Molecular modeling of intercalation complexes of antitumor active 9-aminoacridine and a [d, e]-anellated isoquinoline derivative with base paired deoxytetranucleotides

Thermal stabilisation of the short DNA duplexes by acridine-4-carboxamide derivatives

The short oligodeoxynucleotide (ODN) probes are suitable for good discrimination of point mutations. However, the probes suffer from low melting temperatures. In this work, the strategy of using acridine-4-carboxamide intercalators to improve thermal stabilisation is investigated. The study of large series of acridines revealed that optimal stabilisation is achieved upon decoration of acridine by secondary carboxamide carrying sterically not demanding basic function bound through a two-carbon linker. Two highly active intercalators were attached to short probes (13 or 18 bases; designed as a part of HFE gene) by click chemistry into positions 7 and/or 13 and proved to increase the melting temperate (T_m) of the duplex by almost 8°C for the best combination. The acridines interact with both single- and double-stranded DNAs with substantially preferred interaction for the latter. The study of interaction suggested higher affinity of the acridines toward the GC- than AT-rich sequences. Good discrimination of two point mutations was shown in practical application with HFE gene (wild type, H63D C > G and S65C A > C mutations). Acridine itself can also serve as a fluorophore and also allows discrimination of the fully matched sequences from those with point mutations in probes labelled only with acridine.

Cooperativity effect of the ππ interaction between drug and DNA on intercalative binding induced by H-bonds: a QM/QTAIM investigation of the curcuminadenineH2O model system

In order to reveal the nature of intercalative binding of drug to DNA, the cooperativity effect of the ππ interaction was investigated in the curcuminadenineH2O model system by applying a combined QM and QTAIM computational approach. The H-bonds between the electron-donating group of curcumin and adenine induce the formation of the ππ stacking. The introduction of H2O weakens the H-bonding and ππ interactions, leading to an anti-cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that the anti-cooperative effect is the main driving force for the intercalative binding of drug to DNA bases, which is in agreement with many experimental phenomena. Therefore, the designed DNA-targeted intercalating drugs should possess not only hydrophobic moieties, but also strong electron-donating groups bound to the DNA bases with H-bonds, which can slow the variation rates of the strengths of the H-bonding and ππ interactions between drug and DNA bases in the anti-cooperative process, leading to the intercalation formation. The enthalpy change is the major factor driving the positive thermodynamic cooperativity.

Antibacterial and Photocatalytic Properties of ZnO-9-Aminoacridine Hydrochloride Hydrate Drug Nanoconjugates

The development of nanomaterial-based hybrid systems for healthcare and energy-related materials has attracted significant attention nowadays. Here, we have designed a nanocomposite of ZnO nanoparticles (NPs) with anticancer therapeutic drug 9-aminoacridine hydrochloride hydrate (9AA-HCl) for antibacterial and photocatalytic activities. Spectroscopic studies reveal that the photoinduced electron transfer from photoexcited 9AA-HCl to the conduction band of ZnO NP causes the generation of the reactive oxygen species (ROS), which is responsible for antibacterial activity and photocatalytic properties. It is seen that the efficiency of photodegradation of dye molecules increases in ZnO-9AA-HCl nanoconjugated systems than pure ZnO nanoparticles because of efficient charge separation. In addition, the antibacterial efficacy of the nanoconjugate is investigated using a strain of Gram-negative bacteria where the cell-killing activities are observed 99.99 and 100% for 20 and 21 μL/mL nanoconjugate, respectively, and very little cell-killing activity is observed for free ZnO NPs and free drug. Moreover, it is also observed that the nanoconjugate generates sufficient intracellular ROS that can hydrolyze 2',7'-dichlorodihydrofluoresceindiacetate (DCFH-DA) to highly fluorescent 2',7'-dichlorofluorescein (DCF). The outcome of the study will provide valuable information for designing new-edge nanoconjugate materials for potential applications in photocatalytic and antibacterial activities.

