Development of squaraine based G-quadruplex ligands using click chemistry

Xin Zhang,Xiangjun Liu,Junqing He,Dihua Shangguan,Tao Bing,Yongbiao Wei,Junyan Wang,Bing Jin,Nan Zhang

doi:10.1038/s41598-017-04344-x

Abstract

The G-quadruplex (G4) structures of nucleic acids are considered to play an intrinsic role in gene expression. To this end, the development of new G4 ligands has attracted extensive research interests towards potential applications as G4-targeted drugs and molecular probes. To date, the majority of G4 ligands have been composed of an extended planar aromatic scaffold that interacts with the terminal G-tetrad plane via π-π interactions, and various side chains that interact with the sugar-phosphate backbone, loops or grooves of the G4 structures. The side chains act to modulate the affinity and selectivity of the G4 ligands, alongside influencing their biodistribution. Here, we present a click chemistry methodology to generate a series of squaraine-based G4 ligand derivatives based on our previously reported G4 probe (named CSTS) but with varing side chains. We find that importantly these new G4 ligand derivatives retain the G4 selectivity, optical properties and low cytotoxicity of CSTS, but exhibit different binding behaviors to G4 structures, and distinct cellular uptake efficiencies. Indeed, of these new complexes, several exhibit much higher affinity and cellular uptake than CSTS. Overall, this novel, facile and highly effective strategy has significant future potential for the high-throughput screening of G4 ligands or probes targeted towards in vivo applications.

Highlights

Guanine-rich nucleic acids (DNA or RNA) are known to self-assemble into four-stranded structures defined as G-quadruplexes (G4s), which are composed of the planar arrangement of four guanine bases stabilized by Hoogsteen hydrogen bonds[1,2,3]
The further application of CSTS in cell analysis is not possible owing to its poor cellular uptake, likely due to the two negatively charged sulfonic acid groups on the side chains impeding cell membrane penetration
We note that zidovudine (11) is a clinical drug approved by the Food and Drug Administration (FDA)[39], it is a deoxythymidine derivative which may interact with other nucleic acid bases on the loop of G4s through hydrogen-bond interactions

Summary

Introduction

Guanine-rich nucleic acids (DNA or RNA) are known to self-assemble into four-stranded structures defined as G-quadruplexes (G4s), which are composed of the planar arrangement of four guanine bases stabilized by Hoogsteen hydrogen bonds (known as a G-quartet)[1,2,3]. As the planar aromatic scaffold of CSTS determines its excellent optical characteristics and high selectivity to parallel G4s For such an approach, it is necessary to develop a new modification strategy to readily produce a catalogue of CSTS analogues with different side chains, in particular, in order to screen new probes for G4 recognition and for in vivo applications. We report a new, highly efficient, molecular platform based on a dicyanomethylene-substituted benzothiazole squaraine functionalized with two alkyne groups (compound 1), which is readily coupled to various azides through a 1,3-dipolar cycloaddition reaction (click chemistry) using copper(I) as a catalyst[35, 36] Exploiting this platform, we have synthesized five new CSTS analogues (Fig. 1) with a variety of side chains (Compounds 2–6) and tested their binding behaviors to different G4s and their relative cellular interaction capacity

Methods

Results

Conclusion