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Mokhosoev IM, Astakhov DV, Terentiev AA, Moldogazieva NT. Cytochrome P450 monooxygenase systems: Diversity and plasticity for adaptive stress response. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 193:19-34. [PMID: 39245215 DOI: 10.1016/j.pbiomolbio.2024.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/21/2024] [Accepted: 09/04/2024] [Indexed: 09/10/2024]
Abstract
Superfamily of cytochromes P450 (CYPs) is composed of heme-thiolate-containing monooxygenase enzymes, which play crucial roles in the biosynthesis, bioactivation, and detoxification of a variety of organic compounds, both endogenic and exogenic. Majority of CYP monooxygenase systems are multi-component and contain various redox partners, cofactors and auxiliary proteins, which contribute to their diversity in both prokaryotes and eukaryotes. Recent progress in bioinformatics and computational biology approaches make it possible to undertake whole-genome and phylogenetic analyses of CYPomes of a variety of organisms. Considerable variations in sequences within and between CYP families and high similarity in secondary and tertiary structures between all CYPs along with dramatic conformational changes in secondary structure elements of a substrate binding site during catalysis have been reported. This provides structural plasticity and substrate promiscuity, which underlie functional diversity of CYPs. Gene duplication and mutation events underlie CYP evolutionary diversity and emergence of novel selectable functions, which provide the involvement of CYPs in high adaptability to changing environmental conditions and dietary restrictions. In our review, we discuss the recent advancements and challenges in the elucidating the evolutionary origin and mechanisms underlying the CYP monooxygenase system diversity and plasticity. Our review is in the view of hypothesis that diversity of CYP monooxygenase systems is translated into the broad metabolic profiles, and this has been acquired during the long evolutionary time to provide structural plasticity leading to high adaptative capabilities to environmental stress conditions.
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Affiliation(s)
| | - Dmitry V Astakhov
- Department of Biochemistry, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991, Moscow, Russia
| | - Alexander A Terentiev
- Department of Biochemistry and Molecular Biology, N.I. Pirogov Russian National Research Medical University, 117997, Moscow, Russia
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2
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Queiroz da Silva ML, Ferreira de Sousa N, Dos Santos ATL, de Sousa GR, Fonseca VJA, Douglas Melo Coutinho H, Barbosa Filho JM, de Souza Ferrari J, Scotti MT, Ribeiro-Filho J, Martins de Lima JP, da Rocha JBT, Bezerra Morais-Braga MF. Inhibition of the morphological transition of Candida spp. by riparins I-IV. Fundam Clin Pharmacol 2024:e13007. [PMID: 38738393 DOI: 10.1111/fcp.13007] [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: 06/17/2023] [Revised: 03/19/2024] [Accepted: 04/19/2024] [Indexed: 05/14/2024]
Abstract
Candida spp. is an opportunistic pathogen capable of causing superficial to invasive infections. Morphological transition is one of the main virulence factors of this genus and, therefore, is an important variable to be considered in pharmacological interventions. Riparins I, II, III, and IV are alkamide-type alkaloids extracted from the unripe fruit of Aniba riparia, whose remarkable pharmacological properties were previously demonstrated. This work aimed to evaluate in silico and in vitro the inhibitory effects of Riparins on the morphological transition of Candida albicans, Candida tropicalis, and Candida krusei. Molecular docking was applied to analyze the inhibitory effects of riparins against proteins such as N-acetylglucosamine, CYP-51, and protein kinase A (PKA) using the Ramachandran plot. The ligands were prepared by MarvinSketch and Spartan software version 14.0, and MolDock Score and Rerank Score were used to analyze the affinity of the compounds. In vitro analyses were performed by culturing the strains in humid chambers in the presence of riparins or fluconazole (FCZ). The morphology was observed through optical microscopy, and the size of the hyphae was determined using the ToupView software. In silico analysis demonstrated that all riparins are likely to interact with the molecular targets: GlcNAc (>50%), PKA (>60%), and CYP-51 (>70%). Accordingly, in vitro analysis showed that these compounds significantly inhibited the morphological transition of all Candida strains. In conclusion, this study demonstrated that riparins inhibit Candida morphological transition and, therefore, can be used to overcome the pathogenicity of this genus.
