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Jia H, Brixius B, Bocianoski C, Ray S, Koes DR, Brixius-Anderko S. Deciphering the Role of Fatty Acid-Metabolizing CYP4F11 in Lung Cancer and Its Potential As a Drug Target. Drug Metab Dispos 2024; 52:69-79. [PMID: 37973374 DOI: 10.1124/dmd.123.001463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/25/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. We found that the cytochrome P450 isoform CYP4F11 is significantly overexpressed in patients with lung squamous cell carcinoma. CYP4F11 is a fatty acid ω-hydroxylase and catalyzes the production of the lipid mediator 20-hydroxyeicosatetraenoic acid (20-HETE) from arachidonic acid. 20-HETE promotes cell proliferation and migration in cancer. Inhibition of 20-HETE-generating cytochrome P450 enzymes has been implicated as novel cancer therapy for more than a decade. However, the exact role of CYP4F11 and its potential as drug target for lung cancer therapy has not been established yet. Thus, we performed a transient knockdown of CYP4F11 in the lung cancer cell line NCI-H460. Knockdown of CYP4F11 significantly inhibits lung cancer cell proliferation and migration while the 20-HETE production is significantly reduced. For biochemical characterization of CYP4F11-inhibitor interactions, we generated recombinant human CYP4F11. Spectroscopic ligand binding assays were conducted to evaluate CYP4F11 binding to the unselective CYP4A/F inhibitor HET0016. HET0016 shows high affinity to recombinant CYP4F11 and inhibits CYP4F11-mediated 20-HETE production in vitro with a nanomolar IC 50 Cross evaluation of HET0016 in NCI-H460 cells shows that lung cancer cell proliferation is significantly reduced together with 20-HETE production. However, HET0016 also displays antiproliferative effects that are not 20-HETE mediated. Future studies aim to establish the role of CYP4F11 in lung cancer and the underlying mechanism and investigate the potential of CYP4F11 as a therapeutic target for lung cancer. SIGNIFICANCE STATEMENT: Lung cancer is a deadly cancer with limited treatment options. Cytochrome P450 4F11 (CYP4F11) is significantly upregulated in lung squamous cell carcinoma. Knockdown of CYP4F11 in a lung cancer cell line significantly attenuates cell proliferation and migration with reduced production of the lipid mediator 20-hydroxyeicosatetraenoic acid (20-HETE). Studies with the unselective inhibitor HET0016 show a high inhibitory potency of CYP4F11-mediated 20-HETE production using recombinant enzyme. Overall, our studies demonstrate the potential of targeting CYP4F11 for new transformative lung cancer treatment.
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Affiliation(s)
- Huiting Jia
- Department of Pharmaceutical Sciences, Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania (H.J., B.B., S.R., S.B.-A.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (D.R.K.); and Elizabeth Forward High School, Elizabeth, Pennsylvania (C.B.)
| | - Bjoern Brixius
- Department of Pharmaceutical Sciences, Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania (H.J., B.B., S.R., S.B.-A.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (D.R.K.); and Elizabeth Forward High School, Elizabeth, Pennsylvania (C.B.)
| | - Caleb Bocianoski
- Department of Pharmaceutical Sciences, Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania (H.J., B.B., S.R., S.B.-A.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (D.R.K.); and Elizabeth Forward High School, Elizabeth, Pennsylvania (C.B.)
| | - Sutapa Ray
- Department of Pharmaceutical Sciences, Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania (H.J., B.B., S.R., S.B.-A.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (D.R.K.); and Elizabeth Forward High School, Elizabeth, Pennsylvania (C.B.)
| | - David R Koes
- Department of Pharmaceutical Sciences, Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania (H.J., B.B., S.R., S.B.-A.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (D.R.K.); and Elizabeth Forward High School, Elizabeth, Pennsylvania (C.B.)
| | - Simone Brixius-Anderko
- Department of Pharmaceutical Sciences, Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania (H.J., B.B., S.R., S.B.-A.); Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania (D.R.K.); and Elizabeth Forward High School, Elizabeth, Pennsylvania (C.B.)
