Electrochemical DNA biosensor for the study of ciprofloxacin–DNA interaction

Targeted synthesis of a trimethoxyphenyltetrahydropyrimidine analogue designed as a DNA intercalator: in silico, multi-spectroscopic, thermodynamic, and in vitro approaches

Based on the rational design of DNA intercalators and Topo-II inhibitors and taking into consideration the main pharmacophoric features of doxorubicin (Dox) as a reference standard, we theoretically designed novel substituted tetrahydropyrimidine analogues (T1-35). The designed analogues (T1-35) were investigated for their inhibitory potential towards the hybrid DNA and Topo-II target receptor using molecular docking. Interestingly, the theoretically designed analogue T30 with a 3,4,5-trimethoxy phenyl side chain was found to be the superior candidate, achieving a binding score of -7.06 kcal mol-1, compared with two reference standards, doxorubicin (Dox) and a co-crystal ligand (EVP). Moreover, the docked candidates (T30, Dox, and EVP) were further subjected to molecular dynamics simulations for 500 ns. Furthermore, MM-GBSA calculations showed that the target candidate (T30) achieved superior ΔG binding energy (-33.86 kcal mol-1) compared with Dox and EVP. Moreover, T30 was found to be the most promising candidate that could be conveniently synthesized based on its order in the chemical synthesis scheme. In addition, to evaluate the antiproliferative activity and scope of compound T30, we requested the National Cancer Institute (NCI) to test it against nine cancer cell types. Interestingly, compound T30 exhibited very strong antiproliferative activity with a mean GI% of 122% and a mean GI50 of 4.10 μM. It exhibited the highest anticancer activity towards all 59 cell lines. Moreover, the in vitro binding interaction of compound T30 with calf thymus DNA (ctDNA) was examined using various techniques, such as spectrofluorimetry, UV-vis spectrophotometry, viscosity measurements, ionic strength measurements, and thermodynamics to confirm its mechanism of action. Investigating the intermolecular binding interaction between small compounds and DNA can provide valuable insights for designing drugs with enhanced effectiveness and improved targeted activities.

In silico modelling of ciprofloxacin specific aptamer for the development of high-performance biosensor

Ciprofloxacin (CFX), a widely used fluoroquinolone antibiotic, is critical in healthcare settings for treating patients. However, improper treatment of wastewater from these facilities can lead to environmental contamination with CFX. This underscores the need for an efficient, straightforward method for early detection. In this study, a DNA aptamer was selected through a hierarchical docking workflow, and the stability and interactions were assessed by Molecular Dynamics (MD) simulation. The aptamer-CFX complex that showed the most promise had a docking score of -8.596 kcal/mol and was further analyzed using MD simulation and MM/PBSA. Based on the overall results, the identified ssDNA sequence length of 60 nt (CAGCGCTAGGGCTTTTAGCGTAATGGGTAGGGTGGTGCGGTGCAGATATCGGAATTGGTG) was immobilized over a gold transducer surface through the self-assembled monolayer (SAM; Au-S-ssDNA) method. The ssDNA-modified surface has demonstrated a high affinity towards CFX, which is confirmed by cyclic voltammogram (CV) and electrochemical impedance spectroscopy measurements (EIS). The DNA-aptamer modified electrode demonstrated a good linear range (10 × 10-9 - 200 × 10-9 M), detection limit (1.0 × 10-9 M), selectivity, reproducibility, and stability. The optimized DNA-aptamer-based CFX sensor was further utilized for the accurate determination of CFX with good recoveries in real samples.

