DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes

A comprehensive review of computational methods for Protein-DNA binding site prediction

Accurately identifying protein-DNA binding sites is essential for understanding the molecular mechanisms underlying biological processes, which in turn facilitates advancements in drug discovery and design. While biochemical experiments provide the most accurate way to locate DNA-binding sites, they are generally time-consuming, resource-intensive, and expensive. There is a pressing need to develop computational methods that are both efficient and accurate for DNA-binding site prediction. This study thoroughly reviews and categorizes major computational approaches for predicting DNA-binding sites, including template detection, statistical machine learning, and deep learning-based methods. The 14 state-of-the-art DNA-binding site prediction models have been benchmarked on 136 non-redundant proteins, where the deep learning-based, especially pre-trained large language model-based, methods achieve superior performance over the other two categories. Applications of these DNA-binding site prediction methods are also involved.

Development of cyclopeptide inhibitors of cGAS targeting protein-DNA interaction and phase separation

Cyclic GMP-AMP synthase (cGAS) is an essential sensor of aberrant cytosolic DNA for initiating innate immunity upon invading pathogens and cellular stress, which is considered as a potential drug target for autoimmune and autoinflammatory diseases. Here, we report the discovery of a class of cyclopeptide inhibitors of cGAS identified by an in vitro screening assay from a focused library of cyclic peptides. These cyclopeptides specifically bind to the DNA binding site of cGAS and block the binding of dsDNA with cGAS, subsequently inhibit dsDNA-induced liquid phase condensation and activation of cGAS. The specificity and potency of one optimal lead XQ2B were characterized in cellular assays. Concordantly, XQ2B inhibited herpes simplex virus-1 (HSV-1)-induced antiviral immune responses and enhanced HSV-1 infection in vitro and in vivo. Furthermore, XQ2B significantly suppressed the elevated levels of type I interferon and proinflammatory cytokines in primary macrophages from Trex1-/- mice and systemic inflammation in Trex1-/- mice. XQ2B represents the specific cGAS inhibitor targeting protein-DNA interaction and phase separation and serves as a scaffold for the development of therapies in the treatment of cGAS-dependent inflammatory diseases.

Organometallic Pillarplexes That Bind DNA 4-Way Holliday Junctions and Forks

Holliday 4-way junctions are key to important biological DNA processes (insertion, recombination, and repair) and are dynamic structures that adopt either open or closed conformations, the open conformation being the biologically active form. Tetracationic metallo-supramolecular pillarplexes display aryl faces about a cylindrical core, an ideal structure to interact with open DNA junction cavities. Combining experimental studies and MD simulations, we show that an Au pillarplex can bind DNA 4-way (Holliday) junctions in their open form, a binding mode not accessed by synthetic agents before. Pillarplexes can bind 3-way junctions too, but their large size leads them to open up and expand that junction, disrupting the base pairing, which manifests in an increased hydrodynamic size and lower junction thermal stability. At high loading, they rearrange both 4-way and 3-way junctions into Y-shaped forks to increase the available junction-like binding sites. Isostructural Ag pillarplexes show similar DNA junction binding behavior but lower solution stability. This pillarplex binding contrasts with (but complements) that of metallo-supramolecular cylinders, which prefer 3-way junctions and can rearrange 4-way junctions into 3-way junction structures. The pillarplexes' ability to bind open 4-way junctions creates exciting possibilities to modulate and switch such structures in biology, as well as in synthetic nucleic acid nanostructures. In human cells, the pillarplexes do reach the nucleus, with antiproliferative activity at levels similar to those of cisplatin. The findings provide a new roadmap for targeting higher-order junction structures using a metallo-supramolecular approach, as well as expanding the toolbox available to design bioactive junction binders into organometallic chemistry.

