Recognition of a Single Guanine Bulge by 2-Acylamino-1,8-naphthyridine

Two-Photon-Responsive "TICT + AIE" Active Naphthyridine-BF2 Photoremovable Protecting Group: Application for Specific Staining and Killing of Cancer Cells

The combined effects of twisted intramolecular charge transfer (TICT) and aggregation-induced emission (AIE) phenomena have demonstrated a significant influence on excited-state chemistry. These combined TICT and AIE features have been extensively utilized to enhance photodynamic and photothermal therapy. Herein, we demonstrated the synergistic capabilities of TICT and AIE phenomena in the design of the photoremovable protecting group (PRPG), namely, NMe2-Napy-BF2. This innovative PRPG incorporates TICT and AIE characteristics, resulting in four remarkable properties: (i) red-shifted absorption wavelength, (ii) strong near-infrared (NIR) emission, (iii) viscosity-sensitive emission property, and (iv) accelerated photorelease rate. Inspired by these intriguing attributes, we developed a nanodrug delivery system (nano-DDS) using our PRPG for cancer treatment. In vitro studies showed that our nano-DDS manifested effective cellular internalization, specific staining of cancer cells, high-resolution confocal imaging of cancerous cells in the NIR region, and controlled release of the anticancer drug chlorambucil upon exposure to light, leading to cancer cell eradication. Most notably, our nano-DDS exhibited a substantially increased two-photon (TP) absorption cross section (435 GM), exhibiting its potential for in vivo applications. This development holds promise for significant advancements in cancer treatment strategies.

The role of post-transcriptional modification on a new tRNAIle(GAU) identified from Ganoderma lucidum in its fragments' cytotoxicity on cancer cells

Ganoderma lucidum (Ganoderma) is a famous Chinese herbal medicine which has been used clinically for thousands of years in China. Despite numerous studies on triterpenes and polysaccharides, the bioactivity of RNAs abundant in Ganoderma remains unknown. Here, based on LC-MS techniques, dihydrouracil, 5-methyluridine (m⁵U) and pseudouridine were identified at position 19, 52 and 53 of a new tRNA^Ile(GAU) which was isolated as the most abundant tRNA species in Ganoderma, and is the first purified tRNA from fungus. Cytotoxic screening of tRNA-half (t-half) and tRNA fragment (tRF) derived from this tRNA, as well as their mimics (t-half or tRF as antisense strand), demonstrated that the double-stranded form, i.e., tRF and t-halve mimics, exhibited stronger cytotoxicity than their single-stranded form, and the cytotoxicity of t-half mimic is significantly stronger than that of tRF mimic. Notably, the cytotoxicity of 3'-t-half mimic is not only much more potent than that of taxol, but also is much more potent than that of ganoderic acids, the major bioactive components in Ganoderma. Furthermore, 3'-t-half mimic_M2 (m⁵U modified) exhibited significantly stronger cytotoxicity than unmodified 3'-t-half mimic, which is consistent with the computational simulation showing that m⁵U modification enhances the stability of the tertiary structure of 3'-t-half mimic. Overall, the present study not only indicates t-halves are bioactive components in Ganoderma which should not be neglected, but also reveals an important role of post-transcriptional modification on tRNA in its fragments' cytotoxicity against cancer cells, which benefits the design and development of RNAi drugs from natural resource.

Photo-Thermo-Mechanochemical Approach to Synthesize Quinolines via Addition/Cyclization of Sulfoxonium Ylides with 2-Vinylanilines Catalyzed by Iron(II) Phthalocyanine

A novel photo-thermo-mechanochemical approach to assembling quinolines catalyzed by iron(II) phthalocyanine has been realized for the first time. This transformation features a cost-efficient catalytic system and operational simplicity, is free of solvent, and shows good substrate tolerance, providing a green alternative to existing thermal approaches. Mechanistic experiments demonstrate that the in-situ-formed secondary amine may be the key intermediate for the further cyclization/aromatization process.