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Affiliation(s)
| | - Natália Ferreira de Sousa
- Laboratório de Quimioinformática, Departamento de Química, Universidade Federal da Paraíba (UFPB), São João do Cariri, Brazil
| | | | - Gabriela Ribeiro de Sousa
- Departamento de Ciências da Saúde, Universidade Federal da Paraiba (UFPB), São João do Cariri, Brazil
| | | | | | - José Maria Barbosa Filho
- Departamento de Ciências da Saúde, Universidade Federal da Paraiba (UFPB), São João do Cariri, Brazil
| | | | - Marcus Tullius Scotti
- Laboratório de Quimioinformática, Departamento de Química, Universidade Federal da Paraíba (UFPB), São João do Cariri, Brazil
| | | | | | - João Batista Teixeira da Rocha
- Departamento de Química Biológica, Universidade Regional do Cariri (URCA), Crato, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria (UFSM), Santa Maria, Brazil
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3
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Hargrove T, Lamb DC, Wawrzak Z, Hull M, Kelly SL, Guengerich FP, Lepesheva GI. Identification of Potent and Selective Inhibitors of Acanthamoeba: Structural Insights into Sterol 14α-Demethylase as a Key Drug Target. J Med Chem 2024; 67:7443-7457. [PMID: 38683753 PMCID: PMC11089504 DOI: 10.1021/acs.jmedchem.4c00303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
Acanthamoeba are free-living pathogenic protozoa that cause blinding keratitis, disseminated infection, and granulomatous amebic encephalitis, which is generally fatal. The development of efficient and safe drugs is a critical unmet need. Acanthamoeba sterol 14α-demethylase (CYP51) is an essential enzyme of the sterol biosynthetic pathway. Repurposing antifungal azoles for amoebic infections has been reported, but their inhibitory effects on Acanthamoeba CYP51 enzymatic activity have not been studied. Here, we report catalytic properties, inhibition, and structural characterization of CYP51 from Acanthamoeba castellanii. The enzyme displays a 100-fold substrate preference for obtusifoliol over lanosterol, supporting the plant-like cycloartenol-based pathway in the pathogen. The strongest inhibition was observed with voriconazole (1 h IC50 0.45 μM), VT1598 (0.25 μM), and VT1161 (0.20 μM). The crystal structures of A. castellanii CYP51 with bound VT1161 (2.24 Å) and without an inhibitor (1.95 Å), presented here, can be used in the development of azole-based scaffolds to achieve optimal amoebicidal effectiveness.
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Affiliation(s)
- Tatiana
Y. Hargrove
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - David C. Lamb
- Faculty
of Medicine, Health and Life Science, Swansea
University, Swansea SA2 8PP, U.K.
| | - Zdzislaw Wawrzak
- Synchrotron
Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Marcus Hull
- Faculty
of Medicine, Health and Life Science, Swansea
University, Swansea SA2 8PP, U.K.
| | - Steven L. Kelly
- Faculty
of Medicine, Health and Life Science, Swansea
University, Swansea SA2 8PP, U.K.
