Structural investigation of idarubicin–DNA interaction: Spectroscopic and molecular docking study

Indispensable role of microbes in anticancer drugs and discovery trends

Recent years have seen an increased focus on the advancement of naturally derived products for the treatment of cancer. Since the beginning of recorded history, nature has provided a variety of medicinal agents, and an overwhelming number of drugs that we have today are derived from natural sources. Such natural agents are prominently used to treat several diseases such as diabetes, malaria, Alzheimer's, pulmonary disorders, etc. with cancer being the highlight of this review. Due to the rapid development of resistance to chemotherapeutic drugs, the hunt for effective novel drugs is still a paramount concern in cancer treatment. Moreover, many chemotherapy drugs typically have high toxicity and adverse side effects, which necessitates the need to develop anti-tumor drugs that can be employed to treat deadly tumors with fewer negative effects on health and better efficacy. Isolation of several chemotherapeutic drugs has been conducted from a wide range of natural sources which include plants, microbes, fungi, and marine microorganisms. Considering the trends of previous decades, microbial diversity has grown to play a significant role in the formulation of pharmaceuticals and drugs, especially antibiotics and anti-cancer medications. Microbe-derived antitumor antibiotics such as anthracycline, epothilones, bleomycin, actinomycin, and staurosporine are amongst the widely used cancer chemotherapeutic agents. This review deals majorly with microbe-derived anticancer drugs taking into account their derivatives, mechanism of action, isolation procedures, limitations, and tumors targeted by them. This article also reports the phase of clinical study these drugs are undergoing. Moreover, it intends to portray the indispensable part that these microbes have been playing since time immemorial in the odyssey of chemotherapeutic agents. KEY POINTS: • Microbial diversity contributes heavily towards the formulation of anticancer drugs. • Polypeptides, carbohydrates, and alkaloids are prevalent microbe-based drug classes. • Microbe-derived anticancer agents target various sarcomas, carcinomas, and lymphomas.

Self-assembly CuO-loaded nanocomposite involving functionalized DNA with dihydromyricetin for water-based efficient and controllable antibacterial action

With the antibiotic crisis intensifies, the defense and treatment of pathogen infections in safe and effective fashion has become a critical issue. Herein, we report a novel and advanced type of sterilization agent designed via the functionalization DNA nanocarriers based on dihydromyricetin and CuO-loaded nanoparticles (DNA/DMY-CuO). Firstly, a pure dihydromyricetin (DMY) isolated from Ampelopsis grossedentata is used as a bridge to the stimulate the construction of DNA cross-linking networks by hydrogen bonding. Subsequently, a 3D spherical CuO-loaded nanocomposite (204.39 nm) is customized using the DNA/DMY network as a biological template through a simple coordination-assisted self-assembly method, which exhibits a high dispersibility, water-solubility and physiological stability. The reversible physical interactions in nanocarriers allows the selective separation and automatic release of CuO NPs from DNA/DMY-CuO in neutral and wound exudate environments, thereby extending the survival period of CuO NPs by nearly 24 h. Meanwhile, the nanocarriers system relied on the strong binding ability of DMY to the outer membrane of Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) achieves controlled drug delivery onto the pathogen wall. The advanced antibacterial action of DNA/DMY-CuO also reflected in membrane destruction, cytoplasmic constituent leakages and ATP synthetic pathway cessation, thereby halting cytosolic metalloregulatory mechanisms and minimizing drug-resistant bacteria. In summary, such multi-functional CuO-loaded nanocomposite provides a water-dispersibility, controllable, low cytotoxicity and long-effective platform to address the ever-growing threats of bacterial infections.

