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Published on: April 5, 2022
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Porphyrin-based ligand interaction with G-quadruplex: Metal cation effects
Fahimeh Otovat1, Mohammad Reza Bozorgmehr2, Ali Mahmoudi1
1Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Tehran, Iran.
Journal of Molecular Recognition : JMR
|April 7, 2023
Summary
This study used molecular dynamics to investigate how porphyrin ligands interact with G-quadruplex DNA structures. Ligand L2 showed the strongest interaction, enhancing G-quadruplex stability and offering insights into molecular mechanisms.
Area of Science:
- Biochemistry
- Computational Chemistry
- Molecular Biology
Background:
- G-quadruplex structures are crucial in telomere maintenance and have potential therapeutic applications.
- Planar porphyrin ligands are explored for their ability to interact with and detect various analytes, including metal ions and biomolecules.
- Understanding ligand-G-quadruplex interactions is key to developing novel diagnostic and therapeutic agents.
Purpose of the Study:
- To investigate the molecular dynamics of interactions between three porphyrin ligands (L1, L2, L3) and G-quadruplex DNA from human telomeres.
- To elucidate the effect of different metal ions (monovalent and divalent) on these ligand-G-quadruplex interactions.
- To determine the binding affinity and stability imparted by the ligands to the G-quadruplex structure.
Main Methods:
- Molecular dynamics simulations were employed to model the interactions.
- Analysis focused on hydrogen bonding, structural changes in the G-quadruplex sheets, and inter-guanine distances.
- Binding pockets and binding energies were calculated for the ligand-G-quadruplex complexes.
Main Results:
- Divalent ions (Mg2+, Ca2+) with ligands caused significant changes in the lower G-quadruplex sheet's hydrogen bonds and increased guanine-guanine distances.
- Monovalent ion interactions showed varied effects on hydrogen bonds between sheets depending on the specific ion (e.g., Li+, Na+).
- Ligands stabilized the G-quadruplex by intercalating between sheets and interacting with loops, with ligand L2 exhibiting the highest interaction level.
Conclusions:
- Porphyrin ligands can significantly stabilize G-quadruplex structures through specific binding interactions.
- The study provides a molecular-level understanding of porphyrin-G-quadruplex interactions, consistent with experimental findings.
- These findings support the potential of porphyrin derivatives as tools for G-quadruplex detection and modulation.
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