| | - F. Peter Guengerich
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
| | - Galina I. Lepesheva
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232, United States
- Vanderbilt
Institute of Chemical Biology, Nashville, Tennessee 37232, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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4
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McCarty KD, Sullivan ME, Tateishi Y, Hargrove TY, Lepesheva GI, Guengerich FP. Processive kinetics in the three-step lanosterol 14α-demethylation reaction catalyzed by human cytochrome P450 51A1. J Biol Chem 2023; 299:104841. [PMID: 37209823 PMCID: PMC10285260 DOI: 10.1016/j.jbc.2023.104841] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023] Open
Abstract
Cytochrome P450 (P450, CYP) family 51 enzymes catalyze the 14α-demethylation of sterols, leading to critical products used for membranes and the production of steroids, as well as signaling molecules. In mammals, P450 51 catalyzes the 3-step, 6-electron oxidation of lanosterol to form (4β,5α)-4,4-dimethyl-cholestra-8,14,24-trien-3-ol (FF-MAS). P450 51A1 can also use 24,25-dihydrolanosterol (a natural substrate in the Kandutsch-Russell cholesterol pathway). 24,25-Dihydrolanosterol and the corresponding P450 51A1 reaction intermediates, the 14α-alcohol and -aldehyde derivatives of dihydrolanosterol, were synthesized to study the kinetic processivity of the overall 14α-demethylation reaction of human P450 51A1. A combination of steady-state kinetic parameters, steady-state binding constants, dissociation rates of P450-sterol complexes, and kinetic modeling of the time course of oxidation of a P450-dihydrolanosterol complex showed that the overall reaction is highly processive, with koff rates of P450 51A1-dihydrolanosterol and the 14α-alcohol and 14α-aldehyde complexes being 1 to 2 orders of magnitude less than the forward rates of competing oxidations. epi-Dihydrolanosterol (the 3α-hydroxy analog) was as efficient as the common 3β-hydroxy isomer in the binding and formation of dihydro FF-MAS. The common lanosterol contaminant dihydroagnosterol was found to be a substrate of human P450 51A1, with roughly one-half the activity of dihydrolanosterol. Steady-state experiments with 14α-methyl deuterated dihydrolanosterol showed no kinetic isotope effect, indicating that C-14α C-H bond breaking is not rate-limiting in any of the individual steps. The high processivity of this reaction generates higher efficiency and also renders the reaction less sensitive to inhibitors.
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Affiliation(s)
- Kevin D McCarty
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Molly E Sullivan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yasuhiro Tateishi
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
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5
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Mohamed H, Ghith A, Bell SG. The binding of nitrogen-donor ligands to the ferric and ferrous forms of cytochrome P450 enzymes. J Inorg Biochem 2023; 242:112168. [PMID: 36870164 DOI: 10.1016/j.jinorgbio.2023.112168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/24/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
The cytochrome P450 superfamily of heme-thiolate monooxygenase enzymes can catalyse various oxidation reactions. The addition of a substrate or an inhibitor ligand induces changes in the absorption spectrum of these enzymes and UV-visible (UV-vis) absorbance spectroscopy is the most common and readily available technique used to interrogate their heme and active site environment. Nitrogen-containing ligands can inhibit the catalytic cycle of heme enzymes by interacting with the heme. Here we evaluate the binding of imidazole and pyridine-based ligands to the ferric and ferrous forms of a selection of bacterial cytochrome P450 enzymes using UV-visible absorbance spectroscopy. The majority of these ligands interact with the heme as one would expect for type II nitrogen directly coordinated to a ferric heme-thiolate species. However, the spectroscopic changes observed in the ligand-bound ferrous forms indicated differences in the heme environment across these P450 enzyme/ligand combinations. Multiple species were observed in the UV-vis spectra of the ferrous ligand-bound P450s. None of the enzymes gave rise to the isolation of a single species with a Soret band at ∼442-447 nm, indicative of a 6-coordinate ferrous thiolate species with a nitrogen-donor ligand. A ferrous species with Soret band at ∼427 nm coupled with an α-band of increased intensity was observed with the imidazole ligands. With some enzyme-ligand combinations reduction resulted in breaking of the iron‑nitrogen bond yielding a 5-coordinate high-spin ferrous species. In other instances, the ferrous form was readily oxidised back to the ferric form on addition of the ligand.
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Affiliation(s)
- Hebatalla Mohamed
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | - Amna Ghith
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University Adelaide, Adelaide, SA 5005, Australia.
