Ямпольский Илья Викторович

Личная информация

Илья Викторович Ямпольский родился 25 апреля 1979 года в Москве. Окончил Биокласс Московской школы 1543. С 1996 по 2001 год учился в Высшем Химической Колледже РАН. Будучи студентом работал в лабораториях Института Органической химии им. Н.Д. Зелинского РАН и Института элементоорганических соединений им. А.Н. Несмеянова РАН. С 2000 года работает в ИБХ РАН. В 2009 получил степень кандидата химических наук  в области биохимии за работу по изучению структуры хромофоров в GFP-подобных флуоресцентных белках. 

В 2016 году защитил диссертацию доктора химических наук, посвященную изучению новых люциферинов - субстратов биолюминесцентных реакций.

Научные интересы

Области научных интересов: Медицинская химия, полный синтез, биолюминесценция, люминесцентные и флуорогенные красители, установление механизмов биосинтеза.

Также И. В. Ямпольский посвящает много времени преподаванию химии для школьников и студентов, специализирующихся в области биологии, являеся автором около десятка оригинальных лекционных курсов.
 

Основные научные результаты

ВЫПОЛНЕНО

 

2009-2011

 

Исследован биосинтез химически неустойчивого ацимилина - хромофора красного флюоресцентного белка. В рамках этой задачи разработан способ получения 2-ациламиноимидазолонов - биосинтетических прекурсоров 2-ацилиминолимидазолонов. Показано, что спонтанное окисление прекурсоров кислородом воздуха проходит по необычному механизму.

             

Discosoma

 

2002-2009

 

Полный синтез хромофоров GFP-подобных флуоресцентных белков был использован в качестве инструмента для самостоятельного определения структуры этих хромофоров. Кроме того, изучена взаимосвязь между структурой и спектральные свойствами отношения в этом классе производных имидазола. Разработаны новые подходы к синтезу 2-функционализованных арилиденмидиазолонов. Синтезированы хромофоры из asFP595, Kaede и YFP538.

 

           

Zoanthus

 

           

Trachyphyllia

 

 

           

 

Anemonia

 

2002-2004

 

Выделен, секвенирован и исследован биохимическими методами синий белковый пигмент из Rhizostoma pulmo (медуза, обитающая в Черном море). Определить природу синей окраски (структуру хромофора) не удалось.

 

           

 

Rhizostoma pulmo

 

Избранные публикации

  1. Jiang T., Yang X., Zhou Y., Yampolsky I., Du L., Li M. (2017). New bioluminescent coelenterazine derivatives with various C-6 substitutions. Org. Biomol. Chem. , [+]

    A series of new coelenterazine analogs with varying substituents at the C-6 position of the imidazopyrazinone core have been designed and synthesized for the extension of bioluminescence substrates. Some of them display excellent bioluminescence properties compared to DeepBlueC™ or native coelenterazine with both in vitro and in vivo biological evaluations, thus placing these derivatives among the most ideal substrates for Renilla bioluminescence applications.

    ID:1835
  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. Oba Y., Stevani C.V., Oliveira A.G., Tsarkova A.S., Chepurnykh T.V., Yampolsky I.V. (2017). Selected Least Studied but not Forgotten Bioluminescent Systems. Photochem. Photobiol. 93 (2), 405–415 [+]

    Bioluminescence is a form of chemiluminescence generated by luminous organisms. Luminous taxa have currently been reported from about 800 genera and probably over 10,000 species in the world. On the other hand, their bioluminescent systems, including chemical structures of luciferins/chromophores and the genes encoding luciferases/photoproteins, have been elucidated from only a few taxonomic groups; e.g. beetles, bacteria, dinoflagellates, ostracods, and some cnidarians. Research efforts to understand unknown bioluminescence systems are being conducted around the world, and recently, for example, novel luciferin structures of luminous enchytraeid potworms and fungi were identified by the authors. In this paper, we review the current status and perspectives, in the context of post-genomic era, of most-likely novel but less-revealed bioluminescence systems of ten selected organisms; earthworm, parchment tubeworm, fireworm, scaleworm, limpet, millipede, brittle star, acorn worms, tunicate, and shark, which indeed are the next focus of our international collaboration. This article is protected by copyright. All rights reserved.

