Баранов Михаил Сергеевич

Кандидат химических наук


Руководитель подразделения (Группа химии гетероциклических соединений)

Эл. почта: baranovmikes@gmail.com

Избранные публикации

  1. Bozhanova N.G., Baranov M.S., Sarkisyan K.S., Gritcenko R., Mineev K.S., Golodukhina S.V., Baleeva N.S., Lukyanov K.A., Mishin A.S. (2017). Yellow and Orange Fluorescent Proteins with Tryptophan-based Chromophores. ACS Chem. Biol. , [+]

    Rapid development of new microscopy techniques exposed the need for genetically encoded fluorescent tags with special properties. Recent works demonstrated the potential of fluorescent proteins with tryptophan-based chromophores. We applied rational design and random mutagenesis to the monomeric red fluorescent protein FusionRed and found two groups of mutants carrying a tryptophan-based chromophore: with yellow (535 nm) or orange (565 nm) emission. On the basis of the properties of proteins, a model synthetic chromophore, and a computational modeling, we concluded that the presence of a ketone-containing chromophore in different isomeric forms can explain the observed yellow and orange phenotypes.

    ID:1803
  2. Kaskova Z.M., Dörr F.A., Petushkov V.N., Purtov K.V., Tsarkova A.S., Rodionova N.S., Mineev K.S., Guglya E.B., Kotlobay A., Baleeva N.S., Baranov M.S., Arseniev A.S., Gitelson J.I., Lukyanov S., Suzuki Y., Kanie S., Pinto E., DiMascio P., Waldenmaier H.E., Pereira T.A., Carvalho R.P., Oliveira A.G., Oba Y., Bastos E.L., Stevani C.V., Yampolsky I.V. (2017). Mechanism and Color Modulation of Fungal Bioluminescence. Sci Adv 3 (4), e1602847 [+]

    Bioluminescent fungi are spread throughout the globe, but details on their mechanism of light emission are still scarce. Usually, the process involves three key components: an oxidizable luciferin substrate, a luciferase enzyme, and a light emitter, typically oxidized luciferin, and called oxyluciferin. We report the structure of fungal oxyluciferin, investigate the mechanism of fungal bioluminescence, and describe the use of simple synthetic α-pyrones as luciferins to produce multicolor enzymatic chemiluminescence. A high-energy endoperoxide is proposed as an intermediate of the oxidation of the native luciferin to the oxyluciferin, which is a pyruvic acid adduct of caffeic acid. Luciferase promiscuity allows the use of simple α-pyrones as chemiluminescent substrates.

    ID:1628
  3. Baranov M.S., Kaskova Z.M., Gritсenko R., Postikova S.G., Ivashkin P.E., Kislukhin A.A., Moskvin D.I., Mineev K.S., Arseniev A.S., Labas Yu.A., Yampolsky I.V. (2017). Synthesis of Panal Terpenoid Core. Synlett 28 (5), 583–588 [+]

    Panal is a natural bicyclic cadalane-type sesquiterpenoid with an unusual combination of stereocenters. It was isolated in 1988 as an alleged biosynthetic precursor of luciferin (a light-emitting molecule) in a bioluminescent fungus Panellus stipticus. Herein we present the first approach to the synthesis of the terpenoid skeleton of panal, which includes construction of five stereocenters, one of which is easily epimerizable. The key steps in the synthetic approach presented are high-pressure Diels–Alder reaction disobeying the ‘endo rule’, Barbier reductive allylation, and cyclization of trans-decalin ring via ring-closing metathesis.

    ID:1623
  4. Ямпольский И.В., Петушков В.Н., Пуртов К.В., Родионова Н.С., Баранов М.С. (2016). Патент РФ №2596398 «Метод и реактивы для детекции активности люциферазы». , [+]

    Группа изобретений относится к области биохимии. Предложен метод выявления люциферазы в биологических образцах с использованием 3-гидроксигиспидина или 3-гидроксибиснориангонина в качестве люциферина. Предложено соединение для реализации указанного метода, представляющее собой 3-гидроксигиспидин. Кроме того, предложен метод выявления люциферазы в присутствии гиспидин-3-гидроксилазы в биологических образцах с использованием гиспидина или биснориангонина в качестве прекурсора люциферина и НАД(Ф)Н. Также предложен набор реактивов для реализации указанного метода, включающий гиспидин или биснориангонин и НАД(Ф)Н. Группа изобретений позволяет выявлять люциферазу грибов в биологических образцах и в дальнейшем может быть использована в широком спектре биолюминесцентных анализов in vivo и in vitro.

