Molecular modeling study on orphan human protein CYP4A22 for identification of potential ligand binding site

Poornima Gajendrarao, Navaneethakrishnan Krishnamoorthy, Sugunadevi Sakkiah, Prettina Lazar, Keun Woo Lee

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

A molecular structure is an essential source to identify ligand binding sites in orphan human cytochrome P450 4A22 (CYP4A22) that belongs to family 4, which is known to be involved in the regulation of blood pressure. Thus, a homology model has been constructed for CYP4A22 and refined by molecular dynamics simulation (MDS). Subsequently, molecular docking was performed with possible substrates, arachidonic acid (essential fatty acid, AA) and erythromycin (therapeutic drug, ERY). These complexes were also subjected to MDS, which helped in predicting the energetically favorable binding sites for these ligands. Putative substrate recognition sites (SRSs) of this protein provide highly hydrophobic binding pockets for the target ligands. A few key ligand binding residues identified in this study indicates that they could also play a major role in ligand-channeling (F122, L132 and C230). Furthermore, it appears that they might serve critical support for the catalytic reaction center (E321, F450, P449 and R455). Structural analysis of channels proposed that the conformational changes might have originated from the active site upon ligand binding and transferred to the rest of the protein via SRSs, which could thereby regulate the channels in CYP4A22. Most of our prediction results are supported by other research groups. In summary, the first molecular modeling study of CYP4A22 yields structural knowledge, which would be helpful to design structure-based-drugs and functional experiments for the target protein.

Original languageEnglish
Pages (from-to)524-532
Number of pages9
JournalJournal of Molecular Graphics and Modelling
Volume28
Issue number6
DOIs
Publication statusPublished - 26 Feb 2010
Externally publishedYes

Fingerprint

Molecular modeling
cytochromes
Binding sites
Cytochrome P-450 Enzyme System
Binding Sites
Ligands
proteins
Proteins
ligands
Molecular dynamics
drugs
Substrates
molecular dynamics
blood pressure
Essential Fatty Acids
Blood pressure
homology
Computer simulation
Erythromycin
fatty acids

Keywords

  • Arachidonic acid
  • Cytochrome P450 4A22
  • Erythromycin
  • Homology modeling
  • Ligand binding site
  • Molecular docking
  • Molecular dynamics simulation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Spectroscopy
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

Cite this

Molecular modeling study on orphan human protein CYP4A22 for identification of potential ligand binding site. / Gajendrarao, Poornima; Krishnamoorthy, Navaneethakrishnan; Sakkiah, Sugunadevi; Lazar, Prettina; Lee, Keun Woo.

In: Journal of Molecular Graphics and Modelling, Vol. 28, No. 6, 26.02.2010, p. 524-532.

Research output: Contribution to journalArticle

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