New hopes from old drugs: revisiting DNA-binding small molecules as anticancer agents

Synthesis of Marine-Inspired Multifaceted DNA Damaging Spirooxindoles Combating NSCLC and Associated Bacterial Infection

Targeted therapeutics have gained prominence in combating non-small cell lung carcinoma (NSCLC) and opportunistic bacterial infections like Staphylococcus aureus (S. aureus). This study explores dual-acting marine-inspired spirooxindoles to limit NSCLC and opportunistic bacteria. Pharmacophoric motifs from antitumor and antibacterial marine products were merged into a new series of pyrazole-clubbed spirooxindoles via a stereoselective [3 + 2] cycloaddition reaction. MTT screening identified 4e, 4i, and 4p-4s as potent cytotoxic agents, with 4p showing exceptional activity (IC50 = 0.042 μM) and tumor selectivity (SI = 58.28). 4p exhibited antibacterial efficacy against S. aureus (MIC = 25 μg/mL). DNA damage studies using a terbium(III) chloride biosensor revealed 4p's ability to damage both calf thymus and S. aureus DNA at low concentrations. Docking simulations presumed that 4p binds between DNA strands, while apoptosis studies indicated it induced G1/S phase cell cycle arrest and increased A549 apoptosis by 33.65%. These findings highlight 4p as a promising lead for further studies.

Comprehensive Evaluation of End-Point Free Energy Methods in DNA-Ligand Interaction Predictions

Deoxyribonucleic acid (DNA) serves as a repository of genetic information in cells and is a critical molecular target for various antibiotics and anticancer drugs. A profound understanding of small molecule interaction with DNA is crucial for the rational design of DNA-targeted therapies. While the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics/generalized Born surface area (MM/GBSA) approaches have been well established for predicting protein-ligand binding, their application to DNA-ligand interactions has been less explored. In this study, we systematically investigated the binding of 13 diverse small molecules to DNA, evaluating the accuracy of DNA-ligand interaction predictions across different solvation approaches, interior dielectric constants (εin), and molecular force fields. Our results demonstrate that MM/PBSA, using energy-minimized structures (the bsc1 force field and εin = 20), provides the best correlation (Rp = -0.742) with experimental binding affinities, surpassing the performance of rDock scoring functions (best Rp = -0.481). Notably, the interior dielectric constant was found to significantly impact DNA-ligand binding free energy predictions, especially for MM/PBSA. Moreover, both MM/PBSA and MM/GBSA predictions (εin = 16 or 20) exhibited superior performance in distinguishing native-like binding modes within the top-10 poses from decoys, compared to the molecular docking tools used in this study. However, the popular docking software PLANTS demonstrates notable efficacy in predicting the top-1 binding pose. Given the considerably higher computational cost of MM/PBSA, MM/GBSA rescoring with higher εin = 16 or 20 is more efficient for recognizing the native-like binding poses for DNA-ligand systems. This study presents the first detailed exploration of end-point free energy calculations in the context of DNA-ligand interactions and offers valuable insights for the application of the MM/PB(GB)SA methods in this domain.

Structure optimization and molecular dynamics studies of new tumor-selective s-triazines targeting DNA and MMP-10/13 for halting colorectal and secondary liver cancers

A series of triazole-tethered triazines bearing pharmacophoric features of DNA-targeting agents and non-hydroxamate MMPs inhibitors were synthesized and screened against HCT-116, Caco-2 cells, and normal colonocytes by MTT assay. 7a and 7g surpassed doxorubicin against HCT-116 cells regarding potency (IC50 = 0.87 and 1.41 nM) and safety (SI = 181.93 and 54.41). 7g was potent against liver cancer (HepG-2; IC50 = 65.08 nM), the main metastatic site of CRC with correlation to MMP-13 expression. Both derivatives induced DNA damage at 2.67 and 1.87 nM, disrupted HCT-116 cell cycle and triggered apoptosis by 33.17% compared to doxorubicin (DNA damage at 0.76 nM and 40.21% apoptosis induction). 7g surpassed NNGH against MMP-10 (IC50 = 0.205 μM) and MMP-13 (IC50 = 0.275 μM) and downregulated HCT-116 VEGF related to CRC progression by 38%. Docking and MDs simulated ligands-receptors binding modes and highlighted SAR. Their ADMET profiles, drug-likeness and possible off-targets were computationally predicted.

Exploiting spirooxindoles for dual DNA targeting/CDK2 inhibition and simultaneous mitigation of oxidative stress towards selective NSCLC therapy; synthesis, evaluation, and molecular modelling studies

The unique structure of spirooxindoles and their ability to feature various pharmacophoric motifs render them privileged scaffolds for tailoring new multitarget anticancer agents. Herein, a stereoselective multicomponent reaction was utilized to generate a small combinatorial library of pyrazole-tethered spirooxindoles targeting DNA and CDK2 with free radical scavenging potential as an extra bonus. The designed spirooxindoles were directed to combat NSCLC via inducing apoptosis and alleviating oxidative stress. The series' absolute configuration was assigned by X-ray diffraction analysis. Cytotoxicity screening of the developed spirooxindoles against NSCLC A549 and H460 cells compared to normal lung fibroblasts Wi-38 revealed the sensitivity of A549 cells to the compounds and raised 6e and 6h as the study hits (IC50 ∼ 0.09 μM and SI > 3). They damaged DNA at 24.6 and 35.3 nM, and surpassed roscovitine as CDK2 inhibitors (IC50 = 75.6 and 80.2 nM). Docking and MDs simulations postulated their receptors binding modes. The most potent derivative, 6e, induced A549 apoptosis by 40.85% arresting cell cycle at G2/M phase, and exhibited antioxidant activity in a dose-dependent manner compared to Trolox as indicated by DPPH scavenging assay. Finally, in silico ADMET analysis predicted the drug-likeness properties of 6e.

The role of cGAS in epithelial dysregulation in inflammatory bowel disease and gastrointestinal malignancies

The gastrointestinal tract is lined by an epithelial monolayer responsible for selective permeability and absorption, as well as protection against harmful luminal contents. Recognition of foreign or aberrant DNA within these epithelial cells is, in part, regulated by pattern recognition receptors such as cyclic GMP-AMP synthase (cGAS). cGAS binds double-stranded DNA from exogenous and endogenous sources, resulting in the activation of stimulator of interferon genes (STING) and a type 1 interferon response. cGAS is also implicated in non-canonical pathways involving the suppression of DNA repair and the upregulation of autophagy via interactions with PARP1 and Beclin-1, respectively. The importance of cGAS activation in the development and progression of inflammatory bowel disease and gastrointestinal cancers has been and continues to be explored. This review delves into the intricacies of the complex role of cGAS in intestinal epithelial inflammation and gastrointestinal malignancies, as well as recent therapeutic advances targeting cGAS pathways.

Triggering Breast Cancer Apoptosis via Cyclin-Dependent Kinase Inhibition and DNA Damage by Novel Pyrimidinone and 1,2,4-Triazolo[4,3-a]pyrimidinone Derivatives

Combinations of apoptotic inducers are common clinical practice in breast cancer. However, their efficacy is limited by the heterogeneous pharmacokinetic profiles. An advantageous alternative is merging their molecular entities in hybrid multitargeted scaffolds exhibiting synergistic activities and uniform distribution. Herein, we report apoptotic inducers simultaneously targeting DNA and CDK-2 (cyclin-dependent kinase-2) inspired by studies revealing that CDK-2 inhibition sensitizes breast cancer to DNA-damaging agents. Accordingly, rationally substituted pyrimidines and triazolopyrimidines were synthesized and assayed by MTT against MCF-7, MDA-MB231, and Wi-38 cells compared to doxorubicin. The N-(4-amino-2-((2-hydrazinyl-2-oxoethyl)thio)-6-oxo-1,6-dihydropyrimidin-5-yl)acetamide 5 and its p-nitrophenylhydrazone 8 were the study hits against MCF-7 (IC50 = 0.050 and 0.146 μM) and MDA-MB231 (IC50 = 0.826 and 0.583 μM), induced DNA damage at 10.64 and 30.03 nM, and inhibited CDK-2 (IC50 = 0.172 and 0.189 μM). 5 induced MCF-7 apoptosis by 46.75% and disrupted cell cycle during S phase. Docking and MD simulations postulated their stable key interactions.

