1
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Amaya JA, Manley OM, Bian JC, Rutland CD, Leschinsky N, Ratigan SC, Makris TM. Enhancing ferryl accumulation in H 2O 2-dependent cytochrome P450s. J Inorg Biochem 2024; 252:112458. [PMID: 38141432 DOI: 10.1016/j.jinorgbio.2023.112458] [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: 11/02/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 12/25/2023]
Abstract
A facile strategy is presented to enhance the accumulation of ferryl (iron(IV)-oxo) species in H2O2 dependent cytochrome P450s (CYPs) of the CYP152 family. We report the characterization of a highly chemoselective CYP decarboxylase from Staphylococcus aureus (OleTSA) that is soluble at high concentrations. Examination of OleTSA Compound I (CpdI) accumulation with a variety of fatty acid substrates reveals a dependence on resting spin-state equilibrium. Alteration of this equilibrium through targeted mutagenesis of the proximal pocket favors the high-spin form, and as a result, enhances Cpd-I accumulation to nearly stoichiometric yields.
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Affiliation(s)
- Jose A Amaya
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Olivia M Manley
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America; Department of Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Julia C Bian
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Cooper D Rutland
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Nicholas Leschinsky
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Steven C Ratigan
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America
| | - Thomas M Makris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States of America; Department of Structural and Molecular Biochemistry, North Carolina State University, Raleigh, NC 27695, United States of America; Department of Chemistry, North Carolina State University, Raleigh, NC 27695, United States of America.
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2
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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3
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Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp-Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH-Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α-Helical Metalloprotein. Angew Chem Int Ed Engl 2020; 60:3974-3978. [PMID: 33215801 DOI: 10.1002/anie.202012673] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/19/2020] [Indexed: 11/09/2022]
Abstract
De Novo metalloprotein design assesses the relationship between metal active site architecture and catalytic reactivity. Herein, we use an α-helical scaffold to control the iron coordination geometry when a heme cofactor is allowed to bind to either histidine or cysteine ligands, within a single artificial protein. Consequently, we uncovered a reversible pH-induced switch of the heme axial ligation within this simplified scaffold. Characterization of the specific heme coordination modes was done by using UV/Vis and Electron Paramagnetic Resonance spectroscopies. The penta- or hexa-coordinate thiolate heme (9≤pH≤11) and the penta-coordinate imidazole heme (6≤pH≤8.5) reproduces well the heme ligation in chloroperoxidases or cyt P450 monooxygenases and peroxidases, respectively. The stability of heme coordination upon ferric/ferrous redox cycling is a crucial property of the construct. At basic pHs, the thiolate mini-heme protein can catalyze O2 reduction when adsorbed onto a pyrolytic graphite electrode.
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Affiliation(s)
- Karl J Koebke
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Barbara Schoepp-Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2), Centrale Marseille, Aix-Marseille Univ., CNRS, Marseille, France
| | - Vincent L Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS, Aix-Marseille Univ., Marseille, France
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4
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Koebke KJ, Kühl T, Lojou E, Demeler B, Schoepp‐Cothenet B, Iranzo O, Pecoraro VL, Ivancich A. The pH‐Induced Selectivity Between Cysteine or Histidine Coordinated Heme in an Artificial α‐Helical Metalloprotein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Karl J. Koebke
- Department of Chemistry University of Michigan Ann Arbor MI 48109 USA
| | - Toni Kühl
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Borries Demeler