    ID:1574
  5. Sarkisyan K.S., Bolotin D.A., Meer M.V., Usmanova D.R., Mishin A.S., Sharonov G.V., Ivankov D.N., Bozhanova N.G., Baranov M.S., Soylemez O., Bogatyreva N.S., Vlasov P.K., Egorov E.S., Logacheva M.D., Kondrashov A.S., Chudakov D.M., Putintseva E.V., Mamedov I.Z., Tawfik D.S., Lukyanov K.A., Kondrashov F.A. (2016). Local fitness landscape of the green fluorescent protein. Nature 533 (7603), 397–401 [+]

    Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design.

    ID:1529
  6. Povarova N.V., Bozhanova N.G., Sarkisyan K.S., Gritcenko R., Baranov M.S., Yampolsky I.V., Lukyanov K.A., Mishin A.S. (2016). Docking-guided identification of protein hosts for GFP chromophore-like ligands. J. Mater. Chem. C 4, 3036–3040 [+]

    Synthetic analogs of the Green Fluorescent Protein (GFP) chromophore emerge as promising fluorogenic dyes for labeling in living systems. Here, we report the computational identification of protein hosts capable of binding to and enhancing fluorescence of GFP chromophore derivatives. Automated docking of GFP-like chromophores to over 3000 crystal structures of Escherichia coli proteins available in the Protein Data Bank allowed the identification of a set of candidate proteins. Four of these proteins were tested experimentally in vitro for binding with the GFP chromophore and its red-shifted Kaede chromophore-like analogs. Two proteins were found to possess sub-micromolar affinity for some Kaede-like chromophores and activate fluorescence of these fluorogens.

    ID:1407
  7. Tsarkova A.S., Dubinnyi M.A., Baranov M.S., Oguienko A.D., Yampolsky I.V. (2016). Nambiscalarane, a novel sesterterpenoid comprising a furan ring, and other secondary metabolites from bioluminescent fungus Neonothopanus nambi. Mend. Comm. 26 (3), 191–192 [+]

    In the course of isolation of fungal luciferin from bioluminescent fungus Neonothopanus nambi, structures of novel nambiscalarane, Aurisin Z, trans-α-hydroxy-γ-phenylbutyrolactone, methyl 4-butyramidobenzoate as well as known nambinones A and C and polyhydroxylated sterol were identified.

    ID:1565
  8. Балеева Н.С., Ямпольский И.В., Баранов М.С. (2016). Борированные производные хромофора зеленого флуоресцентного белка как потенциальные флуоресцентные сенсоры. Биоорг. хим. 42 (4), 501–504 [+]

    Борированные производные хромофора зеленого флуоресцентного белка (4-(2-(дифторборил)-бензилиден)-1H-имидазол-5(4H)-оны) предложены в качестве потенциальных флуоресцентных сенсоров. Синтезированы модельные карбаматные производные борированных аналогов хромофора, содержащих аминогруппу в бензилиденовом фрагменте, а также проведен анализ их оптических свойств. Показано, что благодаря заметному смещению максимумов абсорбции и эмиссии, наблюдаемому при разрушении/введении карбаматной группы при атоме азота, подобные производные являются отличным претендентом на роль новых флуоресцентных сенсоров.

    ID:1566
  9. Baleeva N.S., Yampolsky I.V., Baranov M.S. (2016). Conformationally Locked GFP Chromophore Derivatives as Potential Fluorescent Sensors. Russ. J. Bioorgan. Chem. 42 (4), 453–456 [+]

    We propose to use the conformationally locked GFP chromophore derivatives (4-(2(difluoroboryl)benzylidene)-1H-imidazol-5(4H)-ones) as potential fluorescent sensors. The model carbamate derivatives were synthesized and their fluorescent properties were studied. It was shown that the introduction/cleavage of the carbamate groups at the nitrogen atom led to the noticeable shifts in the absorption and emission maxima of the resultant derivatives, which makes them promising candidates for new fluorescent sensors.

