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Evaluating Molecular Docking Software for Small Molecule Binding to G-Quadruplex DNA.

Jonathan Dickerhoff1, Kassandra R Warnecke1, Kaibo Wang1

  • 1Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 W Stadium Ave, West Lafayette, IN 47907, USA.

International Journal of Molecular Sciences
|October 13, 2021
PubMed
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This summary is machine-generated.

This study evaluated molecular docking programs for predicting G-quadruplex DNA (G4 DNA) binding poses. DOCK 6 showed better performance, but scoring functions limit current docking accuracy for G4 DNA-small molecule interactions.

Area of Science:

  • Biochemistry
  • Medicinal Chemistry
  • Computational Biology

Background:

  • G-quadruplexes (G4s) are significant nucleic acid structures and emerging drug targets.
  • The MYC promoter G-quadruplex (MycG4) is a key model for studying parallel G4 structures.
  • Molecular docking is increasingly used for G4 DNA targets, but presents unique challenges compared to protein targets.

Purpose of the Study:

  • To systematically evaluate the performance of four common docking programs for G4 DNA-ligand binding pose prediction.
  • To assess the accuracy of molecular docking in modeling small molecule interactions with the MycG4 structure.
  • To identify limitations in current docking methodologies for G4 DNA targets.

Main Methods:

  • Systematic evaluation of AutoDock Vina, DOCK 6, Glide, and RxDock.
Keywords:
G-quadruplexG4-ligandsdockingdrug designpose predictionscoring

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  • Utilized experimentally determined complex structures of four small molecules with the MycG4.
  • Assessed binding pose prediction accuracy of each docking program.

    • Main Results:

    • Significant performance differences were observed among the evaluated docking programs.
    • DOCK 6 with GB/SA rescoring demonstrated superior performance compared to other tested programs.
    • Docking accuracy for G4 DNA targets is primarily limited by the employed scoring functions.

    Conclusions:

    • Current molecular docking programs should be applied cautiously for predicting G4 DNA-small molecule binding modes.
    • Further development of scoring functions is crucial for improving docking accuracy in G4 DNA drug discovery.
    • This study provides valuable insights into the capabilities and limitations of computational methods for targeting G4 DNA structures.