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Yamazaki S, Hishinuma E, Suzuki Y, Ueda A, Kijogi C, Nakayoshi T, Oda A, Saito S, Tadaka S, Kinoshita K, Maekawa M, Sato Y, Kumondai M, Mano N, Hirasawa N, Hiratsuka M. Functional significance of CYP2B6 gene rare allelic variants identified in Japanese individuals. Biochem Pharmacol 2024; 229:116515. [PMID: 39218044 DOI: 10.1016/j.bcp.2024.116515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/12/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Cytochrome P450 2B6 (CYP2B6) catalyzes the metabolism of many drugs, including efavirenz and propofol. Genetic polymorphisms in CYP2B6 alter its enzymatic activity and substantially affect its pharmacokinetics. High-frequency variants, such as CYP2B6*6, are associated with the risk of developing side effects due to reduced CYP2B6 activity. However, the impact of rare alterations on enzyme function remains unknown, and some of these variants may significantly decrease the CYP2B6 activity. Therefore, in this study, we evaluated in vitro the functional alterations in 29 missense variants of the CYP2B6 gene identified in 8,380 Japanese individuals. Wild-type CYP2B6 and 29 rare CYP2B6 variants were transiently expressed in mammalian cells. The expression levels of variant CYP2B6 proteins in the microsomal fractions extracted from 293FT cells were assessed using western blotting and reduced-carbon monoxide difference spectroscopy, and a specific peak at 450 nm was detected in the wild-type and 19 variants. Furthermore, kinetic parameters were determined by assaying the reactions with efavirenz and propofol and quantifying the metabolite concentrations. We found that 12 variants had significantly lower or abolished enzymatic activity with both the substrates. In silico three-dimensional docking and molecular-dynamics simulations suggested that these functional changes were due to conformational changes in essential regions, such as the heme-binding site and ligand channels involved in transporting substrates to the active site. These findings have implications for predicting the plasma concentrations of CYP2B6 substrates and controlling their side effects.
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Affiliation(s)
- Shuki Yamazaki
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Yuma Suzuki
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Akiko Ueda
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan
| | - Caroline Kijogi
- Research Center for Pharmaceutical Development, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Tomoki Nakayoshi
- Graduate School of Information Sciences, Hiroshima City University, Hiroshima 731-3194, Japan; Department of Pharmacy, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan
| | - Akifumi Oda
- Department of Pharmacy, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan
| | - Sakae Saito
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Shu Tadaka
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; Graduate School of Information Sciences, Tohoku University, Sendai 980-8575, Japan
| | - Masamitsu Maekawa
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Yu Sato
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Masaki Kumondai
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan.
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2
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Massively parallel characterization of CYP2C9 variant enzyme activity and abundance. Am J Hum Genet 2021; 108:1735-1751. [PMID: 34314704 DOI: 10.1016/j.ajhg.2021.07.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/28/2021] [Indexed: 12/19/2022] Open
Abstract
CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these therapeutics. In particular, the anti-coagulant warfarin is prescribed to over 15 million people annually and polymorphisms in CYP2C9 can affect individual drug response and lead to an increased risk of hemorrhage. We developed click-seq, a pooled yeast-based activity assay, to test thousands of variants. Using click-seq, we measured the activity of 6,142 missense variants in yeast. We also measured the steady-state cellular abundance of 6,370 missense variants in a human cell line by using variant abundance by massively parallel sequencing (VAMP-seq). These data revealed that almost two-thirds of CYP2C9 variants showed decreased activity and that protein abundance accounted for half of the variation in CYP2C9 function. We also measured activity scores for 319 previously unannotated human variants, many of which may have clinical relevance.