DNA-Based Electrodes and Computational Approaches on the Intercalation Study of Antitumoral Drugs

The binding between anticancer drugs and double-stranded DNA (dsDNA) is a key issue to understand their mechanism of action, and many chemical methods have been explored on this task. Molecular docking techniques successfully predict the affinity of small molecules into the DNA binding sites. In turn, various DNA-targeted drugs are electroactive; in this regard, their electrochemical behavior may change according to the nature and strength of interaction with DNA. A carbon paste electrode (CPE) modified with calf thymus ds-DNA (CPDE) and computational methods were used to evaluate the drug–DNA intercalation of doxorubicin (DOX), daunorubicin (DAU), idarubicin (IDA), dacarbazine (DAR), mitoxantrone (MIT), and methotrexate (MTX), aiming to evaluate eventual correlations. CPE and CPDE were immersed in pH 7 0.1 mM solutions of each drug with different incubation times. As expected, the CPDE response for all DNA-targeted drugs was higher than that of CPE, evidencing the drug–DNA interaction. A peak current increase of up to 10-fold was observed; the lowest increase was seen for MTX, and the highest increase for MIT. Although this increase in the sensitivity is certainly tied to preconcentration effects of DNA, the data did not agree entirely with docking studies, evidencing the participation of other factors, such as viscosity, interfacial electrostatic interactions, and coefficient of diffusion.

The Interaction between DNA and Three Intercalating Anthracyclines Using Electrochemical DNA Nanobiosensor Based on Metal Nanoparticles Modified Screen-Printed Electrode

The screen-printed electrodes have gained increasing importance due to their advantages, such as robustness, portability, and easy handling. The manuscript presents the investigation of the interaction between double-strand deoxyribonucleic acid (dsDNA) and three anthracyclines: epirubicin (EPI), idarubicin (IDA), and doxorubicin (DOX) by differential pulse voltammetry on metal nanoparticles modified by screen-printed electrodes. In order to investigate the interaction, the voltammetric signals of dsDNA electroactive bases were used as an indicator. The effect of various metal nanomaterials on the signals of guanine and adenine was evaluated. Moreover, dsDNA/PtNPs/AgNPs/SPE (platinum nanoparticles/silver nanoparticles/screen-printed electrodes) was designed for anthracyclines–dsDNA interaction studies since the layer-by-layer modification strategy of metal nanoparticles increases the surface area. Using the signal of multi-layer calf thymus (ct)-dsDNA, the within-day reproducibility results (RSD%) for guanine and adenine peak currents were found as 0.58% and 0.73%, respectively, and the between-day reproducibility results (RSD%) for guanine and adenine peak currents were found as 1.04% and 1.26%, respectively. The effect of binding time and concentration of three anthracyclines on voltammetric signals of dsDNA bases were also evaluated. The response was examined in the range of 0.3–1.3 ppm EPI, 0.1–1.0 ppm IDA and DOX concentration on dsDNA/PtNPs/AgNPs/SPE. Electrochemical studies proposed that the interaction mechanism between three anthracyclines and dsDNA was an intercalation mode.

Evaluation of potential anti-RNA-dependent RNA polymerase (RdRP) drugs against the newly emerged model of COVID-19 RdRP using computational methods

INTRODUCTION

Despite all the efforts to treat COVID-19, no particular cure has been found for this virus. Since developing antiviral drugs is a time-consuming process, the most effective approach is to evaluate the approved and under investigation drugs using in silico methods. Among the different targets within the virus structure, as a vital component in the life cycle of coronaviruses, RNA-dependent RNA polymerase (RdRP) can be a critical target for antiviral drugs. The impact of the existence of RNA in the enzyme structure on the binding affinity of anti-RdRP drugs has not been investigated so far.

METHODS

In this study, the potential anti-RdRP effects of a variety of drugs from two databases (Zinc database and DrugBank) were evaluated using molecular docking. For this purpose, the newly emerged model of COVID-19 (RdRP) post-translocated catalytic complex (PDB ID: 7BZF) that consists of RNA was chosen as the target.

RESULTS

The results indicated that idarubicin (IDR), a member of the anthracycline antibiotic family, and fenoterol (FNT), a known beta-2 adrenergic agonist drug, tightly bind to the target enzyme and could be used as potential anti-RdRP inhibitors of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). These outcomes revealed that due to the ligand-protein interactions, the presence of RNA in this structure could remarkably affect the binding affinity of inhibitor compounds.

