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Ershov PV, Yablokov EO, Mezentsev YV, Chuev GN, Fedotova MV, Kruchinin SE, Ivanov AS. SARS-COV-2 Coronavirus Papain-like Protease PLpro as an Antiviral Target for Inhibitors of Active Site and Protein-Protein Interactions. Biophysics (Nagoya-shi) 2023; 67:902-912. [PMID: 36883182 PMCID: PMC9984130 DOI: 10.1134/s0006350922060082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 03/06/2023] Open
Abstract
The papain-like protease PLpro of the SARS-CoV-2 coronavirus is a multifunctional enzyme that catalyzes the proteolytic processing of two viral polyproteins, pp1a and pp1ab. PLpro also cleaves peptide bonds between host cell proteins and ubiquitin (or ubiquitin-like proteins), which is associated with a violation of immune processes. Nine structures of the most effective inhibitors of the PLpro active center were prioritized according to the parameters of biochemical (IC 50) and cellular tests to assess the suppression of viral replication (EC 50) and cytotoxicity (CC 50). A literature search has shown that PLpro can interact with at least 60 potential protein partners in cells, 23 of which are targets for other viral proteins (human papillomavirus and Epstein-Barr virus). The analysis of protein-protein interactions showed that the proteins USP3, UBE2J1, RCHY1, and FAF2 involved in deubiquitinylation and ubiquitinylation processes contain the largest number of bonds with other proteins; the interaction of viral proteins with them can affect the architecture of the entire network of protein-protein interactions. Using the example of a spatial model of the PLpro/ubiquitin complex and a set of 154 naturally occurring compounds with known antiviral activity, 13 compounds (molecular masses in the range of 454-954 Da) were predicted as potential PLpro inhibitors. These compounds bind to the "hot" amino acid residues of the protease at the positions Gly163, Asp164, Arg166, Glu167, and Tyr264 involved in the interaction with ubiquitin. Thus, pharmacological effects on peripheral PLpro sites, which play important roles in binding protein substrates, may be an additional target-oriented antiviral strategy.
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Affiliation(s)
- P. V. Ershov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | - E. O. Yablokov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
| | | | - G. N. Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Moscow oblast Russia
| | - M. V. Fedotova
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - S. E. Kruchinin
- Krestov Institute of Solution Chemistry, Russian Academy of Sciences, 153045 Ivanovo, Russia
| | - A. S. Ivanov
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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Shumyantseva VV, Bulko TV, Gnedenko OV, Yablokov EO, Usanov SA, Ivanov AS. [Adrenodoxins and their role in the cytochrome P450 systems]. Biomed Khim 2022; 68:47-54. [PMID: 35221296 DOI: 10.18097/pbmc20226801047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The role of partner proteins in the formation of functional complexes in cytochrome P450 systems was investigated by means of optical biosensor technique. Kinetic constants and equilibrium dissociation constants of complexes of cytochrome CYP11A1 (P450scc) with wild-type adrenodoxin (Adx WT) and mutant forms of adrenodoxin R106D and D109R were determined using an optical biosensor. Wild-type adrenodoxin (Kd = (1.23±0.09)⋅10⁻⁶ M) and mutant D109R (Kd = (2.37±0.09)⋅10⁻⁸ M) formed complexes with cytochrome P450scc. For the R106D mutant, no complex formation was detected. To investigate the possibility of the participation of adrenodoxins and their mutant variants in the process of electron transfer as electron donors in mitochondrial cytochrome P450 systems, the electrochemical properties of these iron-sulfur proteins Adx WT and mutant forms of adrenodoxins were studied. Adx WT, mutant forms R106D and D109R have redox potentials E1/2 significantly more negative than cytochromes P450 (-579±10 mV, -590±15 mV, and -528±10 mV, respectively). These results suggest that Adx WT and mutant forms may be electron donors in the cytochrome P450 systems.
