TITLE

Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9

AUTHOR(S)

Cojocaru, Vlad; Winn, Peter J.; Wade, Rebecca C.

PUB. DATE

February 2012

SOURCE

Current Drug Metabolism;Feb2012, Vol. 13 Issue 2, p143

SOURCE TYPE

Academic Journal

DOC. TYPE

Article

ABSTRACT

The active site of liver-specific, drug-metabolizing cytochrome P450 (CYP) monooxygenases is deeply buried in the protein and is connected to the protein surface through multiple tunnels, many of which were found open in different CYP crystal structures. It has been shown that different tunnels could serve as ligand passage routes in different CYPs. However, it is not understood whether one CYP uses multiple routes for substrate access and product release and whether these routes depend on ligand properties. From 300 ns of molecular dynamics simulations of CYP2C9, the second most abundant CYP in the human liver we found four main ligand exit routes, the occurrence of each depending on the ligand type and the conformation of the F-G loop, which is likely to be affected by the CYPmembrane interaction. A non-helical F-G loop favored exit towards the putative membrane-embedded region. Important protein features that direct ligand exit include aromatic residues that divide the active site and whose motions control access to two pathways. The ligands interacted with positively charged residues on the protein surface through hydrogen bonds that appear to select for acidic substrates. The observation of multiple, ligand-dependent routes in a CYP aids understanding of how CYP mutations affect drug metabolism and provides new possibilities for CYP inhibition.

ACCESSION #

72885381

 

Related Articles

• Malleability and Versatility of Cytochrome P450 Active Sites Studied by Molecular Simulations. Oostenbrink, Chris; De Ruiter, Anita; Hritz, Jozef; Vermeulen, Nico // Current Drug Metabolism;Feb2012, Vol. 13 Issue 2, p190 

  As the most important phase I drug metabolizing enzymes, the human Cytochromes P450 display an enormous versatility in the molecular structures of possible substrates. Individual isoforms may preferentially bind specific classes of molecules, but also within these classes, some isoforms show...

• Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations. Hendrychová, Tereza; Berka, Karel; Navrátilová, Veronika; Anzenbacher, Pavel; Otyepka, Michal // Current Drug Metabolism;Feb2012, Vol. 13 Issue 2, p177 

  The flexibility, active site volume, solvation, and access path dynamics of six metabolically active mammalian cytochromes P450 (human 2A6, 2C9, 2D6, 2E1, 3A4 and rabbit 2B4) are extensively studied using molecular dynamics (MD) simulations. On average, the enzymes' overall structures...

• Identification of Selectivity Determinants in CYP Monooxygenases by Modelling and Systematic Analysis of Sequence and Structure. Seifert, Alexander; Pleiss, Jürgen // Current Drug Metabolism;Feb2012, Vol. 13 Issue 2, p197 

  Cytochrome P450 monooxygenases (CYPs) form a large, ubiquitous enzyme family and are of great interest in red and white biotechnology. To investigate the effect of protein structure on selectivity, the binding of substrate molecules near to the active site was modelled by molecular dynamics...

• The Role of Protein Plasticity in Computational Rationalization Studies on Regioselectivity in Testosterone Hydroxylation by Cytochrome P450 BM3 Mutants. De Beer, Stephanie B. A.; Van Bergen, Laura A. H.; Keijzer, Karlijn; Rea, Vanina; Venkataraman, Harini; Guerra, Célia Fonseca; Bickelhaupt, F. Matthias; Vermeulen, Nico P.E.; Commandeur, Jan N.M.; Geerke, Daan P. // Current Drug Metabolism;Feb2012, Vol. 13 Issue 2, p155 

  Recently, it was found that mutations in the binding cavity of drug-metabolizing Cytochrome P450 BM3 mutants can result in major changes in regioselectivity in testosterone (TES) hydroxylation. In the current work, we report the intrinsic reactivity of TES' C-H bonds and our attempts to...

• A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes. Lonsdale, Richard; Rouse, Sarah L.; Sansom, Mark S. P.; Mulholland, Adrian J. // PLoS Computational Biology;Jul2014, Vol. 10 Issue 7, p1 

  Cytochrome P450 enzymes are found in all life forms. P450s play an important role in drug metabolism, and have potential uses as biocatalysts. Human P450s are membrane-bound proteins. However, the interactions between P450s and their membrane environment are not well-understood. To date, all...

• Implication of Crystal Water Molecules in Inhibitor Binding at ALR2 Active Site. Hymavati; Kumar, Vivek; Sobhia, M. Elizabeth // Computational & Mathematical Methods in Medicine;Jan2012, p1 

  Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecule. The solvent environment around such biomolecule controls their structure and plays important role in protein-ligand interactions. An understanding of the nature and role of these water...

• Substrate binding to cytochromes P450. Isin, Emre M.; Guengerich, F. Peter // Analytical & Bioanalytical Chemistry;Nov2008, Vol. 392 Issue 6, p1019 

  P450s have attracted tremendous attention owing to not only their involvement in the metabolism of drug molecules and endogenous substrates but also the unusual nature of the reaction they catalyze, namely, the oxidation of unactivated C–H bonds. The binding of substrates to P450s, which...

• Validation of incorporating flurbiprofen into the Pittsburgh cocktail*. Zgheib, Nathalie K.; Frye, Reginald F.; Tracy, Timothy S.; Romkes, Marjorie; Branch, Robert A. // Clinical Pharmacology & Therapeutics;Sep2006, Vol. 80 Issue 3, p257 

  Background: We have previously shown that flurbiprofen metabolism to 4′-hydroxyflurbiprofen provides an in vivo measure of cytochrome P450 (CYP) 2C9 activity. This study evaluated the possibility of incorporating flurbiprofen into the current 5-drug Pittsburgh cocktail.Methods: In a...

• CYP2C9 Genotype vs. Metabolic Phenotype for Individual Drug Dosing—A Correlation Analysis Using Flurbiprofen as Probe Drug. Vogl, Silvia; Lutz, Roman W.; Schönfelder, Gilbert; Lutz, Werner K. // PLoS ONE;Mar2015, Vol. 10 Issue 3, p1 

  Currently, genotyping of patients for polymorphic enzymes responsible for metabolic elimination is considered a possibility to adjust drug dose levels. For a patient to profit from this procedure, the interindividual differences in drug metabolism within one genotype should be smaller than those...

Read the Article