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Iori S, Lahtela-Kakkonen M, D'Onofrio C, Maietti F, Mucignat G, Bardhi A, Barbarossa A, Zaghini A, Pauletto M, Dacasto M, Giantin M. New insights into aflatoxin B1 mechanistic toxicology in cattle liver: an integrated approach using molecular docking and biological evaluation in CYP1A1 and CYP3A74 knockout BFH12 cell lines. Arch Toxicol 2024:10.1007/s00204-024-03799-y. [PMID: 38834875 DOI: 10.1007/s00204-024-03799-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
Aflatoxin B1 (AFB1) is a pro-carcinogenic compound bioactivated in the liver by cytochromes P450 (CYPs). In mammals, CYP1A and CYP3A are responsible for AFB1 metabolism, with the formation of the genotoxic carcinogens AFB1-8,9-epoxide and AFM1, and the detoxified metabolite AFQ1. Due to climate change, AFB1 cereals contamination arose in Europe. Thus, cattle, as other farm animals fed with grains (pig, sheep and broiler), are more likely exposed to AFB1 via feed with consequent release of AFM1 in milk, posing a great concern to human health. However, knowledge about bovine CYPs involved in AFB1 metabolism is still scanty. Therefore, CYP1A1- and CYP3A74-mediated molecular mechanisms of AFB1 hepatotoxicity were here dissected. Molecular docking of AFB1 into CYP1A1 model suggested AFB1 8,9-endo- and 8,9-exo-epoxide, and AFM1 formation, while docking of AFB1 into CYP3A74 pointed to AFB1 8,9-exo-epoxide and AFQ1 synthesis. To biologically confirm these predictions, CYP1A1 and CYP3A74 knockout (KO) BFH12 cell lines were exposed to AFB1. LC-MS/MS investigations showed the abolished production of AFM1 in CYP1A1 KO cells and the strong increase of parent AFB1 in CYP3A74 KO cells; the latter result, coupled to a decreased cytotoxicity, suggested the major role of CYP3A74 in AFB1 8,9-exo-epoxide formation. Finally, RNA-sequencing analysis indirectly proved lower AFB1-induced cytotoxic effects in engineered cells versus naïve ones. Overall, this study broadens the knowledge on AFB1 metabolism and hepatotoxicity in cattle, and it provides the weight of evidence that CYP1A1 and CYP3A74 inhibition might be exploited to reduce AFM1 and AFBO synthesis, AFB1 toxicity, and AFM1 milk excretion.
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Affiliation(s)
- Silvia Iori
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Maija Lahtela-Kakkonen
- School of Pharmacy, University of Eastern Finland, Yliopistonrinne 3, 70210, Kuopio, Finland
| | - Caterina D'Onofrio
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Federica Maietti
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Greta Mucignat
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Anisa Bardhi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Andrea Barbarossa
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Anna Zaghini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum University of Bologna, Via Tolara di Sopra 50, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Mauro Dacasto
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy
| | - Mery Giantin
- Department of Comparative Biomedicine and Food Science, University of Padua, Viale Dell'Università 16, Legnaro, 35020, Padua, Italy.
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2
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van Vugt-Lussenburg BMA, Capinha L, Reinen J, Rooseboom M, Kranendonk M, Onderwater RCA, Jennings P. " Commandeuring" Xenobiotic Metabolism: Advances in Understanding Xenobiotic Metabolism. Chem Res Toxicol 2022; 35:1184-1201. [PMID: 35768066 PMCID: PMC9297329 DOI: 10.1021/acs.chemrestox.2c00067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The understanding
of how exogenous chemicals (xenobiotics) are
metabolized, distributed, and eliminated is critical to determine
the impact of the chemical and its metabolites to the (human) organism.
This is part of the research and educational discipline ADMET (absorption,
distribution, metabolism, elimination, and toxicity). Here, we review
the work of Jan Commandeur and colleagues who have not only made a
significant impact in understanding of phase I and phase II metabolism
of several important compounds but also contributed greatly to the
development of experimental techniques for the study of xenobiotic
metabolism. Jan Commandeur’s work has covered a broad area
of research, such as the development of online screening methodologies,
the use of a combination of enzyme mutagenesis and molecular modeling
for structure–activity relationship (SAR) studies, and the
development of novel probe substrates. This work is the bedrock of
current activities and brings the field closer to personalized (cohort-based)
pharmacology, toxicology, and hazard/risk assessment.
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Affiliation(s)
| | - Liliana Capinha
- Division of Computational and Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMs), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Jelle Reinen
- Charles River Den Bosch, Hambakenwetering 7, 5203 DL Hertogenbosch, The Netherlands
| | - Martijn Rooseboom
- Shell Global Solutions International B.V., 1030 BN The Hague, The Netherlands
| | - Michel Kranendonk
- Center for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School/Faculty of Medical Sciences, Universidade NOVA de Lisboa, Campo dos Mártires da Pátria 130, 1169-056 Lisboa, Portugal
| | | | - Paul Jennings
- Division of Computational and Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute of Molecular and Life Sciences (AIMMs), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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3
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Molecular probes for human cytochrome P450 enzymes: Recent progress and future perspectives. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213600] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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4
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Glass SM, Martell CM, Oswalt AK, Osorio-Vasquez V, Cho C, Hicks MJ, Mills JM, Fujiwara R, Glista MJ, Kamath SS, Furge LL. CYP2D6 Allelic Variants *34, *17-2, *17-3, and *53 and a Thr309Ala Mutant Display Altered Kinetics and NADPH Coupling in Metabolism of Bufuralol and Dextromethorphan and Altered Susceptibility to Inactivation by SCH 66712. Drug Metab Dispos 2018; 46:1106-1117. [PMID: 29784728 DOI: 10.1124/dmd.117.079871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/09/2018] [Indexed: 01/27/2023] Open
Abstract
Metabolic phenotype can be affected by multiple factors, including allelic variation and interactions with inhibitors. Human CYP2D6 is responsible for approximately 20% of cytochrome P450-mediated drug metabolism but consists of more than 100 known variants; several variants are commonly found in the population, whereas others are quite rare. Four CYP2D6 allelic variants-three with a series of mutations distal to the active site (*34, *17-2, *17-3) and one ultra-metabolizer with mutations near the active site (*53), along with reference *1 and an active site mutant of *1 (Thr309Ala)-were expressed, purified, and studied for interactions with the typical substrates dextromethorphan and bufuralol and the inactivator SCH 66712. We found that *34, *17-2, and *17-3 displayed reduced enzyme activity and NADPH coupling while producing the same metabolites as *1, suggesting a possible role for Arg296 in NADPH coupling. A higher-activity variant, *53, displayed similar NADPH coupling to *1 but was less susceptible to inactivation by SCH 66712. The Thr309Ala mutant showed similar activity to that of *1 but with greatly reduced NADPH coupling. Overall, these results suggest that kinetic and metabolic analysis of individual CYP2D6 variants is required to understand their possible contributions to variable drug response and the complexity of personalized medicine.