The cGAS-STING pathway in cardiovascular diseases: from basic research to clinical perspectives

The cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase-stimulator of interferon genes (cGAS-STING) signaling pathway, an important component of the innate immune system, is involved in the development of several diseases. Ectopic DNA-induced inflammatory responses are involved in several pathological processes. Repeated damage to tissues and metabolic organelles releases a large number of damage-associated molecular patterns (mitochondrial DNA, nuclear DNA, and exogenous DNA). The DNA fragments released into the cytoplasm are sensed by the sensor cGAS to initiate immune responses through the bridging protein STING. Many recent studies have revealed a regulatory role of the cGAS-STING signaling pathway in cardiovascular diseases (CVDs) such as myocardial infarction, heart failure, atherosclerosis, and aortic dissection/aneurysm. Furthermore, increasing evidence suggests that inhibiting the cGAS-STING signaling pathway can significantly inhibit myocardial hypertrophy and inflammatory cell infiltration. Therefore, this review is intended to identify risk factors for activating the cGAS-STING pathway to reduce risks and to simultaneously further elucidate the biological function of this pathway in the cardiovascular field, as well as its potential as a therapeutic target.

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

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

RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method

Small molecule drugs can be used to target nucleic acids (NA) to regulate biological processes. Computational modeling methods, such as molecular docking or scoring functions, are commonly employed to facilitate drug design. However, the accuracy of the scoring function in predicting the closest-to-native docking pose is often suboptimal. To overcome this problem, a machine learning model, RmsdXNA, was developed to predict the root-mean-square-deviation (RMSD) of ligand docking poses in NA complexes. The versatility of RmsdXNA has been demonstrated by its successful application to various complexes involving different types of NA receptors and ligands, including metal complexes and short peptides. The predicted RMSD by RmsdXNA was strongly correlated with the actual RMSD of the docked poses. RmsdXNA also outperformed the rDock scoring function in ranking and identifying closest-to-native docking poses across different structural groups and on the testing dataset. Using experimental validated results conducted on polyadenylated nuclear element for nuclear expression triplex, RmsdXNA demonstrated better screening power for the RNA-small molecule complex compared to rDock. Molecular dynamics simulations were subsequently employed to validate the binding of top-scoring ligand candidates selected by RmsdXNA and rDock on MALAT1. The results showed that RmsdXNA has a higher success rate in identifying promising ligands that can bind well to the receptor. The development of an accurate docking score for a NA-ligand complex can aid in drug discovery and development advancements. The code to use RmsdXNA is available at the GitHub repository https://github.com/laiheng001/RmsdXNA.

Deep-WET: a deep learning-based approach for predicting DNA-binding proteins using word embedding techniques with weighted features

DNA-binding proteins (DBPs) play a significant role in all phases of genetic processes, including DNA recombination, repair, and modification. They are often utilized in drug discovery as fundamental elements of steroids, antibiotics, and anticancer drugs. Predicting them poses the most challenging task in proteomics research. Conventional experimental methods for DBP identification are costly and sometimes biased toward prediction. Therefore, developing powerful computational methods that can accurately and rapidly identify DBPs from sequence information is an urgent need. In this study, we propose a novel deep learning-based method called Deep-WET to accurately identify DBPs from primary sequence information. In Deep-WET, we employed three powerful feature encoding schemes containing Global Vectors, Word2Vec, and fastText to encode the protein sequence. Subsequently, these three features were sequentially combined and weighted using the weights obtained from the elements learned through the differential evolution (DE) algorithm. To enhance the predictive performance of Deep-WET, we applied the SHapley Additive exPlanations approach to remove irrelevant features. Finally, the optimal feature subset was input into convolutional neural networks to construct the Deep-WET predictor. Both cross-validation and independent tests indicated that Deep-WET achieved superior predictive performance compared to conventional machine learning classifiers. In addition, in extensive independent test, Deep-WET was effective and outperformed than several state-of-the-art methods for DBP prediction, with accuracy of 78.08%, MCC of 0.559, and AUC of 0.805. This superior performance shows that Deep-WET has a tremendous predictive capacity to predict DBPs. The web server of Deep-WET and curated datasets in this study are available at https://deepwet-dna.monarcatechnical.com/ . The proposed Deep-WET is anticipated to serve the community-wide effort for large-scale identification of potential DBPs.

Discovery of novel benzimidazole acyclic C-nucleoside DNA intercalators halting breast cancer growth

Breast cancer continues to be the most frequent cancer worldwide. In practice, successful clinical outcomes were achieved via targeting DNA. Along with the advances in introducing new DNA-targeting agents, the "sugar approach" design was employed herein to develop new intercalators bearing pharmacophoric motifs tethered to carbohydrate appendages. Accordingly, new benzimidazole acyclic C-nucleosides were rationally designed, synthesized and assayed via MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay to evaluate their cytotoxicity against MCF-7 and MDA-MB-231 breast cancer cells compared to normal fibroblasts (Wi-38), compared to doxorubicin. (1S,2R,3S,4R)-2-(1,2,3,4,5-Pentahydroxy)pentyl-1H-5,6-dichlorobenzimidazole 7 and (1S,2R,3S,4R)-2-(1,2,3,4,5-pentahydroxy)pentyl-1H-naphthimidazole 13 were the most potent and selective derivatives against MCF-7 (half-maximal inhibitory concentration [IC50 ] = 0.060 and 0.080 µM, selectivity index [SI] = 9.68 and 8.27, respectively) and MDA-MB-231 cells (IC50  = 0.299 and 0.166 µM, SI = 1.94 and 3.98, respectively). Thus, they were identified as the study hits for mechanistic studies. Both derivatives induced DNA damage at 0.24 and 0.29 μM, respectively. The DNA damage kinetics were studied compared to doxorubicin, where they both induced faster damage than doxorubicin. This indicated that 7 and 13 showed a more potent DNA-damaging effect than doxorubicin. Docking simulations within the DNA double strands highlighted the role of both the heterocyclic core and the sugar side chain in exhibiting key H-bond interactions with DNA bases.

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.

Neutral and cationic nickel(II) complexes with substituted salicylaldehydes: Characterization, antibacterial activity, and interaction with biomacromolecules

Four neutral and six cationic nickel(II) complexes of the substituted salicylaldehydes (X-diCl-saloH), namely 3,5-dichloro-salicylaldehyde (3,5-diCl-saloH) and 5-fluoro-salicylaldehyde (5-F-saloH), were synthesized in the absence or presence of the N,N'-donors 1,10-phenanthroline (phen), 2,9-dimethyl-1,10-phenanthroline (neoc), or 2,2'-bipyridylamine (bipyam) as co-ligands and were characterized by various techniques. The obtained complexes bear the general formulas [Ni(X-salo)2(H2O)2], [Ni(3,5-diCl-salo)2(neoc/phen)] and [Ni(X-salo)(N,N'-donor)2](PF6). The crystal structures of three complexes were determined by single-crystal X-ray crystallography revealing a bidentate coordination of the salicylaldehydes. The interaction of the compounds with calf-thymus DNA was studied by diverse techniques which revealed an intercalative interaction for the neutral complexes [Ni(X-salo)2(H2O)2] and [Ni(3,5-diCl-salo)2(neoc/phen)]and the co-existence of electrostatic interactions for the cationic complexes [Ni(X-salo)(N,N'-donor)2](PF6). The compounds bind tightly and reversibly to serum albumins. The antibacterial activity of the compounds was investigated against Staphylococcus aureus ATCC 6538, Bacillus subtilis ATCC 6633, Escherichia coli NCTC 29,212 and Xanthomonas campestris ATCC 1395 and the complexes bearing neoc as co-ligand proved the most potent.