    ID:1567
  10. Yampolsky I.V., Lukyanov K.A., Baranov M.S. (2015). Boron-containing 5-arylidene-3,5-dihydro-4H-imidazol-4-ones. US 20150177254 A1 9 (133), 220 [+]

    Novel compounds of the general formula ##STR00001## are introduced, containing 5-arylidene-3,5-dihydro-4h-imidazol-4-one core. These compounds can be used for fluorescent staining of cell membranes, biomolecules' labeling in vivo and in vitro, a number of compounds also have photoacidic properties. This allows to use them, for example, as instruments to drastically change pH of a medium, and also as dynamic fluorescent probes for investigation of complex objects like proteins and micellae, as well as in studies of hydration dynamics and in photolithography.

    ID:1572
  11. Purtov K.V., Petushkov V.N., Baranov M.S., Mineev K.S., Rodionova N.S., Kaskova Z.M., Tsarkova A.S., Petunin A.I., Bondar V.S., Rodicheva E.K., Medvedeva S.E., Oba Y., Arseniev A.S., Lukyanov S., Gitelson J.I., Yampolsky I.V. (2015). The Chemical Basis of Fungal Bioluminescence. Angew. Chem. Int. Ed. 127 (28), 8242–8246 [+]

    Many species of fungi naturally produce light, a phenomenon known as bioluminescence, however, the fungal substrates used in the chemical reactions that produce light have not been reported. We identified the fungal compound luciferin 3-hydroxyhispidin, which is biosynthesized by oxidation of the precursor hispidin, a known fungal and plant secondary metabolite. The fungal luciferin does not share structural similarity with the other eight known luciferins. Furthermore, it was shown that 3-hydroxyhispidin leads to bioluminescence in extracts from four diverse genera of luminous fungi, thus suggesting a common biochemical mechanism for fungal bioluminescence.

    ID:1295
  12. Povarova N.V., Baranov M.S., Kovalchuk S.N., Semiletova I.V., Lukyanov K.A., Kozhemyak V.B. (2015). Novel Water-Soluble Substrate for Silicateins. Bioorg. Khim. 41 (3), 380–2 [+]

    We suggested to use tetrakis(2-hydroxyethyl)orthosilicate (THEOS) as a substrate for silicateins--an enzyme family playing a key role in formation of skeleton in marine sponges. We compared THEOS with tetraethylorthosilicate (TEOS)--a commonly used substrate for silicateins. These substrates were tested in reaction of amorphous silica formation in vitro catalyzed by silicatein Al from sponge Latrunculia oparinae. It was found that reaction with THEOS occurs more efficiently than with TEOS, probably due to high water solubility and higher hydrolysis rate of THEOS.

    ID:1417
  13. Dubinnyi M.A., Kaskova Z.M., Rodionova N.S., Baranov M.S., Gorokhovatsky A.Y., Kotlobay A., Solntsev K.M., Tsarkova A.S., Petushkov V.N., Yampolsky I.V. (2015). Novel Mechanism of Bioluminescence: Oxidative Decarboxylation of a Moiety Adjacent to the Light Emitter of Fridericia Luciferin. Angew. Chem. Int. Ed. Engl. 54 (24), 7065–7067 [+]

    A novel luciferin from a bioluminescent Siberian earthworm Fridericia heliota was recently described. In this study, the Fridericia oxyluciferin was isolated and its structure elucidated. The results provide insight into a novel bioluminescence mechanism in nature. Oxidative decarboxylation of a lysine fragment of the luciferin supplies energy for light generation, while a fluorescent CompX moiety remains intact and serves as the light emitter.

