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Golczak A, Prukała D, Sikorska E, Gierszewski M, Cherkas V, Kwiatek D, Kubiak A, Varma N, Pędziński T, Murphree S, Cibulka R, Mrówczyńska L, Kolanowski JL, Sikorski M. Tetramethylalloxazines as efficient singlet oxygen photosensitizers and potential redox-sensitive agents. Sci Rep 2023; 13:13426. [PMID: 37591918 PMCID: PMC10435492 DOI: 10.1038/s41598-023-40536-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/12/2023] [Indexed: 08/19/2023] Open
Abstract
Tetramethylalloxazines (TMeAll) have been found to have a high quantum yield of singlet oxygen generation when used as photosensitizers. Their electronic structure and transition energies (S0 → Si, S0 → Ti, T1 → Ti) were calculated using DFT and TD-DFT methods and compared to experimental absorption spectra. Generally, TMeAll display an energy diagram similar to other derivatives belonging to the alloxazine class of compounds, namely π,π* transitions are accompanied by closely located n,π* transitions. Photophysical data such as quantum yields of fluorescence, fluorescence lifetimes, and nonradiative rate constants were also studied in methanol (MeOH), acetonitrile (ACN), and 1,2-dichloroethane (DCE). The transient absorption spectra were also analyzed. To assess cytotoxicity of new compounds, a hemolytic assay was performed using human red blood cells (RBC) in vitro. Subsequently, fluorescence lifetime imaging experiments (FLIM) were performed on RBC under physiological and oxidative stress conditions alone or in the presence of TMeAll allowing for pinpointing changes caused by those compounds on the intracellular environment of these cells.
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Affiliation(s)
- Anna Golczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Dorota Prukała
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Ewa Sikorska
- Poznań University of Economics and Business, Al. Niepodległości 10, 61-875, Poznan, Poland
| | - Mateusz Gierszewski
- Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, 61-614, Poznan, Poland
| | - Volodymyr Cherkas
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Dorota Kwiatek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Adam Kubiak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Naisargi Varma
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Tomasz Pędziński
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - Shaun Murphree
- Department of Chemistry, Allegheny College, 520 N. Main Street, Meadville, PA, USA
| | - Radek Cibulka
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628, Prague 6, Czech Republic.
| | - Lucyna Mrówczyńska
- Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznan, Poland.
| | - Jacek Lukasz Kolanowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
| | - Marek Sikorski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland.
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Kabir MP, Ouedraogo D, Orozco-Gonzalez Y, Gadda G, Gozem S. Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins. J Phys Chem B 2023; 127:1301-1311. [PMID: 36740810 PMCID: PMC9940217 DOI: 10.1021/acs.jpcb.2c06475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin's C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin's N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4-8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.
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Čubiňák M, Varma N, Oeser P, Pokluda A, Pavlovska T, Cibulka R, Sikorski M, Tobrman T. Tuning the Photophysical Properties of Flavins by Attaching an Aryl Moiety via Direct C-C Bond Coupling. J Org Chem 2023; 88:218-229. [PMID: 36525315 DOI: 10.1021/acs.joc.2c02168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Palladium-catalyzed Suzuki reactions of brominated flavin derivatives (5-deazaflavins, alloxazines, and isoalloxazines) with boronic acids or boronic acid esters that occur readily under mild conditions were shown to be an effective tool for the synthesis of a broad range of 7/8-arylflavins. In general, the introduction of an aryl/heteroaryl group by means of a direct C-C bond has been shown to be a promising approach to tuning the photophysical properties of flavin derivatives. The aryl substituents caused a bathochromic shift in the absorption spectra of up to 52 nm and prolonged the fluorescence lifetime by up to 1 order of magnitude. Moreover, arylation of flavin derivatives decreased their ability to generate singlet oxygen.
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Affiliation(s)
- Marek Čubiňák
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Naisargi Varma
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614Poznań, Poland
| | - Petr Oeser
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Adam Pokluda
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Tetiana Pavlovska
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Radek Cibulka
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Marek Sikorski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614Poznań, Poland
| | - Tomáš Tobrman
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
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Kar RK. Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems. Drug Discov Today 2023; 28:103374. [PMID: 36174967 DOI: 10.1016/j.drudis.2022.103374] [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: 03/01/2022] [Revised: 06/27/2022] [Accepted: 09/22/2022] [Indexed: 02/02/2023]
Abstract
Hybrid quantum mechanics/molecular mechanics (QM/MM) is one of the most reliable approaches for accurately modeling and studying the complex pharmaceutical discovery system. Classical mechanics has significantly accelerated the drug discovery process in the past decade. However, the current challenge is the large pool of false positives, which require extensive validation. Hybrid QM/MM is an effective solution for accurately studying ligand binding, structural mechanisms, free energy evaluation, and spectroscopic characterization. This article highlights the methodological details relevant to cost-effective hybrid QM/MM methods. This approach, combined with traditional pharmacoinformatics methods, could be a reliable strategy to balance the cost and accuracy of the calculations.
