Spectroscopic and In Silico Studies on the Interaction of Substituted Pyrazolo[1,2-a]benzo[1,2,3,4]tetrazine-3-one Derivatives with c-Myc G4-DNA

Abstract

Herein we describe a combined experimental and in silico study of the interaction of a series of pyrazolo[1,2-a]benzo[1,2,3,4]tetrazin-3-one derivatives (PBTs) with parallel G-quadruplex (GQ) DNA aimed at correlating their previously reported anticancer activities and the stabilizing effects observed by us on c-myc oncogene promoter GQ structure. Circular dichroism (CD) melting experiments were performed to characterize the effect of the studied PBTs on the GQ thermal stability. CD measurements indicate that two out of the eight compounds under investigation induced a slight stabilizing effect (2–4 °C) on GQ depending on the nature and position of the substituents. Molecular docking results allowed us to verify the modes of interaction of the ligands with the GQ and estimate the binding affinities. The highest binding affinity was observed for ligands with the experimental melting temperatures (Tms). However, both stabilizing and destabilizing ligands showed similar scores, whilst Molecular Dynamics (MD) simulations, performed across a wide range of temperatures on the GQ in water solution, either unliganded or complexed with two model PBT ligands with the opposite effect on the Tms, consistently confirmed their stabilizing or destabilizing ability ascertained by CD. Clues about a relation between the reported anticancer activity of some PBTs and their ability to stabilize the GQ structure of c-myc emerged from our study. Furthermore, Molecular Dynamics simulations at high temperatures are herein proposed for the first time as a means to verify the stabilizing or destabilizing effect of ligands on the GQ, also disclosing predictive potential in GQ-targeting drug discovery.

Anticancer Activity, Reduction Mechanism and G-Quadruplex DNA Binding of a Redox-Activated Platinum(IV)–Salphen Complex

“…In order to shed light on the binding mechanism of Pt(II)-Sal towards G-Q DNA, all-atom classical MD simulations were performed. The parallel G-Q conformation from the promoter region of the oncogene c-myc (PDB ID: 1XAV) [ 35 ] was selected to investigate the Pt(II) complex binding, since it is the quadruplex conformation reported in previous experimental settings [ 19 , 36 ]. At physiological pH, the side chains of the complex are most likely positively charged (see details in Materials and Methods section) due to the protonation of the piperidine’s nitrogen atoms ( Scheme 4 ).…”

One pot-like regiospecific access to 1-aryl-1H-pyrazol-3(2H)-one derivatives and evaluation of the anticancer activity

“…Due to the increasing interest towards pyrazolone derivatives in the anticancer field, either as key intermediates or by incorporation in polycyclic heterocycles, 22 herein new insights into the synthesis and the antiproliferative properties of the 1-aryl-pyrazol-3-ones 7a-i, 8 and 9a-i are reported. In this light, we propose a more advantageous synthetic procedure, involving a step economy with respect to the previously reported methods in the literature, including the possibility to introduce functionalities in the hindered position of the 1-aryl moiety.…”

G-Quadruplexes in c-MYC Promoter as Targets for Cancer Therapy

“…This study showed that the substitution in C8 and C9 ( 27 ) and only in C8 ( 28 ) with chlorine atoms ( Figure 8 ) improves the G4 stabilizing effect of these derivatives (ΔTm = 4.0 and 1.9 °C, respectively). Moreover, molecular docking studies have predicted that these chlorine atoms interact with adenine 3 of the G4 [ 98 ]. These compounds also presented good antiproliferative activity against different cancer cell lines in an MTT assay, with IC 50 values between 13.5 and 13.9 µM for Compound 26 and 17.7 and 20.5 µM for Compound 27 [ 99 ].…”