CONCLUSION

In silico approaches, such as molecular docking, could effectively address the problem of finding appropriate treatment for COVID-19. Our results showed that IDR and FNT have a significant affinity to the RdRP of SARS-CoV-2; therefore, these drugs are remarkable inhibitors of coronaviruses.

Single-molecule brightness analysis for the determination of anticancer drug interactions with DNA

Anthracyclines are one of the most studied anticancer drugs approved for medical treatment. The equilibrium constant (K) of the reaction between these drugs with DNA in both in vitro and in vivo experiments lacks consensus. The K values vary from 10⁴ up to 10⁸ M^-1, which suggest a 1000-fold error in determining the effective concentration needed to form the drug-DNA complex. Until 2014, only one study by García [J. Phys. Chem. B, 2014, 118, 1288-1295] showed that the binding of anthracycline representative doxorubicin occurs in two reactions. We support this result by brightness analysis at a single molecular level for the four most common anthracyclines: doxorubicin, daunorubicin, epirubicin, and idarubicin.

Exploring the binding mode of donepezil with calf thymus DNA using spectroscopic and molecular docking methods

Donepezil (DNP) is one of approved drugs to treat Alzheimer's disease (AD). However, the potential effect of DNP on DNA is still unclear. Therefore, the interaction of DNP with calf thymus DNA (DNA) was studied in vitro using spectroscopic and molecular docking methods. Steady-state and transient fluorescence experiments showed that there was a clear binding interaction between DNP and DNA, resulting from DNP fluorescence being quenched using DNA. DNP and DNA have one binding site between them, and the binding constant (K_b ) was 0.78 × 10⁴ L·mol^-1 at 298 K. In this binding process, hydrophobic force was the main interaction force, because enthalpy change (ΔH) and entropy change (ΔS) of DNP-DNA were 67.92 kJ·mol^-1 and 302.96 J·mol^-1 ·K^-1 , respectively. DNP bound to DNA in a groove-binding mode, which was verified using a competition displacement study and other typical spectroscopic methods. Fourier transform infrared (FTIR) spectrum results showed that DNP interacted with guanine (G) and cytosine (C) bases of DNA. The molecular docking results further supported the results of spectroscopic experiments, and suggested that both Pi-Sigma force and Pi-Alkyl force were the major hydrophobic force functioning between DNP and DNA.

In vitro spectroscopic investigation of groove binding interaction of Fe3O4@CaAl-LDH@L-Dopa with calf thymus DNA

The principal goal of this study is to evaluate the interaction of Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles with calf thymus DNA. The magnetic nanoparticles were previously prepared by a chemical co-precipitation method, and the surface of the Fe₃O₄ nanoparticles was coated with CaAl layered double hydroxides. The antiparkinsonian drug "L-Dopa" was carried by this core-shell nanostructure to achieve the drug delivery system with suitable properties for biological applications. Also, the interaction of Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles with CT-DNA was studied using, UV-Visible spectroscopy, viscosity, circular dichroism (CD), and fluorescence spectroscopy techniques. The results of investigations demonstrated that Fe₃O₄@CaAl-LDH@L-Dopa and Fe₃O₄@CaAl-LDH nanoparticles have interacted via minor groove binding and intercalated to CT-DNA, respectively.

Idarubicin-bromelain combination sensitizes cancer cells to conventional chemotherapy

Objectives

The primary cytotoxic effects of anticancer drugs like idarubicin, a chemotherapeutic agent, are not limited to neoplastic cells; they also produce similar effects in normal cells. In this study, we hypothesized that the combination of idarubicin-bromelain could make cancer cells more susceptible to cytotoxicity and genotoxicity.

Materials and Methods

To test our hypothesis, the optimal concentrations of idarubicin and bromelain were combined and incubated in the HL-60 cancer cell line and normal human mononuclear leukocytes (PBMC) for 24, 48, and 72 hr. Cytotoxicity and genotoxicity were evaluated by measurement of ATP cell viability test, DNA damage, Caspase-3, Acridine orange/ethidium bromide (AO/EB), and DAPI fluorescent dyes in both cell types.

