The Mechanism of Dynamic Interaction between Doxorubicin and Calf Thymus DNA at the Single-Molecule Level Based on Confocal Raman Spectroscopy

An in-depth study of clofarabine's binding mechanism to DNA: A thorough experimental and theoretical investigation

The interaction of medicinal compounds with nucleic acids is a critical challenge in drug development. This research focused on the binding dynamics of clofarabine (CLO), an antineoplastic agent, with fish sperm DNA (dsDNA) under conditions that simulate the physiological environment at a pH of 7.4. The investigations employed multiple techniques, including fluorescence and UV spectroscopy, thermal denaturation analysis, viscosity measurements, electrochemical assessments, and molecular docking studies to elucidate these binding interactions. The binding constant (Kb) for the interaction between CLO and dsDNA, as determined from the Benesi-Hildebrand plot, was found to be 2.74 × 104 at a temperature of 298 K. The entropy (∆S) and enthalpy (∆H) changes associated with this binding interaction were measured as + 43.08 J mol-1 K-1 and -12.44 kJ mol-1, respectively. These values indicate that the predominant forces driving the binding interaction are primarily due to hydrogen bonding. Studies using the ethidium bromide and the Hoechst probe showed that CLO does not bind to dsDNA intercalatively. Findings obtained through UV-Vis absorption spectroscopy, competitive binding assays, and viscosity assessments indicated that CLO associates with dsDNA by binding within the minor groove. Molecular docking analyses demonstrated that CLO is accommodated within the AT-rich segment of the minor groove, with significant hydrogen bonding interactions occurring between CLO and dsDNA. These findings may offer valuable perspectives for elucidating the mechanisms underlying the toxicity, resistance, and adverse effects associated with CLO.

Multifunctional molecular hybrid for targeted colorectal cancer cells: Integrating doxorubicin, AS1411 aptamer, and T9/U4 ASO

Colorectal cancer (CRC) poses a global health challenge, with current treatments often harming both cancerous and normal cells. To improve efficacy, a multifunctional drug delivery platform has been developed, integrating bioactive materials, anticancer agents, and targeted recognition ligands into a single molecule. This study aimed to create a molecular hybrid (MH) containing doxorubicin, AS1411 aptamer, and T9/U4 ASO to regulate SW480 cell proliferation. The AS1411 aptamer targets nucleolin, overexpressed on cancer cell membranes, while T9/U4 ASO inhibits human telomerase RNA activity, further hindering cancer cell proliferation. AS-T9/U4_MH was synthesized via oligonucleotide hybridization, followed by doxorubicin loading and evaluation of its impact on cell proliferation. Binding capability of this MH was verified using fluorescence microscopy and flow cytometry, demonstrating specific recognition of SW480 cells due to nucleolin availability on the cell surface. These findings were corroborated by both microscopy and flow cytometry. AS-T9/U4_MH exhibited anti-proliferative effects, with the doxorubicin-loaded system demonstrating encapsulation and reduced toxicity. Moreover, the presence of Dox within AS-T9/U4_MH led to a notable reduction in hTERT and vimentin expression in SW480 cells. Additionally, examination of apoptotic pathways unveiled a marked decrease in Bcl-2 expression and a simultaneous increase in Bax expression in SW480 cells treated with Dox-loaded AS-T9/U4_MH, indicating its impact on promoting apoptosis. This molecular hybrid shows promise as a platform for integrating chemotherapeutic drugs with bioactive materials for cancer therapy.

Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome

Doxorubicin (DOX) is a widely used chemotherapeutic agent known for intercalating into DNA. However, the exact modes of DOX interactions with various DNA structures remain unclear. Using molecular dynamics (MD) simulations, we explored DOX interactions with DNA duplexes (dsDNA), G-quadruplex, and nucleosome. DOX predominantly stacks on terminal bases of dsDNA and occasionally binds into its minor groove. In the G-quadruplex, DOX stacks on planar tetrads but does not spontaneously intercalate into these structures. Potential of mean force calculations indicate that while intercalation is the most energetically favorable interaction mode for DOX in dsDNA, the process requires overcoming a significant energy barrier. In contrast, DOX spontaneously intercalates into bent nucleosomal DNA, due to the increased torsional stress. This preferential intercalation of DOX into regions with higher torsional stress provides new insights into its mechanism of action and underscores the importance of DNA tertiary and quaternary structures in therapies utilizing DNA intercalation.

