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Kowalski JP, Rettie AE. There and Back Again: A Perspective on 20 Years of CYP4Z1. Drug Metab Dispos 2024; 52:498-507. [PMID: 38604728 DOI: 10.1124/dmd.124.001670] [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: 01/29/2024] [Revised: 03/17/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Cytochrome P450 (CYP)4Z1, a highly expressed CYP gene in breast cancer, was one of the last CYPs to be identified in the human genome, some 20 years ago. CYP4 enzymes typically catalyze ω-hydroxylation and metabolize ω3 and ω6 polyunsaturated fatty acids to bioactive lipid metabolites that can influence tumor growth and metastasis. These attributes of CYP4Z1 make it an attractive target for new chemotherapeutic drug design, as a potential biomarker for selection of patients that might respond favorably to drugs and for developing enzyme inhibitors as potential therapeutic agents. This review summarizes the current state of knowledge regarding the advancing biochemistry of CYP4Z1, its role in breast cancer, and the recent synthesis of selective chemical inhibitors of the enzyme. We identify gaps that need to be filled to further advance this field and present new experimental data on recombinant CYP4Z1 expression and purification of the active catalytic form. SIGNIFICANCE STATEMENT: In breast cancer, an unmet need is the availability of highly effective therapeutic agents, especially for triple negative breast cancer. The relevance of the work summarized in this mini-review is that it identifies a new potential drug target, CYP4Z1, and discusses ways in which the gene product's catalytic activity might be modulated in order to combat this malignancy and limit its spread.
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Affiliation(s)
- John P Kowalski
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington
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Yu Y, Li L, Luo B, Chen D, Yin C, Jian C, You Q, Wang J, Fang L, Cai D, Sun J. Predicting potential therapeutic targets and small molecule drugs for early-stage lung adenocarcinoma. Biomed Pharmacother 2024; 174:116528. [PMID: 38555814 DOI: 10.1016/j.biopha.2024.116528] [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: 01/16/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024] Open
Abstract
Lung cancer is a leading cause of cancer-related mortality worldwide, with non-small cell lung cancer (NSCLC) constituting the majority, and its main subtype being lung adenocarcinoma (LUAD). Despite substantial advances in LUAD diagnosis and treatment, early diagnostic biomarkers inadequately fulfill clinical requirements. Thus, we conducted bioinformatics analysis to identify potential biomarkers and corresponding therapeutic drugs for early-stage LUAD patients. Here we identified a total of 10 differentially expressed genes (DEGs) with survival significance through the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). Subsequently, we identified a promising small molecule drug, Aminopurvalanol A, based on the 10 key genes using the L1000FWD application, which was validated by molecular docking followed by in vivo and in vitro experiments. The results highlighted TOP2A, CDH3, ASPM, CENPF, SLC2A1, and PRC1 as potential detection biomarkers for early LUAD. We confirmed the efficacy and safety of Aminopurvalanol A, providing valuable insights for the clinical management of LUAD.
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Affiliation(s)
- Yongxin Yu
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Lingchen Li
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Bangyu Luo
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Diangang Chen
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Chenrui Yin
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Chunli Jian
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Qiai You
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Jianmin Wang
- Department of Oncology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing 400021, China
| | - Ling Fang
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Dingqin Cai
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China
| | - Jianguo Sun
- Institute of Cancer, Xinqiao Hospital, Army Medical University, Chongqing 400037, China.
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Zhou X, Tan F, Zhang S, Zhang T. Combining single-cell RNA sequencing data and transcriptomic data to unravel potential mechanisms and signature genes of the progression of idiopathic pulmonary fibrosis to lung adenocarcinoma and predict therapeutic agents. Funct Integr Genomics 2023; 23:346. [PMID: 37996625 DOI: 10.1007/s10142-023-01274-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/29/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
Patients with idiopathic pulmonary fibrosis (IPF) have a significantly higher prevalence of lung adenocarcinoma (LUAD) than normal subjects, although the underlying association is unclear. The raw data involved were obtained from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis were used to screen for differentially expressed genes (DEGs) and modular signature genes (MSGs). Genes intersecting DEGs and MSGs were considered hub genes for IPF and LUAD. Machine learning algorithms were applied to capture epithelial cell-derived signature genes (EDSGs) shared. External cohort data were exploited to validate the robustness of EDSGs. Immunohistochemical staining and K-M plots were used to denote the prognostic value of EDSGs in LUAD. Based on EDSGs, we constructed a TF-gene-miRNA regulatory network. Molecular docking can validate the strength of action between candidate drugs and EDSGs. Epithelial cells, 650 DEGs, and 1773 MSGs were shared by IPF and LUAD. As for 379 hub genes, we performed pathway and functional enrichment analysis. By analyzing sc-RNA seq data, we identified 1234 marker genes of IPF epithelial cell-derived and 1481 of LUAD. And these genes shared 8 items with 379 hub genes. Through the machine learning algorithms, we further fished TRIM2, S100A14, CYP4B1, LMO7, and SFN. The ROC curves emphasized the significance of EDSGs in predicting the onset of LUAD and IPF. The TF-gene-miRNA network revealed regulatory relationships behind EDSGs. Finally, we predicted appropriate therapeutic agents. Our study preliminarily identified potential mechanisms between IPF and LUAD, which will inform subsequent studies.
