1
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Li H, Huang Y, Chen F, Zeng Z, Hollmann F, Wu X, Zhang X, Duan P, Su H, Shi J, Sheng X, Zhang W. Unspecific peroxygenase enabled formation of azoxy compounds. Nat Commun 2024; 15:8312. [PMID: 39333130 PMCID: PMC11436639 DOI: 10.1038/s41467-024-52648-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 09/17/2024] [Indexed: 09/29/2024] Open
Abstract
Enzymes are making a significant impact on chemical synthesis. However, the range of chemical products achievable through biocatalysis is still limited compared to the vast array of products possible with organic synthesis. For instance, azoxy products have rarely been synthesized using enzyme catalysts. In this study, we discovered that fungal unspecific peroxygenases are promising catalysts for synthesizing azoxy products from simple aniline starting materials. The catalytic features (up to 48,450 turnovers and a turnover frequency of 6.7 s-1) and substrate transformations (up to 99% conversion with 98% chemoselectivity) highlight the synthetic potential. We propose a mechanism where peroxygenase-derived hydroxylamine and nitroso compounds spontaneously (non-enzymatically) form the desired azoxy products. This work expands the reactivity repertoire of biocatalytic transformations in the underexplored field of azoxy compound formation reactions.
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Affiliation(s)
- Huanhuan Li
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yawen Huang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Fuqiang Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Zhigang Zeng
- School of Nuclear Technology and Chemistry & Biology, Hubei University of Science and Technology, Xianning, Hubei, 437100, China
| | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Vander Maasweg9, 2629 HZ, Delft, The Netherlands
| | - Xin Wu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Xiyang Zhang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Peigao Duan
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Hao Su
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China
| | - Jianjun Shi
- College of Chemistry and Chemical Engineering Hainan Normal University Haikou, 571158, Haikou, China
| | - Xiang Sheng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.
| | - Wuyuan Zhang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin, 300308, China.
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2
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Song Z, Yu X, Zhu M, Wu Z, Fu Z, Chen J. Distinct Species-Specific and Toxigenic Metabolic Profiles for 6PPD and 6PPD Quinone by P450 Enzymes: Insights from In Vitro and In Silico Studies. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024. [PMID: 39120070 DOI: 10.1021/acs.est.4c03361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
The tire rubber antioxidant N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) and its quinone product (6PPDQ) are prevalent emerging contaminants, yet their biotransformation profiles remain poorly understood, hampering the assessment of environmental and health risks. This study investigated the phase-I metabolism of 6PPD and 6PPDQ across aquatic and mammalian species through in vitro liver microsome (LM) incubations and in silico simulations. A total of 40 metabolites from seven pathways were identified using the highly sensitive nano-electrospray ionization mass spectrometry. Notably, 6PPDQ was consistently detected as a 6PPD metabolite with an approximate 2% yield, highlighting biotransformation as a neglected indirect exposure pathway for 6PPDQ in organisms. 6PPDQ was calculated to form through a facile two-step phenyl hydroxylation of 6PPD, catalyzed by cytochrome P450 enzymes. Distinct species-specific metabolic kinetics were observed, with fish LM demonstrating retarded biotransformation rates for 6PPD and 6PPDQ compared to mammalian LM, suggesting the vulnerability of aquatic vertebrates to these contaminants. Intriguingly, two novel coupled metabolites were identified for 6PPD, which were predicted to exhibit elevated toxicity compared to 6PPDQ and result from C-N oxidative coupling by P450s. These unveiled metabolic profiles offer valuable insights for the risk assessment of 6PPD and 6PPDQ, which may inform future studies and regulatory actions.