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Liu Q, Gao J, Zhang Y, Liu X, Zhang X, Lin Q, Zeng W, Zhou Z. A trans-ortho asymmetrically di-strapped metalloporphyrin integrating three key structural features of ligand in heme. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
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3
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Shi Y, Wolf CA, Lotfy R, Sharma SS, Tesfa AF, Wolber G, Bureik M, Clark BR. Deciphering the biotransformation mechanism of dialkylresorcinols by CYP4F11. Bioorg Chem 2023; 131:106330. [PMID: 36565673 DOI: 10.1016/j.bioorg.2022.106330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/15/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Cytochrome P450 enzymes (CYPs) are one of the most important classes of oxidative enzymes in the human body, carrying out metabolism of various exogenous and endogenous substrates. In order to expand the knowledge of these enzymes' specificity and to obtain new natural product derivatives, CYP4F11, a cytochrome P450 monooxygenase, was used in the biotransformation of dialkylresorcinols 1 and 2, a pair of antibiotic microbial natural products. This investigation resulted in four biotransformation products including two oxidative products: a hydroxylated derivative (3) and a carboxylic acid derivative (4). In addition, acetylated (5) and esterified products (6) were isolated, formed by further metabolism by endogenous yeast enzymes. Oxidative transformations were highly regioselective, and took place exclusively at the ω-position of the C-5 alkyl chain. Homology modeling studies revealed that optimal hydrogen bonding between 2 and the enzyme can only be established with the C-5 alkyl chain pointing towards the heme. The closely-related CYP4F12 was not capable of oxidizing the dialkylresorcinol 2. Modeling experiments rationalize these differences by the different shapes of the binding pockets with respect to the non-oxidized alkyl chain. Antimicrobial testing indicated that the presence of polar groups on the side-chains reduces the antibiotic activity of the dialkylresorcinols.
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Affiliation(s)
- Yue Shi
- School of Pharmaceutical Science and Technology, Tianjin University, 92, Weijin Road, Tianjin 300092, People's Republic of China
| | - Clemens A Wolf
- Molecular Design Lab, Freie Universität Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry, Königin-Luise-Straße, 2 + 4, 14195 Berlin, Germany
| | - Rowaa Lotfy
- Molecular Design Lab, Freie Universität Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry, Königin-Luise-Straße, 2 + 4, 14195 Berlin, Germany
| | - Sangeeta S Sharma
- School of Pharmaceutical Science and Technology, Tianjin University, 92, Weijin Road, Tianjin 300092, People's Republic of China
| | - Abel Fekadu Tesfa
- School of Pharmaceutical Science and Technology, Tianjin University, 92, Weijin Road, Tianjin 300092, People's Republic of China
| | - Gerhard Wolber
- Molecular Design Lab, Freie Universität Berlin, Institute of Pharmacy, Pharmaceutical and Medicinal Chemistry, Königin-Luise-Straße, 2 + 4, 14195 Berlin, Germany
| | - Matthias Bureik
- School of Pharmaceutical Science and Technology, Tianjin University, 92, Weijin Road, Tianjin 300092, People's Republic of China
| | - Benjamin R Clark
- School of Pharmaceutical Science and Technology, Tianjin University, 92, Weijin Road, Tianjin 300092, People's Republic of China.
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Sebastiani F, Baroni C, Patil G, Dali A, Becucci M, Hofbauer S, Smulevich G. The Role of the Hydrogen Bond Network in Maintaining Heme Pocket Stability and Protein Function Specificity of C. diphtheriae Coproheme Decarboxylase. Biomolecules 2023; 13:235. [PMID: 36830604 PMCID: PMC9953210 DOI: 10.3390/biom13020235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Monoderm bacteria accumulate heme b via the coproporphyrin-dependent biosynthesis pathway. In the final step, in the presence of two molecules of H2O2, the propionate groups of coproheme at positions 2 and 4 are decarboxylated to form vinyl groups by coproheme decarboxylase (ChdC), in a stepwise process. Decarboxylation of propionate 2 produces an intermediate that rotates by 90° inside the protein pocket, bringing propionate 4 near the catalytic tyrosine, to allow the second decarboxylation step. The active site of ChdCs is stabilized by an extensive H-bond network involving water molecules, specific amino acid residues, and the propionate groups of the porphyrin. To evaluate the role of these H-bonds in the pocket stability and enzyme functionality, we characterized, via resonance Raman and electronic absorption spectroscopies, single and double mutants of the actinobacterial pathogen Corynebacterium diphtheriae ChdC complexed with coproheme and heme b. The selective elimination of the H-bond interactions between propionates 2, 4, 6, and 7 and the polar residues of the pocket allowed us to establish the role of each H-bond in the catalytic reaction and to follow the changes in the interactions from the substrate to the product.
