The Journal was founded in 1975 by Prof. Yurii A. Ovchinnikov. The Editorial Board uses the term "bioorganic chemistry" to cover a wide range of problems related to the investigation of the structure and function of biomolecules using the methods of organic, biochemical and physical chemistry.

The journal is intended for scientists, for those in the health professions, educators, and students in universities and researchers in industrial, medical, agricultural, and environmental control laboratories.

Russian Journal of Bioorganic Chemistry (Bioorganicheskaya Khimiya) welcomes papers on all aspects of bioorganic chemistry, biochemistry, cell and molecular biology, genomics, proteomics, bioinformatics, immunology, molecular virology, molecular evolution and developmental biology.

The Journal publishes reviews, minireviews, research articles and theoretical investigations, hypothesis and short communications.

The Journal is published in Russian (under the name Bioorganicheskaya Khimiya in the Russian Federation) and in English (under the name Russian Journal
of Bioorganic Chemistry) six times a year by Russian Academy of Sciences (IKC "Akademkniga") in Moscow (Russia) and Pleiades Publishing Inc.
in the United States. The English edition is distributed worldwide by Springer.

Articles are published in Russian and English. Publication of articles in the Russian Journal of Bioorganic Chemistry (Bioorganicheskaya Khimiya) – free.

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Vol 49, No 3 (2023)

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pages 223-223 views
Fluorescence Decay Analysis of the Model Compounds as an Approach to Photophysical Engineering of Fluorescent Proteins
Baleeva N.S., Baranov M.S., Bogdanov A.M.

Studying of structure-function relationships between a chromophore and its protein environment plays a key role in photophysical engineering of fluorescent proteins (FPs), specifically, in the guided designing of their new variants with a higher fluorescence quantum yield (FQY). Known approaches to FQY increasing mostly rely on suppression of the excited state nonradiative processes, but no tools have been suggested for the tuning of the radiative rate constant (kr), which is also a potentially “adjustable” value. Here, we propose an experimental approach in which the synthetic chromophore of FP models the “fixation” of the most important radiationless constants and allows monitoring of the fluorescence lifetime flexibility (as an indicator of the kr value). As a proof-of-concept, we studied the time-resolved fluorescence behavior of the green and blue FP chromophore analogs in diverse chemical environments. The conformationally locked analog of the GFP chromophore in most cases showed monophasic fluorescence decay kinetics with a lifetime of 2.7–3.0 ns, thus adequately modeling the typical behavior of GFPs with the highest FQYs. Under the conditions of stimulated ionization of this chromophore, we observed increased (up to 4.3–4.6 ns) fluorescence lifetimes, which can be interpreted in terms of an increase in the radiative constant (kr). The conformationally locked analog of the Sirius chromophore showed biexponential fluorescence decay kinetics, partly simulating the properties of the blue FPs. In an acetic acid solution, this compound exhibited distinct fluorescent properties (elevated fluorescence intensity with a major lifetime population of ~4 ns), which can be interpreted as the emission of an unusual cationic form of the chromophore.

pages 275-284 views
Three-Dimensional Structure of Fab Fragment of Monoclonal Antibody LNKB-2 Complexed with Antigenic Nonaptide from Human Interleukin-2
Goryacheva E.A., Artemyev I.V., Pletnevа N.V., Pletnev V.Z.

The three-dimensional structure of the antigen-binding fragment (Fab) of the monoclonal antibody LNKB-2 in complex with the synthetic antigenic nonapeptide of human interleukin-2 (IL-2; Lys-Pro-Leu-Glu-Glu-Val-Leu-Asn-Leu-O) was determined by X-ray method at a resolution of 2.6 Å in crystal space group P212121. The peptide adopts a somewhat distorted α-helical conformation, close to that of fragment 64–72 of the IL-2 antigen. Four out of the six hypervariable loops in the antigen-binding site of the Fab fragment are involved in nonapeptide association through hydrogen bonding, salt bridge formation, and hydrophobic interactions. Moreover, Tyr residues of an antibody play an important role in antigen-antibody recognition.

pages 285-290 views
Convenient Preparation of -Butyl Amino Acid Esters from -Butanol
Azev V.N., Chulin A.N., Molchanov M.V., Miroshnikov A.I.

