Stabilization and structural alteration of the G-quadruplex DNA made from the human telomeric repeat mediated by Tröger's base based novel benzimidazole derivatives

Design, synthesis, and evaluation of novel quindoline derivatives with fork-shaped side chains as RNA G-quadruplex stabilizers for repressing oncogene NRAS translation

NRAS mutation is the second most common oncogenic factor in cutaneous melanoma. Inhibiting NRAS translation by stabilizing the G-quadruplex (G4) structure with small molecules seems to be a potential strategy for cancer therapy due to the NRAS protein's lack of a druggable pocket. To enhance the effects of previously reported G4 stabilizers quindoline derivatives, we designed and synthesized a novel series of quindoline derivatives with fork-shaped side chains by introducing (alkylamino)alkoxy side chains. Panels of experimental results showed that introducing a fork-shaped (alkylamino)alkoxy side chain could enhance the stabilizing abilities of the ligands against NRAS RNA G-quadruplexes and their anti-melanoma activities. One of them, 10b, exhibited good antitumor activity in the NRAS-mutant melanoma xenograft mouse model, showing the therapeutic potential of this kind of compounds.

An in silico approach to evaluate the bindings of natural flavonoids and RNA-DNA hybrids

Flavonoids, low molecular weight polyphenolic compounds, are important natural products that belong to plant secondary metabolites. They have diverse biomedical applications such as antioxidative, anti-inflammatory, enzyme inhibitory, antimutagenic, anticarcinogenic, aromatase inhibitory effects, etc. Some of the flavonoids have been exported for bindings with certain DNA and tRNA structures both experimentally and computationally. RNA-DNA hybrid (RDH) falls into an important category of noncanonical nucleic acid structures that have many important biological functions. We have investigated the interaction of RDH structures with some of the dietary flavonoids with the aid of computational methods such as docking and molecular dynamics simulation. The presence of the - OH group on the ligand and the availability of a proper binding pocket in the macromolecule are the two main factors driving the binding preference. Thus, this computationally guided report explains the binding of the flavonoids with RDH structures to assist the researchers in designing noncanonical nucleic acid-targeted drug molecules.Communicated by Ramaswamy H. Sarma.

New Xanthone Derivatives as Potent G-Quadruplex Binders for Developing Anti-Cancer Therapeutics

Xanthone is an important scaffold for various medicinally relevant compounds. However, it has received scant attention in the design of agents that are cytotoxic to cancer cells via targeting the stabilization of G-quadruplex (G4) nucleic acids. Specific G4 DNA recognition against double-stranded (ds) DNA is receiving epoch-making interest for the development of G4-mediated anticancer agents. Toward this goal, we have synthesized xanthone-based derivatives with various functionalized side-arm substituents that exhibited significant selectivity for G4 DNA as compared to dsDNA. The specific interaction has been demonstrated by performing various biophysical experiments. Based on the computational study as well as the competitive ligand binding assay, it is inferred that the potent compounds exhibit an end-stacking mode of binding with G4 DNA. Additionally, compound-induced conformational changes in the flanking nucleotides form the binding pocket for effective interaction. Selective action of the compounds on cancer cells suggests their effectiveness as potent anti-cancer agents. This study promotes the importance of structure-based screening approaches to get molecular insights for new scaffolds toward desired specific recognition of non-canonical G4 DNA structures.

Design and Synthesis of Xanthone Analogues Conjugated with Aza-aromatic Substituents as Promising G-Quadruplex Stabilizing Ligands and their Selective Cancer Cell Cytotoxic Action

We have examined the stabilization of higher-order noncanonical G-quadruplex (G4) DNA structures formed by the G-rich sequences in the promoter region of oncogenes such as c-MYC, c-KIT, VEGF and BCl2 by newly synthesized, novel nitrogen-containing aromatics conjugated to xanthone moiety. Compounds with N-heterocyclic substituents such as pyridine (XNiso), benzimidazole (XBIm), quinoxaline (XQX) and fluorophore dansyl (XDan) showed greater effectiveness in stabilizing the G4 DNA as well as selective cytotoxicity for cancer cells (mainly A549) over normal cells both in terms of UV-Vis spectral titrations and cytotoxicity assay. Both fluorescence spectral titrimetric measurements and circular dichroism (CD) melting experiments further substantiated the G4 stabilization phenomenon by these small-molecular ligands. In addition, these compounds could induce the formation of parallel G4 structures in the absence of any added salt condition in Tris⋅HCl buffer at 25 °C. In a polymerase stop assay, the formation of stable G4 structures in the promoter of oncogenes and halting of DNA synthesis in the presence of the above-mentioned compounds was demonstrated by using oncogene promoter as the DNA synthesis template. Apoptosis-mediated cell death of the cancer cells was proved by Annexin V-PI dual staining assay and cell-cycle arrest occurred in the S phase of the cell cycles. The plausible mode of binding involves the stacking of the xanthone core on the G4 DNA plane with the possibility of interaction with the 5'-overhang as indicated by molecular dynamics simulation studies.

