Novel G-quadruplex stabilizing agents: in-silico approach and dynamics

Abstract

The stabilization of overhang G-rich repetitive DNA units at the 3'-end of telomeres, which are well known to form functionally important G-quadruplex structures, is a current goal in designing novel anticancer drugs. In the present study, we have undertaken an in silico approach by molecular docking using a small molecule library to find potential G-quadruplex stabilizing agents. Two molecules, A, [N'1-imino(2-pyridyl)methyl-3,4,5-trimethoxybenzene-1-carbohydrazide] and B, [(3-[4-({[3-({4-[(2cyanoethyl)(methyl)amino]benzylidene}amino)propyl]imino}methyl)(methyl) anilino]propanenitrile)], that had good docking scores have been investigated for interaction with G-quadruplexes in a Molecular Dynamics simulation study. Fluorescence spectroscopy of G-quadruplexes bound to the screened molecules A and B was used to experimentally validate the theoretical results. The binding of ligands A and B to G-quadruplexes resulted in blue shifts of 10-18 nm, respectively, in the fluorescence emission spectra of the G-quadruplexes, demonstrating that both molecules bind to the G-face of the quadruplex. The same experiment was performed for the complexation of these small molecules with a G-rich DNA duplex, [Formula: see text]. Interestingly, no blue shift was observed in the fluorescence emission spectra of the DNA duplex in the presence of these small molecules. Thus, these findings indicated that these ligands very selectively bind to G-quadruplexes instead of the duplex DNA. In addition, a one-dimensional water ligand observed via a gradient spectroscopy Nuclear Magnetic Resonance (NMR) experiment showed that both molecules bound to the 23-mer G-quadruplex DNA. The molecular properties of the ligand-quadruplex complex have been analyzed with the help of the Adaptive Poisson-Boltzmann Solver, revealing that electrostatics govern the binding of the small molecules to G-quadruplexes. Both molecules were investigated in detail using solvation free energy calculations and Absorption, Distribution, Metabolism, Elimination and Toxicity (ADMET) predictions, which provide insight into lead optimization for designing G-quadruplex stabilizing agents; therefore, these molecules have potential as new therapeutic agents.

Membrane disruptive antimicrobial activities of human β-defensin-3 analogs

“…The described systems were continued for a simulation spanning 50 ns time scale. Computation of the electrostatic potential was carried out by solving Adaptive Poisson-Boltzmann solver (APBS) as reported in the literature [31]. All the computations were carried out using GPU workstation enabled with Tesla C2075.…”

G-quadruplexes in viruses: function and potential therapeutic applications

“…telomestatin) and G4-binding proteins (e.g. TRF2) show anti-proliferative and potential anti-tumor activities through telomere interference (36,(58)(59)(60)(61). However, the exact mechanism is more complicated as telomestatin derivatives present telomerase independent activity, most likely through targeting G4s involved in tumor growth elsewhere in the genome (62)(63)(64).…”

LINCRNA00273 promotes cancer metastasis and its G-Quadruplex promoter can serve as a novel target to inhibit cancer invasiveness

“…M2 has been described as a G-quadruplex targeting agent [ 31 ], therefore the significant decrease in the expression of LINC00273 by M2 treatment, prompted us to explore the presence of such a structure in the promoter of the said lnc RNA. Interestingly, we found two Quadruplex forming G rich motifs (i) P1, 5’- GGGCGGTGGGAGGGGGGTGGTGGG-3’ (ii) P2, 5’- GGGCGGGGAGGGGGG-3’) at the promoter of LINC00273 [ Supplementary Figure 4 (IV) C&D) .…”

“…Two dimensional HSQC and HMBC spectra of M2 were recorded using “hsqcetgpsi2” and “hmbcgplpndqf” respectively. Water LOGSY NMR experiment was carried out as per our previous paper [ 31 ]. 1 H NMR(500 MHz): δ 7.63(1H, d, J=8.77 Hz), 6.71(1H, d, J=7.63Hz), 2.6(2H, t, J=13.69 Hz), 3.76(2H, t, J=13.69Hz), 3.64(2H, t, J=13.08 Hz), 2.073(2H, m, J=13.08 Hz), 3.09(3H, s), 8.17(1H, s).…”