    ID:1702
  4. 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
  5. 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
  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., Kaskova Z.M., Yampolsky I.V. (2016). A Tale Of Two Luciferins: Fungal and Earthworm New Bioluminescent Systems. Acc. Chem. Res. 49 (11), 2372–2380 [+]

    Bioluminescence, the ability of a living organism to produce light through a chemical reaction, is one of Nature's most amazing phenomena widely spread among marine and terrestrial species. There are various different mechanisms underlying the emission of "cold light", but all involve a small molecule, luciferin, that provides energy for light-generation upon oxidation, and a protein, luciferase, that catalyzes the reaction. Different species often use different proteins and substrates in the process, which suggests that the ability to produce light evolved independently several times throughout evolution. Currently, it is estimated that there are more than 30 different mechanisms of bioluminescence. Even though the chemical foundation underlying the bioluminescence phenomenon is by now generally understood, only a handful of luciferins have been isolated and characterized. Today, the known bioluminescence reactions are used as indispensable analytical tools in various fields of science and technology. A pressing need for new bioluminescent analytical techniques with a wider range of practical applications stimulates the search and chemical studies of new bioluminescent systems. In the past few years two such systems were unraveled: those of the earthworms Fridericia heliota and the higher fungi. The luciferins of these two systems do not share structural similarity with the previously known ones. This Account will survey structure elucidation of the novel luciferins and identification of their mechanisms of action. Fridericia luciferin is a key component of a novel ATP-dependent bioluminescence system. Structural studies were performed on 0.005 mg of natural substance and revealed its unusual extensively modified peptidic nature. Elucidation of Fridericia oxyluciferin revealed that oxidative decarboxylation of a lysine fragment of luciferin supplies energy for light generation, while a fluorescent CompX moiety remains intact and serves as a light emitter. Along with luciferin, a number of its natural analogs were found in the extracts of worm biomass. They occurred to be highly unusual modified peptides comprising a set of amino acids, including threonine, aminobutyric acid, homoarginine, unsymmetrical N,N-dimethylarginine and extensively modified tyrosine. These natural compounds represent a unique peptide chemistry found in terrestrial animals and raise novel questions concerning their biosynthetic origin. Also in this Account we discuss identification of the luciferin of higher fungi 3-hydroxyhispidin which is biosynthesized by oxidation of the precursor hispidin, a known fungal and plant secondary metabolite. 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:1562
  8. Kaskova Z.M., Tsarkova A.S., Yampolsky I.V. (2016). 1001 lights: luciferins, luciferases, their mechanisms of action and applications in chemical analysis, biology and medicine. Chem. Soc.Rev. 45, 6048–6077 [+]

    Bioluminescence (BL) is a spectacular phenomenon involving light emission by live organisms. It is caused by the oxidation of a small organic molecule, luciferin, with molecular oxygen, which is catalysed by the enzyme luciferase. In nature, there are approximately 30 different BL systems, of which only 9 have been studied to various degrees in terms of their reaction mechanisms. A vast range of in vitro and in vivo analytical techniques have been developed based on BL, including tests for different analytes, immunoassays, gene expression assays, drug screening, bioimaging of live organisms, cancer studies, the investigation of infectious diseases and environmental monitoring. This review aims to cover the major existing applications for bioluminescence in the context of the diversity of luciferases and their substrates, luciferins. Particularly, the properties and applications of D-luciferin, coelenterazine, bacterial, Cypridina and dinoflagellate luciferins and their analogues along with their corresponding luciferases are described. Finally, four other rarely studied bioluminescent systems (those of limpet Latia, earthworms Diplocardia and Fridericia and higher fungi), which are promising for future use, are also discussed.