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Affiliation(s)
- V V Shumyantseva
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - T V Bulko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - O V Gnedenko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S A Usanov
- Institute of Bioorganic Chemistry, Minsk, Belarus
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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Kaluzhskiy LA, Ershov PV, Yablokov EO, Mezentsev YV, Gnedenko OV, Shkel TV, Gilep AA, Usanov SA, Ivanov AS. Screening of Potential Non-Azole Inhibitors of Lanosterol 14-Alpha Demethylase (CYP51) of the Сandida Fungi. Biochem Moscow Suppl Ser B 2021. [DOI: 10.1134/s1990750821030045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yablokov EO, Sushko TA, Kaluzhskiy LA, Kavaleuski AA, Mezentsev YV, Ershov PV, Gilep AA, Ivanov АS, Strushkevich NV. Substrate-induced modulation of protein-protein interactions within human mitochondrial cytochrome P450-dependent system. J Steroid Biochem Mol Biol 2021; 208:105793. [PMID: 33271253 DOI: 10.1016/j.jsbmb.2020.105793] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/18/2020] [Accepted: 11/14/2020] [Indexed: 12/28/2022]
Abstract
Steroidogenesis is strictly regulated at multiple levels, as produced steroid hormones are crucial to maintain physiological functions. Cytochrome P450 enzymes are key players in adrenal steroid hormone biosynthesis and function within short redox-chains in mitochondria and endoplasmic reticulum. However, mechanisms regulating supply of reducing equivalents in the mitochondrial CYP-dependent system are not fully understood. In the present work, we aimed to estimate how the specific steroids, substrates, intermediates and products of multistep reactions modulate protein-protein interactions between adrenodoxin (Adx) and mitochondrial CYP11 s. Using the SPR technology we determined that steroid substrates affect affinity and stability of CYP11s-Adx complexes in an isoform-specific mode. In particular, cholesterol induces a 4-fold increase in the rate of CYP11A1 - Adx complex formation without significant effect on dissociation (koff decreased ∼1.5-fold), overall increasing complex affinity. At the same time steroid substrates decrease the affinity of both CYP11B1 - Adx and CYP11B2 - Adx complexes, predominantly reducing their stability (4-7 fold). This finding reveals differentiation of protein-protein interactions within the mitochondrial pool of CYPs, which have the same electron donor. The regulation of electron supply by the substrates might affect the overall steroid hormones production. Our experimental data provide further insight into protein-protein interactions within CYP-dependent redox chains involved in steroidogenesis.
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Affiliation(s)
- E O Yablokov
- Institute of Biomedical Chemistry, 119121, Pogodinskaya str. 10, Building 8, Moscow, Russia.
| | - T A Sushko
- Department of Bioengineering, School of Engineering, The University of Tokyo, 4-6 - 1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan
| | - L A Kaluzhskiy
- Institute of Biomedical Chemistry, 119121, Pogodinskaya str. 10, Building 8, Moscow, Russia
| | - A A Kavaleuski
- Institute of Bioorganic Chemistry National Academy of Sciences of Belarus, 220141, Kuprevicha str. 5/2, Minsk, Belarus
| | - Y V Mezentsev
- Institute of Biomedical Chemistry, 119121, Pogodinskaya str. 10, Building 8, Moscow, Russia
| | - P V Ershov
- Institute of Biomedical Chemistry, 119121, Pogodinskaya str. 10, Building 8, Moscow, Russia
| | - A A Gilep
- Institute of Bioorganic Chemistry National Academy of Sciences of Belarus, 220141, Kuprevicha str. 5/2, Minsk, Belarus
| | - А S Ivanov
- Institute of Biomedical Chemistry, 119121, Pogodinskaya str. 10, Building 8, Moscow, Russia
| | - N V Strushkevich
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205, Moscow, Russia