Impact of temperature on the binding interaction between dsDNA and curcumin: An electrochemical study

In this study, we investigated the binding mode between double-stranded deoxyribonucleic acid (dsDNA) and curcumin (CU) using differential pulse voltammetry (DPV), UV-Vis spectroscopy, and molecular docking. By employing these techniques, we predicted the binding within the minor groove region of dsDNA and CU. Significantly, we employed electrochemistry, specifically cyclic voltammetry (CV), to explore the temperature effect on the dsDNA and CU binding. To the best of our knowledge, this is the first study to utilize electrochemical methods for investigating the temperature-dependent behavior of this binding interaction. Our findings revealed temperature-dependent variations in the binding constants: 2.42 × 103 M-1 at 25 °C, 4.26 × 103 M-1 at 30 °C, 5.44 × 103 M-1 at 35 °C, 6.29 × 103 M-1 at 40 °C, and 7.52 × 103 M-1 at 45 °C. Notably, the binding constant exhibited an increasing trend with elevated temperatures, indicating a temperature-dependent enhancement of the binding interaction.

Functionalities of electrochemical fluoroquinolone sensors and biosensors

Fluoroquinolones (FQs) are a class of broad-spectrum antimicrobial agents that are used to treat variety of infectious diseases. This class of antibiotics was being used for patients exhibiting early symptoms of a human respiratory disease known as the COVID-19 virus. As a result, this outbreak causes an increase in drug-resistant strains and environmental pollution, both of which pose serious threats to biota and human health. Thus, to ensure public health and prevent antimicrobial resistance, it is crucial to develop effective detection methods for FQs determination in water bodies even at trace levels. Due to their characteristics like specificity, selectivity, sensitivity, and low detection limits, electrochemical biosensors are promising future platforms for quick and on-site monitoring of FQs residues in a variety of samples when compared to conventional detection techniques. Despite their excellent properties, biosensor stability continues to be a problem even today. However, the integration of nanomaterials (NMs) could improve biocompatibility, stability, sensitivity, and speed of response in biosensors. This review concentrated on recent developments and contemporary methods in FQs biosensors. Furthermore, a variety of modification materials on the electrode surface are discussed. We also pay more attention to the practical applications of electrochemical biosensors for FQs detection. In addition, the existing challenges, outlook, and promising future perspectives in this field have been proposed. We hope that this review can serve as a bedrock for future researchers and provide new ideas for the development of electrochemical biosensors for antibiotics detection in the future.

Voltammetric studies and spectroscopic investigations of the interaction of an anticancer drug bevacizumab-DNA and analytical applications of disposable pencil graphite sensor

A sensitive, simple, fast electrochemical biosensor for the DNA interaction of bevacizumab (BEVA), which is used as a targeted drug in cancer treatment, was developed using the differential pulse voltammetry (DPV) technique with pencil graphite electrode (PGE). In the work, PGE was electrochemically activated in a supporting electrolyte medium of +1.4 V/60 s (PBS pH 3.0). Surface characterization of PGE was carried out by SEM, EDX, EIS, and CV techniques. Determination and electrochemical properties of BEVA were examined with CV and DPV techniques. BEVA gave a distinct analytical signal on the PGE surface at a potential of +0.90 V (vs. Ag/AgCl). In the procedure proposed in this study, BEVA gave a linear response on PGE in PBS (pH 3.0 containing 0.02 M NaCl) (0.1 mg mL-1 - 0.7 mg mL-1) with LOD and LOQ values of 0.026 mg mL-1 and 0.086 μg mL-1, respectively. BEVA was reacted with 20 μg mL-1 DNA in PBS for 150 s and analytical peak signals for adenine and guanine bases were evaluated. The interaction between BEVA-DNA was supported by UV-Vis. Absorption spectrometry and the binding constant was determined as 7.3 × 104.

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

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

Electrochemical DNA biosensors developed for the monitoring of biointeractions with drugs: a review

The interaction of drugs with DNA is important for the discovery of novel drug molecules and for understanding the therapeutic effects of drugs as well as the monitoring of side effects. For this reason, many studies have been carried out to investigate the interactions of drugs with nucleic acids. In recent years, a large number of studies have been performed to electrochemically detect drug-DNA interactions. The fast, sensitive, and accurate results of electrochemical techniques have resulted in a leading role for their implementation in this field. By means of electrochemical techniques, it is possible not only to demonstrate drug-DNA interactions but also to quantitatively analyze drugs. In this context, electrochemical biosensors for drug-DNA interactions have been examined under different headings including anticancer, antiviral, antibiotic, and central nervous system drugs as well as DNA-targeted drugs. An overview of the studies related to electrochemical DNA biosensors developed for the detection of drug-DNA interactions that were reported in the last two decades in the literature is presented herein along with their applications and they are discussed together with their future perspectives.