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Affiliation(s)
- Zehua Song
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiaomei Yu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Minghua Zhu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
- Key Laboratory of Integrated Regulation and Resources Development of Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing 210098, China
| | - Zimeng Wu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Zhiqiang Fu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Jingwen Chen
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian Key Laboratory on Chemicals Risk Control and Pollution Prevention Technology, School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
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3
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Ritzefeld M, Zhang L, Xiao Z, Andrei SA, Boyd O, Masumoto N, Rodgers UR, Artelsmair M, Sefer L, Hayes A, Gavriil ES, Raynaud FI, Burke R, Blagg J, Rzepa HS, Siebold C, Magee AI, Lanyon-Hogg T, Tate EW. Design, Synthesis, and Evaluation of Inhibitors of Hedgehog Acyltransferase. J Med Chem 2024; 67:1061-1078. [PMID: 38198226 PMCID: PMC10823475 DOI: 10.1021/acs.jmedchem.3c01363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Hedgehog signaling is involved in embryonic development and cancer growth. Functional activity of secreted Hedgehog signaling proteins is dependent on N-terminal palmitoylation, making the palmitoyl transferase Hedgehog acyltransferase (HHAT), a potential drug target and a series of 4,5,6,7-tetrahydrothieno[3,2-c]pyridines have been identified as HHAT inhibitors. Based on structural data, we designed and synthesized 37 new analogues which we profiled alongside 13 previously reported analogues in enzymatic and cellular assays. Our results show that a central amide linkage, a secondary amine, and (R)-configuration at the 4-position of the core are three key factors for inhibitory potency. Several potent analogues with low- or sub-μM IC50 against purified HHAT also inhibit Sonic Hedgehog (SHH) palmitoylation in cells and suppress the SHH signaling pathway. This work identifies IMP-1575 as the most potent cell-active chemical probe for HHAT function, alongside an inactive control enantiomer, providing tool compounds for validation of HHAT as a target in cellular assays.
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Affiliation(s)
- Markus Ritzefeld
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Leran Zhang
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Zhangping Xiao
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | | | - Olivia Boyd
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Naoko Masumoto
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Ursula R. Rodgers
- National
Heart and Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
| | - Markus Artelsmair
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Lea Sefer
- Division
of Structural Biology, University of Oxford, Oxford OX3 7BN, U.K.
| | - Angela Hayes
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | | | - Florence I. Raynaud
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Julian Blagg
- Division
of Cancer Therapeutics, Centre for Cancer Drug Discovery, Institute of Cancer Research, London SM2 5NG, U.K.
| | - Henry S. Rzepa
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
| | - Christian Siebold
- Division
of Structural Biology, University of Oxford, Oxford OX3 7BN, U.K.
| | - Anthony I. Magee
- National
Heart and Lung Institute, Imperial College
London, London SW7 2AZ, U.K.
| | | | - Edward W. Tate
- Department
of Chemistry, Imperial College London, London W12 0BZ, U.K.
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4
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Rougé V, Nguyen PTTH, Allard S, Lee Y. Reaction of Amino Acids with Ferrate(VI): Impact of the Carboxylic Group on the Primary Amine Oxidation Kinetics and Mechanism. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:18509-18518. [PMID: 36441566 DOI: 10.1021/acs.est.2c03319] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ferrate (Fe(VI)) is a novel oxidant that can be used to mitigate disinfection byproduct (DBP) precursors. However, the reaction of Fe(VI) with organic nitrogen, which is a potential precursor of potent nitrogenous DBPs, remains largely unexplored. The present work aimed to identify the kinetics and products for the reaction of Fe(VI) with primary amines, notably amino acids. A new kinetic model involving ionizable intermediates was proposed and can describe the unusual pH effect on the Fe(VI) reactivity toward primary amines and amino acids. The Fe(VI) oxidation of phenylalanine produced a mixture of nitrile, nitrite/nitrate, amide, and ammonia, while nitroalkane was an additional product in the case of glycine. The product distribution for amino acids significantly differed from that of uncarboxylated primary amines that mainly generate nitriles. A general reaction pathway for primary amines and amino acids was proposed and notably involved the formation of imines, the degradation of which was affected by the presence of a carboxylic group. In comparison, ozonation led to higher yields of nitroalkanes that could be readily converted to potent halonitroalkanes during chlor(am)ination. Based on this study, Fe(VI) can effectively mitigate primary amine-based, nitrogenous DBP precursors with little formation of toxic halonitroalkanes.
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Affiliation(s)
- Valentin Rougé
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju61005, Republic of Korea
| | - Pham Thi Thai Ha Nguyen
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju61005, Republic of Korea
| | | | - Yunho Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju61005, Republic of Korea
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5
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Yamaguchi K, Isobe H, Shoji M, Kawakami T, Miyagawa K. The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations. Molecules 2023; 28:7119. [PMID: 37894598 PMCID: PMC10609222 DOI: 10.3390/molecules28207119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).