Dual FLT3/haspin kinase inhibitor based on 3H-pyrazolo[4,3-f]quinoline scaffold with activities against acute myeloid leukemia

The 3H-pyrazolo[4,3-f]quinoline core, a privileged fusion moiety from quinoline and indazole, facilely synthesized in a one flask multi-component Doebner-Povarov reaction, is a newly described kinase hinge binder. Previous works have demonstrated that the 3H-pyrazolo[4,3-f]quinoline moiety can be tuned, via judicious substitution patterns, to selectively inhibit cancer-associated kinases, such as FLT3 and haspin. A first generation 3H-pyrazolo[4,3-f]quinoline-based haspin inhibitor, HSD972, and FLT3 inhibitor, HSD1169, were previously disclosed as inhibitors of various cancer cell lines. Given the recent revelation that haspin is over-expressed and plays critical proliferative roles in many cancers, and compounds with dual activity against FLT3 and other important kinases are now being actively developed by many groups, we became interested in optimizing the 3H-pyrazolo[4,3-f]quinoline-based compounds to improve activity against both FLT3 and haspin. Herein, we report the discovery of new 3H-pyrazolo[4,3-f]quinoline-based dual FLT3/haspin inhibitor, HSK205. HSK205 has remarkable potencies against FLT3-driven AML cell lines, inhibiting proliferation with GI50 values between 2-25 nM. Western blot analyses of treated AML cells confirm that HSK205 inhibit the phosphorylation of both FLT3 and histone H3 (a haspin target) in cells. While multi-component reactions (MCRs) have been used to make many bioactive molecules, there are very few examples of using MCRs to make compounds that target protein kinases, which have emerged as one of the top drug candidates (especially in oncology). This work highlights our recent efforts to make ultrapotent protein kinase inhibitors using multi-component reactions (especially the Doebner-Povarov reaction).

Peroxidase-Mimicking Ir-Te Nanorods for Photoconversion-Combined Multimodal Cancer Therapy

Owing to multiple physicochemical properties, the combination of hybrid elemental compositions of nanoparticles can be widely utilized for a variety of applications. To combine pristine tellurium nanorods, which act as a sacrificing template, with another element, iridium-tellurium nanorods (IrTeNRs) were synthesized via the galvanic replacement technique. Owing to the coexistence of iridium and tellurium, IrTeNRs exhibited unique properties, such as peroxidase-like activity and photoconversion. Additionally, the IrTeNRs demonstrated exceptional colloidal stability in complete media. Based on these properties, the IrTeNRs were applied to in vitro and in vivo cancer therapy, allowing for the possibility of multiple therapeutic methodologies. The enzymatic therapy was enabled by the peroxidase-like activity that generated reactive oxygen species, and the photoconversion under 473, 660 and 808 nm laser irradiation induced cancer cell apoptosis via photothermal and photodynamic therapy.

Targeting genomic DNAs and oligonucleotide on base specificity: A comparative spectroscopic, computational and in vitro study

Drug discovery in targeted nucleic acid therapeutics encompass several stages and rigorous challenges owing to less specificity of the DNA binders and high failure rate in different stages of clinical trials. In this perspective, we report newly synthesized ethyl 4-(pyrrolo[1,2-a]quinolin-4-yl)benzoate (PQN) with minor groove A-T base pair binding selectivity and encouraging in cell results. This pyrrolo quinolin derivative has shown excellent groove binding ability with three of our inspected genomic DNAs (cpDNA 73 % AT, ctDNA58% AT and mlDNA 28 % AT) with varying A-T and G-C content. Notably in spite of similar binding patterns PQN have strong binding preference with A-T rich groove of genomic cpDNA over the ctDNA and mlDNA. Spectroscopic experiments like steady state absorption and emission results have established the relative binding strengths (K_abs = 6.3 × 10⁵ M^-1, 5.6 × 10⁴ M^-1, 4.3 × 10⁴ M^-1 and K_emiss = 6.1 × 10⁵ M^-1, 5.7 × 10⁴ M^-1 and 3.5 × 10⁴ M^-1 for PQN-cpDNA, PQN-ctDNA and PQN-mlDNA respectively) whereas circular dichroism and thermal melting studies have unveiled the groove binding mechanism. Specific A-T base pair attachment with van der Waals interaction and quantitative hydrogen bonding assessment were characterized by computational modeling. In addition to genomic DNAs, preferential A-T base pair binding in minor groove was also observed with our designed and synthesized deca-nucleotide (primer sequences 5^/-GCGAATTCGC-3^/ and 3^/-CGCTTAAGCG-5^/). Cell viability assays (86.13 % in 6.58 μM and 84.01 % in 9.88 μM concentrations) and confocal microscopy revealed low cytotoxicity (IC₅₀ 25.86 μM) and efficient perinuclear localization of PQN. We propose PQN with excellent DNA-minor groove binding capacity and intracellular permeation properties, as a lead for further studies encompassing nucleic acid therapeutics.

Molecular Mechanism of Ligand Binding to the Minor Groove of DNA

Although DNA-ligand binding is pervasive in biology, little is known about molecular-level binding mechanisms. Using all-atom, explicit-solvent molecular dynamics simulations in conjunction with weighted ensemble (WE)-enhanced sampling, an ensemble of 2562 binding trajectories of Hoechst 33258 (H33258) to d(CGC AAA TTT GCG) was generated from which the binding mechanism was extracted. In particular, the electrostatic interaction between the positively charged H33258 and the negatively charged DNA backbone drives the formation of initial H33258-DNA contacts. After this initial contact, a hinge-like intermediate state is formed in which one end of H33258 inserts into the minor groove of DNA. Following hinge state formation is a concerted motion whereby the second end of H33258 swings into the minor groove and the spine of hydration along the minor groove causing dehydration. This study illustrates how WE-enhanced simulations of biomolecular ligation processes can offer novel mechanistic insights by generating ensembles of binding events.

pH-Sensitive Gold Nanorods for Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) Delivery and DNA-Binding Studies

A facile experimental protocol for the synthesis of poly(ethylene glycol)-modified (PEGylated) gold nanorods (AuNRs@PEG) is presented as well as an effective drug loading procedure using the non-steroidal anti-inflammatory drug (NSAID) naproxen (NAP). The interaction of AuNRs@PEG and drug-loaded AuNRs (AuNRs@PEG@NAP) with calf-thymus DNA was studied at a diverse temperature revealing different interaction modes; AuNRs@PEG may interact via groove-binding and AuNRs@PEG@NAP may intercalate to DNA-bases. The cleavage activity of the gold nanoparticles for supercoiled circular pBR322 plasmid DNA was studied by gel electrophoresis while their affinity for human and bovine serum albumins was also evaluated. Drug-release studies revealed a pH-sensitive behavior with a release up to a maximum of 24% and 33% NAP within the first 180 min at pH = 4.2 and 6.8, respectively. The cytotoxicity of AuNRs@PEG and AuNRs@PEG@NAP was evaluated against MCF-7 and MDA-MB-231 breast cancer cell lines. The development of AuNRs as an efficient non-steroidal anti-inflammatory drugs (NSAIDs) delivery system for chemotherapy is still in its infancy. The present work can shed light and inspire other research groups to work in this direction.

Iron(III) Complexes with Non-Steroidal Anti-Inflammatory Drugs: Structure, Antioxidant and Anticholinergic Activity, and Interaction with Biomolecules

One the main research goals of bioinorganic chemists is the synthesis of novel coordination compounds possessing biological potency. Within this context, three novel iron(III) complexes with the non-steroidal anti-inflammatory drugs diflunisal and diclofenac in the presence or absence of the nitrogen donors 1,10-phenanthroline or pyridine were isolated and characterized by diverse techniques. The complexes were evaluated for their ability to scavenge in vitro free radicals such as hydroxyl, 1,1-diphenyl-2-picrylhydrazyl and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radicals, revealing their selective potency towards hydroxyl radicals. The in vitro inhibitory activity of the complexes towards the enzymes acetylcholinesterase and butyrylcholinesterase was evaluated, and their potential to achieve neuroprotection appeared promising. The interaction of the complexes with calf-thymus DNA was examined in vitro, revealing their ability to intercalate in-between DNA nucleobases. The affinity of the complexes for serum albumins was evaluated in vitro and revealed their tight and reversible binding.