9-AAA inhibits growth and induces apoptosis in human melanoma A375 and rat prostate adenocarcinoma AT-2 and Mat-LyLu cell lines but does not affect the growth and viability of normal fibroblasts

The present study found that, similarly to 5-fluorouracil, low concentrations (1-10 µM) of 9-aminoacridine (9-AAA) inhibited the growth of the two rat prostate cancer AT-2 and Mat-LyLu cell lines and the human melanoma A375 cell line. However, at the same concentrations, 9-AAA had no effect on the growth and apoptosis of normal human skin fibroblasts (HSFs). The differences between the cellular responses of the AT-2 and Mat-LyLu cell lines, which differ in malignancy, were found to be relatively small compared with the differences between normal HSFs and the cancer cell lines. Visible effects on the cell growth and survival of tumor cell lines were observed after 24-48 h of treatment with 9-AAA, and increased over time. The inhibition of cancer cell growth was found to be due to the gradually increasing number of cells dying by apoptosis, which was observed using two methods, direct counting and FlowSight analysis. Simultaneously, cell motile activity decreased to the same degree in cancer and normal cells within the first 8 h of incubation in the presence of 9-AAA. The results presented in the current study suggest that short-lasting tests for potential anticancer substances can be insufficient; which may result in cell type-dependent differences in the responses of cells to tested compounds that act with a delay being overlooked. The observed differences in responses between normal human fibroblasts and cancer cells to 9-AAA show the requirement for additional studies to be performed simultaneously on differently reacting cancer and normal cells, to determine the molecular mechanisms responsible for these differences.

A Spectroscopic Approach with Theoretical Studies to Study the Interaction of 9-aminoacridine with Certain Phenols

The influence of phenols upon the fluorescence quenching of 9-aminoacridine (9-AA) was examined in acetonitrile solution by employing steady state and time-resolved fluorescence measurements. On increasing the concentration of quencher molecules the absorption spectra of 9-AA change with significant bathochromic shift. The fluorescence intensity of 9-AA change in presence of quencher molecules were measured at various temperatures as a function of the quencher concentrations. The observed bimolecular quenching rate constant (kq) depends on the nature and electronic effect of substituent present in the quencher molecules. The bimolecular quenching rate constant (kq) decreases on increasing the oxidation potential of quencher molecules. To examine the quenching behavior, kq values were correlated with the free energy change (ΔG). To get forthcoming in the quenching process, fluorescence quenching experiments were carried out in different solvents of varying polarities. The observed result suggest the involvement of charge-transfer quenching mechanism. Lifetime measurements support static quenching. Further, the radical scavenging potential is calculated from density functional theory (DFT) calculations to address the quenching behavior of the quencher molecules. DFT result reveals that electronic features are important in tuning the quenching ability of the quencher molecules and found to agree with the obtained experiment result.

Identification of modes of interactions between 9-aminoacridine hydrochloride hydrate and serum proteins by low and high resolution spectroscopy and molecular modeling

Photophysical studies on binding interactions of 9-aminoacridine hydrochloride hydrate (9AA-HCl) with serum proteins using low and high resolution spectroscopic techniques in conjunction with molecular modeling.

Pharmacogenomic study using bio- and nanobioelectrochemistry: Drug-DNA interaction

Small molecules that bind genomic DNA have proven that they can be effective anticancer, antibiotic and antiviral therapeutic agents that affect the well-being of millions of people worldwide. Drug-DNA interaction affects DNA replication and division; causes strand breaks, and mutations. Therefore, the investigation of drug-DNA interaction is needed to understand the mechanism of drug action as well as in designing DNA-targeted drugs. On the other hand, the interaction between DNA and drugs can cause chemical and conformational modifications and, thus, variation of the electrochemical properties of nucleobases. For this purpose, electrochemical methods/biosensors can be used toward detection of drug-DNA interactions. The present paper reviews the drug-DNA interactions, their types and applications of electrochemical techniques used to study interactions between DNA and drugs or small ligand molecules that are potentially of pharmaceutical interest. The results are used to determine drug binding sites and sequence preference, as well as conformational changes due to drug-DNA interactions. Also, the intention of this review is to give an overview of the present state of the drug-DNA interaction cognition. The applications of electrochemical techniques for investigation of drug-DNA interaction were reviewed and we have discussed the type of qualitative or quantitative information that can be obtained from the use of each technique.