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Cytochrome P450 2C9 polymorphism: Effect of amino acid substitutions on protein flexibility in the presence of tamoxifen. Comput Biol Chem 2020; 84:107166. [DOI: 10.1016/j.compbiolchem.2019.107166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/29/2019] [Accepted: 11/14/2019] [Indexed: 01/21/2023]
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4
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Multiple drug binding modes in Mycobacterium tuberculosis CYP51B1. J Inorg Biochem 2020; 205:110994. [PMID: 31982812 DOI: 10.1016/j.jinorgbio.2020.110994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/08/2023]
Abstract
The Mycobacterium tuberculosis (Mtb) genome encodes 20 different cytochrome P450 enzymes (CYPs), many of which serve essential biosynthetic roles. CYP51B1, the Mtb version of eukaryotic sterol demethylase, remains a potential therapeutic target. The binding of three drug fragments containing nitrogen heterocycles to CYP51B1 is studied here by continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) techniques to determine how each drug fragment binds to the heme active-site. All three drug fragments form a mixture of complexes, some of which retain the axial water ligand from the resting state. Hyperfine sublevel correlation spectroscopy (HYSCORE) and electron-nuclear double resonance spectroscopy (ENDOR) observe protons of the axial water and on the drug fragments that reveal drug binding modes. Binding in CYP51B1 is complicated by the presence of multiple binding modes that coexist in the same solution. These results aid our understanding of CYP-inhibitor interactions and will help guide future inhibitor design.
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Quiroga I, Scior T. Induced fit for cytochrome P450 3A4 based on molecular dynamics. ADMET AND DMPK 2019; 7:252-266. [PMID: 35359616 PMCID: PMC8963583 DOI: 10.5599/admet.729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/19/2019] [Indexed: 11/18/2022] Open
Abstract
The present study aims at numerically describing to what extent substrate - enzyme complexes in solution may change over time as a natural process of conformational changes for a liganded enzyme in comparison to those movements which occur independently from substrate interaction, i.e. without a ligand. To this end, we selected structurally known pairs of liganded / unliganded CYP450 3A4 enzymes with different geometries hinting at induced fit events. We carried out molecular dynamics simulations (MD) comparing the trajectories in a "cross-over" protocol: (i) we added the ligand to the unliganded crystal form which should adopt geometries similar to the known geometry of the liganded crystal structure during MD, and - conversely - (ii) we removed the bound ligand form the known liganded complex to test if a geometry similar to the known unliganded (apo-) form can be adopted during MD. To compare continues changes we measured root means square deviations and frequencies. Results for case (i) hint at larger conformational changes required for accepting the substrate during its approach to final position - in contrast to case (ii) when mobility is fairly reduced by ligand binding (strain energy). In conclusion, a larger conformational sampling prior to ligand binding and the freezing-in (rigidity) of conformations for bound ligands can be interpreted as two conditions linked to induced-fit.
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Affiliation(s)
- Israel Quiroga
- Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Pue., Mexico
| | - Thomas Scior
- Faculty of Chemical Sciences, Benemérita Universidad Autónoma de Puebla, Puebla, Pue., Mexico
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6
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Louet M, Labbé CM, Fagnen C, Aono CM, Homem-de-Mello P, Villoutreix BO, Miteva MA. Insights into molecular mechanisms of drug metabolism dysfunction of human CYP2C9*30. PLoS One 2018; 13:e0197249. [PMID: 29746595 PMCID: PMC5944999 DOI: 10.1371/journal.pone.0197249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/30/2018] [Indexed: 12/17/2022] Open
Abstract
Cytochrome P450 2C9 (CYP2C9) metabolizes about 15% of clinically administrated drugs. The allelic variant CYP2C9*30 (A477T) is associated to diminished response to the antihypertensive effects of the prodrug losartan and affected metabolism of other drugs. Here, we investigated molecular mechanisms involved in the functional consequences of this amino-acid substitution. Molecular dynamics (MD) simulations performed for the active species of the enzyme (heme in the Compound I state), in the apo or substrate-bound state, and binding energy analyses gave insights into altered protein structure and dynamics involved in the defective drug metabolism of human CYP2C9.30. Our data revealed an increased rigidity of the key Substrate Recognition Sites SRS1 and SRS5 and shifting of the β turn 4 of SRS6 toward the helix F in CYP2C9.30. Channel and binding substrate dynamics analyses showed altered substrate channel access and active site accommodation. These conformational and dynamic changes are believed to be involved in the governing mechanism of the reduced catalytic activity. An ensemble of representative conformations of the WT and A477T mutant properly accommodating drug substrates were identified, those structures can be used for prediction of new CYP2C9 and CYP2C9.30 substrates and drug-drug interactions.
