhibits significant hypolipidemic activity in both animal models and clinical trials. Recently, a large number of studies on the lipid-lowering mechanism of berberine and studies for improving its hypolipidemic activity have been reported, but for the most part, they have been either incomplete or not comprehensive. In addition, there have been a few specific reviews on the lipid-reducing effect of berberine. In this paper, the physicochemical properties, the lipid-lowering mechanism, and studies of the modification of berberine all are discussed to promote the development of berberine as a lipid-lowering agent. Subsequently, this paper provides some insights into the deficiencies of berberine in the study of lipid-lowering drug, and based on the situation, some proposals are put forward.

What Can Electrochemical Methods Offer in Determining DNA-Drug Interactions?

The interactions of compounds with DNA have been studied since the recognition of the role of nucleic acid in organisms. The design of molecules which specifically interact with DNA sequences allows for the control of the gene expression. Determining the type and strength of such interaction is an indispensable element of pharmaceutical studies. Cognition of the therapeutic action mechanisms is particularly important for designing new drugs. Owing to their sensitivity, simplicity, and low costs, electrochemical methods are increasingly used for this type of research. Compared to other techniques, they require a small number of samples and are characterized by a high reliability. These methods can provide information about the type of interaction and the binding strength, as well as the damage caused by biologically active molecules targeting the cellular DNA. This review paper summarizes the various electrochemical approaches used for the study of the interactions between pharmaceuticals and DNA. The main focus is on the papers from the last decade, with particular attention on the voltammetric techniques. The most preferred experimental approaches, the electrode materials and the new methods of modification are presented. The data on the detection ranges, the binding modes and the binding constant values of pharmaceuticals are summarized. Both the importance of the presented research and the importance of future prospects are discussed.

G-Quadruplex binding of cavity-containing anthraquinonesulfonyl-β-cyclodextrin conjugate. Effect of encapsulation of ethidium bromide and berberine

An anthraquinonesulfonyl derivative of β-cyclodextrin is prepared and characterized employing spectroscopic techniques. The binding interactions of the compound with ethidium bromide, berberine, calf-thymus DNA, quadruplex DNAs viz., kit22, telo24, and myc22 are investigated by ultraviolet-visible, and fluorescence spectroscopic methods. Anthraquinonesulfonyl-β-cyclodextrin conjugate acts as a host molecule and enhances ethidium bromide and berberine fluorescence due to their encapsulation in cyclodextrin's cavity. The binding constant values are 9.0 × 10⁵ mol^-1 dm³ and 5.7 × 10⁴ mol^-1 dm³ for the formation of host: guest complexes of the β-CD derivative with ethidium bromide and berberine respectively. The proximity of the protons of ethidium bromide and berberine protons with those of the internal cavity of β-CD in the anthraquinonesulfonyl-β-CD conjugate is confirmed by two-dimensional rotating-frame Overhauser effect spectroscopy. The conjugate displays a quenching of fluorescence selectively to the quadruplexes kit22 and telo24 that is contrast to the spectral behavior with duplex DNA. ctDNA and myc22 exhibit different absorption and emission profiles with ethidium bromide on encapsulation by β-CD. The encapsulation of berberine leads to a fluorescence enhancement on binding to ctDNA, telo24, and myc22 with binding constants of 5.6 × 10⁵, 3.3 × 10⁵ mol^-1 dm³, and 1.5 × 10⁵ mol^-1 dm³ respectively. In contrast, kit22 leads to fluorescence quenching on berberine encapsulated-anthraquinonesulfonyl-β-cyclodextrin conjugate with a Stern-Volmer constant of 3.3 × 10⁵ mol^-1 dm³.Communicated by Ramaswamy H. Sarma.

