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Sánchez-Trasviña C, Galindo-Estrada JD, Tinoco-Valencia R, Serrano-Carreón L, Rito-Palomares M, Willson RC, Mayolo-Deloisa K. Laccase-luminol chemiluminescence system: an investigation of substrate inhibition. LUMINESCENCE 2023; 38:341-349. [PMID: 36760184 DOI: 10.1002/bio.4460] [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: 11/09/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023]
Abstract
Chemiluminescence (CL) reactions are widely used for the detection and quantification of many types of analytes. Laccase has previously been proposed in CL reactions; however, its light emission behaviour has not been characterized. This study was conducted to characterize the laccase-luminol system, determine its kinetic parameters, and analyze the effects of protein and OH- concentration on the CL signal. Laccase from Coriolopsis gallica was combined with different concentrations of luminol (125 nM to 4 mM), and the enzyme kinetics were evaluated using diverse kinetic models. The laccase-luminol system was able to produce CL without an intermediate molecule, but it exhibited substrate-inhibition behaviour. A two-site random model was used and suggested that when the first luminol molecule was bound to the active site, laccase affinity for the second luminol molecule was increased. This inhibition effect could be avoided using a low luminol concentration. At 5 μM luminol concentration, 1 mg/ml (0.13 U) laccase is needed to achieve nearly 90% of the maximum CL signal, suggesting that the available luminol could not bind to all active sites. Furthermore, the concentration of NaOH negatively affected the CL signal. The laccase-luminol system represents an alternative to existing CL systems, with potential uses in molecular detection and quantification.
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Affiliation(s)
- Calef Sánchez-Trasviña
- Tecnologico de Monterrey, The Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico
| | - José Daniel Galindo-Estrada
- Universidad Politécnica del Valle de Toluca, Carretera Toluca-Almoloya de Juárez km. 5.6, Almoloya de Juárez, Estado de México, Mexico
| | - Raunel Tinoco-Valencia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Leobardo Serrano-Carreón
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, Mexico
| | - Marco Rito-Palomares
- Tecnologico de Monterrey, The Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. Morones Prieto 3000 Pte, Monterrey, NL, Mexico
| | - Richard C Willson
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Av. Morones Prieto 3000 Pte, Monterrey, NL, Mexico.,Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA
| | - Karla Mayolo-Deloisa
- Tecnologico de Monterrey, The Institute for Obesity Research, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Tecnologico de Monterrey, Escuela de Ingeniería y Ciencias, Centro de Biotecnología-FEMSA, Av. Eugenio Garza Sada 2501 Sur, Monterrey, NL, Mexico.,Institute of Materials Science of Barcelona (ICMAB-CSIC), Campus UAB, Bellaterra, Spain
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2
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Biotransformation of phenytoin in the electrochemically-driven CYP2C19 system. Biophys Chem 2022; 291:106894. [PMID: 36174335 DOI: 10.1016/j.bpc.2022.106894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
The possibility of the detection of atypical kinetic profiles of drug biotransformation using electrochemical systems based on immobilized cytochromes P450 with phenytoin hydroxylation by cytochrome P450 2C19 (CYP2C19) as an example was evaluated for the first time. For this purpose, we developed an electrochemical system, where one of the electrodes was modified by didodecyldimethylammonium bromide (DDAB) and was used as an electron donor for reduction of heme iron ion of the immobilized CYP2C19 and initiation of the catalytic reaction, while the second electrode was not modified and served for an electrochemical quantitation of 4-hydroxyphenytoin, which is a metabolite of antiepileptic drug phenytoin, by its oxidation peak. It was revealed that the dependence of the rate of 4-hydroxyphenytoin formation on phenytoin concentration is described by the equation for two enzymes or two binding sites indicating the existing of high- and low-affinity forms of the enzyme. The atypical kinetics and the kinetic parameters of CYP2C19-mediated phenytoin hydroxylation in the electrochemical system correlate to the same characteristics obtained by other authors in an alternative enzymatic system. Our results demonstrate the possibility of electrochemical systems based on cytochromes P450 to be applied for the detection of atypical kinetic profiles of drug metabolism.
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3
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Atypical kinetics of cytochrome P450 enzymes in pharmacology and toxicology. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 95:131-176. [PMID: 35953154 DOI: 10.1016/bs.apha.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Atypical kinetics are observed in metabolic reactions catalyzed by cytochrome P450 enzymes (P450). Yet, this phenomenon is regarded as experimental artifacts in some instances despite increasing evidence challenging the assumptions of typical Michaelis-Menten kinetics. As P450 play a major role in the metabolism of a wide range of substrates including drugs and endogenous compounds, it becomes critical to consider the impact of atypical kinetics on the accuracy of estimated kinetic and inhibitory parameters which could affect extrapolation of pharmacological and toxicological implications. The first half of this book chapter will focus on atypical non-Michaelis-Menten kinetics (e.g. substrate inhibition, biphasic and sigmoidal kinetics) as well as proposed underlying mechanisms supported by recent insights in mechanistic enzymology. In particular, substrate inhibition kinetics in P450 as well as concurrent drug inhibition of P450 in the presence of substrate inhibition will be further discussed. Moreover, mounting evidence has revealed that despite the high degree of sequence homology between CYP3A isoforms (i.e. CYP3A4 and CYP3A5), they have the propensities to exhibit vastly different susceptibilities and potencies of mechanism-based inactivation (MBI) with a common drug inhibitor. These experimental observations pertaining to the presence of these atypical isoform- and probe substrate-specific complexities in CYP3A isoforms by several clinically-relevant drugs will therefore be expounded and elaborated upon in the second half of this book chapter.
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4
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Wang Z, Paragas EM, Nagar S, Korzekwa K. Complex Cytochrome P450 Kinetics Due to Multisubstrate Binding and Sequential Metabolism. Part 1. Theoretical Considerations. Drug Metab Dispos 2021; 49:1090-1099. [PMID: 34503952 PMCID: PMC11022900 DOI: 10.1124/dmd.121.000553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 09/06/2021] [Indexed: 11/22/2022] Open
Abstract
Complexities in P450-mediated metabolism kinetics include multisubstrate binding, multiple-product formation, and sequential metabolism. Saturation curves and intrinsic clearances were simulated for single-substrate and multisubstrate models using derived velocity equations and numerical solutions of ordinary differential equations (ODEs). Multisubstrate models focused on sigmoidal kinetics because of their dramatic impact on clearance predictions. These models were combined with multiple-product formation and sequential metabolism, and simulations were performed with random error. Use of single-substrate models to characterize multisubstrate data can result in inaccurate kinetic parameters and poor clearance predictions. Comparing results for use of standard velocity equations with ODEs clearly shows that ODEs are more versatile and provide better parameter estimates. It would be difficult to derive concentration-velocity relationships for complex models, but these relationships can be easily modeled using numerical methods and ODEs. SIGNIFICANCE STATEMENT: The impact of multisubstrate binding, multiple-product formation, and sequential metabolism on the P450 kinetics was investigated. Numerical methods are capable of characterizing complicated P450 kinetics.