Results

The combination of idarubicin-bromelain significantly reduced cell proliferation in the more potent HL-60 compared to PBMC in all incubation times (P<0.05). DNA damage and Caspase-3 levels (except for 24 hr) were also higher in the HL-60 cell line in comparison with PBMC and were statistically significant (P<0.05). The percentages of apoptotic images obtained by DAPI and AO / EB morphological examination were increased in both cells, depending on the combination dose.

Conclusion

Based on these results, it can be concluded that idarubicin combined with bromelain produces more cytotoxic effects in low concentrations in comparison with when it was used per se in the HL-60 cells. Conversely, it was found that this combination in PBMC caused less cytotoxicity and less genotoxicity. Taken together, it can be said that this new combination makes cancer cells more sensitive to conventional therapy.

RNA targeting by an anthracycline drug: spectroscopic and in silico evaluation of epirubicin interaction with tRNA

Anthracyclines are putative anticancer agents used to treat a wide range of cancers. Among these anthracyclines, epirubicin is derived from the doxorubicin by the subtle difference in the orientation of C4-hydroxyl group at sugar molecule. Epirubicin has great significance as it has propitious anticancer potential with lesser cardiotoxicity and faster elimination from the body. The present study is done to understand the molecular aspect of epirubicin binding to tRNA. We have used various spectroscopic techniques like Fourier transform infrared spectroscopy (FTIR), absorption spectroscopy and circular dichroism to illustrate the binding sites, the extent of binding and conformational changes associated with tRNA after interacting with epirubicin. From infrared studies, we infer that epirubicin interacts with guanine and uracil bases of tRNA. Results obtained from infrared and CD studies suggest that epirubicin complexation with tRNA does not result in any conformational change in tRNA structure. Binding constant (2.1 × 10³ M^-1) calculated from the absorbance data illustrates that epirubicin has a weak interaction with tRNA molecule. These spectroscopic results like the binding site of epirubicin and binding energy of epirubicin-tRNA complex were also verified by the molecular docking. Results of the present study provide information that aids in the development of efficient RNA targeted drugs from the existing drugs by certain chemical modification in their structure resulting in lesser side effects and better efficacy.Communicated by Ramaswamy H. Sarma.

Binding of platinum derivative, oxaliplatin to deoxyribonucleic acid: structural insight into antitumor action

Platinum-derived chemodrugs constitute an active class in cancer therapeutics. Besides being potent against various solid tumors, oxaliplatin has been recognized as the first platinum compound to be approved for the treatment of colorectal cancer. Structurally, oxaliplatin consists of a platinum metal complexed to oxalate and diaminocyclohexane (DACH) and exert its anticancer action by inhibiting DNA replication and transcription. The present study highlights the binding properties of oxaliplatin with calf thymus DNA using spectroscopic methods to comprehend its binding mechanism at molecular level to overcome associated cellular resistance and side effects. Attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopic outcomes confirm that oxaliplatin is a covalent binding agent and also provide sequence specificity in DNA molecule. Infrared spectral results further indicate that oxaliplatin alkylates purine nitrogenous bases majorly guanine residues (G) in the major groove via formation of either interstrand or intrastrand guanine-guanine d(GpG) and guanine-adenine d(GpA) (N7 position) crosslinks accompanied with a slight external binding to sugar-phosphate backbone. Again, circular dichroism (CD) spectroscopic results suggest subtle conformational changes in DNA molecule due to its complexation with oxaliplatin and duplex attains an intermediate conformational state, having characteristics of both B- and C-forms. Further, a moderate binding strength of 4.12 ± 0.2 × 10⁴ M^-1 for the interaction has been estimated via ultraviolet-visible spectroscopy. The inferences obtained from these investigations are encouraging and can form the basis for further exploration in the field of rational drug development based on platinum compounds possessing preferential binding for nucleic acid with improved competence. Communicated by Ramaswamy H. Sarma.