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Affiliation(s)
- Xianqiang Zhou
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China
- Department of Pulmonary Diseases, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai, 200072, China
| | - Fang Tan
- Department of Neurology, The First Affiliated Hospital of Anhui University of Traditional Chinese Medicine, Hefei, 230031, Anhui Province, China
| | - Suxian Zhang
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China
| | - Tiansong Zhang
- Department of Traditional Chinese Medicine, Jing'an District Central Hospital Affiliated to Fudan University, Shanghai, 200040, China.
- Department of Pulmonary Diseases, Jing'an District Hospital of Traditional Chinese Medicine, Shanghai, 200072, China.
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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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Hartz P, Fehlmann T, Wagenpfeil G, Unger MM, Bernhardt R. A CYPome-wide study reveals new potential players in the pathogenesis of Parkinson's disease. Front Pharmacol 2023; 13:1094265. [PMID: 36744208 PMCID: PMC9892771 DOI: 10.3389/fphar.2022.1094265] [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: 11/09/2022] [Accepted: 12/22/2022] [Indexed: 01/20/2023] Open
Abstract
Genetic and environmental factors lead to the manifestation of Parkinson's disease (PD) but related mechanisms are only rudimentarily understood. Cytochromes P450 (P450s) are involved in the biotransformation of toxic compounds and in many physiological processes and thus predestinated to be involved in PD. However, so far only SNPs (single nucleotide polymorphisms) in CYP2D6 and CYP2E1 have been associated with the susceptibility of PD. Our aim was to evaluate the role of all 57 human P450s and their redox partners for the etiology and pathophysiology of PD and to identify novel potential players which may lead to the identification of new biomarkers and to a causative treatment of PD. The PPMI (Parkinson's Progression Markers Initiative) database was used to extract the gene sequences of all 57 P450s and their three redox partners to analyze the association of SNPs with the occurrence of PD. Applying statistical analyses of the data, corresponding odds ratios (OR) and confidence intervals (CI) were calculated. We identified SNPs significantly over-represented in patients with a genetic predisposition for PD (GPD patients) or in idiopathic PD (IPD patients) compared to HC (healthy controls). Xenobiotic-metabolizing P450s show a significant accumulation of SNPs in PD patients compared with HC supporting the role of toxic compounds in the pathogenesis of PD. Moreover, SNPs with high OR values (>5) in P450s catalyzing the degradation of cholesterol (CYP46A1, CY7B1, CYP39A1) indicate a prominent role of cholesterol metabolism in the brain for PD risk. Finally, P450s participating in the metabolism of eicosanoids show a strong over-representation of SNPs in PD patients underlining the effect of inflammation on the pathogenesis of PD. Also, the redox partners of P450 show SNPs with OR > 5 in PD patients. Taken together, we demonstrate that SNPs in 26 out of 57 P450s are at least 5-fold over-represented in PD patients suggesting these P450s as new potential players in the pathogenesis of PD. For the first time exceptionally high OR values (up to 12.9) were found. This will lead to deeper insight into the origin and development of PD and may be applied to develop novel strategies for a causative treatment of this disease.