Synthesis of 3-substituted quinolines by ruthenium-catalyzed aza-Michael addition and intramolecular annulation of enaminones with anthranils

A method for the synthesis of 3-substituted quinolines by ruthenium-catalyzed aza-Michael addition and intramolecular annulation of enaminones with anthranils has been developed.

Possibilities and challenges of small molecule organic compounds for the treatment of repeat diseases

The instability of repeat sequences in the human genome results in the onset of many neurological diseases if the repeats expand above a certain threshold. The transcripts containing long repeats sequester RNA binding proteins. The mechanism of repeat instability involves metastable slip-out hairpin DNA structures. Synthetic organic chemists have focused on the development of small organic molecules targeting repeat DNA and RNA sequences to treat neurological diseases with repeat-binding molecules. Our laboratory has studied a series of small molecules binding to mismatched base pairs and found molecules capable of binding CAG repeat DNA, which causes Huntington's disease upon expansion, CUG repeat RNA, a typical toxic RNA causing myotonic dystrophy type 1, and UGGAA repeat RNA causing spinocerebellar ataxia type 31. These molecules exhibited significant beneficial effects on disease models in vivo, suggesting the possibilities for small molecules as drugs for treating these neurological diseases.

Ab initio multi-level layered elongation method and its application to local interaction analysis between DNA bulge and ligand molecules

A multi-level layered elongation method was developed for efficiently analyzing the electronic states of local structures in large bio/nano-systems at the full ab initio level of theory. The original elongation method developed during the last three decades in our group has focused on the system in one direction from one terminal to the other terminal to sequentially construct the electronic states of a polymer, called a theoretical synthesis of polymers. In this study, an important region termed the central (C) part is targeted in a large polymer and the remainder are terminal (T) parts. The electronic structures along with polymer elongation are calculated repeatedly from both end T parts to the C central part at the same time. The important C part is treated with large basis sets (high level) and the other regions are treated with small basis sets (low level) in the ab initio theoretical framework. The electronic structures besides the C part can be reused for other systems with different structures at the C part, which renders the method computationally efficient. This multi-level layered elongation method was applied to the investigation on DNA single bulge recognition of small molecules (ligands). The reliability and validity of our approach were examined in comparison with the results obtained by direct calculations using a conventional quantum chemical method for the entire system. Furthermore, stabilization energies by the formation of the complex of bulge DNA and a ligand were estimated with basis set superposition error corrections incorporated into the elongation method.

Copper-Catalyzed Annulation or Homocoupling of Sulfoxonium Ylides: Synthesis of 2,3-Diaroylquinolines or α,α,β-Tricarbonyl Sulfoxonium Ylides

An unprecedented copper-catalyzed reaction of sulfoxonium ylides and anthranils is reported that enables an easy access to 2,3-diaroylquinolines through a [4+1+1] annulation. Copper-catalyzed homocoupling of sulfoxonium ylides provided α,α,β-tricarbonyl sulfoxonium ylides, which provides a strategy to extend the carbon chain through C-C bond formation. The utility of the products as well as the mechanistic details of the process are presented.

A Novel Ruthenium(II) Polypyridyl Complex Bearing 1,8-Naphthyridine as a High Selectivity and Sensitivity Fluorescent Chemosensor for Cu2+ and Fe3+ Ions

A novel ruthenium(II) polypyridyl complex bearing 1,8-naphthyridine was successfully designed and synthesized. This complex was fully characterized by EI-HRMS, NMR, and elemental analyses. The recognition properties of the complex for various metal ions were investigated. The results suggested that the complex displayed high selectivity and sensitivity for Cu²⁺ and Fe³⁺ ions with good anti-interference in the CH₃CN/H₂O (1:1, v/v) solution. The fluorescent chemosensor showed obvious fluorescence quenching when the Cu²⁺ and Fe³⁺ ions were added. The detection limits of Cu²⁺ and Fe³⁺ were 39.9 nmol/L and 6.68 nmol/L, respectively. This study suggested that this Ru(II) polypyridyl complex can be used as a high selectivity and sensitivity fluorescent chemosensor for Cu²⁺ and Fe³⁺ ions.