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Affiliation(s)
- Federico Sebastiani
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Chiara Baroni
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Gaurav Patil
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrea Dali
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Maurizio Becucci
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
| | - Stefan Hofbauer
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Giulietta Smulevich
- Dipartimento di Chimica “Ugo Schiff”, DICUS, Università di Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Italy
- INSTM Research Unit of Firenze, via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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5
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Spotlight on CYP4B1. Int J Mol Sci 2023; 24:ijms24032038. [PMID: 36768362 PMCID: PMC9916508 DOI: 10.3390/ijms24032038] [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: 12/29/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
The mammalian cytochrome P450 monooxygenase CYP4B1 can bioactivate a wide range of xenobiotics, such as its defining/hallmark substrate 4-ipomeanol leading to tissue-specific toxicities. Similar to other members of the CYP4 family, CYP4B1 has the ability to hydroxylate fatty acids and fatty alcohols. Structural insights into the enigmatic role of CYP4B1 with functions in both, xenobiotic and endobiotic metabolism, as well as its unusual heme-binding characteristics are now possible by the recently solved crystal structures of native rabbit CYP4B1 and the p.E310A variant. Importantly, CYP4B1 does not play a major role in hepatic P450-catalyzed phase I drug metabolism due to its predominant extra-hepatic expression, mainly in the lung. In addition, no catalytic activity of human CYP4B1 has been observed owing to a unique substitution of an evolutionary strongly conserved proline 427 to serine. Nevertheless, association of CYP4B1 expression patterns with various cancers and potential roles in cancer development have been reported for the human enzyme. This review will summarize the current status of CYP4B1 research with a spotlight on its roles in the metabolism of endogenous and exogenous compounds, structural properties, and cancer association, as well as its potential application in suicide gene approaches for targeted cancer therapy.
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Lu Y, Liu X, Lotfy R, Liu S, Tesfa AF, Wolber G, Bureik M, Clark BR. Experimental and Computational Studies on the Biotransformation of Pseudopyronines with Human Cytochrome P450 CYP4F2. JOURNAL OF NATURAL PRODUCTS 2022; 85:2603-2609. [PMID: 36327116 DOI: 10.1021/acs.jnatprod.2c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The secondary metabolite pseudopyronine B, isolated from Pseudomonas mosselii P33, was biotransformed by human P450 enzymes, heterologously expressed in the fission yeast Schizosaccharomyces pombe. Small-scale studies confirmed that both CYP4F2 and CYP4F3A were capable of oxidizing the substrate, with the former achieving a higher yield. In larger-scale studies using CYP4F2, three new oxidation products were obtained, the structures of which were elucidated by UV-vis, 1D and 2D NMR, and HR-MS spectroscopy. These corresponded to hydroxylated, carboxylated, and ester derivatives (1-3) of pseudopyronine B, all of which had been oxidized exclusively at the ω-position of the C-6 alkyl chain. In silico homology modeling experiments highlighted key interactions between oxygen atoms of the pyrone ring and two serine residues and a histidine residue of CYP4F2, which hold the substrate in a suitable orientation for oxidation at the terminus of the C-6 alkyl chain. Additional modeling studies with all three pseudopyronines revealed that the seven-carbon alkyl chain of pseudopyronine B was the perfect length for oxidation, with the terminal carbon lying close to the heme iron. The antibacterial activity of the substrates and three oxidation products was also assessed, revealing that oxidation at the ω-position removes all antimicrobial activity. This study both increases the range of known substrates for human CYF4F2 and CYP4F3A enzymes and demonstrates their utility in producing additional natural product derivatives.