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Affiliation(s)
- Kizashi Yamaguchi
- SANKEN, Osaka University, Ibaraki 567-0047, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka 560-0043, Osaka, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Okayama, Japan;
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan;
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
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6
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Zhang H, Wang X, Song R, Ding W, Li F, Ji L. Emerging Metabolic Profiles of Sulfonamide Antibiotics by Cytochromes P450: A Computational-Experimental Synergy Study on Emerging Pollutants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:5368-5379. [PMID: 36921339 DOI: 10.1021/acs.est.3c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Metabolism, especially by CYP450 enzymes, is the main reason for mediating the toxification and detoxification of xenobiotics in humans, while some uncommon metabolic pathways, especially for emerging pollutants, probably causing idiosyncratic toxicity are easily overlooked. The pollution of sulfonamide antibiotics in aqueous system has attracted increasing public attention. Hydroxylation of the central amine group can trigger a series of metabolic processes of sulfonamide antibiotics in humans; however, this work parallelly reported the coupling and fragmenting initiated by amino H-abstraction of sulfamethoxazole (SMX) catalyzed by human CYP450 enzymes. Elucidation of the emerging metabolic profiles was mapped via a multistep synergy between computations and experiments, involving preliminary DFT computations and in vitro and in vivo assays, profiling adverse effects, and rationalizing the fundamental factors via targeted computations. Especially, the confirmed SMX dimer was shown to potentially act as a metabolism disruptor in humans, while spin aromatic delocalization resulting in the low electron donor ability of amino radicals was revealed as the fundamental factor to enable coupling of sulfonamide antibiotics by CYP450 through the nonconventional nonrebound pathway. This work may further strengthen the synergistic use of computations prior to experiments to avoid wasteful experimental screening efforts in environmental chemistry and toxicology.
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Affiliation(s)
- Huanni Zhang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoqing Wang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, China
| | - Runqian Song
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wen Ding
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
| | - Fei Li
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai 264003, China
| | - Li Ji
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou 221116, China
- International Center for Research on Innovative Biobased Materials (ICRI-BioM)─International Research Agenda, Lodz University of Technology, Zeromskiego 116, Lodz 90-924, Poland
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7
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Kamel EM, Lamsabhi AM. The quasi-irreversible inactivation of cytochrome P450 enzymes by paroxetine: a computational approach. Org Biomol Chem 2021; 18:3334-3345. [PMID: 32301459 DOI: 10.1039/d0ob00529k] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The mechanism-based inactivation (MBI) of P450 by paroxetine was investigated by computational analysis. The drug-enzyme interactions were figured out through studying energy profiles of three competing mechanisms. The potency of paroxetine as P450's inhibitor was estimated based on the availability of two active sites for the MBI in the paroxetine structure. The inactivation by the amino site of paroxetine mainly proceeds via the hydrogen atom transfer pathway because of the lower energy demand of its rate determining step. In addition, the low-spin state is the predominant route in the MBI at the methylenedioxo active site as a result of being rebound barrier-free mechanism. Our comparative investigation showed that inactivation at the secondary amine is thermodynamically more favorable because of the lower energy barrier of the dehydration mechanism of the hydroxylated paroxetine complex than its methylenedioxo counterpart. The results of docking analysis coincided with the outputs of DFT calculations since the docking pose with the lowest binding affinity is that for conformation with polar interaction between the amino group of paroxetine and the oxo moiety of P450's active site. Assessment of the molecular dynamics simulations trajectories revealed the favorable interaction of paroxetine with P450.
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Affiliation(s)
- Emadeldin M Kamel
- Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62514, Egypt. and Departamento de Química, Universidad Autónoma de Madrid, Módulo 13, Campus de Excelencia UAM-CSIC Cantoblanco, Madrid, Spain
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Universidad Autónoma de Madrid, Módulo 13, Campus de Excelencia UAM-CSIC Cantoblanco, Madrid, Spain and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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8
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Shamovsky I, Ripa L, Narjes F, Bonn B, Schiesser S, Terstiege I, Tyrchan C. Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations. J Med Chem 2021; 64:8545-8563. [PMID: 34110134 DOI: 10.1021/acs.jmedchem.1c00514] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Aromatic and heteroaromatic amines (ArNH2) are activated by cytochrome P450 monooxygenases, primarily CYP1A2, into reactive N-arylhydroxylamines that can lead to covalent adducts with DNA nucleobases. Hereby, we give hands-on mechanism-based guidelines to design mutagenicity-free ArNH2. The mechanism of N-hydroxylation of ArNH2 by CYP1A2 is investigated by density functional theory (DFT) calculations. Two putative pathways are considered, the radicaloid route that goes via the classical ferryl-oxo oxidant and an alternative anionic pathway through Fenton-like oxidation by ferriheme-bound H2O2. Results suggest that bioactivation of ArNH2 follows the anionic pathway. We demonstrate that H-bonding and/or geometric fit of ArNH2 to CYP1A2 as well as feasibility of both proton abstraction by the ferriheme-peroxo base and heterolytic cleavage of arylhydroxylamines render molecules mutagenic. Mutagenicity of ArNH2 can be removed by structural alterations that disrupt geometric and/or electrostatic fit to CYP1A2, decrease the acidity of the NH2 group, destabilize arylnitrenium ions, or disrupt their pre-covalent transition states with guanine.