Enhancing Catalytic Activity of Uranyl-Dependent DNAzyme by Flexible Linker Insertion for More Sensitive Detection of Uranyl Ion

The uranyl-dependent DNAzyme 39E cleaves its nucleic acid substrate in the presence of uranyl ion (UO₂²⁺). It has been widely utilized in many sensor designs for selective and sensitive detection of UO₂²⁺ in the environment and inside live cells. In this work, by inserting a flexible linker (C3 Spacer) into one critical site (A₂₀) of the 39E catalytic core, we successfully enhanced the original catalytic activity of 39E up to 8.1-fold at low UO₂²⁺ concentrations. Applying such a modified DNAzyme (39E-A₂₀-C3) in a label-free fluorescent sensor for UO₂²⁺ detection achieved more than 1 order of magnitude sensitivity enhancement over using native 39E, with the UO₂²⁺ detection limit improved from 2.6 nM (0.63 ppb) to 0.19 nM (0.047 ppb), while the high selectivity to UO₂²⁺ over other metal ions was fully preserved. The method was also successfully applied for the detection of UO₂²⁺-spiked environmental water samples to demonstrate its practical usefulness.

A Tetraphenylethene-Naphthyridine-Based AIEgen TPEN with Dual Mechanochromic and Chemosensing Properties

Synthesis of new tetraphenylethene (TPE) conjugates via an innocuous route led to the revelation of a unique TPE-based aggregation-induced emissive fluorogen 3 (TPEN), which showed an interesting mechanochromic property when the emission was changed from blue to green upon grinding and green to blue upon fuming. The mechanochromic property of TPEN has been explored to prepare ink-free rewritable paper for security documentation. A detailed photophysical investigation of the TPE-naphthyridine scaffold led to the discovery of its high sensitivity to silver ions (Ag⁺) over other metal ions with a detection limit of 0.25 μM in an aqueous system. The stoichiometry of the complex of TPEN and silver ion was established to be 2:1 (TPEN:Ag⁺) on the basis of photophysical studies, mass analysis, and high-resolution mass spectrometry analysis.

Determination of mutated genes in the presence of wild-type DNA by using molecular beacons as probe

Low-abundance mutations in the presence of wild-type DNA can be determined using molecular beacon (MB) as probe. A MB is generally used as DNA probe because it can distinguish single-base mismatched target DNA from fully matched target DNA. However, the probe can not determine low-abundance mutations in the presence of wild-type DNA. In this study, this limitation is addressed by enhancing the stability of unpaired base-containing dsDNA with a hydrogen-bonding ligand, which was added after hybridization of the MB to the target DNA. The ligand formed hydrogen bonds with unpaired bases and stabilized the unpaired base-containing dsDNA if target DNA is mutated one. As a result, more MBs were opened by the mutant genes in the presence of the ligand and a further increase in the fluorescence intensity was obtained. By contrast, fluorescence intensity did not change if target DNA is wild-type one. Consequent increase in the fluorescence intensity of the MB was regarded as a signal derived from mutant genes. The proposed method was applied in synthetic template systems to determine point mutation in DNA obtained from PCR analysis. The method also allows rapid and simple discrimination of a signal if it is originated in the presence of mutant gene or alternatively by a lower concentration of wild gene.

Lewis Acid Catalyzed Dehydrogenative Coupling of Tertiary Propargylic Alcohols with Quinoline N-Oxides

An unprecedented Lewis acid catalyzed, high-efficiency synthesis of valuable 2-(quinolin-2-yl)prop-2-en-1-ones via dehydrogenative coupling of propargylic alkynols with quinoline N-oxides is described. This protocol, which tolerates a broad range of functional groups, provides a straightforward pathway to the products 2-(quinolin-2-yl)prop-2-en-1-one scaffolds in satisfactory yields. The conversion could be scaled up to gram scale efficiently, which underlines a latent application of this methodology.

