Ligand-induced conformational preorganization of loops of c-MYC G-quadruplex DNA and its implications in structure-specific drug design

2017 ◽  
Vol 13 (8) ◽  
pp. 1458-1468 ◽  
Author(s):  
S. Harikrishna ◽  
Saikiran Kotaru ◽  
P. I. Pradeepkumar
Keyword(s):  
Drug Design ◽  
Ligand Binding ◽  
Small Molecules ◽  
Conformational Changes ◽  
Specific Drug ◽  
Quadruplex Dna ◽  
G Quadruplex

Ligand binding toc-MYCG-quadruplex DNA induces conformational changes in the loops of the quadruplex.c-MYCquadruplex-specific small molecules can be designed by targeting these loop conformers.

G-quadruplex DNA: a novel target for drug design

2021 ◽  
Author(s):  
Fang-Yuan Teng ◽  
Zong-Zhe Jiang ◽  
Man Guo ◽  
Xiao-Zhen Tan ◽  
Feng Chen ◽  
...  
Keyword(s):  
Drug Design ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Novel Target

scholarly journals Erratum: Corrigendum: Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Paul E. Reyes-Gutiérrez ◽  
Tomáš Kapal ◽  
Blanka Klepetářová ◽  
David Šaman ◽  
Radek Pohl ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cross Link ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Assignment Error

scholarly journals N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA

2019 ◽  
Vol 23 (11n12) ◽  
pp. 1195-1215 ◽  
Author(s):  
Ariana Yett ◽  
Linda Yingqi Lin ◽  
Dana Beseiso ◽  
Joanne Miao ◽  
Liliya A. Yatsunyk
Keyword(s):  
Optical Properties ◽  
Small Molecules ◽  
Genomic Stability ◽  
Water Soluble ◽  
Biological Processes ◽  
Binding Properties ◽  
Quadruplex Dna ◽  
Dna Structures ◽  
G Quadruplex ◽  
High Fluorescence

[Formula: see text]-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect — high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules ([Formula: see text] ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.

Identification of small molecules capable of regulating conformational changes of telomeric G-quadruplex

2018 ◽  
Vol 1154 ◽  
pp. 1-7 ◽  
Author(s):  
Shuo-Bin Chen ◽  
Guo-Cai Liu ◽  
Lian-Quan Gu ◽  
Zhi-Shu Huang ◽  
Jia-Heng Tan
Keyword(s):  
Small Molecules ◽  
Conformational Changes ◽  
G Quadruplex

scholarly journals Visible-light photoswitching of ligand binding mode suggests G-quadruplex DNA as a target for photopharmacology

2020 ◽  
Vol 56 (38) ◽  
pp. 5186-5189 ◽  
Author(s):  
Michael P. O’Hagan ◽  
Javier Ramos-Soriano ◽  
Susanta Haldar ◽  
Sadiyah Sheikh ◽  
Juan C. Morales ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Visible Light ◽  
Binding Mode ◽  
Quadruplex Dna ◽  
G Quadruplex

A pyridinium-decorated photoresponsive dithienylethene selectively targets G-quadruplex DNA, allowing binding mode and toxicity to be controlled exclusively with visible light.

scholarly journals NovelFeIIandCoIIComplexes of Natural Product Tryptanthrin: Synthesis and Binding with G-Quadruplex DNA

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Yi-ning Zhong ◽  
Yan Zhang ◽  
Yun-qiong Gu ◽  
Shi-yun Wu ◽  
Wen-ying Shen ◽  
...  
Keyword(s):  
Natural Products ◽  
Ligand Binding ◽  
Single Crystal ◽  
Natural Product ◽  
Significant Interaction ◽  
Rational Design ◽  
X Ray Diffraction ◽  
Quadruplex Dna ◽  
X Ray ◽  
G Quadruplex

Tryptanthrin is one of the most important members of indoloquinoline alkaloids. We obtained this alkaloid fromIsatis. Two novelFeIIandCoIIcomplexes of tryptanthrin were first synthesized. Single-crystal X-ray diffraction analyses show that these complexes display distorted four-coordinated tetrahedron geometry via two heterocyclic nitrogen and oxygen atoms from tryptanthrin ligand. Binding with G-quadruplex DNA properties revealed that both complexes were found to exhibit significant interaction with G-quadruplex DNA. This study may potentially serve as the basis of future rational design of metal-based drugs from natural products that target the G-quadruplex DNA.

scholarly journals Erratum: Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Paul E. Reyes-Gutiérrez ◽  
Tomáš Kapal ◽  
Blanka Klepetářová ◽  
David Šaman ◽  
Radek Pohl ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cross Link ◽  
Quadruplex Dna ◽  
G Quadruplex ◽  
Assignment Error

scholarly journals Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Paul E. Reyes-Gutiérrez ◽  
Tomáš Kapal ◽  
Blanka Klepetářová ◽  
David Šaman ◽  
Radek Pohl ◽  
...  
Keyword(s):  
Small Molecules ◽  
Cross Link ◽  
Quadruplex Dna ◽  
Mistaken Identity ◽  
G Quadruplex ◽  
Assignment Error

Abstract Two molecules of mistaken identity are addressed. Uncovering these assignment errors led us to formulate more general guidelines about additional misassignments in cases of published bis-imines derived from 1,2-phenylenediamine and hydroxybenzaldehydes having no substituent in ortho-positions. The main purpose of this article is to highlight this repetitive assignment error in the literature and thus increase the likelihood of correct assignments in future papers.

Synthetic Small Molecules Targeting G-Quadruplexes and their Application

2015 ◽  
Vol 1088 ◽  
pp. 507-513
Author(s):  
Hui Yu ◽  
Yan Li Wang ◽  
Xiao Yin Zhao ◽  
Wen Zhang
Keyword(s):  
Drug Design ◽  
Small Molecules ◽  
Small Molecule ◽  
Binding Mode ◽  
Current Understanding ◽  
Promising Target ◽  
G Quadruplex ◽  
Small Molecule Ligands

G-quadruplex is expected to be a promising target for drug design. The manually synthesized small-molecule compounds are able to induce the formation of and stabilize G-quadruplexes. In this paper, we summarize the current understanding of the structure of G-quadruplexes, the binding mode of G-quadruplexes and small-molecule ligands, and important synthesized small molecules targeting G-quadruplexes as potential drugs.

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