The benzylisoquinoline alkaloids, berberine and coptisine, act against camptothecin-resistant topoisomerase I mutants

DNA replication inhibitors are utilized extensively in studies of molecular biology and as chemotherapy agents in clinical settings. The inhibition of DNA replication often triggers double-stranded DNA breaks (DSBs) at stalled DNA replication sites, resulting in cytotoxicity. In East Asia, some traditional medicines are administered as anticancer drugs, although the mechanisms underlying their pharmacological effects are not entirely understood. In this study, we screened Japanese herbal medicines and identified two benzylisoquinoline alkaloids (BIAs), berberine and coptisine. These alkaloids mildly induced DSBs, and this effect was dependent on the function of topoisomerase I (Topo I) and MUS81-EME1 structure-specific endonuclease. Biochemical analysis revealed that the action of BIAs involves inhibiting the catalytic activity of Topo I rather than inducing the accumulation of the Topo I-DNA complex, which is different from the action of camptothecin (CPT). Furthermore, the results showed that BIAs can act as inhibitors of Topo I, even against CPT-resistant mutants, and that the action of these BIAs was independent of CPT. These results suggest that using a combination of BIAs and CPT might increase their efficiency in eliminating cancer cells.

An Integrated Strategy for the Detection, Dereplication, and Identification of DNA-Binding Biomolecules from Complex Natural Product Mixtures

A fundamental factor in natural product drug discovery programs is the necessity to identify the active component(s) from complex chemical mixtures. Whereas this has traditionally been accomplished using bioassay-guided fractionation, we questioned whether alternative techniques could supplement and, in some cases, even supplant this approach. We speculated that a combination of ligand-fishing methods and modern analytical tools (e.g., LC-MS and online natural product databases) offered a route to enhance natural product drug discovery. Herein, a candidate solution referred to as the lickety-split ligand-affinity-based molecular angling system (LLAMAS) is described. This approach utilizes an ultrafiltration-based LC-PDA-MS/MS-guided DNA-binding assay in combination with the (i) Global Natural Products Social Molecular Networking, (ii) Dictionary of Natural Products, and (iii) SciFinder platforms to identify DNA binders in complex chemical mixtures. LLAMAS was initially vetted in tests using known small-molecule DNA binders and then optimized to a 96-well plate-based format. A set of 332 plant samples used in traditional Chinese medicine was screened for DNA-binding activity with LLAMAS, resulting in the identification of seven DNA-binding molecules, including berberine (12), palmatine (13), coptisine (14), fangchinoline (15), tetrandrine (16), daurisoline (17), and dauricine (18). These results demonstrate that LLAMAS is an effective natural product discovery platform for the efficient identification and dereplication of DNA-binding molecules from complex mixtures.

Study of alkaloid berberine and its interaction with the human telomeric i-motif DNA structure

The alkaloid berberine presents many biological activities related to its potential to bind DNA structures, such as duplex or G-quadruplex. Recently, it has been proposed that berberine may interact with i-motif structures formed from the folding of cytosine-rich sequences. In the present work, the interaction of this alkaloid with the i-motif formed by the human telomere cytosine-rich sequence, as well as with several positive and negative controls, has been studied. Molecular fluorescence and circular dichroism spectroscopies, as well as nuclear magnetic resonance spectrometry and competitive dialysis, have been used with this purpose. The results shown here reveal that the interaction of berberine with this i-motif is weak, mostly electrostatics in nature and takes place with bases not involved in C·C⁺ base pairs. Moreover, this ligand is not selective for i-motif structures, as binds equally to both, folded structure, and unfolded strand, without producing any stabilization of the i-motif. As a conclusion, the development of analytical methods based on the interaction of fluorescent ligands, such as berberine, with i-motif structures should consider the thermodynamic aspects related with the interaction, as well as the selectivity of the proposed ligands with different DNA structures, including unfolded strands.

Comparative binding analysis of noscapine and piperine with tRNA: A structural perturbation and energetic study

In this study, we have exploring the binding mechanisms of the two anticancer alkaloid noscapine (NOS) and piperine (PIP) with tRNA using different spectroscopy and computational method. Absorbance and emission spectra revealed that both the drugs show strong binding with tRNA, where NOS intercalate between the base pairs of tRNA and PIP binds in the groove of tRNA. Competitive binding study and steady state anisotropy further confirms the intercalative mode of binding between NOS and tRNA and groove binding in PIP-tRNA complex. The observed thermodynamic parameters suggested that NOS-tRNA complex formation is endothermic and entropy driven, however it was exothermic, and enthalpy driven in case of PIP-tRNA complex. CD and time resolved fluorescence studies show the structural perturbations and conformational change in tRNA structure with NOS as well as PIP. Molecular docking studies are comparable with experimental results and further confirmed that the hydrophobic interactions involved in the NOS-tRNA binding, whereas hydrogen binding and van der Waals interactions play important role in the PIP-tRNA complex formation. This study can be useful to understand the potential binding and resultant tRNA damage by alkaloids and deigned new target specific anticancer drug.

