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Prakinee K, Lawan N, Phintha A, Visitsatthawong S, Chitnumsub P, Jitkaroon W, Chaiyen P. On the Mechanisms of Hypohalous Acid Formation and Electrophilic Halogenation by Non-Native Halogenases. Angew Chem Int Ed Engl 2024; 63:e202403858. [PMID: 38606607 DOI: 10.1002/anie.202403858] [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: 02/24/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/13/2024]
Abstract
Enzymatic electrophilic halogenation is a mild tool for functionalization of diverse organic compounds. Only a few groups of native halogenases are capable of catalyzing such a reaction. In this study, we used a mechanism-guided strategy to discover the electrophilic halogenation activity catalyzed by non-native halogenases. As the ability to form a hypohalous acid (HOX) is key for halogenation, flavin-dependent monooxygenases/oxidases capable of forming C4a-hydroperoxyflavin (FlC4a-OOH), such as dehalogenase, hydroxylases, luciferase and pyranose-2-oxidase (P2O), and flavin reductase capable of forming H2O2 were explored for their abilities to generate HOX in situ. Transient kinetic analyses using stopped-flow spectrophotometry/fluorometry and product analysis indicate that FlC4a-OOH in dehalogenases, selected hydroxylases and luciferases, but not in P2O can form HOX; however, the HOX generated from FlC4a-OOH cannot halogenate their substrates. Remarkably, in situ H2O2 generated by P2O can form HOI and also iodinate various compounds. Because not all enzymes capable of forming FlC4a-OOH can react with halides to form HOX, QM/MM calculations, site-directed mutagenesis and structural analysis were carried out to elucidate the mechanism underlying HOX formation and characterize the active site environment. Our findings shed light on identifying new halogenase scaffolds besides the currently known enzymes and have invoked a new mode of chemoenzymatic halogenation.
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Affiliation(s)
- Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Surawit Visitsatthawong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Penchit Chitnumsub
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA) Thailand Science Park, Pathum Thani, 12120, Thailand
| | - Watcharapa Jitkaroon
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley, Rayong, 21210, Thailand
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Phintha A, Chaiyen P. Unifying and versatile features of flavin-dependent monooxygenases: Diverse catalysis by a common C4a-(hydro)peroxyflavin. J Biol Chem 2023; 299:105413. [PMID: 37918809 PMCID: PMC10696468 DOI: 10.1016/j.jbc.2023.105413] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/04/2023] Open
Abstract
Flavin-dependent monooxygenases (FDMOs) are known for their remarkable versatility and for their crucial roles in various biological processes and applications. Extensive research has been conducted to explore the structural and functional relationships of FDMOs. The majority of reported FDMOs utilize C4a-(hydro)peroxyflavin as a reactive intermediate to incorporate an oxygen atom into a wide range of compounds. This review discusses and analyzes recent advancements in our understanding of the structural and mechanistic features governing the enzyme functions. State-of-the-art discoveries related to common and distinct structural properties governing the catalytic versatility of the C4a-(hydro)peroxyflavin intermediate in selected FDMOs are discussed. Specifically, mechanisms of hydroxylation, dehalogenation, halogenation, and light-emitting reactions by FDMOs are highlighted. We also provide new analysis based on the structural and mechanistic features of these enzymes to gain insights into how the same intermediate can be harnessed to perform a wide variety of reactions. Challenging questions to obtain further breakthroughs in the understanding of FDMOs are also proposed.
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Affiliation(s)
- Aisaraphon Phintha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, Thailand.
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Phonbuppha J, Tinikul R, Ohmiya Y, Chaiyen P. High Sensitivity and Low-Cost Flavin luciferase (FLUX Vc)-based Reporter Gene for Mammalian Cell Expression. J Biol Chem 2023; 299:104639. [PMID: 36965614 PMCID: PMC10164909 DOI: 10.1016/j.jbc.2023.104639] [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: 02/23/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/27/2023] Open
Abstract
Luciferase-based gene reporters generating bioluminescence signals are important tools for biomedical research. Amongst the luciferases, flavin-dependent enzymes use the most economical chemicals. However, their applications in mammalian cells are limited due to their low signals compared to other systems. Here, we constructed Flavin Luciferase from Vibrio campbellii (Vc) for Mammalian Cell Expression (FLUXVc) by engineering luciferase from Vibrio campbellii (the most thermostable bacterial luciferase reported to date) and optimizing its expression and reporter assays in mammalian cells which can improve the bioluminescence light output by >400-fold as compared to the non-engineered version. We found that the FLUXVc reporter gene can be overexpressed in various cell lines and showed outstanding signal-to-background in HepG2 cells, significantly higher than that of firefly luciferase (Fluc). The combined use of FLUXVc/Fluc as target/control vectors gave the most stable signals, better than the standard set of Fluc(target)/Rluc(control). We also demonstrated that FLUXVc can be used for testing inhibitors of the NF-κB signaling pathway. Collectively, our results provide an optimized method for using the more economical flavin-dependent luciferase in mammalian cells.
