Methods for investigating G-quadruplex DNA/ligand interactions

P Murat, Y Singh, E Defrancq - Chemical Society Reviews, 2011 - pubs.rsc.org
DNA is considered an important target for drug design and development. Until recently, the
focus was on double-stranded (duplex) DNA structures. However, it has now been shown …

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

J Šponer, X Cang, TE Cheatham III - Methods, 2012 - Elsevier
The article reviews the application of biomolecular simulation methods to understand the
structure, dynamics and interactions of nucleic acids with a focus on explicit solvent …

Ion binding to quadruplex DNA stems. Comparison of MM and QM descriptions reveals sizable polarization effects not included in contemporary simulations

K Gkionis, H Kruse, JA Platts, A Mladek… - Journal of chemical …, 2014 - ACS Publications
Molecular mechanical (MM) force fields are commonly employed for biomolecular
simulations. Despite their success, the nonpolarizable nature of contemporary additive force …

Binding of BRACO19 to a telomeric G-quadruplex DNA probed by all-atom molecular dynamics simulations with explicit solvent

B Machireddy, HJ Sullivan, C Wu - Molecules, 2019 - mdpi.com
Although BRACO19 is a potent G-quadruplex binder, its potential for clinical usage is
hindered by its low selectivity towards DNA G-quadruplex over duplex. High-resolution …

A new insight into mushroom tyrosinase inhibitors: docking, pharmacophore-based virtual screening, and molecular modeling studies

K Bagherzadeh, F Shirgahi Talari, A Sharifi… - Journal of …, 2015 - Taylor & Francis
Tyrosinase, a widely spread enzyme in micro-organisms, animals, and plants, participates in
two rate-limiting steps in melanin formation pathway which is responsible for skin protection …

Probing the binding pathway of BRACO19 to a parallel-stranded human telomeric G-quadruplex using molecular dynamics binding simulation with AMBER DNA …

B Machireddy, G Kalra, S Jonnalagadda… - Journal of chemical …, 2017 - ACS Publications
Human telomeric DNA G-quadruplex has been identified as a good therapeutic target in
cancer treatment. G-quadruplex-specific ligands that stabilize the G-quadruplex have great …

Binding of Telomestatin, TMPyP4, BSU6037, and BRACO19 to a Telomeric G-Quadruplex–Duplex Hybrid Probed by All-Atom Molecular Dynamics Simulations with …

HJ Sullivan, C Readmond, C Radicella, V Persad… - ACS …, 2018 - ACS Publications
A promising anticancer therapeutic strategy is the stabilization of telomeric G-quadruplexes
using G-quadruplex-binding small molecules. Although many G-quadruplex-specific ligands …

Nemorubicin and doxorubicin bind the G-quadruplex sequences of the human telomeres and of the c-MYC promoter element Pu22

L Scaglioni, R Mondelli, R Artali, FR Sirtori… - Biochimica et Biophysica …, 2016 - Elsevier
Background Intra-molecular G-quadruplex structures are present in the guanine rich regions
of human telomeres and were found to be prevalent in gene promoters. More recently, the …

On characterizing the interactions between proteins and guanine quadruplex structures of nucleic acids

EKS McRae, EP Booy, GP Padilla-Meier… - Journal of nucleic …, 2017 - Wiley Online Library
Guanine quadruplexes (G4s) are four‐stranded secondary structures of nucleic acids which
are stabilized by noncanonical hydrogen bonding systems between the nitrogenous bases …

Extended molecular dynamics of a c-kit promoter quadruplex

B Islam, P Stadlbauer, M Krepl, J Koca… - Nucleic acids …, 2015 - academic.oup.com
The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique
structure, which has been elucidated by crystallographic and NMR methods and shows a …