BzDANP, a Small-Molecule Modulator of Pre-miR-29a Maturation by Dicer

We here report the synthesis of novel molecule BzDANP having a three-ring benzo[c][1,8]naphthyridine system, the evaluation of its binding properties to a single nucleotide bulge in RNA duplexes, and BzDANP-induced suppression of pre-miR-29a processing by Dicer. BzDANP showed much increased affinity to the bulged RNAs as compared with the parent molecule DANP, which possesses the same hydrogen-bonding surface as BzDANP but in a two-ring [1,8]naphthyridine system. Melting temperature analysis of bulged RNAs showed that BzDANP most effectively stabilized the C-bulged RNA. Dicer-mediated processing of pre-miR-29a was suppressed by BzDANP in a concentration dependent manner. The presence of the C-bulge at the Dicer cleavage site was effective for the suppression of pre-miR-29a processing by BzDANP. These results demonstrated that the small molecule binding to the bulged site in the vicinity of the Dicer cleavage site could be a potential modulator for the maturation of pre-miRNA.

Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base

A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site.

Recognition of DNA/RNA bulges by antimicrobial and antitumor metallohelices

Bulged structures have been identified in nucleic acids and have been shown to be linked to biomolecular processes involved in numerous diseases. Thus, chemical agents with affinity for bulged nucleic acids are of general biological significance. Herein, the mechanism of specific recognition and stabilization of bulged DNA and RNA by helical bimetallic species was established through detailed molecular biophysics and biochemistry assays. These agents, known as 'flexicates', are potential mimetics of α-helical peptides in cancer treatment, exhibiting antimicrobial and antitumor effects. The flexicates have positive impacts on the thermal stability of DNA duplexes containing bulges, which means that the flexicates interact with the duplexes containing bulges, and that these interactions stabilize the secondary structures of these duplexes. Notably, the stabilising effect of the flexicates increases with the size of the bulge, the maximal stabilization is observed for the duplexes containing a bulge composed of at least three bases. The flexicates bind most preferentially to the bulges composed of pyrimidines flanked on both sides also by pyrimidines. It is suggested that it is so because these bulges exhibit greatest conformational variability in comparison with other combinations of bases in the bulge loop and bases flanking the bulge. Finally, the results indicate that there is only one dominant binding site for the flexicates on the DNA and RNA bulges and that the flexicates bind directly to the bulge or in its close proximity. It is also shown that the flexicates effectively bind to RNA duplexes containing the bulged region of HIV-1 TAR RNA.

NMR study on the interaction of the conserved CREX 'stem-loop' in the Hepatitis E virus genome with a naphthyridine-based ligand

A 2-amino-1,8-naphthyridine derivative that is described to bind single guanine bulges in RNA-DNA and RNA-RNA duplexes was synthesized and its interaction with the single G bulge in the conserved CREX of the Hepatitis E Virus (HEV) genome was explored by NMR and molecular modeling. Results indicate that the ligand intercalates in the internal loop, though none of the expected hydrogen bonds with the single G in the bulge could be demonstrated.

HIV-1 drug discovery: targeting folded RNA structures with branched peptides

Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.

Palladium-catalyzed direct coupling of 2-vinylanilines and isocyanides: an efficient synthesis of 2-aminoquinolines

A variety of 2-aminoquinolines were prepared in good to excellent yields.

Tandem Cu-catalyzed ketenimine formation and intramolecular nucleophile capture: Synthesis of 1,2-dihydro-2-iminoquinolines from 1-(o-acetamidophenyl)propargyl alcohols

The copper-catalyzed ketenimine formation reaction of 1-(o-acetamidophenyl)propargyl alcohols with various sulfonyl azides is found to undergo a concomitant intramolecular nucleophile attack to generate 1,2-dihydro-2-iminoquinolines after aromatization (via elimination of acetyl and hydroxy groups) and tautomerization. The reaction produces 4-substituted and 3,4-unsubstituted title compounds in moderate to good yields under mild reaction conditions.