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Affiliation(s)
- Sarah M Glass
- Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan
| | | | | | | | - Christi Cho
- Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan
| | - Michael J Hicks
- Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan
| | | | - Rina Fujiwara
- Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan
| | | | - Sharat S Kamath
- Department of Chemistry, Kalamazoo College, Kalamazoo, Michigan
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5
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Zeng J, Zhu Q, Wu Y, Chen H, Lin X. Characterization of a polycyclic aromatic ring-hydroxylation dioxygenase from Mycobacterium sp. NJS-P. CHEMOSPHERE 2017; 185:67-74. [PMID: 28686888 DOI: 10.1016/j.chemosphere.2017.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 06/01/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
Abstract
Ring-hydroxylating dioxygenases (RHDs) play a critical role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). In this study, genes pdoAB encoding a dioxygenase capable of oxidizing various PAHs with up to five-ring benzo[a]pyrene were cloned from Mycobacterium sp. NJS-P. The α-subunit of the PdoAB showed 99% and 93% identity to that from Mycobacterium sp. S65 and Mycobacterium sp. py136, respectively. An Escherichia coli expression experiment revealed that the enzyme is able to oxidize anthracene, phenanthrene, pyrene and benzo[a]pyrene, but not to fluoranthene and benzo[a]anthracene. Furthermore, the results of in silico analysis showed that PdoAB has a large substrate-binding pocket satisfying for accommodation of HMW PAHs, and suggested that the binding energy of intermolecular interaction may predict the substrate conversion of RHDs towards HMW PAHs, especially those may have steric constraints on the substrate-binding pocket, such as benzo[a]pyrene and benzo[a]anthracene.
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Affiliation(s)
- Jun Zeng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Qinghe Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Yucheng Wu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China
| | - Hong Chen
- Soil and Environment Analysis Center, Institute of Soil Science, Chinese Academy of Science, PR China
| | - Xiangui Lin
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Beijing East Road, 71, Nanjing 210008, PR China; Joint Open Laboratory of Soil and the Environment, Hong Kong University and Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, PR China.
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6
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Nair PC, McKinnon RA, Miners JO. Cytochrome P450 structure–function: insights from molecular dynamics simulations. Drug Metab Rev 2016; 48:434-52. [DOI: 10.1080/03602532.2016.1178771] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Wijma HJ, Marrink SJ, Janssen DB. Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations. J Chem Inf Model 2014; 54:2079-92. [PMID: 24916632 DOI: 10.1021/ci500126x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Computational approaches could decrease the need for the laborious high-throughput experimental screening that is often required to improve enzymes by mutagenesis. Here, we report that using multiple short molecular dynamics (MD) simulations makes it possible to accurately model enantioselectivity for large numbers of enzyme-substrate combinations at low computational costs. We chose four different haloalkane dehalogenases as model systems because of the availability of a large set of experimental data on the enantioselective conversion of 45 different substrates. To model the enantioselectivity, we quantified the frequency of occurrence of catalytically productive conformations (near attack conformations) for pairs of enantiomers during MD simulations. We found that the angle of nucleophilic attack that leads to carbon-halogen bond cleavage was a critical variable that limited the occurrence of productive conformations; enantiomers for which this angle reached values close to 180° were preferentially converted. A cluster of 20-40 very short (10 ps) MD simulations allowed adequate conformational sampling and resulted in much better agreement to experimental enantioselectivities than single long MD simulations (22 ns), while the computational costs were 50-100 fold lower. With single long MD simulations, the dynamics of enzyme-substrate complexes remained confined to a conformational subspace that rarely changed significantly, whereas with multiple short MD simulations a larger diversity of conformations of enzyme-substrate complexes was observed.
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Affiliation(s)
- Hein J Wijma
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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8
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Ma LN, Du ZZ, Lian P, Wei DQ. A theoretical study on the mechanism of a superficial mutation inhibiting the enzymatic activity of CYP1A2. Interdiscip Sci 2014; 6:25-31. [DOI: 10.1007/s12539-014-0184-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/03/2013] [Accepted: 09/10/2013] [Indexed: 11/24/2022]
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9
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Schultes S, Nijmeijer S, Engelhardt H, Kooistra AJ, Vischer HF, de Esch IJP, Haaksma EEJ, Leurs R, de Graaf C. Mapping histamine H4 receptor–ligand binding modes. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20212c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Computational prediction of ligand binding modes in G protein-coupled receptors (GPCRs) remains a challenging task. Systematic consideration of different protein modelling templates, ligand binding poses, and ligand protonation states in extensive molecular dynamics (MD) simulation studies enabled the prediction of ligand-specific mutation effects in the histamine H4 receptor, a key player in inflammation.
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Affiliation(s)
- Sabine Schultes
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Saskia Nijmeijer
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Harald Engelhardt
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Albert J. Kooistra
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Henry F. Vischer
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Iwan J. P. de Esch
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Eric E. J. Haaksma
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Rob Leurs
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
| | - Chris de Graaf
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry
- Department of Pharmacochemistry
- Faculty of Exact Sciences
- VU University Amsterdam
- 1081 HV Amsterdam
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10
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Tierney DL. Jahn-Teller dynamics in a series of high-symmetry Co(II) chelates determine paramagnetic relaxation enhancements. J Phys Chem A 2012; 116:10959-72. [PMID: 23095055 DOI: 10.1021/jp309245e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NMR paramagnetic relaxation enhancements (PREs) of a series of structurally characterized, trigonal bis-trispyrazolylborate (Tp) chelates of high-spin Co(II), spanning 100-850 MHz in field, are reported. Prior knowledge of the metal-nucleus distances allows numerical extraction of position-dependent electron spin relaxation rates (τ(c)(-1)) from direct measurement of the individual PREs of the four symmetry distinct protons in Co(Tp)(2), using available closed-form expressions. The data for this electronically complex system where spin-orbit coupling defines the ground state electronic structure are analyzed in terms of the Solomon-Bloembergen-Morgan (SBM) relations, as well as available zero-field splitting limit theories. A simple angular correction is shown to be sufficient to reconcile the individual τ(c)(T) data for the four classes of protons. The data identify a previously unrecognized dynamic Jahn-Teller effect in these historically important complexes, with a barrier of ~230 cm(-1), pointing to a level of dynamics in trispyrazolylborate chemistry that has not been described before, and further show that it is the Jahn-Teller that is responsible for the PREs in fluid solution. A field-dependent component is also identified for the two protons nearest g(//), which is suggested to arise due to Zeeman mixing of excited state character into the ground level.
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Affiliation(s)
- David L Tierney
- Department of Chemistry and Chemical Biology, The University of New Mexico, Albuquerque, New Mexico 87131, United States.
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11
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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
![]()
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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Rydberg P, Olsen L. Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6. ACS Med Chem Lett 2012; 3:69-73. [PMID: 24900373 DOI: 10.1021/ml200246f] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 11/07/2011] [Indexed: 11/30/2022] Open
Abstract
A ligand-based method based on the SMARTCyp approach that predicts the sites of cytochrome P450 2D6-mediated metabolism of druglike molecules has been developed. The method uses only two descriptors besides the reactivity from SMARTCyp: the distance to a protonated nitrogen atom and the distance to the end of the molecule. Hence, the site of metabolism is predicted directly from the 2D structure of a molecule, without requiring calculation of electronic properties or generation of 3D structures. Testing on an independent test set gives an area under the curve value of 0.94, and a site of metabolism is found among the top two ranked atoms for 91% of the compounds.