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Affiliation(s)
- Zeyuan Wang
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Erickson M Paragas
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
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5
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Seibert E, Tracy TS. Fundamentals of Enzyme Kinetics: Michaelis-Menten and Non-Michaelis-Type (Atypical) Enzyme Kinetics. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2342:3-27. [PMID: 34272689 DOI: 10.1007/978-1-0716-1554-6_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This chapter will provide a general introduction to the kinetics of enzyme-catalyzed reactions, including a general discussion of catalysts, reaction rates, and binding constants. This section will be followed by a discussion of various types of enzyme kinetics observed in drug metabolism reactions. A large number of enzymatic reactions can be adequately described by Michaelis-Menten kinetics. The Michaelis-Menten equation represents a rectangular hyperbola, with a y-asymptote at the Vmax value. However, in other cases, more complex kinetic models are required to explain the observed data. Atypical kinetic profiles are believed to arise from the simultaneous binding of multiple molecules within the active site of the enzyme (Tracy and Hummel, Drug Metab Rev 36:231-242, 2004). Several cytochromes P450 (CYPs) have large active sites that enable binding of multiple molecules (Yano et al., J Biol Chem 279:38091-38094, 2004; Wester et al., J Biol Chem 279:35630-35637, 2004). Thus, atypical kinetics are not uncommon in in vitro drug metabolism studies.
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Affiliation(s)
- Eleanore Seibert
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA.
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6
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Numerical Methods for Modeling Enzyme Kinetics. Methods Mol Biol 2021; 2342:147-168. [PMID: 34272694 DOI: 10.1007/978-1-0716-1554-6_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
Abstract
Differential equations are used to describe time-dependent changes in enzyme kinetics and pharmacokinetics. Analytical and numerical methods can be used to solve differential equations. This chapter describes the use of numerical methods in solving differential equations and its applications in characterizing the complexities observed in enzyme kinetics. A discussion is included on the use of numerical methods to overcome limitations of explicit equations in the analysis of metabolism kinetics, reversible inhibition kinetics, and inactivation kinetics. The chapter describes the advantages of using numerical methods when Michaelis-Menten assumptions do not hold.
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7
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Tang LWT, Verma RK, Yong RP, Li X, Wang L, Lin Q, Fan H, Chan ECY. Differential Reversible and Irreversible Interactions between Benzbromarone and Human Cytochrome P450s 3A4 and 3A5. Mol Pharmacol 2021; 100:224-236. [PMID: 34210765 DOI: 10.1124/molpharm.121.000256] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022] Open
Abstract
Mounting evidence has revealed that despite the high degree of sequence homology between cytochrome P450 3A isoforms (i.e., CYP3A4 and CYP3A5), they have the propensities to exhibit vastly different irreversible and reversible interactions with a single substrate. We have previously established that benzbromarone (BBR), a potent uricosuric agent used in the management of gout, irreversibly inhibits CYP3A4 via mechanism-based inactivation (MBI). However, it remains unelucidated if CYP3A5-its highly homologous counterpart-is susceptible to inactivation by BBR. Using three structurally distinct probe substrates, we consistently demonstrated that MBI was not elicited in CYP3A5 by BBR. Our in silico covalent docking models and molecular dynamics simulations suggested that disparities in the susceptibilities toward MBI could be attributed to the specific effects of BBR covalent adducts on the F-F' loop. Serendipitously, we also discovered that BBR reversibly activated CYP3A5-mediated rivaroxaban hydroxylation wherein apparent V max increased and K m decreased with increasing BBR concentration. Fitting data to the two-site model yielded interaction factors α and β of 0.44 and 5.88, respectively, thereby confirming heterotropic activation of CYP3A5 by BBR. Furthermore, heteroactivation was suppressed by the CYP3A inhibitor ketoconazole in a concentration-dependent manner and decreased with increasing preincubation time, implying that activation was incited via binding of parent BBR molecule within the enzymatic active site. Finally, noncovalent docking revealed that CYP3A5 can more favorably accommodate both BBR and rivaroxaban in concert as compared with CYP3A4, which further substantiated our experimental observations. SIGNIFICANCE STATEMENT: Although it has been previously demonstrated that benzbromarone (BBR) inactivates CYP3A4, it remains uninterrogated whether it also elicits mechanism-based inactivation in CYP3A5, which shares ∼85% sequence similarity with CYP3A4. This study reported that BBR exhibited differential irreversible and reversible interactions with both CYP3A isoforms and further unraveled the molecular determinants underpinning their diverging interactions. These data offer important insight into differential kinetic behavior of CYP3A4 and CYP3A5, which potentially contributes to interindividual variabilities in drug disposition.
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Affiliation(s)
- Lloyd Wei Tat Tang
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
| | - Ravi Kumar Verma
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
| | - Ren Ping Yong
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
| | - Xin Li
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
| | - Lili Wang
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
| | - Qingsong Lin
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
| | - Hao Fan
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
| | - Eric Chun Yong Chan
- Department of Pharmacy, Faculty of Science (L.W.T.T., R.P.Y., E.C.Y.C.), and Protein and Proteomics Centre (PPC), SingMass (X.L., L.W., Q.L.), National University of Singapore, Singapore; and Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore (R.K.V., H.F.)
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8
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Srinivasan B. Explicit Treatment of Non-Michaelis-Menten and Atypical Kinetics in Early Drug Discovery*. ChemMedChem 2020; 16:899-918. [PMID: 33231926 DOI: 10.1002/cmdc.202000791] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Indexed: 12/27/2022]
Abstract
Biological systems are highly regulated. They are also highly resistant to sudden perturbations enabling them to maintain the dynamic equilibrium essential to sustain life. This robustness is conferred by regulatory mechanisms that influence the activity of enzymes/proteins within their cellular context to adapt to changing environmental conditions. However, the initial rules governing the study of enzyme kinetics were mostly tested and implemented for cytosolic enzyme systems that were easy to isolate and/or recombinantly express. Moreover, these enzymes lacked complex regulatory modalities. Now, with academic labs and pharmaceutical companies turning their attention to more-complex systems (for instance, multiprotein complexes, oligomeric assemblies, membrane proteins and post-translationally modified proteins), the initial axioms defined by Michaelis-Menten (MM) kinetics are rendered inadequate, and the development of a new kind of kinetic analysis to study these systems is required. This review strives to present an overview of enzyme kinetic mechanisms that are atypical and, oftentimes, do not conform to the classical MM kinetics. Further, it presents initial ideas on the design and analysis of experiments in early drug-discovery for such systems, to enable effective screening and characterisation of small-molecule inhibitors with desirable physiological outcomes.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling Discovery Sciences, R&D, AstraZeneca, 310, Milton Rd, Milton CB4 0WG, Cambridge, UK
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9
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Kumar S, Bouic PJ, Rosenkranz B. In Vitro Assessment of the Interaction Potential of Ocimum basilicum (L.) Extracts on CYP2B6, 3A4, and Rifampicin Metabolism. Front Pharmacol 2020; 11:517. [PMID: 32425779 PMCID: PMC7204527 DOI: 10.3389/fphar.2020.00517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Ocimum basilicum L. or basilicum is a common culinary herb, used as a traditional medicine for various medical conditions including HIV/AIDS and tuberculosis, in Africa. The objective of this study was to evaluate the effect of methanol, ethanol, aqueous and ethyl acetate extracts of the dried leaves and inflorescence of O. basilicum, on the activity of cytochrome P450 enzymes (CYPs) CYP2B6 and 3A4, as well as esterase-mediated metabolism of rifampicin to 25-O-desacetyl rifampicin (25ODESRIF). Human liver microsomes (HLM) were used to evaluate inhibition and CYP2B6/3A4 mRNA expression HepG2 assays were used to measure induction. Furthermore, the phytoconstituents likely involved in causing the observed effect were analyzed using biochemical tests and LC-MS. The aqueous and methanolic extracts showed reversible and time-dependent inhibition (TDI) of CYP2B6 with TDI-IC50s 33.35 μg/ml (IC50 shift-fold >1.5) and 4.93 μg/ml (IC50 shift-fold >7) respectively, while the methanolic and ethanolic extracts inhibited 25ODESRIF formation (IC50s 31 μg/ml, 8.94 μg/ml). In HepG2 assays, the methanolic and ethanolic extracts moderately induced CYP2B6, 3A4 mRNA with 38%-, 28%-fold shift, and 22%-, 44%-fold shift respectively. LC-MS full scans identified phenols rosmarinic acid [m/z 359 (M-H)-, approximately 2298 mg/L in aqueous extract] and caftaric acid along with flavones salvigenin [m/z 329 (M+H)+, approximately 1855 mg/L in ethanolic extract], eupatorin [m/z 345 (M+H)+, 668.772 mg/L in ethanolic extract], rutin [m/z 609 (M-H)-] and isoquercetin [m/z 463 (M-H)-] and other compounds—linalool [m/z 153 (M-H)-], hydroxyjasmonic acid [m/z 225 (M-H)-], eucommiol [m/z 187 (M-H)-] and trihydroxy octadecenoic acid [m/z 329 (M-H)-, 530 mg/L in ethanolic extract]. The putative gastrointestinal tract (GIT) concentration for all extracts was calculated as 2,400 μg/ml and hepatic circulation concentrations were estimated at 805.68 μg/ml for the aqueous extract, and 226.56 μg/ml for methanolic extract. Based on the putative GIT concentration, estimated hepatic circulation concentration [I] and inhibition constant Ki, the predicted percentile of inhibition in vivo was highest for the aqueous extract on CYP2B6 (96.7%). The observations indicated that O. basilicum extracts may have the potential to cause clinically relevant herb-drug interactions (HDI) with CYP2B6 and rifampicin metabolism in vivo, if sufficient hepatic concentrations are reached in humans.
