Targeting DNA with novel diphenylcarbazoles

Palindromic carbazole derivatives: unveiling their antiproliferative effect via topoisomerase II catalytic inhibition and apoptosis induction

Human DNA topoisomerases are essential for crucial cellular processes, including DNA replication, transcription, chromatin condensation, and maintenance of its structure. One of the significant strategies employed in cancer treatment involves the inhibition of a specific type of topoisomerase, known as topoisomerase II (Topo II). Carbazole derivatives, recognised for their varied biological activities, have recently become a significant focus in oncological research. This study assesses the efficacy of three symmetrically substituted carbazole derivatives: 2,7-Di(2-furyl)-9H-carbazole (27a), 3,6-Di(2-furyl)-9H-carbazole (36a), and 3,6-Di(2-thienyl)-9H-carbazole (36b) - as anticancer agents. Among investigated carbazole derivatives, compound 3,6-di(2-furyl)-9H-carbazole bearing two furan moieties emerged as a novel catalytic inhibitor of Topo II. Notably, 3,6-di(2-furyl)-9H-carbazole effectively selectively inhibited the relaxation and decatenation activities of Topo IIα, with minimal effects on the IIβ isoform. These findings underscore the potential of compound 3,6-Di(2-furyl)-9H-carbazole as a promising lead candidate warranting further investigation in the realm of anticancer drug development.

An insight into DNA binding properties of newly designed cationic δ,δ'‑diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies

Two cationic δ,δ'‑diazacarbazoles, 1‑Methyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (MPDPI) and 1,5‑Dimethyl‑5H‑pyrrolo[3,2‑b:4,5‑b']dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ'‑diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV-Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ'‑diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV-Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to CH₃ (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5‑NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ'‑diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ'‑diazacarbazoles and DNA were weakened, but δ,δ'‑diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.

Turning intercalators into groove binders: synthesis, photophysics and DNA binding properties of tetracationic mononuclear ruthenium(ii)-based chromophore–quencher complexes

Despite incorporating an extended planar polyaromatic ligand two newly synthesized Ru^II complexes are not DNA intercalators but groove binders.

Recognition and discrimination of DNA quadruplexes by acridine-peptide conjugates

We have explored a series of trisubstituted acridine-peptide conjugates for their ability to recognize and discriminate between DNA quadruplexes derived from the human telomere, and the c-kit and N-ras proto-oncogenes. Quadruplex affinity was measured as the peptide sequences were varied, together with their substitution position on the acridine, and the identity of the C-terminus (acid or amide). Surface plasmon resonance measurements revealed that all compounds bound to the human telomeric quadruplex with sub-micromolar affinity. Docking calculations from molecular modelling studies were used to model the effects of substituent orientation and peptide sequence. Modelling and experiment were in agreement that placement of the peptide over the face of the acridine is detrimental to binding affinity. The highest degrees of selectivity were observed towards the N-ras quadruplex by compounds capable of forming simultaneous contacts with their acridine and peptide moieties. The ligands that bound best displayed quadruplex affinities in the 1-5 nM range and at least 10-fold discrimination between the quadruplexes studied.

Effect of spermine conjugation on the interaction of acridine with alternating purine-pyrimidine oligodeoxyribonucleotides studied by CD, fluorescence and absorption spectroscopies

We studied by electronic spectroscopies the interaction between double-stranded oligonucleotides containing either adenine-thymine or guanine-cytosine alternating sequences and N(1)-(acridin-9-yl)-1,16-diamino-4,8,13-triazahexadecane, which is a conjugated molecule formed by the covalent binding of spermine and 9-aminoacridine moieties via a trimethylene chain. Solutions containing the oligonucleotides and the conjugate, at different molar ratios, were studied by using electronic absorption, fluorescence emission and circular dichroism. Calculated association constants and fluorescence emission spectra showed that spermine conjugation induces sequence selectivity. The orientation of the intercalated acridine rings with respect to the oligonucleotide base planes was deduced from the electronic circular dichroism spectra. Evidence of the formation of spermine-induced aggregated structures, with potential applications to DNA packaging, gene therapy and anti-tumor therapy, was also achieved. Our data demonstrates that this spermine-acridine conjugate adds several specific characteristics provided by the polyamine moiety, as sequence selectivity, to the interesting properties of acridine derivatives.