Synthesis and Antibacterial Activity of Spiro[4H-pyran-3,3'-oxindoles] Catalyzed by Tröger's Base Derivative

OBJECTIVE

Two classes of spiro[4H-pyran-3,3'-oxindole] derivatives were prepared via the one pot reaction of chain diketones (1-phenyl-1,3-butanedione or dibenzoyl methane), substituted isatins and malononitrile successfully catalyzed by a Tröger's base derivative 1b (5,12-dimethyl-3,10-diphenyl-bis-1H-pyrazol[b,f][4,5]-1,5-diazadicyclo[3.3.1]-2,6-octadiene). The antibacterial activity of products against three wild-type bacteria (B. subtilis, S. aureus, and E. coli) and two resistant strains (Methicillin-resistant S. aureus (18H8) and E. coli carrying the BlaNDM-1 gene (18H5)) was evaluated using the minimum inhibitory concentration (MIC)..

METHODS

1-Phenyl-1,3-butanedione 2 or dibenzoylmethane 2' (0.42 mmol), substituted isatin 3 (0.4 mmol), malononitrile 4 (0.8 mmol), Tröger's base derivative 1b (0.08 mmol), and 10 mL of acetonitrile were added to a 50 mL round bottom flask and refluxed. After the completion (TLC monitoring), water (10 mL) was added to the reaction mixture; pH = 7 was adjusted with saturated NaHCO3 (aq.), and the mixture was extracted with CH2Cl2 (50 mL × 3). Organic layers were combined and dried with anhydrous Na2SO4; the solvent was removed under vacuum, and the residue was purified by column chromatography (VDCM: VMeOH = 80: 1) to afford product 5. The antibacterial activity was tested by the MTT method.

RESULTS

Seventeen spiro[4H-pyran-3,3'-oxindole] derivatives were synthesized through the reaction of chain diketones (1-phenyl-1,3-butanedione or dibenzoyl methane), substituted isatins, and malononitrile in one-pot in medium to high yields. Four compounds showed antibacterial activity, and two of them showed the same activity as the positive control Ceftazidime on S. aureus (MIC = 12.5 μg/mL).

CONCLUSION

Two classes of spiro[4H-pyran-3,3'-oxindole] derivatives were prepared, and their antibacterial activity was evaluated. Tröger's base derivative 1b (5,12-dimethyl-3,10-diphenyl-bis-1H-pyrazol[b,f][4,5]- 1,5-diazadicyclo[3,3,1]-2,6-octadiene) was used as an efficient organocatalyst for the reaction of low reactive chain diketones (1-phenyl-1,3-butanedione or dibenzoyl methane), substituted isatins, and malononitrile in one-pot successfully and effectively by providing multiple active sites and alkaline environment. By the theoretical calculation, we explained the possible reaction sequence and mechanism. Due to the superiority and high efficiency of the TB framework as an organocatalyst, the reaction showed many advantages, including mild reaction conditions, low catalyst loading, and a wide substrate range. It expanded the application of Tröger's base to the multicomponent reaction in organocatalysis. Some products were screened due to their high antibacterial activity in vitro, showing their potential in new antibacterial drug development.

Chemical Information and Computational Modeling of Targeting Hybrid Nucleic Acid Structures of PIM1 Sequences by Synthetic Pyrrole-Imidazole Carboxamide Drugs

DNA can adopt various distinct structural motifs, such as quadruplex, duplex, i-motifs, etc. which have multifarious applications in biomedical therapeutics. Quadruplex-duplex hybrids (QDHs) consist of the juxtaposed quadruplex and duplex motifs and are thermally stable and biologically relevant. Selective binding toward these secondary structures plays an important role in the evaluation of the structure-specific ligands. Herein, several small molecules containing anthraquinone conjugated oligopyrrole, oligoimidazole, and pyrrole-imidazole derivatives have been screened for the binding of the quadruplex-duplex nucleic acid hybrids formed in PIM1 sequences through docking and molecular dynamics (MD) simulation studies. The binding interaction of the anthraquinone polypyrrole ligands has also been checked by performing different biophysical experiments. PIM1, being a coactivator of the MYC oncogene, can be targeted by these small molecules to control MYC expression which is overexpressed in the majority of human cancer cells. Accordingly, these cancer cell-specific and blood-compatible anthraquinone conjugated oligopyrrole ligands can be employed for anticancer therapeutic applications. Thus, the structure-activity relationship (SAR) of the screened ligands manifested prudent structural information for designing PIM1 QDHs targeting small molecules.

