The long-term goal of this project is to elucidate the interrelationships between the structure and conformational dynamics of cytochrome P450 enzymes, their catalytic mechanisms, and the consequences of these interactions in terms of catalytic outcome and substrate specificity. The phase of the work proposed here has three major goals: (a) To utilize NMR and fluorescent probes to elucidate the conformational range of bacterial P450 enzymes and the nature of the environment in the vicinity of the thiolate-iron ligand;(b) to investigate the mechanisms by which mutations distant from the active site alter the catalytic process, focusing on the possible role of coupled protein motions and conformational links;(c) to further stabilize the monomeric state of solubilized human P450 enzymes and to extend the NMR and fluorescent conformational probe studies to these proteins;and (d) to apply cutting edge computational docking techniques to the conformational ensembles emerging from the combined use of molecular dynamics and NMR to construct refined protocols for the prediction and rationalization of cytochrome P450 substrate and inhibitor specificity, focusing initially on CYP2C9 The work proposed in this application rests on a number of technical advances. First, efforts to determine the structures of membrane-bound human P450 enzymes have succeeded in the past decade and more than a dozen P450 enzyme structures in various ligation states are now available. Second, the rapid progress in NMR techniques has allowed us to demonstrate the utility of site-specific NMR probes in conformational analysis of proteins as large as the P450 enzymes. Third, methods for the site-specific incorporation of unnatural and labeled amino acids now make it possible to tag individual positions in a protein with NMR or fluorescent probes. Fourth, advances in computational algorithms and the increase in computer speed now allow long-term molecular dynamics studies and computational docking of flexible ligands in flexible active sites. This is a broad study of the interplay of conformational dynamics and its role in modulating catalysis and determining substrate specificity in a set of enzymes that are notoriously malleable and challenging. The results should have a major impact in the pharmaceutical industry, for which the P450 specificity for a given drug candidate can determine whether it progresses or is discarded. They will also impact the design of inhibitors for P450 enzyme targeted in cancer and other diseases, and the design of P450 catalysts for biotechnological applications. Beyond P450, the conformational issues dealt with in this project and the techniques being explored have broader applicability and will have an impact in completely different areas of biochemistry and biology.

Public Health Relevance

Cytochrome P450 enzymes fulfill critical roles in the metabolism of drugs and environmental chemicals, the biosynthesis of endogenous factors such as the sterol hormones, and the termination of the action of endogenous factors such as retinoic acid. They are of major practical interest because: (a) they are important targets for clinically used antifungal, antiparasitic, and anticancer drugs, (b) they are major determinants of drug pharmacokinetics and drug action, (c) they are responsible for a broad range of metabolism-dependent drug toxicities, and (d) they have high potential as biotechnological catalysts. The ability to predict P450 substrate and inhibitor specificity, and the effect of mutations on catalytic function, is central to all of these areas.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Xenobiotic and Nutrient Disposition and Action Study Section (XNDA)
Program Officer
Okita, Richard T
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Francisco
Schools of Pharmacy
San Francisco
United States
Zip Code
de Montellano, Paul R Ortiz (2018) 1-Aminobenzotriazole: A Mechanism-Based Cytochrome P450 Inhibitor and Probe of Cytochrome P450 Biology. Med Chem (Los Angeles) 8:
Zhao, Yan; Wan, Debin; Yang, Jun et al. (2016) Catalytic Activities of Tumor-Specific Human Cytochrome P450 CYP2W1 Toward Endogenous Substrates. Drug Metab Dispos 44:771-80
Conner, Kip P; Cruce, Alex A; Krzyaniak, Matthew D et al. (2015) Drug modulation of water-heme interactions in low-spin P450 complexes of CYP2C9d and CYP125A1. Biochemistry 54:1198-207
Basudhar, Debashree; Madrona, Yarrow; Kandel, Sylvie et al. (2015) Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography. J Biol Chem 290:10000-17
Varfaj, Fatbardha; Zulkifli, Siti N A; Park, Hyoung-Goo et al. (2014) Carbon-carbon bond cleavage in activation of the prodrug nabumetone. Drug Metab Dispos 42:828-38
Frank, Daniel J; Madrona, Yarrow; Ortiz de Montellano, Paul R (2014) Cholesterol ester oxidation by mycobacterial cytochrome P450. J Biol Chem 289:30417-25
Conner, Kip P; Schimpf, Alina M; Cruce, Alex A et al. (2014) Strength of axial water ligation in substrate-free cytochrome P450s is isoform dependent. Biochemistry 53:1428-34
Nishida, Clinton R; Everett, Steven; Ortiz de Montellano, Paul R (2013) Specificity determinants of CYP1B1 estradiol hydroxylation. Mol Pharmacol 84:451-8
Straub, Wesley E; Nishida, Clinton R; de Montellano, Paul R Ortiz (2013) Expression in Escherichia coli of a cytochrome P450 enzyme with a cobalt protoporphyrin IX prosthetic group. Methods Mol Biol 987:107-13
Ortiz de Montellano, Paul R (2013) Cytochrome P450-activated prodrugs. Future Med Chem 5:213-28

Showing the most recent 10 out of 154 publications