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Affiliation(s)
- Saneesh Kumar
- Division of Clinical Pharmacology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa
| | - Patrick J Bouic
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa.,Synexa Life Sciences, Cape Town, South Africa
| | - Bernd Rosenkranz
- Division of Clinical Pharmacology, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town, South Africa.,Fundisa African Academy of Medicines Development, Cape Town, South Africa
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10
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Atypical Michaelis-Menten kinetics in cytochrome P450 enzymes: A focus on substrate inhibition. Biochem Pharmacol 2019; 169:113615. [DOI: 10.1016/j.bcp.2019.08.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022]
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11
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Yadav J, Korzekwa K, Nagar S. Impact of Lipid Partitioning on the Design, Analysis, and Interpretation of Microsomal Time-Dependent Inactivation. Drug Metab Dispos 2019; 47:732-742. [PMID: 31043439 PMCID: PMC6556519 DOI: 10.1124/dmd.118.085969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/30/2019] [Indexed: 12/20/2022] Open
Abstract
Nonspecific drug partitioning into microsomal membranes must be considered for in vitro-in vivo correlations. This work evaluated the effect of including lipid partitioning in the analysis of complex TDI kinetics with numerical methods. The covariance between lipid partitioning and multiple inhibitor binding was evaluated. Simulations were performed to test the impact of lipid partitioning on the interpretation of TDI kinetics, and experimental TDI datasets for paroxetine (PAR) and itraconazole (ITZ) were modeled. For most kinetic schemes, modeling lipid partitioning results in statistically better fits. For MM-IL simulations (KI,u = 0.1 µM, kinact = 0.1 minute-1), concurrent modeling of lipid partitioning for an fumic range (0.01, 0.1, and 0.5) resulted in better fits compared with post hoc correction (AICc: -526 vs. -496, -579 vs. -499, and -636 vs. -579, respectively). Similar results were obtained with EII-IL. Lipid partitioning may be misinterpreted as double binding, leading to incorrect parameter estimates. For the MM-IL datasets, when fumic = 0.02, MM-IL, and EII model fits were indistinguishable (δAICc = 3). For less partitioned datasets (fumic = 0.1 or 0.5), the inclusion of partitioning resulted in better models. The inclusion of lipid partitioning can lead to markedly different estimates of KI,u and kinact A reasonable alternate experimental design is nondilution TDI assays, with post hoc fumic incorporation. The best fit models for PAR (MIC-M-IL) and ITZ (MIC-EII-M-IL and MIC-EII-M-Seq-IL) were consistent with their reported mechanism and kinetics. Overall, experimental fumic values should be concurrently incorporated into TDI models with complex kinetics, when dilution protocols are used.
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Affiliation(s)
- Jaydeep Yadav
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Ken Korzekwa
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
| | - Swati Nagar
- Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania
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12
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Buchholz PCF, Ohs R, Spiess AC, Pleiss J. Progress Curve Analysis Within BioCatNet: Comparing Kinetic Models for Enzyme-Catalyzed Self-Ligation. Biotechnol J 2018; 14:e1800183. [DOI: 10.1002/biot.201800183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/15/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart; Stuttgart Germany
| | - Rüdiger Ohs
- Institute for Biochemical Engineering, Technical University of Braunschweig; Braunschweig Germany
| | - Antje C. Spiess
- Institute for Biochemical Engineering, Technical University of Braunschweig; Braunschweig Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart; Stuttgart Germany
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13
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Tang S, Chen A, Zhou X, Zeng L, Liu M, Wang X. Assessment of the inhibition risk of shikonin on cytochrome P450 via cocktail inhibition assay. Toxicol Lett 2017; 281:74-83. [DOI: 10.1016/j.toxlet.2017.09.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/18/2017] [Accepted: 09/19/2017] [Indexed: 12/30/2022]
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14
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Venkatachalam A, Parashar A, Manoj KM. Functioning of drug-metabolizing microsomal cytochrome P450s: In silico probing of proteins suggests that the distal heme 'active site' pocket plays a relatively 'passive role' in some enzyme-substrate interactions. In Silico Pharmacol 2016; 4:2. [PMID: 26894412 PMCID: PMC4760962 DOI: 10.1186/s40203-016-0016-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/05/2016] [Indexed: 01/01/2023] Open
Abstract
PURPOSE The currently held mechanistic understanding of microsomal cytochrome P450s (CYPs) seeks that diverse drug molecules bind within the deep-seated distal heme pocket and subsequently react at the heme centre. To explain a bevy of experimental observations and meta-analyses, we indulge a hypothesis that involves a "diffusible radical mediated" mechanism. This new hypothesis posits that many substrates could also bind at alternate loci on/within the enzyme and be reacted without the pertinent moiety accessing a bonding proximity to the purported catalytic Fe-O enzyme intermediate. METHODS Through blind and heme-distal pocket centered dockings of various substrates and non-substrates (drug molecules of diverse sizes, classes, topographies etc.) of microsomal CYPs, we explored the possibility of access of substrates via the distal channels, its binding energies, docking orientations, distance of reactive moieties (or molecule per se) to/from the heme centre, etc. We investigated specific cases like- (a) large drug molecules as substrates, (b) classical marker drug substrates, (c) class of drugs as substrates (Sartans, Statins etc.), (d) substrate preferences between related and unrelated CYPs, (e) man-made site-directed mutants' and naturally occurring mutants' reactivity and metabolic disposition, (f) drug-drug interactions, (g) overall affinities of drug substrate versus oxidized product, (h) meta-analysis of in silico versus experimental binding constants and reaction/residence times etc. RESULTS It was found that heme-centered dockings of the substrate/modulator drug molecules with the available CYP crystal structures gave poor docking geometries and distances from Fe-heme centre. In conjunction with several other arguments, the findings discount the relevance of erstwhile hypothesis in many CYP systems. Consequently, the newly proposed hypothesis is deemed a viable alternate, as it satisfies Occam's razor. CONCLUSIONS The new proposal affords expanded scope for explaining the mechanism, kinetics and overall phenomenology of CYP mediated drug metabolism. It is now understood that the heme-iron and the hydrophobic distal pocket of CYPs serve primarily to stabilize the reactive intermediate (diffusible radical) and the surface or crypts of the apoprotein bind to the xenobiotic substrate (and in some cases, the heme distal pocket could also serve the latter function). Thus, CYPs enhance reaction rates and selectivity/specificity via a hitherto unrecognized modality.