A preparation of tert-butyl esters of amino acid is described that proceeds from protected amino acids and tert-butanol using anhydrous magnesium sulfate and an excess of boron trifluoride diethyl etherate as additional reagents. The method affords tert-butyl esters in good yields and a variety of amino acid side chains and substituents tolerate the reaction conditions.

pages 291-295 views
A New Peptide from the Venom of the Madagascar Cat-Eyed Snake Blocks Nicotinic Acetylcholine Receptor
Kryukova E.V., Ivanov D.A., Kopylova N.V., Starkov V.G., Andreeva T.V., Ivanov I.A., Tsetlin V.I., Utkin Y.N.

In screening the venoms of various snake species, we found that the venom of the Madagascar cat-eyed snake Madagascarophis colubrinus competes with α-bungarotoxin for binding to the nicotinic acetylcholine receptor from Torpedo californica. Using liquid chromatography, a peptide, called macoluxin and inhibiting the binding of the toxin to the receptor, was isolated from the venom. The amino acid sequence of this 23-amino acid peptide was determined by automatic Edman degradation. Comparison with amino acid sequences of known proteins showed that the macoluxin sequence is homologous to the α-helical region of the sequence of snake venom metalloproteinases. The peptide was synthesized by solid-phase peptide synthesis, and the study of its biological activity showed that it inhibits the binding of α-bungarotoxin to the Torpedo receptor with an IC50 of 47 μM. Macoluxin also reversibly inhibited acetylcholine-induced currents in the muscle-type nicotinic acetylcholine receptor. This is the first data on the presence in the venom of rear fanged snakes of a peptide that can inhibit the nicotinic acetylcholine receptor.

pages 296-305 views
Dynamics of 24 Self-Assembling H-(RADA)-OH Peptides Complexed in Bi-Layered Structure with Layers in and Orientation
Danilkovich A.V., Tikhonov D.A., Lipkin V.M.

H-(RADA)4-OH peptide in water tends to form biolgels at physiological conditions. Thusly made scaffold is formed of fibrils resulted from peptides self-assembling. Fibrils have two external hydrophilic layers, while hydrophobic one is situated between of them. Bio gels by the H-(RADA)4-OH peptides are considered to be a prominent source for designed extra cellular matrix aimed to cell cultures of different types. Little is known about detailed structure the filament structure and β-sheets peptide composition. We have designed and studied molecular dynamics of bi-layered protofilament structures with β-sheets formed of parallel or anti-parallel peptide chains. Method of molecular dynamics was used to study H-(RADA)4-OH peptide complexes at 80 and 300 K. While the most stable peptide complex was found to consist of anti-parallel peptides, had the lowest free energy and the least deviation of atom coordinates, yet another stable structure of the peptide complex was identified as 24-mer of parallel peptides with two β-sheets placed in syn orientation. These results underlined the importance of factors, directing the initial stages of the H-(RADA)4-OH peptide self-assembling in solution.

pages 306-318 views
Development of a System for Biosynthesis, Isolation and Purification of Holoform of Recombinant Human Neuroglobin and Its Characteristics
Semenova M.A., Dolgikh D.A., Kirpichnikov M.P., Maksimov G.V., Brazhe N.A., Bocharov E.V., Ziganshin .H., Parshina E.Y., Ignatova A.A., Smirnova O.M., Bochkova Z.V., Chertkova R.V.

An efficient system for the biosynthesis, isolation and purification of recombinant human neuroglobin has been developed and optimized, which makes it possible to produce protein in quantities sufficient to study its properties. According to UV-visible, IR-, CD-, and NMR spectroscopy data, recombinant neuroglobin is a structured protein in the holoform state. The data of chromato-mass-spectrometric analysis made it possible to conclude that there is a correctly formed disulfide bond in the structure of the oxidized form of the protein. Using Raman and surface-enhanced Raman spectroscopy with laser excitation at 532 nm, it was shown that heme in the reduced and oxidized forms of neuroglobin has vibrational degrees of freedom typical of b-type hemes, and the iron atom is six-coordinated. Using Raman spectroscopy with laser excitation at 633 nm, it was found that reduced –SH-groups were present in reduced neuroglobin, while in oxidized neuroglobin disulfide bridge was formed. The results obtained serve as the basis for detailed studies of the mechanism of the functioning of neuroglobin as a neuroprotector, in particular, during its interaction with oxidized cytochrome c, which is released from mitochondria in violation of their functioning and/or morphology.

pages 319-330 views


From Peptides to Receptors
Tsetlin V.I.

