Influence of the amino substituents in the interaction of ethidium bromide with DNA

Unveiling the multifaceted interactions of antitumor drug mitoxantrone with ct-DNA through biophysical and in silico studies

Mitoxantrone, an anthraquinone derivative, is a widely used anticancer drug with its well-known ability to engage in complex interactions with DNA. Although known for its intercalating ability, the enigma surrounding its binding modes with DNA persists. The existing corpus of literature primarily focuses on mitoxantrone-DNA interactions with short DNA sequences, thereby yielding insights into its interactive nature is limited to this specific sequence. This study aims to elucidate the diverse modes with which mitoxantrone interacts with calf thymus DNA using a combination of spectroscopy, calorimetry and in silico studies. The findings from spectroscopic, calorimetric and molecular dynamic results in correlation with existing literature, unveil a fascinating narrative: mitoxantrone intercalates at lower concentrations but promotes condensation at higher concentrations. Although intercalation with side chains positioned in the minor/major groove is the major binding mode in GC-rich sequences, molecular modelling studies hint at an alternative binding mode in AT-rich sequences where it exclusively displays pure electrostatic interaction. These findings underscore the pivotal role of both drug structure and base sequence in dictating binding mode and affinity. Such insights not only deepen the understanding of structure-activity relationships but also hold promise for guiding future drug design strategies.

Palladium(II)-Indenyl Complexes Bearing N-Heterocyclic Carbene (NHC) Ligands as Potent and Selective Metallodrugs toward High-Grade Serous Ovarian Cancer Models

In this study, we synthesized novel Pd(II)-indenyl complexes using various N-heterocyclic carbene (NHC) ligands, including chelating NHC-picolyl, NHC-thioether, and diNHC ligands, and two monodentate NHCs. Transmetalation reactions between a Pd(II)-indenyl precursor and silver-NHC complexes were generally employed, except for chelating diNHC derivatives, which required direct reaction with bisimidazolium salts and potassium carbonate. Characterization included NMR, HRMS analysis, and single-crystal X-ray diffraction. In vitro on five ovarian cancer cell lines showed notable cytotoxicity, with IC50 values in the micro- and submicromolar range. Some compounds exhibited intriguing selectivity for cancer cells due to higher tumor cell uptake. Mechanistic studies revealed that monodentate NHCs induced mitochondrial damage while chelating ligands caused DNA damage. One chelating NHC-picolyl ligand showed promising cytotoxicity and selectivity in high-grade serous ovarian cancer models, supporting its consideration for preclinical study.

Elucidating the Interaction of Indole-3-Propionic Acid and Calf Thymus DNA: Multispectroscopic and Computational Modeling Approaches

Indole-3-propionic acid (IPA) is a plant growth regulator with good specificity and long action. IPA may be harmful to human health because of its accumulation in vegetables and fruits. Therefore, in this study, the properties of the interaction between calf thymus DNA (ctDNA) and IPA were systematically explored using multispectroscopic and computational modeling approaches. Analysis of fluorescence spectra showed that IPA binding to ctDNA to spontaneously form a complex was mainly driven by hydrogen bonds and hydrophobic interaction. DNA melting analysis, viscosity analysis, DNA cleavage study, and circular dichroism measurement revealed the groove binding of IPA to ctDNA and showed that the binding did not significantly change ctDNA confirmation. Furthermore, molecular docking found that IPA attached in the A-T rich minor groove region of the DNA. Molecular dynamics simulation showed that DNA and IPA formed a stable complex and IPA caused slight fluctuations for the residues at the binding site. Gel electrophoresis experiments showed that IPA did not significantly disrupt the DNA structure. These findings may provide useful information on the potential toxicological effects and environmental risk assessments of IPA residue in food at the molecular level.

New insights into self-structure induction in poly (rA) by Quinacrine through non-classical intercalation: Spectroscopic and theoretical perspectives

Self-structure induction in a single stranded polyriboadenylic acid [poly (rA)] is an auspicious physiological phenomenon which switches off protein production in tumor cells. In the present study, the self-structure induction process in poly (rA) moiety was thoroughly investigated using various steady state and time resolved techniques. Optical melting pattern directly evidenced the formation of self-structured assembly in single stranded poly (rA) upon complexation with quinacrine. Further, UV-absorption spectroscopic studies revealed that quinacrine binds to poly (rA) in co-operative fashion and the indication of intercalative mode of binding first came out with the involvement of around two base pairs of poly (rA) in the complexation. Experimental observations established the unconventional or non-classical intercalation of quinacrine molecule inside self-structured duplex poly (rA) moiety. This complexation was accompanied with negative enthalpy change and positive entropy change; suggesting strong van der Waals and the H-bonding interactions as the major governing forces in the complexation. Moreover, ionic strength dependent binding study established that the non-polyelectrolytic forces were the dominating forces. Further, the photo physical behavior of QN was authenticated using time dependent density functional theory (TDDFT) where both the ground and excited states were exploited.

Enhanced enzymatic activity and conformational stability of catalase in presence of tetrahedral DNA nanostructures: A biophysical and kinetic study

The emergence of DNA nanotechnology has shown enormous potential in a vast array of applications, particularly in the medicinal and theranostics fields. Nevertheless, the knowledge of the compatibility between DNA nanostructures and cellular proteins is largely unknown. Herein, we report the biophysical interaction between proteins (circulatory protein bovine serum albumin, BSA, and the cellular enzyme bovine liver catalase, BLC) and tetrahedral DNA (tDNAs), which are well-known nanocarriers for therapeutics. Interestingly, the secondary conformation of BSA or BLC was unaltered in the presence of tDNAs which supports the biocompatible property of tDNA. In addition, thermodynamic studies showed that the binding of tDNAs with BLC has a stable non-covalent interaction via hydrogen bond and van der Waals contact, which is indicative of a spontaneous reaction. Furthermore, the catalytic activity of BLC was increased in the presence of tDNAs during 24 h of incubation. These findings indicate that the presence of tDNA nanostructures not only ensures a steady secondary conformation of proteins, but also stabilize the intracellular proteins like BLC. Surprisingly, our investigation discovered that tDNAs have no effect on albumin proteins, either by interfering or by adhering to the extracellular proteins. These findings will aid in the design of future DNA nanostructures for biomedical applications by increasing the knowledge on the biocompatible interaction of tDNAs with biomacromolecules.