Mechanisms of Surfactin from Bacillus subtilis SF1 against Fusarium foetens: A Novel Pathogen Inducing Potato Wilt

Fusarium wilt is a severe and worldwide disease in potato cultivation. In this study, Fusarium foetens was first identified as the pathogen of potato wilt. Bacillus subtilis SF1 has the potential for controlling potato wilt induced by F. foetens, resulting in a mycelium growth inhibition of 52.50 ± 2.59% in vitro and a significant decrease in incidence rate by 45.56% in vivo. This research highlighted the antifungal activity of surfactin from B. subtilis SF1 and attempted to reveal the unknown antifungal mechanisms. Surfactin inhibited F. foetens mycelium growth beyond the concentration of 20 μg/μL. Surfactin-treated mycelium appeared to have morphological malformation. Surfactin enhanced reduced glutathione production and caused the increase in values of the extracellular fluids in OD260 and OD280. Surfactin induced differential protein expression and changed the genes’ transcription levels. Surfactin binds to fungal DNA via groove-binding mode, with a binding constant of Kb 2.97 × 104 M−1. Moreover, B. subtilis SF1 harbored genes encoding plant-promoting determinants, making potato seedlings grow vigorously. The results will help provide a comprehensive understanding of the mechanisms of surfactin against filamentous fungi and the application of surfactin-producing microbial in the biocontrol of plant pathogenic fungi.

Lighting-Up the Far-Red Fluorescence of RNA-Selective Dyes by Switching from Ortho to Para Position

Fluorescence imaging is constantly searching for new far-red emitting probes whose turn-on response is selective upon the interaction with specific biological targets. Cationic push-pull dyes could indeed respond to these requirements due to their intramolecular charge transfer (ICT) character, by which their optical properties can be tuned, and their ability to interact strongly with nucleic acids. Starting from the intriguing results recently achieved with some push-pull dimethylamino-phenyl dyes, two isomers obtained by switching the cationic electron acceptor head (either a methylpyridinium or a methylquinolinium) from the ortho to the para position have been scrutinized for their ICT dynamics, their affinity towards DNA and RNA, and in vitro behavior. By exploiting the marked fluorescence enhancement observed upon complexation with polynucleotides, fluorimetric titrations were employed to evaluate the dyes' ability as efficient DNA/RNA binders. The studied compounds exhibited in vitro RNA-selectivity by localizing in the RNA-rich nucleoli and within the mitochondria, as demonstrated by fluorescence microscopy. The para-quinolinium derivative showed some modest antiproliferative effect on two tumor cell lines as well as improved properties as an RNA-selective far-red probe in terms of both turn-on response (100-fold fluorescence enhancement) and localized staining ability, attracting interest as a potential theranostic agent.

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.

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.

Synthesis, Structural Investigations, and In Vitro/In Silico Bioactivities of Flavonoid Substituted Biguanide: A Novel Schiff Base and Its Diorganotin (IV) Complexes

Quercetin is one of the most powerful bioactive dietary flavonoids. The in vivo biological study of quercetin is extremely difficult due to its very low solubility. However, diorganotin complexes of quercetin are more useful when contrasted with quercetin due to increased solubility. In the present study, quercetin, substituted biguanide synthesized in the form of Schiff base and its di-alkyl/aryl tin (IV) complexes were obtained by condensing Schiff base with respective di-alkyl/aryl tin (IV) dichloride. Advanced analytical techniques were used for structural elucidation. The results of biological screening against Gram-positive/Gram-negative bacteria and fungi showed that these diorganotin (IV) derivatives act as potent antimicrobial agents. The in silico investigation with dihydropteroate (DHPS) disclosed a large ligand-receptor interaction and revealed a strong relationship between the natural exercises and computational molecular docking results.

N-substituted benzenesulfonamide compounds: DNA binding properties and molecular docking studies

Benzenesulfonamide-based imine compounds 5-8 were prepared and screened for their binding properties to the FSdsDNA. The structures of synthesized compounds were elucidated by the spectroscopic and analytical methods. Compounds 5-8 were screened for their interactions with the FSdsDNA. Compound 8 showed the highest binding affinity to the FSdsDNA with intrinsic binding constant of 3.10 × 104 M-1. The compounds caused the quenching of the DNA-EB emission indicating displacement of EB (ethidium bromide) from the FSdsDNA. Finally, the binding interactions between the DNA and binder molecules 5-8 were examined by the molecular docking studies. The compounds locate approximately same region of the minor groove of DNA via hydrogen bonding contacts between the sulfonamide oxygen atoms and the DG10/DG16 nucleotides of DNA.Communicated by Ramaswamy H. Sarma.

