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Stanková J, Jurášek M, Hajdúch M, Džubák P. Terpenes and Terpenoids Conjugated with BODIPYs: An Overview of Biological and Chemical Properties. JOURNAL OF NATURAL PRODUCTS 2024; 87:1306-1319. [PMID: 38482846 PMCID: PMC11061839 DOI: 10.1021/acs.jnatprod.3c00961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 05/03/2024]
Abstract
Advancements in small-molecule research have created the need for sensitive techniques to accurately study biological processes in living systems. Fluorescent-labeled probes have become indispensable tools, particularly those that use boron-dipyrromethene (BODIPY) dyes. Terpenes and terpenoids are organic compounds found in nature that offer diverse biological activities, and BODIPY-based probes play a crucial role in studying these compounds. Monoterpene-BODIPY conjugates have exhibited potential for staining bacterial and fungal cells. Sesquiterpene-BODIPY derivatives have been used to study sarcoplasmic/endoplasmic reticulum calcium ATPase (SERCA), indicating their potential for drug development. Owing to their unique properties, diterpenes have been investigated using BODIPY conjugates to evaluate their mechanisms of action. Triterpene-BODIPY conjugates have been synthesized for biological studies, with different spacers affecting their cytotoxicity. Fluorescent probes, inspired by terpenoid-containing vitamins, have also been developed. Derivatives of tocopherol, coenzyme Q10, and vitamin K1 can provide insights into their oxidation-reduction abilities. All these probes have diverse applications, including the study of cell membranes to investigate immune responses and antioxidant properties. Further research in this field can help better understand and use terpenes and terpenoids in various biological contexts.
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Affiliation(s)
- Jarmila Stanková
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, 77900 Olomouc, Czech Republic
| | - Michal Jurášek
- Department
of Chemistry of Natural Compounds, University
of Chemistry and Technology Prague, 16628 Prague, Czech Republic
| | - Marián Hajdúch
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, 77900 Olomouc, Czech Republic
- Laboratory
of Experimental Medicine, Institute of Molecular and Translational
Medicine, University Hospital Olomouc, 77900 Olomouc, Czech Republic
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, 77900 Olomouc, Czech Republic
- Laboratory
of Experimental Medicine, Institute of Molecular and Translational
Medicine, University Hospital Olomouc, 77900 Olomouc, Czech Republic
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Guseva GB, Eremeeva YV, Antina EV, Gilfanov IR, Lisovskaya SA, Ostolopovskaya OV, Trizna EY, Kayumov AR, Nikitina LE. Effect of meso-substituents and medium properties on the photo- and pH-stability, penetration efficiency into bacterial and microscopic fungi cells of terpene-BODIPY conjugates. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123701. [PMID: 38070313 DOI: 10.1016/j.saa.2023.123701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/17/2023] [Accepted: 11/26/2023] [Indexed: 01/13/2024]
Abstract
In order to expand the arsenal of tools and areas for practical use of BODIPY dyes as bifunctional fluorescent theranostics, we studied the effect of the meso-substituents nature and medium properties on photo- and pH-stability, efficiency of singlet oxygen generation, and affinity to biostructures of terpene-BODIPY conjugates. The BODIPYs fused with myrtenol or thiotherpenoid via carboxylic acid residues exhibit high stability over a wide pH range and the presence of a bulky substituent at the meso-position of BODIPY conjugates increases their photostability two-fold compared to structurally related meso-unsubstituted analogues. Furthermore, the photodegradation rate of the conjugates directly depends on their ability to generate singlet oxygen and the course probability of the corresponding red-ox reactions involving reactive oxygen species. The conjugate of BODIPY with a thiotherpenoid demonstrated high ability to penetrate the membranes of filamentous and yeast-like fungi and bind to membrane of organelles in the fungal cell. At the same time, this compound also had a high ability to penetrate into biofilms of Staphylococcus aureus and Klebsiella pneumoniae and into bacterial cells within the matrix, which makes this compound promising for staining intracellular structures of eukaryotic cells and bacteria embedded into biofilms.
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Affiliation(s)
- Galina B Guseva
- G.A. Krestov Institute of Solution Chemistry of Russian Academy of Sciences, 153045 Ivanovo, Russia.
| | - Yuliya V Eremeeva
- G.A. Krestov Institute of Solution Chemistry of Russian Academy of Sciences, 153045 Ivanovo, Russia.
| | - Elena V Antina
- G.A. Krestov Institute of Solution Chemistry of Russian Academy of Sciences, 153045 Ivanovo, Russia.
| | - Ilmir R Gilfanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia.
| | - Svetlana A Lisovskaya
- Kazan State Medical University, Faculty of Medicine and Biology, 420012 Kazan, Russia; Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; Scientific Research Institute of Epidemiology and Microbiology, 420015 Kazan, Russia.
| | - Olga V Ostolopovskaya
- Kazan State Medical University, Faculty of Medicine and Biology, 420012 Kazan, Russia; Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia.
| | - Elena Y Trizna
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia.
| | - Airat R Kayumov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia.
| | - Liliya E Nikitina
- Kazan State Medical University, Faculty of Medicine and Biology, 420012 Kazan, Russia; Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia.