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

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

Synthesis, X-ray, Hirshfeld surface analysis, exploration of DNA binding, urease enzyme inhibition and anticancer activities of novel adamantane-naphthyl thiourea conjugate

1-(adamantane-1-carbonyl-3-(1-naphthyl)) thiourea (C₂₂H₂₄N₂OS (4), was synthesized by the reaction of freshly prepared adamantane-1-carbonyl chloride from corresponding acid (3) with ammonium thiocyanate in 1:1 M ratio in dry acetone to afford the adamantane-1-carbonyl isothiocyanate (2) in situ followed by treatment with 1-naphthyl amine (3). The structure was established by elemental analyses, FTIR, ¹H, ¹³C NMR and mass spectroscopy. The molecular and crystal structure were determined by single crystal X-ray analysis. It belongs to triclinic system P - 1 space group with a = 6.7832(5) Å, b = 11.1810(8) Å, c = 13.6660(10) Å, α = 105.941(6)°, β = 103.730(6)°, γ = 104.562(6)°, Z = 2, V = 910.82(11) ų. The naphthyl group is almost planar. In the crystal structure, intermolecular CH···O hydrogen bonds link the molecules into centrosymmetric dimers, enclosing R₂²(14) ring motifs, while the intramolecular NH···O hydrogen bonds enclose S(6) ring motifs, in which they may be effective in the stabilization of the structure. The Hirshfeld surface analysis of the crystal structure indicates that the most important contributions for the crystal packing are from H … H (59.3%), H … C/C … H (19.8%) and H … S/S … H (10.1%) interactions. Hydrogen bonding and van der Waals interactions are the dominant interactions in the crystal packing. DFT, molecular docking and urease inhibition studies revealed stability and electron withdrawing nature of 4 as compared to DNA base pairs and residues of urease. The DNA binding results from docking, UV- visible spectroscopy, and viscosity studies indicated significant binding of 4 with the DNA via intercalation and groove binding. Further investigation of the compound was done on hepatocellular carcinoma; Huh-7 cell line as well as normal human embryonic kidney; Hek-293 cell line. The compound showed significant cytotoxic activity against Huh-7 cells in comparison to normal Hek-293 cells indicating selective cytotoxicity towards cancer cells.

Synthesis, X-ray crystal structure elucidation and Hirshfeld surface analysis of N-((4-(1H-benzo[d]imidazole-2-yl)phenyl)carbamothioyl)benzamide: investigations for elastase inhibition, antioxidant and DNA binding potentials for biological applications

The interest in the present study pertains to the development of a new compound based upon a benzimidazole thiourea moiety that has unique properties related to elastase inhibition, free radical scavenging activity and its DNA binding ability. The title compound, N-(4-(1H-benzo[d]imidazol-2-yl)phenyl)-3-benzoyl thiourea (C21H18N4O2SH2O:TUBC), was synthesized by reacting an acid chloride of benzoic acid with potassium thiocyanate (KSCN) along with the subsequent addition of 4-(1H-benzo[d]imidazol-2-yl)benzenamine via a one-pot three-step procedure. The structure of the resulting benzimidazole based thiourea was confirmed by spectroscopic techniques including FTIR, 1H-NMR, 13C-NMR and single crystal X-ray diffraction and further examined by Hirshfeld surface analysis. TUBC was also investigated by using both in silico methodology including molecular docking for elastase inhibition along with quantum chemical studies and in vitro experimental methodology utilizing elastase inhibition and free radical scavenging assay along with DNA binding experiments. Docking results confirmed that TUBC binding was within the active region of elastase. In comparison to the reference drug oleanolic acid, the low IC50 value of TUBC also indicated its high tendency towards elastase inhibition. TUBC scavenged 80% of DPPH˙ radicals which pointed towards its promising antioxidant activity. TUBC-DNA binding by DFT, docking, UV-visible spectroscopy and viscosity measurements revealed TUBC to be a potential drug candidate that binds spontaneously and reversibly with DNA via a mixed binding mode. All theoretical and experimental findings pointed to TUBC as a potential candidate for a variety of biological applications.