    ID:1265
  14. Dubinnyi M.A., Tsarkova A.S., Petushkov V.N., Kaskova Z.M., Rodionova N.S., Kovalchuk S.I., Ziganshin R.H., Baranov M.S., Mineev K.S., Yampolsky I.V. (2015). Novel Peptide Chemistry in Terrestrial Animals: Natural Luciferin Analogues from the Bioluminescent Earthworm Fridericia heliota. Chem. Eur. J. 21 (10), 3942–3947 [+]

    Пресс-релиз по теме статьи Новый класс природных пептидов: аналоги люциферина почвенного червя Fridericia heliota

    ID:1243
  15. Tsarkova A.S., Dubinnyi M.A., Baranov M.S., Petushkov N., Rodionova S., Zagudaylova B., Yampolsky I.V. (2015). Total synthesis of AsLn2 – a luciferin analogue from the Siberian bioluminescent earthworm Fridericia heliota. Mendeleev Communications 25 (2), 99–100 [+]

    Total synthesis of AsLn2, a luciferin analogue isolated from the Siberian bioluminescent earthworm F. heliota, was performed from (Z)-5-(2,3-dimethoxy-3-oxoprop-1-en-1-yl)-2-hydroxybenzoic acid in six steps.

    ID:1264
  16. Baleeva N.S., Myannik K.A., Yampolsky I.V., Baranov M.S. (2015). Bioinspired Fluorescent Dyes Based on a Conformationally Locked Chromophore of the Fluorescent Protein Kaede. Eur.J.Org.Chem 2015 (26), 5716–5721 [+]

    A novel class of fluorescent dyes based on the conformationally locked heterocyclic core of the chromophore of the fluorescent protein Kaede was discovered. Introduction of a single conformational lock at the benzylidene fragment of the Kaede chromophore resulted in an increase in the fluorescence quantum yield (FQY) by one order of magnitude and a redshift of ca. 60 nm in the emission spectrum. Imposing the second lock at the ethylene fragment of the Kaede chromophore provided a further increase in the FQY. Locked analogues demonstrated bright and redshifted emission in a broad range of solvents, which makes them good candidates for a wide spectrum of fluorescent-labeling applications.

    ID:1564
  17. Baranov M.S., Solntsev K.M., Baleeva N.S., Mishin A.S., Lukyanov S.A., Lukyanov K.A., Yampolsky I.V. (2014). Red-shifted fluorescent aminated derivatives of a conformationally locked GFP chromophore. Chem. Eur. J. 20 (41), 13234–41 [+]

    A novel class of fluorescent dyes based on conformationally locked GFP chromophore is reported. These dyes are characterized by red-shifted spectra, high fluorescence quantum yields and pH-independence in physiological pH range. The intra- and intermolecular mechanisms of radiationless deactivation of ABDI-BF2 fluorophore by selective structural locking of various conformational degrees of freedom were studied. A unique combination of solvatochromic and lipophilic properties together with "infinite" photostability (due to a dynamic exchange between free and bound dye) makes some of the novel dyes promising bioinspired tools for labeling cellular membranes, lipid drops and other organelles.

    ID:1294
  18. Petushkov V.N., Dubinnyi M.A., Tsarkova A.S., Rodionova N.S., Baranov M.S., Kublitski V.S., Shimomura O., Yampolsky I.V. (2014). A Novel Type of Luciferin from the Siberian Luminous Earthworm Fridericia heliota: Structure Elucidation by Spectral Studies and Total Synthesis. Angew. Chem. Int. Ed. Engl. 53 (22), 5566–5568 [+]

    Пресс-релиз по материалам этой статьи: "Восьмая формула света".

    ID:1016
  19. Baranov M.S., Fedyakina I.T., Shchelkanov M.Y., Yampolsky I.V. (2014). Ring-expanding rearrangement of 2-acyl-5-arylidene-3,5-dihydro-4H-imidazol-4-ones in synthetis of flutimide analogs. Tetrahedron 70 (23), 3714–3719 ID:1038
  20. Frizler M., Yampolsky I.V., Baranov M.S., Stirnberg M., Gütschow M. (2013). Chemical introduction of the green fluorescence: imaging of cysteine cathepsins by an irreversibly locked GFP fluorophore. Org. Biomol. Chem. 11 (35), 5913–21 [+]

    An activity-based probe, containing an irreversibly locked GFP-like fluorophore, was synthesized and evaluated as an inhibitor of human cathepsins and, as exemplified with cathepsin K, it proved to be suitable for ex vivo imaging and quantification of cysteine cathepsins by SDS-PAGE.