- Department of Chemistry and Biochemistry University of Lethbridge Lethbridge AB T1K 3M4 Canada
| | - Barbara Schoepp‐Cothenet
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
| | - Olga Iranzo
- Institut des Sciences Moléculaires de Marseille (iSm2) Centrale Marseille Aix-Marseille Univ. CNRS Marseille France
| | | | - Anabella Ivancich
- Laboratoire de Bioénergétique et Ingénierie des Protéines (UMR 7281), IMM FR3479, CNRS Aix-Marseille Univ. Marseille France
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5
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Rimal H, Subedi P, Kim KH, Park H, Lee JH, Oh TJ. Characterization of CYP125A13, the First Steroid C-27 Monooxygenase from Streptomyces peucetius ATCC27952. J Microbiol Biotechnol 2020; 30:1750-1759. [PMID: 32958729 PMCID: PMC9728343 DOI: 10.4014/jmb.2007.07004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/15/2022]
Abstract
The characterization of cytochrome P450 CYP125A13 from Streptomyces peucetius was conducted using cholesterol as the sole substrate. The in vitro enzymatic assay utilizing putidaredoxin and putidaredoxin reductase from Pseudomonas putida revealed that CYP125A13 bound cholesterol and hydroxylated it. The calculated KD value, catalytic conversion rates, and Km value were 56.92 ± 11.28 μM, 1.95 nmol min-1 nmol-1, and 11.3 ± 2.8 μM, respectively. Gas chromatography-mass spectrometry (GC-MS) analysis showed that carbon 27 of the cholesterol side-chain was hydroxylated, characterizing CYP125A13 as steroid C27-hydroxylase. The homology modeling and docking results also revealed the binding of cholesterol to the active site, facilitated by the hydrophobic amino acids and position of the C27-methyl group near heme. This orientation was favorable for the hydroxylation of the C27-methyl group, supporting the in vitro analysis. This was the first reported case of the hydroxylation of cholesterol at the C-27 position by Streptomyces P450. This study also established the catalytic function of CYP125A13 and provides a solid basis for further studies related to the catabolic potential of Streptomyces species.
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Affiliation(s)
- Hemraj Rimal
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea
| | - Pradeep Subedi
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea
| | - Ki -Hwa Kim
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 0841, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Research for Practical Application, Korea Polar Research Institute, Incheon 21990, Republic of Korea,Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea,Corresponding author J.H.Lee Phone: +82-32-760-5555 E-mail:
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, SunMoon University, Asan 3460, Republic of Korea,Genome-based BioIT Convergence Institute, Asan 31460, Republic of Korea,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, Asan 3140, Republic of Korea,T-J.Oh Phone: +82-41-530-2677 E-mail:
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6
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Wright WC, Chenge J, Wang J, Girvan HM, Yang L, Chai SC, Huber AD, Wu J, Oladimeji PO, Munro AW, Chen T. Clobetasol Propionate Is a Heme-Mediated Selective Inhibitor of Human Cytochrome P450 3A5. J Med Chem 2020; 63:1415-1433. [PMID: 31965799 PMCID: PMC7087482 DOI: 10.1021/acs.jmedchem.9b02067] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human cytochrome P450 (CYP) enzymes CYP3A4 and CYP3A5 metabolize most drugs and have high similarities in their structure and substrate preference. Whereas CYP3A4 is predominantly expressed in the liver, CYP3A5 is upregulated in cancer, contributing to drug resistance. Selective inhibitors of CYP3A5 are, therefore, critical to validating it as a therapeutic target. Here we report clobetasol propionate (clobetasol) as a potent and selective CYP3A5 inhibitor identified by high-throughput screening using enzymatic and cell-based assays. Molecular dynamics simulations suggest a close proximity of clobetasol to the heme in CYP3A5 but not in CYP3A4. UV-visible spectroscopy and electron paramagnetic resonance analyses confirmed the formation of an inhibitory type I heme-clobetasol complex in CYP3A5 but not in CYP3A4, thus explaining the CYP3A5 selectivity of clobetasol. Our results provide a structural basis for selective CYP3A5 inhibition, along with mechanistic insights, and highlight clobetasol as an important chemical tool for target validation.