Revelation of potential bioactive water-soluble Boc-L-valine and imidazole appended metal complexes {M = Co(II), Cu(II) & Zn(II)}: synthesis, characterization, ct-DNA binding, pBR322 cleavage, SOD mimetic, and cytotoxicity studies

Bio-compatible water-soluble conjugates of Co(II), Cu(II) and Zn(II) (1-3), [Co(Boc-L-valine)2(imidazole)2], [Cu(Boc-L-valine)2(imidazole)2], and [Zn(Boc-L-valine)2(imidazole)2], were synthesized and comprehensively characterized by various spectroscopic techniques (UV-visible, FT-IR, ESI-MS, EPR, 1H NMR, 13C NMR) and single crystal X-ray diffraction which showed that the complexes 1-3 crystallized in an orthorhombic crystal system, in a slightly distorted octahedral geometry having the space group P21212. Density functional theory calculations were performed to correlate the energy of frontier molecular orbitals with the stability and reactivity of the complexes. In vitro DNA binding interaction studies of complexes were performed by employing various biophysical techniques and their corroborative results revealed (i) the electrostatic mode of binding in the groove region of DNA, (ii) pBR322 plasmid cleavage at a low concentration of 5-12.5 μM via an oxidative pathway in complexes 1 and 2 and the hydrolytic mechanism in the case of 3, (iii) changes in the 1H NMR chemical shift values of the NH2 group of GMP after interaction with complex 3, (iv) alteration in the EPR parameters of complex 2 after complexation with DNA, (v) SOD mimetic activity of complex 2 with the IC50 value of 2.08 μM and (vi) a good and selective cytotoxicity profile against chemo-resistant MCF-7 and MDA-MB-231 cancer cell lines by complex 1. Molecular docking studies complemented the spectroscopic results and confirmed the electrostatic interaction of complexes in the groove region of DNA.

DNA binding properties and cytotoxic effects of two double rollover cycloplatinated (II) complexes on cancer cell lines

In this study, the DNA binding capacity and cytotoxic effects of two double rollovers cycloplatinated complexes, [Pt₂(μ-bpy-2H)(CF₃COO)₂(PPh₃)₂] and [Pt₂(μ-bpy-2H)(I)₂(PPh₃)₂] denoted as C1 and C2, respectively, were evaluated. By using UV-Visible spectroscopy the intrinsic binding constant (K_b) of C1 and C2 to DNA were determined as 2.9 × 10⁵ M^-1, and 5.4 × 10⁵ M^-1, respectively. Both the compounds were able to quench the fluorescence of ethidium bromide as a well known DNA intercalator. The calculated Stern-Volmer quenching constants (K_sv) for C1 and C2 were 3.5 × 10³ M^-1, and 1.2 × 10⁴ M^-1, respectively. Upon interaction of both the compounds with DNA, increase in viscosity of DNA solution were observed, further confiming the involvement of intercalative interactions between the complexes and DNA. The cytotoxic effects of complexes in compare to cisplatin were evaluated on different cancer cell lines by MTT assay. Interestingly, C2 showed the highest cytotoxicity on A2780R, a cisplatin resistant-cell line. Induction of apoptosis by the complexes was proved by flowcytometry. In all the studied cell lines, the extent of apoptosis induced by C2 was comparable or higher than cisplatin. Cisplatin induced more necrosis in all the cancer cell lines in the tested concentration.

Application of the SwitchSense Technique for the Study of Small Molecules’ (Ethidium Bromide and Selected Sulfonamide Derivatives) Affinity to DNA in Real Time

The discovery and introduction of the switchSense technique in the chemical laboratory have drawn well-deserved interest owing to its wide range of applications. Namely, it can be used to determine the diameter of proteins, alterations in their tertiary structures (folding), and many other conformational changes that are important from a biological point of view. The essence of this technique is based on its ability to study of the interactions between an analyte and a ligand in real time (in a buffer flow). Its simplicity, on the other hand, is based on the use of a signaling system that provides information about the ongoing interactions based on the changes in the fluorescence intensity. This technique can be extremely advantageous in the study of new pharmaceuticals. The design of compounds with biological activity, as well as the determination of their molecular targets and modes of interactions, is crucial in the search for new drugs and the fight against drug resistance. This article presents another possible application of the switchSense technique for the study of the binding kinetics of small model molecules such as ethidium bromide (EB) and selected sulfonamide derivatives with DNA in the static and dynamic modes at three different temperatures (15, 25, and 37 °C) each. The experimental results remain in very good agreement with the molecular dynamics docking ones. These physicochemical insights and applications obtained from the switchSense technique allow for the design of an effective strategy for molecular interaction assessments of small but pharmaceutically important molecules with DNA.

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.

Interaction of organoruthenium(II)-polypyridyl complexes with DNA and BSA

The interaction of four arene ruthenium complexes [(η⁶-p-cymene)Ru(Me₂dppz)Cl]PF₆ (1) with Me₂dppz = 11,12-dimethyldipyrido[3,2-a:2',3'-c]phenazine, [(η⁶-p-cymene)Ru(aip)Cl]PF₆ (2) with aip = 2-(9-anthryl)-1H-imidazo[4,5-f][1,10] phenanthroline), ([(ƞ⁶-toluene)Ru(ppf)Cl]PF₆) (3) and ([(ƞ⁶-p-cymene)Ru(ppf)Cl]PF₆) (4) with ppf = pyrido[2',3':5,6] pyrazino[2,3-f][1,10]phenanthroline with calf thymus DNA were investigated. All of four complexes exhibit DNA-binding activity. UV-Vis spectroscopic studies revealed the intrinsic binding constants of the order 10⁴ M^-1 of magnitude, indicating non-intercalative mode. Fluorescence quenching analysis showed that all complexes interfere with intercalator ethidium bromide and minor groove binder Hoechst 33258 by a singular non-intercalative mode with extent that differs by two orders of magnitude. Gel electrophoresis results on DNA cleavage assay demonstrated that all complexes produced conformational changes of supercoiled circular plasmid pUC19 in concentration dependent way. The results of fluorescence titration bovine serum albumin by 1, 2, 3 and 4 showed that all complexes significantly quench tryptophan residues fluorescence through a static quenching mechanism. The antimicrobial activity against both Gram-positive and Gram-negative bacteria analyzed. Complex 1 was most active, even on Escherichia coli was more active than positive control compound.