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Affiliation(s)
- Jittima Phonbuppha
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan valley, Rayong 21210 Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok 10400 Thailand
| | - Yoshihiro Ohmiya
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan valley, Rayong 21210 Thailand; National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Osaka 563-8577, Japan; Osaka Institute of Technology (OIT), Osaka, Osaka 535-8585, Japan
| | - Pimchai Chaiyen
- School of Biomolecular Science & Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan valley, Rayong 21210 Thailand.
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Pimviriyakul P, Chaiyen P. Formation and stabilization of C4a-hydroperoxy-FAD by the Arg/Asn pair in HadA monooxygenase. FEBS J 2023; 290:176-195. [PMID: 35942637 DOI: 10.1111/febs.16591] [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: 06/15/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 01/14/2023]
Abstract
HadA monooxygenase catalyses the detoxification of halogenated phenols and nitrophenols via dehalogenation and denitration respectively. C4a-hydroperoxy-FAD is a key reactive intermediate wherein its formation, protonation and stabilization reflect enzyme efficiency. Herein, transient kinetics, site-directed mutagenesis and pH-dependent behaviours of HadA reaction were employed to identify key features stabilizing C4a-adducts in HadA. The formation of C4a-hydroperoxy-FAD is pH independent, whereas its decay and protonation of distal oxygen are associated with pKa values of 8.5 and 8.4 respectively. These values are correlated with product formation within a pH range of 7.6-9.1, indicating the importance of adduct stabilization to enzymatic efficiency. We identified Arg101 as a key residue for reduced FAD (FADH- ) binding and C4a-hydroperoxy-FAD formation due to the loss of these abilities as well as enzyme activity in HadAR101A and HadAR101Q . Mutations of the neighbouring Asn447 do not affect the rate of C4a-hydroperoxy-FAD formation; however, they impair FADH- binding. The disruption of Arg101/Asn447 hydrogen bond networking in HadAN447A increases the pKa value of C4a-hydroperoxy-FAD decay to 9.5; however, this pKa was not altered in HadAN447D (pKa of 8.5). Thus, Arg101/Asn447 pair should provide important interactions for FADH- binding and maintain the pKa associated with H2 O2 elimination from C4a-hydroperoxy-FAD in HadA. In the presence of substrate, the formation of C4a-hydroxy-FAD at the hydroxylation step is pH insensitive, and it dehydrates to form the oxidized FAD with pKa of 7.9. This structural feature might help elucidate how the reactive intermediate was stabilized in other flavin-dependent monooxygenases.
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Affiliation(s)
- Panu Pimviriyakul
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
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Mohammadi M, Siadati SA, Ahmadi S, Habibzadeh S, Poor Heravi MR, Hossaini Z, Vessally E. Carbon fixation of CO2 via cyclic reactions with borane in gaseous atmosphere leading to formic acid (and metaboric acid); A potential energy surface (PES) study. Front Chem 2022; 10:1003086. [PMID: 36324523 PMCID: PMC9620423 DOI: 10.3389/fchem.2022.1003086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Carbon dioxide (CO2), a stable gaseous species, occupies the troposphere layer of the atmosphere. Following it, the environment gets warmer, and the ecosystem changes as a consequence of disrupting the natural order of our life. Due to this, in the present reasearch, the possibility of carbon fixation of CO2 by using borane was investigated. To conduct this, each of the probable reaction channels between borane and CO2 was investigated to find the fate of this species. The results indicate that among all the channels, the least energetic path for the reaction is reactant complex (RC) to TS (A-1) to Int (A-1) to TS (A-D) to formic acid (and further meta boric acid production from the transformation of boric acid). It shows that use of gaseous borane might lead to controlling these dangerous greenhouse gases which are threatening the present form of life on Earth, our beautiful, fragile home.
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Affiliation(s)
- Marziyeh Mohammadi
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
- *Correspondence: Marziyeh Mohammadi, ; Seyyed Amir Siadati,
| | - Seyyed Amir Siadati
- Department of Chemistry, Qaemshahr Branch, Islamic Azad University, Qaemshahr, Iran
- *Correspondence: Marziyeh Mohammadi, ; Seyyed Amir Siadati,
| | - Sheida Ahmadi
- Department of Chemistry, Payame Noor University, Tehran, Iran
| | | | | | | | - Esmail Vessally
- Department of Chemistry, Payame Noor University, Tehran, Iran
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Pi S, Luo Y, Liu YJ. Thorough Understanding of Bioluminophore Production in Bacterial Bioluminescence. J Phys Chem A 2022; 126:6604-6616. [DOI: 10.1021/acs.jpca.2c04311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shuangqi Pi
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yanling Luo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
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Strong proton transfer from phenolic ring to imine functionality in 1D azido and dicyanamido bridged Mn(II) coordination polymers: Synthesis, crystal structure and magnetic studies. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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