Group of chemistry of heterocyclic compounds
The main direction of the group's research is the development of new approaches to the synthesis of heterocyclic compounds, as well as the application of these approaches in the synthesis of substances which have biological activity or are models in the study of biological processes.
The main activity of the group is aimed at the development of new and improvement of old approaches to the synthesis of heterocyclic compounds, as well as the applied use of the methods obtained in the synthesis of the target compounds. The next ones act in the capacity of the target compounds:
- Model compounds which simulate chromophores of fluorescent proteins
- New fluorescent dyes
- New fluorogenic dyes
- Other biologically active compounds
One of the main directions of our research is the study of the structure of stained and fluorescent proteins chromophores. Counter-synthesis is certainly the key tool of such studies. Earlier this approach allowed to confirm the structure of chromophores of proteins asFP595, Kaede and zFP538, as well as to understand the mechanism of dsRed protein chromophore formation.
Currently, within the framework of project 16-33-60116-mol-a-dk ("Study of the chromophores of fluorescent proteins: from structural and functional studies to the search for new fluorophores for living systems"), we also confirmed the structure of the chromophores of yellow and orange proteins, which contain the residue tryptophan, and also work on the synthesis of a model compound, which simulate the chromophore structure of the laRFP protein was started.
Study of a new class of fluorescent dyes based on the borated chromophore GFP
Another interesting result of our studies was the detection of the dependence of the quantum yield of fluorescence of chromophores on their mobility, which helped us synthesize a number of high fluorescence derivatives of the GFP chromophore by means of coordination fixation with a boron atom, which ones can be reliably attributed to a new separate group of fluorescent markers called BOBDI BOronBenzyliDeneImidazolone). This discovery made it possible in practice to demonstrate the possibility of using such compounds as fluorescent labels for living systems (the work was realized within the framework of the RFBR project 14-03-31162 mol_a, "A new class of fluorescent dyes for biology").
Existing fluorescent dyes used for staining living systems have a number of significant disadvantages and are unsuitable for solving a certain range of problems (for example, there are practically no compounds with Stokes shifts of more than 100 nm among them). At the same time, the chromophores of fluorescent proteins do not have many of the disadvantages inherent in the existing dyes, and therefore they are an excellent basis for creating new dyes.
Development of new fluorogenic dyes, including ones based on the chromophores of fluorescent proteins
One of the new and modern methods of fluorescent labeling of biological cells is the use of so-called fluorogenic dyes – substances, which do not have a pronounced fluorescence in a free form and acquire it only when bound to the target object.
One of the promising candidates for the role of such substances are the chromophores of fluorescent proteins and their derivatives.
In this regard, in our group, the creation and study of various fluorogenic compounds is actively conducted.
Development of new approaches to the synetze of heterocyclic compounds
Our team has long been studying the chemistry of chromophores of fluorescent proteins based on the molecule - 4-benzylidene-imidazole-5-ones. During this work we have created several new approaches to the synthesis of these compounds, and in parallel many unexpected transformations associated with the use of esters of nitroacetic and azidoacetic acids were discovered.
In particular, the method of synthesis of 5-hydroxy-1,2-oxazine-6-ones discovered by us allows us to take a new look at one of the methods for the synthesis of isoxazole-3,5-dicarboxylic acid derivatives, the Dornow reaction. Preliminary results strongly suggest that we have discovered the true mechanism of this transformation, which does not correspond to the schemes proposed in the scientific literature.
Similarly, the transformations of the derivatives of azidoacetic acid and their phosphazenes observed by us are also not reflected in the scientific literature, which suggests the possibility of creating new ways of synthesizing heterocyclic systems and from these reagents.