Interaction of the platinum complex of tyrosine-β-cyclodextrin with G-quadruplex DNA

The telomeric quadruplex structures formed by the guanine-rich sequences of DNA have emerged as targets for small molecules designed and synthesized to stabilize the G-quadruplexes. This report presents a newly synthesized tyrosine-tethered cyclodextrin derivative and its platinum complex. Their structures are characterized using IR, NMR, and mass spectral techniques. The binding interactions of the platinum complex with CT-DNA and the kit22, myc22, and telo24 G-quadruplexes are investigated employing absorption and fluorescence spectral titrations. The binding constant or KSV values of the interaction with the G-quadruplexes are more significant than those with the duplex DNA by order of 10. It presents the compound as a G-quadruplex-selective binder. Further, the well-known G-quadruplex binding molecule Berberine is encapsulated in the Tyr- β-CD through a host: guest association. The structure of the host: guest complex is investigated employing 2D ROESY spectroscopy. In addition, the study on the binding interaction of the complex to the DNA targets is also carried out. The mode and strength of interaction of the free and the Berberine-loaded Tyr-β-CD to the duplex and the quadruplexes are reported.

Nanomolar Binding of an Antibiotic Peptide to DNA Measured with Raman Spectroscopy

Immobilization of DNA to surfaces offers a convenient means of screening the binding affinity and selectivity of potential small-molecule therapeutic candidates. Unfortunately, most surface-sensitive methods for detecting these binding interactions are not informative of the molecular structure, information that is valuable for understanding the non-covalent interactions that stabilize binding. In this work, we report a method to meet this challenge by employing confocal Raman microscopy to quantify the association of a minor-groove-binding antimicrobial peptide, netropsin, to duplex DNA hairpin sequences immobilized on the interior surfaces of porous silica particles. To assess binding selectivity, particles functionalized with different sequences of DNA were equilibrated with solutions of 100 nM netropsin, and selective association was detected based on the presence of netropsin Raman scattering in the particles. The selectivity study revealed that netropsin binds to sequences of duplex DNA having AT-rich recognition regions. To quantify binding affinities, these AT-rich DNA sequences were equilibrated with a range of netropsin solution concentrations (1 to 100 nM). Raman scattering intensities of netropsin versus solution concentration were well described by single-binding-site Langmuir isotherms with nanomolar dissociation constants, in agreement with previous isothermal calorimetry and surface plasmon resonance results. Target sequence binding was accompanied with changes in netropsin and DNA vibrational modes consistent with the hydrogen bonding between the amide groups of netropsin and adenine and thymine bases in the DNA minor groove. The binding of netropsin to a control sequence lacking the AT-rich recognition region exhibited an affinity nearly 4 orders of magnitude weaker than found for the target sequences. The Raman spectrum of netropsin interacting with this control sequence showed broad pyrrole and amide mode vibrations at frequencies similar to a free solution, revealing less constrained conformations compared with the specific binding interactions observed with AT-rich sequences.

Metal Complexes with Naphthalene-Based Acetic Acids as Ligands: Structure and Biological Activity

Naproxen (6-methoxy-α-methyl-2-naphthaleneacetic acid), 1-naphthylacetic acid, 2-naphthylacetic acid and 1-pyreneacetic acid are derivatives of acetic acid bearing a naphthalene-based ring. In the present review, the coordination compounds of naproxen, 1- or 2-naphthylacetato and 1-pyreneacetato ligands are discussed in regard to their structural features (nature and nuclearity of metal ions and coordination mode of ligands), their spectroscopic and physicochemical properties and their biological activities.

Inhibition of Cancer Cell Proliferation and Bacterial Growth by Silver(I) Complexes Bearing a CH3-Substituted Thiadiazole-Based Thioamide

Ag(I) coordination compounds have recently attracted much attention as antiproliferative and antibacterial agents against a wide range of cancer cell lines and pathogens. The bioactivity potential of these complexes depends on their structural characteristics and the nature of their ligands. Herein, we present a series of four Ag(I) coordination compounds bearing as ligands the CH₃-substituted thiadiazole-based thioamide 5-methyl-1,3,4-thiadiazole-2-thiol (mtdztH) and phosphines, i.e., [AgCl(mtdztH)(PPh₃)₂] (1), [Ag(mtdzt)(PPh₃)₃] (2), [AgCl(mtdztH)(xantphos)] (3), and [AgmtdztH)(dppe)(NO₃)]_n (4), where xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene and dppe = 1,2-bis(diphenylphosphino)ethane, and the assessment of their in vitro antibacterial and anti-cancer efficiency. Among them, diphosphine-containing compounds 3 and 4 were found to exhibit broad-spectrum antibacterial activity characteristics against both Gram-(+) and Gram-(-) bacterial strains, showing high in vitro bioactivity with IC₅₀ values as low as 4.6 μΜ. In vitro cytotoxicity studies against human ovarian, pancreatic, lung, and prostate cancer cell lines revealed the strong cytotoxic potential of 2 and 4, with IC₅₀ values in the range of 3.1-24.0 μΜ, while 3 and 4 maintained the normal fibroblast cells' viability at relatively higher levels. Assessment of these results, in combination with those obtained for analogous Ag(I) complexes bearing similar heterocyclic thioamides, suggest the pivotal role of the substituent groups of the thioamide heterocyclic ring in the antibacterial and anti-cancer efficacy of the respective Ag(I) complexes. Compounds 1-4 exhibited moderate in vitro antioxidant capacity for free radicals scavenging, as well as reasonably strong ability to interact with calf-thymus DNA, suggesting the likely implication of these properties in their bioactivity mechanisms. Complementary insights into the possible mechanism of their anti-cancer activity were provided by molecular docking calculations, exploring their ability to bind to the overexpressed fibroblast growth factor receptor 1 (FGFR1), affecting cancer cells' functionalities.

Revisiting recent unusual drug-DNA complex structures: Implications for cancer and neurological disease diagnostics and therapeutics

DNA plays a crucial role in various biological processes such as protein production, replication, recombination etc. by adopting different conformations. Targeting these conformations by small molecules is not only important for disease therapy, but also improves our understanding of the mechanisms of disease development. In this review, we provide an overview of some of the most recent ligand-DNA complexes that have diagnostic and therapeutic applications in neurological diseases caused by abnormal repeat expansions and in cancer associated with mismatches. In addition, we have discussed important implications of ligands targeting higher-order structures, such as four-way junctions, G-quadruplexes and triplexes for drug discovery and DNA nanotechnology. We provide an overview of the results and perspectives of such structural studies on ligand-DNA interactions.

Anticancer potential of mebendazole against chronic myeloid leukemia: in silico and in vitro studies revealed new insights about the mechanism of action

Chronic myeloid leukemia (CML) is caused by constitutively active fusion protein BCR-ABL1, and targeting ABL1 is a promising therapy option. Imatinib, dasatinib, and nilotinib have all been shown to work effectively in clinical trials. ABL1 mutations, particularly the T315I gate-keeper mutation, cause resistance in patients. As a result, broad-spectrum ABL1 medicines are desperately needed. In order to screen potential drugs targeting CML, mebendazole (MBZ) was subjected to the in vitro test against CML cell lines (K562 and FEPS) and computational assays. The antiproliferative effect of MBZ and the combination with tyrosine kinase inhibitors (TKIs) was tested using end-point viability assays, cell cycle distribution analysis, cell membrane, and mitochondrial dyes. By interrupting the cell cycle and causing cell death, MBZ and its combination with imatinib and dasatinib have a significant antiproliferative effect. We identified MBZ as a promising “new use” drug targeting wild-type and mutant ABL1 using molecular docking. Meanwhile, we determined which residues in the allosteric site are important in ABL1 drug development. These findings may not only serve as a model for repositioning current authorized medications but may also provide ABL1-targeted anti-CML treatments a fresh lease of life.