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Affiliation(s)
- Avanthika Venkatachalam
- Formerly at PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004, India.
| | - Abhinav Parashar
- Formerly at Hemoproteins Lab, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India, 632014.
| | - Kelath Murali Manoj
- Formerly at PSG Institute of Advanced Studies, Avinashi Road, Peelamedu, Coimbatore, Tamil Nadu, 641004, India.
- Formerly at Hemoproteins Lab, School of Bio Sciences and Technology, VIT University, Vellore, Tamil Nadu, India, 632014.
- Satyamjayatu: The Science & Ethics Foundation, Kulappully, Shoranur-2 (PO), Kerala, 679122, India.
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Shaik AN, Bohnert T, Williams DA, Gan LL, LeDuc BW. Mechanism of Drug-Drug Interactions Between Warfarin and Statins. J Pharm Sci 2016; 105:1976-1986. [PMID: 27103011 DOI: 10.1016/j.xphs.2016.03.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 11/25/2022]
Abstract
The anticoagulant drug warfarin and the lipid-lowering statin drugs are commonly co-administered to patients with cardiovascular diseases. Clinically significant drug-drug interactions (DDIs) between these drugs have been recognized through case studies for many years, but the biochemical mechanisms causing these interactions have not been explained fully. Previous theories include kinetic alterations in cytochrome P-450-mediated drug metabolism or disturbances of drug-protein binding, leading to anticoagulant activity of warfarin; however, neither the enantioselective effects on warfarin metabolism nor the potential disruption of drug transporter function have been well investigated. This study investigated the etiology of the DDIs between warfarin and statins. Liquid chromatography-mass spectrometry methods were developed and validated to quantify racemic warfarin, 6 of its hydroxylated metabolites, and pure enantiomers of warfarin; these methods were applied to study the role of different absorption, distribution, metabolism, and excretion properties, leading to DDIs. Plasma protein binding displacement of warfarin was performed in the presence of statins using equilibrium dialysis method. Substrate kinetics of warfarin and pure enantiomers were performed with human liver microsomes to determine the kinetic parameters (Km and Vmax) for the formation of all 6 hydroxywarfarin metabolites, inhibition of warfarin metabolism in the presence of statins, was determined. Uptake transport studies of warfarin were performed using overexpressing HEK cell lines and efflux transport using human adenocarcinoma colonic cell line cells. Fluvastatin significantly displaced plasma protein binding of warfarin and pure enantiomers; no other statin resulted in significant displacement of warfarin. All the statins that inhibited the formation of 10-hydroxywarfarin, atorvastatin, pitavastatin, and simvastatin were highly potent compared to other statins; in contrast, only fluvastatin was found to be a potent inhibitor of formation of 7-hydroxy warfarin. Uptake and efflux drug transporters do not play any role in these DDIs. The results showed that DDIs between warfarin and statins are primarily caused by cytochrome P-450 inhibition.
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Affiliation(s)
- Abdul Naveed Shaik
- Department of Pharmaceutical Sciences, MCPHS University, 179 Longwood Avenue, Boston, Massachusetts 02115; Department of Drug Metabolism and Pharmacokinetics, Biogen, 14 Cambridge Center, Cambridge, Massachusetts 02140.
| | - Tonika Bohnert
- Department of Drug Metabolism and Pharmacokinetics, Biogen, 14 Cambridge Center, Cambridge, Massachusetts 02140
| | - David A Williams
- Department of Pharmaceutical Sciences, MCPHS University, 179 Longwood Avenue, Boston, Massachusetts 02115
| | - Lawrence L Gan
- Development Center for Biotechnology, Taipei 221, Taiwan
| | - Barbara W LeDuc
- Department of Pharmaceutical Sciences, MCPHS University, 179 Longwood Avenue, Boston, Massachusetts 02115
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16
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Sun D, Zhu L, Xiao L, Xia Y, Ge G, Cao Y, Wu Y, Yin J, Yang L. In vitroglucuronidation of Armillarisin A: UDP-glucuronosyltransferase 1A9 acts as a major contributor and significant species differences. Xenobiotica 2014; 44:988-95. [DOI: 10.3109/00498254.2014.927084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Al-Jenoobi FI, Al-Thukair AA, Alam MA, Abbas FA, Al-Mohizea AM, Alkharfy KM, Al-Suwayeh SA. Modulation of CYP2D6 and CYP3A4 metabolic activities by Ferula asafetida resin. Saudi Pharm J 2014; 22:564-9. [PMID: 25561870 PMCID: PMC4281599 DOI: 10.1016/j.jsps.2014.03.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 03/26/2014] [Indexed: 11/30/2022] Open
Abstract
Present study investigated the potential effects of Ferula asafetida resin on metabolic activities of human drug metabolizing enzymes: CYP2D6 and CYP3A4. Dextromethorphan (DEX) was used as a marker to assess metabolic activities of these enzymes, based on its CYP2D6 and CYP3A4 mediated metabolism to dextrorphan (DOR) and 3-methoxymorphinan (3-MM), respectively. In vitro study was conducted by incubating DEX with human liver microsomes and NADPH in the presence or absence of Asafetida alcoholic extract. For clinical study, healthy human volunteers received a single dose of DEX alone (phase-I) and repeated the same dose after a washout period and four-day Asafetida treatment (phase-II). Asafetida showed a concentration dependent inhibition on DOR formation (in vitro) and a 33% increase in DEX/DOR urinary metabolic ratio in clinical study. For CYP3A4, formation of 3-MM in microsomes was increased at low Asafetida concentrations (10, 25 and 50 μg/ml) but slightly inhibited at the concentration of 100 μg/ml. On the other hand, in vivo observations revealed that Asafetida significantly increased DEX/3-MM urinary metabolic ratio. The findings of this study suggest that Asafetida may have a significant effect on CYP3A4 metabolic activity. Therefore, using Ferula asafetida with CYP3A4 drug substrates should be cautioned especially those with narrow therapeutic index such as cyclosporine, tacrolimus and carbamazepine.
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Affiliation(s)
- Fahad I. Al-Jenoobi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Corresponding author. Address: Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh-11451, Saudi Arabia. Tel.: +966 504187374.
| | - Areej A. Al-Thukair
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohd Aftab Alam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Fawkeya A. Abbas
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah M. Al-Mohizea
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Khalid M. Alkharfy
- Department of Clinical Pharmacy, College of Pharmacy and Biomarkers Research Program, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A. Al-Suwayeh
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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18
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Brantley SJ, Argikar AA, Lin YS, Nagar S, Paine MF. Herb-drug interactions: challenges and opportunities for improved predictions. Drug Metab Dispos 2014; 42:301-17. [PMID: 24335390 PMCID: PMC3935140 DOI: 10.1124/dmd.113.055236] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/11/2013] [Indexed: 01/23/2023] Open
Abstract
Supported by a usage history that predates written records and the perception that "natural" ensures safety, herbal products have increasingly been incorporated into Western health care. Consumers often self-administer these products concomitantly with conventional medications without informing their health care provider(s). Such herb-drug combinations can produce untoward effects when the herbal product perturbs the activity of drug metabolizing enzymes and/or transporters. Despite increasing recognition of these types of herb-drug interactions, a standard system for interaction prediction and evaluation is nonexistent. Consequently, the mechanisms underlying herb-drug interactions remain an understudied area of pharmacotherapy. Evaluation of herbal product interaction liability is challenging due to variability in herbal product composition, uncertainty of the causative constituents, and often scant knowledge of causative constituent pharmacokinetics. These limitations are confounded further by the varying perspectives concerning herbal product regulation. Systematic evaluation of herbal product drug interaction liability, as is routine for new drugs under development, necessitates identifying individual constituents from herbal products and characterizing the interaction potential of such constituents. Integration of this information into in silico models that estimate the pharmacokinetics of individual constituents should facilitate prospective identification of herb-drug interactions. These concepts are highlighted with the exemplar herbal products milk thistle and resveratrol. Implementation of this methodology should help provide definitive information to both consumers and clinicians about the risk of adding herbal products to conventional pharmacotherapeutic regimens.