A chitosan gold nanoparticles molecularly imprinted polymer based ciprofloxacin sensor

In this work, we present a novel study on the development of an electrochemical biomimetic sensor to detect the ciprofloxacin (CIP) antibiotic. A chitosan gold nanoparticles decorated molecularly imprinted polymer (Ch-AuMIP) was used to modify the glassy carbon electrode (GCE) for preparation of the sensor. The Ch-AuMIP was characterized to understand various properties like chemical composition, morphology, roughness, and conduction using Fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), atomic force microscopy (AFM) and cyclic voltammetry (CV) respectively. Several experimental conditions affecting the Ch-AuMIP/GCE sensor such as the CIP removal agent, the extraction time, the volume of Ch-AuMIP drop-cast onto GCE and the rebinding time were studied and optimized. The Ch-AuMIP sensor sensitivity was studied in the concentration range of 1-100 μmol L-1 exhibiting a limit of detection of 210 nmol L-1. The synergistic combination of Au nanoparticles and Ch-MIP helps detect the CIP antibiotic with good sensitivity and selectivity, respectively. We investigated the selectivity aspect by using some possible interfering species and the developed sensing system showed good selectivity for CIP with a 66% response compared to the other compounds (≤45% response). The proposed sensing strategy showed its applicability for successful detection of CIP in real samples like tap water, mineral water, milk, and pharmaceutical formulation. The developed sensor showed good selectivity towards CIP even among the analogue molecules of Norfloxacin (NFX) and Ofloxacin (OFX). The developed sensor was successfully applied to determine the CIP in different samples with a satisfactory recovery in the range of 94 to 106%.

Sm2O3 nanorod-modified graphite paste electrode for trace level voltammetric determination of acetaminophen and ciprofloxacin

Illustration of drug molecule electro-oxidation at Sm₂O₃ nanorods.

Highly efficient detection of ciprofloxacin in water using a nitrogen-doped carbon electrode fabricated through plasma modification

We developed a novel electrochemical sensor based on nitrogen plasma modification to effectively detect ciprofloxacin in water.

Selective Electrochemical Detection of Ciprofloxacin with a Porous Nafion/Multiwalled Carbon Nanotube Composite Film Electrode

This study focuses on the development of electrochemical sensors for the detection of Ciprofloxacin (CFX) in natural waters and wastewater effluents. The sensors are prepared by depositing a layer of multiwalled carbon nanotubes (MWCNTs) dispersed in a porous Nafion film on to a boron-doped diamond (BDD) electrode substrate. The porous-Nafion-MWCNT/BDD electrode enhanced detection of CFX due to selective adsorption, which was accomplished by a combination of electrostatic attraction at -SO3(-) sites in the porous Nafion film and the formation of charge assisted hydrogen bonding between CFX and -COOH MWCNT surface functional groups. By contrast, the bare BDD electrode did not show any activity for CFX oxidation. The sensors were selective for CFX detection in the presence of other antibiotics (i.e., amoxicillin) and other nontarget water constituents (i.e., Cl(-), Ca(2+), humic acid, sodium dodecylbenzenesulfonate, salicylic acid, 4-aminobenzoic acid, and 4-hydroxybenzoic acid). A limit of detection of 5 nM (S/N = 5.04 ± 0.26) in a 0.1 M KH2PO4 supporting electrolyte (pH = 4.5) was obtained using differential pulse voltammetry. The linear dynamic ranges with respect to CFX concentration were 0.005-0.05 μM and 0.05-10 μM, and the sensitivities were 41 ± 5.2 μA μM(-1) and 2.1 ± 0.22 μA μM(-1), respectively. Sensor fouling was observed at high concentrations of some organic compounds such as 1 mM 4-aminobenzoic acid and 4-hydroxybenzoic acid. However, a short cathodic treatment fully restores sensor response. The results indicate that these sensors have application in detecting CFX in natural waters and wastewater effluents.