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9
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Jaladanki CK, Khatun S, Gohlke H, Bharatam PV. Reactive Metabolites from Thiazole-Containing Drugs: Quantum Chemical Insights into Biotransformation and Toxicity. Chem Res Toxicol 2021; 34:1503-1517. [PMID: 33900062 DOI: 10.1021/acs.chemrestox.0c00450] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Drugs containing thiazole and aminothiazole groups are known to generate reactive metabolites (RMs) catalyzed by cytochrome P450s (CYPs). These RMs can covalently modify essential cellular macromolecules and lead to toxicity and induce idiosyncratic adverse drug reactions. Molecular docking and quantum chemical hybrid DFT study were carried out to explore the molecular mechanisms involved in the biotransformation of thiazole (TZ) and aminothiazole (ATZ) groups leading to RM epoxide, S-oxide, N-oxide, and oxaziridine. The energy barrier required for the epoxidation is 13.63 kcal/mol, that is lower than that of S-oxidation, N-oxidation, and oxaziridine formation (14.56, 17.90, and 20.20, kcal/mol respectively). The presence of the amino group in ATZ further facilitates all the metabolic pathways, for example, the barrier for the epoxidation reaction is reduced by ∼2.5 kcal/mol. Some of the RMs/their isomers are highly electrophilic and tend to form covalent bonds with nucleophilic amino acids, finally leading to the formation of metabolic intermediate complexes (MICs). The energy profiles of these competitive pathways have also been explored.
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Affiliation(s)
- Chaitanya K Jaladanki
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Samima Khatun
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany.,Forschungszentrum Jülich GmbH, John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector -67, S. A. S. Nagar (Mohali), 160 062 Punjab, India
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10
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Banerjee A, Shah JK. Elucidating the effect of the ionic liquid type and alkyl chain length on the stability of ionic liquid-iron porphyrin complexes. J Chem Phys 2020; 153:034306. [PMID: 32716177 DOI: 10.1063/5.0007815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The present study is motivated by the long-term objective of understanding how ionic liquids are biodegraded by cytochrome P450, which contains iron porphyrin (FeP) serving as the catalytic center. To this end, the current study is designed to elucidate the impact of types and conformations of ionic liquids on the binding energy with FeP, the key interactions that stabilize the ionic liquid-FeP complex, and how the electron uptake ability of FeP is altered in the presence of ionic liquids. Four classes of ionic liquids are considered: 1-alkyl-3-methylimidazolium, 1-alkyl-pyridinium, 1-alkylsulfonium, and N-methyl-N-alkylpyrrolidinium. The influence of linear alkyl chains of ethyl, butyl, hexyl, octyl, and decyl is examined on the favorable binding modes with FeP, considering two widely different conformations: tail up and tail down with respect to FeP. Electronic structure calculations are performed at the M06 level of theory with the 6-31G(d,p) basis set for C, H, and N atoms, while the Lanl2DZ basis set is employed for Fe. Donor-acceptor interactions contributing to the binding of ionic liquids to FeP are unraveled through the natural bond orbital analysis. The results from this study indicate that the binding energies are dependent not only on the class of ionic liquids but also on the conformations presented to FeP. The propensity of FeP to acquire an electron is significantly enhanced in the presence of ionic liquid cations, irrespective of the type and the alkyl chain length.
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Affiliation(s)
- Atiya Banerjee
- School of Chemical Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Jindal K Shah
- School of Chemical Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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11
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Fu Z, Yang L, Sun D, Qu Z, Zhao Y, Gao J, Wang Y. Coupled electron and proton transfer in the piperidine drug metabolism pathway by the active species of cytochromes P450. Dalton Trans 2020; 49:11099-11107. [DOI: 10.1039/c9dt03056e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
KS-DFT and MSDFT studies reveal a novel CEPT step that triggers ring contraction of piperidines by P450.