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Affiliation(s)
- Maxime Louet
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
| | - Céline M. Labbé
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
| | - Charline Fagnen
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
- Université Pierre et Marie Curie, Sorbonne Universités, UMR 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Paris, France
| | - Cassiano M. Aono
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Santo André, Brazil
| | - Paula Homem-de-Mello
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas, Santo André, Brazil
| | - Bruno O. Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
| | - Maria A. Miteva
- Université Paris Diderot, Sorbonne Paris Cité, Inserm UMR-S 973, Molécules Thérapeutiques In silico, Paris, France
- INSERM, U973, Paris, France
- * E-mail:
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7
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Lockart MM, Rodriguez CA, Atkins WM, Bowman MK. CW EPR parameters reveal cytochrome P450 ligand binding modes. J Inorg Biochem 2018. [PMID: 29530595 DOI: 10.1016/j.jinorgbio.2018.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cytochrome P450 (CYP) monoxygenses utilize heme cofactors to catalyze oxidation reactions. They play a critical role in metabolism of many classes of drugs, are an attractive target for drug development, and mediate several prominent drug interactions. Many substrates and inhibitors alter the spin state of the ferric heme by displacing the heme's axial water ligand in the resting enzyme to yield a five-coordinate iron complex, or they replace the axial water to yield a nitrogen-ligated six-coordinate iron complex, which are traditionally assigned by UV-vis spectroscopy. However, crystal structures and recent pulsed electron paramagnetic resonance (EPR) studies find a few cases where molecules hydrogen bond to the axial water. The water-bridged drug-H2O-heme has UV-vis spectra similar to nitrogen-ligated, six-coordinate complexes, but are closer to "reverse type I" complexes described in older liteature. Here, pulsed and continuous wave (CW) EPR demonstrate that water-bridged complexes are remarkably common among a range of nitrogenous drugs or drug fragments that bind to CYP3A4 or CYP2C9. Principal component analysis reveals a distinct clustering of CW EPR spectral parameters for water-bridged complexes. CW EPR reveals heterogeneous mixtures of ligated states, including multiple directly-coordinated complexes and water-bridged complexes. These results suggest that water-bridged complexes are under-represented in CYP structural databases and can have energies similar to other ligation modes. The data indicates that water-bridged binding modes can be identified and distinguished from directly-coordinated binding by CW EPR.
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Affiliation(s)
- Molly M Lockart
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States
| | - Carlo A Rodriguez
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States
| | - William M Atkins
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA 98195-7610, United States
| | - Michael K Bowman
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States.
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8
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Daly AK, Rettie AE, Fowler DM, Miners JO. Pharmacogenomics of CYP2C9: Functional and Clinical Considerations. J Pers Med 2017; 8:E1. [PMID: 29283396 PMCID: PMC5872075 DOI: 10.3390/jpm8010001] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023] Open
Abstract
CYP2C9 is the most abundant CYP2C subfamily enzyme in human liver and the most important contributor from this subfamily to drug metabolism. Polymorphisms resulting in decreased enzyme activity are common in the CYP2C9 gene and this, combined with narrow therapeutic indices for several key drug substrates, results in some important issues relating to drug safety and efficacy. CYP2C9 substrate selectivity is detailed and, based on crystal structures for the enzyme, we describe how CYP2C9 catalyzes these reactions. Factors relevant to clinical response to CYP2C9 substrates including inhibition, induction and genetic polymorphism are discussed in detail. In particular, we consider the issue of ethnic variation in pattern and frequency of genetic polymorphisms and clinical implications. Warfarin is the most well studied CYP2C9 substrate; recent work on use of dosing algorithms that include CYP2C9 genotype to improve patient safety during initiation of warfarin dosing are reviewed and prospects for their clinical implementation considered. Finally, we discuss a novel approach to cataloging the functional capabilities of rare 'variants of uncertain significance', which are increasingly detected as more exome and genome sequencing of diverse populations is conducted.
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Affiliation(s)
- Ann K Daly
- Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Douglas M Fowler
- Department of Genome Sciences and Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - John O Miners
- Department of Clinical Pharmacology, Flinders University School of Medicine, Adelaide 5042, Australia.