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Affiliation(s)
- Scott J Brantley
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina (S.J.B.); Department of Pharmaceutical Sciences, Temple University School of Pharmacy, Philadelphia, Pennsylvania (A.A.A., S.N.); Department of Pharmaceutics, University of Washington, Seattle, Washington (Y.S.L.); and College of Pharmacy, Washington State University, Spokane, Washington (M.F.P.)
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Abstract
As described in Chapter 2 , a large number of enzymatic reactions can be adequately described by Michaelis-Menten kinetics. The Michaelis-Menten equation represents a rectangular hyperbola, with a y-asymptote at the V max value. In many cases, more complex kinetic models are required to explain the observed data. Atypical kinetic profiles are believed to arise from the simultaneous binding of multiple molecules within the active site of the enzyme (Tracy and Hummel, Drug Metab Rev 36:231-242, 2004). Several cytochromes P450 have large active sites that enable binding of multiple molecules (Wester et al. J Biol Chem 279:35630-35637, 2004; Yano et al. J Biol Chem 279:38091-38094, 2004). Thus, atypical kinetics are not uncommon in in vitro drug metabolism studies. This chapter covers enzyme kinetic reactions in which a single enzyme has multiple binding sites for substrates and/or inhibitors as well as reactions catalyzed by multiple enzymes.
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Affiliation(s)
- Eleanore Seibert
- R&D Project Management, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
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20
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Farrow SC, Facchini PJ. Dioxygenases catalyze O-demethylation and O,O-demethylenation with widespread roles in benzylisoquinoline alkaloid metabolism in opium poppy. J Biol Chem 2013; 288:28997-9012. [PMID: 23928311 DOI: 10.1074/jbc.m113.488585] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
In opium poppy, the antepenultimate and final steps in morphine biosynthesis are catalyzed by the 2-oxoglutarate/Fe(II)-dependent dioxygenases, thebaine 6-O-demethylase (T6ODM) and codeine O-demethylase (CODM). Further investigation into the biochemical functions of CODM and T6ODM revealed extensive and unexpected roles for such enzymes in the metabolism of protopine, benzo[c]phenanthridine, and rhoeadine alkaloids. When assayed with a wide range of benzylisoquinoline alkaloids, CODM, T6ODM, and the functionally unassigned paralog DIOX2, renamed protopine O-dealkylase, showed novel and efficient dealkylation activities, including regio- and substrate-specific O-demethylation and O,O-demethylenation. Enzymes catalyzing O,O-demethylenation, which cleave a methylenedioxy bridge leaving two hydroxyl groups, have previously not been reported in plants. Similar cleavage of methylenedioxy bridges on substituted amphetamines is catalyzed by heme-dependent cytochromes P450 in mammals. Preferred substrates for O,O-demethylenation by CODM and protopine O-dealkylase were protopine alkaloids that serve as intermediates in the biosynthesis of benzo[c]phenanthridine and rhoeadine derivatives. Virus-induced gene silencing used to suppress the abundance of CODM and/or T6ODM transcripts indicated a direct physiological role for these enzymes in the metabolism of protopine alkaloids, and they revealed their indirect involvement in the formation of the antimicrobial benzo[c]phenanthridine sanguinarine and certain rhoeadine alkaloids in opium poppy.
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Affiliation(s)
- Scott C Farrow
- From the Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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21
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Zhang H, Gay SC, Shah M, Foroozesh M, Liu J, Osawa Y, Zhang Q, Stout CD, Halpert JR, Hollenberg PF. Potent mechanism-based inactivation of cytochrome P450 2B4 by 9-ethynylphenanthrene: implications for allosteric modulation of cytochrome P450 catalysis. Biochemistry 2013; 52:355-64. [PMID: 23276288 DOI: 10.1021/bi301567z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism-based inactivation of cytochrome P450 2B4 (CYP2B4) by 9-ethynylphenanthrene (9EP) has been investigated. The partition ratio and k(inact) are 0.2 and 0.25 min(-1), respectively. Intriguingly, the inactivation exhibits sigmoidal kinetics with a Hill coefficient of 2.5 and an S(50) of 4.5 μM indicative of homotropic cooperativity. Enzyme inactivation led to an increase in mass of the apo-CYP2B4 by 218 Da as determined by electrospray ionization liquid chromatography and mass spectrometry, consistent with covalent protein modification. The modified CYP2B4 was purified to homogeneity and its structure determined by X-ray crystallography. The structure showed that 9EP is covalently attached to Oγ of Thr 302 via an ester bond, which is consistent with the increased mass of the protein. The presence of the bulky phenanthrenyl ring resulted in inward rotations of Phe 297 and Phe 206, leading to a compact active site. Thus, binding of another molecule of 9EP in the active site is prohibited. However, results from the quenching of 9EP fluorescence by unmodified or 9EP-modified CYP2B4 revealed at least two binding sites with distinct affinities, with the low-affinity site being the catalytic site and the high-affinity site on the protein periphery. Computer-aided docking and molecular dynamics simulations with one or two ligands bound revealed that the high-affinity site is situated at the entrance of a substrate access channel surrounded by the F' helix, β1-β2 loop, and β4 loop and functions as an allosteric site to enhance the efficiency of activation of the acetylenic group of 9EP and subsequent covalent modification of Thr 302.
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Affiliation(s)
- Haoming Zhang
- Department of Pharmacology, The University of Michigan Medical School , Ann Arbor, Michigan 48109, USA
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22
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Physiologically Based Pharmacokinetic (PBPK) Modeling of Metabolic Pathways of Bromochloromethane in Rats. J Toxicol 2012; 2012:629781. [PMID: 22719758 PMCID: PMC3377357 DOI: 10.1155/2012/629781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/27/2012] [Accepted: 03/30/2012] [Indexed: 11/18/2022] Open
Abstract
Bromochloromethane (BCM) is a volatile compound and a by-product of disinfection of water by chlorination. Physiologically based pharmacokinetic (PBPK) models are used in risk assessment applications. An updated PBPK model for BCM is generated and applied to hypotheses testing calibrated using vapor uptake data. The two different metabolic hypotheses examined are (1) a two-pathway model using both CYP2E1 and glutathione transferase enzymes and (2) a two-binding site model where metabolism can occur on one enzyme, CYP2E1. Our computer simulations show that both hypotheses describe the experimental data in a similar manner. The two pathway results were comparable to previously reported values (Vmax = 3.8 mg/hour, Km = 0.35 mg/liter, and kGST = 4.7 /hour). The two binding site results were Vmax1 = 3.7 mg/hour, Km1 = 0.3 mg/hour, CL2 = 0.047 liter/hour. In addition, we explore the sensitivity of different parameters for each model using our obtained optimized values.