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Affiliation(s)
- Zhiqiang Fu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- School of Environmental Science and Technology
- Dalian University of Technology
- Dalian 116024
- China
| | - Lili Yang
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- China
| | - Dongru Sun
- Institute of Drug Discovery Technology
- Ningbo University
- Ningbo 315211
- China
| | - Zexing Qu
- Laboratory of Theoretical and Computational Chemistry
- Institute of Theoretical Chemistry
- Jilin University
- Changchun 130023
- China
| | - Yufen Zhao
- Institute of Drug Discovery Technology
- Ningbo University
- Ningbo 315211
- China
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute
- University of Minnesota
- Minneapolis
- USA
- Institute of Systems and Physical Biology
| | - Yong Wang
- Institute of Drug Discovery Technology
- Ningbo University
- Ningbo 315211
- China
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12
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Theoretical study on the mechanism of N- and α-carbon oxidation of lapatinib catalyzed by cytochrome P450 monooxygenase. J Mol Model 2019; 25:225. [PMID: 31312984 DOI: 10.1007/s00894-019-4125-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 07/07/2019] [Indexed: 10/26/2022]
Abstract
Lapatinib, an orally active dual tyrosine kinase inhibitor, is efficacious in combination therapy with capecitabine for advanced metastatic breast cancer. Despite its importance, it has been associated with hepatotoxicity observed in clinical trials and postmarketing surveillance. The mechanisms of hepatotoxicity at the chemical and cellular levels may link to drug metabolism. In this study, the N- and α-carbon oxidation processes of lapatinib catalyzed by CYP3A4 were explored by density functional theory method. The calculation results show that oxidation of C6 is the primary metabolic process and carboxylic acid is the main metabolic product. Both hydroxylation of C8 and subsequent formation of primary amines are feasible. However, it is not easy for the primary amines to form active metabolites nitroso, which indicates that there are other paths for the production of nitroso. Carboxylic acid is not the main metabolite of N7 oxidation because of higher hydrolysis energy barrier of intermediate nitrone. It is worthy to study subsequent N-hydroxylation and its downstream reaction, which may be the main pathway for the formation of nitroso. These results lay the foundation for drug design and optimization.
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13
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Delgado JL, Lentz SRC, Kulkarni CA, Chheda PR, Held HA, Hiasa H, Kerns RJ. Probing structural requirements for human topoisomerase I inhibition by a novel N1-Biphenyl fluoroquinolone. Eur J Med Chem 2019; 172:109-130. [PMID: 30959322 DOI: 10.1016/j.ejmech.2019.03.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 03/13/2019] [Accepted: 03/16/2019] [Indexed: 11/28/2022]
Abstract
Fluoroquinolones substituted with N-1 biphenyl and napthyl groups were discovered to act as catalytically inhibitors of human topoisomerases I and II, and to possess anti-proliferative activity in vivo. Structural requirements for these novel quinolones to inhibit catalytic activity of human topoisomerase I have not been explored. In this work novel derivatives of the N-1 biphenyl fluoroquinolone were designed, synthesized and evaluated to understand structural requirements of the C-3 carboxylic acid, C-6 fluorine, C-7 aminomethylpyrrolidine, C-8 methoxy, and the N-1 biphenyl functional groups for hTopoI inhibition. Characterization of each analog for inhibition of hTopoI catalytic inhibition reveals critical insight into structural requirements of these novel quinolones for activity. Additionally, results of DNA binding and modeling studies suggest that N-1 biphenyl fluoroquinolones intercalate between the DNA base pairs with the N-1 biphenyl functional group, rather than the quinolone core, and that this mode of DNA intercalation contributes to inhibition of hTopoI by these novel structures. The results presented here support further development and evaluation of N-1 biphenyl fluoroquinolone analogs as a novel class of anti-cancer agents that act through catalytic inhibition of hTopoI.
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Affiliation(s)
- Justine L Delgado
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA
| | - Sarah R C Lentz
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Chaitanya A Kulkarni
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA
| | - Pratik R Chheda
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA
| | - Hailey A Held
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Robert J Kerns
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, College of Pharmacy, University of Iowa, 115 S Grand Ave., S321 Pharmacy Building, Iowa City, IA, 52242, USA.