Novel ametantrone-amsacrine related hybrids as topoisomerase IIβ poisons and cytotoxic agents

The precise definition of the structural requirements for effective topoisomerase II poisoning by drug molecules is still an elusive issue. In the attempt to better define a pharmacophoric pattern, we prepared several conjugates combining the chemical features of two well-known topoisomerase II poisons, amsacrine and ametantrone. Indeed, an appropriate fusion geometry, which entails the anthracenedione moiety of ametantrone appropriately connected to the methanesulfonamidoaniline side chain of amsacrine, elicits DNA-intercalating properties, the capacity to inhibit the human topoisomerase IIβ isoform, and cytotoxic activity resembling that of the parent compounds. In addition, the properties of the lateral groups linked to the anthracenedione group play an important role in modulating DNA binding and cell cytotoxicity. Among the compounds tested, 10, 11, and 19 appear to be promising for further development.

Excimer of 9-aminoacridine hydrochloride hydrate in confined medium: an integrated experimental and theoretical study

We aim to find out the extent of stability of the excimer of 9-aminoacridine hydrochloride hydrate (9AA), a prospective PDT drug, in different confined media with varying cavity size. When confined in cetyltrimethyl ammonium bromide micelles, although at low concentration of 9AA, only a single distinct peak (λ(max) at 460 nm) with a shoulder at 485 nm is observed in steady-state fluorescence spectrum, yet with increase in concentration the peak and the shoulder merge with simultaneous emergence of another peak at 535 nm, which is assigned to excimer. Similar behavior is also observed in Triton-X, crown ether, α-cyclodextrin, β-cyclodextrin, and homogeneous aqueous medium. The formation of excimer, which reflects the extent of confinement of 9AA, is maximum in β-cyclodextrin followed by others. Steady-state and time-resolved fluorescence studies along with TRES and TRANES analyses coupled with anisotropy data and transient absorption studies reveal the presence of monomer-dimer equilibrium of 9AA in the excited state. Molecular modeling indicates that the structure of excimer is stabilized by locking of the two monomeric species via four hydrogen bonds formed between the amino-H and imino-N of 9AA monomers, whereas the dimer in the ground state has only two such hydrogen bonds.

Spectroscopic investigation on the interaction of 9-aminoacridine with certain dyes

The fluorescence quenching of 9-Aminoacridine (9-AA) by various dyes were probed in aqueous medium using steady state and time resolved fluorescence spectroscopic techniques. From these techniques, we had rationalized the interaction of 9-AA with various dyes via ground state complex formation. The binding constant (K) and number of binding sites (n) were calculated from the relevant fluorescence quenching data. The fluorescence emission of 9-Aminoacridine was quenched by the dyes through static quenching followed by the mechanism of energy transfer. The static quenching mechanism was confirmed by lifetime measurements. The thermodynamic parameters such as free energy change (ΔG), enthalpy change (ΔH) and entropy change (ΔS), were calculated by thermodynamic equations. The results showed that Van der Waals interaction or hydrogen bond formation played a major role in the binding of 9-AA with these dyes.

Quinoline alkaloids as intercalative topoisomerase inhibitors

Quinoline alkaloids are abundant in the Rutaceae, and many have exhibited cytotoxic activity. Because structurally related antitumor alkaloids such as camptothecin and fagaronine are known to function as intercalative topoisomerase poisons, it is hypothesized that cytotoxic Stauranthus alkaloids may also serve as intercalative topoisomerase inhibitors. To test this hypothesis theoretically, ten Stauranthus quinoline alkaloids were examined for potential intercalation into DNA using a molecular docking approach. Four of the alkaloids (stauranthine, skimmianine, 3',6'-dihydroxy-3',6'-dihydrostauranthine, and trans-3',4'-dihydroxy-3',4'-dihydrostauranthine) were able to intercalatively dock consistently into DNA. In order to probe the intermolecular interactions that may be responsible for intercalation of these quinoline alkaloids, density functional calculations have been carried out using both the B3LYP and M06 functionals. M06 calculations indicated favorable pi-pi interactions between either skimmianine or stauranthine and the guanine-cytosine base pair. Furthermore, the lowest-energy face-to-face orientation of stauranthine with guanine is consistent with favorable dipole-dipole orientations, favorable electrostatic interactions, and favorable frontier molecular orbital interactions. Likewise, the lowest-energy face-to-face orientation of stauranthine with the guanine-cytosine base pair reveals favorable electrostatic interactions as well as frontier molecular orbital interactions. Thus, not only can quinoline alkaloids dock intercalatively into DNA, but the docked orientations are also electronically favorable.