Deciphering the Binding Insights of Novel Disubstituted Anthraquinone Derivatives with G-Quadruplex DNA to Exhibit Selective Cancer Cell Cytotoxicity

Anthraquinone-based compounds are well-known as duplex DNA as well as G-quadruplex DNA binders. Implications of various anthraquinone derivatives for specific recognition of G-quadruplex DNA over duplex DNA is a 'challenging' research work that requires adequate experience with molecular design. To address this important issue, we designed and synthesized ten new 2,6-disubstituted anthraquinone-based derivatives with different functionalized piperazinyl side-chains. Among these, particular compounds with certain distant groups have shown selective and significant binding affinities toward the c-MYC and c-KIT G-quadruplex DNA over the duplex DNA, as noticed from various biophysical experiments. The structural difference of quadruplex and duplex DNA was utilized to probe these derivatives for the end-stacking mode of binding with G-quadruplex DNA. The ability of the ligands to halt DNA synthesis by stabilizing G-quadruplex structures is one of the crucial points to further apply them for quadruplex-mediated anti-cancer therapeutics. Interestingly, these ligands trigger apoptosis to exhibit selective cytotoxicity toward cancer cells over normal cells. This was further evidenced by ligand-induced cell cycle arrest as well as cellular apoptotic morphological changes. These blood-compatible ligands provided detailed structure-activity relationship approaches for the molecular design of anthraquinone-based G-quadruplex binders.

Base-Catalyzed, Solvent-Free Synthesis of Rigid V-Shaped Epoxydibenzo[b,f][1,5]diazocines

A novel method for the synthesis of epoxydibenzo[b,f][1,5]diazocines exhibiting a V-shaped molecular architecture is reported. The unique approach is based on unprecedented base-catalyzed, solvent-free autocondensation and cross-condensation of fluorinated o-aminophenones. The structure of the newly synthesized diazocines was confirmed independently by X-ray analysis and chiroptical methods. The rigidity of the diazocine scaffold allowed for the separation of the racemate into single enantiomers that proved to be thermally stable up to 140 °C. Furthermore, the inertness of the diazocine scaffold was demonstrated by performing a series of typical transformations, including transition metal-catalyzed reactions, proceeding without affecting the bis-hemiaminal subunit.

Theoretical Insight into the Library Screening Approach for Binding of Intermolecular G-Quadruplex RNA and Small Molecules through Docking and Molecular Dynamics Simulation Studies

The interactions of intermolecular G-quadruplex RNA and small molecules have been investigated by computational studies. Various anthraquinone, bisbenzimidazole, and carbazole-benzimidazole based ligands have shown a distinct preference to G-quadruplex structures as opposed to the corresponding duplex forms of DNA that were docked with telomeric G-quadruplex RNA. The comparative binding study of such ligands with G-quadruplex (G4) RNA showed higher binding affinities toward carbazole-benzimidazole ligands than those of the anthraquinone and bisbenzimidazole based ligands. A molecular dynamics simulation study was used to examine quadruplex-ligand interactions. Analysis of the binding free energy indicated the formation of the thermodynamically favorable RNA-ligand complex. The formation of several H-bonding interactions and the change of the solvent accessible surface area (SASA) also support the effective binding of the carbazole-benzimidazole ligands with G4 RNA structures. Thus, the library screening approach has assisted in getting a structure-activity relationship for the selected small molecules toward the G-quadruplex RNA binding, which can be applied in the targeting of G-quadruplex RNA medicated anticancer therapeutics.

Benzimidazole-1,2,3-triazole hybrid molecules: synthesis and study of their interaction with G-quadruplex DNA

A series of new benzimidazole-1,2,3-triazole hybrid derivatives have been synthesized via 'click' reaction and evaluated for their in vitro cytotoxicity as well as DNA binding affinity. MTT assay showed that all the six compounds are cytotoxic to PC3 and B16-F10 cancer cell lines. Though all the compounds showed moderate interaction with G4, c-Myc promoter DNA and dsDNA, 4f exhibited selective interaction with G-quadruplex DNA over duplex DNA as demonstrated by spectroscopic experiments like UV-vis spectroscopy, fluorescence spectroscopy, CD spectroscopy, thermal melting and fluorescence lifetime experiments. They also confirm the G-quadruplex DNA stabilizing potential of 4f. Viscosity measurements also confirm that 4f exhibits high G-quadruplex DNA selectivity over duplex DNA. Docking studies supported the spectroscopic observations. Cell cycle analysis showed that 4f induces G₂/M phase arrest and induces apoptosis. Hence, from these experimental results it is evident that compound 4f may be a G-quadruplex DNA groove binding molecule with anticancer activity.

Monofunctional Platinum(II) Anticancer Agents

Platinum-based anticancer drugs represented by cisplatin play important roles in the treatment of various solid tumors. However, their applications are largely compromised by drug resistance and side effects. Much effort has been made to circumvent the drug resistance and general toxicity of these drugs. Among multifarious designs, monofunctional platinum(II) complexes with a general formula of [Pt(3A)Cl]⁺ (A: Ammonia or amine) stand out as a class of "non-traditional" anticancer agents hopeful to overcome the defects of current platinum drugs. This review aims to summarize the development of monofunctional platinum(II) complexes in recent years. They are classified into four categories: fluorescent complexes, photoactive complexes, targeted complexes, and miscellaneous complexes. The intention behind the designs is either to visualize the cellular distribution, or to reduce the side effects, or to improve the tumor selectivity, or inhibit the cancer cells through non-DNA targets. The information provided by this review may inspire researchers to conceive more innovative complexes with potent efficacy to shake off the drawbacks of platinum anticancer drugs.