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Affiliation(s)
- Patrik Rydberg
- Biostructural Research, Department
of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100
Copenhagen, Denmark
| | - Lars Olsen
- Biostructural Research, Department
of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100
Copenhagen, Denmark
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13
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Wasik AM, Gandy MN, McIldowie M, Holder MJ, Chamba A, Challa A, Lewis KD, Young SP, Scheel-Toellner D, Dyer MJ, Barnes NM, Piggott MJ, Gordon J. Enhancing the anti-lymphoma potential of 3,4-methylenedioxymethamphetamine ('ecstasy') through iterative chemical redesign: mechanisms and pathways to cell death. Invest New Drugs 2011; 30:1471-83. [PMID: 21850491 DOI: 10.1007/s10637-011-9730-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 08/01/2011] [Indexed: 11/29/2022]
Abstract
While 3,4-methylenedioxymethamphetamine (MDMA/'ecstasy') is cytostatic towards lymphoma cells in vitro, the concentrations required militate against its translation directly to a therapeutic in vivo. The possibility of 'redesigning the designer drug', separating desired anti-lymphoma activity from unwanted psychoactivity and neurotoxicity, was therefore mooted. From an initial analysis of MDMA analogues synthesized with a modified α-substituent, it was found that incorporating a phenyl group increased potency against sensitive, Bcl-2-deplete, Burkitt's lymphoma (BL) cells 10-fold relative to MDMA. From this lead, related analogs were synthesized with the 'best' compounds (containing 1- and 2-naphthyl and para-biphenyl substituents) some 100-fold more potent than MDMA versus the BL target. When assessed against derived lines from a diversity of B-cell tumors MDMA analogues were seen to impact the broad spectrum of malignancy. Expressing a BCL2 transgene in BL cells afforded only scant protection against the analogues and across the malignancies no significant correlation between constitutive Bcl-2 levels and sensitivity to compounds was observed. Bcl-2-deplete cells displayed hallmarks of apoptotic death in response to the analogues while BCL2 overexpressing equivalents died in a caspase-3-independent manner. Despite lymphoma cells expressing monoamine transporters, their pharmacological blockade failed to reverse the anti-lymphoma actions of the analogues studied. Neither did reactive oxygen species account for ensuing cell death. Enhanced cytotoxic performance did however track with predicted lipophilicity amongst the designed compounds. In conclusion, MDMA analogues have been discovered with enhanced cytotoxic efficacy against lymphoma subtypes amongst which high-level Bcl-2--often a barrier to drug performance for this indication--fails to protect.
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Affiliation(s)
- Agata M Wasik
- School of Immunity & Infection, The Medical School, Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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14
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Structural features of cytochromes P450 and ligands that affect drug metabolism as revealed by X-ray crystallography and NMR. Future Med Chem 2011; 2:1451-68. [PMID: 21103389 DOI: 10.4155/fmc.10.229] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cytochromes P450 (P450s) play a major role in the clearance of drugs, toxins, and environmental pollutants. Additionally, metabolism by P450s can result in toxic or carcinogenic products. The metabolism of pharmaceuticals by P450s is a major concern during the design of new drug candidates. Determining the interactions between P450s and compounds of very diverse structures is complicated by the variability in P450-ligand interactions. Understanding the protein structural elements and the chemical attributes of ligands that dictate their orientation in the P450 active site will aid in the development of effective and safe therapeutic agents. The goal of this review is to describe P450-ligand interactions from two perspectives. The first is the various structural elements that microsomal P450s have at their disposal to assume the different conformations observed in X-ray crystal structures. The second is P450-ligand dynamics analyzed by NMR relaxation studies.
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15
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CYP1A2-mediated biotransformation of cardioactive 2-thienylidene-3,4-methylenedioxybenzoylhydrazine (LASSBio-294) by rat liver microsomes and human recombinant CYP enzymes. Eur J Med Chem 2011; 46:349-55. [DOI: 10.1016/j.ejmech.2010.11.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 11/10/2010] [Accepted: 11/15/2010] [Indexed: 11/24/2022]
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16
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Schyman P, Usharani D, Wang Y, Shaik S. Brain chemistry: how does P450 catalyze the O-demethylation reaction of 5-methoxytryptamine to yield serotonin? J Phys Chem B 2010; 114:7078-89. [PMID: 20405876 DOI: 10.1021/jp1008994] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory has been applied to elucidate the mechanism of the O-demethylation reaction that generates serotonin from 5-methoxytryptamine (5-MT); a process that is efficiently catalyzed by P450 CYP2D6. Two substrates, the neutral 5-MT and the protonated 5-MTH(+), were used to probe the reactivity of CYP2D6 compound I. Notably, the H-abstraction process is found to be slightly more facile for 5-MT. However, our DFT augmented by docking results show that the amino acid Glu216 in the active site holds the NH(3)(+) tail of the 5-MTH(+) substrate in an upright conformation and thereby controls the regioselectivity of the bond activation. Thus, the substrate protonation serves an important function in maximizing the yield of serotonin. This finding is in accord with experimental conclusions that 5-MTH(+) serves as the substrate for the CYP2D6 enzyme. The study further shows that the H-abstraction follows two-state reactivity (TSR), whereas the rebound path may involve more states due to the appearance of both Fe(IV) and Fe(III) electromers during the reaction of 5-MTH(+).
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Affiliation(s)
- Patric Schyman
- Institute of Chemistry and The Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91940 Jerusalem, Israel
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Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1. mBio 2010; 1. [PMID: 20714442 PMCID: PMC2921158 DOI: 10.1128/mbio.00135-10] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Accepted: 05/05/2010] [Indexed: 11/20/2022] Open
Abstract
The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons.
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Wang B, Yang LP, Zhang XZ, Huang SQ, Bartlam M, Zhou SF. New insights into the structural characteristics and functional relevance of the human cytochrome P450 2D6 enzyme. Drug Metab Rev 2010; 41:573-643. [PMID: 19645588 DOI: 10.1080/03602530903118729] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
To date, the crystal structures of at least 12 human CYPs (1A2, 2A6, 2A13, 2C8, 2C9, 2D6, 2E1, 2R1, 3A4, 7A1, 8A1, and 46A1) have been determined. CYP2D6 accounts for only a small percentage of all hepatic CYPs (< 2%), but it metabolizes approximately 25% of clinically used drugs with significant polymorphisms. CYP2D6 also metabolizes procarcinogens and neurotoxins, such as 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, 1,2,3,4-tetrahydroquinoline, and indolealkylamines. Moreover, the enzyme utilizes hydroxytryptamines and neurosteroids as endogenous substrates. Typical CYP2D6 substrates are usually lipophilic bases with an aromatic ring and a nitrogen atom, which can be protonated at physiological pH. Substrate binding is generally followed by oxidation (5-7 A) from the proposed nitrogen-Asp301 interaction. A number of homology models have been constructed to explore the structural features of CYP2D6, while antibody studies also provide useful structural information. Site-directed mutagenesis studies have demonstrated that Glu216, Asp301, Phe120, Phe481, and Phe483 play important roles in determining the binding of ligands to CYP2D6. The structure of human CYP2D6 has been recently determined and shows the characteristic CYP fold observed for other members of the CYP superfamily. The lengths and orientations of the individual secondary structural elements in the CYP2D6 structure are similar to those seen in other human CYP2 members, such as CYP2C9 and 2C8. The 2D6 structure has a well-defined active-site cavity located above the heme group with a volume of approximately 540 A(3), which is larger than equivalent cavities in CYP2A6 (260 A(3)), 1A2 (375 A(3)), and 2E1 (190 A(3)), but smaller than those in CYP3A4 (1385 A(3)) and 2C8 (1438 A(3)). Further studies are required to delineate the molecular mechanisms involved in CYP2D6 ligand interactions and their implications for drug development and clinical practice.
