Characterization of clinically used oral antiseptics as quadruplex-binding ligands

Abstract

Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a widely used oral antiseptic, and the G-quadruplex (G4) structure in the KRAS oncogene promoter. The interaction of chlorhexidine and related drugs to the KRAS G4 is evaluated using multiple biophysical methods, including thermal melt, fluorescence titration and surface plasmon resonance (SPR) assays. Chlorhexidine has a specific low micromolar binding interaction with the G4, while related drugs have weaker and/or less specific interactions. Through NMR experiments and docking studies, we propose a plausible binding mode driven by both aromatic stacking and groove binding interactions. Additionally, cancer cell lines harbouring oncogenic mutations in the KRAS gene exhibit increased sensitivity to chlorhexidine. Treatment of breast cancer cells with chlorhexidine decreases KRAS protein levels, while a KRAS gene transiently expressed by a promoter lacking a G4 is not affected. This work confirms that known ligands bind broadly to G4 structures, while other drugs and druglike compounds can have more selective interactions that may be biologically relevant.

Selective Small-Molecule Targeting of a Triple Helix Encoded by the Long Noncoding RNA, MALAT1

“…Our small molecule microarray (SMM) approach (Figure 1a) has successfully identified several chemotypes targeting RNA and DNA motifs, including the HIV TAR hairpin, 27,28 miR21, 29 Myc, and KRAS G-quadruplexes. 30,31 Here, a minimal 5′-fluorescently labeled Malat1 (Figure 1a) RNA construct was used to screen a ~ 26 000 compound library. To select the most promising compounds, a pipeline composed of statistical analysis, inspection of pharmacophore properties ( i.e ., whether compound would be amenable to later medicinal chemistry efforts), selectivity, commercial availability, and cell-based evaluation of the top 28 compounds was developed (Figure 1b).…”

Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe

“…GQ-forming sequences are widely present in the genome (12,13) and have been proven to play important roles in chromosome maintenance, telomerase dysfunction and regulation of expression of several oncogenes (14−21). Consequently, several small molecule ligands that bind and modulate GQ function have been evaluated as chemotherapeutic agents (22−29). However, the druggability of GQs in a clinical setup has not yet been realized.…”

The study of antiviral drugs targeting SARS-CoV-2 nucleocapsid and spike proteins through large-scale compound repurposing

“…The library includes FDA-approved medicines, traditional Chinese medicine monomers, and additional developing small molecule inhibitors. This library chip is suitable for pure/total protein-small molecule interactions 17 , 18 , 19 , 20 and nucleic acid-small molecule interactions 21 , 22 . Comparing to novel drug development, the known pharmacological and safety profiles would streamline the drug development, which subsequently benefits both preclinical and clinical evaluation of these drugs for potential therapeutics.…”