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzgskiy LA, Ivanov AS, Gnuchev NV, Mitkevich VA, Makarov AA, Kozin SA. Direct Molecular Fishing of Zinc-Dependent Protein Partners of Amyloid-beta 1–16 with the Taiwan (D7H) Mutation and Phosphorylated Ser8 Residue. Mol Biol 2021. [DOI: 10.1134/s0026893320060035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Kaluzhskiy LA, Ershov PV, Yablokov EO, Mezentsev YV, Gnedenko OV, Shkel TV, Gilep AA, Usanov SA, Ivanov AS. [Screening of potential non-azole inhibitors of lanosterol14-alpha demethylase (CYP51) of Candida fungi]. Biomed Khim 2021; 67:42-50. [PMID: 33645521 DOI: 10.18097/pbmc20216701042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Currently, opportunistic fungi of the genus Candida are the main causative agents of mycoses, which are especially severe upon condition of acquired immunodeficiency. The main target for the development of new antimycotics is the cytochrome P450 51 (CYP51) of the pathogenic fungus. Due to the widespread distribution of Candida strains resistancy to inhibitors of the azole class, the screening for CYP51 inhibitors both among non-azole compounds and among clinically used drugs repurposing as antimycotics is becoming urgent. To identify potential inhibitors from the non-azole group, an integrated approach was applied, including bioinformatics analysis, computer molecular modeling, and a surface plasmon resonance (SPR) technology. Using in silico modeling, the binding sites for acetylsalicylic acid, ibuprofen, chlorpromazine and haloperidol (this compounds, according to the literature, showed antimycotic activity) were predicted in the active site of CYP51 of Candida albicans and Candida glabrata. The Kd values of molecular complexes of acetylsalicylic acid, ibuprofen and haloperidol with CYP51, determined by SPR analysis, ranged from 18 μM to 126 μM. It was also shown that structural derivatives of haloperidol, containing various substituents, could be positioned in the active site of CYP51 of Candida albicans with the possible formation of coordination bonds between the hydroxyl groups of the derivatives and the iron atom in the heme of CYP51. Thus, the potential basic structures of non-azole compounds have been proposed, which can be used for the design of new CYP51 inhibitors of Candida fungi.
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Affiliation(s)
| | - P V Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - O V Gnedenko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - T V Shkel
- Institute of Bioorganic Chemistry, Minsk, Belarus
| | - A A Gilep
- Institute of Bioorganic Chemistry, Minsk, Belarus
| | - S A Usanov
- Institute of Bioorganic Chemistry, Minsk, Belarus
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzgskiy LA, Ivanov AS, Gnuchev NV, Mitkevich VA, Makarov AA, Kozin SA. [Direct Molecular Fishing of Zinc-Dependent Protein Partners of Amyloid-beta 1-16 with the Taiwan (D7H) Mutation and Phosphorylated Ser8 Residue]. Mol Biol (Mosk) 2020; 54:1029-1036. [PMID: 33276366 DOI: 10.31857/s0026898420060038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/10/2020] [Indexed: 11/24/2022]
Abstract
We previously showed that the metal-binding domain 1-16 of intact amyloid-beta (Aβ) is involved in interactions with a number of proteins from the cytosolic fraction of SK-N-SH human neuroblastoma cells in a zinc-dependent manner only. It is known that hereditary mutations in the Aβ metal-binding domain (Aβ(1-16)), which accelerate the development of Alzheimer's disease and post-translational modifications of amino acid residues, can significantly affect the domain's structure in the presence of zinc ions. In this work, using the molecular fishing methodology for Aβ(l-16) isoforms with the Taiwanese mutation (D7H) and a phosphorylated Ser8 residue, proteins from the cytosol of SK-N-SH cells were found that are able to form zinc-dependent non-covalent complexes with these domains. The partner proteins identified for these isoforms differed from those for intact Aβ(1-16). In contrast, the Aβ(1-16) isoform with the English mutation (H6R) and the Aβ(1-16) isoform containing both an isomerized Asp7 residue and phosphorylated Ser8 residue did not interact with cytosolic proteins. The results are useful for developing methods for rational modulation of protein-protein interactions involving natural isoforms of beta-amyloid, and also indicate the possible role of beta-amyloid with phosphorylated Ser8 as a molecule involved in normal physiological processes.
