Identification of the bioactive conformation for mucin epitope peptides

Adrian Kalaszi, Gabor Imre, Imre Jakli, O. Farkas

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Most of the drug molecules exhibit their biological activity through binding to the target protein. When the 3D structure of the binding site is unknown, pure ligand-based approaches are often used to perceive the 3D pharmacophore. However, dealing with conformational flexibility of ligands in such methods is still in the frontline of the current research. The special thermodynamic properties of the binding of flexible molecules, as derived here, show that the probability of the bioactive conformations in solution can determine the likelihood of binding. The binding activities can be obtained experimentally, while the probability of conformations in solution can be computed. Our present paper discusses the thermodynamic basis of performing 3D QSAR studies on molecules, with considerable conformational flexibility. In addition, we supply an algorithm to locate the bioactive conformations. The work is initiated to find the binding conformation of the therapeutically promising mucin epitope pentapeptides.

Original languageEnglish
Pages (from-to)16-27
Number of pages12
JournalJournal of Molecular Structure: THEOCHEM
Volume823
Issue number1-3
DOIs
Publication statusPublished - Dec 1 2007

Fingerprint

Epitopes
Mucins
activity (biology)
Thermodynamics
Peptides
peptides
Conformations
Ligands
Quantitative Structure-Activity Relationship
Molecules
Binding Sites
flexibility
Binding sites
molecules
Bioactivity
Research
ligands
Pharmaceutical Preparations
Proteins
Thermodynamic properties

Keywords

  • Binding free energy
  • Bioactive structures
  • Conformational flexibility
  • Conformational search
  • Drug design
  • Molecular dynamics
  • Rational library design

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computational Theory and Mathematics
  • Atomic and Molecular Physics, and Optics

Cite this

Identification of the bioactive conformation for mucin epitope peptides. / Kalaszi, Adrian; Imre, Gabor; Jakli, Imre; Farkas, O.

In: Journal of Molecular Structure: THEOCHEM, Vol. 823, No. 1-3, 01.12.2007, p. 16-27.

Research output: Contribution to journalArticle

Kalaszi, Adrian ; Imre, Gabor ; Jakli, Imre ; Farkas, O. / Identification of the bioactive conformation for mucin epitope peptides. In: Journal of Molecular Structure: THEOCHEM. 2007 ; Vol. 823, No. 1-3. pp. 16-27.
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