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9
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Lockhart CM, Smith TB, Yang P, Naidu M, Rettie AE, Nath A, Weleber R, Kelly EJ. Longitudinal characterisation of function and structure of Bietti crystalline dystrophy: report on a novel homozygous mutation in CYP4V2. Br J Ophthalmol 2017; 102:187-194. [PMID: 28698241 DOI: 10.1136/bjophthalmol-2016-309696] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/03/2017] [Accepted: 05/06/2017] [Indexed: 01/11/2023]
Abstract
BACKGROUND Bietti crystalline dystrophy (BCD) is a rare inherited disorder characterised by fine crystalline deposits in the corneal limbus and retinal posterior pole. In 2004, mutations in the CYP4V2 gene were identified as the cause of BCD. Here, we describe the report of a homozygous point mutation in a patient with BCD and provide detailed characterisation of functional and structural changes over 20 years. METHODS At regular intervals, the patient underwent repeat ophthalmic evaluations. DNA was extracted from buccal swabs, amplified by standard PCR and analysed for homology to the CYP4V2 sequence. Homology modelling was conducted using Iterative Threading ASSEmbly Refinement and molecular dynamics simulations using GROningen MAchine for Chemical Simulations. RESULTS The proband, a 47-year-old woman of German ancestry was diagnosed with crystalline retinopathy at age 25. Over the next 20 years, visual acuity and function gradually declined with progression of retinal pigment epithelium and choroidal atrophy. When first tested at 39 years of age, the multifocal electroretinogram (ERG) was markedly abnormal, more so for the right eye, whereas the full-field ERG was more symmetrical and lagged other measures of visual function. Gene sequencing showed a single C>T point mutation in exon 9 encoding a R400C amino acid change. Computational modelling suggests the mutation impairs function due to loss of a hydrogen bonding interaction with the propionate side chains of the haeme prosthetic group. CONCLUSION This is the first report of a homozygous R400C mutation in CYP4V2 with protein modelling showing high likelihood of enzyme dysfunction. The comprehensive long-term clinical follow-up provides insight into disease progression and highlights possible anti-inflammatory modulation of disease severity.
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Affiliation(s)
| | - Travis B Smith
- Casey Eye Institute, Oregon Health Sciences University, Portland, Oregon, USA
| | - Paul Yang
- Casey Eye Institute, Oregon Health Sciences University, Portland, Oregon, USA
| | - Malini Naidu
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Abhinav Nath
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Richard Weleber
- Casey Eye Institute, Oregon Health Sciences University, Portland, Oregon, USA
| | - Edward J Kelly
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
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Vazquez-Albacete D, Montefiori M, Kol S, Motawia MS, Møller BL, Olsen L, Nørholm MHH. The CYP79A1 catalyzed conversion of tyrosine to (E)-p-hydroxyphenylacetaldoxime unravelled using an improved method for homology modeling. PHYTOCHEMISTRY 2017; 135:8-17. [PMID: 28088302 DOI: 10.1016/j.phytochem.2016.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/01/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin. Docking experiments identified key regions of the active site involved in binding of the substrate and facilitating catalysis. Arginine 152 and threonine 534 were identified as key residues interacting with the substrate. The model was validated experimentally using site-directed mutagenesis. The new CYP79A1 model provides detailed insights into the mechanism of the initial steps in cyanogenic glycoside biosynthesis. The approach could guide functional characterization of other membrane-bound P450s and provide structural guidelines for elucidation of key structure-function relationships of other plant P450s.
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Affiliation(s)
- Dario Vazquez-Albacete
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Marco Montefiori
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Lars Olsen
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark.
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11
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Reed JR, Backes WL. Physical Studies of P450-P450 Interactions: Predicting Quaternary Structures of P450 Complexes in Membranes from Their X-ray Crystal Structures. Front Pharmacol 2017; 8:28. [PMID: 28194112 PMCID: PMC5276844 DOI: 10.3389/fphar.2017.00028] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/16/2017] [Indexed: 01/15/2023] Open
Abstract
Cytochrome P450 enzymes, which catalyze oxygenation reactions of both exogenous and endogenous chemicals, are membrane bound proteins that require interaction with their redox partners in order to function. Those responsible for drug and foreign compound metabolism are localized primarily in the endoplasmic reticulum of liver, lung, intestine, and other tissues. More recently, the potential for P450 enzymes to exist as supramolecular complexes has been shown by the demonstration of both homomeric and heteromeric complexes. The P450 units in these complexes are heterogeneous with respect to their distribution and function, and the interaction of different P450s can influence P450-specific metabolism. The goal of this review is to examine the evidence supporting the existence of physical complexes among P450 enzymes. Additionally, the review examines the crystal lattices of different P450 enzymes derived from X-ray diffraction data to make assumptions regarding possible quaternary structures in membranes and in turn, to predict how the quaternary structures could influence metabolism and explain the functional effects of specific P450-P450 interactions.