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.

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.

Phytochemicals toward Green (Bio)sensing

Because of numerous inherent and unique characteristics of phytochemicals as bioactive compounds derived from plants, they have been widely used as one of the most interesting nature-based compounds in a myriad of fields. Moreover, a wide variety of phytochemicals offer a plethora of fascinating optical and electrochemical features that pave the way toward their development as optical and electrochemical (bio)sensors for clinical/health diagnostics, environmental monitoring, food quality control, and bioimaging. In the current review, we highlight how phytochemicals have been tailored and used for a wide variety of optical and electrochemical (bio)sensing and bioimaging applications, after classifying and introducing them according to their chemical structures. Finally, the current challenges and future directions/perspective on the optical and electrochemical (bio)sensing applications of phytochemicals are discussed with the goal of further expanding their potential applications in (bio)sensing technology. Regarding the advantageous features of phytochemicals as highly promising and potential biomaterials, we envisage that many of the existing chemical-based (bio)sensors will be replaced by phytochemical-based ones in the near future.

Synthesis of novel calix[4]arene p-benzazole derivatives and investigation of their DNA binding and cleavage activities with molecular docking and experimental studies

In this study, novel p-benzimidazole-derived calix[4]arene compounds with different structures, and a benzothiazole-derived calix[4]arene compound, were synthesized by a microwave-assisted method and their structures were determined by FTIR, 1H NMR, 13C NMR, MALDI-TOF mass spectroscopy, and elemental analysis. The effects of functional calixarenes against bacterial (pBR322 plasmid DNA) and eukaryotic DNA (calf thymus DNA = CT-DNA) were investigated. The studies with plasmid DNA have shown that compounds 6 and 10 containing methyl and benzyl groups, respectively, have DNA cleavage activity at the highest concentrations (10 000 μM). Interactions with plasmid DNA using some restriction enzymes (BamHI and HindIII) were also investigated. The binding ability of p-substituted calix[4]arene compounds towards CT-DNA was examined using UV-vis and fluorescence spectroscopy and it was determined that some compounds showed efficiency. In particular, it was observed that the functional compounds (10 and 5) containing benzyl and chloro-groups had higher activity (K b binding constants were found to be 7.1 × 103 M-1 and 9.3 × 102 M-1 respectively) on DNA than other compounds. Competitive binding experiments using ethidium bromide also gave an idea about the binding properties. Docking studies of the synthesized compounds with DNA were performed to predict the binding modes, affinities and noncovalent interactions stabilizing the DNA-compound complexes at the molecular level. Docking results were in good agreement with the experimental findings on the DNA binding activities of compounds. Based on these results, this preliminary study could shed light on future experimental antibacterial and/or anticancer research.

Determination of Drug Efflux Pump Efficiency in Drug-Resistant Bacteria Using MALDI-TOF MS

Multidrug efflux pumps play an essential role in antibiotic resistance. The conventional methods, including minimum inhibitory concentration and fluorescent assays, to monitor transporter efflux activity might have some drawbacks, such as indirect evidence or interference from color molecules. In this study, MALDI-TOF MS use was explored for monitoring drug efflux by a multidrug transporter, and the results were compared for validation with the data from conventional methods. Minimum inhibitory concentration was used first to evaluate the activity of Escherichia coli drug transporter AcrB, and this analysis showed that the E. coli overexpressing AcrB exhibited elevated resistance to various antibiotics and dyes. Fluorescence-based studies indicated that AcrB in E. coli could decrease the accumulation of intracellular dyes and display various efflux rate constants for different dyes, suggesting AcrB’s efflux activity. The MALDI-TOF MS analysis parameters were optimized to maintain a detection accuracy for AcrB’s substrates; furthermore, the MS data showed that E. coli overexpressing AcrB led to increased ions abundancy of various dyes and drugs in the extracellular space at different rates over time, illustrating continuous substrate efflux by AcrB. This study concluded that MALDI-TOF MS is a reliable method that can rapidly determine the drug pump efflux activity for various substrates.