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Affiliation(s)
- William C. Wright
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
- Integrated Biomedical Sciences Program, University of
Tennessee Health Science Center, Memphis, Tennessee 38163, USA
| | - Jude Chenge
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jingheng Wang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Hazel M. Girvan
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Sergio C. Chai
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Peter O. Oladimeji
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Natural
Sciences, Department of Chemistry, The University of Manchester, Manchester, M1 7DN,
UK
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105-3678, USA
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7
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Nguyen RC, Yang Y, Wang Y, Davis I, Liu A. Substrate-Assisted Hydroxylation and O-Demethylation in the Peroxidase-like Cytochrome P450 Enzyme CYP121. ACS Catal 2020; 10:1628-1639. [PMID: 32391185 DOI: 10.1021/acscatal.9b04596] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CYP121 is a P450 enzyme from Mycobacterium tuberculosis that catalyzes a C-C coupling reaction between the two aromatic rings on its native substrate cyclo(l-Tyr-l-Tyr) (cYY) to form mycocyclosin, a necessary product for cell survival. Unlike the typical P450 enzymes for hydroxylation, CYP121 is believed to behave like a peroxidase and conduct radical-mediated C-C bond formation. Here, we probe whether the phenolic hydrogen of the substrate is the site of the postulated hydrogen atom abstraction for radical formation. We synthesized a singly O-methylated substrate analogue, cYF-4-OMe, and characterized its interaction with CYP121 by ultraviolet-visible and electron paramagnetic resonance spectroscopies and X-ray crystallography. We found that cYF-4-OMe can function as a substrate of CYP121 using the established assay via the peroxide shunt. Analysis of the enzymatic reaction revealed an O-demethylation of cYF-4-OMe instead of cyclization, yielding cYY and formaldehyde. A hydroxylated substrate, cYF-4-OMeOH, is expected to be the intermediate product, which was trapped and structurally characterized by X-ray crystallography. We further determined that the deformylation reaction of cYF-4-OMeOH proceeds via an alkyl-oxygen rather than aryl-oxygen bond cleavage by the 18O-labeling studies. Finally, the pH dependence catalytic study on the native substrate and the methoxy analogue further supports the mechanistic understanding that the hydrogen atom abstraction is the critical first oxidation step exerted by a heme-based oxidant during the cyclization reaction of cYY. The switch in catalytic activity reveals the power of CYP121 as a P450 enzyme and provides insight into the peroxidase-like catalytic mechanism.
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Affiliation(s)
- Romie C. Nguyen
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Yu Yang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Yifan Wang
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, Texas 78249, United States
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8
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Multiple drug binding modes in Mycobacterium tuberculosis CYP51B1. J Inorg Biochem 2020; 205:110994. [PMID: 31982812 DOI: 10.1016/j.jinorgbio.2020.110994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/08/2023]
Abstract
The Mycobacterium tuberculosis (Mtb) genome encodes 20 different cytochrome P450 enzymes (CYPs), many of which serve essential biosynthetic roles. CYP51B1, the Mtb version of eukaryotic sterol demethylase, remains a potential therapeutic target. The binding of three drug fragments containing nitrogen heterocycles to CYP51B1 is studied here by continuous wave (CW) and pulsed electron paramagnetic resonance (EPR) techniques to determine how each drug fragment binds to the heme active-site. All three drug fragments form a mixture of complexes, some of which retain the axial water ligand from the resting state. Hyperfine sublevel correlation spectroscopy (HYSCORE) and electron-nuclear double resonance spectroscopy (ENDOR) observe protons of the axial water and on the drug fragments that reveal drug binding modes. Binding in CYP51B1 is complicated by the presence of multiple binding modes that coexist in the same solution. These results aid our understanding of CYP-inhibitor interactions and will help guide future inhibitor design.
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9
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Lau ICK, Feyereisen R, Nelson DR, Bell SG. Analysis and preliminary characterisation of the cytochrome P450 monooxygenases from Frankia sp. EuI1c (Frankia inefficax sp.). Arch Biochem Biophys 2019; 669:11-21. [PMID: 31082352 DOI: 10.1016/j.abb.2019.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 10/26/2022]
Abstract
Frankia bacteria are nitrogen fixing species from the Actinobacterium phylum which live on the root nodules of plants. They have been hypothesised to have significant potential for natural product biosynthesis. The cytochrome P450 monooxygenase complement of Frankia sp. EuI1c (Frankia inefficax sp.), which comprises 68 members, was analysed. Several members belonged to previously uncharacterised bacterial P450 families. There was an unusually high number of CYP189 family members (21) suggesting that this family has undergone gene duplication events which are classified as "blooms". The likely electron transfer partners for the P450 enzymes were also identified and analysed. These consisted of predominantly [3Fe-4S] cluster containing ferredoxins (eight), a single [2Fe-2S] ferredoxin and a couple of ferredoxin reductases. Three of these CYP family members were produced and purified, using Escherichia coli as a host, and their substrate range was characterised. CYP1027H1 and CYP150A20 bound a broad range of norisoprenoids and terpenoids. CYP1074A2 was highly specific for certain steroids including testosterone, progesterone, stanolone and 4-androstene-3,17-dione. It is likely that steroids are the physiological substrates of CYP1074A2. These results also give an indication that terpenoids are the likely substrates of CYP1027H1 and CYP150A2. The large number of P450s belonging to distinct families as well as the associated electron transfer partners found in different Frankia strains highlights the importance of this family of enzymes has in the secondary metabolism of these bacteria.