G-Quadruplex selectivity and cytotoxicity of a guanidine-encapsulated porphyrin-cyclodextrin conjugate

G-Quadruplex DNAs represent out-of-the-way nucleic acid conformations, frequently formed by guanine-rich sequences. They have emanated as cancer-associated targets for designed small molecules. The variation in the binding affinity of the synthesized compounds to duplex and quadruplex structures is an intriguing quest, solved by spectroscopic analysis. In this paper, we report the synthesis of a porphyrin-cyclodextrin conjugate, characterized by utilizing FT-IR, NMR, and mass spectrometry. Further, two benzimidazolylguanidines are synthesized which form host: guest complexes with the porphyrin-cyclodextrin conjugate. The structure of the complexes is optimized by analyzing their 2D ROESY spectra. The interactions of the host, guest, and the host: guest complexes with the duplex (calf thymus DNA) and quadruplex (kit22) nucleic acids are investigated employing UV-vis, fluorescence, circular dichroism, and DNA melting experiments. The calculated strengths of the compounds' binding with kit22 are in the order of 10⁶, which is larger than those observed for the duplex DNA binding. The significant G-quadruplex selectivity of the host: guest complex of anthracenyl-benzimidazolylguanidine is discussed in detail. Further, the in vitro cytotoxicity of the compounds on MCF-7 cell lines is examined. The host: guest complexes show enhanced half-maximal inhibitory concentration values compared to the un-complexed compounds.

Palladium(II) Complexes of Substituted Salicylaldehydes: Synthesis, Characterization and Investigation of Their Biological Profile

Five palladium(II) complexes of substituted salicylaldehydes (X-saloH, X = 4-Et2N (for 1), 3,5-diBr (for 2), 3,5-diCl (for 3), 5-F (for 4) or 4-OMe (for 5)) bearing the general formula [Pd(X-salo)2] were synthesized and structurally characterized. The crystal structure of complex [Pd(4-Et2N-salo)2] was determined by single-crystal X-ray crystallography. The complexes can scavenge 1,1-diphenyl-picrylhydrazyl and 2,2′-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radicals and reduce H2O2. They are active against two Gram-positive (Staphylococcus aureus and Bacillus subtilis) and two Gram-negative (Escherichia coli and Xanthomonas campestris) bacterial strains. The complexes interact strongly with calf-thymus DNA via intercalation, as deduced by diverse techniques and via the determination of their binding constants. Complexes interact reversibly with bovine and human serum albumin. Complementary insights into their possible mechanisms of bioactivity at the molecular level were provided by molecular docking calculations, exploring in silico their ability to bind to calf-thymus DNA, Escherichia coli and Staphylococcus aureus DNA-gyrase, 5-lipoxygenase, and membrane transport lipid protein 5-lipoxygenase-activating protein, contributing to the understanding of the role complexes 1–5 can play both as antioxidant and antibacterial agents. Furthermore, in silico predictive tools have been employed to study the chemical reactivity, molecular properties and drug-likeness of the complexes, and also the drug-induced changes of gene expression profile (as protein- and mRNA-based prediction results), the sites of metabolism, the substrate/metabolite specificity, the cytotoxicity for cancer and non-cancer cell lines, the acute rat toxicity, the rodent organ-specific carcinogenicity, the anti-target interaction profiles, the environmental ecotoxicity, and finally the activity spectra profile of the compounds.

Low doses of niclosamide and quinacrine combination yields synergistic effect in melanoma via activating autophagy-mediated p53-dependent apoptosis

Malignant melanoma is a highly aggressive, malignant, and drug-resistant tumor. It lacks an efficient treatment approach. In this study, we developed a novel anti-melanoma strategy by using anti-tapeworm drug niclosamide and anti-malarial drug quinacrine, and investigated the molecular mechanism by in vitro and in vivo assays. Meanwhile, other types of tumor cells, immortalized epithelial cells and bone marrow mesenchymal stem cells were used to evaluate the universal role of anti-cancer and safety of the strategy. The results showed, briefly, an exposure to niclosamide and quinacrine led to an increased apoptosis-related protein p53, cleaved caspase-3 and cleaved PARP and autophagy-related protein LC3B expression, and a decreased expression of autophagy-related protein p62, finally leading to cell apoptosis and autophage. After inhibiting autophagy by Baf-A1, flow cytometry and western blot showed that the expression of apoptosis-related proteins was down-regulated and the number of apoptotic cells decreased. Subsequently, in the siRNA-mediated p53 knockdown cells, the expression of apoptosis-related proteins and the number of apoptotic cells were also reduced, while the expression of autophagy-related proteins including LC3B, p62 did not change significantly. To sum up, we developed a new, safe strategy for melanoma treatment by using low doses of niclosamide and quinacrine to treat melanoma; and found a novel mechanism by which the combination application of low doses of niclosamide and quinacrine exerts an efficient anti-melanoma effect through activation of autophagy-mediated p53-dependent apoptosis. The novel strategy was verified to exert a universal anti-cancer role in other types of cancer.

Silver(I) complexes bearing heterocyclic thioamide ligands with NH2 and CF3 substituents: effect of ligand group substitution on antibacterial and anticancer properties

In recent years, there has been an increasing interest in the study of Ag(I) coordination compounds as potent antibacterial and anticancer agents. Herein, a series of Ag(I) complexes bearing phosphines and heterocyclic thioamide ligands with highly electronegative NH₂- and CF₃-group substituents, i.e. [AgCl(atdztH)(xantphos)] (1), [Ag(μ-atdztH)(DPEphos)]₂(NO₃)₂ (2), [Ag(atdzt)(PPh₃)₃] (3), [Ag(μ-atdzt)(DPEphos)]₂ (4), and [Ag(μ-mtft)(DPEphos)]₂ (5), where atdztH = 5-amino-1,3,4-thiadiazole-2-thiol, mtftH = 4-methyl-5-(trifluoromethyl)-1,2,4-triazol-3-thiol, xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene, and DPEphos = bis(2-diphenylphosphino-phenyl)ether, were synthesized, and their in vitro antibacterial and anticancer properties were evaluated. Complexes 1-4 bearing the NH₂-substituted thioamide exhibited moderate-to-high activity against S. aureus, B. subtilis, B. cereus and E. coli bacterial strains. A high antiproliferative activity was also observed for 1-3 against SKOV-3, Hup-T3, DMS114 and PC3 cancer cell lines (IC₅₀ = 4.0-11.7 μM), as well as some degree of selectivity against MRC-5 normal cells. Interestingly, 5 bearing the CF₃-substituted thioamide is completely inactive in all bioactivity studies. Binding of 1-3 to drug-carrier proteins BSA and HSA is reasonably strong for their uptake and subsequent release to possible target sites. The three complexes show a significant in vitro antioxidant ability for scavenging free radicals, suggesting likely implication of this property in the mechanism of their bioactivity, but a low potential to destroy the double-strand structure of CT-DNA by intercalation. Complementary insights into possible bioactivity mechanisms were provided by molecular docking calculations, exploring the ability of complexes to bind to bacterial DNA gyrase, and to the overexpressed in the aforementioned cancer cells Fibroblast Growth Factor Receptor 1, affecting their functionalities.

Decrypting the interaction pattern of Piperlongumine with calf thymus DNA and dodecamer d(CGCGAATTCGCG)2 B-DNA: Biophysical and molecular docking analysis

The mechanisms of interaction of DNA with pharmacological molecules are critical to understanding their therapeutic actions on physiological systems. Piperlongumine is widely studied for its anticancer potential. Multi-spectrometry, calorimetry and in silico studies were employed to study the interaction of piperlongumine and calf thymus DNA. UV-Vis spectroscopy illustrated a hyperchromic pattern in spectra of the calf thymus DNA-piperlongumine complex, while fluorescent quenching was observed in emission spectral studies. Competitive displacement assay demonstrated higher displacement and binding constant for DNA-rhodamine B complex by piperlongumine than DNA-methylene blue complex. Differential scanning calorimetry presented non-significant changes in melting temperature and molecular docking presented the precise interaction site of piperlongumine with calf thymus DNA at minor groove. Further, piperlongumine treatment did not result in pBluescript KS plasmid DNA cleavage as revealed from the DNA topology assay. All these experiments confirmed the binding of piperlongumine with DNA through minor groove binding mode.