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Affiliation(s)
- James R Reed
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
| | - Wayne L Backes
- Department of Pharmacology and Experimental Therapeutics, Louisiana State University Health Sciences Center New Orleans LA, USA
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12
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Krzyaniak MD, Cruce AA, Vennam P, Lockart M, Berka V, Tsai AL, Bowman MK. The tetrahydrobiopterin radical interacting with high- and low-spin heme in neuronal nitric oxide synthase - A new indicator of the extent of NOS coupling. Free Radic Biol Med 2016; 101:367-377. [PMID: 27989753 PMCID: PMC5362310 DOI: 10.1016/j.freeradbiomed.2016.10.503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 10/07/2016] [Accepted: 10/26/2016] [Indexed: 01/10/2023]
Abstract
Reaction intermediates trapped during the single-turnover reaction of the neuronal ferrous nitric oxide synthase oxygenase domain (Fe(II)nNOSOX) show four EPR spectra of free radicals. Fully-coupled nNOSOX with cofactor (tetrahydrobiopterin, BH4) and substrate (l-arginine) forms the typical BH4 cation radical with an EPR spectrum ~4.0mT wide and hyperfine tensors similar to reports for a biopterin cation radical in inducible NOSOX (iNOSOX). With excess thiol, nNOSox lacking BH4 and l-arg is known to produce superoxide. In contrast, we find that nNOSOX with BH4 but no l-arg forms two radicals with rather different, fast (~250μs at 5K) and slower (~500μs at 20K), electron spin relaxation rates and a combined ~7.0mT wide EPR spectrum. Rapid freeze-quench CW- and pulsed-EPR measurements are used to identify these radicals and their origin. These two species are the same radical with identical nuclear hyperfine couplings, but with spin-spin couplings to high-spin (4.0mT component) or low-spin (7.0mT component) Fe(III) heme. Uncoupled reactions of nNOS leave the enzyme in states that can be chemically reduced to sustain unregulated production of NO and reactive oxygen species in ischemia-reperfusion injury. The broad EPR signal is a convenient indicator of uncoupled nNOS reactions producing low-spin Fe(III) heme.
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Affiliation(s)
- Matthew D Krzyaniak
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Alex A Cruce
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Preethi Vennam
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Molly Lockart
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Vladimir Berka
- Division of Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ah-Lim Tsai
- Division of Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Michael K Bowman
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA.
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13
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Bostick CD, Hickey KM, Wollenberg LA, Flora DR, Tracy TS, Gannett PM. Immobilized Cytochrome P450 for Monitoring of P450-P450 Interactions and Metabolism. ACTA ACUST UNITED AC 2016; 44:741-9. [PMID: 26961240 DOI: 10.1124/dmd.115.067637] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/09/2016] [Indexed: 11/22/2022]
Abstract
Cytochrome P450 (P450) protein-protein interactions have been shown to alter their catalytic activity. Furthermore, these interactions are isoform specific and can elicit activation, inhibition, or no effect on enzymatic activity. Studies show that these effects are also dependent on the protein partner cytochrome P450 reductase (CPR) and the order of protein addition to purified reconstituted enzyme systems. In this study, we use controlled immobilization of P450s to a gold surface to gain a better understanding of P450-P450 interactions between three key drug-metabolizing isoforms (CYP2C9, CYP3A4, and CYP2D6). Molecular modeling was used to assess the favorability of homomeric/heteromeric P450 complex formation. P450 complex formation in vitro was analyzed in real time utilizing surface plasmon resonance. Finally, the effects of P450 complex formation were investigated utilizing our immobilized platform and reconstituted enzyme systems. Molecular modeling shows favorable binding of CYP2C9-CPR, CYP2C9-CYP2D6, CYP2C9-CYP2C9, and CYP2C9-CYP3A4, in rank order.KDvalues obtained via surface plasmon resonance show strong binding, in the nanomolar range, for the above pairs, with CYP2C9-CYP2D6 yielding the lowestKD, followed by CYP2C9-CYP2C9, CYP2C9-CPR, and CYP2C9-CYP3A4. Metabolic incubations show that immobilized CYP2C9 metabolism was activated by homomeric complex formation. CYP2C9 metabolism was not affected by the presence of CYP3A4 with saturating CPR concentrations. CYP2C9 metabolism was activated by CYP2D6 at saturating CPR concentrations in solution but was inhibited when CYP2C9 was immobilized. The order of addition of proteins (CYP2C9, CYP2D6, CYP3A4, and CPR) influenced the magnitude of inhibition for CYP3A4 and CYP2D6. These results indicate isoform-specific P450 interactions and effects on P450-mediated metabolism.
