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Rationalizing the structural basis of organic-platinum hybrid complexes binding towards quadruplex-duplex hybrids

Salvatore Muscarella1, Irene Treccarichi1, Luisa D'Anna1

  • 1Università di Palermo, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy.

Journal of Inorganic Biochemistry
|April 8, 2025
PubMed
Summary

Researchers used atomistic simulations to understand how platinum complexes bind to quadruplex-duplex hybrid (QDH) structures. Binding affinity is driven by π-π stacking and hydrogen bonds, guiding the design of new QDH-targeting compounds.

Keywords:
DockingMolecular dynamicsPt complexesQuadruplex-duplex hybrids

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Medicinal Chemistry

Background:

  • Guanine-rich sequences form non-canonical quadruplex-duplex hybrid (QDH) structures.
  • QDHs present unique binding pockets distinct from G-quadruplexes (G4) or double helices.
  • Organic-metal hybrid platinum complexes show selective binding to QDHs with lateral duplex stem-loops.

Purpose of the Study:

  • To elucidate the atomistic features governing the selective binding of organic-platinum hybrid complexes to QDH structures.
  • To address the lack of solution structures for some investigated compounds and understand binding affinity variations.

Main Methods:

  • All-atom molecular dynamics simulations were employed.
  • Analysis focused on interactions within the QDH binding pocket.

Main Results:

  • Binding affinity is determined by a balance of π-π stacking interactions within the QDH pocket.
  • Stable hydrogen bonds with surrounding nucleobases significantly influence binding affinity.
  • Key structural determinants for high selectivity were identified at the atomistic level.

Conclusions:

  • The study provides crucial insights into the molecular recognition mechanisms of QDH structures by platinum complexes.
  • Findings will guide the rational design of novel compounds for targeted QDH therapies.