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6
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Jing Y, Usai R, Liu Y, Kincaid JR. Revealing substrate-induced structural changes in active site of human CYP51 in the presence of its physiological substrates. J Inorg Biochem 2023; 242:112167. [PMID: 36870163 PMCID: PMC10082466 DOI: 10.1016/j.jinorgbio.2023.112167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
The human sterol 14α-demethylases (CYP51, CYP is an abbreviation for cytochrome P450) catalyze three-step oxidative removal of 14α-methyl group of lanosterol by first forming an alcohol, then an aldehyde, and finally conducting a CC bond cleavage reaction. This present study utilizes a combination of Resonance Raman spectroscopy and Nanodisc technology to probe the active site structure of CYP51 in the presence of its hydroxylase and lyase substrates. Ligand-binding induced partial low-to-high-spin conversion is observed by applying electronic absorption spectroscopy and Resonance Raman (RR) spectroscopy. This low degree of spin conversion of CYP51 is contributed by the retention of the water ligand coordinated to the heme iron as well as direct interaction between the hydroxyl group of lyase substrate and the iron center. No significant changes in active site structure are found between detergent-stabilized CYP51 and nanodisc-incorporated CYP51, nevertheless, it is demonstrated that nanodisc-incorporated assemblies provide much more well-defined active site RR spectroscopic responses, which induces a larger conversion from low-to-high-spin state in presence of the substrates. Moreover, a positive polar environment around the exogenous diatomic ligand is detected, providing insight into the mechanism of this essential CC bond cleavage reaction.
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Affiliation(s)
- Yuanqi Jing
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Remigio Usai
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
| | - Yilin Liu
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA.
| | - James R Kincaid
- Department of Chemistry, Marquette University, Milwaukee, WI 53233, USA
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7
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Hargrove TY, Lamb DC, Smith JA, Wawrzak Z, Kelly SL, Lepesheva GI. Unravelling the role of transient redox partner complexes in P450 electron transfer mechanics. Sci Rep 2022; 12:16232. [PMID: 36171457 PMCID: PMC9519919 DOI: 10.1038/s41598-022-20671-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/16/2022] [Indexed: 01/05/2023] Open
Abstract
The molecular evolution of cytochromes P450 and associated redox-driven oxidative catalysis remains a mystery in biology. It is widely believed that sterol 14α-demethylase (CYP51), an essential enzyme of sterol biosynthesis, is the ancestor of the whole P450 superfamily given its conservation across species in different biological kingdoms. Herein we have utilized X-ray crystallography, molecular dynamics simulations, phylogenetics and electron transfer measurements to interrogate the nature of P450-redox partner binding using the naturally occurring fusion protein, CYP51-ferredoxin found in the sterol-producing bacterium Methylococcus capsulatus. Our data advocates that the electron transfer mechanics in the M. capsulatus CYP51-ferredoxin fusion protein involves an ensemble of ferredoxin molecules in various orientations and the interactions are transient. Close proximity of ferredoxin, however, is required to complete the substrate-induced large-scale structural switch in the P450 domain that enables proton-coupled electron transfer and subsequent oxygen scission and catalysis. These results have fundamental implications regarding the early evolution of electron transfer proteins and for the redox reactions in the early steps of sterol biosynthesis. They also shed new light on redox protein mechanics and the subsequent diversification of the P450 electron transfer machinery in nature.
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Affiliation(s)
- Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - David C Lamb
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - Jarrod A Smith
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, IL, 60439, USA
| | - Steven L Kelly
- Faculty of Medicine, Health and Life Science, Swansea University, Swansea, SA2 8PP, UK
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232, USA.