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Affiliation(s)
- Chris D Bostick
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Katherine M Hickey
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Lance A Wollenberg
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Darcy R Flora
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Timothy S Tracy
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
| | - Peter M Gannett
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, West Virginia (C.D.B., K.M.H.); Array BioPharma, Boulder, Colorado (L.A.W.); Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota (D.R.F.); College of Pharmacy, University of Kentucky, Lexington, Kentucky (T.S.T.); and Department of Pharmaceutical Sciences, College of Pharmacy, Nova Southeastern University, Ft. Lauderdale, Florida (P.M.G.)
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Conner KP, Cruce AA, Krzyaniak MD, Schimpf AM, Frank DJ, Ortiz de Montellano P, Atkins WM, Bowman MK. Drug modulation of water-heme interactions in low-spin P450 complexes of CYP2C9d and CYP125A1. Biochemistry 2015; 54:1198-207. [PMID: 25591012 DOI: 10.1021/bi501402k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Azoles and pyridines are commonly incorporated into small molecule inhibitor scaffolds that target cytochromes P450 (CYPs) as a strategy to increase drug binding affinity, impart isoform-dependent selectivity, and improve metabolic stability. Optical absorbance spectra of the CYP-inhibitor complex are widely used to infer whether these inhibitors are ligated directly to the heme iron as catalytically inert, low-spin (type II) complexes. Here, we show that the low-spin complex between a drug-metabolizing CYP2C9 variant and 4-(3-phenylpropyl)-1H-1,2,3-triazole (PPT) retains an axial water ligand despite exhibiting elements of "classic" type II optical behavior. Hydrogens of the axial water ligand are observed by pulsed electron paramagnetic resonance (EPR) spectroscopy for both inhibitor-free and inhibitor-bound species and show that inhibitor binding does not displace the axial water. A (15)N label incorporated into PPT is 0.444 nm from the heme iron, showing that PPT is also in the active site. The reverse type I inhibitor, LP10, of CYP125A1 from Mycobacterium tuberculosis, known from X-ray crystal structures to form a low-spin water-bridged complex, is found by EPR and by visible and near-infrared magnetic circular dichroism spectroscopy to retain the axial water ligand in the complex in solution.
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Affiliation(s)
- Kip P Conner
- Department of Medicinal Chemistry, Box 357610, and Department of Chemistry, Box 351700, University of Washington , Seattle, Washington 98195, United States
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16
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Kubrycht J, Sigler K, Souček P, Hudeček J. Structures composing protein domains. Biochimie 2013; 95:1511-24. [DOI: 10.1016/j.biochi.2013.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/02/2013] [Indexed: 12/21/2022]
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Cheesman MJ, Traylor MJ, Hilton ME, Richards KE, Taylor MC, Daborn PJ, Russell RJ, Gillam EMJ, Oakeshott JG. Soluble and membrane-bound Drosophila melanogaster CYP6G1 expressed in Escherichia coli: purification, activity, and binding properties toward multiple pesticides. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:455-465. [PMID: 23470655 DOI: 10.1016/j.ibmb.2013.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/11/2013] [Accepted: 02/12/2013] [Indexed: 06/01/2023]
Abstract
Cytochrome P450 CYP6G1 has been implicated in the resistance of Drosophila melanogaster to numerous pesticides. While in vivo and in vitro studies have provided insight to the diverse functions of this enzyme, direct studies on the isolated CYP6G1 enzyme have not been possible due to the need for a source of recombinant enzyme. In the current study, the Cyp6g1 gene was isolated from D. melanogaster and re-engineered for heterologous expression in Escherichia coli. Approximately 460 nmol L⁻¹ of P450 holoenzyme were obtained in 500 mL cultures. The recombinant enzyme was located predominantly within the bacterial cytosol. A two-step purification protocol using Ni-chelate affinity chromatography followed by removal of detergent on a hydroxyapatite column produced essentially homogenous enzyme from both soluble and membrane fractions. Recombinant CYP6G1 exhibited p-nitroanisole O-dealkylation activity but was not active against eleven other typical P450 marker substrates. Substrate-induced binding spectra and IC₅₀ values for inhibition of p-nitroanisole O-dealkylation were obtained for a wide selection of pesticides, namely DDT, imidacloprid, chlorfenvinphos, malathion, endosulfan, dieldrin, dicyclanil, lufenuron and carbaryl, supporting previous in vivo and in vitro studies on Drosophila that have suggested that the enzyme is involved in multi-pesticide resistance in insects.