Synthesis and Characterization of Macrocyclic Chiral Tröger's Base Phenhomazine Candidates as Anticancer Agent

1,4,7,10-Tetraoxa[10](2,8)trögerophane 5 was synthesized from its corresponding precursors. Heating of 2 with p-nitrophenoxide afforded bis(p-nitrophenyl)ether 3, which was treated with hydrazine hydrate to give bis(p-aminophenyl)ether 4. Treatment of 4 with paraformaldehyde and triflouroacetic anhydride gave trögerophane 5. Reaction of 5 with trifluroacetic anhydride afforded phenhomazine derivative 6, which was treated with potassium carbonate to afford tetrahydrophenhomazine 7. Finally, reaction of 7 with phenacylchloride, bromoacetic acid, or ethyl bromoacetate in the presence of triethyl amine under reflux, afforded the corresponding macrocyclic compounds 8, 9 and 10, respectively. The synthesized trögerophane,precursors and its newly synthesized phenhomazines derivatives were screened for anticancer activity. Results revealed that 1,4,7,10-tetraoxa[10](2,8)trögerophane had a promising selectivity towards colon cancer cell line with an IC₅₀ of 92.7 µg/ml.

Recent Update on Targeting c-MYC G-Quadruplexes by Small Molecules for Anticancer Therapeutics

Guanine-rich DNA sequences have the propensity to adopt four-stranded tetrahelical G-quadruplex (G4) structures that are overrepresented in gene promoters. The structural polymorphism and physicochemical properties of these non-Watson-Crick G4 structures make them important targets for drug development. The guanine-rich nuclease hypersensitivity element III₁ present in the upstream of P1 promoter of c-MYC oncogene has the ability to form an intramolecular parallel G4 structure. The G4 structure that forms transiently in the c-MYC promoter functions as a transcriptional repressor element. The c-MYC oncogene is overexpressed in a wide variety of cancers and plays a key role in cancer progression. Till now, a large number of compounds that are capable of interacting and stabilizing thec-MYC G4 have been reported. In this review, we summarize various c-MYC G4 specific molecules and discuss their effects on c-MYC gene expression in vitro and in vivo.

Synthesis and antitumor activities of transition metal complexes of a bis-Schiff base of 2-hydroxy-1-naphthalenecarboxaldehyde

The complexes of Schiff base have attracted much attention for their potential biological activities. In this research, five transition metal complexes TM₃L₂(OAc)₂ (TM = Cu, 1; Ni, 2; Co, 3; Mn, 4; Fe, 5) were prepared using a bis-Schiff base of N,N'-bis[(2-hydroxy-1-naphthalenyl)methylene]-propane-1,3-diamine (H₂L), which present similar linear trinuclear structures with their three metal ions consolidated by two bis-Schiff base ligands and two acetate ligands. Their antitumor activities in vitro were screened through seven human cancer cell lines by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. It revealed that complexes 1, 2 and 5 show much higher antitumor activities than the bis-Schiff base ligand and complexes 3 and 4, and even than cisplatin. Among them, complex 1 has the highest inhibitory effects on tumor cells with its IC₅₀ value (half-inhibitory concentration) being less than 0.5 μM for human bladder cancer cell line T-24, at which concentration complex 1 shows nearly no toxicity to the normal cell HL-7702 as revealed by flow cytometry. All of these demonstrate a potential anti-cancer candidate for complex 1, which induces tumor cell apoptosis by blocking T-24 tumor cells at the G2/M phase of the cell cycle, reducing mitochondrial membrane potential, increasing the concentration of reactive oxygen species and Ca²⁺ in the cell, and changing the expression of proteins.

Specific stabilization of promoter G-Quadruplex DNA by 2,6-disubstituted amidoanthracene-9,10-dione based dimeric distamycin analogues and their selective cancer cell cytotoxicity

We have designed and synthesized anthraquinone containing compounds which have oligopyrrole side chains of varying lengths. These compounds stabilized the G-quadruplex DNA formed in the promoter regions of c-MYC oncogenes selectively over the duplex DNA. These observations were recorded using UV-vis spectroscopic titrations, fluorescence measurements and circular dichroism (CD) spectral titrations. The potency of the compounds to stabilize the G4 DNA has been shown from the thermal denaturation experiments. The compound interacts with c-MYC G-quadruplex DNA through stacking mode as obtained from ethidium bromide displacement assay, cyclic voltammetric titration, and docking experiments. Molecular modeling studies suggested that the stacking of the anthraquinone moiety over the G-tetrad of the G4 structures are responsible for the stability of such quadruplex secondary structure. Furthermore, polymerase stop assay also supported the formation of stable G4 structures in the presence of the above-mentioned compounds. The compounds have shown selective cancer cell (HeLa and HEK293T) cytotoxicity over normal cells (NIH3T3 and HDFa) under in vitro conditions as determined from MTT based cell viability assay. Apoptosis was found to be the mechanistic pathway underlying the cancer cell cytotoxicity as obtained from Annexin V-FITC and PI dual staining assay which was further substantiated by nuclear morphological changes as observed by AO/EB dual staining assay. Cellular morphological changes, as well as nuclear condensation and fragmentation upon treatment with these compounds, were observed under bright field and confocal microscopy.

