Surface Dependent Dual Recognition of a G-quadruplex DNA With Neomycin-Intercalator Conjugates

Abstract

G-quadruplexes have been characterized as structures of vital importance in the cellular functioning of several life forms. They have subsequently been established to serve as a therapeutic target of several diseases including cancer, HIV, tuberculosis and malaria. In this paper, we report the binding of aminosugar-intercalator conjugates with a well-studied anti-parallel G-quadruplex derived from Oxytricha Nova G-quadruplex DNA. Of the four neomycin-intercalator conjugates studied with varying surface areas, BQQ-neomycin conjugate displayed the best binding to this DNA G-quadruplex structure with an association constant of K a = (1.01 ±0.03) × 10 7 M −1 which is nearly 100-fold higher than the binding of neomycin to this quadruplex. The binding of BQQ-neomycin displays a binding stoichiometry of 1:1 indicating the presence of a single and unique binding site for this G-quadruplex. In contrast, the BQQ-neomycin displays very weak binding to the bacterial A-site rRNA sequence showing that BQQ-does not enhance the neomycin binding to its natural target, the bacterial rRNA A-site. The BQQ-neomycin conjugate is prone to aggregation even at low micromolar concentrations (4 µM) leading to some ambiguities in the analysis of thermal denaturation profiles. Circular dichroism experiments showed that binding of BQQ-neomycin conjugate causes some structural changes in the quadruplex while still maintaining the overall anti-parallel structure. Finally, the molecular docking experiments suggest that molecular surface plays an important role in the recognition of a second site on the G-quadruplex. Overall, these results show that molecules with more than one binding moieties can be made to specifically recognize G-quadruplexes with high affinities. The dual binding molecules comprise of quadruplex groove binding and intercalator units, and the molecular surface of the intercalator plays an important part in enhancing binding interaction to the G-quadruplex structure.

Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery

“…Moreover, stacking interactions were observed only for the smallest polycyclic ring, the anthraquinone intercalator. 143 …”

“…The molecular modeling part of the study, performed with Vina, revealed for all the conjugates that neomycin was positioned in the wide groove with a linker extending the intercalating moieties more toward the thymine loop regions. Moreover, stacking interactions were observed only for the smallest polycyclic ring, the anthraquinone intercalator …”

“…Moreover, stacking interactions were observed only for the smallest polycyclic ring, the anthraquinone intercalator. 143 Glide (grid-based ligand docking with energetics) is the docking engine of the Schrodinger suite. It relies on an exhaustive search algorithm where an initial rough positioning and scoring is followed by torsionally flexible energy optimization with the OPLS ff.…”

Parallel G-quadruplex recognition by neomycin

“…Some of the fluorescent modifications were also used in developing DNA- and RNA-based screening assays for rapid drug discovery of several classes of small-molecule binders ( Watkins et al, 2013 ; Ranjan and Arya, 2019 ). In comparison to DNA-binding studies with duplexes and triplexes, our investigations with DNA G-quadruplexes were limited with most of the binding studies with antiparallel G-quadruplex structures ( Ranjan et al, 2010 ; Ranjan et al, 2013b ; Ranjan et al, 2020 ). Detailed studies involving aminoglycoside binding to parallel G-quadruplexes remain unknown until now.…”