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Affiliation(s)
- Ian C K Lau
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - René Feyereisen
- Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David R Nelson
- University of Tennessee Health Science Center, Dept. of Microbiology, Immunology and Biochemistry, 858 Madison Ave. Suite G01, Memphis, TN, 38163, USA
| | - Stephen G Bell
- Department of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia.
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10
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Hargrove TY, Wawrzak Z, Fisher PM, Child SA, Nes WD, Guengerich FP, Waterman MR, Lepesheva GI. Binding of a physiological substrate causes large-scale conformational reorganization in cytochrome P450 51. J Biol Chem 2018; 293:19344-19353. [PMID: 30327430 DOI: 10.1074/jbc.ra118.005850] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/15/2018] [Indexed: 11/06/2022] Open
Abstract
Sterol 14α-demethylases (CYP51s) are phylogenetically the most conserved cytochromes P450, and their three-step reaction is crucial for biosynthesis of sterols and serves as a leading target for clinical and agricultural antifungal agents. The structures of several (bacterial, protozoan, fungal, and human) CYP51 orthologs, in both the ligand-free and inhibitor-bound forms, have been determined and have revealed striking similarity at the secondary and tertiary structural levels, despite having low sequence identity. Moreover, in contrast to many of the substrate-promiscuous, drug-metabolizing P450s, CYP51 structures do not display substantial rearrangements in their backbones upon binding of various inhibitory ligands, essentially representing a snapshot of the ligand-free sterol 14α-demethylase. Here, using the obtusifoliol-bound I105F variant of Trypanosoma cruzi CYP51, we report that formation of the catalytically competent complex with the physiological substrate triggers a large-scale conformational switch, dramatically reshaping the enzyme active site (3.5-6.0 Å movements in the FG arm, HI arm, and helix C) in the direction of catalysis. Notably, our X-ray structural analyses revealed that the substrate channel closes, the proton delivery route opens, and the topology and electrostatic potential of the proximal surface reorganize to favor interaction with the electron-donating flavoprotein partner, NADPH-cytochrome P450 reductase. Site-directed mutagenesis of the amino acid residues involved in these events revealed a key role of active-site salt bridges in contributing to the structural dynamics that accompanies CYP51 function. Comparative analysis of apo-CYP51 and its sterol-bound complex provided key conceptual insights into the molecular mechanisms of CYP51 catalysis, functional conservation, lineage-specific substrate complementarity, and druggability differences.
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Affiliation(s)
- Tatiana Y Hargrove
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Argonne, Illinois 60439
| | - Paxtyn M Fisher
- the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, and
| | - Stella A Child
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - W David Nes
- the Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, and
| | - F Peter Guengerich
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Michael R Waterman
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Galina I Lepesheva
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, .,the Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232
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11
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Ravula T, Barnaba C, Mahajan M, Anantharamaiah GM, Im SC, Waskell L, Ramamoorthy A. Membrane environment drives cytochrome P450's spin transition and its interaction with cytochrome b 5. Chem Commun (Camb) 2018; 53:12798-12801. [PMID: 29143058 DOI: 10.1039/c7cc07520k] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Heme's spin-multiplicity is key in determining the enzymatic function of cytochrome P450 (cytP450). The origin of the low-spin state in ferric P450 is still under debate. Here, we report the first experimental demonstration of P450's membrane interaction altering its spin equilibrium which is accompanied by a stronger affinity for cytochrome b5. These results highlight the importance of lipid membrane for the function of P450.