Investigation on Quantitative Structure-Activity Relationships of 1,3,4-Oxadiazole Derivatives as Potential Telomerase Inhibitors

BACKGROUND

Telomerase, a reverse transcriptase, maintains telomere and chromosomes integrity of dividing cells, while it is inactivated in most somatic cells. In tumor cells, telomerase is highly activated, and works in order to maintain the length of telomeres causing immortality, hence it could be considered as a potential marker to tumorigenesis.A series of 1,3,4-oxadiazole derivatives showed significant broad-spectrum anticancer activity against different cell lines, and demonstrated telomerase inhibition.

METHODS

This series of 24 N-benzylidene-2-((5-(pyridine-4-yl)-1,3,4-oxadiazol-2yl)thio)acetohydrazide derivatives as telomerase inhibitors has been considered to carry out QSAR studies. The endpoint to build QSAR models is determined by the IC50 values for telomerase inhibition, i.e., the concentration (μM) of inhibitor that produces 50% inhibition. These values were converted to pIC50 (- log IC50) values. We used the most common and transparent method, where models are described by clearly expressed mathematical equations: Multiple Linear Regression (MLR) by Ordinary Least Squares (OLS).

RESULTS

Validated models with high correlation coefficients were developed. The Multiple Linear Regression (MLR) models, by Ordinary Least Squares (OLS), showed good robustness and predictive capability, according to the Multi-Criteria Decision Making (MCDM = 0.8352), a technique that simultaneously enhances the performances of a certain number of criteria. The descriptors selected for the models, such as electrotopological state (E-state) descriptors, and extended topochemical atom (ETA) descriptors, showed the relevant chemical information contributing to the activity of these compounds.

CONCLUSION

The results obtained in this study make sure about the identification of potential hits as prospective telomerase inhibitors.

Dual mode of binding of anti cancer drug epirubicin to G-quadruplex [d-(TTAGGGT)]4 containing human telomeric DNA sequence induces thermal stabilization

Epirubicin exerts its anti cancer action by blocking DNA/RNA synthesis and inhibition of topoisomerase-II enzyme. Recent reports on its influence on telomere maintenance, suggest interaction with G-quadruplex DNA leading to multiple strategies of action. The binding of epirubicin with parallel stranded inter molecular G-quadruplex DNA [d-(TTAGGGT)]₄ comprising human telomeric DNA sequence TTAGGG was investigated by absorption, fluorescence, circular dichroism and nuclear magnetic resonance spectroscopy. The epirubicin binds as monomer to G-quadruplex DNA with affinity, K_b1 = 3.8 × 10⁶ M^-1 and K_b2 = 2.7 × 10⁶ M^-1, at two independent sites externally. The specific interactions induce thermal stabilization of DNA by 13.2-26.3 °C, which is likely to come in the way of telomere association with telomerase enzyme and contribute to epirubicin-induced apoptosis in cancer cell lines. The findings pave the way for drug designing in view of the possibility of altering substituent groups on anthracyclines to enhance efficacy using alternate mechanism of its interaction with G4 DNA, causing interference in telomere maintenance pathway by inducing telomere dysfunction.

Design, Synthesis and Molecular Docking Analysis of Flavonoid Derivatives as Potential Telomerase Inhibitors

Based on the structural scaffolds of natural products, two series of flavonoid derivatives, for a total of twelve compounds, were designed and synthesized as potential human telomerase inhibitors. Using a modified TRAP-PCR assay, compound 5c exhibited the most potent inhibitory activity against human telomerase with an IC₅₀ value of less than 50 μM. In vitro, the results demonstrated that compound 5c had potent anticancer activity against five classes of tumor cell lines. The molecular docking and molecular dynamics analyses binding to the human telomerase holoenzyme were performed to elucidate the binding mode of active compound 5c. This finding helps the rational design of more potent telomerase inhibitors based on the structural scaffolds of natural products.

Glycoconjugates Based on Supramolecular Tröger's Base Scaffold: Synthesis, Photophysics, Docking, and BSA Association Study

This study presents new Tröger's bases bearing glycosyl moieties obtained from a copper-catalyzed azide-alkyne cycloaddition reaction. The Tröger's bases present absorption maxima close to 275 nm related to fully spin and symmetry-allowed electronic transitions. The main fluorescence emission located at 350 nm was observed with no influence on the glycosyl moieties. Furthermore, protein detection studies have been performed using bovine serum albumin (BSA) as a model protein, and results have shown a strong interaction between some of the compounds through a static fluorescence suppression mechanism related to the formation of a glycoconjugate-BSA complex favored by the glycosyl subunit. Moreover, docking was also studied for better understanding the suppression mechanism and indicated that the glycosyl and triazole moieties increase the affinity with BSA.