    ID:1563
  9. 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
  10. 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
  11. 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
  12. Walker C.L., Lukyanov K.A., Yampolsky I.V., Mishin A.S., Bommarius A.S., DurajThatte A.M., Azizi B., Tolbert L.M., Solntsev K.M. (2015). Fluorescence imaging using synthetic GFP chromophores. Curr Opin Chem Biol 27, 64–74 [+]

    Green fluorescent protein and related proteins carry chromophores formed within the protein from their own amino acids. Corresponding synthetic compounds are non-fluorescent in solution due to photoinduced isomerization of the benzylideneimidiazolidinone core. Restriction of this internal rotation by binding to host molecules leads to pronounced, up to three orders of magnitude, increase of fluorescence intensity. This property allows using GFP chromophore analogs as fluorogenic dyes to detect metal ions, proteins, nucleic acids, and other hosts. For example, RNA aptamer named Spinach, which binds to and activates fluorescence of some GFP chromophores, was proved to be a unique label for live-cell imaging of specific RNAs, endogenous metabolites and target proteins. Chemically locked GFP chromophores are brightly fluorescent and represent potentially useful dyes due to their small size and high water solubility.

    ID:1372
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. Petushkov V.N., Dubinnyi M.A., Rodionova N.S., Nadezhdin K.D., Marques S.M., EstevesdaSilva J.C.G., Shimomura O., Yampolsky I.V. (2014). AsLn2, a luciferin-related modified tripeptide from the bioluminescent earthworm Fridericia heliota. Tetrahedron Lett. 55 (2), 463–465 ID:1039
  23. Petushkov V.N., Tsarkova A.S., Dubinnyi M.A., Rodionova N.S., Marques S.M., EstevesdaSilva J.C.G., Shimomura O., Yampolsky I.V. (2014). CompX, a luciferin-related tyrosine derivative from the bioluminescent earthworm Fridericia heliota. Tetrahedron Lett. 55 (2), 460–462 ID:1040
  24. 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
  25. Pletnev V.Z., Pletneva N.V., Lukyanov K.A., Souslova E.A., Fradkov A.F., Chudakov D.M., Chepurnykh T., Yampolsky I.V., Wlodawer A., Dauter Z., Pletnev S. (2013). Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine. Acta Crystallogr. D Biol. Crystallogr. 69 (Pt 9), 1850–60 [+]
    ID:1017
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. Sarkisyan K.S., Yampolsky I.V., Solntsev K.M., Lukyanov S.A., Lukyanov K.A., Mishin A.S. (2012). Tryptophan-based chromophore in fluorescent proteins can be anionic. Sci Rep 2, 608 [+]

    Cyan fluorescent proteins (CFP) with tryptophan66-based chromophore are widely used for live cell imaging. In contrast to green and red fluorescent proteins, no charged states of the CFP chromophore have been described. Here, we studied synthetic CFP chromophore and found that its indole group can be deprotonated rather easily (pKa 12.4).We then reproduced this effect in the CFP mCerulean by placing basic amino acids in the chromophore microenvironment. As a result, green-emitting variant with an anionic chromophore and key substitution Val61Lys was obtained. This is the first evidence strongly suggesting that tryptophan-based chromophores in fluorescent proteins can exist in an anionic charged state. Switching between protonated and deprotonated Trp66 in fluorescent proteins represents a new unexplored way to control their spectral properties.

