Reassessment of Cytochrome P450 2B2:  Catalytic Specificity and Identification of Four Active Site Residues†

Although the residues that determine the preference of CYP2D6 (cytochrome P450 2D6) for compounds containing a basic nitrogen are well characterized, the contribution of other active site residues to substrate binding and orientation is less well understood. Our structural model of CYP2D6 identifies the aromatic residue Phe120 as a likely major feature of the active site. To examine the role of Phe120, mutants of CYP2D6 in which this residue has been substituted by alanine, leucine, tyrosine, serine, histidine, tryptophan or methionine residues have been prepared in bacterial membranes co-expressing human cytochrome NADPH cytochrome P450 oxidoreductase. The mutants have been characterized using the prototypical bufuralol 1´ hydroxylase and dextromethorphan O- and N-demethylase activities of CYP2D6. Larger effects on Km values are observed for dextromethorphan O-demethylation than for bufuralol 1´ hydroxylation, indicating that the Phe120 side chain is more important in dextromethorphan than in bufuralol binding. A role for this side chain in determining the regiospecificity of substrate oxidation was indicated by changes in the relative rates of O- and N-demethylation of dextromethorphan and, notably, by the formation of 7-hydroxy dextromethrophan, a novel dextromethorphan metabolite, in mutants in which it had been substituted. Computational studies of dextromethorphan binding to the active site of the Phe120→Ala mutant were carried out to throw light on the way in which the removal of this side chain leads to different modes of ligand binding.

Download Full-text

Cytochrome P450: Probes of Active Site Residues

Cytochrome P450 - Handbook of Experimental Pharmacology ◽

10.1007/978-3-642-77763-9_12 ◽

1993 ◽

pp. 183-194

Author(s):

L. S. Kaminsky ◽

R. S. Obach ◽

M. J. Fasco

Keyword(s):

Cytochrome P450 ◽

Active Site ◽

Active Site Residues

Download Full-text

Active-site residues move independently from the rest of the protein in a 200ns molecular dynamics simulation of cytochrome P450 CYP119

Archives of Biochemistry and Biophysics ◽

10.1016/j.abb.2011.02.020 ◽

2011 ◽

Vol 509 (2) ◽

pp. 127-132 ◽

Cited By ~ 13

Author(s):

Relly Brandman ◽

Jed N. Lampe ◽

Yigal Brandman ◽

Paul R. Ortiz de Montellano

Keyword(s):

Molecular Dynamics ◽

Cytochrome P450 ◽

Molecular Dynamics Simulation ◽

Active Site ◽

Dynamics Simulation ◽

Active Site Residues

Download Full-text

Faculty Opinions recommendation of 13C NMR analysis of electrostatic interactions between NAD+ and active site residues of UDP-galactose 4-epimerase: implications for the activation induced by uridine nucleotides.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1000833.9459 ◽

2001 ◽

Author(s):

Hung-Wen Liu

Keyword(s):

13C Nmr ◽

Active Site ◽

Electrostatic Interactions ◽

Nmr Analysis ◽

Active Site Residues ◽

13C Nmr Analysis ◽

Uridine Nucleotides

Download Full-text

Development of Xanthine Based Inhibitors Targeting Phosphodiesterase 9A

Letters in Drug Design & Discovery ◽

10.2174/1570180813666161102125423 ◽

2017 ◽

Vol 14 (10) ◽

pp. 1122-1137 ◽

Cited By ~ 1

Author(s):

Nivedita Singh ◽

Parameswaran Saravanan ◽

M.S. Thakur ◽

Sanjukta Patra

Keyword(s):