Conjugate of Natural Bacteriochlorin with Doxorubicin for Combined Photodynamic and Chemotherapy

Chemotherapy is among the main classical approaches to the treatment of oncologic diseases. Its efficiency has been comprehensively proven by clinical examinations; however, the low selectivity of chemotherapeutic agents limits the possibilities of this method, making it necessary to search for new approaches to the therapy of oncologic diseases. Photodynamic therapy is the least invasive method and a very efficient alternative for the treatment of malignant tumors; however, its efficiency depends on the depth of light penetration into the tissue and on the degree of oxygenation of the treatment zone. In this work, a hitherto unknown conjugate of a natural bacteriochlorin derivative and doxorubicin was obtained. In vitro and in vivo studies showed a more pronounced activity of the conjugate against MCF-7 and 4T1 cells and its higher tumorotropicity in animal tumor-bearing animals compared to free anthracycline antibiotic. The suggested conjugate implements the advantages of photodynamic therapy and chemotherapy and has great potential in cancer treatment.

Analysis of Structural Heterogeneity in Low-Rank Coal and Its Pyrolyzed Char Using Multi-Point Scanning Micro-Raman Spectroscopy

Understanding the changes in carbon structure during the mid-low-temperature pyrolysis of low-rank coal is important for efficient utilization. Raman spectroscopy is commonly used to analyze the structural order of carbonaceous materials, but traditional methods may overlook the heterogeneity of coal/char. This research explores the heterogeneity of char structure derived from low-rank coal at 700 °C through multi-point micro-Raman analysis. The analysis of parameters such as area (A), intensity (I), full width at half maximum (FWHM/W), and peak position (P) reveals that the carbon structure becomes less ordered as coal transforms into char due to the deposition of small molecules on the surface. The study emphasizes the benefits of multi-point detection for gaining in-depth insights into the structural evolution of carbonaceous materials. The increased standard deviation of Raman parameters indicates diverse structural characteristics resulting from pyrolysis at this temperature, which traditional methods may not capture effectively. The mapping method used in this research visually illustrates the distribution of carbon structures in the region.

Synergistic effects and competitive relationships between DOC and DOX as acting on DNA molecules: Studied with confocal Raman spectroscopy and molecular docking technology

Docetaxel (DOC) is one of the second-generation antineoplastic drugs of the taxanes family with excellent antitumor activity. However, the mechanism of DOC inducing tumor cell apoptosis and treating cancer diseases, especially its interaction with DNA in the nucleus, and its adjuvant or combined Doxorubicin (DOX) acting on DNA molecules are unclear. In this study, the interaction mechanism between DOC and DNA, as well as the synergistic effects and competitive relationships among DOC and DOX when they simultaneously interact with DNA molecules were studied by laser confocal Raman spectroscopy combined with UV-visible absorption spectroscopy and molecular docking technology. The spectroscopic results showed that the binding constant of DOC to DNA is 5.25 × 103 M-1, the binding modes of DOC and DNA are non-classical intercalation and electrostatic binding, and the DNA-DOC complex has good stability. When DOC or DOX interacts with DNA alone, both of them can bind with bases and phosphate backbone of DNA, and also lead to DNA conformation changes; when DOC and DOX interact with DNA at the same time, the orders of interaction not only affect their binding sites with DNA, but also cause changes in the surrounding environment of the binding sites. In addition, the molecular docking results further verified that DOC and DOX have synergy and competition when they interact with DNA molecules simultaneously. The docking energies of DNA-DOC and DNA-DOX indicate the important role of van der Waals forces and hydrogen bonds. This study has practical significance for the design and development of antitumor drugs with less toxic based on the taxanes family and the combination with other drugs for the treatment of cancer.

Studying the Effects and Competitive Mechanisms of YOYO-1 on the Binding Characteristics of DOX and DNA Molecules Based on Surface-Enhanced Raman Spectroscopy and Molecular Docking Techniques

Revealing the interaction mechanisms between anticancer drugs and target DNA molecules at the single-molecule level is a hot research topic in the interdisciplinary fields of biophysical chemistry and pharmaceutical engineering. When fluorescence imaging technology is employed to carry out this kind of research, a knotty problem due to fluorescent dye molecules and drug molecules acting on a DNA molecule simultaneously is encountered. In this paper, based on self-made novel solid active substrates NpAA/(ZnO-ZnCl2)/AuNPs, we use a surface-enhanced Raman spectroscopy method, inverted fluorescence microscope technology, and a molecular docking method to investigate the action of the fluorescent dye YOYO-1 and the drug DOX on calf thymus DNA (ctDNA) molecules and the influencing effects and competitive relationships of YOYO-1 on the binding properties of the ctDNA-DOX complex. The interaction sites and modes of action between the YOYO-1 and the ctDNA-DOX complex are systematically examined, and the DOX with the ctDNA-YOYO-1 are compared, and the impact of YOYO-1 on the stability of the ctDNA-DOX complex and the competitive mechanism between DOX and YOYO-1 acting with DNA molecules are elucidated. This study has helpful experimental guidance and a theoretical foundation to expound the mechanism of interaction between drugs and biomolecules at the single-molecule level.