    ID:831
  32. Baranov M.S., Yampolsky I.V. (2012). Unusual transformations of anthranilic acid imidazolides. Chemistry of Heterocyclic compounds 48, 1108–1110 ID:1043
  33. Ivashkin P.E., Lukyanov K.A., Yampolsky I.V. (2011). Synthesis of biosynthetic precursors of chromophores of red fluorescent proteins. Russ. J. Bioorgan. Chem. 37 (4), 411–420 [+]
    ID:1023
  34. Ivashkin P.E., Lukyanov K.A., Lukyanov S., Yampolsky I.V. (2011). A synthetic GFP-like chromophore undergoes base-catalyzed autoxidation into acylimine red form. J. Org. Chem. 76 (8), 2782–91 [+]

    Fluorescent proteins are widely used in modern experimental biology, but much controversy exists regarding details of maturation of different types of their chromophores. Here we studied possible mechanisms of DsRed-type red chromophore formation using synthetic biomimetic GFP-like chromophores, bearing an acylamino substituent, corresponding to an amino acid residue at position 65. We have shown these model compounds to readily react with molecular oxygen to produce a highly unstable DsRed-like acylimine, isolated in the form of stable derivatives. Under the same aerobic conditions an unusual red-shifted imide chromophore--a product of 4-electron oxidation of Gly65 residue--is formed. Our data showed that GFP chromophore is prone to autoxidation at position 65 Cα by its chemical nature with basic conditions being the only key factor required.

    ID:513
  35. Yampolsky I.V., Balashova T.A., Lukyanov K.A. (2009). Synthesis and spectral and chemical properties of the yellow fluorescent protein zFP538 chromophore. Biochemistry 48 (33), 8077–82 [+]

    Members of the green fluorescent protein (GFP) family become chromophoric through a unique pathway based on autocatalytic modifications of their amino acid residues. The yellow fluorescent protein zFP538 from the button polyp Zoanthus possesses unique spectral characteristics that are intermediate between those of the green and orange-red fluorescent proteins. In this study, we used chemical synthesis to resolve conflicting data from crystallographic and biochemical analyses of the zFP538 chromophore structure. We synthesized 2-(5-amino-1-oxopentyl)-5-(4-hydroxybenzylidene)-3-methyl-3,5-dihydro-4H-imidazol-4-one (5), which can spontaneously react intramolecularly to form cyclic imine (7). Compound 7 represents the native chromophore structure reported in the crystallographic study. We have also discovered an unusual isomerization of a 2-acylimidazolone to a 2,6-diketopiperazine derivative. The zFP538 chromophore is a complex system with intriguing chemical and spectral behavior, properties that have led to discrepancies in the interpretation of its structure. Our study supports the findings of previous crystallographic work, which postulated a cyclic imine chromophore structure within the native zFP538 protein, and also provides an explanation for experimental results obtained in the biochemical characterization of zFP538-derived chromopeptides.

    ID:514
  36. Bogdanov A.M., Mishin A.S., Yampolsky I.V., Belousov V.V., Chudakov D.M., Subach F.V., Verkhusha V.V., Lukyanov S., Lukyanov K.A. (2009). Green fluorescent proteins are light-induced electron donors. Nat. Chem. Biol.  (5), 459–461 [+]

    Proteins of the green fluorescent protein (GFP) family are well known owing to their unique biochemistry and extensive use as in vivo markers. We discovered that GFPs of diverse origins can act as light-induced electron donors in photochemical reactions with various electron acceptors, including biologically relevant ones. Moreover, via green-to-red GFP photoconversion, this process can be observed in living cells without additional treatment.

    ID:22
  37. Ivashkin P.E., Yampolsky I.V., Lukyanov K.A. (2009). Synthesis and properties of chromophores of fluorescent proteins. Russ. J. Bioorgan. Chem. 35 (6), 652–669 [+]

    We describe the existing approaches to the synthesis of 5-arylidene-3,5-dihydro-4H-imidazol-4-ones - model chromophores of fluorescent proteins and their nonnatural analogs. We discuss in detail the chemical (acid-base and redox reactions, cis-trans isomery, etc.) and spectral properties of the chromophores and the influence of substitutes and the environment. The study of synthetic chromophores allows for modeling of the photophysical characteristics of fluorescent proteins.

