Combating multidrug-resistance in S. pneumoniae: a G-quadruplex binding inhibitor of efflux pump and its bio-orthogonal assembly.

Antibiotic resistance poses a significant global health threat, necessitating innovative strategies to combat multidrug-resistant bacterial infections. Streptococcus pneumoniae, a pathogen responsible for various infections, harbors highly conserved DNA quadruplexes in genes linked to its pathogenesis. In this study, we introduce a novel approach to counter antibiotic resistance by stabilizing G-quadruplex structures within the open reading frames of key resistance-associated genes (pmrA, recD and hsdS). We synthesized An4, a bis-anthracene derivative, using Cu(I)-catalyzed azide-alkyne cycloaddition, which exhibited remarkable binding and stabilization of the G-quadruplex in the pmrA gene responsible for drug efflux. An4 effectively permeated multidrug-resistant S. pneumoniae strains, leading to a substantial 12.5-fold reduction in ciprofloxacin resistance. Furthermore, An4 downregulated pmrA gene expression, enhancing drug retention within bacterial cells. Remarkably, the pmrA G-quadruplex cloned into the pET28a(+) plasmid transformed into Escherichia coli BL21 cells can template Cu-free bio-orthogonal synthesis of An4 from its corresponding alkyne and azide fragments. This study presents a pioneering strategy to combat antibiotic resistance by genetically reducing drug efflux pump expression through G-quadruplex stabilization, offering promising avenues for addressing antibiotic resistance.

Guanosine-based hydrogel as a supramolecular scaffold for template-assisted macrocyclization.

The G-quartet-like supramolecular assembly present in guanosine hydrogel templates macrocyclization between bis-azide and bis-alkyne fragments. The resulting macrocycle enhances viscoelastic properties, and strengthens the hydrogel network. This approach holds potential for the in situ synthesis of drugs and their simultaneous delivery in a stimuli-responsive manner.

Bioorthogonal Chemistry in Translational Research: Advances and Opportunities.

Bioorthogonal chemistry is a rapidly expanding field of research that involves the use of small molecules that can react selectively with biomolecules in living cells and organisms, without causing any harm or interference with native biochemical processes. It has made significant contributions to the field of biology and medicine by enabling selective labeling, imaging, drug targeting, and manipulation of bio-macromolecules in living systems. This approach offers numerous advantages over traditional chemistry-based methods, including high specificity, compatibility with biological systems, and minimal interference with biological processes. In this review, we provide an overview of the recent advancements in bioorthogonal chemistry and their current and potential applications in translational research. We present an update on this innovative chemical approach that has been utilized in cells and living systems during the last five years for biomedical applications. We also highlight the nucleic acid-templated synthesis of small molecules by using bioorthogonal chemistry. Overall, bioorthogonal chemistry provides a powerful toolset for studying and manipulating complex biological systems, and holds great potential for advancing translational research.

Expanding the Toolbox of Target Directed Bio-Orthogonal Synthesis: In Situ Direct Macrocyclization by DNA Templates.

Herein, we demonstrate for the first time that noncanonical DNA can direct macrocyclization-like challenging reactions to synthesize gene modulators. The planar G-quartets present in DNA G-quadruplexes (G4s) provide a size complementary reaction platform for the bio-orthogonal macrocyclization of bifunctional azide and alkyne fragments over oligo- and polymerization. G4s immobilized on gold-coated magnetic nanoparticles have been used as target templates to enable easy identification of a selective peptidomimetic macrocycle. Structurally similar macrocycles have been synthesized to understand their functional role in the modulation of gene function. The innate fluorescence of the in situ formed macrocycle has been utilized to monitor its cellular localization using a G4 antibody and its in cell formation from the corresponding azide and alkyne fragments. The successful execution of in situ macrocyclization in vitro and in cells would open up a new dimension for target-directed therapeutic applications.

Thiazole Containing PNA Mimic Regulates c-MYC Gene Expression through DNA G-Quadruplex.

Peptide nucleic acids (PNAs), besides hybridizing to complementary DNA and RNAs, bind and stabilize DNA secondary structures. Herein, we illustrate the design and synthesis of PNA-like scaffolds by incorporating five-membered thiazole rings as modified bases instead of nucleobases and their subsequent effects on gene regulation by biophysical and in vitro assays. A thiazole-modified PNA trimer selectively recognizes c-MYC G-quadruplex (G4) DNA over other G4s and duplex DNA. It displays a high stabilization potential for the c-MYC G4 DNA and shows remarkable fluorescence enhancement with the c-MYC G4. It is flexible enough to bind at 5' and 3' ends as well as in the groove region of c-MYC G4. Furthermore, the PNA trimer easily permeates the cellular membrane and suppresses c-MYC mRNA expression in HeLa cells by targeting the promoter G4. This study illuminates modified PNAs as flexible molecular tools for selective targeting of noncanonical nucleic acids and modulating gene function.

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.

Ionophore constructed from non-covalent assembly of a G-quadruplex and liponucleoside transports K+-ion across biological membranes.

The selective transport of ions across cell membranes, controlled by membrane proteins, is critical for a living organism. DNA-based systems have emerged as promising artificial ion transporters. However, the development of stable and selective artificial ion transporters remains a formidable task. We herein delineate the construction of an artificial ionophore using a telomeric DNA G-quadruplex (h-TELO) and a lipophilic guanosine (MG). MG stabilizes h-TELO by non-covalent interactions and, along with the lipophilic side chain, promotes the insertion of h-TELO within the hydrophobic lipid membrane. Fluorescence assays, electrophysiology measurements and molecular dynamics simulations reveal that MG/h-TELO preferentially transports K+-ions in a stimuli-responsive manner. The preferential K+-ion transport is presumably due to conformational changes of the ionophore in response to different ions. Moreover, the ionophore transports K+-ions across CHO and K-562 cell membranes. This study may serve as a design principle to generate selective DNA-based artificial transporters for therapeutic applications.

A Competitive Pull-Down Assay Using G-quadruplex DNA Linked Magnetic Nanoparticles To Determine Specificity of G-quadruplex Ligands.

Herein, we develop a competitive screening method in which G-quadruplex DNA linked magnetic nanoparticles pull down selective ligands for a particular quadruplex topology from a series of small molecules. The screening strategy is first optimized with known G-quadruplex ligands and then used with a new series of G-quadruplex interactive bis-triazolyl ligands that are synthesized by Cu(I)-catalyzed azide-alkyne cycloaddition. The assay enables the identification of c-MYC and BCL2 G-quadruplex selective bis-triazole ligands that specifically target promoter G-quadruplexes in cancer cells.

Cytidine-Derived Hydrogels with Tunable Antibacterial Activities.

We herein report the preparation of hydrogels by the Ag+ ion induced assembly of cytidine and boronic acids. These hydrogels, presumably formed by an i-motif like arrangement of cytidine and its boronate ester analogues, possess excellent thixotropic and self-healing properties. The hydrogels exhibit potent antimicrobial activity that can be tuned by varying the functional groups in their boronic acid component. These hydrogels could find potential use as antimicrobial agents and stimuli-responsive drug delivery systems.