Electroanalysis in Pharmacogenomic Studies: Mechanisms of Drug Interaction with DNA

The review discusses electrochemical methods for analysis of drug interactions with DNA. The electroanalysis method is based on the registration of interaction-induced changes in the electrochemical oxidation potential of heterocyclic nitrogenous bases in the DNA molecule and in the maximum oxidation current amplitude. The mechanisms of DNA-drug interactions can be identified based on the shift in the electrooxidation potential of heterocyclic nitrogenous bases toward more negative (cathodic) or positive (anodic) values. Drug intercalation into DNA shifts the electrochemical oxidation potential to positive values, indicating thermodynamically unfavorable process that hinders oxidation of nitrogenous bases in DNA. The potential shift toward the negative values indicates electrostatic interactions, e.g., drug binding in the DNA minor groove, since this process does not interfere with the electrochemical oxidation of bases. The concentration-dependent decrease in the intensity of electrochemical oxidation of DNA bases allows to quantify the type of interaction and calculate the binding constants.

Studying the Interaction between Bendamustine and DNA Molecule with SERS Based on AuNPs/ZnCl2/NpAA Solid-State Substrate

Bendamustine (BENDA) is a bifunctional alkylating agent with alkylating and purinergic antitumor activity, which exerts its anticancer effects by direct binding to DNA, but the detailed mechanism of BENDA-DNA interaction is poorly understood. In this paper, the interaction properties of the anticancer drug BENDA with calf thymus DNA (ctDNA) were systematically investigated based on surface-enhanced Raman spectroscopy (SERS) technique mainly using a novel homemade AuNPs/ZnCl2/NpAA (NpAA: nano porous anodic alumina) solid-state substrate and combined with ultraviolet-visible spectroscopy and molecular docking simulation to reveal the mechanism of their interactions. We experimentally compared and studied the SERS spectra of ctDNA, BENDA, and BENDA-ctDNA complexes with different molar concentrations (1:1, 2:1, 3:1), and summarized their important characteristic peak positions, their peak position differences, and hyperchromic/hypochromic effects. The results showed that the binding modes include covalent binding and hydrogen bonding, and the binding site of BENDA to DNA molecules is mainly the N7 atom of G base. The results of this study help to understand and elucidate the mechanism of BENDA at the single-molecule level, and provide guidance for the further development of effective new drugs with low toxicity and side effects.

Interaction of Doxorubicin Embedded into Phospholipid Nanoparticles and Targeted Peptide-Modified Phospholipid Nanoparticles with DNA

The interactions of dsDNA with new targeted drug delivery derivatives of doxorubicin (DOX), such as DOX embedded into phospholipid nanoparticles (NPhs) and DOX with the NGR targeted peptide-modified NPhs were studied electrochemically by differential pulse voltammetry technique. Screen-printed electrodes (SPEs), modified with stable fine dispersions of carbon nanotubes (CNTs), were used for quantitative electrochemical investigations of direct electrochemical oxidation of guanine, adenine, and thymine heterocyclic bases of dsDNA, and their changes in the presence of DOX nanoderivatives. Analysing the shifts of peak potentials of nucleobases in the presence of drug, we have shown that the doxorubicin with NGR targeted peptide changed the mode of interaction in DNA-drug complexes from intercalative to electrostatic. Binding constants (K_b) of DNA-drug complexes were calculated in accordance with adenine, guanine, and thymine oxidation signals. Based on our experiments, we have proven that the surface modification of a drug delivery system with NGR targeted peptide dramatically changed the mechanism of interaction of drug with genetic material. DNA-mediated drug toxicity was calculated based on the concentration-dependent "response" of heterocyclic nucleobases on drug influence. DOX, DOX-loaded phospholipid nanoparticles (NPhs), and DOX with NGR addressed peptide-modified NPhs were moderately toxic in the concentration range of 0.5-290 µM.

Editorial for the Special Issue on Optics and Photonics in Micromachines

Micromachines, as a platform for manipulation, assembling, detection and imaging, is a typical interdisciplinary field related to broad areas, e [...].

UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA

UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.