In the 1960s and 1970s, the Institute of Chemistry of Natural Compounds developed a topochemical approach for designing new biologically active peptide compounds, the applicability of which to the creation of inhibitors and effective substrates of proteolytic enzymes was shown by the author of this review under the direct supervision of V.T. Ivanov. The next task was to establish the conformation of protein neurotoxins from snake venoms and to study the topography of their binding to the target, the nicotinic acetylcholine receptor (nAChR) from the electric organ of the Torpedo marmorata ray. With selectively labeled derivatives containing one fluorescent or spin label on established amino acid residues, neurotoxin residues in contact with nAChR were identified for the first time. Later, in collaboration with the laboratory of V.T. Ivanov, new analogues of α-conotoxins (peptide neurotoxins from poisonous mollusks Conus), were synthesized including their photoactivated derivatives, which showed the participation of all Torpedo nAChR subunits in the binding of α‑conotoxins. The final part of the review briefly presents the recent achievements of the Department of Molecular Neuroimmune Signaling (headed by V.I. Tsetlin) concerning the isolation and synthesis of new peptide and protein neurotoxins and the study of their mechanism of action.

pages 224-228 views
Evolution of Peptide Biopharmaceuticals
Ivanov V.T., Deigin V.I.

Peptides are small molecule substances involved in numerous essential physiological functions such as human growth and development, stress, regulation of the emotional state, sexual behavior, and immune responses. Their mechanisms of action are based on receptor-ligand interaction, which leads to highly selective effects. These properties and low toxicity allow them to be considered potent drugs. The production of peptide preparations became possible at the beginning of the 20th century after a method for the selective synthesis of peptides was developed. However, after the successful synthesis of the first peptide drugs, many issues related to increasing stability, bioavailability, half-life, and the ability to move through cell membranes remained unresolved. The review considers the historical path of development of the synthesis and production of peptides, as well as modern approaches to the creation of peptide drugs and their use in biopharmaceutics, including the development of original peptide drugs in Russia.

pages 229-242 views
Therapeutic Potential and Application Prospects of Antimicrobial Peptides in the Era of Global Spread of Antibiotic Resistance
Safronova V.N., Bolosov I.A., Panteleev P.V., Balandin S.V., Ovchinnikova T.V.

In the era of the growing global threat of antibiotic resistance, antimicrobial peptides (AMPs) are considered as new generation drugs for treatment of various infectious diseases. In this review, AMPs are seen as an alternative to traditional antibiotics, many of which have already lost or are gradually reducing their effectiveness against a number of critically important pathogenic microorganisms. Recent outbreaks of secondary infections during the COVID-19 pandemic have increased the interest in AMPs due to an acute shortage of effective agents against bacterial and fungal infections. The review summarized current data on clinical studies of AMPs, assembled a list of developed drugs based on AMPs at various stages of clinical trials, highlighted the urgency of study of new AMPs, and systematized the most relevant clinical data and application of AMPs.

pages 243-258 views
Multifunctional Proteins and Their Role in the Vital Activity of Cells
Korshunov D.A., Sereda E.E., Kondakova I.V.

The function of a newly discovered protein is often assessed by matching its new sequence to sequences of proteins with known functions. However, protein superfamilies can contain homologous elements that catalyze different reactions. Some homologous proteins differ in that they perform a second or even a third function and are called moonlighting proteins, which can be translated as mate proteins or underwork proteins. Also, such proteins are called multifunctional. In addition to these, the superfamilies of proteins with multiple functions also include pseudoenzymes that have a common catalytically active domain but no catalytic activity, as well as metamorphs and morpheins. This review discusses examples of such proteins, their diversity of functions, and their importance in the life of the cell.

pages 259-274 views

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