Unusual dimeric flavonoids (brachydins) induce ultrastructural membrane alterations associated with antitumor activity in cancer cell lines

Notwithstanding the advances in molecular target-based drugs, chemotherapy remains the most common cancer treatment, despite its high toxicity. Consequently, effective anticancer therapies with fewer adverse effects are needed. Therefore, this study aimed to determine the anticancer activity of the dichloromethane fraction (DCMF) isolated from Arrabidae brachypoda roots, whose components are three unusual dimeric flavonoids. The toxicity of DCMF was investigated in breast (MCF-7), prostate (DU145), and cervical (HeLa) tumor cells, as well as non-tumor cells (PNT2), using sulforhodamine B (cell viability), Comet (genotoxicity), clonogenicity (reproductive capacity) and wound healing (cell migration) assays, and atomic force microscopy (AFM) for ultrastructural cell membrane alterations. Molecular docking revealed affinity between albumin and each rare flavonoid, supporting the impact of fetal bovine serum in DCMF antitumor activity. The IC₅₀ values for MCF7, HeLa, and DU145 were 2.77, 2.46, and 2.51 µg/mL, respectively, and 4.08 µg/mL for PNT2. DCFM was not genotoxic to tumor or normal cells when exposed to twice the IC₅₀ for up to 24 h, but it inhibited tumor cell migration and reproduction compared to normal cells. Additionally, AFM revealed alterations in the ultrastructure of tumor nuclear membrane surfaces, with a positive correlation between DCMF concentration and tumor cell roughness. Finally, we found a negative correlation between roughness and the ability of DCMF-treated tumor cells to migrate and form colonies with more than 50 cells. These findings suggest that DCFM acts by causing ultrastructural changes in tumor cell membranes while having fewer toxicological effects on normal cells.

Effect of Bis-Dimethylamine Substitution on DNA Binding Property and Cytotoxic Activity of Polyhydroxyxanthone

A bis-dimethylamine substituted xanthone (Xan-2) was obtained by cationic modification of the free C3 and C6 hydroxy groups of 1,3,6-trihydroxyxanthone (Xan-1) which was isolated from Polygala hongkongensis Hemsl.. The results of the spectroscopic analysis, melting profiles, electrophoretic migration, PCR assay and molecular docking indicated that the hydrophobic plane of Xan-1 and Xan-2 could intercalate into the DNA base pairs meanwhile the basic amine alkyl chain of Xan-2 could bind with DNA phosphate framework via electrostatic interaction. Thus, Xan-2 exhibited higher DNA binding affinity than Xan-1. Further study showed that Xan-2 could inhibit the proliferation of HeLa, SGC-7901 and A549 cells effectively by MTT assay and induce apoptosis of HeLa cells as detected by AO/EB staining and flow cytometry assay. Interestingly, Xan-2 exhibited selective cytotoxicity to cells, which was proved by its relatively low inhibitory effect on Raw 264.7 cell. What these studies mean is that disubstituted amine alkyl chains will play an important role in DNA binding property and cytotoxic activity, providing a direction for the development of novel potential antitumor agents.

Repurposing of Anti-Malarial Drug Quinacrine for Cancer Treatment: A Review

Quinacrine (QC), a synthetic drug belonging to the 9-aminoacridine family, has been used extensively to treat malaria and multiple ailments over the past several decades. Following its discovery in the 1920s and extensive use for the treatment of malaria for nearly two decades, numerous studies have explored its antineoplastic potential in both preclinical and clinical settings. Multiple studies spanning over seven decades have examined a wide range of QC anticancer activities across various types of cancers, along with the underlying mechanisms. Many of these mechanisms, including activation of the p53 signaling cascade and simultaneous NF-κB signaling inhibition, have been reported in various studies, bringing QC to a unique polypharmacological category drug possessing the potential to treat a wide variety of diseases, including cancer. This article summarizes most of the research conducted over several decades to uncover new molecular mechanisms activated or inactivated and directly correlate with antineoplastic activity QC.

Deciphering the sensing of α-amyrin acetate with hs-DNA: a multipronged biological probe

In this study, we focus on the biomimetic development of small molecules and their biological sensing with DNA. The binding of herring sperm deoxyribonucleic acid (hs-DNA) with naturally occurring bioactive small molecule α-amyrin acetate (α-AA), a biomimetic - isolated from the leaves of Ficus (F.) arnottiana is investigated. Collective information from various imaging, spectroscopic and biophysical experiments provides evidence that α-AA is a minor groove sensor of hs-DNA and preferentially binds to the A-T-rich regions. Interactions of different concentrations of small molecule α-AA with hsDNA were evaluated via various analytical techniques such as UV-Vis, circular dichroism (CD) and fluorescence emission spectroscopy. Fluorescence emission spectroscopy results suggest that α-AA decreases the emission level of hsDNA. DNA minor groove sensor Hoechst 33258 and intercalative sensor EB, melting transition analysis (T M) and viscosity analysis clarified that α-AA binds to hs-DNA via a groove site. Biophysical chemistry and molecular docking studies show that hydrophobic interactions play a major role in this binding. The present research deals with a natural product biosynthesis-linked chemical-biology interface sensor as a biological probe for α-AA: hs-DNA.

Biocompatible silver(I) complexes with heterocyclic thioamide ligands for selective killing of cancer cells and high antimicrobial activity - A combined in vitro and in silico study

A series of heteroleptic Ag(I) complexes bearing 4,6-dimethyl-2-pyrimidinethiol (dmp2SH), i.e., [AgCl(dmp2SH)(PPh₃)₂] (1), [Ag(dmp2SH)(PPh₃)₂]NO₃ (2), [Ag(dmp2SΗ)(xantphos)]NO₃ (3), [Ag(μ-dmp2S)(PPh₃)]₂ (4), [Ag(dmp2S)(xantphos)] (5), [Ag(μ-dmp2S)(DPEphos)]₂ (6) (xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene and DPEPhos = bis[(2-diphenylphosphino)phenyl]ether) were synthesized. The complexes display systematic variation of particular structural characteristics which were proved to have a significant impact on their in vitro cytotoxicity and antimicrobial properties. A moderate-to-high potential for bacteria growth inhibition was observed for all complexes, with 2, 3 and 5 being particularly effective against Gram-(+) bacteria (IC₅₀ = 1.6-4.5 μM). The three complexes exhibit high in vitro cytotoxicity against HeLa and MCF-7 cancer cells (IC₅₀ = 0.32-3.00 μΜ), suggesting the importance of coordination unsaturation and cationic charge for effective bioactivity. A very low cytotoxicity against HDFa normal cells was observed, revealing a high degree of selectivity (selectivity index ~10) and, hence, biocompatibility. Fluorescence microscopy using 2 showed effective targeting on the membrane of the HeLa cancer cells, subsequently inducing cell death. Binding of the complexes to serum albumin proteins is reasonably strong for potential uptake and subsequent release to target sites. A moderate in vitro antioxidant capacity for free radicals scavenging was observed and a low potential to destroy the double-strand structure of calf-thymus DNA by intercalation, suggesting likely implication of these properties in the bioactivity mechanisms of these complexes. Further insight into possible mechanisms of bioactivity was obtained by molecular modeling calculations, by exploring their ability to act as potential inhibitors of DNA-gyrase, human estrogen receptor alpha, human cyclin-dependent kinase 6, and human papillomavirus E6 oncoprotein.

Docking and scoring for nucleic acid-ligand interactions: Principles and current status

Nucleic acid (NA)-ligand interactions have crucial roles in many cellular processes and, thus, are increasingly attracting therapeutic interest in drug discovery. Molecular docking is a valuable tool for studying molecular interactions. However, because NAs differ significantly from proteins in both their physical and chemical properties, traditional docking algorithms and scoring functions for protein-ligand interactions might not be applicable to NA-ligand docking. Therefore, various sampling strategies and scoring functions for NA-ligand interactions have been developed. Here, we review the basic principles and current status of docking algorithms and scoring functions for DNA/RNA-ligand interactions. We also discuss challenges and limitations of current docking and scoring approaches.