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Affiliation(s)
- P V Ershov
- Orekhovich Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - Yu V Mezentsev
- Orekhovich Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - E O Yablokov
- Orekhovich Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - L A Kaluzgskiy
- Orekhovich Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - A S Ivanov
- Orekhovich Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - N V Gnuchev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - V A Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - A A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - S A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia.,
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Kulbatskii DS, Shulepko MA, Sluchanko NN, Yablokov EO, Kamyshinsky RA, Chesnokov YM, Kirpichnikov MP, Lyukmanova EN. Efficient screening of ligand-receptor complex formation using fluorescence labeling and size-exclusion chromatography. Biochem Biophys Res Commun 2020; 532:127-133. [PMID: 32828540 DOI: 10.1016/j.bbrc.2020.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 08/09/2020] [Indexed: 11/19/2022]
Abstract
Evidence of a complex formation is a crucial step in the structural studies of ligand-receptor interactions. Here we presented a simple and fast approach for qualitative screening of the complex formation between the chimeric extracellular domain of the nicotinic acetylcholine receptor (α7-ECD) and three-finger proteins. Complex formation of snake toxins α-Bgtx and WTX, as well as of recombinant analogs of human proteins Lynx1 and SLURP-1, with α7-ECD was confirmed using fluorescently labeled ligands and size-exclusion chromatography with simultaneous absorbance and fluorescence detection. WTX/α7-ECD complex formation also was confirmed by cryo-EM. The proposed approach could easily be adopted to study the interaction of other receptors with their ligands.
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Affiliation(s)
- D S Kulbatskii
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - M A Shulepko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - N N Sluchanko
- A. N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect 33, Building 1, Moscow, 119071, Russia
| | - E O Yablokov
- Federal State Budgetary Institution "V.N. Orekhovich Research Institute of Biomedical Chemistry", Pogodinskaya 10k8, Moscow, 119121, Russia
| | - R A Kamyshinsky
- National Research Center "Kurchatov Institute", Academic Kurchatov Sq. 1, Moscow, 123182, Russia; Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Leninskiy Prospect 59, Moscow, 119333, Russia
| | - Y M Chesnokov
- National Research Center "Kurchatov Institute", Academic Kurchatov Sq. 1, Moscow, 123182, Russia; Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Leninskiy Prospect 59, Moscow, 119333, Russia
| | - M P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia; Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1k12, Moscow, 119192, Russia
| | - E N Lyukmanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia; Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1k12, Moscow, 119192, Russia.
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Kaluzhskiy LA, Ershov PV, Kurpedinov KS, Sonina DS, Yablokov EO, Shkel TV, Haidukevich IV, Sergeev GV, Usanov SA, Ivanov AS. [SPR analysis of protein-protein interactions with P450 cytochromes and cytochrome b5 integrated into lipid membrane]. Biomed Khim 2019; 65:374-379. [PMID: 31666408 DOI: 10.18097/pbmc20196505374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Identification of new protein-protein interactions (PPI) and characterization of quantitative parameters of complex formation represent one of central tasks of protein interactomics. This work is a logical continuation of the cycle of our previous works devoted to the study of PPIs among the components of cytochrome P450-dependent monooxygenase system. Using an optical biosensor of Surface Plasmon Resonance (SPR biosensor), a comparative analysis on the determination of kinetic and equilibrium parameters of complex formation between the membrane-bound hemoprotein cytochrome b5 with cytochrome P450s was performed using two different protocols for protein immobilization: 1) covalent non-oriented one on to the carboxymethyl dextran chip type CM and 2) non-covalent oriented immobilization in the lipid environment on the chip type L1 with internal control of liposomes surface distribution. In the second protocol it was shown that the complex formation was characterized by 2.5 times higher affinity due to an decrease in rate dissociation constants. The appropriateness of using both experimental models is discussed.
