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.
Nadezhda Baleevaj. r.
Snezhana Zaytsevastud.
Alexander Smirnoveng.

Selected publications

  1. Povarova N.V., Markina N.M., Baranov M.S., Barinov N.A., Klinov D.V., Kozhemyako V.B., Lukyanov K.A. (2018). A water-soluble precursor for efficient silica polymerization by silicateins. Biochem. Biophys. Res. Commun. 495 (2), 2066–2070 [+]

    Silicateins, the spicule-forming proteins from marine demosponges capable to polymerize silica, are popular objects of biomineralization studies due to their ability to form particles varied in shape and composition under physiological conditions. Despite the occurrence of the many approaches to nanomaterial synthesis using silicateins, biochemical properties of this protein family are poorly characterized. The main reason for this is that tetraethyl orthosilicate (TEOS), the commonly used silica acid precursor, is almost insoluble in water and thus is poorly available for the protein. To solve this problem, we synthesized new water-soluble silica precursor, tetra(glycerol)orthosilicate (TGS), and characterized biochemical properties of the silicatein A1 from marine sponge Latrunculia oparinae. Compared to TEOS, TGS ensured much greater activity of silicatein and was less toxic for the mammalian cell culture. We evaluated optimum conditions for the enzyme - pH range, temperature and TGS concentration. We concluded that TGS is a useful silica acid precursor that can be used for silica particles synthesis and in vivo applications.

  2. Bozhanova N.G., Baranov M.S., Klementieva N.V., Sarkisyan K.S., Gavrikov A.S., Yampolsky I.V., Zagaynova E.V., Lukyanov S.A., Lukyanov K.A., Mishin A.S. (2017). Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chemical Science 8 (10), 7138–7142 [+]

    We present protein-PAINT – the implementation of the general principles of PAINT (Point Accumulation for Imaging in Nanoscale Topography) for live-cell protein labeling. Our method employs the specific binding of cell-permeable fluorogenic dyes to genetically encoded protein tags. We engineered three mutants of the bacterial lipocalin Blc that possess different affinities to a fluorogenic dye and exhibit a strong increase in fluorescence intensity upon binding. This allows for rapid labeling and washout of intracellular targets on a time scale from seconds to a few minutes. We demonstrate an order of magnitude higher photostability of the fluorescence signal in comparison with spectrally similar fluorescent proteins. Protein-PAINT ensures prolonged super-resolution fluorescence microscopy of living cells in both single molecule detection and stimulated emission depletion regimes.


Mikhail Baranov