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8
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Mohamed H, Child SA, Bruning JB, Bell SG. A comparison of the bacterial CYP51 cytochrome P450 enzymes from Mycobacterium marinum and Mycobacterium tuberculosis. J Steroid Biochem Mol Biol 2022; 221:106097. [PMID: 35346833 DOI: 10.1016/j.jsbmb.2022.106097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
Members of the CYP51 family of cytochrome P450 enzymes are classified as sterol demethylases involved in the metabolic formation of cholesterol and related derivatives. The CYP51 enzyme from Mycobacterium marinum was studied and compared to its counterpart from Mycobacterium tuberculosis to determine the degree of functional conservation between them. Spectroscopic analyses of substrate and inhibitor binding of the purified CYP51 enzymes from M. marinum and M. tuberculosis were performed. The catalytic oxidation of lanosterol and related steroids was investigated. M. marinum CYP51 was structurally characterized by X-ray crystallography. The CYP51 enzyme of M. marinum is sequentially closely related to CYP51B1 from M. tuberculosis. However, differences in the heme spin state of each enzyme were observed upon the addition of steroids and other ligands. Both enzymes displayed different binding properties to those reported for the CYP51-Fdx fusion protein from the bacterium Methylococcus capsulatus. The enzymes were able to oxidatively demethylate lanosterol to generate 14-demethylanosterol, but no products were detected for the related species dihydrolanosterol and eburicol. The crystal structure of CYP51 from M. marinum in the absence of added substrate but with a Bis-Tris molecule within the active site was resolved. The CYP51 enzyme of M. marinum displays differences in how steroids and other ligands bind compared to the M. tuberculosis enzyme. This was related to structural differences between the two enzymes. Overall, both of these CYP51 enzymes from mycobacterial species displayed significant differences to the CYP51 enzymes of eukaryotic species and the bacterial CYP51-Fdx enzyme of Me. capsulatus.
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Affiliation(s)
| | - Stella A Child
- Department of Chemistry, University of Adelaide, SA 5005, Australia
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, SA 5005, Australia
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, SA 5005, Australia.
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9
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Examination of multiple Trypanosoma cruzi targets in a new drug discovery approach for Chagas disease. Bioorg Med Chem 2022; 58:116577. [DOI: 10.1016/j.bmc.2021.116577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022]
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10
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Hargrove TY, Wawrzak Z, Rachakonda G, Nes WD, Villalta F, Guengerich FP, Lepesheva GI. Relaxed Substrate Requirements of Sterol 14α-Demethylase from Naegleria fowleri Are Accompanied by Resistance to Inhibition. J Med Chem 2021; 64:17511-17522. [PMID: 34842434 PMCID: PMC8667612 DOI: 10.1021/acs.jmedchem.1c01710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Naegleria fowleri is the protozoan pathogen that causes primary amoebic meningoencephalitis (PAM), with the death rate exceeding 97%. The amoeba makes sterols and can be targeted by sterol biosynthesis inhibitors. Here, we characterized N. fowleri sterol 14-demethylase, including catalytic properties and inhibition by clinical antifungal drugs and experimental substituted azoles with favorable pharmacokinetics and low toxicity. None of them inhibited the enzyme stoichiometrically. The highest potencies were displayed by posaconazole (IC50 = 0.69 μM) and two of our compounds (IC50 = 1.3 and 0.35 μM). Because both these compounds penetrate the brain with concentrations reaching minimal inhibitory concentration (MIC) values in an N. fowleri cellular assay, we report them as potential drug candidates for PAM. The 2.1 Å crystal structure, in complex with the strongest inhibitor, provides an explanation connecting the enzyme weaker substrate specificity with lower sensitivity to inhibition. It also provides insight into the enzyme/ligand molecular recognition process and suggests directions for the design of more potent inhibitors.
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Affiliation(s)
- Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - Girish Rachakonda
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, Tennessee 37208, United States
| | - W David Nes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Fernando Villalta
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, Nashville, Tennessee 37208, United States
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
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11
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Structural Insights into the Azole Resistance of the Candida albicans Darlington Strain Using Saccharomyces cerevisiae Lanosterol 14α-Demethylase as a Surrogate. J Fungi (Basel) 2021; 7:jof7110897. [PMID: 34829185 PMCID: PMC8621857 DOI: 10.3390/jof7110897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Target-based azole resistance in Candida albicans involves overexpression of the ERG11 gene encoding lanosterol 14α-demethylase (LDM), and/or the presence of single or multiple mutations in this enzyme. Overexpression of Candida albicans LDM (CaLDM) Y132H I471T by the Darlington strain strongly increased resistance to the short-tailed azoles fluconazole and voriconazole, and weakly increased resistance to the longer-tailed azoles VT-1161, itraconazole and posaconazole. We have used, as surrogates, structurally aligned mutations in recombinant hexahistidine-tagged full-length Saccharomyces cerevisiae LDM6×His (ScLDM6×His) to elucidate how differential susceptibility to azole drugs is conferred by LDM of the C. albicans Darlington strain. The mutations Y140H and I471T were introduced, either alone or in combination, into ScLDM6×His via overexpression of the recombinant enzyme from the PDR5 locus of an azole hypersensitive strain of S. cerevisiae. Phenotypes and high-resolution X-ray crystal structures were determined for the surrogate enzymes in complex with representative short-tailed (voriconazole) and long-tailed (itraconazole) triazoles. The preferential high-level resistance to short-tailed azoles conferred by the ScLDM Y140H I471T mutant required both mutations, despite the I471T mutation conferring only a slight increase in resistance. Crystal structures did not detect changes in the position/tilt of the heme co-factor of wild-type ScLDM, I471T and Y140H single mutants, or the Y140H I471T double-mutant. The mutant threonine sidechain in the Darlington strain CaLDM perturbs the environment of the neighboring C-helix, affects the electronic environment of the heme, and may, via differences in closure of the neck of the substrate entry channel, increase preferential competition between lanosterol and short-tailed azole drugs.