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Affiliation(s)
| | - P V Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - K S Kurpedinov
- Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - D S Sonina
- Mendeleev University of Chemical Technology of Russia, Moscow, Russia
| | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - T V Shkel
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - I V Haidukevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - G V Sergeev
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - S A Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzhskiy LA, Florinskaya AV, Gnedenko OV, Zgoda VG, Vakhrushev IV, Raeva OS, Yarygin KN, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Direct Molecular Fishing of Protein Partners for Proteins Encoded by Genes of Human Chromosome 18 in HepG2 Cell Lysate. Russ J Bioorg Chem 2019. [DOI: 10.1134/s1068162019010059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzhsky LA, Florinskaya AV, Buneeva OA, Medvedev AE, Ivanov AS. Effect of Bioregulator Isatin on Protein–Protein Interactions Involving Isatin-Binding Proteins. Russ J Bioorg Chem 2018. [DOI: 10.1134/s1068162018010053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Ershov PV, Mezentsev YV, Yablokov EO, Kaluzhskiy LA, Florinskaya AV, Svirid AV, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Specificity of Isatin Interaction with Cytochromes P450. Biochem Moscow Suppl Ser B 2018. [DOI: 10.1134/s1990750818020026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Florinskaya AV, Ershov PV, Mezentsev YV, Kaluzhskiy LA, Yablokov EO, Buneeva OA, Zgoda VG, Medvedev AE, Ivanov AS. [The analysis of participation of individual proteins in the protein interactome formation]. Biomed Khim 2018; 64:169-174. [PMID: 29723146 DOI: 10.18097/pbmc20186402169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
It becomes increasingly clear that most proteins of living systems exist as components of various protein complexes rather than individual molecules. The use of various proteomic techniques significantly extended our knowledge not only about functioning of individual complexes but also formed a basis for systemic analysis of protein-protein interactions. In this study gel-filtration chromatography accompanied by mass-spectrometry was used for the interactome analysis of human liver proteins. In six fractions (with average molecular masses of 45 kDa, 60 kDa, 85 kDa, 150 kDa, 250 kDa, and 440 kDa) 797 proteins were identified. In dependence of their distribution profiles in the fractions, these proteins could be subdivided into four groups: (1) single monomeric proteins that are not involved in formation of stable protein complexes; (2) proteins existing as homodimers or heterodimers with comparable partners; (3) proteins that are partially exist as monomers and partially as components of protein complexes; (4) proteins that do not exist in the monomolecular state, but also exist within protein complexes containing three or more subunits. Application of this approach to known isatin-binding proteins resulted in identification of proteins involved in formation of the homo- and heterodimers and mixed protein complexes.
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Affiliation(s)
| | - P V Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - O A Buneeva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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14
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Ershov PV, Mezentsev YV, Yablokov EO, Kalushskiy LA, Florinskaya AV, Svirid AV, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. [Study specificity of isatin interactions with P450 cytochromes]. Biomed Khim 2018; 64:61-65. [PMID: 29460836 DOI: 10.18097/pbmc20186401061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cytochrome P450-dependent monooxygenase systems exist basically in all living organisms, where they perform various important functions. The coordinated functioning of these systems involves many proteins participating in different protein-protein interactions (PPI). Previously, we have found that the endogenous non-peptide bioregulator isatin (indoledione-2,3), synthesized from indole by means of certain cytochromes P450 (e.g. P450 2E1, P450 2C19, P450 2A6) regulates affinity of some PPI. In this work, an attempt has been undertaken to register a direct interaction of isatin with a set of different proteins related to the functioning of cytochrome P450-dependent monooxygenase: five isoforms of cytochromes P450, two isoforms of cytochrome b5, cytochrome P450 reductase, adrenodoxin, adrenodoxin reductase and ferrochelatase. The study has shown that isatin binds specifically only to cytochromes P450 with high affinity (the equilibrium dissociation constant (Kd) is about 10-8 M).
