Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model

Haizhen Zhong, Karl N. Kirschner, Moses Lee, J. Phillip Bowen

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

The 3 ns unrestrained MD simulations were carried out on the DNA/duocarmycin complex based on (1) the classic RESP charge model, and (2) the QM-polarized ligand docking (QPLD)-based charge model. The RMSDs of the trajectories and the ΔGbind of the QPLD model perform much better than the RESP model, with the ΔGbind estimation for QPLD model (-16.11 kcal/mol) versus ΔGbind estimation for RESP model (-10.05 kcal/mol).

Original languageEnglish (US)
Pages (from-to)542-545
Number of pages4
JournalBioorganic and Medicinal Chemistry Letters
Volume18
Issue number2
DOIs
StatePublished - Jan 15 2008

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Free energy
Ligands
DNA
Trajectories

Keywords

  • DNA/duocarmycin complex
  • MD simulations
  • MM/GBSA
  • QM-polarized ligand docking (QPLD)
  • RESP charge model

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry

Cite this

Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model. / Zhong, Haizhen; Kirschner, Karl N.; Lee, Moses; Bowen, J. Phillip.

In: Bioorganic and Medicinal Chemistry Letters, Vol. 18, No. 2, 15.01.2008, p. 542-545.

Research output: Contribution to journalArticle

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