Molecular dynamics study on the binding of an anticancer DNA G-quadruplex stabilizer, CX-5461, to human telomeric, C-Kit1, and c-Myc G-quadruplexes and a DNA duplex

Holli Joi Sullivan, Brian Chen, Chun Wu

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

DNA G-quadruplex (G4) stabilizer, CX-5461, is in phase I/II clinical trials for advanced cancers with BRCA1/2 deficiencies. A FRET-melting temperature increase assay measured the stabilizing effects of CX-5461 to a DNA duplex (∼10 K), and three G4 forming sequences negatively implicated in the cancers upon its binding: human telomeric (∼30 K), c-KIT1 (∼27 K), and c-Myc (∼25 K). Without experimentally solved structures of these CX-5461-G4 complexes, CX-5461’s interactions remain elusive. In this study, we performed a total of 73.5 μs free ligand molecular dynamics binding simulations of CX-5461 to the DNA duplex and three G4s. Three binding modes (top, bottom, and side) were identified for each system and their thermodynamic, kinetic, and structural nature were deciphered. The molecular mechanics/Poisson Boltzmann surface area binding energies of CX-5461 were calculated for the human telomeric (-28.6 kcal/mol), c-KIT1 (-23.9 kcal/mol), c-Myc (-22.0 kcal/mol) G4s, and DNA duplex (-15.0 kcal/mol) systems. These energetic differences coupled with structural differences at the 3′ site explained the different melting temperatures between the G4s, while CX-5461’s lack of intercalation to the duplex explained the difference between the G4s and duplex. Based on the interaction insight, CX-5461 derivatives were designed and docked, showing higher selectivity to the G4s over the duplex.

Original languageEnglish (US)
Pages (from-to)5203-5224
Number of pages22
JournalJournal of chemical information and modeling
Volume60
Issue number10
DOIs
StatePublished - Oct 26 2020
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • General Chemical Engineering
  • Computer Science Applications
  • Library and Information Sciences

Fingerprint

Dive into the research topics of 'Molecular dynamics study on the binding of an anticancer DNA G-quadruplex stabilizer, CX-5461, to human telomeric, C-Kit1, and c-Myc G-quadruplexes and a DNA duplex'. Together they form a unique fingerprint.

Cite this