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14
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Leth R, Ercig B, Olsen L, Jørgensen FS. Both Reactivity and Accessibility Are Important in Cytochrome P450 Metabolism: A Combined DFT and MD Study of Fenamic Acids in BM3 Mutants. J Chem Inf Model 2019; 59:743-753. [DOI: 10.1021/acs.jcim.8b00750] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rasmus Leth
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Bogac Ercig
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Lars Olsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Flemming Steen Jørgensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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15
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The importance of evaluating the chemical structures and strategies to avoid pitfalls in quantitative bioanalysis. Bioanalysis 2019; 11:85-101. [DOI: 10.4155/bio-2018-0211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Quantitative bioanalytical data are crucial in pharmaceutical research and development, allowing project teams to make informed scientific decisions on the progression of candidate molecules to medicines. Many challenges are often encountered during the bioanalysis of drugs in biological matrices which require resolution in a timely manner. In this publication, guidance is provided to bioanalytical scientists on how to identify potential problems before they become an obstacle for the drug development and to share our experiences dealing some of most common problems encountered in the bioanalytical laboratory. Relevant topics in bioanalysis such as stabilization approaches for glucuronides (Acyl and N-); prodrugs (phosphate and esters), amides, amines, N-oxides; bioanalysis of light sensitive molecules, halogenated drugs and lactones are discussed in this publication.
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16
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Vickers C, Backfisch G, Oellien F, Piel I, Lange UEW. Enzymatic Late‐Stage Oxidation of Lead Compounds with Solubilizing Biomimetic Docking/Protecting groups. Chemistry 2018; 24:17936-17947. [DOI: 10.1002/chem.201802331] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/12/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Clare Vickers
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Gisela Backfisch
- Development Sciences, DMPK and Bioanalytical ResearchAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Frank Oellien
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Isabel Piel
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
| | - Udo E. W. Lange
- Neuroscience Discovery, Medicinal ChemistryAbbVie (Deutschland) GmbH & Co. KG Knollstrasse D-67061 Ludwigshafen Germany
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17
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Abstract
The nitro group is considered to be a versatile and unique functional group in medicinal chemistry. Despite a long history of use in therapeutics, the nitro group has toxicity issues and is often categorized as a structural alert or a toxicophore, and evidence related to drugs containing nitro groups is rather contradictory. In general, drugs containing nitro groups have been extensively associated with mutagenicity and genotoxicity. In this context, efforts toward the structure-mutagenicity or structure-genotoxicity relationships have been undertaken. The current Perspective covers various aspects of agents that contain nitro groups, their bioreductive activation mechanisms, their toxicities, and approaches to combat their toxicity issues. In addition, recent advances in the field of anticancer, antitubercular and antiparasitic agents containing nitro groups, along with a patent survey on hypoxia-activated prodrugs containing nitro groups, are also covered.
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Affiliation(s)
- Kunal Nepali
- School of Pharmacy, College of Pharmacy , Taipei Medical University , 250 Wuxing Street , Taipei 11031 , Taiwan
| | - Hsueh-Yun Lee
- School of Pharmacy, College of Pharmacy , Taipei Medical University , 250 Wuxing Street , Taipei 11031 , Taiwan
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy , Taipei Medical University , 250 Wuxing Street , Taipei 11031 , Taiwan
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18
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Huang X, Groves JT. Oxygen Activation and Radical Transformations in Heme Proteins and Metalloporphyrins. Chem Rev 2018; 118:2491-2553. [PMID: 29286645 PMCID: PMC5855008 DOI: 10.1021/acs.chemrev.7b00373] [Citation(s) in RCA: 591] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/20/2022]
Abstract
As a result of the adaptation of life to an aerobic environment, nature has evolved a panoply of metalloproteins for oxidative metabolism and protection against reactive oxygen species. Despite the diverse structures and functions of these proteins, they share common mechanistic grounds. An open-shell transition metal like iron or copper is employed to interact with O2 and its derived intermediates such as hydrogen peroxide to afford a variety of metal-oxygen intermediates. These reactive intermediates, including metal-superoxo, -(hydro)peroxo, and high-valent metal-oxo species, are the basis for the various biological functions of O2-utilizing metalloproteins. Collectively, these processes are called oxygen activation. Much of our understanding of the reactivity of these reactive intermediates has come from the study of heme-containing proteins and related metalloporphyrin compounds. These studies not only have deepened our understanding of various functions of heme proteins, such as O2 storage and transport, degradation of reactive oxygen species, redox signaling, and biological oxygenation, etc., but also have driven the development of bioinorganic chemistry and biomimetic catalysis. In this review, we survey the range of O2 activation processes mediated by heme proteins and model compounds with a focus on recent progress in the characterization and reactivity of important iron-oxygen intermediates. Representative reactions initiated by these reactive intermediates as well as some context from prior decades will also be presented. We will discuss the fundamental mechanistic features of these transformations and delineate the underlying structural and electronic factors that contribute to the spectrum of reactivities that has been observed in nature as well as those that have been invented using these paradigms. Given the recent developments in biocatalysis for non-natural chemistries and the renaissance of radical chemistry in organic synthesis, we envision that new enzymatic and synthetic transformations will emerge based on the radical processes mediated by metalloproteins and their synthetic analogs.