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23
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Denisov IG, Sligar SG. A novel type of allosteric regulation: functional cooperativity in monomeric proteins. Arch Biochem Biophys 2012; 519:91-102. [PMID: 22245335 PMCID: PMC3329180 DOI: 10.1016/j.abb.2011.12.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 10/14/2022]
Abstract
Cooperative functional properties and allosteric regulation in cytochromes P450 play an important role in xenobiotic metabolism and define one of the main mechanisms of drug-drug interactions. Recent experimental results suggest that ability to bind simultaneously two or more small organic molecules can be the essential feature of cytochrome P450 fold, and often results in rich and complex pattern of allosteric behavior. Manifestations of non-Michaelis kinetics include homotropic and heterotropic activation and inhibition effects depending on the stoichiometric ratios of substrate and effector, changes in the regio- and stereospecificity of catalytic transformations, and often give rise to the clinically important drug-drug interactions. In addition, functional response of P450 systems is modulated by the presence of specific and non-specific effector molecules, metal ions, membrane incorporation, formation of homo- and hetero-oligomers, and interactions with the protein redox partners. In this article we briefly overview the main factors contributing to the allosteric effects in cytochromes P450 with the main focus on the sources of cooperative behavior in xenobiotic metabolizing monomeric heme enzymes with their conformational flexibility and extremely broad substrate specificity. The novel mechanism of functional cooperativity in P450 enzymes does not require substantial binding cooperativity, rather it implies the presence of one or more binding sites with higher affinity than the single catalytically active site in the vicinity of the heme iron.
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Affiliation(s)
- Ilia G. Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801
| | - Stephen G. Sligar
- Department of Biochemistry, University of Illinois, Urbana, IL, 61801
- Beckman Institute, University of Illinois, Urbana, IL, 61801
- School of Molecular and Cellular Biology, University of Illinois, Urbana, IL, 61801
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Li Y, Xu J, Lai WG, Whitcher-Johnstone A, Tweedie DJ. Metabolic Switching of BILR 355 in the Presence of Ritonavir. II. Uncovering Novel Contributions by Gut Bacteria and Aldehyde Oxidase. Drug Metab Dispos 2012; 40:1130-7. [DOI: 10.1124/dmd.111.044362] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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25
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Dong D, Wu B. Substrate selectivity of drug-metabolizing cytochrome P450s predicted from crystal structures andin silicomodeling. Drug Metab Rev 2012; 44:1-17. [DOI: 10.3109/03602532.2011.645581] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Dong D, Wu B, Chow D, Hu M. Substrate selectivity of drug-metabolizing cytochrome P450s predicted from crystal structures and in silico modeling. Drug Metab Rev 2012; 44:192-208. [PMID: 22251142 DOI: 10.3109/03602532.2011.645580] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Enormous efforts toward predicting the metabolic fate of a drug have been driven by the high attrition rate in drug development. To accelerate such efforts, it is critical to elucidate the molecular mechanisms of drug recognition by drug-metabolizing enzymes. Therefore, it is not surprising that an increasing number of crystal structures have been determined (by X-ray crystallography) and numerous insightful in silico (computational) models have been established for the most important metabolic enzymes, cytochrome P450s (CYPs). In this review, we provide a detailed analysis of the available crystal structures for CYPs to reveal the structural features and protein flexibility determining substrate selectivity. The ligand-based in silico models (including pharmacophore and molecular field analysis models) are also discussed, with a focus on their ability to characterize the structural features of the substrates for various CYP isoforms.
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Affiliation(s)
- Dong Dong
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas 77030, USA
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27
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Evidence of CYP3A allosterism in vivo: analysis of interaction between fluconazole and midazolam. Clin Pharmacol Ther 2011; 91:442-9. [PMID: 22048224 PMCID: PMC3830930 DOI: 10.1038/clpt.2011.178] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The allosteric effect of fluconazole (effector) on the formation of 1’-hydroxymidazolam (1’-OH-MDZ) and 4-hydroxymidazolam (4-OH-MDZ) from the CYP3A4/5 substrate, midazolam (MDZ), was examined in healthy volunteers. Following pre-treatment of fluconazole, AUC4-OH/AUCMDZ increased 35–62%, while AUC1’-OH/AUCMDZ decreased 5–37%; AUC1’-OH/AUC4-OH ratio decreased 46–58% by fluconazole and had no association with CYP3A5 genotype. 1’-OH-MDZ formation in vitro was more susceptible than 4-OH-MDZ formation to inhibition by fluconazole. Fluconazole decreased the intrinsic formation clearance ratio of 1’-OH-MDZ/4-OH-MDZ to an extent that was quantitatively comparable to in vivo observations. The elimination clearance of midazolam metabolites appeared unaffected by fluconazole. This study demonstrated that fluconazole alters midazolam product formation both in vivo and in vitro in a manner consistent with an allosteric interaction. The 1'-OH-MDZ/4-OH-MDZ ratio may serve as a biomarker of such interactions between midazolam, CYP3A4/5 and other putative effectors.
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28
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Abstract
Inhibition of enzyme activity at high substrate concentrations, so-called "substrate inhibition," is commonly observed and has been recognized in drug metabolism reactions since the last decade. Although the importance of such "atypical" kinetics in vivo remains poorly understood, a substrate with substrate inhibition kinetics has been shown to unconventionally alter the metabolism of other substrates. In recent years, it is becoming increasingly evident that the mechanisms for substrate inhibition are highly complex, which are possibly contributed by multiple (at least two) binding sites within the enzyme protein, the formation of a ternary dead-end enzyme complex, and/or the ligand-induced changes in enzyme conformation. This review primarily discusses the mechanisms for substrate inhibition displayed by the important drug-metabolizing enzymes, such as cytochrome p450s, UDP-glucuronyltransferases, and sulfotransferases. Kinetic modeling of substrate inhibition in the absence or presence of a modifier is another central issue in this review because of its importance in the determination of kinetic parameters and in vitro/in vivo predictions.
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Affiliation(s)
- Baojian Wu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Texas, USA.
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29
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Atkins WM, Qian H. Stochastic ensembles, conformationally adaptive teamwork, and enzymatic detoxification. Biochemistry 2011; 50:3866-72. [PMID: 21473615 DOI: 10.1021/bi200275r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
It has been appreciated for a long time that enzymes exist as conformational ensembles throughout multiple stages of the reactions they catalyze, but there is renewed interest in the functional implications. The energy landscape that results from conformationlly diverse poteins is a complex surface with an energetic topography in multiple dimensions, even at the transition state(s) leading to product formation, and this represents a new paradigm. At the same time there has been renewed interest in conformational ensembles, a new paradigm concerning enzyme function has emerged, wherein catalytic promiscuity has clear biological advantages in some cases. "Useful", or biologically functional, promiscuity or the related behavior of "multifunctionality" can be found in the immune system, enzymatic detoxification, signal transduction, and the evolution of new function from an existing pool of folded protein scaffolds. Experimental evidence supports the widely held assumption that conformational heterogeneity promotes functional promiscuity. The common link between these coevolving paradigms is the inherent structural plasticity and conformational dynamics of proteins that, on one hand, lead to complex but evolutionarily selected energy landscapes and, on the other hand, promote functional promiscuity. Here we consider a logical extension of the overlap between these two nascent paradigms: functionally promiscuous and multifunctional enzymes such as detoxification enzymes are expected to have an ensemble landscape with more states accessible on multiple time scales than substrate specific enzymes. Two attributes of detoxification enzymes become important in the context of conformational ensembles: these enzymes metabolize multiple substrates, often in substrate mixtures, and they can form multiple products from a single substrate. These properties, combined with complex conformational landscapes, lead to the possibility of interesting time-dependent, or emergent, properties. Here we demonstrate these properties with kinetic simulations of nonequilibrium steady state (NESS) behavior resulting from energy landscapes expected for detoxification enzymes. Analogous scenarios with other promiscuous enzymes may be worthy of consideration.
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Affiliation(s)
- William M Atkins
- Department of Medicinal Chemistry and Department of Applied Mathematics, University of Washington, Seattle, Washington 98190, United States.