Complexes of Zinc(II)- and Copper(II) Perchlorates with Nicotinamide: Synthesis, Structure, Cytotoxicity

Interaction of zinc(II)- and copper(II) perchlorate hexahydrates with nicotinamide (Nia – nicotinamide, niacinamide, 3-pyridinecarboxamide, C₅H₄NС(O)NH₂) has been studied. It has been demonstrated that complex compounds [Zn(Nia)₂(H₂O)₄](ClO₄)₂ (1) and [Cu(Nia)₂(H₂O)₂](ClO₄)₂ ⋅ 2H₂O (2) are formed in aqueous media at the molar ratio M(ClO₄)₂ ⋅ 6H₂O : Nia = 1 : 2. Both compounds are the ionic ones. Geometry of complex cation (1) may be represented as a distorted octahedron in which nicotinamide molecules are in the trans-position. The same position of ligands is found for planar complex cation (2). Cytotoxicity of the prepared compounds (MTT assay) has been determined with respect to dental pulp stem cells (DPSC) and breast cancer cell line MCF-7. Antiproliferative activity has been studied relative to 10 cancer cell lines, complex compound (1) being the most toxic for C6, Panc-1, U251 cell lines (survivability below 15%).

Selective Impedimetric Chemosensing of Carcinogenic Heterocyclic Aromatic Amine in Pork by dsDNA-Mimicking Molecularly Imprinted Polymer Film-Coated Electrodes

Inspired by the easy intercalation of quinoxaline heterocyclic aromatic amines (HAAs) in double-stranded DNA (dsDNA), we synthesized a nucleobase-functionalized molecularly imprinted polymer (MIP) as the recognition unit of an impedimetric chemosensor for the selective determination of a 2-amino-3,7,8-trimethyl-3H-imidazo[4,5-f]quinoxaline (7,8-DiMeIQx) HAA. HAAs are generated in meat and fish processed at high temperatures. They are considered to be potent hazardous carcinogens. The MIP film was prepared by potentiodynamic electropolymerization of a pre-polymerization complex of two adenine- and one thymine-substituted bis(2,2'-bithien-5-yl)methane functional monomer molecules with one 7,8-DiMeIQx template molecule, in the presence of the 2,4,5,2',4',5'-hexa(thiophene-2-yl)-3,3'-bithiophene cross-linking monomer, in solution. The as-formed MIP chemosensor allowed for the selective impedimetric determination of 7,8-DiMeIQx in the 47 to 400 μM linear dynamic concentration range with a limit of detection of 15.5 μM. The chemosensor was successfully applied for 7,8-DiMeIQx determination in the pork meat extract as a proof of concept.

Covalent and noncovalent interactions of coordination compounds with DNA: An overview

Deoxyribonucleic acid plays a central role in crucial cellular processes, and many drugs exert their effects through binding to DNA. Since the discovery of cisplatin and its derivatives considerable attention of researchers has been focused on the development of novel anticancer metal-based drugs. Transition metal complexes, due to their great diversity in size and structure, have a big potential to modify DNA through diverse types of interactions, making them the prominent class of compounds for DNA targeted therapy. In this review we describe various binding modes of metal complexes to duplex DNA based on covalent and noncovalent interactions or combination of both. Specific examples of each binding mode as well as possible cytotoxic effects of metal complexes in tumor cells are presented.

Förster Resonance Energy Transfer from Carbon Nanoparticles to a DNA-Bound Compound: A Method to Detect the Nature of Binding

A drug molecule can bind in various orientations to a DNA strand. Nature of the binding decides the functionality and efficacy of the drug. To innovate a new method to detect the nature of binding of a drug to DNA strands, herein we have used the dipole-dipole interaction driven Förster resonance energy transfer (FRET) between carbon nanoparticles (CNPs) and a DNA-bound small molecule, (E)-3-ethyl-2-(4-(pyrrolidin-1-yl)styryl)benzo[d]thiazol-3-ium (EPSBT), which belongs to the hemicyanine family and binds typically to the minor groove of a DNA duplex. EPSBT was designed to obtain appreciable fluorescence quantum yield, which constructed an efficient FRET pair with the synthesized CNPs. The tested compound prefers the thymine nucleobase to bind to the DNA strand. Orientation of its dipole on attachment to the DNA strand and the donor-acceptor distance dictate the FRET efficiency with the CNPs. The results provided a precise estimation of the nature of binding of EPSBT to the DNA backbone and, hence, supposedly will help in deciding the functional efficacy.