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Affiliation(s)
- Xiongyi Huang
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department
of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - John T. Groves
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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19
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Alberro N, Torrent-Sucarrat M, Arrieta A, Rubiales G, Cossío FP. Density Functional Theory Study on the Demethylation Reaction between Methylamine, Dimethylamine, Trimethylamine, and Tamoxifen Catalyzed by a Fe(IV)-Oxo Porphyrin Complex. J Phys Chem A 2018; 122:1658-1671. [PMID: 29320849 DOI: 10.1021/acs.jpca.7b10654] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In this work, we studied computationally the N-demethylation reaction of methylamine, dimethylamine, and trimethylamine as archetypal examples of primary, secondary, and tertiary amines catalyzed by high-field low-spin Fe-containing enzymes such as cytochromes P450. Using DFT calculations, we found that the expected C-H hydroxylation process was achieved for trimethylamine. When dimethylamine and methylamine were studied, two different reaction mechanisms (C-H hydroxylation and a double hydrogen atom transfer) were computed to be energetically accessible and both are equally preferred. Both processes led to the formation of formaldehyde and the N-demethylated substrate. Finally, as an illustrative example, the relative contribution of the three primary oxidation routes of tamoxifen was rationalized through energetic barriers obtained from density functional calculations and docking experiments involving CYP3A4 and CYP2D6 isoforms. We found that the N-demethylation process was the intrinsically favored one, whereas other oxidation reactions required most likely preorganization imposed by the residues close to the active sites.
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Affiliation(s)
- Nerea Alberro
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain.,Ikerbasque, Basque Foundation for Science , María Díaz de Haro 3, 6°, 48013 Bilbao, Spain
| | - Ana Arrieta
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Gloria Rubiales
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Fernando P Cossío
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO-CINQA) , Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain.,Donostia International Physics Center (DIPC) , Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain
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20
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Muñoz-Muñoz AC, Pekol T, Schubring D, Johnson C, Andrade L. Identification of Novel Opioid Interferences using High-Resolution Mass Spectrometry†. J Anal Toxicol 2017; 42:6-16. [DOI: 10.1093/jat/bkx065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/02/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Teresa Pekol
- Dominion Diagnostics, 211 Circuit Drive, North Kingstown, RI 02852, USA
| | - Dana Schubring
- Dominion Diagnostics, 211 Circuit Drive, North Kingstown, RI 02852, USA
| | - Charlene Johnson
- Dominion Diagnostics, 211 Circuit Drive, North Kingstown, RI 02852, USA
| | - Lawrence Andrade
- Dominion Diagnostics, 211 Circuit Drive, North Kingstown, RI 02852, USA
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21
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Vazquez-Albacete D, Montefiori M, Kol S, Motawia MS, Møller BL, Olsen L, Nørholm MHH. The CYP79A1 catalyzed conversion of tyrosine to (E)-p-hydroxyphenylacetaldoxime unravelled using an improved method for homology modeling. PHYTOCHEMISTRY 2017; 135:8-17. [PMID: 28088302 DOI: 10.1016/j.phytochem.2016.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/01/2016] [Accepted: 11/27/2016] [Indexed: 06/06/2023]
Abstract
The vast diversity and membrane-bound nature of plant P450s makes it challenging to study the structural characteristics of this class of enzymes especially with respect to accurate intermolecular enzyme-substrate interactions. To address this problem we here apply a modified hybrid structure strategy for homology modeling of plant P450s. This allows for structural elucidation based on conserved motifs in the protein sequence and secondary structure predictions. We modeled the well-studied Sorghum bicolor cytochrome P450 CYP79A1 catalyzing the first step in the biosynthesis of the cyanogenic glucoside dhurrin. Docking experiments identified key regions of the active site involved in binding of the substrate and facilitating catalysis. Arginine 152 and threonine 534 were identified as key residues interacting with the substrate. The model was validated experimentally using site-directed mutagenesis. The new CYP79A1 model provides detailed insights into the mechanism of the initial steps in cyanogenic glycoside biosynthesis. The approach could guide functional characterization of other membrane-bound P450s and provide structural guidelines for elucidation of key structure-function relationships of other plant P450s.