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30
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Al-Jenoobi FI. Effects of some commonly used Saudi folk herbal medications on the metabolic activity of CYP2C9 in human liver microsomes. Saudi Pharm J 2010; 18:167-71. [PMID: 23964176 DOI: 10.1016/j.jsps.2010.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 04/14/2010] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE To investigate the potential effects of eleven of the most commonly used Saudi folk herbal medications on the metabolic activity of CYP2C9 in human liver microsomes. METHOD CYP2C9-mediated 4'-hydroxylation of tolbutamide (TB) to 4'-hydroxytolbutamide (4-OH-TB) was utilized to assess the metabolic activity of CYP2C9. In the present study, an initial screening of the eleven herbs was carried out by incubating TB with microsomes and NADPH in absence or presence of a fixed concentration (25 μg/ml) of alcoholic extracts of different herbs and the metabolite formed was measured by HPLC. Herbs that showed significant effects were further investigated at a lower range of concentration. RESULTS Among the investigated herbal extracts, only aniseed and curcuma showed statistically significant effects on the formation of 4-OH-TB in human liver microsomes. Curcuma produced a potent inhibition on the metabolite formation and its maximum (about 45% inhibition) was observed at the highest extract concentrations (10 and 25 μg/ml). On the other hand, aniseed significantly activates the formation of 4-OH-TB and the maximum activation (about 55%) was observed at 2.5 μg/ml of aniseed extract. CONCLUSION The results of this study have shown that alcoholic extracts of curcuma and aniseed were capable of inhibiting and activating; respectively, the CYP2C9-mediated 4-OH-TB formation in human liver microsomes, suggesting that these herbs have the potential to interact with CYP2C9 drug substrates. None of the other nine investigated herbs was able to produce any statistically significant effect.
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Affiliation(s)
- Fahad I Al-Jenoobi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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Kumar S. Engineering cytochrome P450 biocatalysts for biotechnology, medicine and bioremediation. Expert Opin Drug Metab Toxicol 2010; 6:115-31. [PMID: 20064075 DOI: 10.1517/17425250903431040] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
IMPORTANCE OF THE FIELD Cytochrome P450 enzymes comprise a superfamily of heme monooxygenases that are of considerable interest for the: i) synthesis of novel drugs and drug metabolites; ii) targeted cancer gene therapy; iii) biosensor design; and iv) bioremediation. However, their applications are limited because cytochrome P450, especially mammalian P450 enzymes, show a low turnover rate and stability, and require a complex source of electrons through cytochrome P450 reductase and NADPH. AREAS COVERED IN THIS REVIEW In this review, we discuss the recent progress towards the use of P450 enzymes in a variety of the above-mentioned applications. We also present alternate and cost-effective ways to perform P450-mediated reaction, especially using peroxides. Furthermore, we expand upon the current progress in P450 engineering approaches describing several recent examples that are utilized to enhance heterologous expression, stability, catalytic efficiency and utilization of alternate oxidants. WHAT THE READER WILL GAIN The review provides a comprehensive knowledge in the design of P450 biocatalysts for potentially practical purposes. Finally, we provide a prospective on the future aspects of P450 engineering and its applications in biotechnology, medicine and bioremediation. TAKE HOME MESSAGE Because of its wide applications, academic and pharmaceutical researchers, environmental scientists and healthcare providers are expected to gain current knowledge and future prospects of the practical use of P450 biocatalysts.
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Affiliation(s)
- Santosh Kumar
- University of Missouri-Kansas City, School of Pharmacy, Division of Pharmacology and Toxicology, 2464 Charlotte St., Kansas City, MO 64108, USA.
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Evans MV, Caldwell JC. Evaluation of two different metabolic hypotheses for dichloromethane toxicity using physiologically based pharmacokinetic modeling for in vivo inhalation gas uptake data exposure in female B6C3F1 mice. Toxicol Appl Pharmacol 2010; 244:280-90. [PMID: 20153349 DOI: 10.1016/j.taap.2010.01.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 01/25/2010] [Accepted: 01/30/2010] [Indexed: 11/25/2022]
Abstract
Dichloromethane (DCM, methylene chloride) is a lipophilic volatile compound readily absorbed and then metabolized to several metabolites that may lead to chronic toxicity in different target organs. Physiologically based pharmacokinetic (PBPK) models are useful tools for calculation of internal and target organ doses of parent compound and metabolites. PBPK models, coupled with in vivo inhalation gas-uptake data, can be useful to estimate total metabolism. Previously, such an approach was used to make predictions regarding the metabolism and to make subsequent inferences of DCM's mode of action for toxicity. However, current evidence warrants re-examination of this approach. The goal of this work was to examine two different hypotheses for DCM metabolism in mice. One hypothesis describes two metabolic pathways: one involving cytochrome P450 2E1 (CYP2E1) and a second glutathione (GSH). The second metabolic hypothesis describes only one pathway mediated by CYP2E1 that includes multiple binding sites. The results of our analysis show that the in vivo gas-uptake data fit both hypotheses well and the traditional analysis of the chamber concentration data is not sufficient to distinguish between them. Gas-uptake data were re-analyzed by construction of a velocity plot as a function of increasing DCM initial concentration. The velocity (slope) analysis revealed that there are two substantially different phases in velocity, one rate for lower exposures and a different rate for higher exposures. The concept of a "metabolic switch," namely that due to conformational changes in the enzyme after one site is occupied - a different metabolic rate is seen - is also consistent with the experimental data. Our analyses raise questions concerning the importance of GSH metabolism for DCM. Recent research results also question the importance of this pathway in the toxicity of DCM. GSH-related DNA adducts were not formed after in vivo DCM exposure in mice and DCM-induced DNA damage has been detected in human lung cultures without GSH metabolism. In summary, a revised/updated metabolic hypothesis for DCM has been examined using in vivo inhalation data in mice combined with PBPK modeling that is consistent with up-to-date models of the active site for CYP2E1 and suggests that this pathway is the major metabolizing pathway for DCM metabolism.
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Affiliation(s)
- M V Evans
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC 27711, USA.
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Westholm DE, Salo DR, Viken KJ, Rumbley JN, Anderson GW. The blood-brain barrier thyroxine transporter organic anion-transporting polypeptide 1c1 displays atypical transport kinetics. Endocrinology 2009; 150:5153-62. [PMID: 19819953 DOI: 10.1210/en.2009-0769] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Organic anion-transporting polypeptide (Oatp) 1c1 is a high-affinity T(4) transporter expressed in brain barrier cells. Oatp1c1 transports a variety of additional ligands including the conjugated sterol estradiol 17beta-glucuronide (E(2)17betaG). Intriguingly, published data suggest that E(2)17betaG inhibition of Oatp1c1-mediated T(4) transport exhibits characteristics suggestive of atypical transport kinetics. To determine whether Oatp1c1 exhibits atypical transport kinetics, we first performed detailed T(4) and E(2)17betaG uptake assays using Oatp1c1 stably transfected HEK293 cells and a wide range of T(4) and E(2)17betaG concentrations (100 pm to 300 nm and 27 nm to 200 mum, respectively). Eadie-Hofstee plots derived from these detailed T(4) and E(2)17betaG uptake experiments display a biphasic profile consistent with atypical transport kinetics. These data along with T(4) and E(2)17betaG cis-inhibition dose-response measurements revealed shared high- and low-affinity Oatp1c1 binding sites for T(4) and E(2)17betaG. T(4) and E(2)17betaG recognized these Oatp1c1 binding sites with opposite preferences. In addition, sterols glucuronidated in the 17 or 21 position, exhibited preferential substrate-dependent inhibition of Oatp1c1 transport, inhibiting Oatp1c1-mediated E(2)17betaG transport more strongly than T(4) transport. Together these data reveal that Oatp1c1-dependent substrate transport is a complex process involving substrate interaction with multiple binding sites and competition for binding with a variety of other substrates. A thorough understanding of atypical Oatp1c1 transport processes and substrate-dependent inhibition will allow better prediction of endo- and xenobiotic interactions with the Oatp transporter.