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Affiliation(s)
- Philip Hartz
- Institut für Biochemie, Fachbereich Biologie, Universität des Saarlandes, Naturwissenschaftlich-Technische Fakultät, Saarbrücken, Germany
| | - Tobias Fehlmann
- Institut für Klinische Bioinformatik, Universität des Saarlandes, Saarbrücken, Germany
| | - Gudrun Wagenpfeil
- Institut für Medizinische Biometrie, Epidemiologie und Medizinische Informatik, Universität des Saarlandes, Homburg, Germany
| | - Marcus Michael Unger
- KLinik für Neurologie, Fachbereich Klinische Medizin, Universität des Saarlandes, Homburg, Germany,Klinik für Neurologie, SHG Kliniken Sonnenberg, Saarbrücken, Germany,*Correspondence: Marcus Michael Unger, ; Rita Bernhardt,
| | - Rita Bernhardt
- Institut für Biochemie, Fachbereich Biologie, Universität des Saarlandes, Naturwissenschaftlich-Technische Fakultät, Saarbrücken, Germany,*Correspondence: Marcus Michael Unger, ; Rita Bernhardt,
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Lin Q, Guan H, Ma C, Chen L, Cao L, Liu H, Cheng X, Wang C. Biotransformation patterns of dictamnine in vitro/in vivo and its relative molecular mechanism of dictamnine-induced acute liver injury in mice. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 85:103628. [PMID: 33652109 DOI: 10.1016/j.etap.2021.103628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/12/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Dictamnine (DIC), a typical furan-quinoline alkaloid, has a wide range of pharmacological and toxicological effects, such as anti-bacterial, antifungal, anti-cancer, and hepatoxicity. But the molecular mechanism of DIC-induced hepatoxicity in mice remains unclear. This study aimed to clarify the biotransformation patterns of DIC in vitro/in vivo and the relative molecular mechanism of DIC-induced hepatoxicity in mice. All metabolites of DIC were identified by comparing the blank and drug-containing urine, feces, plasma, and liver samples. The structure of epoxide intermediate derived from DIC was confirmed by trapping assay. Oxidative stress injury and inflammation have been confirmed to be involved in the toxicological process of DIC-induced hepatoxicity in mice by detecting the relative biochemical indexes. The results will help to develop a deeper understanding about the biotransformation patterns of DIC, structure of the epoxide intermediate, and the molecular mechanism of DIC-induced hepatoxicity in mice.
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Affiliation(s)
- Qiyan Lin
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China
| | - Huida Guan
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China
| | - Chao Ma
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China
| | - Liangni Chen
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China
| | - Lanlan Cao
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China
| | - Hanze Liu
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China
| | - Xuemei Cheng
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China
| | - Changhong Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines, Shanghai R&D Centre for Standardization of Chinese Medicines, 1200 Cailun Road, Shanghai, 201203, China.
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Khojasteh SC, Driscoll JP, Jackson KD, Miller GP, Mitra K, Rietjens IMCM, Zhang D. Novel advances in biotransformation and bioactivation research-2019 year in review .. Drug Metab Rev 2020; 52:333-365. [PMID: 32645275 PMCID: PMC10805366 DOI: 10.1080/03602532.2020.1772281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 05/14/2020] [Indexed: 01/25/2023]
Abstract
Biotransformation is one of the main mechanisms used by the body to eliminate drugs. As drug molecules become more complicated, the involvement of drug metabolizing enzymes increases beyond those that are typically studied, such as the cytochrome P450 enzymes. In this review, we try to capture the many outstanding articles that were published in the past year in the field of biotransformation (see Table 1). We have divided the articles into two categories of (1) metabolites and drug metabolizing enzymes, and (2) bioactivation and safety. This annual review is the fifth of its kind since 2016 (Baillie et al. 2016; Khojasteh et al. 2017, 2018, 2019). This effort in itself also continues to evolve. We have followed the same format we used in previous years in terms of the selection of articles and the authoring of each section. I am pleased of the continued support of Rietjens, Miller, Zhang, Driscoll and Mitra to this review. We would like to welcome Klarissa D. Jackson as a new author for this year's issue. We strive to maintain a balance of authors from academic and industry settings. We would be pleased to hear your opinions of our commentary, and we extend an invitation to anyone who would like to contribute to a future edition of this review. Cyrus Khojasteh, on behalf of the authors.
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Affiliation(s)
- S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
| | - James P Driscoll
- Department of Drug Metabolism and Pharmacokinetics, MyoKardia, Inc, South San Francisco, CA, USA
| | - Klarissa D Jackson
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kaushik Mitra
- Department of Safety Assessment and Laboratory Animal Resources, Merck Research Laboratories (MRL), Merck & Co., Inc, West Point, PA, USA
| | | | - Donglu Zhang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc, South San Francisco, CA, USA
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Kowalski JP, McDonald MG, Pelletier RD, Hanenberg H, Wiek C, Rettie AE. Design and Characterization of the First Selective and Potent Mechanism-Based Inhibitor of Cytochrome P450 4Z1. J Med Chem 2020; 63:4824-4836. [DOI: 10.1021/acs.jmedchem.0c00101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- John P. Kowalski
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington 98105, United States
| | - Matthew G. McDonald
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington 98105, United States
| | - Robert D. Pelletier
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington 98105, United States
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children’s Hospital Essen, University of Duisburg−Essen, 45122 Essen, Germany
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Allan E. Rettie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, Washington 98105, United States
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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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