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Affiliation(s)
- Ya Lu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300092, People's Republic of China
| | - Xueling Liu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300092, People's Republic of China
- The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou 450008, People's Republic of China
| | - Rowaa Lotfy
- Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Institute of Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Sijie Liu
- Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Institute of Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Abel Fekadu Tesfa
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300092, People's Republic of China
| | - Gerhard Wolber
- Pharmaceutical and Medicinal Chemistry (Computer-Aided Drug Design), Institute of Pharmacy, Freie Universität Berlin, Berlin 14195, Germany
| | - Matthias Bureik
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300092, People's Republic of China
| | - Benjamin R Clark
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, Tianjin 300092, People's Republic of China
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7
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Chen J, Hao X, Tan R, Li Y, Wang B, Pan J, Ma W, Ma L. Functional Study on Cytochrome P450 in Response to L(-)-Carvone Stress in Bursaphelenchus xylophilus. Genes (Basel) 2022; 13:1956. [PMID: 36360193 PMCID: PMC9689654 DOI: 10.3390/genes13111956] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 09/12/2023] Open
Abstract
Bursaphelenchus xylophilus (PWN) causes pine wilt disease (PWD), which is one of the most devastating pine diseases worldwide. Cytochrome P450 (CYP) catalyzes the biosynthetic metabolism of terpenoids and plays an important role in the modification of secondary metabolites in all living organisms. We investigated the molecular characteristics and biological functions of Bx-cyp29A3 in B. xylophilus. The bioinformatics analysis results indicated that Bx-cyp29A3 has a transmembrane domain and could dock with L(-)-carvone. The gene expression pattern indicated that Bx-cyp29A3 was expressed in 0.2, 0.4, 0.6, 0.8, and 1.0 mg/mL L(-)-carvone solutions. The Bx-cyp29A3 expression increased in a dose-dependent manner and peaked at 24 h of exposure when the L(-)-carvone solution concentration was 0.8 mg/mL. However, the gene expression peaked at 0.6 mg/mL after 36 h. Furthermore, RNA interference (RNAi) indicated that Bx-cyp29A3 played an essential role in the response to L(-)-carvone. The mortality rates of the Bx-cyp29A3 knockdown groups were higher than those of the control groups in the 0.4, 0.6, 0.8, and 1.0 mg/mL carvone solutions after 24 h of exposure or 36 h of exposure. In summary, bioinformatics provided the structural characteristics and conserved sequence properties of Bx-cyp29A3 and its encoded protein, which provided a target gene for the study of the P450 family of B. xylophilus. Gene silencing experiments clarified the function of Bx-cyp29A3 in the immune defense of B. xylophilus. This study provides a basis for the screening of new molecular targets for the prevention and management of B. xylophilus.
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Affiliation(s)
- Jie Chen
- School of Forestry, Northeast Forestry University, Harbin 150040, China
- Plant Science, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Xin Hao
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ruina Tan
- School of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Yang Li
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bowen Wang
- School of Art and Archaeology, Zhejiang University, Zhejiang University, Hangzhou 310028, China
| | - Jialiang Pan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang 110034, China
| | - Wei Ma
- College of Pharmaceutical Sciences, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| | - Ling Ma
- School of Forestry, Northeast Forestry University, Harbin 150040, China
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Zhao N, Yan Y, Liu W, Wang J. Cytochrome P450 CYP709C56 metabolizing mesosulfuron-methyl confers herbicide resistance in Alopecurus aequalis. Cell Mol Life Sci 2022; 79:205. [PMID: 35334005 PMCID: PMC11072224 DOI: 10.1007/s00018-022-04171-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 12/15/2022]
Abstract