Current Developments of N-Heterocyclic Carbene Au(I)/Au(III) Complexes toward Cancer Treatment

Since their first discovery, N-heterocyclic carbenes have had a significant impact on organometallic chemistry. Due to their nature as strong σ-donor and π-acceptor ligands, they are exceptionally well suited to stabilize Au(I) and Au(III) complexes in biological environments. Over the last decade, the development of rationally designed NHCAu(I/III) complexes to specifically target DNA has led to a new “gold rush” in bioinorganic chemistry. This review aims to summarize the latest advances of NHCAu(I/III) complexes that are able to interact with DNA. Furthermore, the latest advancements on acyclic diamino carbene gold complexes with anticancer activity are presented as these typically overlooked NHC alternatives offer great additional design possibilities in the toolbox of carbene-stabilized gold complexes for targeted therapy.

Multi-Spectroscopic and Molecular Simulation Approaches to Characterize the Intercalation Binding of 1-Naphthaleneacetic Acid With Calf Thymus DNA

1-Naphthaleneacetic acid (NAA), having high-quality biological activity and great yield-increasing potential in agricultural production, is a broad-spectrum plant growth regulator. Although NAA is of low toxicity, it can affect the balance of the human metabolism and damage the body if it is used in high quantity for a long time. In this study, the interaction of NAA with calf thymus DNA (ctDNA) was investigated under simulated human physiological acidity (pH 7.4) using fluorescence, ultraviolet-visible absorption, and circular dichroism spectroscopy combined with viscosity measurements and molecular simulation techniques. The quenching of the endogenous fluorescence of NAA by ctDNA, observed in the fluorescence spectrum experiment, was a mixed quenching process that mainly resulted from the formation of the NAA-ctDNA complex. NAA mainly interacted with ctDNA through hydrophobic interaction, and the binding constant and quenching constant at room temperature (298 K) were 0.60 × 10⁵ L mol^-1 and 1.58 × 10⁴ L mol^-1, respectively. Moreover, the intercalation mode between NAA and ctDNA was verified in the analysis of melting point, KI measurements, and the viscosity of ctDNA. The results were confirmed by molecular simulation, and it showed that NAA was enriched near the C-G base of ctDNA. As shown in circular dichroism spectra, the positive peak intensity of ctDNA intensified along with a certain degree of redshift, while the negative peak intensity decreased after binding with NAA, suggesting that the binding of NAA induced the transformation of the secondary structure of ctDNA from B-form to A-form. These researches will help to understand the hazards of NAA to the human body more comprehensively and concretely, to better guide the use of NAA in industry and agriculture.

Metallointercalators-DNA Tetrahedron Supramolecular Self-Assemblies with Increased Serum Stability

Self-assembly of metallointercalators into DNA nanocages is a rapid and facile approach to synthesize discrete bioinorganic host/guest structures with a high load of metal complexes. Turberfield's DNA tetrahedron can accommodate one intercalator for every two base pairs, which corresponds to 48 metallointercalators per DNA tetrahedron. The affinity of the metallointercalator for the DNA tetrahedron is a function of both the structure of the intercalating ligand and the overall charge of the complex, with a trend in affinity [Ru(bpy)2(dppz)]2+ > [Tb-DOTAm-Phen]3+ ≫ Tb-DOTA-Phen. Intercalation of the metal complex stabilizes the DNA tetrahedron, resulting in an increase of its melting temperature and, importantly, a significant increase in its stability in the presence of serum. [Ru(bpy)2(dppz)]2+, which has a greater affinity for DNA than [Tb-DOTAm-Phen]3+, increases the melting point and decreases degradation in serum to a greater extent than the TbIII complex. In the presence of Lipofectamine, the metallointercalator@DNA nanocage assemblies substantially increase the cell uptake of their respective metal complex. Altogether, the facile incorporation of a large number of metal complexes per assembly, the higher stability in serum, and the increased cell penetration of metallointercalator@DNA make these self-assemblies well-suited as metallodrugs.

Substituent effect of benzyl moiety in nitroquinoxaline small molecules upon DNA binding: Cumulative destacking of DNA nucleobases leading to histone eviction

Cooperative disruption of Watson-Crick hydrogen bonds, as well as base-destacking, is shown to be triggered by a quinoxaline-based small molecule consisting of an N,N-dimethylaminopropyl tether, and a para-substituted benzyl moiety. This events lead to superstructure formation and DNA condensation as evident from biophysical experiments and classical molecular dynamics simulations. The DNA superstructure formation by mono-quinoxaline derivatives is highly entropically favored and predominantly driven by hydrophobic interactions. Furthermore, oversupercoiling of DNA and base-destacking cumulatively induces histone eviction from in-vitro assembled nucleosomes at lower micromolar concentrations implicating biological relevance. The DNA structural modulation and histone eviction capacity of the benzyl para-substituents are in the order: -I > -CF₃> -Br > -Me > -OMe > -OH, which is largely guided by the polarity of benzyl para-substituent and the resulting molecular topology. The most hydrophobic derivative 3c with para-iodo benzyl moiety causes maximal disruption of base pairing and generation of superstructures. Both these events gradually diminish as the polarity of the benzyl para-substituent increases. On the other hand, quinoxaline derivatives having heterocyclic ring instead of benzyl ring, or in the absence of N,N-dimethylamino head-group, is incapable of inducing any DNA structural change and histone eviction. Further, the quinoxaline compounds displayed potent anticancer activities against different cancer cell lines which directly correlates with the hydrophobic effects of the benzyl para-substituents. Overall, the present study provides new insights into the mechanistic approach of DNA structural modulation driven histone eviction guided by the hydrophobicity of synthesized compounds leading to cellular cytotoxicity towards cancer cells.