Acridine-O6-benzylguanine hybrids: Synthesis, DNA binding, MGMT inhibition and antiproliferative activity

O⁶-Methylguanine-DNA-methyltransferase (MGMT) is a key DNA repair enzyme involved in chemoresistance to DNA-alkylating anti-cancer drugs such as Temozolomide (TMZ) through direct repair of drug-induced O⁶-methylguanine residues in DNA. MGMT substrate analogues, such as O⁶-benzylguanine (BG), efficiently inactivate MGMT in vitro and in cells; however, these drugs failed to reach the clinic due to adverse side effects. Here, we designed hybrid drugs combining a BG residue covalently linked to a DNA-interacting moiety (6-chloro-2-methoxy-9-aminoacridine). Specifically, two series of hybrids, encompassing three compounds each, were obtained by varying the position of the attachment point of BG (N⁹ of guanine vs. the benzyl group) and the length and nature of the linker. UV/vis absorption and fluorescence data indicate that all six hybrids adopt an intramolecularly stacked conformation in aqueous solutions in a wide range of temperatures. All hybrids interact with double-stranded DNA, as clearly evidenced by spectrophotometric titrations, without intercalation of the acridine ring and do not induce thermal stabilization of the duplex. All hybrids, as well as the reference DNA intercalator (6-chloro-2-methoxy-9-aminoacridine 8), irreversibly inhibit MGMT in vitro with variable efficiency, comparable to that of BG. In a multidrug-resistant glioblastoma cell line T98G, benzyl-linked hybrids 7a-c and the N⁹-linked hybrid 19b are moderately cytotoxic (GI₅₀ ≥ 15 μM after 96 h), while N⁹-linked hybrids 19a and 19c are strongly cytotoxic (GI₅₀ = 1-2 μM), similarly to acridine 8 (GI₅₀ = 0.6 μM). Among all compounds, hybrids 19a and 19c, similarly to BG, display synergic cytotoxic effect upon co-treatment with subtoxic doses of TMZ, with combination index (CI) values as low as 0.2-0.3. In agreement with in vitro results, compound 19a inactivates cellular MGMT but, unlike BG, does not induce significant levels of DNA damage, either alone or in combination with TMZ, as indicated by the results of γH2AX immunostaining experiments. Instead, and unlike BG, compound 19a alone induces significant apoptosis of T98G cells, which is not further increased in a combination with TMZ. These results indicate that molecular mechanisms underlying the cytotoxicity of 19a and its combination with TMZ are distinct from that of BG. The strongly synergic properties of this combination represent an interesting therapeutic opportunity in treating TMZ-resistant cancers.

Quinacrine Has Preferential Anticancer Effects on Mesothelioma Cells With Inactivating NF2 Mutations

Mesothelioma is a rare cancer with disproportionately higher death rates for shipping and mining populations. These patients have few treatment options, which can be partially attributed to limited chemotherapy responses for tumors. We initially hypothesized that quinacrine could be combined with cisplatin or pemetrexed to synergistically eliminate mesothelioma cells. The combination with cisplatin resulted in synergistic cell death and the combination with pemetrexed was not synergistic, although novel artificially-generated pemetrexed-resistant cells were more sensitive to quinacrine. Unexpectedly, we discovered cells with NF2 mutations were very sensitive to quinacrine. This change of quinacrine sensitivity was confirmed by NF2 ectopic expression and knockdown in NF2 mutant and wildtype cell lines, respectively. There are few common mutations in mesothelioma and inactivating NF2 mutations are present in up to 60% of these tumors. We found quinacrine alters the expression of over 3000 genes in NF2-mutated cells that were significantly different than quinacrine-induced changes in NF2 wildtype cells. Changes to NF2/hippo pathway biomarkers were validated at the mRNA and protein levels. Additionally, quinacrine induces a G1 phase cell cycle arrest in NF2-mutated cells versus the S phase arrest in NF2-wildtype cells. This study suggests quinacrine may have repurposing potential for a large subset of mesothelioma patients.

Quinacrine Induces Nucleolar Stress in Treatment-Refractory Ovarian Cancer Cell Lines

A considerable subset of gynecologic cancer patients experience disease recurrence or acquired resistance, which contributes to high mortality rates in ovarian cancer (OC). Our prior studies showed that quinacrine (QC), an antimalarial drug, enhanced chemotherapy sensitivity in treatment-refractory OC cells, including artificially generated chemoresistant and high-grade serous OC cells. In this study, we investigated QC-induced transcriptomic changes to uncover its cytotoxic mechanisms of action. Isogenic pairs of OC cells generated to be chemoresistant and their chemosensitive counterparts were treated with QC followed by RNA-seq analysis. Validation of selected expression results and database comparison analyses indicated the ribosomal biogenesis (RBG) pathway is inhibited by QC. RBG is commonly upregulated in cancer cells and is emerging as a drug target. We found that QC attenuates the in vitro and in vivo expression of nucleostemin (NS/GNL3), a nucleolar RBG and DNA repair protein, and the RPA194 catalytic subunit of Pol I that results in RBG inhibition and nucleolar stress. QC promotes the redistribution of fibrillarin in the form of extranuclear foci and nucleolar caps, an indicator of nucleolar stress conditions. In addition, we found that QC-induced downregulation of NS disrupted homologous recombination repair both by reducing NS protein levels and PARylation resulting in reduced RAD51 recruitment to DNA damage. Our data suggest that QC inhibits RBG and this inhibition promotes DNA damage by directly downregulating the NS-RAD51 interaction. Additionally, QC showed strong synergy with PARP inhibitors in OC cells. Overall, we found that QC downregulates the RBG pathway, induces nucleolar stress, supports the increase of DNA damage, and sensitizes cells to PARP inhibition, which supports new therapeutic stratagems for treatment-refractory OC. Our work offers support for targeting RBG in OC and determines NS to be a novel target for QC.

Anticancer Activity of Indeno[1,2-b]-Pyridinol Derivative as a New DNA Minor Groove Binding Catalytic Inhibitor of Topoisomerase IIα

Topoisomerase IIα has been a representative anti-cancer target for decades thanks to its functional necessity in highly proliferative cancer cells. As type of topoisomerase IIα targeting drugs, topoisomerase II poisons are frequently in clinical usage. However, topoisomerase II poisons result in crucial consequences resulted from mechanistically induced DNA toxicity. For this reason, it is needed to develop catalytic inhibitors of topoisomerase IIα through the alternative mechanism of enzymatic regulation. As a catalytic inhibitor of topoisomerase IIα, AK-I-191 was previously reported for its enzyme inhibitory activity. In this study, we clarified the mechanism of AK-I-191 and conducted various types of spectroscopic and biological evaluations for deeper understanding of its mechanism of action. Conclusively, AK-I-191 represented potent topoisomerase IIα inhibitory activity through binding to minor groove of DNA double helix and showed synergistic effects with tamoxifen in antiproliferative activity.

Synthesis, antiproliferative and antitrypanosomal activities, and DNA binding of novel 6-amidino-2-arylbenzothiazoles

A series of 6-amidinobenzothiazoles, linked via phenoxymethylene or directly to the 1,2,3-triazole ring with a p-substituted phenyl or benzyl moiety, were synthesised and evaluated in vitro against four human tumour cell lines and the protozoan parasite Trypanosoma brucei. The influence of the type of amidino substituent and phenoxymethylene linker on antiproliferative and antitrypanosomal activities was observed, showing that the imidazoline moiety had a major impact on both activities. Benzothiazole imidazoline 14a, which was directly connected to N-1-phenyl-1,2,3-triazole, had the most potent growth-inhibitory effect (IC₅₀ = 0.25 µM) on colorectal adenocarcinoma (SW620), while benzothiazole imidazoline 11b, containing a phenoxymethylene linker, exhibited the best antitrypanosomal potency (IC₉₀ = 0.12 µM). DNA binding assays showed a non-covalent interaction of 6-amidinobenzothiazole ligands, indicating both minor groove binding and intercalation modes of DNA interaction. Our findings encourage further development of novel structurally related 6-amidino-2-arylbenzothiazoles to obtain more selective anticancer and anti-HAT agents.