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Affiliation(s)
- Bo Wang
- Department of Pediatrics, Guangdong Women and Children's Hospital, Guangzhou, China
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19
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Veselovsky A, Sobolev B, Zharkova M, Archakov A. Computer-based substrate specifity prediction for cytochrome P450. ACTA ACUST UNITED AC 2010; 56:90-100. [DOI: 10.18097/pbmc20105601090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cytochrome P450 is important class of enzymes metabolizing numerous drugs. The composition and activity of these enzymes are determined the drug distribution in organism, its pharmacological and toxic effect. Thus the prediction of the behaviour of compounds in organism is essential for discovery and development of new drugs in the early stages of this process. The different isoforms of cytochrome P450 can oxidized wide range of chemical compounds and their substrate specifity do not correlate with their taxonomical classification. The main methods of cytochrome P450 substrate specifity prediction is reviewed. These methods divided based on primary informations that used: prediction based on amino acid sequences, ligand-based (pharmacophore and QSAR models) and structure-based (molecular docking, affinity prediction) methods. The common problem of cytochrome P450 substrate prediction and advantage and disadvantages of these methods are discussed.
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Kim DN, Cho KH, Oh WS, Lee CJ, Lee SK, Jung J, No KT. EaMEAD: Activation energy prediction of cytochrome P450 mediated metabolism with effective atomic descriptors. J Chem Inf Model 2009; 49:1643-54. [PMID: 19545128 DOI: 10.1021/ci900011g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In an effort to improve drug design and predictions for pharmacokinetics (PK), an empirical model was developed to predict the activation energies (Ea) of cytochrome P450 (CYP450) mediated metabolism. The model, EaMEAD (Activation energy of Metabolism reactions with Effective Atomic Descriptors), predicts the Ea of four major metabolic reactions of the CYP450 enzyme: aliphatic hydroxylation, N-dealkylation, O-dealkylation, and aromatic hydroxylation. To build and validate the empirical model, the E(a) values of the substrates with diverse chemical structures (394 metabolic sites for aliphatic hydroxylation, 27 metabolic sites for N-dealkylation, 9 metabolic sites for O-dealkylation, and 85 metabolic sites for aromatic hydroxylation) were calculated by AM1 molecular orbital (MO). Empirical equations, Quantitative Structure Activity Relationship (QSAR) models, were derived using effective atomic charge, effective atomic polarizability, and bond dipole moments of the substrates as descriptors. EaMEAD is shown to accurately predict Ea with a correlation coefficient (R) of 0.94 and root-mean-square error (RMSE, unit is kcal/mol) of 0.70 for aliphatic hydroxylation, N-dealkylation, and O-dealkylation, and R of 0.83 and RMSE of 0.80 for aromatic hydroxylation, respectively. Physical origin and the role of the effective atomic descriptors of the models are presented in detail. With this model, the Ea of the metabolism can be rapidly predicted without any experimental parameters or time-consuming QM calculation. Regioselectivity prediction with our model is presented in the case of CYP3A4 metabolism. The reliability and ease of use of this model will greatly facilitate early stage PK predictions and rational drug design. Moreover, the model can be applied to develop the Ea prediction model of various types of chemical reactions.
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Affiliation(s)
- Doo Nam Kim
- Bioinformatics and Molecular Design Research Center, Seoul 120-749, Korea
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23
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Keizers PHJ, Van Dijk BR, De Graaf C, Van Vugt-Lussenburg BMA, Vermeulen NPE, Commandeur JNM. Metabolism ofN-substituted 7-methoxy-4-(aminomethyl) -coumarins by cytochrome P450 2D6 mutants and the indication of additional substrate interaction points. Xenobiotica 2009; 36:763-71. [PMID: 16971342 DOI: 10.1080/00498250600765325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Previous studies have shown the critical roles residues F120 and F483 play in the oxidative metabolism of 7-methoxy-4-(aminomethyl)-coumarin (MAMC) by cytochrome P450 2D6 (CYP2D6). In the present study, a series of N-alkyl-7-methoxy-4-(aminomethyl)-coumarins (MAMC analogues) were used as substrates for the F120A and F483A mutants in order to probe the CYP2D6 active site. The F120A and F483A mutants of CYP2D6 displayed significant activity towards the MAMC analogues. Automated docking studies of the MAMC analogues in a CYP2D6 homology model suggested a distal hydrophobic active site binding cleft for the substrate N-alkyl chains, consisting of the residues L213 and V308.
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Affiliation(s)
- P H J Keizers
- Department of Pharmacochemistry, Division of Molecular Toxicology, Leiden Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, Amsterdam, The Netherlands
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24
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Understanding CYP2D6 interactions. Drug Discov Today 2009; 14:964-72. [PMID: 19638317 DOI: 10.1016/j.drudis.2009.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 07/15/2009] [Accepted: 07/17/2009] [Indexed: 11/20/2022]
Abstract
Owing to the polymorphic nature of CYP2D6, clinically significant issues can arise when drugs rely on that enzyme either for clearance, or metabolism to an active metabolite. Available screening methods to determine if the compound is likely to cause drug-drug interactions, or is likely to be a victim of inhibition of CYP2D6 by other compounds will be described. Computational models and examples will be given on strategies to design out the CYP2D6 liabilities for both heme-binding compounds and non-heme-binding compounds.
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25
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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26
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Meyer MR, Peters FT, Maurer HH. The Role of Human Hepatic Cytochrome P450 Isozymes in the Metabolism of Racemic 3,4-Methylenedioxyethylamphetamine and Its Single Enantiomers. Drug Metab Dispos 2009; 37:1152-6. [DOI: 10.1124/dmd.108.026203] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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27
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Stjernschantz E, Vermeulen NPE, Oostenbrink C. Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450. Expert Opin Drug Metab Toxicol 2008; 4:513-27. [PMID: 18484912 DOI: 10.1517/17425255.4.5.513] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Early in-vitro consideration of metabolism and inhibition of cytochrome P450 has proven its merits over the last 15 years. Simultaneously, many computational drug-design methods have been developed, and are being applied to study the interactions between drug candidates and cytochrome P450 enzymes (P450s). OBJECTIVE This review discusses the recent advances of these methods and the implications that are specific for P450s. METHODS Mainly focusing on the prediction of binding affinity and ligand selectivity, we outline the applicability of the different methods to answer specific questions. Special emphasis is put on the different levels of theory that are being used in recent computational descriptions of ligand-P450 interactions. CONCLUSION P450s offer an additional challenge for computational methods, considering the ambiguities of the catalytic cycle and the significant flexibility of the active site. Different computational methods display different limitations, which is crucial to take into account when choosing the method appropriate to each application.