Multiple herbicide resistance in diverse weed species endowed by enhanced herbicide detoxification or degradation is rapidly growing into a great threat to herbicide sustainability and global food safety. Although metabolic resistance is frequently documented in the economically damaging arable weed species shortawn foxtail (Alopecurus aequalis Sobol.), relevant molecular knowledge has been lacking. Previously, we identified a field population of A. aequalis (R) that had evolved metabolic resistance to the commonly used acetolactate synthase (ALS)-inhibiting herbicide mesosulfuron-methyl. RNA sequencing was used to discover potential herbicide metabolism-related genes, and four cytochrome P450s (CYP709C56, CYP71R18, CYP94C117, and CYP94E14) were identified with higher expressions in the R vs. susceptible (S) plants. Here the full-length P450 complementary DNA transcripts were each cloned with identical sequences between the S and R plants. Transgenic Arabidopsis overexpressing CYP709C56 became resistant to the sulfonylurea herbicide mesosulfuron-methyl and the triazolo-pyrimidine herbicide pyroxsulam. This resistance profile generally but does not completely in accordance with what is evident in the R A. aequalis. Transgenic lines exhibited enhanced capacity for detoxifying mesosulfuron-methyl into O-demethylated metabolite, which is in line with the detection of O-demethylated herbicide metabolite in vitro in transformed yeast. Structural modeling predicted that mesosulfuron-methyl binds to CYP709C56 involving amino acid residues Thr-328, Thr-500, Asn-129, Gln-392, Phe-238, and Phe-242 for achieving O-demethylation. Constitutive expression of CYP709C56 was highly correlated with the metabolic mesosulfuron-methyl resistance in A. aequalis. These results indicate that CYP709C56 degrades mesosulfuron-methyl and its up-regulated expression in A. aequalis confers resistance to mesosulfuron-methyl.
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Affiliation(s)
- Ning Zhao
- Anhui Province Key Laboratory of Integrated Pest Management On Crops, School of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Yanyan Yan
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China
| | - Weitang Liu
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jinxin Wang
- College of Plant Protection, Shandong Agricultural University, Tai'an, 271018, China.
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Xiao Y, Shen Q, Gu M, Jiao Y, Liu Y. Changes in transcriptome of goat muscle during frozen, ice‐temperature and chilled storage within 7 days. Int J Food Sci Technol 2022. [DOI: 10.1111/ijfs.15637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Xiao
- College of Food Engineering and Nutritional Science Shaanxi Normal University Xi’an Shaanxi 710062 China
| | - Qian Shen
- College of Food Engineering and Nutritional Science Shaanxi Normal University Xi’an Shaanxi 710062 China
| | - Minghui Gu
- College of Food Engineering and Nutritional Science Shaanxi Normal University Xi’an Shaanxi 710062 China
| | - Yang Jiao
- College of Food Engineering and Nutritional Science Shaanxi Normal University Xi’an Shaanxi 710062 China
| | - Yongfeng Liu
- College of Food Engineering and Nutritional Science Shaanxi Normal University Xi’an Shaanxi 710062 China
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Bergmann J, Oksanen E, Ryde U. Combining crystallography with quantum mechanics. Curr Opin Struct Biol 2021; 72:18-26. [PMID: 34392061 DOI: 10.1016/j.sbi.2021.07.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 11/19/2022]
Abstract
In standard crystallographic refinement of biomacromolecules, the crystallographic raw data are supplemented by empirical restraints that ensure that the structure makes chemical sense. These restraints are typically accurate for amino acids and nucleic acids, but less so for cofactors, substrates, inhibitors, ligands and metal sites. In quantum refinement, this potential is replaced by more accurate quantum mechanical (QM) calculations. Several implementations have been presented, differing in the level of QM and whether it is used for the entire structure or only for a site of particular interest. It has been shown that the method can improve and correct errors in crystal structures and that it can be used to determine protonation and tautomeric states of various ligands and to decide what is really seen in the structure by refining different interpretations and using standard crystallographic and QM quality measures to decide which fits the structure best.