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Affiliation(s)
- Thirupathi Ravula
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA.
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12
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Lockart MM, Rodriguez CA, Atkins WM, Bowman MK. CW EPR parameters reveal cytochrome P450 ligand binding modes. J Inorg Biochem 2018. [PMID: 29530595 DOI: 10.1016/j.jinorgbio.2018.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cytochrome P450 (CYP) monoxygenses utilize heme cofactors to catalyze oxidation reactions. They play a critical role in metabolism of many classes of drugs, are an attractive target for drug development, and mediate several prominent drug interactions. Many substrates and inhibitors alter the spin state of the ferric heme by displacing the heme's axial water ligand in the resting enzyme to yield a five-coordinate iron complex, or they replace the axial water to yield a nitrogen-ligated six-coordinate iron complex, which are traditionally assigned by UV-vis spectroscopy. However, crystal structures and recent pulsed electron paramagnetic resonance (EPR) studies find a few cases where molecules hydrogen bond to the axial water. The water-bridged drug-H2O-heme has UV-vis spectra similar to nitrogen-ligated, six-coordinate complexes, but are closer to "reverse type I" complexes described in older liteature. Here, pulsed and continuous wave (CW) EPR demonstrate that water-bridged complexes are remarkably common among a range of nitrogenous drugs or drug fragments that bind to CYP3A4 or CYP2C9. Principal component analysis reveals a distinct clustering of CW EPR spectral parameters for water-bridged complexes. CW EPR reveals heterogeneous mixtures of ligated states, including multiple directly-coordinated complexes and water-bridged complexes. These results suggest that water-bridged complexes are under-represented in CYP structural databases and can have energies similar to other ligation modes. The data indicates that water-bridged binding modes can be identified and distinguished from directly-coordinated binding by CW EPR.
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Affiliation(s)
- Molly M Lockart
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States
| | - Carlo A Rodriguez
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States
| | - William M Atkins
- Department of Medicinal Chemistry, Box 357610, University of Washington, Seattle, WA 98195-7610, United States
| | - Michael K Bowman
- Department of Chemistry and Biochemistry, Box 870336, University of Alabama, Tuscaloosa, AL 35487-0336, United States.
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13
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Fielding AJ, Dornevil K, Ma L, Davis I, Liu A. Probing Ligand Exchange in the P450 Enzyme CYP121 from Mycobacterium tuberculosis: Dynamic Equilibrium of the Distal Heme Ligand as a Function of pH and Temperature. J Am Chem Soc 2017; 139:17484-17499. [PMID: 29090577 PMCID: PMC5765751 DOI: 10.1021/jacs.7b08911] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CYP121 is a cytochrome P450 enzyme from Mycobacterium tuberculosis that catalyzes the formation of a C-C bond between the aromatic groups of its cyclodityrosine substrate (cYY). The crystal structure of CYP121 in complex with cYY reveals that the solvent-derived ligand remains bound to the ferric ion in the enzyme-substrate complex. Whereas in the generally accepted P450 mechanism, binding of the primary substrate in the active-site triggers the release of the solvent-derived ligand, priming the metal center for reduction and subsequent O2 binding. Here we employed sodium cyanide to probe the metal-ligand exchange of the enzyme and the enzyme-substrate complex. The cyano adducts were characterized by UV-vis, EPR, and ENDOR spectroscopies and X-ray crystallography. A 100-fold increase in the affinity of cyanide binding to the enzyme-substrate complex over the ligand-free enzyme was observed. The crystal structure of the [CYP121(cYY)CN] ternary complex showed a rearrangement of the substrate in the active-site, when compared to the structure of the binary [CYP121(cYY)] complex. Transient kinetic studies showed that cYY binding resulted in a lower second-order rate constant (kon (CN)) but a much more stable cyanide adduct with 3 orders of magnitude slower koff (CN) rate. A dynamic equilibrium between multiple high- and low-spin species for both the enzyme and enzyme-substrate complex was also observed, which is sensitive to changes in both pH and temperature. Our data reveal the chemical and physical properties of the solvent-derived ligand of the enzyme, which will help to understand the initial steps of the catalytic mechanism.