|Mikhail Baranov, Ph.D.||depart. firstname.lastname@example.org, |
|Nadezhda Baleeva||j. r. f.||Dyuhaemail@example.com|
|Alexander Smirnov||j. r. f.|
- (2018). Primary Structure Analysis of Antifungal Peptides from Cultivated and Wild Cereals. Plants (Basel) 7 (3),
- (2018). Azidoacetic Acid Amides in the Synthesis of Substituted Arylidene-1-H-imidazol-5-(4H)-ones. ChemistrySelect 3 (30), 8593–8596
- (2018). A Novel Fluorescent GFP Chromophore Analog-Based Dye for Quantitative PCR. Biochemistry (Mosc) 83 (7), 855–860
- (2018). An effective method for the synthesis of 1,5-disubstituted 4-halo-1H-1,2,3-triazoles from magnesium acetylides. Chem Heterocycl Compd (N Y) 54 (7), 755–757
- (2018). The Role of C2-Substituents in the Imidazolone Ring in the Degradation of GFP Chromophore Derivatives. Russ. J. Bioorganic Chem. 44 (3), 354–357
- (2018). Pyridinium Analogues of Green Fluorescent Protein Chromophore: Fluorogenic Dyes with Large Solvent-Dependent Stokes Shift. J Phys Chem Lett 9 (8), 1958–1963
- (2018). Derivatives of Azidocinnamic Acid in the Synthesis of 2-Amino-4-Arylidene-1H-Imidazol-5(4H)-Ones. Chem Heterocycl Compd (N Y) 54 (6), 625–629
- (2018). Antibiotic Potential of Defense Peptides Derived from the Seeds of a Wild Grass - Barnyard Grass (Echinochloa crusgalli L.). Antibiot Med Biotekhnol 63 (34), 8–11
- (2018). Новая метка для количественной ПЦР на основе синтетического аналога хромофора зелёного флуоресцентного белка. 87 (7), 1089–1095
- (2017). Unveiling Structural Motions of a Highly Fluorescent Superphotoacid by Locking and Fluorinating the GFP Chromophore in Solution. J Phys Chem Lett 8 (23), 5921–5928
- (2017). The Role of N-Substituents in Radiationless Deactivation of Aminated Derivatives of a Locked GFP Chromophore. European J Org Chem 2017 (35), 5219–5224
- (2017). The Sonogashira reaction as a new method for the modification of borated analogues of the green fluorescence protein chromophore. Russ. J. Bioorganic Chem. 43 (5), 612–615
- (2017). Synthesis of 2-arylidene-6,7-dihydroimidazo[1,2-a]pyrazine-3,8(2H,5H)-diones by oxidation of 4-arylidene-2-methyl-1H-imidazol-5(4H)-ones with selenium dioxide. Chem Heterocycl Compd (N Y) 53 (8), 930–933
- (2017). Yellow and Orange Fluorescent Proteins with Tryptophan-based Chromophores. ACS Chem Biol 12 (7), 1867–1873
- (2017). Novel Thionins from Black Seed (Nigella sativa L.) Demonstrate Antimicrobial Activity. Int J Pept Res Ther 23 (2), 171–180
- (2017). Mechanism and color modulation of fungal bioluminescence. Sci Adv 3 (4), e1602847
- (2017). Synthesis of Panal Terpenoid Core. Synlett 28 (5), 583–588
- (2017). A water-soluble precursor for efficient silica polymerization by silicateins. Biochem Biophys Res Commun 495 (2), 2066–2070
- (2017). Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem Sci 8 (10), 7138–7142
- (патент) (2016). Метод и реактивы для детекции активности люциферазы. №2596398 (изобретение)
- (2016). Synthesis and properties of 5-methylidene-3,5-dihydro-4H-imidazol-4-ones (microreview). Chem Heterocycl Compd (N Y) 52 (7), 444–446
- (2016). Conformationally locked GFP chromophore derivatives as potential fluorescent sensors. Russ. J. Bioorganic Chem. 42 (4), 453–456
- (2016). Local fitness landscape of the green fluorescent protein. Nature 533 (7603), 397–401
- (2016). Nambiscalarane, a novel sesterterpenoid comprising a furan ring, and other secondary metabolites from bioluminescent fungus Neonothopanus nambi. MENDELEEV COMMUN 26 (3), 191–192
- (2016). Docking-guided identification of protein hosts for GFP chromophore-like ligands. J Mater Chem C Mater Opt Electron Devices 4 (14), 3036–3040