Photoinduced binding of malachite green copolymer to parallel G-quadruplex DNA

Designing ligands that selectively target G-quadruplex DNAs has gained attention due to their possible roles in regulation of gene expression and as anti-cancer agents. In this article, we report irradiation-induced ligand binding to G-quadruplex DNAs which offers a novel approach to targeting specific G-quadruplexes. Photoinduced binding to G-quadruplex DNAs was observed for copolymers of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG). This molecule has an aromatic ring with cationic charge, which after irradiation becomes a binding site for G-quadruplex DNA. PVAMGs acted as neutral polymers with no binding affinity under dark conditions. The photoinduced binding was revealed by fluorescence spectroscopy, NMR spectroscopy, UV melting curve, and DNA polymerase stop assay. PVAMGs showed preference to parallel G-quadruplex structures over mixed parallel/antiparallel structures. PVAMGs were found to be noncytotoxic under both dark and irradiated conditions up to a concentration of 20 μM.

In vitro and in vivo activity of novel platinum(ii) complexes with naphthalene imide derivatives inhibiting human non-small cell lung cancer cells

3 induced NCI-H460 cell apoptosis via inhibition of the telomerase and dysfunction of mitochondria. Remarkably, 3 obviously inhibited NCI-H460 xenograft tumor growth in vivo.

DNA G-quadruplexes binding and antitumor activity of palladium aryl oxime ligand complexes encapsulated in either albumin or algal cellulose nanoparticles

The interactions between two Pd complexes, designated as [Pd₃(C,N-(C₆H₄C(Cl) = NO)-4)₆] (complex 1) and [Pd₃(C₁₂H₈C = NO)₆] (complex 2), with the human telomeric G-quadruplex DNA, 5'-G₃(T₂AG₃)₃-3' (HTG21), were monitored using spectroscopic, biological, and molecular modeling studies. According to the UV-vis results, these complexes can strongly induce and stabilize G-quadruplex DNA structure with K_b1 = 4.5(±0.3) × 10⁶ M^-1 and K_b2 = 1.0(±0.2) × 10⁷ M^-1via groove mode in comparison with duplex DNA. The release mechanism of the Pd complexes from BSA nanoparticles followed a biphasic pattern unlike that of algal cellulose nanoparticles in vitro. In addition, the cytotoxicity of these complexes on MCF-7 cancer cells and PBMC normal cells was evaluated and compared with cisplatin under similar experimental conditions. Furthermore, to determine and verify the interaction mode of these compounds with G-quadruplex, the molecular docking technique was also performed. Our data clearly demonstrated that complex 2 had higher activity and cytotoxicity than that of complex 1 and could be further investigated in the future as a drug discovery platform.

Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex-Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands have been developed, their low potency and selectivity to G-quadruplexes over duplex remains unsolved. Recently, a crystal structure of a telomeric 3' quadruplex-duplex hybrid was reported and the quadruplex-duplex interface was suggested to a good target to address the issues. However, there are no high-resolution complex structures reported for G-quadruplex ligands except for a docked BSU6037. In this study, molecular dynamic (MD) binding simulations with a free ligand were used to study binding poses and dynamics of four representative ligands: telomestatin, TMPyP4, BSU6037, and BRACO19. The MD data showed that BSU6037 was able to fully intercalate into the interface whereas TMPyP4 and BRACO19 could only maintain partial intercalation into the interface and telomestatin only binds at the quadruplex and duplex ends. Both linear ligands, BSU6037 and BRACO19, were able to interact with the interface, yet they were not selective over duplex DNA. The DNA geometry, binding modes, and binding pathways were systematically characterized, and the binding energy was calculated and compared for each system. The interaction of the ligands to the interface was by the means of an induced-fit binding mechanism rather than a lock-key mechanism, consisting of the DNA unfolding at the interface to allow entrance of the drug and then the refolding and repacking of the DNA and the ligand to further stabilize the G-quadruplex. On the basis of the findings in this study, modifications were suggested to optimize the interface binding for TMPyp4 and telomestatin.

Synthesis of Chiral Carbo-Nanotweezers for Enantiospecific Recognition and DNA Duplex Winding in Cancer Cells

Targeting the DNA of tumor cells with small molecules may offer effective clinical strategies for transcriptional inhibition. We unveil synthesis and characterization of ∼20 nm chiral carbon nanoparticles for enantiospecific recognition of DNA. Our approach inculcates chirality in carbon nanoparticles by controlled tethering of minor groove binders, i.e., Tröger's base (TB). The chiral particles positively enriched the cellular nucleus in MCF-7 breast cancer cells, irrespective of the TB asymmetry tethered on the particle surface, but negatively induced chiral carbon nanoparticles exhibited improved efficiency at inhibiting cell growth. Further studies indicated that these chiral particles act as nanotweezers to perturb the genomic DNA and induce apoptosis cascade in cancer cells.