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Affiliation(s)
- Justin Bergmann
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Esko Oksanen
- European Spallation Source ESS ERIC, P. O. Box 176, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
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11
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Négrerie M. Iron transitions during activation of allosteric heme proteins in cell signaling. Metallomics 2020; 11:868-893. [PMID: 30957812 DOI: 10.1039/c8mt00337h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Allosteric heme proteins can fulfill a very large number of different functions thanks to the remarkable chemical versatility of heme through the entire living kingdom. Their efficacy resides in the ability of heme to transmit both iron coordination changes and iron redox state changes to the protein structure. Besides the properties of iron, proteins may impose a particular heme geometry leading to distortion, which allows selection or modulation of the electronic properties of heme. This review focusses on the mechanisms of allosteric protein activation triggered by heme coordination changes following diatomic binding to proteins as diverse as the human NO-receptor, cytochromes, NO-transporters and sensors, and a heme-activated potassium channel. It describes at the molecular level the chemical capabilities of heme to achieve very different tasks and emphasizes how the properties of heme are determined by the protein structure. Particularly, this reviews aims at giving an overview of the exquisite adaptability of heme, from bacteria to mammals.
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Affiliation(s)
- Michel Négrerie
- Laboratoire d'Optique et Biosciences, INSERM, CNRS, Ecole Polytechnique, 91120 Palaiseau, France.
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12
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Lim S, Alshagga M, Ong CE, Chieng JY, Pan Y. Cytochrome P450 4B1 (CYP4B1) as a target in cancer treatment. Hum Exp Toxicol 2020; 39:785-796. [PMID: 32054340 DOI: 10.1177/0960327120905959] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cytochrome P450 4B1 (CYP4B1) plays crucial roles in biotransforming of xenobiotics. Its predominant extrahepatic expression has been associated with certain tissue-specific toxicities. However, the expressions of CYP4B1 in various cancers and hence their potential roles in cancer development were inclusive. In this work, existing knowledge on expression and regulation of CYP4B1 gene and protein, catalysis of CYP4B1, association of CYP4B1 with cancers, contradicting findings about human CYP4B1 activities as well as the employing CYP4B1 in suicide gene approach for cancer treatment were reviewed. To date, it appears that there is a wide spectrum of tissue distribution of CYP4B1 with lungs as the predominant sites. Several nuclear receptors are possibly responsible for regulating its gene expression. The involvement of CYP4B1 in cancer was considered via activation of procarcinogens and neovascularization. However, human CYP4B1 was found to be inactive due to a substitution of proline with serine at position 427. Suicide gene approach combining reengineered CYP4B1 and prodrug 4-ipomeanol (4-IPO) has shown a promising potential for targeted cancer therapy. Further studies should focus on the verification of human CYP4B1 catalytic activities. More compounds with similar structure as 4-IPO should be tested to identify more alternative agents for the suicide gene approach in cancer treatment.
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Affiliation(s)
- Sym Lim
- Division of Biomedical Science, School of Pharmacy, University of Nottingham Malaysia, Selangor, Malaysia
| | - M Alshagga
- Division of Biomedical Science, School of Pharmacy, University of Nottingham Malaysia, Selangor, Malaysia
| | - C E Ong
- School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - J Y Chieng
- Hospital Pantai Ampang, Kuala Lumpur, Malaysia
| | - Y Pan
- Division of Biomedical Science, School of Pharmacy, University of Nottingham Malaysia, Selangor, Malaysia
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Thesseling FA, Hutter MC, Wiek C, Kowalski JP, Rettie AE, Girhard M. Novel insights into oxidation of fatty acids and fatty alcohols by cytochrome P450 monooxygenase CYP4B1. Arch Biochem Biophys 2020; 679:108216. [PMID: 31801692 DOI: 10.1016/j.abb.2019.108216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/29/2019] [Indexed: 10/25/2022]
Abstract
CYP4B1 is an enigmatic mammalian cytochrome P450 monooxygenase acting at the interface between xenobiotic and endobiotic metabolism. A prominent CYP4B1 substrate is the furan pro-toxin 4-ipomeanol (IPO). Our recent investigation on metabolism of IPO related compounds that maintain the furan functionality of IPO while replacing its alcohol group with alkyl chains of varying structure and length revealed that, in addition to cytotoxic reactive metabolite formation (resulting from furan activation) non-cytotoxic ω-hydroxylation at the alkyl chain can also occur. We hypothesized that substrate reorientations may happen in the active site of CYP4B1. These findings prompted us to re-investigate oxidation of unsaturated fatty acids and fatty alcohols with C9-C16 carbon chain length by CYP4B1. Strikingly, we found that besides the previously reported ω- and ω-1-hydroxylations, CYP4B1 is also capable of α-, β-, γ-, and δ-fatty acid hydroxylation. In contrast, fatty alcohols of the same chain length are exclusively hydroxylated at ω, ω-1, and ω-2 positions. Docking results for the corresponding CYP4B1-substrate complexes revealed that fatty acids can adopt U-shaped bonding conformations, such that carbon atoms in both arms may approach the heme-iron. Quantum chemical estimates of activation energies of the hydrogen radical abstraction by the reactive compound 1 as well as electron densities of the substrate orbitals led to the conclusion that fatty acid and fatty alcohol oxidations by CYP4B1 are kinetically controlled reactions.