Molecular modeling of tricyclic compounds with anilino substituents and their intercalation complexes with DNA sequences

Although 9-anilinoacridines are among the best studied antitumoral intercalators, there are few studies about the effect of isosteric substitution of a benzene moiety for a heterocycle ring in the acridine framework. According to these studies, this approach may lead to effective cytotoxic agents, but good cytotoxic activity depends on structural requirements in the aniline ring which differ from those in 9-anilinoacridines. The present paper deals with molecular modeling studies of some 9-anilino substituted tricyclic compounds and their intercalation complexes (in various DNA sequences) resulting from docking the compounds into various DNA sequences. As expected, the isosteric substitution in 9-anilinoacridines influences the LUMO energy values and orbital distribution, the dipole moment, electrostatic charges and the conformation of the anilino ring. Other important differences are observed during the docking studies, for example, changes in the spatial arrangement of the tricyclic nucleus and the anilino ring at the intercalation site. Semiempirical calculations of the intercalation complexes show that the isosteric replacement of a benzene ring in the acridine nucleus affects not only DNA affinity but also base pair selectivity. These findings explain, at least partially, the different structural requirements observed in several 9-anilino substituted tricyclic compounds for cytotoxic activity. Thus, the data presented here may guide the rational design of new agents with different DNA binding properties and/or a cytotoxic profile by isosteric substitution of known intercalators.

Synthesis, antitumour activity and structure–activity relationships of 5H-benzo[b]carbazoles

A series of novel 5H-benzo[b]carbazoles related to the ellipticines was obtained from the reactions of p-benzoquinones with 2-aminomethylene-1-indanones. Most of the compounds were evaluated for their antitumour activity in the National Cancer Institute's in vitro human tumour cell line screening panel. Among them, particularly derivative 15c bearing a p-quinone methide moiety in ring C of the heterocycle was found to show in vitro activity comparable to clinically well established anticancer agents such as amsacrine or mitomycin C. Compounds 9d, 9e and 12k showed increased potency to distinct cell lines like the leukemia or melanoma subpanel of cell lines. Based on the test results, structure-activity relationships for this series of compounds were developed. For instance, it was found that a quinonoid substructure in ring C leads to a noticeable increase in activity. The same observation was made for a 2-hydroxyl substituent at the ring system. 2-Acetoxy and 2-methoxy derivatives as well as 2-unsubstituted 5H-benzo[b]carbazoles either had a decreased potency or were found to be inactive. A COMPARE analysis with some of these compounds showed poor or no correlation with anticancer drugs of the NCI's standard agents database indicating a novel mechanism of action. Additionally, UV-vis titrations in the series of 5H-benzo[b]carbazoles indicated interactions with calf thymus DNA only for the highly active quinone methide 15c.

Interaction of antitumoral 9-aminoacridine drug with DNA and dextran sulfate studied by fluorescence and surface-enhanced Raman spectroscopy

Fluorescence spectroscopy and surface-enhanced Raman spectroscopy are applied to study the interaction of the drug 9-aminoacridine (9AA) with DNA and dextran sulfate. The effect of the electrostatic interaction between the positively charged 9AA and negatively charged groups in relation to the excimer or exciplex emission is investigated. The exciplex emission of 9AA is connected to the intercalation of this drug between nucleic base residues. The importance of negative groups in this interaction is evaluated by using dextran and dextran sulfate as model polymers. The existence of negative charges seems to induce an increase of the drug concentration in the vicinity of the polymers. The role of electrostatic attraction in the 9AA dimerization is confirmed by the excimer emission of 9AA in the presence of dextran sulfate. In the case of DNA, the phosphate groups may induce the drug approach to the DNA chain, but the exciplex fluorescence emission could be due to a charge transfer between the drug and adenine-rich sequences of DNA.