Near-Infrared Small Molecule as a Specific Fluorescent Probe for Ultrasensitive Recognition of Antiparallel Human Telomere G-Quadruplexes

In the past 10 years, many fluorescent probes have been developed to recognize G-quadruplexes (G4s) since G4s play an important role in biological systems. However, the selectivity and sensitivity of existing probes for G4s limit their further applications. Herein, we design and synthesize a new probe (TOVJ) by introducing 9-vinyljulolidine into TO. The new probe exhibits almost no fluorescence in an aqueous solution. Upon interacting with G4s, especially the antiparallel G4s, the fluorescence intensity was greatly enhanced (maximum 2742-fold) with a large Stokes shift of 198 nm and the maximum emission peak at 694 nm (near-infrared region). TOVJ showed high sensitivity and selectivity to G4s over other DNA topologies (ssDNA/dsDNA), especially to antiparallel G4s. For antiparallel human telomere G4 detection, the limits of detection of Hum24 and 22AG Na⁺ were as low as 164 and 231 pM, respectively. This indicates that TOVJ is a highly sensitive fluorescence sensor that can be effectively used for antiparallel human telomere G4 detection. The result of live-cell imaging showed that TOVJ could enter live cells and locate in the mitochondria.

Structure and biological profile of transition metal complexes with (E)-4-(2-(pyridin-2-ylmethylene)hydrazinyl)quinazoline

The interaction of the recently reported quinazoline derivative (E)-4-(2-(pyridin-2-ylmethylene)hydrazinyl)quinazoline (L) with a series of metal(II) (= copper(II), nickel(II), cobalt(II) and cadmium(II)) chlorides or nitrates resulted in the formation of mononuclear complexes which were characterized by spectroscopic techniques and single-crystal X-ray crystallography, i.e. [Cu(L)₂]Cl₂·4H₂O (1·4H₂O), [Ni(L)₂]Cl₂·4H₂O (2·4H₂O), [Ni(L)₂](NO₃)₂·MeOH (3·MeOH), [Co(L)₂]Cl₂·4H₂O (4·4H₂O), [Co(L)₂](NO₃)₂·H₂O (5·H₂O), [Co(L)₂](NO₃)₃·2.5H₂O (6·2.5H₂O), [Cd(L)(Cl)₂]·H₂O (7·H₂O) and [Cd(L)(CH₃OH)(H₂O)(NO₃)](NO₃) (8). The biological profile of the complexes was further assessed in regard to their binding affinity with calf-thymus DNA, their cleavage ability towards pBluescript II KS plasmid DNA in the absence or presence of irradiation of various wavelengths, their interaction with bovine serum albumin and finally, their ability to scavenge 1,1-diphenyl-picrylhydrazyl and 2,2΄-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) radicals and to reduce H₂O₂.

Elucidating the intercalation of methylated 1,10-phenanthroline with DNA: the important weight of the CH/H interactions and the selectivity of CH/π and CH/n interactions

Flat molecules like phenanthroline derivatives intercalate between base pairs of deoxyribonucleic acid and produce cytotoxic effects against tumoral cells. Elucidating the way of intercalation and its modulation on their efficiency by substitution still remains a challenging topic of research. In this work we analysed the intercalation via the major groove of methylated derivatives of phenanthroline, in different number and position, between guanine-cytosine base pairs. We studied our systems by using semi-empirical methods and density functional theory including dispersion corrections with the PM6-DH2 Hamiltonian and the B3LYP-D3 functional. We explored the geometry and electronic structure by means of the quantum theory of atoms in molecules and non-covalent interactions index analyses, whereas the interaction energy was estimated by means of two different approaches: one taking into account the results from the quantum theory of atoms in molecules analysis and the other based on the so-called energy decomposition analysis. The effect of solvation was also taken into consideration. Our studies show that CH/π and CH/n interactions by means of the -CH3 groups of methylated phen follow a clear pattern for any number of -CH3 groups and their position in the methylated phen ligand. That is, they try to produce the CH/π and CH/n interactions with the O and N heteroatoms of the base pairs and with the O atoms of the sugar and phosphate backbone. These findings suggest that the modulation of the intercalation of ligands that are able to form CH/π and CH/n weak interactions with the deoxyribonucleic acid is ruled not only by the number and position of the substitutions of the ligands but also by some key sites, which are the O and N atoms of the deoxyribonucleic acid in our analysed systems. It suggests some key and lock mechanism in which the interacting fragments fit like puzzle pieces in order to achieve the optimal interaction for the stabilization of the system. Interaction energies were calculated by using different approaches which converged to similar trends about the number and position of the -CH3 groups. The important weight of the CH/H interactions in the total interaction energy must be highlighted.