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Affiliation(s)
- Florian A Thesseling
- Institute of Biochemistry, Heinrich-Heine University, 40225, Düsseldorf, Germany.
| | - Michael C Hutter
- Center for Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225, Düsseldorf, Germany.
| | - John P Kowalski
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, 98195, USA.
| | - Allan E Rettie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, 98195, USA.
| | - Marco Girhard
- Institute of Biochemistry, Heinrich-Heine University, 40225, Düsseldorf, Germany.
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Molecular Functionality of Cytochrome P450 4 (CYP4) Genetic Polymorphisms and Their Clinical Implications. Int J Mol Sci 2019; 20:ijms20174274. [PMID: 31480463 PMCID: PMC6747359 DOI: 10.3390/ijms20174274] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 01/03/2023] Open
Abstract
Enzymes in the cytochrome P450 4 (CYP4) family are involved in the metabolism of fatty acids, xenobiotics, therapeutic drugs, and signaling molecules, including eicosanoids, leukotrienes, and prostanoids. As CYP4 enzymes play a role in the maintenance of fatty acids and fatty-acid-derived bioactive molecules within a normal range, they have been implicated in various biological functions, including inflammation, skin barrier, eye function, cardiovascular health, and cancer. Numerous studies have indicated that genetic variants of CYP4 genes cause inter-individual variations in metabolism and disease susceptibility. Genetic variants of CYP4A11, 4F2 genes are associated with cardiovascular diseases. Mutations of CYP4B1, CYP4Z1, and other CYP4 genes that generate 20-HETE are a potential risk for cancer. CYP4V2 gene variants are associated with ocular disease, while those of CYP4F22 are linked to skin disease and CYP4F3B is associated with the inflammatory response. The present study comprehensively collected research to provide an updated view of the molecular functionality of CYP4 genes and their associations with human diseases. Functional analysis of CYP4 genes with clinical implications is necessary to understand inter-individual variations in disease susceptibility and for the development of alternative treatment strategies.
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Park HG, Kim V, Kim H, Lee R, Cho MA, Park SW, Chun YJ, Kim D. CYP52A23 from Candida albicans and its Substrate Preference for Fatty Acid Hydroxylation. Arch Biochem Biophys 2019; 671:27-34. [PMID: 31181182 DOI: 10.1016/j.abb.2019.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 01/07/2023]
Abstract
The pathogenic fungus Candida albicans contains genes encoding five fatty acid hydroxylases belonging to the CYP52 family in its genome. Our previous study reported that CYP52A21 demonstrated typical omega-hydroxylation of lauric acid (Kim D, Cryle MJ, De Voss JJ, Ortiz de Montellano PR (2007) Arch Biochem Biophys 464, 213-220). Functional characterization of CYP52 fatty acid hydroxylases was studied, and their selectivity for hydroxylation was analyzed. Genes for four other CYP52 members (CYP52A22, CYP52A23, CYP52A24, and CYP52C3) from C. albicans were cloned, and their recombinant enzymes were expressed in Escherichia coli. CO-binding spectral analyses showed that the functional P450 holoenzyme was obtained only in CYP52A23, while no holoenzyme peak was observed in the other three CYP52 enzymes. Spectral change of the type II binding was observed in purified CYP52A23 when titrated with fatty acids but none was observed with alkanes. The gas chromatography-mass spectrometry (GC-MS) analysis revealed that CYP52A23 predominantly exhibited omega-hydroxylation activity during the oxidation reaction of fatty acids. Interestingly, it was found that CYP52A23 preferred longer-chain fatty acids (stearic acid and arachidic acid) for its catalytic activities while CYP52A21 preferred mid-chain fatty acids (lauric acid and mystic acid). To analyze the selectivity of fatty acids, hybrid mutagenesis of genes encoding CYP52A21 and CYP52A23 by overlap extension polymerase chain reaction was conducted. Two hybrid mutants containing the N-terminal fragments of CYP52A21 and C-terminal fragments of CYP52A23 displayed higher catalytic activity in palmitic acid and arachidic acid. These results suggested that the C-terminal part of CYP52A23 may be responsible for its preference to longer-chain fatty acids.