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Affiliation(s)
- Dario Vazquez-Albacete
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Marco Montefiori
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Stefan Kol
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Mohammed Saddik Motawia
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark
| | - Lars Olsen
- Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, University of Copenhagen, Denmark
| | - Morten H H Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Center for Synthetic Biology bioSYNergy, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, Copenhagen, Denmark.
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22
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Dixit VA, Deshpande S. Advances in Computational Prediction of Regioselective and Isoform-Specific Drug Metabolism Catalyzed by CYP450s. ChemistrySelect 2016. [DOI: 10.1002/slct.201601051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
| | - Shirish Deshpande
- Department of Pharmaceutical Chemistry; School of Pharmacy and Technology Management (SPTM), Shri Vile Parle Kelavani Mandal's (SVKM's) Narsee Monjee Institute of Management Studies (NMIMS), Mukesh Patel Technology Park, Babulde, Bank of Tapi River; Mumbai-Agra Road Shirpur, Dist. Dhule−425405 India
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23
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Alberro N, Torrent-Sucarrat M, Arrastia I, Arrieta A, Cossío FP. Two-State Reactivity of Histone Demethylases Containing Jumonji-C Active Sites: Different Mechanisms for Different Methylation Degrees. Chemistry 2016; 23:137-148. [DOI: 10.1002/chem.201604219] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Nerea Alberro
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
- Ikerbasque; Basque Foundation for Science; María Díaz de Haro 3, 6 floor 48013 Bilbao Spain
| | - Iosune Arrastia
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
| | - Ana Arrieta
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I; Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU); Centro de Innovación en Química Avanzada (ORFEO-CINQA); Manuel Lardizabal Ibilbidea 3 20018 San Sebastián/Donostia Spain
- Donostia International Physics Center (DIPC); Manuel Lardizabal Ibilbidea 4 20018 San Sebastián/Donostia Spain
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24
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LC-MS Supported Studies on the in Vitro Metabolism of both Enantiomers of Flubatine and the in Vivo Metabolism of (+)-[(18)F]Flubatine-A Positron Emission Tomography Radioligand for Imaging α4β2 Nicotinic Acetylcholine Receptors. Molecules 2016; 21:molecules21091200. [PMID: 27617996 PMCID: PMC6273452 DOI: 10.3390/molecules21091200] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/01/2016] [Accepted: 09/02/2016] [Indexed: 12/27/2022] Open
Abstract
Both enantiomers of [18F]flubatine are promising radioligands for neuroimaging of α4β2 nicotinic acetylcholine receptors (nAChRs) by positron emission tomography (PET). To support clinical studies in patients with early Alzheimer’s disease, a detailed examination of the metabolism in vitro and in vivo has been performed. (+)- and (−)-flubatine, respectively, were incubated with liver microsomes from mouse and human in the presence of NADPH (β-nicotinamide adenine dinucleotide 2′-phosphate reduced tetrasodium salt). Phase I in vitro metabolites were detected and their structures elucidated by LC-MS/MS (liquid chromatography-tandem mass spectrometry). Selected metabolite candidates were synthesized and investigated for structural confirmation. Besides a high level of in vitro stability, the microsomal incubations revealed some species differences as well as enantiomer discrimination with regard to the formation of monohydroxylated products, which was identified as the main metabolic pathway in this assay. Furthermore, after injection of 250 MBq (+)-[18F]flubatine (specific activity > 350 GBq/μmol) into mouse, samples were prepared from brain, liver, plasma, and urine after 30 min and investigated by radio-HPLC (high performance liquid chromatography with radioactivity detection). For structure elucidation of the radiometabolites of (+)-[18F]flubatine formed in vivo, identical chromatographic conditions were applied to LC-MS/MS and radio-HPLC to compare samples obtained in vitro and in vivo. By this correlation approach, we assigned three of four main in vivo radiometabolites to products that are exclusively C- or N-hydroxylated at the azabicyclic ring system of the parent molecule.
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25
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Lonsdale R, Fort RM, Rydberg P, Harvey JN, Mulholland AJ. Quantum Mechanics/Molecular Mechanics Modeling of Drug Metabolism: Mexiletine N-Hydroxylation by Cytochrome P450 1A2. Chem Res Toxicol 2016; 29:963-71. [DOI: 10.1021/acs.chemrestox.5b00514] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Richard Lonsdale
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Rachel M. Fort
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Patrik Rydberg
- Department
of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Jeremy N. Harvey
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Adrian J. Mulholland
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
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