Synthesis, DNA-Binding, Anticancer Evaluation, and Molecular Docking Studies of Bishomoleptic and Trisheteroleptic Ru-Diimine Complexes Bearing 2-(2-Pyridyl)-quinoxaline

Herein, we report the synthesis and characterization of a bishomoleptic and a trisheteroleptic ruthenium (II) polypyridyl complex, namely, [Ru(bpy)2(2, 2'-pq)](PF6)2 (1) and [Ru(bpy) (phen) (2, 2'-pq)](PF6)2 (2), respectively, where bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline, and 2, 2'-pq = 2-(2'-pyridyl)-quinoxaline. The complexes were characterized by elemental analysis, TGA, 1H-NMR, FT-IR, UV-Vis, emission spectroscopy, and electrochemistry. Their structures were confirmed by single-crystal X-ray diffraction analysis. Complexes 1 and 2 were crystalized in orthorhombic, Pbca, and monoclinic, P21/n systems, respectively. Various spectroscopic techniques were employed to investigate the interaction of both complexes with calf thymus DNA (CT-DNA). The experimental data were confirmed by molecular docking studies, employing two different DNA sequences. Both complexes, 1 and 2, bind with DNA via a minor groove mode of binding. MTT experiments revealed that both complexes induce apoptosis of MCF-7 (breast cancer) cells in low concentrations. Confocal microscopy indicated that 2 localizes in the nucleus and internalizes more efficiently in MCF-7 than in HEK-293.

Processing of the spectrofluorimetric data using the graphical methods and the maximum likelihood approach

The present work describes the calculation of the binding constants from spectrofluorimetric data using simple graphical methods and specialized software implementing the maximum likelihood approach. The following popular cases are analyzed: 1) protein-small molecule; 2) protein-metal complex; 3) DNA-small molecule; 4) DNA-metal complex interactions. The inability of graphical plots to return the correct results except for the simplest situation (single reaction with a non-fluorescent product) is demonstrated. The possibility of determining the most probable stoichiometric model using the maximum likelihood estimation (LSQ as its special case) is discussed as well as the limitations.

Synthesis, DNA-binding and antiproliferative properties of diarylquinolizinium derivatives

A series of ten 2,7- and 2,8-diarylquinolizinium derivatives was synthesized and their DNA-binding and cytotoxic properties were investigated. Except for one nitro-substituted derivative all tested diarylquinolizinium ions bind to DNA with sufficient affinity (2 × 10⁴ M^-1-2 × 10⁵ M^-1). It was shown with photometric, fluorimetric and polarimetric titrations as well as with flow-LD analysis that the ligands bind mainly by intercalation to duplex DNA, however, depending on the ligand-DNA ratio, groove binding and backbone association were also observed with some derivatives. The biological activity was further investigated with tests of cytotoxicity and antiproliferative properties towards non-tumor cells and selected cancer cells, along with cell cycle analysis and an annexin-V assay. Notably, substrates that carry donor-functionalities in the 4-position of the phenyl substituents revealed a strong, and in some cases selective, antiproliferative activity as quantified by the growth inhibition, GI₅₀, at very low micromolar and even submicromolar level both in leukemia and solid tumors.

DANPY (dimethylaminonaphthylpyridinium): an economical and biocompatible fluorophore

Dyes with nonlinear optical (NLO) properties enable new imaging techniques and photonic systems. We have developed a dye (DANPY-1) for photonics applications in biological substrates such as nucleic acids; however, the design specification also enables it to be used for visualizing biomolecules. It is a prototype dye demonstrating a water-soluble, NLO-active fluorophore with high photostability, a large Stokes shift, and a favorable toxicity profile. A practical and scalable synthetic route to DANPY salts has been optimized featuring: (1) convergent Pd-catalyzed Suzuki coupling with pyridine 4-boronic acid, (2) site-selective pyridyl N-methylation, and (3) direct recovery of crystalline intermediates without chromatography. We characterize the optical properties, biocompatibility, and biological staining behavior of DANPY-1. In addition to stability and solubility across a range of polar media, the DANPY-1 chromophore shows a first hyperpolarizability similar to common NLO dyes such as Disperse Red 1 and DAST, a large two-photon absorption cross section for its size, substantial affinity to nucleic acids in vitro, an ability to stain a variety of cellular components, and strong sensitivity of its fluorescence properties to its dielectric environment.

The 1,10-Phenanthroline Ligand Enhances the Antiproliferative Activity of DNA-Intercalating Thiourea-Pd(II) and -Pt(II) Complexes Against Cisplatin-Sensitive and -Resistant Human Ovarian Cancer Cell Lines

Ovarian cancer is the most lethal gynecological malignancy, often because of the frequent insurgence of chemoresistance to the drugs currently used. Thus, new therapeutical agents are needed. We tested the toxicity of 16 new DNA-intercalating agents to cisplatin (cDDP)-sensitive human ovarian carcinoma cell lines and their resistant counterparts. The compounds were the complexes of Pt(II) or Pd(II) with bipyridyl (bipy) and phenanthrolyl (phen) and with four different thiourea ancillary ligands. Within each of the four series of complexes characterized by the same thiourea ligand, the Pd(phen) drugs invariably showed the highest anti-proliferative efficacy. This paralleled both a higher intracellular drug accumulation and a more efficient DNA intercalation than all the other metal-bidentate ligand combinations. The consequent inhibition of topoisomerase II activity led to the greatest inhibition of DNA metabolism, evidenced by the inhibition of the expression of the folate cycle enzymes and a marked perturbation of cell-cycle distribution in both cell lines. These findings indicate that the particular interaction of Pd(II) with phenanthroline confers the best pharmacokinetic and pharmacodynamic properties that make this class of DNA intercalators remarkable inhibitors, even of the resistant cell growth.