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Affiliation(s)
- Eva Stjernschantz
- Vrije Universiteit Amsterdam, Leiden/Amsterdam Centre for Drug Research, Division of Molecular Toxicology, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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28
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Costache AD, Trawick D, Bohl D, Sem DS. AmineDB: Large scale docking of amines with CYP2D6 and scoring for druglike properties—towards defining the scope of the chemical defense against foreign amines in humans. Xenobiotica 2008; 37:221-45. [PMID: 17624022 DOI: 10.1080/00498250601089162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Organic amines are prevalent in nature and in drugs, especially the psychotherapeutic agents, and a major defense against potentially toxic amines is metabolism by CYP2D6. In order to understand better the constraints on the broad specificity of CYP2D6, 4207 amines were docked into the binding site of this enzyme. Docking poses were found predominantly with the positively charged amino groups closest to Asp301, with aromatic rings close to Phe120 and sometimes extending as far as Phe483. Organic amines that bind best to CYP2D6 tend to have larger molecular weights and logP values. Organic amines that score highly as being druglike, based on a Bayesian model constructed using a 5223-drug training set, are least likely to bind to CYP2D6. This correlation suggests that the set of known drugs, which have been largely designed or selected to avoid high affinity CYP binding, partially encodes the binding site preferences (or rather anti-preferences) of CYP2D6. Finally, in order to benchmark our docking and druglike scoring procedures, an analysis of psychotherapeutic agents is presented. All of these data, including the 4207 AM1-optimized ligand structures in proper ionization states, docking poses and scores, Druglike Scores and Lipinski properties, can be viewed from an online database, the AmineDB.
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Affiliation(s)
- A D Costache
- Chemical Proteomics Facility at Marquette, Department of Chemistry, P.O. Box 1881, Marquette University, Milwaukee, Wisconsin 53201, USA
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29
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Abstract
The advent of therapeutic strategies aimed at targeting specific macromolecular components of deregulated signaling pathways associated with particular disease states has given rise to the idea that it should be possible to design ligands as drug candidates to these targets from first principles. This concept has been beckoning for a long time but structure-based ligand design only became feasible once it was possible to determine the 3-D structures of molecular targets at atomic resolution. However, structure-based design turned out to be difficult, chiefly because under physiological conditions both receptors and ligands are not static but they behave dynamically. While it is possible to design ligands with high steric and electronic complementarity to a receptor site, it is always uncertain how biologically relevant the assumed conformations of both ligand and receptor actually are. The fact that it remains beyond our current abilities to predict with sufficient accuracy the affinity between hypothetical ligand and receptor poses is in part connected with this problem and continues to confound the reliable prediction of drug-like ligands for therapeutic targets. Nevertheless, significant progress has been made and so-called virtual screening methods that use computational methods to dock candidate ligands into receptor sites and to score the resulting complexes are now used routinely as one of the components in drug discovery screening campaigns. Here an overview is given of the underlying principles, implementations, and applications of structure-guided computational design technologies. Although the emphasis is on receptor-based strategies, mention will also be made of some of the more established ligand-based approaches, such as similarity analyses and quantitative structure-activity relationship methods.
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Affiliation(s)
- Peter M Fischer
- Centre for Biomolecular Sciences and School of Pharmacy, University of Nottingham, University Park, Nottingham, UK.
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30
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Branco RJ, Seifert A, Budde M, Urlacher VB, Ramos MJ, Pleiss J. Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium. Proteins 2008; 73:597-607. [DOI: 10.1002/prot.22083] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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31
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Stjernschantz E, van Vugt-Lussenburg BMA, Bonifacio A, de Beer SBA, van der Zwan G, Gooijer C, Commandeur JNM, Vermeulen NPE, Oostenbrink C. Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3. Proteins 2008; 71:336-52. [DOI: 10.1002/prot.21697] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Abstract
Since the late 1980s computational methods such as quantitative structure-activity relationship (QSAR) and pharmacophore approaches have become more widely applied to assess interactions between drug-like molecules and transporters, starting with P-glycoprotein (P-gp). Identifying molecules that interact with P-gp and other transporters is important for drug discovery, but it is normally ascertained using laborious in vitro and in vivo studies. Computational QSAR and pharmacophore models can be used to screen commercial databases of molecules rapidly and suggest those likely to bind as substrates or inhibitors for transporters. These predictions can then be readily verified in vitro, thus representing a more efficient route to screening. Recently, the application of this approach has seen the identification of new substrates and inhibitors for several transporters. The successful application of computational models and pharmacophore models in particular to predict transporter binding accurately represents a way to anticipate drug-drug interactions of novel molecules from molecular structure. These models may also see incorporation in future pharmacokinetic-pharmacodynamic models to improve predictions of in vivo drug effects in patients. The implications of early assessment of transporter activity, current advances in QSAR, and other computational methods for future development of these and systems-based approaches will be discussed.
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Affiliation(s)
- S Ekins
- Collaborations in Chemistry, Jenkintown, PA, USA.
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33
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Bonifacio A, Millo D, Keizers PHJ, Boegschoten R, Commandeur JNM, Vermeulen NPE, Gooijer C, van der Zwan G. Active-site structure, binding and redox activity of the heme-thiolate enzyme CYP2D6 immobilized on coated Ag electrodes: a surface-enhanced resonance Raman scattering study. J Biol Inorg Chem 2008; 13:85-96. [PMID: 17899220 PMCID: PMC2099460 DOI: 10.1007/s00775-007-0303-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 09/08/2007] [Indexed: 11/28/2022]
Abstract
Surface-enhance resonance Raman scattering spectra of the heme-thiolate enzyme cytochrome P450 2D6 (CYP2D6) adsorbed on Ag electrodes coated with 11-mercaptoundecanoic acid (MUA) were obtained in various experimental conditions. An analysis of these spectra, and a comparison between them and the RR spectra of CYP2D6 in solution, indicated that the enzyme's active site retained its nature of six-coordinated low-spin heme upon immobilization. Moreover, the spectral changes detected in the presence of dextromethorphan (a CYP2D6 substrate) and imidazole (an exogenous heme axial ligand) indicated that the immobilized enzyme also preserved its ability to reversibly bind a substrate and form a heme-imidazole complex. The reversibility of these processes could be easily verified by flowing alternately solutions of the various compounds and the buffer through a home-built spectroelectrochemical flow cell which contained a sample of immobilized protein, without the need to disassemble the cell between consecutive spectral data acquisitions. Despite immobilized CYP2D6 being effectively reduced by a sodium dithionite solution, electrochemical reduction via the Ag electrode was not able to completely reduce the enzyme, and led to its extensive inactivation. This behavior indicated that although the enzyme's ability to exchange electrons is not altered by immobilization per se, MUA-coated electrodes are not suited to perform direct electrochemistry of CYP2D6.