Study by optical spectroscopy and molecular dynamics of the interaction of acridine-spermine conjugate with DNA

We report a spectroscopic and theoretical study of the interaction between double-stranded oligonucleotides containing either adenine-thymine or guanine-cytosine alternating sequences and N1-(Acridin-9-ylcarbonyl)-1,5,9,14,18-pentazaoctadecane, or ASC, which is formed by the covalent bonding of spermine and 9-amidoacridine moieties via a trimethylene chain. Solutions containing the oligonucleotides and the conjugate at different molar ratios were studied using complementary spectroscopic techniques, including electronic absorption, fluorescence emission, circular dichroism, and Raman spectroscopy. The spectroscopical properties of ASC at both the vibrational and the electronic levels were described by means of ab initio quantum-chemical calculations on 9-amidoacridine, used as a model compound. Molecular dynamics calculations, based on the QM/MM methodology, were also performed using previously docked structures of two oligonucleotide-ASC complexes containing the A-T and the G-C sequence. Our data, taken all together, allowed us to demonstrate that conjugation of spermine to acridine modulates and gives additional properties to the interaction of the latter with DNA. As the ASC molecule has a high affinity by the polyamine transport system, these results are promising for their application in the development of new anti-tumour drugs.

A hitchhiker's guide to G-quadruplex ligands

Over the past decade, nucleic acid chemists have seen the spectacular emergence of molecules designed to interact efficiently and selectively with a peculiar DNA structure named G-quadruplex. Initially derived from classical DNA intercalators, these G-quadruplex ligands progressively became the focal point of new excitement since they appear to inhibit selectively the growth of cancer cells thereby opening interesting perspectives towards the development of novel anti-cancer drugs. The present article aims to help researchers enter this exciting research field, and to highlight recent advances in the design of G-quadruplex ligands.

Molecular Recognition of DNA by Rigid [n]-Polynorbornane-Derived Bifunctional Intercalators: Synthesis and Evaluation of Their Binding Properties

We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27 degrees and a binding constant of about 8 microM. 9-aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding.

Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding

Binding of a small molecule to a macromolecular target reduces its conformational freedom, resulting in a negative entropy change that opposes the binding. The goal of this study is to estimate the configurational entropy change of two minor-groove-binding ligands, netropsin and distamycin, upon binding to the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). Configurational entropy upper bounds based on 10-ns molecular dynamics simulations of netropsin and distamycin in solution and in complex with DNA in solution were estimated using the covariance matrix of atom-positional fluctuations. The results suggest that netropsin and distamycin lose a significant amount of configurational entropy upon binding to the DNA minor groove. The estimated changes in configurational entropy for netropsin and distamycin are -127 J K(-1) mol(-1) and -104 J K(-1) mol(-1), respectively. Estimates of the configurational entropy contributions of parts of the ligands are presented, showing that the loss of configurational entropy is comparatively more pronounced for the flexible tails than for the relatively rigid central body.

Structure-specific recognition of quadruplex DNA by organic cations: influence of shape, substituents and charge

Combining structure-specific recognition of nucleic acids with limited sequence reading is a promising method to reduce the size of the recognition unit required to achieve the necessary selectivity and binding affinity to control function. It has been demonstrated recently that G-quadruplex DNA structures can be targeted by organic cations in a structure-specific manner. Structural targets of quadruplexes include the planar end surfaces of the G-tetrad stacked columns and four grooves. These provide different geometries and functional groups relative to duplex DNA. We have used surface plasmon resonance and isothermal titration calorimetry to show that binding affinity and selectivity of a series of quadruplex end-stacking molecules to human telomeric DNA are sensitive to compound shape as well as substituent type and position. ITC results indicate that binding is largely enthalpy driven. Circular dichroism was also used to identify a group of structurally related compounds that selectively target quadruplex grooves.