Factors for the emission enhancement of dimidium in specific media such as in DNA and on a clay surface

Dimidium (3,8-diamino-5-methyl-6-phenylphenanthridinium: NH2PhP) is a well-known fluorophore as a DNA probe, although its fluorescence enhancement mechanism is not clear. In this study, we investigated the fluorescence enhancement mechanism of NH2PhP on a clay surface by observing the fluorescence behavior. Four systematically selected phenanthridinium derivatives (PDs): NH2PhP, 3,8-bisdimethylamino-5-methyl-6-phenylphenanthridinium (NMe2PhP), 5-methyl-6-phenylphenanthridinium (PhP) and 5-methylphenanthridinium (P) and synthetic clay were used as guest and host materials, respectively. It was revealed that the suppression of hydrogen bonding with water (N-HOH or NH-OH2) is the dominant factor for the fluorescence enhancement on the clay surface for NH2PhP and NMe2PhP. In addition, judging from the fluorescence enhancement for NH2PhP, NMe2PhP and PhP and no fluorescence enhancement for P on the clay surface, the suppression of rotation of the phenyl ring was indicated to make a partial contribution to the fluorescence enhancement mechanism. Because the fluorescence enhancement behavior was quite similar on the clay surface and in DNA, the obtained results afford an important clue to discuss the fluorescence enhancement mechanism of NH2PhP in DNA.

Explication of bovine serum albumin binding with naphthyl hydroxamic acids using a multispectroscopic and molecular docking approach along with its antioxidant activity

In the present investigation, the protein-binding properties of naphthyl-based hydroxamic acids (HAs), N-1-naphthyllaurohydroxamic acid (1) and N-1-naphthyl-p-methylbenzohydroxamic acid (2) were studied using bovine serum albumin (BSA) and UV-visible spectroscopy, fluorescence spectroscopy, diffuse reflectance spectroscopy-Fourier transform infrared (DRS-FTIR), circular dichroism (CD), and cyclic voltammetry along with computational approaches, i.e. molecular docking. Alteration in the antioxidant activities of compound 1 and compound 2 during interaction with BSA was also studied. From the fluorescence studies, thermodynamic parameters such as Gibb's free energy (ΔG), entropy change (ΔS) and enthalpy change (ΔH) were calculated at five different temperatures (viz., 298, 303, 308, 313 or 318 K) for the HAs-BSA interaction. The results suggested that the binding process was enthalpy driven with dominating hydrogen bonds and van der Waals' interactions for both compounds. Warfarin (WF) and ibuprofen (IB) were used for competitive site-specific marker binding interaction and revealed that compound 1 and compound 2 were located in subdomain IIA (Sudlow's site I) on the BSA molecule. Conclusions based on above-applied techniques signify that various non-covalent forces were involved during the HAs-BSA interaction. Therefore the resulted HAs-BSA interaction manifested its effect in transportation, distribution and metabolism for the drug in the blood circulation system, therefore establishing HAs as a drug-like molecule.

Chiral self-assembly of fullerene clusters on CT-DNA templates

Herein we discuss the differential interaction of three monosubstituted fullerene derivatives possessing pyridinium, aniline or phenothiazine end groups (F-Py, F-An and F-PTz, respectively) with calf thymus DNA (CT-DNA), probed via spectroscopic and imaging techniques. The pyridinium derivative, F-Py becomes molecularly dissolved in 10% DMSO-PBS and interacts with CT-DNA via groove binding and electrostatic interactions, leading to the initial condensation of CT-DNA into micrometer sized aggregates and subsequent precipitation. On the other hand, the aniline derivative F-An, which is reported to form nanoclusters of 3-5 nm size, interacts with DNA through ordered, chiral assemblies on the CT-DNA template, thus perturbing the highly networked structure of CT-DNA to form nanonetworks, which eventually transform into condensed aggregates. The binding interactions between CT-DNA and F-An nanoclusters were established via UV-Vis, AFM and TEM analysis, and the chiral nature of the fullerene nanocluster assemblies on CT-DNA was confirmed by the presence of induced circular dichroism that was exhibited around the 250-370 nm region, corresponding to F-An nanocluster absorption. In contrast, the phenothiazine derivative F-PTz, which forms larger nanoclusters of ∼70 nm size in 10% DMSO-PBS, exhibited only weak interactions with CT-DNA without affecting its network structure. These results demonstrate the role of the hydrophobic-hydrophilic balance in the design of DNA interacting fullerene derivatives by controlling their cluster size and interactions with CT-DNA, and are significant in applications such as DNA condensation, gene delivery and dimension controlled nanomaterial fabrication.

Interaction of proflavine with the RNA polynucleotide polyriboadenylic acid-polyribouridylic acid: photophysical and calorimetric studies

The binding of proflavine, an acriflavine derivative, with the RNA polynucletodide polyadenylic acid-polyuridylic acid is investigated here to understand the structural and thermodynamic basis of the binding process. Such binding data are crucial for designing viable theraperutic agents. Spectroscopic studies clearly suggest a strong binding interaction between proflavine and polyadenylic acid-polyuridylic acid leading to efficient energy transfer between the poly AU base pairs and proflavine. The stoichiometry of proflavine polyadenylic acid-polyuridylic acid binding was independently estimated by continuous variation analysis of Job. An intercalative binding model is envisaged for the binding from hydrodynamic studies. Circular dichroism experiments revealed that the binding induced conformational changes in the RNA, and also led to induction of optical activity in the bound dye molecules. The binding affinity of the complex was deduced to be (6.57 ± 0.75) 10⁵ M^-1 at (298.15 ± 0.10) K from isothermal titration calorimetry experiment. Positive entropy and negative enthalpy changes characterized the complexation. The binding was observed to be weaker both at higher temperatures and increased [Na⁺]. The affinity of binding decreased with increasing [Na⁺]. When the Gibbs energy was parsed between polyelectrolytic and nonpolyelectropytic components, it surprisingly revealed a higher role for the non-polyelectrolytic forces. These results present new data for developing RNA targeted ligands.Communicated by Ramaswamy H. Sarma.