Free Energy ◽

Active Site ◽

Signal Transduction Pathway ◽

Docking Study ◽

Primary Objective ◽

Cgmp Level ◽

Active Site Residues ◽

Aromatic Fragment ◽

Docking Approach ◽

Free Energy Of Binding

Background: Phosphodiesterases 9A (PDE9A) is one of the prominent regulating enzymes of the signal transduction pathway having highest catalytic affinity for second messenger, cGMP. When the cGMP level is lowered, an uncontrolled expression of PDE9A may lead to various neurodegenerative diseases. To regulate the catalytic activity of PDE9A, potent inhibitors are needed. Objective: The primary objective of the present study was to develop new xanthine based inhibitors targeting PDE9A. This study was an attempt to bring structural diversification in PDE9A inhibitor development because most of the existing inhibitors are constructed over pyrazolopyrimidinone scaffold. Methods: Manual designing and parallel molecular docking approach were used for the development of xanthine derivatives. In this study, N1, N3, N9 and C8 positions of xanthine scaffold were selected as substitution sites to design 200 new compounds. Reverse docking and pharmaceutical analyses were used for final validation of most promising compounds. Results: By keeping free energy of binding cut-off of -6.0 kcal/mol, 52 compounds were screened. The compounds with substitution at N1, N3 and C8 positions of xanthine showed good occupancy in PDE9A active site pocket with a significant interaction pattern. This was further validated by screening different factors such as free energy of binding, inhibition constant and interacting active site residues in the 5Å region. Substitution at C8 position with phenyl substituent determined the inhibition affinity of compounds towards PDE9A by establishing a strong hydrophobic - hydrophobic interaction. The alkyl chain at N1 position generated selectivity of compounds towards PDE9A. The aromatic fragment at N3 position increased the binding affinity of compounds. Thus, by comparative docking study, it was found that compound 39-42 formed selective interaction towards PDE9A over other members of the PDE superfamily. Conclusion: From the present study, N1, N3 and C8 positions of xanthine were concluded as the best sites for substitution for the generation of potent PDE9A inhibitors.

Download Full-text

The Molecular and Enzyme Kinetic Basis for Altered Activity of Three Cytochrome P450 2C19 Variants Found in the Chinese Population

Current Molecular Pharmacology ◽

10.2174/1874467212666191111110429 ◽

2020 ◽

Vol 13 (3) ◽

pp. 233-244

Author(s):

Amelia Nathania Dong ◽

Nafees Ahemad ◽

Yan Pan ◽

Uma Devi Palanisamy ◽

Beow Chin Yiap ◽

...

Keyword(s):

Cytochrome P450 ◽

Molecular Docking ◽

Active Site ◽

Chinese Population ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

In Vitro Assays ◽

Access Channel ◽

Cytochrome P450 2C19

Background: There is a large inter-individual variation in cytochrome P450 2C19 (CYP2C19) activity. The variability can be caused by the genetic polymorphism of CYP2C19 gene. This study aimed to investigate the molecular and kinetics basis for activity changes in three alleles including CYP2C19*23, CYP2C19*24 and CYP2C19*25found in the Chinese population. Methods: The three variants expressed by bacteria were investigated using substrate (omeprazole and 3- cyano-7-ethoxycoumarin[CEC]) and inhibitor (ketoconazole, fluoxetine, sertraline and loratadine) probes in enzyme assays along with molecular docking. Results: All alleles exhibited very low enzyme activity and affinity towards omeprazole and CEC (6.1% or less in intrinsic clearance). The inhibition studies with the four inhibitors, however, suggested that mutations in different variants have a tendency to cause enhanced binding (reduced IC50 values). The enhanced binding could partially be explained by the lower polar solvent accessible surface area of the inhibitors relative to the substrates. Molecular docking indicated that G91R, R335Q and F448L, the unique mutations in the alleles, have caused slight alteration in the substrate access channel morphology and a more compact active site cavity hence affecting ligand access and binding. It is likely that these structural alterations in CYP2C19 proteins have caused ligand-specific alteration in catalytic and inhibitory specificities as observed in the in vitro assays. Conclusion: This study indicates that CYP2C19 variant selectivity for ligands was not solely governed by mutation-induced modifications in the active site architecture, but the intrinsic properties of the probe compounds also played a vital role.

Download Full-text