Recognition of DNA bulges by dinuclear iron(II) metallosupramolecular helicates

Bulged DNA structures are of general biological significance because of their important roles in a number of biochemical processes. Compounds capable of targeting bulged DNA sequences can be used as probes for studying their role in nucleic acid function, or could even have significant therapeutic potential. The interaction of [Fe(2)L(3)](4+) metallosupramolecular helicates (L = C(25)H(20)N(4)) with DNA duplexes containing bulges has been studied by measurement of the DNA melting temperature and gel electrophoresis. This study was aimed at exploring binding affinities of the helicates for DNA bulges of various sizes and nucleotide sequences. The studies reported herein reveal that both enantiomers of [Fe(2)L(3)](4+) bind to DNA bulges containing at least two unpaired nucleotides. In addition, these helicates show considerably enhanced affinity for duplexes containing unpaired pyrimidines in the bulge and/or pyrimidines flanking the bulge on both sides. We suggest that the bulge creates the structural motif, such as the triangular prismatic pocket formed by the unpaired bulge bases, to accommodate the [Fe(2)L(3)](4+) helicate molecule, and is probably responsible for the affinity for duplexes with a varying number of bulge bases. Our results reveal that DNA bulges represent another example of unusual DNA structures recognized by dinuclear iron(II) ([Fe(2)L(3)](4+)) supramolecular helicates.

Naphthyridine-based lanthanide complexes worked as magnetic resonance imaging contrast for guanosine 5'-monophosphate in vivo

New lanthanide complex Gd-ANAMD containing 2-amino-7-methyl-1,8-naphthyridine was achieved for selective magnetic resonance imaging towards guanosine 5'-monophosphate over other ribonucleotide polyphosphates in aqueous media and in vivo. The formation of strong multi-hydrogen bonds between naphthyridine and guanosine made the phosphate in guanosine 5'-monophosphate positioned on a suitable site to coordinate with the lanthanide ion. The substitution of the coordination naphthyridine by the phosphate oxygen atoms caused obvious relaxivity decrease. The negligible cytotoxicity and appropriate blood circulation time of Gd-ANAMD allow potential application of Magnetic Resonance Imaging in vivo. (1)H NMR confirmed that the selectivity of these lanthanide complexes towards guanosine was attributed to the formation of hydrogen bonds between the guanine moeity and the naphthyridine. The fluorescence detection and lifetime measurement of Tb-ANAMD and Eu-ANAMD suggested that the decrease of the relaxivity is not attributed to the change of the q value, but caused by the prolonging of the residence lifetime of inner-sphere water.

Cyclic GMP recognition using ratiometric QD-fluorophore conjugate nanosensors

Novel luminescent ratiometric nanosensors (QD-NAPTHs) were prepared based on cadmium telluride (CdTe655) quantum dots as luminescent nanoscaffolds with naphthyridine dyes as fluorescent receptors. This biosensing bifluorophoric nanosystem has been designed to achieve detection of guanosine 3',5'-cyclic monophosphate (cyclic GMP) in buffered media. Cyclic GMP is a secondary messenger that is an important factor for detecting cancer, diabetes and, cardiovascular diseases. Due to low concentration levels, even in pathological conditions, sensitive cGMP detection remains a challenge for modern biomedical diagnostics. Here, QD-NAPTH nanosensors were tested in the presence of a target nucleotide and with various structural cGMP analogues. Steady-state fluorescence spectroscopy was used to monitor a change in the nucleotide concentration. A 5-fold increase in naphthyridine fluorescence with a simultaneous decrease in QD luminescence was observed after adding 50 μM of cGMP. Using this novel nanosystem with ratiometric detection, it was possible to recognize cGMP with limit of detection (3σ) equal to 70 ng/ml. Moreover, the enhancement in fluorescence upon interaction with the target nucleotide constitutes a favourable approach towards the detection of cGMP in buffered media. These bifluorophoric nanosensors have a potential for application in fluorescence microscopy imaging and in-vitro assays.