Binding of Gemini Bisbenzimidazole Drugs with Human Telomeric G-Quadruplex Dimers: Effect of the Spacer in the Design of Potent Telomerase Inhibitors

Ananya Paul,Basudeb Maji,Akash K Jain,Santosh K Misra,Santanu Bhattacharya,K Muniyappa,Aamir Ahmad

doi:10.1371/journal.pone.0039467

Ananya Paul, Basudeb Maji + Show 5 more

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https://doi.org/10.1371/journal.pone.0039467

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Abstract

The study of anticancer agents that act via stabilization of telomeric G-quadruplex DNA (G4DNA) is important because such agents often inhibit telomerase activity. Several types of G4DNA binding ligands are known. In these studies, the target structures often involve a single G4 DNA unit formed by short DNA telomeric sequences. However, the 3′-terminal single-stranded human telomeric DNA can form higher-order structures by clustering consecutive quadruplex units (dimers or n-mers). Herein, we present new synthetic gemini (twin) bisbenzimidazole ligands, in which the oligo-oxyethylene spacers join the two bisbenzimidazole units for the recognition of both monomeric and dimeric G4DNA, derived from d(T2AG3)4 and d(T2AG3)8 human telomeric DNA, respectively. The spacer between the two bisbenzimidazoles in the geminis plays a critical role in the G4DNA stability. We report here (i) synthesis of new effective gemini anticancer agents that are selectively more toxic towards the cancer cells than the corresponding normal cells; (ii) formation and characterization of G4DNA dimers in solution as well as computational construction of the dimeric G4DNA structures. The gemini ligands direct the folding of the single-stranded DNA into an unusually stable parallel-stranded G4DNA when it was formed in presence of the ligands in KCl solution and the gemini ligands show spacer length dependent potent telomerase inhibition properties.

Highlights

The 39-end of the telomeric DNA plays a crucial role in chromosome stability and in the protection from degradation, fusion or recombination [1,2,3]
Using a series of ligands based on 1, 3-phenylene-bis previously we have shown the stability, topological changes and induction of G4DNA derived from the sequence d(T2G4)4, telomeric repeat from tetrahymena thermophilia [29] and human
For the sequence d(T2AG3)8, a dimeric hybrid-12 quadruplex structure and a propeller G4DNA have been suggested to be the most stable structure in K+ stabilized conditions based on computational studies [19]

Summary

Introduction

The 39-end of the telomeric DNA plays a crucial role in chromosome stability and in the protection from degradation, fusion or recombination [1,2,3]. Few hundred nucleotides at the terminal end of chromosomes, called telomere, remain singlestranded and are folded into four stranded structures, called the Gquadruplex DNA (G4DNA), a structure induced by Na+ or K+ ions or by some small organic ligands [4,5,6,7,8]. This structure is refractory to telomerase, a ribonucleoprotein of about 170 kDa, which is up-regulated in about 85% of human tumors and is undetectable in most of the normal somatic cells [4,5]. Long RNA transcripts of human telomeric repeats (TERRA), i.e., r(UUAG3)n have been predicted to form multimeric G-quadruplexes, and the eight repeat sequence, i.e., r(UUAG3) forms a dimeric G-quadruplex [22]

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