Ethenesulfonyl fluoride derivatives as telomerase inhibitors: structure-based design, SAR, and anticancer evaluation in vitro

Based on our previous docking model, in order to carry out more rational drug design, totally 82 vinyl sulfonyl fluorides, including some 2-(hetero)arylethenesulfonyl fluorides and 1,3-dienylsulfonyl fluorides derivatives as potential human telomerase inhibitors were designed and synthesised. The in vitro anticancer activity assay showed that compound 57 (1E,3E)-4-(4-((E)-2-(fluorosulfonyl)vinyl)phenyl)buta-1,3-diene-1-sulfonyl fluoride exhibited high activity against A375 and MDA-MB-231 cell lines with IC₅₀ 1.58 and 3.22 µM, but it manifested obvious un-toxic effect against GES-1 and L-02 with IC₅₀ with IC₅₀ values less than 2.00 mM. By the modified TRAP assay, some compounds including 57 exhibited potent inhibitory activities against telomerase with IC₅₀ values of 0.71–0.97 µM.

Design of Modular G-quadruplex Ligands

Guanine-rich nucleic acid sequences able to form four-stranded structures (G-quadruplexes, G4) play key cellular regulatory roles and are considered as promising drug targets for anticancer therapy. On the basis of the organization of their structural elements, G4 ligands can be divided into three major families: one, fused heteroaromatic polycyclic systems; two, macrocycles; three, modular aromatic compounds. The design of modular G4 ligands emerged as the answer to achieve not only more drug-like compounds but also more selective ligands by targeting the diversity of the G4 loops and grooves. The rationale behind the design of a very comprehensive set of ligands, with particular focus on the structural features required for binding to G4, is discussed and combined with the corresponding biochemical/biological data to highlight key structure-G4 interaction relationships. Analysis of the data suggests that the shape of the ligand is the major factor behind the G4 stabilizing effect of the ligands. The information here critically reviewed will certainly contribute to the development of new and better G4 ligands with application either as therapeutics or probes.

Tryptanthrin derivative copper(ii) complexes with high antitumor activity by inhibiting telomerase activity, and inducing mitochondria-mediated apoptosis and S-phase arrest in BEL-7402

Try-Cu exhibited its antitumor activity mainly via inhibiting telomerase by interaction with the c-myc promoter and disrupting mitochondrial functions.

Discovery of (4-bromophenyl)(3-hydroxy-4-methoxyphenyl)methanone through upregulating hTERT induces cell apoptosis and ERS

Dominant-negative mutants of telomerase hTERT were demonstrated to have selective effects in tumor cells. However, no any effective and highly selective hTERT inhibitor has been developed so far. We focused on developing new hTERT modulators and synthesized a small molecular compound, named (4-bromophenyl)(3-hydroxy-4-methoxyphenyl)methanone. Our in vitro studies found that title compound showed high inhibitory activity against telomerase, had high antiproliferative capacity on SMMC-7721 cells with IC₅₀ value 88 nm, and had no obvious toxic effect on human normal hepatocyte cells with IC₅₀ value 10 μM. Our in vivo studies showed that this compound significantly inhibited tumor growth in xenograft tumor models. The further molecular mechanisms of title compound inhibition SMMC-7721 cell proliferation by modulating hTERT were explored; the results showed that endoplasmic reticulum stress (ERS) through ER over response (EOR) activates the expression of hTERT, and then induces ERS, which is believed to be intricately associated with oxidative stress and mitochondrial dysfunction, resulting in apoptotic cell death, thereby modulating the expression of downstream signaling molecules including CHOP (CAAT/enhancer-binding protein homologous protein)) and mitochondrion pathway of apoptosis, leading to inhibition of cell proliferation.

Enhanced G-Quadruplex DNA Stabilization and Telomerase Inhibition by Novel Fluorescein Derived Salen and Salphen Based Ni(II) and Pd(II) Complexes

Metal based salen complexes have been considered as an important scaffold toward targeting of DNA structures. In the present work, we have synthesized nickel(II) and palladium(II) salen and salphen complexes by using readily available fluorescein as the backbone to provide an extended aromatic surface. The metal complexes exhibit affinity toward the human telomeric G-quadruplex DNA with promising inhibition of telomerase activity. This has been ascertained by their efficiency in the long term cell proliferation assay which showed significant cancer cell toxicity in the presence of the metal complexes. Confocal microscopy showed cellular internalization followed by localization in the nucleus and mitochondria. Considerable population at the sub-G1 phase of the cell cycle showed cell death via apoptotic pathway.

Experimental and theoretical investigations into the stability of cyclic aminals

Background: Cyclic aminals are core features of natural products, drug molecules and important synthetic intermediates. Despite their relevance, systematic investigations into their stability towards hydrolysis depending on the pH value are lacking. Results: A set of cyclic aminals was synthesized and their stability quantified by kinetic measurements. Steric and electronic effects were investigated by choosing appropriate groups. Both molecular mechanics (MM) and density functional theory (DFT) based studies were applied to support and explain the results obtained. Rapid decomposition is observed in acidic aqueous media for all cyclic aminals which occurs as a reversible reaction. Electronic effects do not seem relevant with regard to stability, but the magnitude of the conformational energy of the ring system and pKa values of the N-3 nitrogen atom. Conclusion: Cyclic aminals are stable compounds when not exposed to acidic media and their stability is mainly dependent on the conformational energy of the ring system. Therefore, for the preparation and work-up of these valuable synthetic intermediates and natural products, appropriate conditions have to be chosen and for application as drug molecules their sensitivity towards hydrolysis has to be taken into account.