Azouracil and Its Cu(II)-Catalyzed Cyclization to an Anticancer Active Triazole Derivative: Symmetrical and Asymmetrical Reductive Cleavage, DNA Interaction, and Molecular Docking Studies

The 6-amino-1,3-dimethyl uracil-based azo derivative (p-carboxy phenylazouracil, L11) undergoes Cu(II)-catalyzed cyclization to a triazole derivative, namely, 1,3-dimethyl-8-(p-carboxy phenyl) azapurine (L11P). Interestingly, the azo functionality of L11 undergoes both symmetrical and asymmetrical reductive cleavage at two different reaction conditions. The chloride salts of Mn(II), Ni(II), and Pd(II) catalyze reductive cleavage of an azo moiety in an asymmetric manner, producing a new uracil hydrazine derivative (A3). On the other hand, hydrazine catalyzes symmetrical reductive cleavage of the azo moiety of L11, resulting in 5,6-diamino-1,3-dimethyl uracil (A2) along with the starting p-aminobenzoic acid (A1). Time-dependent density functional theoretical (TD-DFT) studies provide optimized geometries of L11, L11P, and A3 along with their orbital energies. The L11 and L11P bind firmly to genomic DNA of E. coli with a site size n ∼ 9 and n ∼ 8. The L11P shows anticancer activity on selected murine lymphoma cancer cell lines (DL, YAC1, and 2PK3). In addition, its antiproliferative activity is measured with several cancer cell lines and found hemocompatible toward blood cells. Corresponding molecular docking studies of L11P with caspase-3 (cysteine-aspartic proteases) unlock their mode of interaction.

Interaction of cobalt(II) and copper(II) hydroxamates with polyriboadenylic acid: An insight into RNA based drug designing

The polyadenylic acid [poly(A)] tail of mRNA plays a noteworthy role in the initiation of the translation, maturation, and stability of mRNA. It also significantly contributes to the production of alternate proteins in eukaryotic cells. Hence, it has recently been recognized as a prospective drug target. Binding affinity of bis(N-p-tolylbenzohydroxamato)Cobalt(II), [N-p-TBHA-Co(II)] (1) and bis(N-p-naphthylbenzohydroxamato)Copper(II), [N-p-NBHA-Cu(II)] (2) complexes with poly(A) have been investigated by biophysical techniques namely, absorption spectroscopy, fluorescence spectroscopy, diffuse reflectance infrared Fourier transform spectroscopy, circular dichroism spectroscopy, viscometric measurements and through molecular docking studies. The intrinsic binding constants (Kb) of complexes were determined following the order of N-p-TBHA-Co(II)] > N-p-NBHA-Cu(II), along with hyperchromism and a bathochromic shift for both complexes. The fluorescence quenching method revealed an interaction between poly(A)-N-p-TBHA-Co(II)/poly(A)-N-p-NBHA-Cu(II). The mode of binding was also determined via the fluorescence ferrocyanide quenching method. The increase in the viscosity of poly(A) that occurred from increasing the concentration of the N-p-TBHA-Co(II)/N-p-NBHA-Cu(II) complex was scrutinized. The characteristics of the interaction site of poly(A) with N-p-TBHA-Co(II)/N-p-NBHA-Cu(II) were adenine and phosphate groups, as revealed by DRS-FTIR spectroscopy. Based on these observations, a partial intercalative mode of the binding of poly(A) has been proposed for both complexes. Circular dichroism confirmed the interaction of both the complexes with poly(A). The molecular docking results illustrated that complexes strongly interact with poly(A) via the relative binding energies of the docked structure as -259.39eV and -226.30eV for N-p-TBHA-Co(II) and N-p-NBHA-Cu(II) respectively. Moreover, the binding affinity of N-p-TBHA-Co(II) is higher in all aspects than N-p-NBHA-Cu(II) for poly(A).

Synthesis, characterization and nucleic acid binding studies of mononuclear copper(II) complexes derived from azo containing O, O donor ligands

Azo linked salicyldehyde and a new 2-hydroxy acetophenone based ligands (HL1 and HL2) with their copper(II) complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) were synthesized and characterized by spectroscopic methods such as 1H, 13C NMR, UV-Vis spectroscopy and elemental analyses. Calculation based on Density Functional Theory (DFT), have been performed to obtain optimized structures. Binding studies of these copper (II) complexes with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) were analyzed by absorption spectra, emission spectra and Viscosity studies and Molecular Docking techniques. The absorption spectral study indicated that the copper(II) complexes of 1 and 2 had intrinsic binding constants with DNA or RNA in the range of 7.6 ± 0.2 × 103 M-1 or 6.5 ± 0.3 × 103M-1 and 5.7 ± 0.4 × 104 M-1 or 1.8 ± 0.5 × 103 M-1 respectively. The synthesized compounds and nucleic acids were simulated by molecular docking to explore more details mode of interaction of the complexes and their orientations in the active site of the receptor.

Binding Mode of Cationic Porphyrin with CT-DNA: Importance of the Location and the Number of Positively Charged of Periphery Cationic Ions of Porphyrin

The binding modes of o-, m-, and p-trans-BMPyP with DNA were studied using their spectroscopic properties. Also, the binding modes were compared based on the location and number of periphery cationic methylpyridine ions of the cationic porphyrins. The optical absorption spectra of the o-, m-, and p-trans-BMPyP when bound to DNA presented red shifts and hypochromicity compared to the optical absorption spectrum of DNA-free cationic porphyrins. m-trans-BMPyP-DNA presented the largest red shifts and hypochromicity. The results of the circular dichroism spectral analysis indicated positive and negative bisignate absorption bands in the Soret band of the porphyrins in the case of all concentration ratios of o- and p-trans-BMPyP-DNA, and two negative absorption bands were observed in m-trans-BMPyP-DNA. Compared to the size of the absorption band of the DNA optical absorption spectrum, the results of the reduced linear (LD^r) spectral analysis indicated mainly small sizes of Soret absorption bands (the absorption spectrum of porphyrins) and positive LD^r values for o- and p-trans-BMPyP-DNA. In consideration of several of such spectroscopic properties, the binding of o- and p-trans-BMPyP with DNA can be said to be distant to insertion modes. Although the case of m-trans-BMPyP to DNA is an insertion mode, the m-trans-BMPyP molecular surface presented much tilt within the intercalation pocket. The results of comparing the binding modes of TMPyP having four periphery cationic methylpyridine ions of cationic porphyrin indicated that regardless of the number of periphery cationic methylpyridine ions of cationic porphyrin, in the case of the ortho-position, nonplanarity due to steric hindrance of the periphery cationic methylpyridine ions presented outside or groove-binding modes indicative of interaction with DNA phosphates. Unlike the ortho-position, the para-position presented different binding modes based on the number of periphery cationic methylpyridine ions. Only cationic porphyrins having four periphery cationic methylpyridine ions were inserted into the DNA. Lastly, regardless of the number of periphery cationic methylpyridine ions, all meta-positions were inserted into the DNA. This indicated that at the least the location and the number of periphery cationic methylpyridine ions of the porphyrins used in this experiment were important elements that determine insertion into DNA base pairs.