Electrochemical determination of the anticancer drug taxol at a ds-DNA modified pencil-graphite electrode and its application as a label-free electrochemical biosensor

In this study a novel biosensor for determination of taxol is described. The interaction of taxol with salmon-sperm double-stranded DNA (ds-DNA) based on the decreasing of the oxidation signals of guanine and adenine bases was studied electrochemically with a pencil-graphite electrode (PGE) using a differential pulse voltammetry (DPV) method. The decreases in the intensity of the guanine and adenine oxidation signals after interaction with taxol were used as indicator signals for the sensitive determination of taxol. DPV exhibits a linear dynamic range of 2.0×10(-7)-1.0×10(-5) M for taxol with a detection limit of 8.0×10(-8) M. Finally, this modified electrode was used for determination of taxol in some real samples.

Impedimetric detection of in situ interaction between anti-cancer drug bleomycin and DNA

Surface confined interaction of anti-cancer drug bleomycin (BLM) with nucleic acids: single stranded and double stranded DNA was investigated herein by using electrochemical impedance spectroscopy (EIS) technique in combination with a graphite sensor technology. The experimental conditions were optimized: such as, dsDNA concentration, BLM concentration and interaction time. The main features of impedimetric DNA biosensor, such as its detection limit and the repeatability, were also discussed. The in situ interaction of BLM with dsDNA was also tested impedimetrically in the absence or presence of other chemotherapeutic agents, such as mitomycin C (MC) and cis-platin (cis-DDP) for testing the selectivity.

Interaction study of ciprofloxacin with human telomeric DNA by spectroscopy and molecular docking

The interaction of ciprofloxacin (CIP) with human telomeric DNA was studied in vitro using multi-spectroscopy and molecular modeling methods. The hypochromic effect with a red shift in ultraviolet (UV) absorption indicated the occurrence of the interaction between CIP and DNA. The fluorescence quenching of CIP was observed with the addition of DNA and was proved to be the static quenching. The binding constant was found to be 9.62×10(4) L mol(-1). Electrospray ionization mass spectrometry (ESI-MS) result further confirmed the formation of 1:1 non-covalent complex between DNA and CIP. Combined with the UV melting results, circular dichroism (CD) results confirmed the existence of groove binding mode, as well as conformational changes of DNA. Molecular docking studies illustrated the visual display of the CIP binding to the GC region in the minor groove of DNA. Specific hydrogen bonds and van der Waals forces were demonstrated as main acting forces between CIP and guanine bases of DNA.

Nanomaterial-assisted signal enhancement of hybridization for DNA biosensors: a review

Detection of DNA sequences has received broad attention due to its potential applications in a variety of fields. As sensitivity of DNA biosensors is determined by signal variation of hybridization events, the signal enhancement is of great significance for improving the sensitivity in DNA detection, which still remains a great challenge. Nanomaterials, which possess some unique chemical and physical properties caused by nanoscale effects, provide a new opportunity for developing novel nanomaterial-based signal-enhancers for DNA biosensors. In this review, recent progress concerning this field, including some newly-developed signal enhancement approaches using quantum-dots, carbon nanotubes and their composites reported by our group and other researchers are comprehensively summarized. Reports on signal enhancement of DNA biosensors by non-nanomaterials, such as enzymes and polymer reagents, are also reviewed for comparison. Furthermore, the prospects for developing DNA biosensors using nanomaterials as signal-enhancers in future are also indicated.