    ID:1028
  21. Baranov M.S., Solntsev K.M., Lukyanov K.A., Yampolsky I.V. (2013). A synthetic approach to GFP chromophore analogs from 3-azidocinnamates. Role of methyl rotors in chromophore photophysics. Chem. Commun. (Camb.) 49 (51), 5778–80 [+]

    We have suggested a novel combinatorial approach for synthesis of otherwise inaccessible GFP chromophore analogs, and studied the influence of aliphatic substituents on their pH-dependent spectral properties. We found that the demethylation at C or N positions of the imidazolone ring leads to a decrease in the excited state lifetime.

    ID:1029
  22. Baranov M.S., Lukyanov K.A., Yampolsky I.V. (2013). Synthesis of the chromophores of fluorescent proteins and their analogs. Russ. J. Bioorgan. Chem. 39 (3), 223–244 [+]

    Members of the green fluorescent protein (GFP) family are widely used in experimental biology as genetically encoded fluorescent tags. Chromophores of GFP-like proteins share a common structural core: 3,5-dihydro-4H-imidazol-4-one. This review covers synthetic approaches to 3,5-dihydro-4H-imidazol-4-ones, substituted at different positions. General, as well as specific methods, represented by single examples are considered. The most popular synthetic route to substituted 3,5-dihydro-4H-imidazol-4-ones includes synthesis of azlactones, followed by transformation into N-acyldehydroaminoacids and, finally, cyclization into target heterocycles. Accordingly, the review is divided into three parts: the first part covers syntheses of azlactones, the second part covers main approaches to N-acyldehydroaminoacids, and in the third part we summarize cyclizations of N-acyldehydroaminoacids, as well as all other approaches to 3,5-dihydro-4H-imidazol-4-ones.

    ID:1032
  23. Baranov M.S., Lukyanov K.A., Ivashkin P.E., Yampolsky I.V. (2013). Efficient synthetic approach to fluorescent oxazole-4-carboxylate derivatives. Synt. Comm. 43 (17), 2337–2342 ID:1041
  24. Baranov M.S., Yampolsky I.V. (2013). Novel condensations of nitroacetic esters with aromatic aldehydes leading to 5-hydroxy-1,2-oxazin-6-ones. Tetrahedron Lett. 54 (7), 628–629 ID:1042
  25. Baranov M.S., Lukyanov K.A., Borissova A.O., Shamir J., Kosenkov D., Slipchenko L.V., Tolbert L.M., Yampolsky I.V., Solntsev K.M. (2012). Conformationally locked chromophores as models of excited-state proton transfer in fluorescent proteins. J. Am. Chem. Soc. 134 (13), 6025–32 [+]

    Members of the green fluorescent protein (GFP) family form chromophores by modifications of three internal amino acid residues. Previously, many key characteristics of chromophores were studied using model compounds. However, no studies of intermolecular excited-state proton transfer (ESPT) with GFP-like synthetic chromophores have been performed because they either are nonfluorescent or lack an ionizable OH group. In this paper we report the synthesis and photochemical study of two highly fluorescent GFP chromophore analogues: p-HOBDI-BF2 and p-HOPyDI:Zn. Among known fluorescent compounds, p-HOBDI-BF(2) is the closest analogue of the native GFP chromophore. These irrreversibly (p-HOBDI-BF(2)) and reversibly (p-HOPyDI:Zn) locked compounds are the first examples of fully planar GFP chromophores, in which photoisomerization-induced deactivation is suppressed and protolytic photodissociation is observed. The photophysical behavior of p-HOBDI-BF2 and p-HOPyDI:Zn (excited state pK(a)'s, solvatochromism, kinetics, and thermodynamics of proton transfer) reveals their high photoacidity, which makes them good models of intermolecular ESPT in fluorescent proteins. Moreover, p-HOPyDI:Zn is a first example of "super" photoacidity in metal-organic complexes.

    ID:717
  26. Baranov M.S., Yampolsky I.V. (2012). Unusual transformations of anthranilic acid imidazolides. Chemistry of Heterocyclic compounds 48, 1108–1110 ID:1043