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Affiliation(s)
- Hyoung-Goo Park
- Department of Biological Sciences, Konkuk University, Seoul, 05029, South Korea
| | - Vitchan Kim
- Department of Biological Sciences, Konkuk University, Seoul, 05029, South Korea
| | - Harim Kim
- Department of Biological Sciences, Konkuk University, Seoul, 05029, South Korea
| | - Rowoon Lee
- Department of Biological Sciences, Konkuk University, Seoul, 05029, South Korea
| | - Myung-A Cho
- Department of Biological Sciences, Konkuk University, Seoul, 05029, South Korea
| | - Sung-Woo Park
- Division of Respiratory and Allergy, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, 14584, South Korea
| | - Young-Jin Chun
- College of Pharmacy, Chung-Ang University, Seoul, 06974, South Korea
| | - Donghak Kim
- Department of Biological Sciences, Konkuk University, Seoul, 05029, South Korea.
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Albertolle ME, Song HD, Wilkey CJ, Segrest JP, Guengerich FP. Glutamine-451 Confers Sensitivity to Oxidative Inhibition and Heme-Thiolate Sulfenylation of Cytochrome P450 4B1. Chem Res Toxicol 2019; 32:484-492. [PMID: 30701961 PMCID: PMC7279892 DOI: 10.1021/acs.chemrestox.8b00353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Human cytochrome P450 (P450) family 4 enzymes are involved in the metabolism of fatty acids and the bioactivation of carcinogenic arylamines and toxic natural products, e.g., 4-ipomeanol. These and other drug-metabolizing P450s are redox sensitive, showing a loss of activity resulting from preincubation with H2O2 and recovery with mild reducing agents [Albertolle, M. W., et al. (2017) J. Biol. Chem. 292, 11230-11242]. The inhibition is due to sulfenylation of the heme-thiolate ligand, as determined by chemopreoteomics and spectroscopy. This phenomenon may have implications for chemical toxicity and observed disease-drug interactions, in which the decreased metabolism of P450 substrates occurs in patients with inflammatory diseases (e.g., influenza and autoimmunity). Human P450 1A2 was determined to be redox insensitive. To determine the mechanism underlying the differential redox sensitivity, molecular dynamics (MD) simulations were employed using the crystal structure of rabbit P450 4B1 (Protein Data Bank entry 5T6Q ). In simulating either the thiolate (Cys-S-) or the sulfenic acid (Cys-SOH) at the heme ligation site, MD revealed Gln-451 in either an "open" or "closed" conformation, respectively, between the cytosol and heme-thiolate cysteine. Mutation to either an isosteric leucine (Q451L) or glutamate (Q451E) abrogated the redox sensitivity, suggesting that this "open" conformation allows for reduction of the sulfenic acid and religation of the thiolate to the heme iron. In summary, MD simulations suggest that Gln-451 in P450 4B1 adopts conformations that may stabilize and protect the heme-thiolate sulfenic acid; mutating this residue destabilizes the interaction, producing a redox insensitive enzyme.
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Affiliation(s)
- Matthew E. Albertolle
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Hyun D. Song
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232-6300, United States
| | - Clayton J. Wilkey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Jere P. Segrest
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee 37232-6300, United States
| | - F. Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, United States
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