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Affiliation(s)
- Rajiv K Kar
- Jyoti and Bhupat Mehta School of Health Sciences and Technology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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Unusual reactivity of a flavin in a bifurcating electron-transferring flavoprotein leads to flavin modification and a charge-transfer complex. J Biol Chem 2022; 298:102606. [PMID: 36257407 PMCID: PMC9713284 DOI: 10.1016/j.jbc.2022.102606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
From the outset, canonical electron transferring flavoproteins (ETFs) earned a reputation for containing modified flavin. We now show that modification occurs in the recently recognized bifurcating (Bf) ETFs as well. In Bf ETFs, the 'electron transfer' (ET) flavin mediates single electron transfer via a stable anionic semiquinone state, akin to the FAD of canonical ETFs, whereas a second flavin mediates bifurcation (the Bf FAD). We demonstrate that the ET FAD undergoes transformation to two different modified flavins by a sequence of protein-catalyzed reactions that occurs specifically in the ET site, when the enzyme is maintained at pH 9 in an amine-based buffer. Our optical and mass spectrometric characterizations identify 8-formyl flavin early in the process and 8-amino flavins (8AFs) at later times. The latter have not previously been documented in an ETF to our knowledge. Mass spectrometry of flavin products formed in Tris or bis-tris-aminopropane solutions demonstrates that the source of the amine adduct is the buffer. Stepwise reduction of the 8AF demonstrates that it can explain a charge transfer band observed near 726 nm in Bf ETF, as a complex involving the hydroquinone state of the 8AF in the ET site with the oxidized state of unmodified flavin in the Bf site. This supports the possibility that Bf ETF can populate a conformation enabling direct electron transfer between its two flavins, as has been proposed for cofactors brought together in complexes between ETF and its partner proteins.
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Derat E, Kamerlin SCL. Computational Advances in Protein Engineering and Enzyme Design. J Phys Chem B 2022; 126:2449-2451. [PMID: 35387452 DOI: 10.1021/acs.jpcb.2c01198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Etienne Derat
- Institut Parisien de Chimie Moléculaire, UMR 8232 CNRS, Sorbonne Université, 75005 Paris, France
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Mohamed-Raseek N, Miller AF. Contrasting roles for two conserved arginines: stabilizing flavin semiquinone or quaternary structure, in bifurcating electron transfer flavoproteins. J Biol Chem 2022; 298:101733. [PMID: 35176283 PMCID: PMC8958531 DOI: 10.1016/j.jbc.2022.101733] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/11/2022] [Accepted: 02/12/2022] [Indexed: 01/02/2023] Open
Abstract
Bifurcating electron transfer flavoproteins (Bf ETFs) are important redox enzymes that contain two flavin adenine dinucleotide (FAD) cofactors, with contrasting reactivities and complementary roles in electron bifurcation. However, for both the “electron transfer” (ET) and the “bifurcating” (Bf) FADs, the only charged amino acid within 5 Å of the flavin is a conserved arginine (Arg) residue. To understand how the two sites produce different reactivities utilizing the same residue, we investigated the consequences of replacing each of the Arg residues with lysine, glutamine, histidine, or alanine. We show that absence of a positive charge in the ET site diminishes accumulation of the anionic semiquinone (ASQ) that enables the ET flavin to act as a single electron carrier, due to depression of the oxidized versus. ASQ reduction midpoint potential, E°OX/ASQ. Perturbation of the ET site also affected the remote Bf site, whereas abrogation of Bf FAD binding accelerated chemical modification of the ET flavin. In the Bf site, removal of the positive charge impaired binding of FAD or AMP, resulting in unstable protein. Based on pH dependence, we propose that the Bf site Arg interacts with the phosphate(s) of Bf FAD or AMP, bridging the domain interface via a conserved peptide loop (“zipper”) and favoring nucleotide binding. We further propose a model that rationalizes conservation of the Bf site Arg even in non-Bf ETFs, as well as AMP's stabilizing role in the latter, and provides a mechanism for coupling Bf flavin redox changes to domain-scale motion.
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