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12
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Lamb DC, Hargrove TY, Zhao B, Wawrzak Z, Goldstone JV, Nes WD, Kelly SL, Waterman MR, Stegeman JJ, Lepesheva GI. Concerning P450 Evolution: Structural Analyses Support Bacterial Origin of Sterol 14α-Demethylases. Mol Biol Evol 2021; 38:952-967. [PMID: 33031537 PMCID: PMC7947880 DOI: 10.1093/molbev/msaa260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an "orphan" P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in >1,000 bacteria from nine different phyla, >50 of them being natural CYP51fx fusion proteins.
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Affiliation(s)
- David C Lamb
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | - Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN
| | - Bin Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, IL
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - William David Nes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX
| | - Steven L Kelly
- Institute of Life Science, Swansea University Medical School, Swansea, United Kingdom
| | - Michael R Waterman
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN.,Center for Structural Biology, Vanderbilt University, Nashville, TN
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13
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Monk BC, Keniya MV. Roles for Structural Biology in the Discovery of Drugs and Agrochemicals Targeting Sterol 14α-Demethylases. J Fungi (Basel) 2021; 7:67. [PMID: 33498194 PMCID: PMC7908997 DOI: 10.3390/jof7020067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/08/2021] [Accepted: 01/17/2021] [Indexed: 02/06/2023] Open
Abstract
Antifungal drugs and antifungal agrochemicals have significant limitations. These include several unintended consequences of their use including the growing importance of intrinsic and acquired resistance. These problems underpin an increasingly urgent need to improve the existing classes of antifungals and to discover novel antifungals. Structural insights into drug targets and their complexes with both substrates and inhibitory ligands increase opportunity for the discovery of more effective antifungals. Implementation of this promise, which requires multiple skill sets, is beginning to yield candidates from discovery programs that could more quickly find their place in the clinic. This review will describe how structural biology is providing information for the improvement and discovery of inhibitors targeting the essential fungal enzyme sterol 14α-demethylase.
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Affiliation(s)
- Brian C. Monk
- Department of Oral Sciences, Sir John Walsh Research Institute, University of Otago, Dunedin 9016, New Zealand;
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14
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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15
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Ogris I, Zelenko U, Sosič I, Gobec M, Skubic C, Ivanov M, Soković M, Kocjan D, Rozman D, Golič Grdadolnik S. Pyridylethanol(phenylethyl)amines are non-azole, highly selective Candida albicans sterol 14α-demethylase inhibitors. Bioorg Chem 2020; 106:104472. [PMID: 33261849 DOI: 10.1016/j.bioorg.2020.104472] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022]
Abstract
Sterol 14α-demethylase (CYP51) is the main drug target for the treatment of fungal infections. The worldwide increase in the incidence of opportunistic fungal infections and the emerging resistance to available azole-based antifungal drugs, raise the need to develop structurally distinct and selective fungal CYP51 inhibitors. In this work we have, for the first time, investigated the binding of pyridylethanol(phenylethyl)amines to any fungal CYP51. The comparison of the binding to Candida albicans and human CYP51 studied by spectroscopic and modeling methods revealed moieties decisive for selectivity and potency and resulted in the development of highly selective derivatives with significantly increased inhibitory potency. The structure-based insight into the selectivity requirements of this new chemical class of fungal CYP51 inhibitors, their unique binding properties and the low molecular weight of lead derivatives offer novel directions for the targeted development of antifungal clinical candidates.