Analysis of the interaction between the cocaine-binding aptamer and its ligands using fluorescence spectroscopy

We used fluorescence spectroscopy to measure the binding affinity and provide new insights into the binding mechanism of cocaine and quinine with the cocaine-binding DNA aptamer. Using the intrinsic fluorescence of quinine and cocaine, we have observed quenching of ligand fluorescence upon binding of the aptamer. Quantification of this quenching provides an easy method to measure the binding constant using small amounts of sample. The observed quenching coupled with a red shift of the Stokes shift in the emission spectrum indicates that quinine and cocaine interact with the aptamer through stacking interactions.

DNA and BSA binding and cytotoxic properties of copper(ii) and iron(iii) complexes with arylhydrazone of ethyl 2-cyanoacetate or formazan ligands

Copper(ii) and iron(iii) complexes with arylhydrazone of ethyl 2-cyanoacetate or formazan ligands show DNA and BSA binding and anticancer abilities.

Fluorescent zinc(ii) complexes for gene delivery and simultaneous monitoring of protein expression

Two new zinc(ii) complexes, [Zn(l-His)(NIP)]+(1) and [Zn(acac)2(NIP)](2) (where NIP is 2-(naphthalen-1-yl)-1H-imidazo[4,5-f][1,10]phenanthroline, acac = acetyl acetone), have been synthesized and characterized by elemental analysis, UV-vis, fluorescence, IR, 1H NMR and electron spray ionization mass spectroscopies. Gel retardation assay, atomic force microscopy and dynamic light scattering studies show that 1 and 2 can induce the condensation of circular plasmid pBR322 DNA into nanometer size particles under ambient conditions. Treatment of 2 with 5 mM EDTA restored 30% of the supercoiled form of DNA, revealing partial reversibility of DNA condensation. The in vitro transfection experiment demonstrates that the complexes can be used to deliver pCMV-tdTomato-N1 plasmid which expresses red fluorescent protein. The confocal studies show that the fluorescent nature of complexes is advantageous for visualizing the intracellular delivery of metal complexes as well as transfection efficiency using two distinct emission windows.

Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts

DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

Exploring the comparative binding aspects of benzophenanthridine plant alkaloid chelerythrine with RNA triple and double helices: a spectroscopic and calorimetric approach

A comparative study on the interaction of a benzophenanthridine alkaloid chelerythrine (CHL) with RNA triplex poly(U).poly(A)*poly(U) (hereafter U.A*U, .(dot) and *(asterisk) represent Watson-Crick and Hoogsteen base pairing respectively) and its parent duplex poly(A).poly(U) (A.U) was carried out by using a combination of various spectroscopic, viscometric and calorimetric techniques. The interaction was characterized by hypochromic and bathochromic effects in the absorption spectrum, the increase of thermal melting temperature, enhancement in solution viscosity, and perturbation in the circular dichroic spectrum. The binding constant calculated by using spectrophotometric data was in the order of 10(5) for both forms of RNA, but it was greater for triplex RNA (30.2 × 10(5) M(-1)) than duplex RNA (3.6 × 10(5) M(-1)). Isothermal titration calorimetric data are in good agreement with the spectrophotometric data. The data indicated stronger binding of CHL to the triplex structure of RNA compared to the native duplex structure. Thermal melting studies indicated greater stabilization of the Hoogsteen base paired third strand of the RNA triplex compared to its Watson-Crick strands. The mode of binding of CHL to both U.A*U and A.U was intercalation as revealed from fluorescence quenching, viscosity measurements and sensitization of the fluorescence experiment. Thermodynamic data obtained from isothermal calorimetric measurements revealed that association was favoured by both a negative enthalpy change and a positive entropy change. Taken together, our results suggest that chelerythrine binds and stabilizes the RNA triplex more strongly than its respective parent duplex. The results presented here may be useful for formulating effective antigene strategies involving benzophenanthridine alkaloids and the RNA triplex.

Ni(ii) complex with bishydrazone ligand: synthesis, characterization, DNA binding studies and pro-apoptotic and pro-differentiation induction in human cancerous cell lines

A new Ni(ii) complex, [Ni(L)(H₂O)] (1), with diethyl 3,3′-(2,2′-(1,1′-(pyridine-2,6-diyl)bis(ethan-1-yl-1-ylidene))bis(hydrazin-1-yl-2-ylidene))bis(3-oxopropanoate) ligand (H₂L) was synthesized as a potential chemotherapeutic agent.

The Plant-Derived Chalcone 2,2',5'-Trihydroxychalcone Provides Neuroprotection against Toll-Like Receptor 4 Triggered Inflammation in Microglia

Chalcones are plant metabolites with potential for therapeutic exploitation as antioxidant, anti-inflammatory, and antiproliferative agents. Here we explored the neuroprotective effects of 2,2',5'-trihydroxychalcone (225THC), a potent antioxidant with radical-scavenging properties. 225THC was found to be a potent inhibitor of apoptosis in stimulated primary rat neuronal cultures. This was likely mediated by an anti-inflammatory effect on microglial cells since 225THC inhibited LPS-stimulated TNF-α and IL-6 secretion from primary rat microglia and modulated the cytokine/chemokine profile of BV2 microglial cells. Additionally, 225THC inhibited LPS-evoked inducible nitric oxide synthase expression but did not influence endogenous superoxide generation. Microglial flow cytometric analyses indicated the 225THC treatment induced a shift from an M1-like phenotype to a more downregulated microglial profile. Taken together these data suggest that the chalcone 2,2',5'-trihydroxychalcone can modulate neuroinflammatory activation in brain-derived microglia and holds promise as a therapeutic in neuroinflammatory conditions.