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Affiliation(s)
- Matthew J Cheesman
- CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, Australian Capital Territory 2601, Australia.
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Conner KP, Vennam P, Woods CM, Krzyaniak MD, Bowman MK, Atkins WM. 1,2,3-Triazole-heme interactions in cytochrome P450: functionally competent triazole-water-heme complexes. Biochemistry 2012; 51:6441-57. [PMID: 22809252 DOI: 10.1021/bi300744z] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In comparison to imidazole (IMZ) and 1,2,4-triazole (1,2,4-TRZ), the isosteric 1,2,3-triazole (1,2,3-TRZ) is unrepresented among cytochrome P450 (CYP) inhibitors. This is surprising because 1,2,3-TRZs are easily obtained via "click" chemistry. To understand this underrepresentation of 1,2,3-TRZs among CYP inhibitors, thermodynamic and density functional theory computational studies were performed with unsubstituted IMZ, 1,2,4-TRZ, and 1,2,3-TRZ. The results indicate that the lower affinity of 1,2,3-TRZ for the heme iron includes a large unfavorable entropy term likely originating in solvent-1,2,3-TRZ interactions; the difference is not solely due to differences in the enthalpy of heme-ligand interactions. In addition, the 1,2,3-TRZ fragment was incorporated into a well-established CYP3A4 substrate and mechanism-based inactivator, 17-α-ethynylestradiol (17EE), via click chemistry. This derivative, 17-click, yielded optical spectra consistent with low-spin ferric heme iron (type II) in contrast to 17EE, which yields a high-spin complex (type I). Furthermore, the rate of CYP3A4-mediated metabolism of 17-click was comparable to that of 17EE, with a different regioselectivity. Surprisingly, continuous-wave electron paramagnetic resonance (EPR) and HYSCORE EPR spectroscopy indicate that 17-click does not displace water from the sixth axial ligand position of CYP3A4 as expected for a type II ligand. We propose a binding model in which 17-click pendant 1,2,3-TRZ hydrogen bonds with the sixth axial water ligand. The results demonstrate the potential for 1,2,3-TRZ to form metabolically labile water-bridged low-spin heme complexes, consistent with recent evidence that nitrogenous type II ligands of CYPs can be efficiently metabolized. The specific case of [CYP3A4·17-click] highlights the risk of interpreting CYP-ligand complex structure on the basis of optical spectra.
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Affiliation(s)
- Kip P Conner
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA 98195-7610, USA
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Kirchmair J, Williamson MJ, Tyzack JD, Tan L, Bond PJ, Bender A, Glen RC. Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model 2012; 52:617-48. [PMID: 22339582 PMCID: PMC3317594 DOI: 10.1021/ci200542m] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
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Metabolism of xenobiotics remains a central challenge
for the discovery
and development of drugs, cosmetics, nutritional supplements, and
agrochemicals. Metabolic transformations are frequently related to
the incidence of toxic effects that may result from the emergence
of reactive species, the systemic accumulation of metabolites, or
by induction of metabolic pathways. Experimental investigation of
the metabolism of small organic molecules is particularly resource
demanding; hence, computational methods are of considerable interest
to complement experimental approaches. This review provides a broad
overview of structure- and ligand-based computational methods for
the prediction of xenobiotic metabolism. Current computational approaches
to address xenobiotic metabolism are discussed from three major perspectives:
(i) prediction of sites of metabolism (SOMs), (ii) elucidation of
potential metabolites and their chemical structures, and (iii) prediction
of direct and indirect effects of xenobiotics on metabolizing enzymes,
where the focus is on the cytochrome P450 (CYP) superfamily of enzymes,
the cardinal xenobiotics metabolizing enzymes. For each of these domains,
a variety of approaches and their applications are systematically
reviewed, including expert systems, data mining approaches, quantitative
structure–activity relationships (QSARs), and machine learning-based
methods, pharmacophore-based algorithms, shape-focused techniques,
molecular interaction fields (MIFs), reactivity-focused techniques,
protein–ligand docking, molecular dynamics (MD) simulations,
and combinations of methods. Predictive metabolism is a developing
area, and there is still enormous potential for improvement. However,
it is clear that the combination of rapidly increasing amounts of
available ligand- and structure-related experimental data (in particular,
quantitative data) with novel and diverse simulation and modeling
approaches is accelerating the development of effective tools for
prediction of in vivo metabolism, which is reflected by the diverse
and comprehensive data sources and methods for metabolism prediction
reviewed here. This review attempts to survey the range and scope
of computational methods applied to metabolism prediction and also
to compare and contrast their applicability and performance.