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Affiliation(s)
- Iza Ogris
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Urška Zelenko
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Cene Skubic
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Marija Ivanov
- Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia
| | - Marina Soković
- Institute for Biological Research "Siniša Stanković"- National Institute of Republic of Serbia, University of Belgrade, Bulevar Despota Stefana 142, 11000 Belgrade, Serbia
| | - Darko Kocjan
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia
| | - Damjana Rozman
- Center for Functional Genomics and Bio-Chips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Simona Golič Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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16
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Hargrove TY, Wawrzak Z, Guengerich FP, Lepesheva GI. A requirement for an active proton delivery network supports a compound I-mediated C-C bond cleavage in CYP51 catalysis. J Biol Chem 2020; 295:9998-10007. [PMID: 32493730 DOI: 10.1074/jbc.ra120.014064] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/29/2020] [Indexed: 12/27/2022] Open
Abstract
CYP51 enzymes (sterol 14α-demethylases) are cytochromes P450 that catalyze multistep reactions. The CYP51 reaction occurs in all biological kingdoms and is essential in sterol biosynthesis. It removes the 14α-methyl group from cyclized sterol precursors by first forming an alcohol, then an aldehyde, and finally eliminating formic acid with the introduction of a Δ14-15 double bond in the sterol core. The first two steps are typical hydroxylations, mediated by an electrophilic compound I mechanism. The third step, C-C bond cleavage, has been proposed to involve either compound I (i.e. FeO3 +) or, alternatively, a proton transfer-independent nucleophilic ferric peroxo anion (compound 0, i.e. Fe3 +O2 -). Here, using comparative crystallographic and biochemical analyses of WT human CYP51 (CYP51A1) and its D231A/H314A mutant, whose proton delivery network is destroyed (as evidenced in a 1.98-Å X-ray structure in complex with lanosterol), we demonstrate that deformylation of the 14α-carboxaldehyde intermediate requires an active proton relay network to drive the catalysis. These results indicate a unified, compound I-based mechanism for all three steps of the CYP51 reaction, as previously established for CYP11A1 and CYP19A1. We anticipate that our approach can be applied to mechanistic studies of other P450s that catalyze multistep reactions, such as C-C bond cleavage.
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Affiliation(s)
- Tatiana Y Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Galina I Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA .,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
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17
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Friggeri L, Hargrove TY, Wawrzak Z, Guengerich FP, Lepesheva GI. Validation of Human Sterol 14α-Demethylase (CYP51) Druggability: Structure-Guided Design, Synthesis, and Evaluation of Stoichiometric, Functionally Irreversible Inhibitors. J Med Chem 2019; 62:10391-10401. [PMID: 31663733 PMCID: PMC6881533 DOI: 10.1021/acs.jmedchem.9b01485] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Sterol 14α-demethylases (CYP51) are the cytochrome P450 enzymes required for biosynthesis of sterols in eukaryotes, the major targets for antifungal agents and prospective targets for treatment of protozoan infections. Human CYP51 could be and, for a while, was considered as a potential target for cholesterol-lowering drugs (the role that is now played by statins, which are also in clinical trials for cancer) but revealed high intrinsic resistance to inhibition. While microbial CYP51 enzymes are often inhibited stoichiometrically and functionally irreversibly, no strong inhibitors have been identified for human CYP51. In this study, we used comparative structure/functional analysis of CYP51 orthologs from different biological kingdoms and employed site-directed mutagenesis to elucidate the molecular basis for the resistance of the human enzyme to inhibition and also designed, synthesized, and characterized new compounds. Two of them inhibit human CYP51 functionally irreversibly with their potency approaching the potencies of azole drugs currently used to inhibit microbial CYP51.
