Berenil Binds Tightly to Parallel and Mixed Parallel/Antiparallel G-Quadruplex Motifs with Varied Thermodynamic Signatures

Abstract

Diminazene, DMZ, (or berenil) has been reported as a tight binder of G-quadruplexes. G-Quadruplex structures are often located in the promotor regions of oncogenes and may play a regulatory role in gene expression based on the stability of the folding topology. In this study, attempts have been made to characterize the specificity of DMZ binding toward multiple G-quadruplex topologies or foldamers. Mutant sequences of the G-quadruplex forming promotor regions of several oncogenes were designed to exhibit restricted loop lengths and folding topologies. Circular dichroism was used to confirm the quadruplex topology of mutant BCL2, KRAS, and c-MYC sequences, human telomere (Na+ and K+) G-quadruplexes and their complexes with DMZ and analogs thereof. Isothermal titration calorimetry was used to generate a complete thermodynamic profile (ΔG, ΔH, −TΔS) for the formation of DMZ and analog complexes with the target G-quadruplexes. DMZ binds to parallel and/or mixed parallel/antiparallel quadruplex DNA motifs with stoichiometries up to 8:1 and via three binding modes with varying affinities. In the case of the parallel G-quadruplexes, with the exception of the long-looped c-MYC mutant, the highest affinity binding event (mode 1) is driven by enthalpy. DMZ binding to the long-looped c-MYC mutant exhibits a very favorable entropy change in addition to a moderately favorable enthalpy change. Mode 1 binding to the antiparallel and mixed parallel/antiparallel hTel quadruplexes is also driven by favorable enthalpy changes. In all cases, the intermediate DMZ affinity binding (mode 2) is driven almost entirely by entropy, with small or unfavorable enthalpic contributions. The weakest binding event (mode 3) is also entropically driven with small or moderate enthalpic contributions.

The potential actions of angiotensin‐converting enzyme II (ACE2) activator diminazene aceturate (DIZE) in various diseases

“…56 Interestingly, the literature has also suggested a possible mechanism of DIZE on G-quadruplex, 61 which is a target in cancer therapy. 62 Previous studies have shown evidence to support stabilisation of the mutated G-quadruplex decreased activity of c-MYC oncogene and thus allows for anti-tumour abilities [63][64][65] and that DIZE is able to bind to G-quadruplexes located in the promoter region of c-MYC oncogene. 65 F I G U R E 4 The activation of ACE2 by DIZE allows ACE2 to produce the vasoprotective peptides of the nonclassical RAS to elicit vasodilation that is important to restore in endothelial dysfunction.…”

“…Interestingly, the literature has also suggested a possible mechanism of DIZE on G‐quadruplex, which is a target in cancer therapy . Previous studies have shown evidence to support stabilisation of the mutated G‐quadruplex decreased activity of c‐MYC oncogene and thus allows for anti‐tumour abilities and that DIZE is able to bind to G‐quadruplexes located in the promoter region of c‐MYC oncogene …”

“…and that DIZE is able to bind to G-quadruplexes located in the promoter region of c-MYC oncogene 65. …”

Co‐Assembly of Peptide with G‐Quadruplex DNA: A Strategic Approach to Develop Anticancer Therapeutics

“…The basic building blocks of G4 are the G‐tetrads which are formed by Hoogsteen G−G base pairing in the presence of cations such as Na + , K + , Pb 2+ , Li + etc [2a,b] . The G4 structures are found all through the human genome, particularly in the telomeric region, promoter oncogenes, immunoglobulin switch regions, ribosomal DNA etc [3] . Formation of G4 plays an important regulatory role in maintaining telomere and expression of oncogenes [4] .…”

Ligand-Based Stability Changes in Duplex DNA Measured with a Microscale Electrochemical Platform

“…While our proof-of-concept work was done with known duplex DNA binders, the method could be easily employed to test induced stability changes for a variety of other ligands. We note that these selected ligands have also shown binding to other nucleotide structures such as c-di-GMP and G-quadruplexes [40,41,42]. The magnitude of changes in T m upon binding of these ligands was readily observable.…”