Electronic structure and vibrational assignments of 2,5-bis[4-(n-cyclobutyldiaminomethyl)phenyl]furan

Several DNA minor groove binders exhibit numerous therapeutic applications. The crystal structure demonstrating 2,5-bis[4-(N-cyclobutyldiaminomethyl)phenyl]furan binding within the minor groove of DNA has been reported by Simpson et al (2000 Bioorg. Med. Chem. Lett. 10 2593). In the present study, computational investigations on the title compound have been carried out which comprise geometry optimization, HOMO-LUMO, dipole moment, Molecular electrostatic potential(MEP), thermodynamic parameters, and IR assignments using the B3LYP/6-31G** method. The true minimum was long-established by the nonappearance of negative wavenumbers. A comparison of optimized parameters with crystallographic structure demonstrates slight variations in the conformations of the cyclobutyl groups. A small HOMO-LUMO gap indicates the high chemical reactivity and inter molecule charge transferability. The vibrational spectra of the molecule calculated in 400–3800 cm−1 region, reproduce reliable IR assignments. Bearing in mind the high pharmaceutical significance of minor groove binders and a variety of flexible options accessible for lead optimization will be a bountiful ground for the development of drugs targeting minor grooves.

Chromomycin A3 suppresses cholangiocarcinoma growth by induction of S phase cell cycle arrest and suppression of Sp1‑related anti‑apoptotic proteins

Cholangiocarcinoma (CCA) is a cancer of biliary epithelium. Late diagnosis and resistance to conventional chemotherapy are the major obstacles in CCA treatment. Increased expression of anti‑apoptotic proteins are observed in CCA, which might confer chemoresistance. Thus, modulations of anti‑apoptotic proteins leading to apoptotic induction is the focus of this study. Chromomycin A3 (CMA3), an anthraquinone glycoside‑mithramycin A analog, was selected. CMA3 strongly binds to GC‑rich regions in DNA, where specificity protein 1 (Sp1), a common transcription factor of apoptosis‑related proteins, is preferentially bounded. The effects of CMA3 on anti‑proliferation, cell cycle arrest and apoptosis induction in CCA cells were demonstrated by MTT assay, flow cytometry and western blot analysis. The results showed CMA3 suppressed cell proliferation in vitro in the nM range. At low doses, CMA3 inhibited cell cycle progression at S phase, while it promoted caspase‑dependent apoptosis at higher doses. CMA3 induced effects of apoptosis were through the suppression of Sp1‑related anti‑apoptotic proteins, FADD‑like IL‑1β‑converting enzyme‑inhibitory protein, myeloid cell leukemia‑1, X‑linked inhibitor of apoptosis protein, cellular inhibitor of apoptosis and survivin. The anti‑CCA effects of CMA3 were confirmed in the xenograft mouse model. CMA3 retarded xenograft tumor growth. Taken together, CMA3 induced apoptosis in CCA cells by diminishing the Sp1‑related anti‑apoptotic proteins is demonstrated. CMA3 might be useful as a chemosensitizing agent.