Copper(II) complexes with non-steroidal anti-inflammatory drugs: Structural characterization, in vitro and in silico biological profile

Six novel copper(II) complexes with the non-steroidal anti-inflammatory drugs ibuprofen, loxoprofen, fenoprofen and clonixin as ligands were synthesized and characterized by diverse techniques including single-crystal X-ray crystallography. The in vitro scavenging activity of the complexes against 1,1-diphenyl-picrylhydrazyl and 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) free radicals and the ability to reduce H₂O₂ were studied in the context of the antioxidant activity studies. The complexes may interact with calf-thymus DNA via intercalation as revealed by the techniques employed. The affinity of the complexes for bovine and human serum albumins was evaluated by fluorescence emission spectroscopy and the corresponding binding constants were determined. Molecular docking simulations on the crystal structure of calf-thymus DNA, human and bovine serum albumins were also employed in order to study in silico the ability of the studied compounds to bind to these target biomacromolecules, in terms of impairment of DNA and transportation through serum albumins, to explain the observed in vitro activity and to establish a possible mechanism of action.

Effects of the Autophagy-Inhibiting Agent Chloroquine on Acute Myeloid Leukemia Cells; Characterization of Patient Heterogeneity

Autophagy is a highly conserved cellular degradation process that prevents cell damage and promotes cell survival, and clinical efforts have exploited autophagy inhibition as a therapeutic strategy in cancer. Chloroquine is a well-known antimalarial agent that inhibits late-stage autophagy. We evaluated the effects of chloroquine on cell viability and proliferation of acute myeloid leukemia acute myeloid leukemia (AML) cells derived from 81 AML patients. Our results show that chloroquine decreased AML cell viability and proliferation for the majority of patients. Furthermore, a subgroup of AML patients showed a greater susceptibility to chloroquine, and using hierarchical cluster analysis, we identified 99 genes upregulated in this patient subgroup, including several genes related to leukemogenesis. The combination of chloroquine with low-dose cytarabine had an additive inhibitory effect on AML cell proliferation. Finally, a minority of patients showed increased extracellular constitutive mediator release in the presence of chloroquine, which was associated with strong antiproliferative effects of chloroquine as well as cytarabine. We conclude that chloroquine has antileukemic activity and should be further explored as a therapeutic drug against AML in combination with other cytotoxic or metabolic drugs; however, due to the patient heterogeneity, chloroquine therapy will probably be effective only for selected patients.

Metabolites from halophilic bacterial isolates Bacillus VITPS16 are cytotoxic against HeLa cells

The present study was aimed at evaluating the cytotoxic potential of selected halophilic bacterial metabolites. The use of the metabolomics approach in identifying the unexplored bioactive metabolites from halophilic bacterial isolate reduces time and complex experiments. In our study, we used UV/Visible spectroscopy, LC-MS/MS, and NMR to identify the metabolites present in the methanolic extract of the halophilic bacterium Bacillus VITPS16. MTT assay revealed that metabolite fractions (S1-79.61% and S2-85.74%) possess cytotoxic activity. Colonogenic assay confirmed the cytotoxic potential of the fractions and apoptosis assays showed that 83.37% of the cells undergo apoptosis at 10 mg/mL concentration (MF-S2). The DNA binding studies revealed the metabolite fraction interacts with DNA resulting in cytotoxicity. The study states that MF- S2 induced an antiproliferative effect that led to apoptosis through DNA binding as one of the possible pathways. The toxicity analysis using zebrafish indicated that the metabolite fractions are non-toxic even at 10 mg/mL concentration. Fraction MF-S2 is found to contain phosphoethanolamines, glycerophospholipids, sphingolipids, apocarotenoid, enigmol and its analogue, ankaflavin and flavonoid type of metabolites, which have been previously reported to have anti-cancer activity.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02724-9.

Natural DNA Intercalators as Promising Therapeutics for Cancer and Infectious Diseases

Cancer and infectious diseases are one of the greatest challenges of modern medicine. An unhealthy lifestyle, the improper use of drugs, or their abuse are conducive to the increase of morbidity and mortality caused by these diseases. The imperfections of drugs currently used in therapy for these diseases and the increasing problem of drug resistance have forced a search for new substances with therapeutic potential. Throughout history, plants, animals, fungi and microorganisms have been rich sources of biologically active compounds. Even today, despite the development of chemistry and the introduction of many synthetic chemotherapeutics, a substantial part of the new compounds being tested for treatment are still of natural origin. Natural compounds exhibit a great diversity of chemical structures, and thus possess diverse mechanisms of action and molecular targets. Nucleic acids seem to be a good molecular target for substances with anticancer potential in particular, but they may also be a target for antimicrobial compounds. There are many types of interactions of small-molecule ligands with DNA. This publication focuses on the intercalation process. Intercalators are compounds that usually have planar aromatic moieties and can insert themselves between adjacent base pairs in the DNA helix. These types of interactions change the structure of DNA, leading to various types of disorders in the functioning of cells and the cell cycle. This article presents the most promising intercalators of natural origin, which have aroused interest in recent years due to their therapeutic potential.

Quinacrine-Induced Autophagy in Ovarian Cancer Triggers Cathepsin-L Mediated Lysosomal/Mitochondrial Membrane Permeabilization and Cell Death

Simple Summary

Ovarian cancer (OC) is the most common cause of cancer-related deaths among women worldwide, and its incidence has been increasing and has continued to prove resistant to a variety of therapeutics. This observation is principally disturbing given the amount of money invested in identifying novel therapies for this disease. A comparatively rapid and economical pipeline for identification of novel drugs is drug repurposing. We reported earlier that the antimalarial drug Quinacrine (QC) also has anticancer activity and here we discovered that QC significantly upregulates cathepsin L (CTSL) and promoting autophagic flux in ovarian cancer. QC-induced CTSL activation promotes lysosomal membrane permeability resulting in active CTSL release into the cytosol, which promotes Bid cleavage, mitochondrial membrane permeability, cytochrome-c release and cell death in both in-vitro and in-vivo models. Therefore, QC is a promising candidate for OC treatment.

Abstract

We previously reported that the antimalarial compound quinacrine (QC) induces autophagy in ovarian cancer cells. In the current study, we uncovered that QC significantly upregulates cathepsin L (CTSL) but not cathepsin B and D levels, implicating the specific role of CTSL in promoting QC-induced autophagic flux and apoptotic cell death in OC cells. Using a Magic Red^® cathepsin L activity assay and LysoTracker red, we discerned that QC-induced CTSL activation promotes lysosomal membrane permeability (LMP) resulting in the release of active CTSL into the cytosol to promote apoptotic cell death. We found that QC-induced LMP and CTSL activation promotes Bid cleavage, mitochondrial outer membrane permeabilization (MOMP), and mitochondrial cytochrome-c release. Genetic (shRNA) and pharmacological (Z-FY(tBU)-DMK) inhibition of CTSL markedly reduces QC-induced autophagy, LMP, MOMP, apoptosis, and cell death; whereas induced overexpression of CTSL in ovarian cancer cell lines has an opposite effect. Using recombinant CTSL, we identified p62/SQSTM1 as a novel substrate of CTSL, suggesting that CTSL promotes QC-induced autophagic flux. CTSL activation is specific to QC-induced autophagy since no CTSL activation is seen in ATG5 knockout cells or with the anti-malarial autophagy-inhibiting drug chloroquine. Importantly, we showed that upregulation of CTSL in QC-treated HeyA8MDR xenografts corresponds with attenuation of p62, upregulation of LC3BII, cytochrome-c, tBid, cleaved PARP, and caspase3. Taken together, the data suggest that QC-induced autophagy and CTSL upregulation promote a positive feedback loop leading to excessive autophagic flux, LMP, and MOMP to promote QC-induced cell death in ovarian cancer cells.