Synthesis and antiproliferative activity of benzo[d]isothiazole hydrazones

Several benzo[d]isothiazole hydrazones have been evaluated for their potential antiretroviral activity. Since a number of these compounds were found to be inactive against viruses, but showed cytotoxicity at micromolar concentrations against the human CD4+ lymphocytes (MT-4) that were used to support HIV-1 growth, they were further tested for antiproliferative activity. The compounds resulted as being cytotoxic for MT-4 cells and new derivatives which were rationally designed and synthesized, were tested for antiproliferative activity against several leukaemia and solid tumour cell lines. In addition, these compounds were evaluated against "normal" cell lines. Compound 2h proved to be the most active compound and the fragment -CO-NH-N=CH-2-hydroxyphenyl was identified as being very important for biological activity, suggesting intramolecular hydrogen bond formation or favourable mutual disposition between two important centres in the pharmacophore. 1H-NMR spectra have been explained with the support of a conformational analysis.

Synthesis and Biological Evaluation of Novel Phenylcarbazoles as Potential Anticancer Agents

We here report the synthesis and biological evaluation of new phenylcarbazole derivatives designed as potential anticancer agents. Indole and hydroxyindole were used to generate three scaffolds that were successively exploited to introduce various substituents on the maleimide moiety. The synthesis includes a final intramolecular key Heck-type reaction, which was carried out with a triflate derivative or with a bromophenyl derivative. Each step was optimized and the complete chemical strategy is detailed. Several compounds showed a marked cytotoxicity against CEM human leukemia cells with IC(50) values in the 10-100 nM range. Precise structure-activity relationships were delineated. Cell cycle analysis, topoisomerase I inhibition, and interaction with DNA were evaluated, and inhibition of CDK activity was also investigated. Although binding of the drugs to DNA likely contributes to the cytotoxic action, the exact molecular targets of these molecules remain undiscovered. The efficient chemical routes reported here for the design of highly cytotoxic compounds provide novel opportunities to identify antitumor agents in the phenylcarbazole series.

Relaxation Dynamics of 2,7- and 3,6-Distyrylcarbazoles in Solutions and in Solid Films: Mechanism for Efficient Nonradiative Deactivation in the 3,6-Linked Carbazole

We performed time-resolved spectral investigations of two distyrylcarbazole derivatives, 2,7- and 3,6-distyrylcarbazole (2,7-DPVTCz and 3,6-DPVTCz, respectively), in dilute toluene solution and in solid films mixed with poly(methyl methacrylate) (PMMA). The lifetime of 2,7-DPVTCz in its excited state in solution is approximately 100 times as great as that of 3,6-DPVTCz, consistent with their photophysical nature. The former shows intense emission, but the latter is nearly nonfluorescent in a free environment. Moreover, the lifetime of 3,6-DPVTCz in its excited state increased also approximately 100 times when the molecule was encapsulated in a 3,6-DPVTCz/PMMA solid film, indicating that intramolecular motion of the molecule significantly affects the observed relaxation dynamics in a confined environment. Calculations on the excited states indicate that an efficient intersystem crossing is activated upon twisting of the bridged C-C single bond in a free 3,6-linked carbazole; such efficient deactivation is impractical in 2,7-linked carbazole or for 3,6-linked carbazole in a PMMA matrix. Information obtained from experiments on femtosecond fluorescence enables us to distinguish crucial relaxation processes in the excited state for a profound understanding of the details of vibrational and electronic relaxations of 3,6-DPVTCz in solution.

Survey of the year 2004 commercial optical biosensor literature

The year 2004 represents a milestone for the biosensor research community: in this year, over 1000 articles were published describing experiments performed using commercially available systems. The 1038 papers we found represent an approximately 10% increase over the past year and demonstrate that the implementation of biosensors continues to expand at a healthy pace. We evaluated the data presented in each paper and compiled a 'top 10' list. These 10 articles, which we recommend every biosensor user reads, describe well-performed kinetic, equilibrium and qualitative/screening studies, provide comparisons between binding parameters obtained from different biosensor users, as well as from biosensor- and solution-based interaction analyses, and summarize the cutting-edge applications of the technology. We also re-iterate some of the experimental pitfalls that lead to sub-optimal data and over-interpreted results. We are hopeful that the biosensor community, by applying the hints we outline, will obtain data on a par with that presented in the 10 spotlighted articles. This will ensure that the scientific community at large can be confident in the data we report from optical biosensors.