- (2016). PH-Sensitive fluorophores from locked GFP chromophores by a non-alternant analogue of the photochemical: Meta effect. Phys Chem Chem Phys 18 (38), 26703–26711
- (2016). Борированные производные хромофора зеленого флуоресцентного белка как потенциальные флуоресцентные сенсоры. 42 (4), 501–504
- (2016). Conformationally locked chromophores of CFP and Sirius protein. Tetrahedron Lett 57 (2728), 3043–3045
- (2015). Bioinspired Fluorescent Dyes Based on a Conformationally Locked Chromophore of the Fluorescent Protein Kaede. European J Org Chem 2015 (26), 5716–5721
- (2015). A novel antifungal peptide from leaves of the weed Stellaria media L. B SOC CHIM BIOL 116 (0), 125–132
- (2015). The Chemical Basis of Fungal Bioluminescence. Angew Chem Int Ed Engl 54 (28), 8124–8128
- (2015). Boron-containing 5-arylidene-3,5-dihydro-4H-imidazol-4-ones. 9 (133), 220
- (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
- (2015). A novel water-soluble substrate for silicateins. Russ. J. Bioorganic Chem. 41 (3), 338–339
- (2015). Total synthesis of AsLn2 - A luciferin analogue from the Siberian bioluminescent earthworm Fridericia heliota. MENDELEEV COMMUN 25 (2), 99–100
- (2014). Novel peptide chemistry in terrestrial animals: Natural luciferin analogues from the bioluminescent earthworm fridericia heliota. Chemistry 21 (10), 3942–3947
- (2014). Red-Shifted Fluorescent Aminated Derivatives of a Conformationally Locked GFP Chromophore. Chemistry 20 (41), 13234–13241
- (2014). Ring-expanding rearrangement of 2-acyl-5-arylidene-3,5-dihydro-4H-imidazol- 4-ones in synthesis of flutimide analogs. Tetrahedron 70 (23), 3714–3719
- (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
- (2013). Comparative analysis of extracts of nigella sativa exhibiting antifungal activity against the oomycete phytophthora infestans. CHEM NAT COMPD 49 (5), 985–987
- (2013). Chemical introduction of the green fluorescence: Imaging of cysteine cathepsins by an irreversibly locked GFP fluorophore. Org Biomol Chem 11 (35), 5913–5921
- (2013). Efficient synthetic approach to fluorescent oxazole-4-carboxylate derivatives. Synth Commun 43 (17), 2337–2342
- (2013). A synthetic approach to GFP chromophore analogs from 3-azidocinnamates. Role of methyl rotors in chromophore photophysics. Chem Commun (Camb) 49 (51), 5778–5780
- (2013). Synthesis of the chromophores of fluorescent proteins and their analogs. Russ. J. Bioorganic Chem. 39 (3), 223–244
- (2013). Novel condensations of nitroacetic esters with aromatic aldehydes leading to 5-hydroxy-1,2-oxazin-6-ones. Tetrahedron Lett 54 (7), 628–629
- (2012). Conformationally locked chromophores as models of excited-state proton transfer in fluorescent proteins. J Am Chem Soc 134 (13), 6025–6032
- (2012). Formation of RNA spatial structures. Mol Biol 46 (1), 34–46
- (2012). Unusual transformations of anthranilic acid imidazolides. Chem Heterocycl Compd (N Y) 48 (7), 1108–1110
- (2010). Antifungal activity of storage 2S albumins from seeds of the invasive weed dandelion Taraxacum officinale Wigg. Protein Pept Lett 17 (4), 522–529
- (2009). The purification and characterization of a novel lipid transfer protein from caryopsis of barnyard grass (Echinochloa crusgalli). APPL BIOCHEM MICRO+ 45 (4), 363–368
- (2009). Isolation of the lipid-transporting protein Ns-LTP1 from seeds of the garden fennel flower (Nigella sativa). Russ. J. Bioorganic Chem. 35 (3), 315–319
- (2000). Specific features of a Thalictrum minus cell culture as a source of alkaloids. Russ J Plant Physiol 47 (1), 58–64
- (1999). Chromatographic properties of Gefil, novel hydrophilic dextran gels. J ANAL CHEM+ 54 (7), 629–632