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Affiliation(s)
- Andrew J. Fielding
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Kednerlin Dornevil
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Li Ma
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Ian Davis
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Aimin Liu
- Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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Wise CE, Makris TM. Recruitment and Regulation of the Non-ribosomal Peptide Synthetase Modifying Cytochrome P450 Involved in Nikkomycin Biosynthesis. ACS Chem Biol 2017; 12:1316-1326. [PMID: 28300390 DOI: 10.1021/acschembio.7b00081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The β-hydroxylation of l-histidine is the first step in the biosynthesis of the imidazolone base of the antifungal drug nikkomycin. The cytochrome P450 (NikQ) hydroxylates the amino acid while it is appended via a phosphopantetheine linker to the non-ribosomal peptide synthetase (NRPS) NikP1. The latter enzyme is comprised of an MbtH and single adenylation and thiolation domains, a minimal composition that allows for detailed binding and kinetics studies using an intact and homogeneous NRPS substrate. Electron paramagnetic resonance studies confirm that a stable complex is formed with NikQ and NikP1 when the amino acid is tethered. Size exclusion chromatography is used to further refine the principal components that are required for this interaction. NikQ binds NikP1 in the fully charged state, but binding also occurs when NikP1 is lacking both the phosphopantetheine arm and appended amino acid. This demonstrates that the interaction is mainly guided by presentation of the thiolation domain interface, rather than the attached amino acid. Electrochemistry and transient kinetics have been used to probe the influence of l-His-NikP1 binding on catalysis by NikQ. Unlike many P450s, the binding of substrate fails to induce significant changes on the redox potential and autoxidation properties of NikQ and slows down the binding of dioxygen to the ferrous enzyme to initiate catalysis. Collectively, these studies demonstrate a complex interplay between the NRPS maturation process and the recruitment and regulation of an auxiliary tailoring enzyme required for natural product biosynthesis.
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Affiliation(s)
- Courtney E. Wise
- Department of Chemistry and
Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
| | - Thomas M. Makris
- Department of Chemistry and
Biochemistry, University of South Carolina, 631 Sumter Street, Columbia, South Carolina 29208, United States
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15
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Dhers L, Pietrancosta N, Ducassou L, Ramassamy B, Dairou J, Jaouen M, André F, Mansuy D, Boucher JL. Spectral and 3D model studies of the interaction of orphan human cytochrome P450 2U1 with substrates and ligands. Biochim Biophys Acta Gen Subj 2017; 1861:3144-3153. [DOI: 10.1016/j.bbagen.2016.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/06/2016] [Accepted: 07/21/2016] [Indexed: 02/08/2023]
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16
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Krzyaniak MD, Cruce AA, Vennam P, Lockart M, Berka V, Tsai AL, Bowman MK. The tetrahydrobiopterin radical interacting with high- and low-spin heme in neuronal nitric oxide synthase - A new indicator of the extent of NOS coupling. Free Radic Biol Med 2016; 101:367-377. [PMID: 27989753 PMCID: PMC5362310 DOI: 10.1016/j.freeradbiomed.2016.10.503] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 10/07/2016] [Accepted: 10/26/2016] [Indexed: 01/10/2023]
Abstract
Reaction intermediates trapped during the single-turnover reaction of the neuronal ferrous nitric oxide synthase oxygenase domain (Fe(II)nNOSOX) show four EPR spectra of free radicals. Fully-coupled nNOSOX with cofactor (tetrahydrobiopterin, BH4) and substrate (l-arginine) forms the typical BH4 cation radical with an EPR spectrum ~4.0mT wide and hyperfine tensors similar to reports for a biopterin cation radical in inducible NOSOX (iNOSOX). With excess thiol, nNOSox lacking BH4 and l-arg is known to produce superoxide. In contrast, we find that nNOSOX with BH4 but no l-arg forms two radicals with rather different, fast (~250μs at 5K) and slower (~500μs at 20K), electron spin relaxation rates and a combined ~7.0mT wide EPR spectrum. Rapid freeze-quench CW- and pulsed-EPR measurements are used to identify these radicals and their origin. These two species are the same radical with identical nuclear hyperfine couplings, but with spin-spin couplings to high-spin (4.0mT component) or low-spin (7.0mT component) Fe(III) heme. Uncoupled reactions of nNOS leave the enzyme in states that can be chemically reduced to sustain unregulated production of NO and reactive oxygen species in ischemia-reperfusion injury. The broad EPR signal is a convenient indicator of uncoupled nNOS reactions producing low-spin Fe(III) heme.