Naphthalene Imide Conjugates: Formation of Supramolecular Assemblies, and the Encapsulation and Release of Dyes through DNA-Mediated Disassembly

We report the synthesis of two new amphiphilic conjugates 1 and 2 based on naphthalene di- and monoimide chromophores and the investigation of their photophysical, self-assembly and DNA-binding properties. These conjugates showed aqueous good solubility and exhibited strong interactions with DNA and polynucleotides such as poly(dG⋅dC)-poly(dG⋅dC) and poly(dA⋅dT)-poly(dA⋅dT). The interaction of these conjugates with DNA was evaluated by photo- and biophysical techniques. These studies revealed that the conjugates interact with DNA through intercalation with association constants in the order of 5-8×10(4)  M(-1) . Of these two conjugates, bolaamphiphile 1 exhibited a supramolecular assembly that formed vesicles with an approximate diameter of 220 nm in the aqueous medium at a critical aggregation concentration of 0.4 mM, which was confirmed by SEM and TEM. These vesicular structures showed a strong affinity for hydrophobic molecules such as Nile red through encapsulation. Uniquely, when exposed to DNA the vesicles disassembled, and therefore this transformation could be utilised for the encapsulation and release of hydrophobic molecules by employing DNA as a stimulus.

RNA-Binding Efficacy of N-Phenylbenzohydroxamic Acid: An Invitro and Insilico Approach

RNA has attracted recent attention for its key role in gene expression and hence targeting by small molecules for therapeutic intervention. This study is aimed to elucidate the specificity of RNA binding affinity of parent compound of N-arylhydroxamic acids series, N-phenylbenzohydroxamic acid trivially named as PBHA,C6H5NOH.C6H5C˭O. The binding behavior was examined by various biophysical methods such as absorption, fluorescence, and viscosity measurements. Molecular docking was also done. The value of affinity constant and overall binding constant was calculated 5.79±0.03×10(4) M(-1) and K'=1.09±0.03×10(5) M(-1), respectively. The Stern-Volmer constant Ksv obtained was 2.28±0.04×10(4) M(-1). The compound (PBHA) shows a concentration-based enhancement of fluorescence intensity with increasing RNA concentration. Fluorescence quenching of PBHA-RNA complex in presence of K4 [Fe(CN)6] was also observed. Viscometric studies complimented the UV results where a continuous increase in relative viscosity of the RNA solution was observed with added optimal PBHA concentration. All the experimental evidences indicate that PBHA can strongly bind to RNA through an intercalative mode.

The effect of LNA nucleobases as enhancers for the binding of amiloride to an abasic site in DNA/DNA and DNA/RNA duplexes

We report on a significant effect of locked nucleic acid (LNA) nucleobases on the binding of amiloride for abasic site (AP)-containing DNA duplexes. Fluorescence titration experiments showed that the binding affinity of amiloride for the target thymine (T) opposite an AP site significantly improves for the DNA duplexes possessing LNA nucleobases that flank the AP site, compared to the corresponding normal DNA duplexes. In particular, LNA flanking nucleobases on both 5'- and 3'-sides of the AP site are found to be effective for the enhancement of the binding affinity. From thermodynamic characterization of the amiloride binding, the loss in the binding entropy is remarkably reduced for the LNA-containing DNA duplexes, which is indeed responsible for the enhanced affinity of amiloride. Moreover, such an effect of LNA nucleobases was also observed for amiloride binding to DNA/RNA hybrid duplexes.

Development of a PET radiotracer for non-invasive imaging of the reactive oxygen species, superoxide, in vivo

Reactive oxygen species (ROS) have been implicated in the pathogenesis of a wide range of human disease states and drug toxicities, but development of imaging tools to study ROS biology in vivo remains a challenge. Here we synthesized and validated a novel PET tracer (12) and its (18)F radiolabeled version [(18)F]12 to allow PET ( positron emission tomography) imaging of superoxide in vivo. Initial analysis of ROS reaction kinetics found that compound 12 was rapidly and selectively oxidized by superoxide, but not other ROS. Cell culture studies in EMT6 cells exposed to the cancer chemotherapeutic agent Doxorubicin (DOX), which activates the superoxide-generating enzyme, NADPH oxidase, showed that compound 12 was a sensitive and specific probe for superoxide in cells. The microPET imaging of heart in mice with DOX-induced cardiac inflammation observed 2-fold greater oxidation of [(18)F]12 in the DOX-treated mice compared to controls (p = 0.02), the results were confirmed by distribution studies on organs subsequently removed from the mice and HPLC analysis of [(18)F] radioactivity compounds. These data indicate that compound 12 is a useful PET tracer to imaging ROS in vivo.

Zn(ii) complex with 2-quinolinecarboxaldehyde selenosemicarbazone: synthesis, structure, interaction studies with DNA/HSA, molecular docking and caspase-8 and -9 independent apoptose induction

A new Zn(ii)-based complex shows a concentration-dependent apoptotic response in highly resistant pancreatic adenocarcinoma cells with extensive activation of caspase-8 and -9.

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

Phenanthridine derivatives are one of the most intensively studied families of biologically active compounds with efficient DNA binding capability. Attracting attention since DNA structure discovery (1960s), they were early recognized as a symbol of DNA intercalative binding, for many decades applied as gold-standard DNA- and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of phenanthridine derivatives resulted in the strong increase of the scientific interest about the turn of this century. Here are summarized phenanthridine-related advances in the 21st century (2000-present period) with emphasis on the supramolecular interactions and bioorganic chemistry, as well as novel or improved synthetic approaches.