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Ksenofontov AA, Isaev YI, Lukanov MM, Makarov DM, Eventova VA, Khodov IA, Berezin MB. Accurate prediction of 11B NMR chemical shift of BODIPYs via machine learning. Phys Chem Chem Phys 2023; 25:9472-9481. [PMID: 36935644 DOI: 10.1039/d3cp00253e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
In this article, we present the results of developing a model based on an RFR machine learning method using the ISIDA fragment descriptors for predicting the 11B NMR chemical shift of BODIPYs. The model is freely available at https://ochem.eu/article/146458. The model demonstrates the high quality of predicting the 11B NMR chemical shift (RMSE, 5CV (FINALE training set) = 0.40 ppm, RMSE (TEST set) = 0.14 ppm). In addition, we compared the "cost" and the user-friendliness for calculations using the quantum-chemical model with the DFT/GIAO approach. The 11B NMR chemical shift prediction accuracy (RMSE) of the model considered is more than three times higher and tremendously faster than the DFT/GIAO calculations. As a result, we provide a convenient tool and database that we collected for all researchers, that allows them to predict the 11B NMR chemical shift of boron-containing dyes. We believe that the new model will make it easier for researchers to correctly interpret the 11B NMR chemical shifts experimentally determined and to select more optimal conditions to perform an NMR experiment.
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Affiliation(s)
- Alexander A Ksenofontov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street, 153045 Ivanovo, Russia.
| | - Yaroslav I Isaev
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street, 153045 Ivanovo, Russia. .,Ivanovo State University of Chemistry and Technology, 7, Sheremetevskiy Avenue, Ivanovo 153000, Russia
| | - Michail M Lukanov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street, 153045 Ivanovo, Russia.
| | - Dmitry M Makarov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street, 153045 Ivanovo, Russia.
| | - Varvara A Eventova
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street, 153045 Ivanovo, Russia. .,Ivanovo State University of Chemistry and Technology, 7, Sheremetevskiy Avenue, Ivanovo 153000, Russia
| | - Ilya A Khodov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street, 153045 Ivanovo, Russia.
| | - Mechail B Berezin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street, 153045 Ivanovo, Russia.
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Guseva GB, Antina EV, Berezin MB, Smirnova AS, Pavelyev RS, Gilfanov IR, Shevchenko OG, Pestova SV, Izmest’ev ES, Rubtsova SA, Ostolopovskaya OV, Efimov SV, Klochkov VV, Rakhmatullin IZ, Timerova AF, Khodov IA, Lodochnikova OA, Islamov DR, Dorovatovskii PV, Nikitina LE, Boichuk SV. Design, Spectral Characteristics, Photostability, and Possibilities for Practical Application of BODIPY FL-Labeled Thioterpenoid. Bioengineering (Basel) 2022; 9:bioengineering9050210. [PMID: 35621488 PMCID: PMC9138141 DOI: 10.3390/bioengineering9050210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/16/2022] Open
Abstract
This paper presents the design and a comparative analysis of the structural and solvation factors on the spectral and biological properties of the BODIPY biomarker with a thioterpene fragment. Covalent binding of the thioterpene moiety to the butanoic acid residue of meso-substituted BODIPY was carried out to find out the membranotropic effect of conjugate to erythrocytes, and to assess the possibilities of its practical application in bioimaging. The molecular structure of the conjugate was confirmed via X-ray, UV/vis-, NMR-, and MS-spectra. It was found that dye demonstrates high photostability and high fluorescence quantum yield (to ~100%) at 514–519 nm. In addition, the marker was shown to effectively penetrate the erythrocytes membrane in the absence of erythrotoxicity. The conjugation of BODIPY with thioterpenoid is an excellent way to increase affinity dyes to biostructures, including blood components.