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Affiliation(s)
- Matthew D Krzyaniak
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Alex A Cruce
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Preethi Vennam
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Molly Lockart
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA
| | - Vladimir Berka
- Division of Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Ah-Lim Tsai
- Division of Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Michael K Bowman
- Department of Chemistry, The University of Alabama, Tuscaloosa, AL 35487-0336, USA.
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17
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Conner KP, Cruce AA, Krzyaniak MD, Schimpf AM, Frank DJ, Ortiz de Montellano P, Atkins WM, Bowman MK. Drug modulation of water-heme interactions in low-spin P450 complexes of CYP2C9d and CYP125A1. Biochemistry 2015; 54:1198-207. [PMID: 25591012 DOI: 10.1021/bi501402k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Azoles and pyridines are commonly incorporated into small molecule inhibitor scaffolds that target cytochromes P450 (CYPs) as a strategy to increase drug binding affinity, impart isoform-dependent selectivity, and improve metabolic stability. Optical absorbance spectra of the CYP-inhibitor complex are widely used to infer whether these inhibitors are ligated directly to the heme iron as catalytically inert, low-spin (type II) complexes. Here, we show that the low-spin complex between a drug-metabolizing CYP2C9 variant and 4-(3-phenylpropyl)-1H-1,2,3-triazole (PPT) retains an axial water ligand despite exhibiting elements of "classic" type II optical behavior. Hydrogens of the axial water ligand are observed by pulsed electron paramagnetic resonance (EPR) spectroscopy for both inhibitor-free and inhibitor-bound species and show that inhibitor binding does not displace the axial water. A (15)N label incorporated into PPT is 0.444 nm from the heme iron, showing that PPT is also in the active site. The reverse type I inhibitor, LP10, of CYP125A1 from Mycobacterium tuberculosis, known from X-ray crystal structures to form a low-spin water-bridged complex, is found by EPR and by visible and near-infrared magnetic circular dichroism spectroscopy to retain the axial water ligand in the complex in solution.
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Affiliation(s)
- Kip P Conner
- Department of Medicinal Chemistry, Box 357610, and Department of Chemistry, Box 351700, University of Washington , Seattle, Washington 98195, United States
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18
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19
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Gerlach DL, Bhagan S, Cruce AA, Burks DB, Nieto I, Truong HT, Kelley SP, Herbst-Gervasoni CJ, Jernigan KL, Bowman MK, Pan S, Zeller M, Papish ET. Studies of the Pathways Open to Copper Water Oxidation Catalysts Containing Proximal Hydroxy Groups During Basic Electrocatalysis. Inorg Chem 2014; 53:12689-98. [DOI: 10.1021/ic501018a] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Deidra L. Gerlach
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Salome Bhagan
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Alex A. Cruce
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Dalton B. Burks
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Ismael Nieto
- Department
of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Hai T. Truong
- Department
of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Steven P. Kelley
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Corey J. Herbst-Gervasoni
- Department
of Chemistry, Drexel University, 3141 Chestnut Street, Philadelphia, Pennsylvania 19104, United States
| | - Katherine L. Jernigan
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Michael K. Bowman
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Shanlin Pan
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
| | - Matthias Zeller
- Department
of Chemistry, Youngstown State University, One University Plaza, Youngstown, Ohio 44555, United States
| | - Elizabeth T. Papish
- Department
of Chemistry, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, United States
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