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Affiliation(s)
- Alois Bonifacio
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Diego Millo
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Peter H. J. Keizers
- Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Roald Boegschoten
- Mechanical Workshop, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Jan N. M. Commandeur
- Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- Molecular Toxicology, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Cees Gooijer
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
| | - Gert van der Zwan
- Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, De Boelelaan 1083a, 1081 HV Amsterdam, The Netherlands
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Kool J, van Liempd SM, Harmsen S, Beckman J, van Elswijk D, Commandeur JNM, Irth H, Vermeulen NPE. Cytochrome P450 bio-affinity detection coupled to gradient HPLC: on-line screening of affinities to cytochrome P4501A2 and 2D6. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 858:49-58. [PMID: 17826363 DOI: 10.1016/j.jchromb.2007.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2007] [Revised: 06/21/2007] [Accepted: 08/07/2007] [Indexed: 11/29/2022]
Abstract
Here we describe novel on-line human CYP1A2 and CYP2D6 Enzyme Affinity Detection (EAD) systems coupled to gradient HPLC. The use of the systems lies in the detection of individual inhibitory ligands in mixtures (e.g. metabolic mixtures or herbal extracts) towards two relevant drug metabolizing human CYPs. The systems can rapidly detect individual compounds in mixtures with affinities to CYP1A2 or 2D6. The HPLC-EAD systems were first evaluated and validated in flow injection analysis mode. IC50 values of known ligands for both CYPs, tested both in flow injection and in HPLC mode, were well comparable with those measured in microplate reader formats. Both EAD systems were also connected to gradient HPLC and used to screen known compound mixtures for the presence of CYP1A2 and 2D6 inhibitors. Finally, the on-line CYP2D6 EAD system was used to screen for the inhibitory activities of stereoisomers of a mixture of five methylenedioxy-alkylamphetamines (XTC analogs) on a chiral analytical column.
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Affiliation(s)
- Jeroen Kool
- LACDR-Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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35
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Yun CH, Kim KH, Kim DH, Jung HC, Pan JG. The bacterial P450 BM3: a prototype for a biocatalyst with human P450 activities. Trends Biotechnol 2007; 25:289-98. [PMID: 17532492 DOI: 10.1016/j.tibtech.2007.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 03/20/2007] [Accepted: 05/09/2007] [Indexed: 11/18/2022]
Abstract
The use of cytochrome P450 (P450 or CYP) enzymes as biocatalysts for the production of fine chemicals, including pharmaceuticals, has been of increasing interest, primarily owing to their catalytic diversity and broad substrate range. CYP102A1 (P450 BM3) from Bacillus megaterium integrates an entire monooxygenase system into one polypeptide and represents an appropriate prokaryotic model for industrial applications of mammalian P450 activities. CYP102A1 not only exhibits the highest catalytic activity ever detected in a P450 monooxygenase but also provides a potentially versatile biocatalyst for the production of human P450 metabolites. CYP102A1 can be further engineered to be a drug-metabolizing enzyme, making it a promising candidate to use as a biocatalyst in drug discovery and synthesis.
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Affiliation(s)
- Chul-Ho Yun
- School of Biological Sciences and Technology and Hormone Research Center, Chonnam National University, Gwangju 500-757, Republic of Korea.
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36
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Eitrich T, Kless A, Druska C, Meyer W, Grotendorst J. Classification of highly unbalanced CYP450 data of drugs using cost sensitive machine learning techniques. J Chem Inf Model 2007; 47:92-103. [PMID: 17238253 DOI: 10.1021/ci6002619] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
In this paper, we study the classifications of unbalanced data sets of drugs. As an example we chose a data set of 2D6 inhibitors of cytochrome P450. The human cytochrome P450 2D6 isoform plays a key role in the metabolism of many drugs in the preclinical drug discovery process. We have collected a data set from annotated public data and calculated physicochemical properties with chemoinformatics methods. On top of this data, we have built classifiers based on machine learning methods. Data sets with different class distributions lead to the effect that conventional machine learning methods are biased toward the larger class. To overcome this problem and to obtain sensitive but also accurate classifiers we combine machine learning and feature selection methods with techniques addressing the problem of unbalanced classification, such as oversampling and threshold moving. We have used our own implementation of a support vector machine algorithm as well as the maximum entropy method. Our feature selection is based on the unsupervised McCabe method. The classification results from our test set are compared structurally with compounds from the training set. We show that the applied algorithms enable the effective high throughput in silico classification of potential drug candidates.
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Affiliation(s)
- T Eitrich
- Central Institute for Applied Mathematics, Research Centre Jülich, Germany
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37
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de Graaf C, Oostenbrink C, Keizers PHJ, van Vugt-Lussenburg BMA, Commandeur JNM, Vermeulen NPE. Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:589-99. [PMID: 17333164 PMCID: PMC1914272 DOI: 10.1007/s00249-006-0126-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 12/01/2006] [Accepted: 12/21/2006] [Indexed: 11/21/2022]
Abstract
Detailed molecular dynamics (MD) simulations have been performed to reproduce and rationalize the experimental finding that the F483A mutant of CYP2D6 has lower affinity for R-propranolol than for S-propranolol. Wild-type (WT) CYP2D6 does not show this stereospecificity. Four different approaches to calculate the free energy differences have been investigated and were compared to the experimental binding data. From the differences between calculations based on forward and backward processes and the closure of thermodynamic cycles, it was clear that not all simulations converged sufficiently. The approach that calculates the free energies of exchanging R-propranolol with S-propranolol in the F483A mutant relative to the exchange free energy in WT CYP2D6 accurately reproduced the experimental binding data. Careful inspection of the end-points of the MD simulations involved in this approach, allowed for a molecular interpretation of the observed differences.
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Affiliation(s)
- Chris de Graaf
- Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Leiden Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris Oostenbrink
- Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Leiden Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Peter H. J. Keizers
- Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Leiden Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Barbara M. A. van Vugt-Lussenburg
- Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Leiden Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jan N. M. Commandeur
- Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Leiden Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Leiden Amsterdam Center for Drug Research (LACDR), Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Abstract
Drug metabolism information is a necessary component of drug discovery and development. The key issues in drug metabolism include identifying: the enzyme(s) involved, the site(s) of metabolism, the resulting metabolite(s), and the rate of metabolism. Methods for predicting human drug metabolism from in vitro and computational methodologies and determining relationships between the structure and metabolic activity of molecules are also critically important for understanding potential drug interactions and toxicity. There are numerous experimental and computational approaches that have been developed in order to predict human metabolism which have their own limitations. It is apparent that few of the computational tools for metabolism prediction alone provide the major integrated functions needed to assist in drug discovery. Similarly the different in vitro methods for human drug metabolism themselves have implicit limitations. The utilization of these methods for pharmaceutical and other applications as well as their integration is discussed as it is likely that hybrid methods will provide the most success.