Synthesis of 6,12-Epiminodibenzo[b,f][1,5]diazocines via an Ytterbium Triflate-Catalyzed, AB2 Three-Component Reaction

An efficient and selective procedure for the synthesis of epiminodibenzo[b,f][1,5]diazocines involving a AB₂ three-component reaction is developed. Two equivalents of suitably substituted 2-aminoarylaldehydes reacted with arylamines in the presence of Yb(OTf)₃ to afford the desired products in high yields. The reaction is highly atom-economic and waste-free, in addition to allowing the generation of two heterocyclic rings and four C-N bonds in a single operation. Significantly, this approach is complementary to the existing literature procedures, affording arylamine-derived products that could not be accessed previously. A plausible mechanism is proposed involving an imine formation-intermolecular annulation-intramolecular iminium ion cyclization sequence.

Crystal structure of 1,1′-diformyl-4,4′-(6H,12H-5,11-methano-dibenzo[b,f][11,5]diazocine-2,8-diyl)dibenzene, C29H22N2O2

C29H22N2O2, triclinic, P1̅ (no. 2), a = 22.4995(6) Å, b = 9.9370(3) Å, c = 21.6466(6) Å, β = 115.941(1)°, V = 4352.1(2) Å3, Z = 4, R gt (F) = 0.0487, wR ref (F 2 ) = 0.1473, T = 296 K.

Relative stability of G-quadruplex structures: Interactions between the human Bcl2 promoter region and derivatives of carbazole and diphenylamine

The bcl2 promoter region forms a G-quadruplex structure, which is a crucial target for anticancer drug development. In this study, we provide theoretical predictions of the stability of different G-quadruplex folds of the 23-mer bcl2 promoter region and G-quadruplex ligand. We take into account the whole G-quadruplex structure, including bound-cations and solvent effects, in order to compute the ligand binding free energy using molecular dynamics simulation. Two series of the carbazole and diphenylamine derivatives are used to screen for the most potent drug in terms of stabilization. The energy analysis identifies the predominant energy components affecting the stability of the various different G-quadruplex folds. The energy associated with the stability of the G-quadruplex-K(+) structures obtained displays good correlation with experimental Tm measurements. We found that loop orientation has an intrinsic influence on G-quadruplex stability and that the basket structure is the most stable. Furthermore, parallel loops are the most effective drug binding site. Our studies also demonstrate that rigidity and planarity are the key structural elements of a drug that stabilizes the G-quadruplex structure. BMVC-4 is the most potential G-quadruplex ligand. This approach demonstrates significant promise and should benefit drug design.

New dimeric carbazole-benzimidazole mixed ligands for the stabilization of human telomeric G-quadruplex DNA and as telomerase inhibitors. A remarkable influence of the spacer

The development of G-quadruplex (G4) DNA binding small molecules has become an important strategy for selectively targeting cancer cells. Herein, we report the design and evolution of a new kind of carbazole-based benzimidazole dimers for their efficient telomerase inhibition activity. Spectroscopic titrations reveal the ligands high affinity toward the G4 DNA with significantly higher selectivity over duplex-DNA. The electrophoretic mobility shift assay shows that the ligands efficiently promote the formation of G4 DNA even at a lower concentration of the stabilizing K(+) ions. The TRAP-LIG assay demonstrates the ligand's potential telomerase inhibition activity and also establishes that the activity proceeds via G4 DNA stabilization. An efficient nuclear internalization of the ligands in several common cancer cells (HeLa, HT1080, and A549) also enabled differentiation between normal HFF cells in co-cultures of cancer and normal ones. The ligands induce significant apoptotic response and antiproliferative activity toward cancer cells selectively when compared to the normal cells.

Dihydropyrazole derivatives as telomerase inhibitors: Structure-based design, synthesis, SAR and anticancer evaluation in vitro and in vivo

It is of our interest to generate and identify novel compounds with regulation telomerase for cancer therapy. In order to carry out more rational design, based on structure-based drug design, several series of N-substituted-dihydropyrazole derivatives, totally 78 compounds as potential human telomerase inhibitors were designed and synthesized. The results demonstrated that some compounds had potent anticancer activity against four tumor cell lines, and showed good selectivity on tumor cells over somatic cells. By the modified TRAP assay, compound 13i exhibited the most potent inhibitory activity against telomerase with an IC50 value of 0.98 μM. In vivo evaluation results indicated that compound 13i could inhibit growth of S180 and HepG2 tumor-bearing mice, and it also significantly enhanced the survival rate of EAC tumor-bearing mice. The further results in vivo confirmed that it could significantly improve pathological changes of N,N-diethylnitrosamine (DEN)-induced rat hepatic tumor. These data support further studies to assess rational design of more efficient telomerase inhibitors in the future.