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Affiliation(s)
- Laura Friggeri
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Tatiana Y. Hargrove
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439, United States
| | - F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Galina I. Lepesheva
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232, United States
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18
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Virelli M, Wang W, Kuniyil R, Wu J, Zanoni G, Fernandez A, Scott J, Vendrell M, Ackermann L. BODIPY‐Labeled Cyclobutanes by Secondary C(sp
3
)−H Arylations for Live‐Cell Imaging. Chemistry 2019; 25:12712-12718. [DOI: 10.1002/chem.201903461] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/19/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Matteo Virelli
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Germany
- Department of ChemistryUniversity of Pavia Viale Taramelli 10 27100 Pavia Italy
| | - Wei Wang
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Germany
| | - Rositha Kuniyil
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Germany
| | - Jun Wu
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Germany
| | - Giuseppe Zanoni
- Department of ChemistryUniversity of Pavia Viale Taramelli 10 27100 Pavia Italy
| | - Antonio Fernandez
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Jamie Scott
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Lutz Ackermann
- Institut für Organische und Biomolekulare ChemieGeorg-August-Universität Göttingen Tammannstraße 2 37077 Göttingen Germany
- Department of ChemistryUniversity of Pavia Viale Taramelli 10 27100 Pavia Italy
- German Center for Cardiovascular Research (DZHK) Potsdamer Strasse 58 10785 Berlin Germany
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19
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Xia C, Shen AL, Duangkaew P, Kotewong R, Rongnoparut P, Feix J, Kim JJP. Structural and Functional Studies of the Membrane-Binding Domain of NADPH-Cytochrome P450 Oxidoreductase. Biochemistry 2019; 58:2408-2418. [PMID: 31009206 PMCID: PMC6873807 DOI: 10.1021/acs.biochem.9b00130] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NADPH-cytochrome P450 oxidoreductase (CYPOR), the essential flavoprotein of the microsomal cytochrome P450 monooxygenase system, is anchored in the phospholipid bilayer by its amino-terminal membrane-binding domain (MBD), which is necessary for efficient electron transfer to cytochrome P450. Although crystallographic and kinetic studies have established the structure of the soluble catalytic domain and the role of conformational motions in the control of electron transfer, the role of the MBD is largely unknown. We examined the role of the MBD in P450 catalysis through studies of amino-terminal deletion mutants and site-directed spin labeling. We show that the MBD spans the membrane and present a model for the orientation of CYPOR on the membrane capable of forming a complex with cytochrome P450. EPR power saturation measurements of CYPOR mutants in liposomes containing a lipid/Ni(II) chelate identified a region of the soluble domain interacting with the membrane. The deletion of more than 29 residues from the N-terminus of CYPOR decreases cytochrome P450 activity concomitant with alterations in electrophoretic mobility and an increased resistance to protease digestion. The altered kinetic properties of these mutants are consistent with electron transfer through random collisions rather than via formation of a stable CYPOR-P450 complex. Purified MBD binds weakly to cytochrome P450, suggesting that other interactions are also required for CYPOR-P450 complex formation. We propose that the MBD and flexible tether region of CYPOR, residues 51-63, play an important role in facilitating the movement of the soluble domain relative to the membrane and in promoting multiple orientations that permit specific interactions of CYPOR with its varied partners.
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Affiliation(s)
- Chuanwu Xia
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Anna L Shen
- McArdle Laboratory for Cancer Research , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Panida Duangkaew
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
- Department of Biochemistry, Faculty of Science , Mahidol University , Bangkok 10400 , Thailand
| | - Rattanawadee Kotewong
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
- Department of Biochemistry, Faculty of Science , Mahidol University , Bangkok 10400 , Thailand
| | - Pornpimol Rongnoparut
- Department of Biochemistry, Faculty of Science , Mahidol University , Bangkok 10400 , Thailand
| | - Jimmy Feix
- Department of Biophysics , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
| | - Jung-Ja P Kim
- Department of Biochemistry , Medical College of Wisconsin , Milwaukee , Wisconsin 53226 , United States
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