Comparative studies on the interaction of anticancer drug irinotecan with dsDNA and ssDNA

The binding mode and thermodynamic characteristics of the anticancer drug irinotecan (Irino) with dsDNA were investigated. The interaction of Irino with dsDNA indicated its intercalation into the base stacking domain of dsDNA double helix.

Preparation, characterization and evaluation of (186) Re-idarubicin: a novel agent for diagnosis and treatment of hepatocellular carcinoma

Hepatocellular carcinoma is a widely prevalent cancer, and hence, the development of radiopharmaceuticals for its management is an important issue. In the current investigation, the complexation of idarubicin with (186) Re was studied. Optimum labelling conditions were found to be 4 mg idarubicin, 1.5 mg stannous chloride dihydrate and ~70 MBq Re-186 at pH 7. The complex showed ~97.6% RCY value at 20 min and remained stable up to 24 h in the presence of 2.5 mg ascorbic acid. Molecular docking was performed to evaluate the complex binding to its target DNA-human topoisomerase II complex. Result of the in vivo evaluation showed that the complex tends to preferentially localize in cancerous tissues. The in vitro cell growth inhibition assay showed that the effect of the (186) Re-idarubicin was stronger than the effect of cold idarubicin, which strongly suggested that its cytotoxicity was mainly because of radiotoxicity rather than chemotherapeutic activity.

Binding studies of terbutaline sulfate to calf thymus DNA using multispectroscopic and molecular docking techniques

The interaction of terbutaline sulfate (TS) with calf thymus DNA (ctDNA) were investigated by fluorescence quenching, UV-vis absorption, viscosity measurements, ionic strength effect, DNA melting experiments and molecular docking. The binding constants (Ka) of TS to ctDNA were determined as 4.92×10(4), 1.26×10(4) and 1.16×10(4) L mol(-1) at 17, 27 and 37 °C, respectively. Stern-Volmer plots suggested that the quenching of fluorescence of TS by ctDNA was a static quenching. The absorption spectra of TS with ctDNA revealed a slight blue shift and hyperchromic effect. The relative viscosity ctDNA was hardly changed by TS, and melting temperature varied slightly. For the system of TS-ctDNA, the intensity of fluorescence decreased with the increase of ionic strength. Also, the Ka for TS-double stranded DNA (dsDNA) was clearly weaker than that for TS-single stranded DNA (ssDNA). All these results revealed that the binding mode of TS with ctDNA should be groove binding. The enthalpy change and entropy change suggested that van der Waals force or hydrogen bonds was a main binding force between TS and ctDNA. Furthermore, the quantum yield of TS was measured by comparing with the standard solution. Based on the Förster energy transference theory (FRET), the binding distance between the acceptor and donor was calculated. Molecular docking showed that TS was a minor groove binder of ctDNA and preferentially bound to A-T rich regions.

In vitro DNA binding studies of anticancer drug idarubicin using spectroscopic techniques

The interaction between idarubicin and double stranded deoxyribonucleic acid (ds-DNA) was investigated by UV-VIS spectrophotometry, fluorescence and Raman spectroscopy techniques. The absorption spectra of idarubicin with ds-DNA showed a slight red shift and hypochromic effect. In the fluorescence experiments, emission peaks were decreased by adding ds-DNA. Using ethidium bromide (ETB) as a fluorescence probe, fluorescence quenching of the emission peak was observed in the ETB-DNA system when idarubicin was added. Moreover, similar results were obtained in Raman spectroscopy. Binding constants of idarubicin with ds-DNA were determined as 5.14×10(5) M(-1) and 5.8×10(5) M(-1) for UV-VIS spectrophotometry and fluorescence spectroscopy, respectively. The large binding constant indicated that idarubicin has a high affinity with ds-DNA. All the evidences indicated that the binding mode of idarubicin with DNA was an intercalative binding. Furthermore, quantitative determination of idarubicin in pharmaceutical formulation was done.