    ID:1037
  38. Mishin A.S., Subach F.V., Yampolsky I.V., King W., Lukyanov K.A., Verkhusha V.V. (2008). The first mutant of the Aequorea victoria green fluorescent protein that forms a red chromophore. Biochemistry 47 (16), 4666–73 [+]

    Green fluorescent protein (GFP) from a jellyfish, Aequorea victoria, and its mutants are widely used in biomedical studies as fluorescent markers. In spite of the enormous efforts of academia and industry toward generating its red fluorescent mutants, no GFP variants with emission maximum at more than 529 nm have been developed during the 15 years since its cloning. Here, we used a new strategy of molecular evolution aimed at generating a red-emitting mutant of GFP. As a result, we have succeeded in producing the first GFP mutant that substantially matures to the red-emitting state with excitation and emission maxima at 555 and 585 nm, respectively. A novel, nonoxidative mechanism for formation of the red chromophore in this mutant that includes a dehydration of the Ser65 side chain has been proposed. Model experiments showed that the novel dual-color GFP mutant with green and red emission is suitable for multicolor flow cytometry as an additional color since it is clearly separable from both green and red fluorescent tags.

    ID:515
  39. Yampolsky I.V., Kislukhin A.A., Amatov T.T., Shcherbo D., Potapov V.K., Lukyanov S., Lukyanov K.A. (2008). Synthesis and properties of the red chromophore of the green-to-red photoconvertible fluorescent protein Kaede and its analogs. Bioorg. Chem. 36 (2), 96–104 [+]

    Green fluorescent protein (GFP) and homologous proteins possess a unique pathway of chromophore formation based on autocatalytic modification of their own amino acid residues. Green-to-red photoconvertible fluorescent protein Kaede carries His-Tyr-Gly chromophore-forming triad. Here, we describe synthesis of Kaede red chromophore (2-[(1E)-2-(5-imidazolyl)ethenyl]-4-(p-hydroxybenzylidene)-5-imidazolone) and its analogs that can be potentially formed by natural amino acid residues. Chromophores corresponding to the following tripeptides were obtained: His-Tyr-Gly, Trp-Tyr-Gly, Phe-Trp-Gly, Tyr-Trp-Gly, Asn-Tyr-Gly, Phe-Tyr-Gly, and Tyr-Tyr-Gly. In basic conditions they fluoresced red with relatively high quantum yield (up to 0.017 for Trp-derived compounds). The most red-shifted absorption peak at 595nm was found for the chromophore Trp-Tyr-Gly in basic DMSO. Surprisingly, in basic DMF non-aromatic Asn-derived chromophore Asn-Tyr-Gly demonstrated the most red-shifted emission maximum at 642 nm. Thus, Asn residue may be a promising substituent, which can potentially diversify posttranslational chemistry in GFP-like proteins.

    ID:516
  40. Evdokimov A.G., Pokross M.E., Egorov N.S., Zaraisky A.G., Yampolsky I.V., Merzlyak E.M., Shkoporov A.N., Sander I., Lukyanov K.A., Chudakov D.M. (2006). Structural basis for the fast maturation of Arthropoda green fluorescent protein. EMBO Rep. 7 (10), 1006–12 [+]

    Since the cloning of Aequorea victoria green fluorescent protein (GFP) in 1992, a family of known GFP-like proteins has been growing rapidly. Today, it includes more than a hundred proteins with different spectral characteristics cloned from Cnidaria species. For some of these proteins, crystal structures have been solved, showing diversity in chromophore modifications and conformational states. However, we are still far from a complete understanding of the origin, functions and evolution of the GFP family. Novel proteins of the family were recently cloned from evolutionarily distant marine Copepoda species, phylum Arthropoda, demonstrating an extremely rapid generation of fluorescent signal. Here, we have generated a non-aggregating mutant of Copepoda fluorescent protein and solved its high-resolution crystal structure. It was found that the protein beta-barrel contains a pore, leading to the chromophore. Using site-directed mutagenesis, we showed that this feature is critical for the fast maturation of the chromophore.