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Affiliation(s)
- P V Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - A V Svirid
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - A A Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - S A Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Belarus
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
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15
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Svirid AV, Ershov PV, Yablokov EO, Kaluzhskiy LA, Mezentsev YV, Florinskaya AV, Sushko TA, Strushkevich NV, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Direct Molecular Fishing of New Protein Partners for Human Thromboxane Synthase. Acta Naturae 2017. [DOI: 10.32607/20758251-2017-9-4-92-100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thromboxane synthase (TBXAS1) catalyzes the isomerization reaction of prostaglandin H2 producing thromboxane A2, the autocrine and paracrine factor in many cell types. A high activity and metastability by these arachidonic acid derivatives suggests the existence of supramolecular structures that are involved in the regulation of the biosynthesis and directed translocation of thromboxane to the receptor. The objective of this study was to identify TBXAS1 protein partners from human liver tissue lysate using a complex approach based on the direct molecular fishing technique, LC-MS/MS protein identification, and protein-protein interaction validation by surface plasmon resonance (SPR). As a result, 12 potential TBXAS1 protein partners were identified, including the components regulating cytoskeleton organization (BBIP1 and ANKMY1), components of the coagulation cascade of human blood (SERPINA1, SERPINA3, APOH, FGA, and FN1), and the enzyme involved in the metabolism of xenobiotics and endogenous bioregulators (CYP2E1). SPR validation on the Biacore 3000 biosensor confirmed the effectiveness of the interaction between CYP2E1 (the enzyme that converts prostaglandin H2 to 12-HHT/thromboxane A2 proantagonist) and TBXAS1 (Kd = (4.3 0.4) 10-7 M). Importantly, the TBXAS1CYP2E1 complex formation increases fivefold in the presence of isatin (indole-2,3-dione, a low-molecular nonpeptide endogenous bioregulator, a product of CYP2E1). These results suggest that the interaction between these hemoproteins is important in the regulation of the biosynthesis of eicosanoids.
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Svirid AV, Ershov PV, Yablokov EO, Kaluzhskiy LA, Mezentsev YV, Florinskaya AV, Sushko TA, Strushkevich NV, Strushkevich NV, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Direct Molecular Fishing of New Protein Partners for Human Thromboxane Synthase. Acta Naturae 2017. [DOI: 10.32607/2075-8251-2017-9-4-92-100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Svirid AV, Ershov PV, Yablokov EO, Kaluzhskiy LA, Mezentsev YV, Florinskaya AV, Sushko TA, Strushkevich NV, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Direct Molecular Fishing of New Protein Partners for Human Thromboxane Synthase. Acta Naturae 2017; 9:92-100. [PMID: 29340222 PMCID: PMC5762833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 11/17/2022] Open
Abstract
Thromboxane synthase (TBXAS1) catalyzes the isomerization reaction of prostaglandin H2 producing thromboxane A2, the autocrine and paracrine factor in many cell types. A high activity and metastability by these arachidonic acid derivatives suggests the existence of supramolecular structures that are involved in the regulation of the biosynthesis and directed translocation of thromboxane to the receptor. The objective of this study was to identify TBXAS1 protein partners from human liver tissue lysate using a complex approach based on the direct molecular fishing technique, LC-MS/MS protein identification, and protein-protein interaction validation by surface plasmon resonance (SPR). As a result, 12 potential TBXAS1 protein partners were identified, including the components regulating cytoskeleton organization (BBIP1 and ANKMY1), components of the coagulation cascade of human blood (SERPINA1, SERPINA3, APOH, FGA, and FN1), and the enzyme involved in the metabolism of xenobiotics and endogenous bioregulators (CYP2E1). SPR validation on the Biacore 3000 biosensor confirmed the effectiveness of the interaction between CYP2E1 (the enzyme that converts prostaglandin H2 to 12-HHT/thromboxane A2 proantagonist) and TBXAS1 (Kd = (4.3 ± 0.4) × 10-7 M). Importantly, the TBXAS1•CYP2E1 complex formation increases fivefold in the presence of isatin (indole-2,3-dione, a low-molecular nonpeptide endogenous bioregulator, a product of CYP2E1). These results suggest that the interaction between these hemoproteins is important in the regulation of the biosynthesis of eicosanoids.