Targeting the Oncogenic TBX2 Transcription Factor With Chromomycins

The TBX2 transcription factor plays critical roles during embryonic development and it is overexpressed in several cancers, where it contributes to key oncogenic processes including the promotion of proliferation and bypass of senescence. Importantly, based on compelling biological evidences, TBX2 has been considered as a potential target for new anticancer therapies. There has therefore been a substantial interest to identify molecules with TBX2-modulatory activity, but no such substance has been found to date. Here, we adopt a targeted approach based on a reverse-affinity procedure to identify the ability of chromomycins A₅ (CA₅) and A₆ (CA₆) to interact with TBX2. Briefly, a TBX2-DNA-binding domain recombinant protein was N-terminally linked to a resin, which in turn, was incubated with either CA₅ or CA₆. After elution, bound material was analyzed by UPLC-MS and CA₅ was recovered from TBX2-loaded resins. To confirm and quantify the affinity (K_D) between the compounds and TBX2, microscale thermophoresis analysis was performed. CA₅ and CA₆ modified the thermophoretic behavior of TBX2, with a K_D in micromolar range. To begin to understand whether these compounds exerted their anti-cancer activity through binding TBX2, we next analyzed their cytotoxicity in TBX2 expressing breast carcinoma, melanoma and rhabdomyosarcoma cells. The results show that CA₅ was consistently more potent than CA₆ in all tested cell lines with IC₅₀ values in the nM range. Of the cancer cell types tested, the melanoma cells were most sensitive. The knockdown of TBX2 in 501mel melanoma cells increased their sensitivity to CA₅ by up to 5 times. Furthermore, inducible expression of TBX2 in 501mel cells genetically engineered to express TBX2 in the presence of doxycycline, were less sensitive to CA₅ than the control cells. Together, the data presented in this study suggest that, in addition to its already recognized DNA-binding properties, CA₅ may be binding the transcription factor TBX2, and it can contribute to its cytotoxic activity.

The 3D Genome as a Target for Anticancer Therapy

The role of 3D genome organization in the precise regulation of gene expression is well established. Accordingly, the mechanistic connections between 3D genome alterations and disease development are becoming increasingly apparent. This opinion article provides a snapshot of our current understanding of the 3D genome alterations associated with cancers. We discuss potential connections of the 3D genome and cancer transcriptional addiction phenomenon as well as molecular mechanisms of action of 3D genome-disrupting drugs. Finally, we highlight issues and perspectives raised by the discovery of the first pharmaceutical strongly affecting 3D genome organization.

Canonical DNA minor groove insertion of bisbenzamidine-Ru(ii) complexes with chiral selectivity

We report the first Ru(ii) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis-benzamidine minor groove DNA-binding agent with a ruthenium(ii) complex. Importantly, one of the enantiomers (Δ-[Ru(bpy)2 b4bpy]2+, Δ-4Ru) shows a considerably higher DNA affinity than the parent organic ligand and the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.

Synthesis of a 3,4-Disubstituted 1,8-Naphthalimide-Based DNA Intercalator for Direct Imaging of Legionella pneumophila

The development of organic molecules to target nucleic acid is an active area of research at the interface of chemistry and biochemistry, which involves DNA binding, nuclear imaging, and antitumor studies. These molecules bind with DNA through covalent interactions, electrostatic interactions, or intercalation. However, they are less permeable to membrane, and they have a significant cytotoxicity, which limits their application under in vivo conditions. In the present work, various mono- and disubstituted 1,8-naphthalimides-based derivatives (S-12, S-13, S-15, and S-21) have been synthesized and characterized through various spectroscopic techniques. Among these, 3-amino-4-bromo-1,8-naphthalimide (S-15) was found to have an attractive water solubility and act as a nuclear imaging agent. The spectroscopic absorption and emission data showed that S-15 has a strong affinity for salmon sperm DNA with a binding constant of 6.61 × 10⁴ M^-1, and the ratiometric fluorescence intensity (I ₄₈₉/I ₅₅₂) of S-15 has a linear relationship in the 0-50 μM range of DNA concentrations. It intercalates with DNA through the hydrophobic planar naphthalimide core as confirmed through cyclic voltammetry, circular dichroism, ¹H NMR titration, and thermal denaturation studies. Positively charged amine groups also participate in H-bonding with the bases and backbone of DNA. The S-15 intercalator showed a large Stokes shift and photostability, which made it attractive for direct imaging of Legionella pneumophila, without the need for a prior membrane permeabilization.

