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Insight Derived from Molecular Dynamics Simulation into the Selectivity Mechanism Targeting c-MYC G-Quadruplex.

Zhiguo Wang¹, Guo Li², Zhou Tian¹

¹Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou 311121, Zhejiang, China.

The Journal of Physical Chemistry. B

|October 22, 2020

Summary

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This summary is machine-generated.

A new molecule, IZCZ-3, selectively targets the c-MYC G-quadruplex (G4) by stabilizing dimeric structures. This finding offers a promising strategy for developing targeted cancer therapies.

Area of Science:

Medicinal Chemistry
Computational Biology
Oncology

Background:

Stabilizing G-quadruplex (G4) structures in oncogenes like c-MYC is a key cancer therapy approach.
Current G4 stabilizers often lack selectivity, targeting multiple G4 structures genome-wide.

Purpose of the Study:

To investigate the binding characteristics of the imidazole/carbazole molecule IZCZ-3 with G4 structures.
To understand the selectivity of IZCZ-3 for the c-MYC G4 over c-KIT and telomeric G4s.

Main Methods:

Molecular docking and molecular dynamics simulations were employed.
Analysis of binding affinities and interactions with monomeric and dimeric G4s.

Main Results:

IZCZ-3 shows inconsistent binding with monomeric G4s but effectively targets dimeric c-MYC and c-KIT G4s via π-π stacking.

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IZCZ-3 exhibits higher affinity for c-MYC G4 due to stabilizing intermolecular aggregates with two exposed G-tetrads.

The observed binding affinity order (c-MYC > c-KIT > telomeric G4) aligns with experimental data when aggregation effects are considered.

Conclusions:

The selectivity of IZCZ-3 for c-MYC G4 arises from its ability to stabilize dimeric aggregates.
This study provides a foundation for designing selective c-MYC G4 stabilizers for cancer treatment.