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Affiliation(s)
- Larry J Jolivette
- Preclinical Drug Discovery, Cardiovascular and Urogenital Centre of Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
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39
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Sousa SF, Fernandes PA, Ramos MJ. Protein-ligand docking: current status and future challenges. Proteins 2006; 65:15-26. [PMID: 16862531 DOI: 10.1002/prot.21082] [Citation(s) in RCA: 600] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Understanding the ruling principles whereby protein receptors recognize, interact, and associate with molecular substrates and inhibitors is of paramount importance in drug discovery efforts. Protein-ligand docking aims to predict and rank the structure(s) arising from the association between a given ligand and a target protein of known 3D structure. Despite the breathtaking advances in the field over the last decades and the widespread application of docking methods, several downsides still exist. In particular, protein flexibility-a critical aspect for a thorough understanding of the principles that guide ligand binding in proteins-is a major hurdle in current protein-ligand docking efforts that needs to be more efficiently accounted for. In this review the key concepts of protein-ligand docking methods are outlined, with major emphasis being given to the general strengths and weaknesses that presently characterize this methodology. Despite the size of the field, the principal types of search algorithms and scoring functions are reviewed and the most popular docking tools are briefly depicted. Recent advances that aim to address some of the traditional limitations associated with molecular docking are also described. A selection of hand-picked examples is used to illustrate these features.
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Affiliation(s)
- Sérgio Filipe Sousa
- REQUIMTE, Departamento de Química, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
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40
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van Vugt-Lussenburg BMA, Damsten MC, Maasdijk DM, Vermeulen NPE, Commandeur JNM. Heterotropic and homotropic cooperativity by a drug-metabolising mutant of cytochrome P450 BM3. Biochem Biophys Res Commun 2006; 346:810-8. [PMID: 16777067 DOI: 10.1016/j.bbrc.2006.05.179] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 05/28/2006] [Indexed: 11/30/2022]
Abstract
Recently, we described a triple mutant of the bacterial cytochrome P450 BM3 as the first mutant with affinity for drug-like compounds. In this paper, we show that this mutant, but not wild-type BM3, is able to metabolise testosterone and several drug-like molecules such as amodiaquine, dextromethorphan, acetaminophen, and 3,4-methylenedioxymethylamphetamine that are known substrates of human P450s. Interestingly, the metabolism of 3,4-methylenedioxymethylamphetamine and acetaminophen could be stimulated up to 70-fold by the addition of caffeine, a known activator of rat P450 3A2. With testosterone metabolism, homotropic cooperativity was observed. This shows that heterotropic and homotropic cooperativity, known to occur in the P450 3A family, can also take place in BM3. BM3 therefore can be used as a model system to study atypical kinetics in mammalian P450s. Second, this study shows that BM3 can be engineered to a drug-metabolising enzyme, making it a promising candidate to use as biocatalyst in drug discovery and synthesis.
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Affiliation(s)
- Barbara M A van Vugt-Lussenburg
- LACDR/Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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41
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de Graaf C, Oostenbrink C, Keizers PHJ, van der Wijst T, Jongejan A, Vermeulen NPE. Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J Med Chem 2006; 49:2417-30. [PMID: 16610785 DOI: 10.1021/jm0508538] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Automated docking strategies successfully applied to binding mode predictions of ligands in Cyt P450 crystal structures in an earlier study (de Graaf et al. J. Med. Chem. 2005, 7, 2308-2318) were used for the catalytic site prediction (CSP) of 65 substrates in a CYP2D6 homology model. The consideration of water molecules at predicted positions in the active site and the rescoring of pooled docking poses from four different docking programs (AutoDock, FlexX, GOLD-Goldscore, and GOLD-Chemscore) with the SCORE scoring function enabled the successful prediction of experimentally reported sites of catalysis of more than 80% of the substrates. Three docking algorithms (FlexX, GOLD-Goldscore, and GOLD-Chemscore) were subsequently used in combination with six scoring functions (Chemscore, DOCK, FlexX, GOLD, PMF, and SCORE) to assess the ability of docking-based virtual screening methods to prioritize known CYP2D6 substrates seeded into a drug-like chemical database (in the absence and presence of active-site water molecules). Finally, the optimal docking strategy in terms of virtual screening accuracy, GOLD-Chemscore with the consideration of active-site water (60% of known substrates recovered in the top 5% of the ranked drug-like database), was verified experimentally; it was successfully used to identify high-affinity CYP2D6 ligands among a larger proprietary database.
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Affiliation(s)
- Chris de Graaf
- Leiden/Amsterdam Center for Drug Research, Division of Molecular Toxicology, Division of Pharmaceutical Sciences, Department of Chemistry and Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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42
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Yu J, Paine MJI, Maréchal JD, Kemp CA, Ward CJ, Brown S, Sutcliffe MJ, Roberts GCK, Rankin EM, Wolf CR. IN SILICO PREDICTION OF DRUG BINDING TO CYP2D6: IDENTIFICATION OF A NEW METABOLITE OF METOCLOPRAMIDE. Drug Metab Dispos 2006; 34:1386-92. [PMID: 16698891 DOI: 10.1124/dmd.106.009852] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Patients with cancer often take many different classes of drugs to treat the effects of their malignancy and the side effects of treatment, as well as their comorbidities. The potential for drug-drug interactions that may affect the efficacy of anticancer treatment is high, and a major source of such interactions is competition for the drug-metabolizing enzymes, cytochromes P450 (P450s). We have examined a series of 20 drugs commonly prescribed to cancer patients to look for potential interactions via CYP2D6. We used a homology model of CYP2D6, together with molecular docking techniques, to perform an in silico screen for binding to CYP2D6. Experimental IC50 values were determined for these compounds and compared with the model predictions to reveal a correlation with a regression coefficient of r2= 0.61. Importantly, the docked conformation of the commonly prescribed antiemetic metoclopramide predicted a new site of metabolism that was further investigated through in vitro analysis with recombinant CYP2D6. An aromatic N-hydroxy metabolite of metoclopramide, consistent with predictions from our modeling studies, was identified by high-performance liquid chromatography/mass spectrometry. This metabolite was found to represent a major product of metabolism in human liver microsomes, and CYP2D6 was identified as the main P450 isoform responsible for catalyzing its formation. In view of the prevalence of interindividual variation in the CYP2D6 genotype and phenotype, we suggest that those experiencing adverse reactions with metoclopramide, e.g., extrapyramidal syndrome, are likely to have a particular CYP2D6 genotype/phenotype. This warrants further investigation.
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Affiliation(s)
- Jinglei Yu
- Division of Cancer Medicine, Biomedical Research Centre, University of Dundee, Ninewells Hospital & Medical School, Dundee, DD1 9SY, UK
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43
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Bonifacio A, Keizers PHJ, Commandeur JNM, Vermeulen NPE, Robert B, Gooijer C, van der Zwan G. Binding of bufuralol, dextromethorphan, and 3,4-methylenedioxymethylamphetamine to wild-type and F120A mutant cytochrome P450 2D6 studied by resonance Raman spectroscopy. Biochem Biophys Res Commun 2006; 343:772-9. [PMID: 16563352 DOI: 10.1016/j.bbrc.2006.03.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 03/07/2006] [Indexed: 11/21/2022]
Abstract
Cytochrome P450 2D6 (CYP2D6) is one of the most important drug-metabolizing enzymes in humans. Resonance Raman data, reported for the first time for CYP2D6, show that the CYP2D6 heme is found to be in a six-coordinated low-spin state in the absence of substrates, and it is perturbed to different extents by bufuralol, dextromethorphan, and 3,4-methylenedioxymethylamphetamine (MDMA). Dextromethorphan and MDMA induce in CYP2D6 a significant amount of five-coordinated high-spin heme species and reduce the polarity of its heme-pocket, whereas bufuralol does not. Spectra of the F120A mutant CYP2D6 suggest that Phe120 is involved in substrate-binding of dextromethorphan and MDMA, being responsible for the spectral differences observed between these two compounds and bufuralol. These differences could be explained postulating a different substrate mobility for each compound in the CYP2D6 active site, consistently with the role previously suggested for Phe120 in binding dextromethorphan and MDMA.