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Affiliation(s)
- Galina B. Guseva
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Elena V. Antina
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Mikhail B. Berezin
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Anastassia S. Smirnova
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
- Faculty of Fundamental and Applied Chemistry, Ivanovo State University of Chemistry and Technology, 7, Sheremetevskiy Avenue, 153000 Ivanovo, Russia
| | - Roman S. Pavelyev
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ilmir R. Gilfanov
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- Varnishes and Paints Department, Kazan National Research Technological University, 68 K. Marksa Street, 420015 Kazan, Russia
| | - Oksana G. Shevchenko
- Center of Collective Usage Molecular Biology, Institute of Biology, Komi Science Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya Street, 167982 Syktyvkar, Russia;
| | - Svetlana V. Pestova
- Medical Chemistry Laboratory, Institute of Chemistry, Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 48 Pervomaiskaya Street, 167000 Syktyvkar, Russia; (S.V.P.); (E.S.I.); (S.A.R.)
| | - Evgeny S. Izmest’ev
- Medical Chemistry Laboratory, Institute of Chemistry, Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 48 Pervomaiskaya Street, 167000 Syktyvkar, Russia; (S.V.P.); (E.S.I.); (S.A.R.)
| | - Svetlana A. Rubtsova
- Medical Chemistry Laboratory, Institute of Chemistry, Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 48 Pervomaiskaya Street, 167000 Syktyvkar, Russia; (S.V.P.); (E.S.I.); (S.A.R.)
| | - Olga V. Ostolopovskaya
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- General and Organic Chemistry Department, Kazan State Medical University, 49 Butlerova Street, 420012 Kazan, Russia
| | - Sergey V. Efimov
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Vladimir V. Klochkov
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ilfat Z. Rakhmatullin
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ayzira F. Timerova
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
| | - Ilya A. Khodov
- G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, 1 Akademicheskaya Street, 153045 Ivanovo, Russia; (G.B.G.); (E.V.A.); (M.B.B.); (A.S.S.); (I.A.K.)
| | - Olga A. Lodochnikova
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzova Street, 420029 Kazan, Russia;
| | - Daut R. Islamov
- Laboratory for Structural Analysis of Biomacromolecules, Kazan Scientific Center, Russian Academy of Sciences, 18 Kremlevskaya Street, 420008 Kazan, Russia;
| | - Pavel V. Dorovatovskii
- National Research Centre “Kurchatov Institute”, 1 Academician Kurchatov Street, 123098 Moscow, Russia;
| | - Liliya E. Nikitina
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- General and Organic Chemistry Department, Kazan State Medical University, 49 Butlerova Street, 420012 Kazan, Russia
| | - Sergei V. Boichuk
- Biologically Active Terpenoids Laboratory, Kazan Federal University, 18 Kremlevskaya Street, 420008 Kazan, Russia; (R.S.P.); (I.R.G.); (O.V.O.); (S.V.E.); (V.V.K.); (I.Z.R.); (A.F.T.); (L.E.N.)
- General and Organic Chemistry Department, Kazan State Medical University, 49 Butlerova Street, 420012 Kazan, Russia
- Correspondence:
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Si Y, Grazon C, Clavier G, Audibert JF, Sclavi B, Méallet-Renault R. FRET-mediated quenching of BODIPY fluorescent nanoparticles by methylene blue and its application to bacterial imaging. Photochem Photobiol Sci 2022; 21:1249-1255. [PMID: 35428949 DOI: 10.1007/s43630-022-00215-1] [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: 12/10/2021] [Accepted: 03/21/2022] [Indexed: 11/28/2022]
Abstract
High resolution and a good signal to noise ratio are a requirement in cell imaging. However, after labelling with fluorescent entities, and after several washing steps, there is often an unwanted fluorescent background that reduces the images resolution. For this purpose, we developed an approach to remove the signal from extra-cellular fluorescent nanoparticles (FNPs) during bacteria imaging, without the need for any washing steps. Our idea is to use methylene blue to quench > 90% of the emission of BODIPY-based fluorescent polymer nanoparticle by a FRET process. This "Hide-and-Seek Game" approach offers a novel strategy to apply fluorescence quenching in bioimaging to improve image accuracy.
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Affiliation(s)
- Yang Si
- PPSM, Université Paris-Saclay, ENS Paris-Saclay, CNRS, 91190, Gif-sur-Yvette, France.,LBPA, Université Paris-Saclay, ENS Paris-Saclay, CNRS, 91190, Gif-sur-Yvette, France.,Epigenetic Chemical Biology, CNRS UMR3523, Institut Pasteur, 28 Rue du Dr Roux, 75015, Paris, France
| | - Chloé Grazon
- PPSM, Université Paris-Saclay, ENS Paris-Saclay, CNRS, 91190, Gif-sur-Yvette, France.,University of Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, 33400, Talence, France
| | - Gilles Clavier
- PPSM, Université Paris-Saclay, ENS Paris-Saclay, CNRS, 91190, Gif-sur-Yvette, France
| | | | - Bianca Sclavi
- LBPA, Université Paris-Saclay, ENS Paris-Saclay, CNRS, 91190, Gif-sur-Yvette, France. .,LCQB, CNRS UMR 7238, Sorbonne Université, 4 Place Jussieu, 75005, Paris, France.
| | - Rachel Méallet-Renault
- PPSM, Université Paris-Saclay, ENS Paris-Saclay, CNRS, 91190, Gif-sur-Yvette, France. .,ISMO, Université Paris-Saclay, CNRS, 91405, Orsay, France.
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