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Affiliation(s)
- Johannes Kirchmair
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
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Exploration of the binding of curcumin analogues to human P450 2C9 based on docking and molecular dynamics simulation. J Mol Model 2011; 18:2599-611. [DOI: 10.1007/s00894-011-1275-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 10/09/2011] [Indexed: 11/26/2022]
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Cojocaru V, Balali-Mood K, Sansom MSP, Wade RC. Structure and dynamics of the membrane-bound cytochrome P450 2C9. PLoS Comput Biol 2011; 7:e1002152. [PMID: 21852944 PMCID: PMC3154944 DOI: 10.1371/journal.pcbi.1002152] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/18/2011] [Indexed: 11/21/2022] Open
Abstract
The microsomal, membrane-bound, human cytochrome P450 (CYP) 2C9 is a liver-specific monooxygenase essential for drug metabolism. CYPs require electron transfer from the membrane-bound CYP reductase (CPR) for catalysis. The structural details and functional relevance of the CYP-membrane interaction are not understood. From multiple coarse grained molecular simulations started with arbitrary configurations of protein-membrane complexes, we found two predominant orientations of CYP2C9 in the membrane, both consistent with experiments and conserved in atomic-resolution simulations. The dynamics of membrane-bound and soluble CYP2C9 revealed correlations between opening and closing of different tunnels from the enzyme's buried active site. The membrane facilitated the opening of a tunnel leading into it by stabilizing the open state of an internal aromatic gate. Other tunnels opened selectively in the simulations of product-bound CYP2C9. We propose that the membrane promotes binding of liposoluble substrates by stabilizing protein conformations with an open access tunnel and provide evidence for selective substrate access and product release routes in mammalian CYPs. The models derived here are suitable for extension to incorporate other CYPs for oligomerization studies or the CYP reductase for studies of the electron transfer mechanism, whereas the modeling procedure is generally applicable to study proteins anchored in the bilayer by a single transmembrane helix. We describe the first atomic-detail models and simulations of a full-length, membrane-bound mammalian cytochrome P450. To date, all the structural studies of microsomal, drug-metabolizing cytochrome P450s have been performed using engineered, solubilized forms of the enzymes and it is not yet understood how the membrane influences their structure, dynamics, and ability to bind substrates. We focused on CYP2C9, the second most abundant cytochrome P450 in the human liver which oxidizes 20% of all marketed drugs. Here, we have derived models of CYP2C9-membrane complexes with a modeling procedure based on molecular dynamics simulations started with arbitrary configurations of the protein in the membrane and performed using both coarse grained and atomic-detail molecular representations. This procedure is expected to be generally applicable to proteins that are anchored in the membrane with a single transmembrane helix. The models and simulations provide evidence for selective substrate access and product release routes in membrane-bound CYPs. This observation may contribute to new strategies to manipulate the activity of CYPs and other enzymes with buried active sites. We anticipate that this study will bring about a paradigm shift towards studying microsomal CYPs as dynamic structures in their natural, lipid environment rather than in artificially solubilized forms.
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Affiliation(s)
- Vlad Cojocaru
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- * E-mail: (VC); (RCW)
| | - Kia Balali-Mood
- Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Mark S. P. Sansom
- Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Rebecca C. Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- * E-mail: (VC); (RCW)
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