Crystal structure of human cytochrome P450 2C9 with bound warfarin

Abstract

Cytochrome P450 proteins (CYP450s) are membrane-associated haem proteins that metabolize physiologically important compounds in many species of microorganisms, plants and animals. Mammalian CYP450s recognize and metabolize diverse xenobiotics such as drug molecules, environmental compounds and pollutants. Human CYP450 proteins CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4 are the major drug-metabolizing isoforms, and contribute to the oxidative metabolism of more than 90% of the drugs in current clinical use. Polymorphic variants have also been reported for some CYP450 isoforms, which has implications for the efficacy of drugs in individuals, and for the co-administration of drugs. The molecular basis of drug recognition by human CYP450s, however, has remained elusive. Here we describe the crystal structure of a human CYP450, CYP2C9, both unliganded and in complex with the anti-coagulant drug warfarin. The structure defines unanticipated interactions between CYP2C9 and warfarin, and reveals a new binding pocket. The binding mode of warfarin suggests that CYP2C9 may undergo an allosteric mechanism during its function. The newly discovered binding pocket also suggests that CYP2C9 may simultaneously accommodate multiple ligands during its biological function, and provides a possible molecular basis for understanding complex drug-drug interactions.

Combining Computational and Biochemical Studies for a Rationale on the Anti‐Aromatase Activity of Natural Polyphenols

“…One of these models was proposed by Favia et al [20] (PDB code 1TQA from the theoretical model section) using the human cytochrome P450 2C9 as template. [27] This model was used in the current study to predict possible binding modes for the compounds under evaluation by using MIFs calculated within the active site with appropriate probes, and the results obtained were compared with the 3D QSAR virtual receptor site. DRY (hydrophobic) and OH (aromatic hydroxy group) probes were initially computed.…”

A comparison of substrate dynamics in human CYP2E1 and CYP2A6

“…Interestingly, the static crystal structures of modified human CYPs have provided insight into the dynamic nature of the CYPs. In some structures the substrate is positioned so far away from the heme that some motion or translation by the substrate and/or protein is required for substrate oxidation [5]. In other cases, the structural changes observed in comparisons of the substratefree versus substrate-bound structures are indicative of significant protein motion [6;7].…”

Conformational dynamics in the F/G segment of CYP51 from Mycobacterium tuberculosis monitored by FRET

“…Contrary to the P450s mentioned above, in the structure of MTCYP51 (ligand free [1h5z] versus inhibitor bound (4-phenylimidazole [1e9x], fluconazole [1ea1]) or the estriol (substrate analog) bound form [1×8v]) the BC and FG loop regions are superimposed very well, with the exception of the C-terminal part of the BC-loop, which is not seen in the ligand-free and estriol-bound MTCYP51; the active site volume remaining the largest amongst known P450 structures, 2,600 Å 3 [14]. For comparison, the calculated active site volumes of some other CYPs are: 256 and 264 Å 3 for cytochrome P450cin (CYP176A) and cytochrome P450cam (CYP101) [15]), 645 Å 3 for CYP2C5 [16], 670Å 3 for CYP2C9 [17], 1440 Å 3 for CYP2C8 [18] and 520 to 1386 Å 3 for CYP3A4 [19 and 20, respectively]. An assumption that the distant location of the F/G segment (~30 Å from the heme iron) may be largely preserved in the substrate-bound sterol 14α-demethylase suggested that substrate recognition sites (SRS) 2 and 3 [21] in this CYP family (or perhaps particularly in MTCYP51) might be non-functional [22].…”