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Affiliation(s)
- Daniel E Westholm
- Department of Pharmacy Practice and Pharmaceutical Sciences, College of Pharmacy, University of Minnesota-Duluth, Duluth, Minnesota 55812, USA
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Denisov IG, Frank DJ, Sligar SG. Cooperative properties of cytochromes P450. Pharmacol Ther 2009; 124:151-67. [PMID: 19555717 DOI: 10.1016/j.pharmthera.2009.05.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Accepted: 05/28/2009] [Indexed: 02/07/2023]
Abstract
Cytochromes P450 form a large and important class of heme monooxygenases with a broad spectrum of substrates and corresponding functions, from steroid hormone biosynthesis to the metabolism of xenobiotics. Despite decades of study, the molecular mechanisms responsible for the complex non-Michaelis behavior observed with many members of this superfamily during metabolism, often termed 'cooperativity', remain to be fully elucidated. Although there is evidence that oligomerization may play an important role in defining the observed cooperativity, some monomeric cytochromes P450, particularly those involved in xenobiotic metabolism, also display this behavior due to their ability to simultaneously bind several substrate molecules. As a result, formation of distinct enzyme-substrate complexes with different stoichiometry and functional properties can give rise to homotropic and heterotropic cooperative behavior. This review aims to summarize the current understanding of cooperativity in cytochromes P450, with a focus on the nature of cooperative effects in monomeric enzymes.
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Affiliation(s)
- Ilia G Denisov
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, United States of America
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35
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Wei X, Dai G, Liu Z, Cheng H, Xie Z, Klisovic R, Marcucci G, Chan KK. Enzyme kinetics of GTI-2040, a phosphorothioate oligonucleotide targeting ribonucleotide reductase. Drug Metab Dispos 2008; 36:2227-33. [PMID: 18653746 DOI: 10.1124/dmd.108.021295] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Enzyme kinetics of GTI-2040 (5'-GGC TAA ATC GCT CCA CCA AG-3'), a phosphorothioate ribonucleotide reductase antisense, were investigated for the first time in 3' exonuclease solution and human liver microsomes (HLMs), using the ion-pair high-performance liquid chromatogram method for quantification of the parent drug and two major 3'N-1 and 3'N-2 metabolites. Enzyme kinetics of GTI-2040 in 3'-exonuclease solution were found to be well characterized by the Michaelis-Menten model, using the sum of formation rates of 3'N-1 and 3'N-2 (approximately total metabolism) because of sequential metabolism. In HLMs, a biphasic binding was observed for GTI-2040 with high- and low-affinity constants (K(d)s) of 0.03 and 3.8 microM, respectively. Enzyme kinetics of GTI-2040 in HLMs were found to deviate from Michaelis-Menten kinetics when the total GTI-2040 substrate was used. However, after correction for the unbound fractions, the formation rate of total metabolites could be described by Michaelis-Menten kinetics. Using the free substrate fraction, the K(m) and V(max) of GTI-2040 were determined to be 6.33 +/- 3.2 microM and 16.5 +/- 8.4 nmol/mg/h, respectively. Using these values, in vitro hepatic intrinsic clearance (CL(int)) in HLM was estimated to be 2.61 +/- 0.56 ml/h. The CL(int) was then used to predict GTI-2040's in vivo intrinsic clearance in humans by a microsomal protein scaling factor, which gave a mean value of 182.7 l/h, representing 24.1% of the observed in vivo mean scaled hepatic intrinsic clearance of 758.7 l/h in patients with acute myeloid leukemia. We concluded that the saturable nonspecific binding of GTI-2040 in HLMs complicated the interpretation of its enzyme kinetics, and scaled intrinsic clearance from HLMs only partially predicted the in vivo intrinsic clearance.
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Affiliation(s)
- Xiaohui Wei
- Division of Pharmaceutics, College of Pharmacy, Ohio State University, Columbus, OH 43210, USA
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36
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Isin EM, Guengerich FP. Substrate binding to cytochromes P450. Anal Bioanal Chem 2008; 392:1019-30. [PMID: 18622598 DOI: 10.1007/s00216-008-2244-0] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/10/2008] [Accepted: 06/11/2008] [Indexed: 01/08/2023]
Abstract
P450s have attracted tremendous attention owing to not only their involvement in the metabolism of drug molecules and endogenous substrates but also the unusual nature of the reaction they catalyze, namely, the oxidation of unactivated C-H bonds. The binding of substrates to P450s, which is usually viewed as the first step in the catalytic cycle, has been studied extensively via a variety of biochemical and biophysical approaches. These studies were directed towards answering different questions related to P450s, including mechanism of oxidation, substrate properties, unusual substrate oxidation kinetics, function, and active-site features. Some of the substrate binding studies extending over a period of more than 40 years of dedicated work have been summarized in this review and categorized by the techniques employed in the binding studies.
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Affiliation(s)
- Emre M Isin
- Biotransformation Section, Department of Discovery DMPK & Bioanalytical Chemistry, AstraZeneca R & D Mölndal, 431 83, Mölndal, Sweden.
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Isin EM, Sohl CD, Eoff RL, Guengerich FP. Cooperativity of cytochrome P450 1A2: interactions of 1,4-phenylene diisocyanide and 1-isopropoxy-4-nitrobenzene. Arch Biochem Biophys 2008; 473:69-75. [PMID: 18328798 PMCID: PMC4662254 DOI: 10.1016/j.abb.2008.02.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2008] [Revised: 02/19/2008] [Accepted: 02/22/2008] [Indexed: 11/26/2022]
Abstract
Homotropic cooperativity of 1-alkoxy-4-nitrobenzene substrates and also their heterotropic cooperative binding interactions with the iron ligand 1,4-phenylene diisocyanide (Ph(NC)2) had been demonstrated previously with rabbit cytochrome P450 (P450) 1A2 [G.P. Miller, F.P. Guengerich, Biochemistry 40 (2001) 7262-7272]. Multiphasic kinetics were observed for the binding of Ph(NC)2 to both ferric and ferrous P450 1A2, including relatively slow steps. Ph(NC)2 induced an apparently rapid change in the circular dichroism spectrum, consistent with a structural change, but had no effect on tryptophan fluorescence. Ph(NC)2 binds the P450 iron in both the ferric and ferrous forms; ferric P450 1A2 was reduced rapidly in the absence of added ligands, and the rate was attenuated when Ph(NC)2 was bound. No oxidation products of Ph(NC)2 were detected. Docking studies with a rabbit P450 1A2 homology model based on the published structure of a human P450 1A2.alpha-naphthoflavone (alphaNF) complex indicated adequate room for a complex with either two 1-isopropoxy-4-nitrobenzene molecules or a combination of one 1-isopropoxy-4-nitrobenzene and one Ph(NC)2; in the case of alphaNF no space for an extra ligand was available. The patterns of homotropic cooperativity seen with 1-alkoxy-4-nitrobenzenes (biphasic plots of v vs. S) differ from those seen with polycyclic hydrocarbons (positive cooperativity), suggesting that only with the latter does the ligand interaction produce improved catalysis. Consistent with this view, Ph(NC)2 inhibited the oxidation of 1-isopropoxy-4-nitrobenzene and other substrates.
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Affiliation(s)
- Emre M Isin
- Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, 638 Robinson Research Building, 2200 Pierce Avenue, Nashville, TN 37232-0146, USA
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