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Affiliation(s)
- Alois Bonifacio
- Laser Centre/Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit Amsterdam, The Netherlands
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44
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van Waterschoot RAB, Keizers PHJ, de Graaf C, Vermeulen NPE, Tschirret-Guth RA. Topological role of cytochrome P450 2D6 active site residues. Arch Biochem Biophys 2006; 447:53-8. [PMID: 16466686 DOI: 10.1016/j.abb.2006.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2005] [Revised: 01/04/2006] [Accepted: 01/05/2006] [Indexed: 10/25/2022]
Abstract
Recent reports have identified Phe120, Asp301, Thr309, and Glu216 as important residues in cytochrome P450 2D6 (CYP2D6) substrate binding and catalysis. Complementary homology models have located these amino acids within the binding pocket of CYP2D6 and in the present study we have used aryldiazenes to test these models and gain further insight in the role these amino acids have in maintaining the integrity of the active site cavity. When Phe120 was replaced to alanine, there was a significant increase in probe migration to pyrrole nitrogens C and D, in agreement with homology models which have located the phenyl side-chain of Phe120 above these two pyrrole rings. No changes in topology were observed with the D301Q mutant, supporting claims that in this mutant the electrostatic interactions with the B/C-loop are largely maintained and the loop retains its native orientation. The T309V mutation resulted in significant topological alteration suggesting that, in addition to its potential role in dioxygen activation, Thr309 plays an important structural role within the active site crevice. Replacement of Ile106 with Glu, engineered to cause electrostatic repulsion with Glu216, had a profound topological effect in the higher region within the active site cavity and impaired the catalytic activity towards CYP2D6 probe substrates.
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Affiliation(s)
- Robert A B van Waterschoot
- LACDR/Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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45
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Stortelder A, Keizers P, Oostenbrink C, De Graaf C, De Kruijf P, Vermeulen N, Gooijer C, Commandeur J, Van Der Zwan G. Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy. Biochem J 2006; 393:635-43. [PMID: 16190863 PMCID: PMC1360716 DOI: 10.1042/bj20051169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 09/02/2005] [Accepted: 09/28/2005] [Indexed: 11/17/2022]
Abstract
Enzyme structure and dynamics may play a main role in substrate binding and the subsequent steps in the CYP (cytochrome P450) catalytic cycle. In the present study, changes in the structure of human CYP2D6 upon binding of the substrate are studied using steady-state and time-resolved fluorescence methods, focusing not only on the emission of the tryptophan residues, but also on emission of the substrate. As a substrate, MAMC [7-methoxy-4-(aminomethyl)-coumarin] was selected, a compound exhibiting native fluorescence. As well as the wild-type, the W128F (Trp128-->Phe) mutant of CYP2D6 was studied. After binding, a variety of energy transfer possibilities exist, and molecular dynamics simulations were performed to calculate distances and relative orientations of donors and acceptors. Energy transfer from Trp128 to haem appeared to be important; its emission was related to the shortest of the three average tryptophan fluorescence lifetimes observed for CYP2D6. MAMC to haem energy transfer was very efficient as well: when bound in the active site, the emission of MAMC was fully quenched. Steady-state anisotropy revealed that besides the MAMC in the active site, another 2.4% of MAMC was bound outside of the active site to wild-type CYP2D6. The tryptophan residues in CYP2D6 appeared to be less accessible for the external quenchers iodide and acrylamide in presence of MAMC, indicating a tightening of the enzyme structure upon substrate binding. However, the changes in the overall enzyme structure were not very large, since the emission characteristics of the enzyme were not very different in the presence of MAMC.
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Key Words
- cytochrome p450
- energy transfer
- enzyme structure
- substrate binding
- time-resolved fluorescence
- cyp, cytochrome p450
- das, decay-associated spectra
- fret, förster resonance energy transfer
- hamc, 7-hydroxy-4-(aminomethyl)-coumarin
- mamc, 7-methoxy-4-(aminomethyl)-coumarin
- md, molecular dynamics
- ni-nta, ni2+-nitrilotriacetate
- r.m.s.d., root-mean-square deviation
- sasa, solvent-accessible surface area
- tcspc, time-correlated single-photon counting
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Affiliation(s)
- Aike Stortelder
- *Laser Centre VU, Department of Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Peter H. J. Keizers
- †LACDR, Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris Oostenbrink
- †LACDR, Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris De Graaf
- †LACDR, Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Petra De Kruijf
- †LACDR, Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Nico P. E. Vermeulen
- †LACDR, Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Cees Gooijer
- *Laser Centre VU, Department of Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jan N. M. Commandeur
- †LACDR, Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Gert Van Der Zwan
- *Laser Centre VU, Department of Analytical Chemistry and Applied Spectroscopy, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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46
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Keizers PHJ, Schraven LHM, de Graaf C, Hidestrand M, Ingelman-Sundberg M, van Dijk BR, Vermeulen NPE, Commandeur JNM. Role of the conserved threonine 309 in mechanism of oxidation by cytochrome P450 2D6. Biochem Biophys Res Commun 2005; 338:1065-74. [PMID: 16269134 DOI: 10.1016/j.bbrc.2005.10.066] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 10/09/2005] [Indexed: 11/18/2022]
Abstract
Based on sequence alignments and homology modeling, threonine 309 in cytochrome P450 2D6 (CYP2D6) is proposed to be the conserved I-helix threonine, which is supposed to be involved in dioxygen activation by CYPs. The T309V mutant of CYP2D6 displayed a strong shift from O-dealkylation to N-dealkylation reactions in oxidation of dextromethorphan and 3,4-methylenedioxymethylamphetamine. This may be explained by an elevated ratio of hydroperoxo-iron to oxenoid-iron of the oxygenating species. In consistence, using cumene hydroperoxide, which directly forms the oxenoid-iron, the T309V mutant again selectively catalyzed the O-dealkylation reactions. The changed ratio of oxygenating species can also explain the decreased activity and changed regioselectivity that were observed in 7-methoxy-4-(aminomethyl)-coumarin and bufuralol oxidation, respectively, by the T309V mutant. Interestingly, the T309V mutant always showed a significantly increased, up to 75-fold, higher activity compared to that of the wild-type when using cumene hydroperoxide. These results indicate that T309 in CYP2D6 is involved in maintaining the balance of multiple oxygenating species and thus influences substrate and regioselectivity.
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Affiliation(s)
- Peter H J Keizers
- Leiden Amsterdam Center for Drug Research (LACDR), Division of Molecular Toxicology, Department of Pharmacochemistry, Vrije Universiteit, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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