Synthesis and in vitro cytotoxic activity of pyrrolo[2,3-e]indole derivatives and a dihydro benzoindole analogue

The synthesis of pyrrolo[2,3-e]indole derivatives with the structural characteristics of DNA bis- and mono-intercalators are described. A dihydro benzoindol analogue was also synthesised to elucidate the major structural requirements for cytotoxic activity. A biological evaluation of the test compounds was carried out in six different tumoral cell lines. The factors that affect the cytotoxic activity appear to be the substituents on the phenyl group, the presence of an amide group capable of strong interactions such as hydrogen bonding and solubility.

Surface-enhanced Raman and steady fluorescence study of interaction between antitumoral drug 9-aminoacridine and trypsin-like protease related to metastasis processes, guanidinobenzoatase

Fluorescence spectroscopy and surface-enhanced Raman spectroscopy (SERS) were applied to study the interaction of the antitumoral drug 9-aminoacridine (9AA) with a trypsin-like protease guanidinobenzoatase (GB) extracted from a mouse Erlich tumor. As a consequence of this interaction, a strong 9AA exciplex emission was detected in the emission fluorescence spectra at certain drug and enzyme concentrations. A SERS study was accomplished on silver colloids at several excitation wavelengths in order to obtain more information about the interaction mechanism. The results derived from Raman spectroscopy indicated that 9AA in the amino monomeric form may interact with the enzyme by means of two different bonds: an ionic bond with a negatively charged amino acid and a ring stacking interaction with an aromatic residue placed in the catalytic site of GB. This interaction mechanism was responsible for a strong exciplex emission detected at a longer wavelength than the expected value of the normal fluorescence emission. Moreover, the GB concentration dependence of the interaction suggested that the drug was sensitive to the quaternary structure of the enzyme.

Synthesis and cytotoxic evaluation of N1,Nm-bis[(tetrahydrobenzo[a]acridin-12-yl)phenyl]alkanediamides and N1,Nm-bi

The title compounds were synthesized in four steps from 5,5-dimethyl-1, 3-cyclohexanedione as starting material. These compounds were evaluated against 60 tumoral cell lines, whereas the N1,Nm-bis[benzo[c]acridin-7-yl]phenyl]alkanediamides displaying significant cytotoxic activity, the corresponding N1,Nm-bis[benzo[a]acridin-12-yl]phenyl]alkanediamides derivatives were found to be less cytotoxic.

Fluorescence and surface-enhanced Raman study of 9-aminoacridine in relation to its aggregation and excimer emission in aqueous solution and on silver surface

Fluorescence spectroscopy and surface-enhanced Raman spectroscopy (SERS) have been applied to study the aggregation and excimer emission of 9-aminoacridine (9AA) and 9-aminoacridine hydrochloride (9AA-HCl) in aqueous solution and on silver colloids. The effect of the drug concentration, pH, and chloride concentration on these processes has been investigated. The excimer emission of 9AA is connected to the dimerization of this drug in solution: the formation of 9AA dimers is greatly favored when the drug is under the amino form at neutral and acidic pH, while at alkaline pH the imino 9AA form tends to form large-size aggregates which cannot be excited to render excimer emission. 9AA is adsorbed on the silver surface under two different forms: strongly and weakly attached 9AA, each one corresponding to the different drug tautomers: imino and amino. The interaction of 9AA with silver induces a charge transfer from the adsorbate to the metal leading to a remarkable fluorescence quenching, a basicity decrease of the adsorbed drug and a considerable weakening of the dimer-excimer emission. Furthermore, an attribution of the main Raman features appearing in the SERS spectra has been proposed, providing marker bands for the imino and amino 9AA tautomers, and a mechanism for the molecular dimerization is also suggested.