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Affiliation(s)
- A. V. Svirid
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - P. V. Ershov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - E. O. Yablokov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - L. A. Kaluzhskiy
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - Yu. V. Mezentsev
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - A. V. Florinskaya
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - T. A. Sushko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan
| | - N. V. Strushkevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - A. A. Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - S. A. Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - A. E. Medvedev
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - A. S. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
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Ivanov AS, Ershov PV, Molnar AA, Mezentsev YV, Kaluzhskiy LA, Yablokov EO, Florinskaya AV, Gnedenko OV, Medvedev AE, Kozin SA, Mitkevich VA, Makarov AA, Gilep AA, Luschik AY, Gaidukevich IV, Usanov SA. Direct molecular fishing in molecular partners investigation in protein–protein and protein–peptide interactions. Russ J Bioorg Chem 2016. [DOI: 10.1134/s1068162016010052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ivanov AS, Medvedev AE, Buneeva OA, Gnedenko OV, Ershov PV, Mezencev YV, Yablokov EO, Kaluzhsky LA, Florinskaya AV, Moskaleva NE, Zgoda VG. [Influence of gravity discharge on the content of isatin-binding proteins in mice: results of ground-based and space research under the program Bion-M №1]. Biomed Khim 2015; 61:632-5. [PMID: 26539872 DOI: 10.18097/pbmc20156105632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Isatin-binding activity of mice liver proteins has been investigated in the samples from the control and flight groups by using the methods of biosensor and proteomic analysis. It was found the higher isatin-binding activity in mice of flight group. The content of a number of individual isatin-binding proteins in the samples of the flight groups differ slightly from the ground control. However, in samples from animals which have weekly post-flight adaptation, the level of certain proteins was significantly increased. The latter allows us to assume that the main events in the proteome of mice (at least in subproteome of isatin-binding proteins), occurs in early post-flight period.
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Affiliation(s)
- A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A E Medvedev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - O A Buneeva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - O V Gnedenko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - P V Ershov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - Y V Mezencev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
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Gnedenko OV, Ivanov AS, Yablokov EO, Usanov SA, Mukha DV, Sergeev GV, Kuzikov AV, Bulko TV, Moskaleva NE, Shumyantseva VV, Archakov AI. [Protein-protein interactions of cytochromes P450 3A4 and 3A5 with their intermediate redox partners cytochromes b5]. Biomed Khim 2015; 61:468-73. [PMID: 26350737 DOI: 10.18097/pbmc20156104468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Molecular interactions between proteins redox partners (cytochromes Р450 3А4, 3А5 and cytochrome b5) within the monooxygenase system, which is known to be involved in drug biotransformation, were investigated. Human cytochromes Р450 3А4 and 3А5 (CYP3A4 and CYP3A5) form complexes with various cytochromes b5: the microsomal (b5mc) and mitochondrial (b5om) forms of this protein, as well as with 2 "chimeric" proteins, b5(om-mc), b5(mc-om). Kinetic constants and equilibrium dissociation constants were determined by the SPR biosensor. Essential distinction between CYP3A4 and CYP3A5 was only observed upon their interactions with cytochrome b5om. Electroanalytical characteristics of electrodes with immobilized hemoproteins were obtained. The electrochemical analysis of CYP3A4, CYP3A5, b5mc, b5om, b5(om-mc), and b5(mc-om) immobilized on screen printed graphite electrodes modified with membranous matrix revealed that these proteins have very close reduction potentials -0.435 -0.350 V (vs. Ag/AgCl). Cytochrome b5mc was shown to be capable of stimulating the electrocatalytic activity of CYP3A4 in the presence of its substrate testosterone.
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Affiliation(s)
- O V Gnedenko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A S Ivanov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E O Yablokov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S A Usanov
- Institute of Bioorganic Chemistry of NAS, Minsk, Belarus
| | - D V Mukha
- Institute of Bioorganic Chemistry of NAS, Minsk, Belarus
| | - G V Sergeev
- Institute of Bioorganic Chemistry of NAS, Minsk, Belarus
| | - A V Kuzikov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | | | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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Gnedenko OV, Ivanov AS, Yablokov EO, Usanov SA, Mukha DV, Sergeev GV, Kuzikov AV, Moskaleva NE, Bulko TV, Shumyantseva VV, Archakov AI. Protein-protein interactions in the systems of cytochromes P450 3A4 and 3A5. Biochem Moscow Suppl Ser B 2014. [DOI: 10.1134/s1990750814030068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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