    ID:280
  41. Yampolsky I.V., Remington S.J., Martynov V.I., Potapov V.K., Lukyanov S., Lukyanov K.A. (2005). Synthesis and properties of the chromophore of the asFP595 chromoprotein from Anemonia sulcata. Biochemistry 44 (15), 5788–93 [+]

    A model compound for the chromophore within the purple nonfluorescent GFP-like chromoprotein asFP595 was synthesized. The postulated structure of the chromophore, 2-acetyl-4-(p-hydroxybenzylidene)-1-methyl-5-imidazolone, was taken from the high-resolution crystal structure analysis of intact asFP595 [Quillin, M. L., Anstrom, D., Shu, X., O'Leary, S., Kallio, K., Lukyanov, K. A., and Remington, S. J. (2005) Kindling Fluorescent Protein from Anemonia sulcata: Dark-State Structure at 1.38 A Resolution, Biochemistry 44, 5774-5787]. Erlenmeyer lactonization and oxidation of the methylene group attached to the heteroaromatic moiety with selenium dioxide were used at the key stages of the synthesis. The spectral properties of the model chromophore in solution and their dependence on the pH and polarity of the solvent were investigated. In water, the chromophore was found to exist in two forms, neutral and anionic, with a pK(a) of 7.1. In a dimethylformamide solution, the spectral properties of the anionic form closely match those of the native protein, demonstrating that under these conditions, the compound is an excellent model for the chromophore within native asFP595.

    ID:517
  42. Bulina M.E., Lukyanov K.A., Yampolsky I.V., Chudakov D.M., Staroverov D.B., Shcheglov A.S., Gurskaya N.G., Lukyanov S. (2004). New class of blue animal pigments based on Frizzled and Kringle protein domains. J. Biol. Chem. 279 (42), 43367–70 [+]

    The nature of coloration in many marine animals remains poorly investigated. Here we studied the blue pigment of a scyfoid jellyfish Rhizostoma pulmo and determined it to be a soluble extracellular 30-kDa chromoprotein with a complex absorption spectrum peaking at 420, 588, and 624 nm. Furthermore, we cloned the corresponding cDNA and confirmed its identity by immunoblotting and mass spectrometry experiments. The chromoprotein, named rpulFKz1, consists of two domains, a Frizzled cysteine-rich domain and a Kringle domain, inserted into one another. Generally, Frizzleds are members of a basic Wnt signal transduction pathway investigated intensely with regard to development and cancerogenesis. Kringles are autonomous structural domains found throughout the blood clotting and fibrinolytic proteins. Neither Frizzled and Kringle domains association with any type of coloration nor Kringle intrusion into Frizzled sequence was ever observed. Thus, rpulFKz1 represents a new class of animal pigments, whose chromogenic group remains undetermined. The striking homology between a chromoprotein and members of the signal transduction pathway provides a novel node in the evolution track of growth factor-mediated morphogenesis compounds.

    ID:290
  43. Pastukhov F.V., Yampolsky I.V., Bubnov Y.N. (2002). Allylboration of functionalized isoquinolines. J. Organomet. Chem  (657), 123–128 ID:1033
  44. Bubnov Y.N., Klimkina E.V., Zhun I.V., Pastukhov F.V., Yampolsky I.V. (2000). Allylic boron and zinc derivatives in synthesis and transformations of nitrogen heterocycles. Pure Appl. Chem. 72 (9), 1641–1644 ID:1034
  45. Bubnov Y.N., Pastukhov F.V., Yampolsky I.V., Ignatenko A.V. (2000). A convenient synthesis of 2,2-diallylated nitrogen heterocycles by allylboration of lactams. Eur.J.Org.Chem 200 (8), 1503–1505 ID:1035