CYP enzymes catalyze the formation of a terminal olefin from 2-ethylhexanoic acid in rat and human liver

Structural and energetic analysis to provide insight residues of CYP2C9, 2C11 and 2E1 involved in valproic acid dehydrogenation selectivity

Docking and molecular dynamics (MD) simulation have been two computational techniques used to gain insight about the substrate orientation within protein active sites, allowing to identify potential residues involved in the binding and catalytic mechanisms. In this study, both methods were combined to predict the regioselectivity in the binding mode of valproic acid (VPA) on three cytochrome P-450 (CYP) isoforms CYP2C9, CYP2C11, and CYP2E1, which are involved in the biotransformation of VPA yielding reactive hepatotoxic intermediate 2-n-propyl-4-pentenoic acid (4nVPA). There are experimental data about hydrogen atom abstraction of the C4-position of VPA to yield 4nVPA, however, there are not structural evidence about the binding mode of VPA and 4nVPA on CYPs. Therefore, the complexes between these CYP isoforms and VPA or 4nVPA were studied to explore their differences in binding and energetic stabilization. Docking results showed that VPA and 4nVPA are coupled into CYPs binding site in a similar conformation, but it does not explain the VPA hydrogen atom abstraction. On the other hand, MD simulations showed a set of energetic states that reorient VPA at the first ns, then making it susceptible to a dehydrogenation reaction. For 4nVPA, multiple binding modes were observed in which the different states could favor either undergo other reaction mechanism or ligand expulsion from the binding site. Otherwise, the energetic and entropic contribution point out a similar behavior for the three CYP complexes, showing as expected a more energetically favorable binding free energy for the complexes between CYPs and VPA than with 4nVPA.

Crystal structure of CYP199A2, a para-substituted benzoic acid oxidizing cytochrome P450 from Rhodopseudomonas palustris

CYP199A2, a cytochrome P450 enzyme from Rhodopseudomonas palustris, oxidatively demethylates 4-methoxybenzoic acid to 4-hydroxybenzoic acid. 4-Ethylbenzoic acid is converted to a mixture of predominantly 4-(1-hydroxyethyl)-benzoic acid and 4-vinylbenzoic acid, the latter being a rare example of CC bond dehydrogenation of an unbranched alkyl group. The crystal structure of CYP199A2 has been determined at 2.0-A resolution. The enzyme has the common P450 fold, but the B' helix is missing and the G helix is broken into two (G and G') by a kink at Pro204. Helices G and G' are bent back from the extended BC loop and the I helix to open up a clearly defined substrate access channel. Channel openings in this region of the P450 fold are rare in bacterial P450 enzymes but more common in eukaryotic P450 enzymes. The channel is hydrophobic except for the basic residue Arg246 at the entrance, which probably plays a role in the specificity of this enzyme for charged benzoates over neutral phenols and benzenes. The substrate binding pocket is hydrophobic, with Ser97 and Ser247 being the only polar residues. Computer docking of 4-ethylbenzoic acid into the active site suggests that the substrate carboxylate oxygens interact with Ser97 and Ser247, and the beta-methyl group is located over the heme iron by Phe185, the side chain of which is only 6.35 A above the iron in the native structure. This binding orientation is consistent with the observed product profile of exclusive attack at the para substituent. Putidaredoxin of the CYP101A1 system from Pseudomonas putida supports substrate oxidation by CYP199A2 at approximately 6% of the activity of the physiological ferredoxin. Comparison of the heme proximal faces of CYP199A2 and CYP101A1 suggests that charge reversal surrounding the surface residue Leu369 in CYP199A2 may be a significant factor in this low cross-activity.

Cytochrome P450-dependent desaturation of lauric acid: isoform selectivity and mechanism of formation of 11-dodecenoic acid

Cytochrome P450-catalyzed desaturation reactions have been reported infrequently in the literature. Previously, we documented the formation of the terminal olefinic metabolite of valproic acid by various members of the CYP2B and CYP4B sub-families. However, despite the extensive use of fatty acid substrates in drug metabolism studies, other examples of terminal desaturation at non-activated carbon centers are lacking. The goals of the present studies were to determine whether the archetypal P450 substrate, lauric acid (dodecanoic acid; DDA), also undergoes desaturation reactions, identify specific rabbit P450 isoforms which catalyze this reaction and examine its mechanism. A highly sensitive, capillary GC/MS assay was developed to separate and quantitate the trimethylsilyl derivatives of 11-ene-DDA, cis- and trans-10-ene-DDA and cis- and trans-9-ene-DDA. Among all of these potential olefinic metabolites, only 11-ene-DDA was formed at a significant rate by rabbit liver microsomes. The formation of 11-ene-DDA was NADPH-dependent, and was induced markedly by acetone pre-treatment, but not by phenobarbital, rifampin or Arochlor 1254. Studies with seven purified, reconstituted rabbit P450 isoforms showed that the most rapid rates of desaturation were obtained with CYP2E1, CYP4A5/7 and CYP4B1. Non-competitive, intermolecular isotope effect experiments, conducted with [12,12,12-2H3]DDA and [11,11-2H2]DDA, demonstrated further that CYP4B1-mediated terminal desaturation of DDA is initiated by removal of a hydrogen atom from the omega-1 rather than the omega position.