Binding interaction of a heteroleptic silver(I) complex with DNA: A joint experimental and computational study

A new heteroleptic Ag(I) complex formulated as [Ag(daf)(phen)]NO₃, where daf and phen stand for 4,5-diazafluoren-9-one and 1,10-phenanthroline, respectively, has been prepared and structurally characterized by elemental analysis, spectroscopic methods (IR, ¹HNMR, and UV-Vis) and cyclic voltammetry. The geometry optimization around Ag(I) at the level of DFT has demonstrated that the Ag(I) center has been nested in a tetrahedral N4 coordination geometry which found to be in close agreement with the experimentally proposed structure. The bond lengths, angles, and the HOMO/LUMO energies have been calculated to substantiate the geometry of the complex. The DNA binding property of the Ag(I) complex has been explored in detail both theoretically (DFT and molecular docking) and experimentally (UV-Vis absorption spectroscopy, circular dichroism spectroscopy, luminescence quenching, competitive binding with ethidium bromide, cyclic voltammetry, and gel electrophoresis), indicating the good affinity of the Ag(I) complex for the intercalation (K_b (binding constant) = 3.45 × 10⁵ M^-1). Providing a fuller picture of Ag(I) complex-DNA interaction, the energy-minimized structure of the complex has been docked to the DNA with a d(AGACGTCT)₂ sequence and the results are in close agreement with experimental achievements and make a deeper insight into the relationship between the structure and biological activity of the complex.

Multispectroscopic and Computational Investigation of ct-DNA Binding Properties with Hydroxybenzylidene Containing Tetrahydrocarbazole Derivative

Mode of interaction of a new tetrahydrocarbazole derivative with ct-DNA has been investigated systematically using fluorescence spectroscopy, UV-Vis spectroscopy and circular dichroism spectroscopy. It is concluded that TAH could intercalate into the base pairs of ct-DNA, and the fluorescence quenching by ct-DNA was static quenching type. Beside the multispectroscopic results, computational studies were done. Molecular docking results revealed that the TAH-DNAs complexes might be classified as druggable molecule in drug design. Additionally, DNA binding studies exhibited that TAH complexes have different interaction and orientation abilities to each DNA isomer. Combination of experimental and computational data showed that reported TAH is promising structure and deserves further applications.

A New Protocol for the Synthesis of New Thioaryl-Porphyrins Derived from 5,10,15,20-Tetrakis(pentafluorophenyl)porphyrin: Photophysical Evaluation and DNA-Binding Interactive Studies

A new protocol for the preparation of thioaryl-porphyrins is described. The compounds were prepared from different disulfides employing NaBH₄ as a reducing agent. The methodology allowed the preparation of four different thioaryl-porphyrins in very-good to excellent yields under soft conditions, such as short reaction times and smooth heating. Additionally, the photophysical properties of new compounds were determined and experimental and theoretical DNA interactions were assessed.

Poly Organotin Acetates against DNA with Possible Implementation on Human Breast Cancer

Two known tin-based polymers of formula {[R₃Sn(CH₃COO)]_n} where R = n-Bu– (1) and R = Ph– (2),were evaluated for their in vitro biological properties. The compounds were characterized via their physical properties and FT-IR, ¹¹⁹Sn Mössbauer, and ¹H NMR spectroscopic data. The molecular structures were confirmed by single-crystal X-Ray diffraction crystallography. The geometry around the tin(IV) ion is trigonal bi-pyramidal. Variations in O–Sn–O···Sn′ torsion angles lead to zig-zag and helical supramolecular assemblies for 1 and 2, respectively. The in vitro cell viability against human breast adenocarcinoma cancer cell lines: MCF-7 positive to estrogens receptors (ERs) and MDA-MB-231 negative to ERs upon their incubation with 1 and 2 was investigated. Their toxicity has been studied against normal human fetal lung fibroblast cells (MRC-5). Compounds 1 and 2 exhibit 134 and 223-fold respectively stronger antiproliferative activity against MDA-MB-231 than cisplatin. The type of the cell death caused by 1 or 2 was also determined using flow cytometry assay. The binding affinity of 1 and 2 towards the CT-DNA was suspected from the differentiation of the viscosity which occurred in the solution containing increasing amounts of 1 and 2. Changes in fluorescent emission light of Ethidium bromide (EB) in the presence of DNA confirmed the intercalation mode of interactions into DNA of both complexes 1 and 2 which have been ascertained from viscosity measurements. The corresponding apparent binding constants (K_app) of 1 and 2 towards CT-DNA calculated through fluorescence spectra are 4.9 × 10⁴ (1) and 7.3 × 10⁴ (2) M⁻¹ respectively. Finally, the type of DNA binding interactions with 1 and 2 was confirmed by docking studies.