Alexis S Ivanov

Publications (10)16.47 Total impact

• Article: Highly sensitive detection of human cardiac myoglobin using a reverse sandwich immunoassay with a gold nanoparticle-enhanced surface plasmon resonance biosensor.

  Oksana V Gnedenko, Yury V Mezentsev, Andrey A Molnar, Andrey V Lisitsa, Alexis S Ivanov, Alexander I Archakov
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  ABSTRACT: A highly sensitive reverse sandwich immunoassay for the detection of human cardiac myoglobin (cMb) in serum was designed utilizing a gold nanoparticle (AuNP)-enhanced surface plasmon resonance (SPR) biosensor. First, a monoclonal anti-cMb antibody (Mab1) was covalently immobilized on the sensor surface. AuNPs were covalently conjugated to the second monoclonal anti-cMb antibody (Mab2) to form an immuno-gold reagent (Mab2-AuNP). The reverse sandwich immunoassay consists of two steps: (1) mixing the serum sample with Mab2-AuNP and incubation for the formation of cMb/Mab2-AuNP complexes and (2) sample injection over the sensor surface and evaluation of the Mab1/cMb/Mab2-AuNP complex formation, with the subsequent calculation of the cMb concentration in the serum. The biosensor signal was amplified approximately 30-fold compared with the direct reaction of cMb with Mab1 on the sensor surface. The limit of detection of cMb in a human blood serum sample was found to be as low as 10pM (approx. 0.18ngmL(-1)), and the inter-assay coefficient of variation was less than 3%. Thus, the developed SPR-based reverse sandwich immunoassay has a sensitivity that is sufficient to measure cMb across a wide range of normal and pathological concentrations, allowing an adequate estimation of the disease severity and the monitoring of treatment.
  Analytica chimica acta 01/2013; 759C:105-109. · 4.31 Impact Factor
• Article: Combinatorial antibody library from multiple sclerosis patients reveals antibodies that cross-react with myelin basic protein and EBV antigen.

  Alexander G Gabibov, Alexey A Belogurov, Yakov A Lomakin, Maria Yu Zakharova, Marat E Avakyan, Viktorya V Dubrovskaya, Ivan V Smirnov, Alexis S Ivanov, Andrey A Molnar, Vladimir E Gurtsevitch, Sergey V Diduk, Ksenia V Smirnova, Bérangère Avalle, Svetlana N Sharanova, Alfonso Tramontano, Alain Friboulet, Alexey N Boyko, Natalia A Ponomarenko, Nina V Tikunova
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  ABSTRACT: Multiple sclerosis (MS) is a widespread neurodegenerative autoimmune disease with unknown etiology. It is increasingly evident that, together with pathogenic T cells, autoreactive B cells are among the major players in MS development. The analysis of myelin neuroantigen-specific antibody repertoires and their possible cross-reactivity against environmental antigens, including viral proteins, could shed light on the mechanism of MS induction and progression. A phage display library of single-chain variable fragments (scFvs) was constructed from blood lymphocytes of patients with MS as a potential source of representative MS autoantibodies. Structural alignment of 13 clones selected toward myelin basic protein (MBP), one of the major myelin antigens, showed high homology within variable regions with cerebrospinal fluid MS-associated antibodies as well as with antibodies toward Epstein-Barr latent membrane protein 1 (LMP1). Three scFv clones showed pronounced specificity to MBP fragments 65-92 and 130-156, similar to the serum MS antibodies. One of these clones, designated E2, in both scFv and full-size human antibody constructs, was shown to react with both MBP and LMP1 proteins in vitro, suggesting natural cross-reactivity. Thus, antibodies induced against LMP1 during Epstein-Barr virus infection might act as inflammatory trigger by reacting with MBP, suggesting molecular mimicry in the mechanism of MS pathogenesis.
  The FASEB Journal 08/2011; 25(12):4211-21. · 5.71 Impact Factor
• Article: FMN binding site of yeast NADPH-cytochrome P450 reductase exposed at the surface is highly specific.

  Alexis S Ivanov, Oksana V Gnedenko, Andrey A Molnar, Alexander I Archakov, Larissa M Podust
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  ABSTRACT: NADPH-cytochrome P450 reductase (CPR) transfers two reducing equivalents derived from NADPH via FAD and FMN to microsomal P450 monooxygenases in one-electron transfer steps. The crystal structure of yeast CPR (yCPR) contains a surface-exposed FMN binding site (FMN2 site) at the interface of the FMN binding and connecting domains, in addition to the single buried site that has been observed in rat CPR. This finding provides a testable hypothesis of how intramolecular (between FAD and FMN) and intermolecular (between FMN and P450) electron transfer may occur in CPR. To verify that occupancy of the FMN2 site is not an artifact of crystallization, a surface plasmon resonance (SPR) biosensor technique has been applied to probe the selectivity of this site under functional conditions. A series of kinetic and equilibrium binding experiments involving yCPR immobilized on different sensor chip surfaces was performed using FMN and FAD, as well as FMN-derived compounds, including riboflavin, dimethylalloxazine, and alloxazine, and other molecules that resemble the planar isoalloxazine ring structure. Only FMN and FAD showed stoichiometric binding responses. Binding affinity for FMN was in the submicromolar range, 30 times higher than that for FAD. Association kinetic rates for the yCPR/FMN complex were up to 60-fold higher than for the yCPR/FAD complex. Taken together, these data indicate that (i) the surface-exposed site in yCPR is highly selective toward binding flavins, (ii) binding of FMN in this site is notably favored, and finally, (iii) both the phosphate group and the isoalloxazine ring of FMN are essential for binding.
  ACS Chemical Biology 08/2010; 5(8):767-76. · 6.45 Impact Factor
• Chapter: Bioinformatics Platform Development

  Alexis S. Ivanov, Alexander V. Veselovsky, Alexander V. Dubanov, Vladlen S. Skvortsov
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  ABSTRACT: In the past 10 yr, the field of bioinformatics has been characterized by the mapping of many genomes. These efforts have stimulated explosive development of novel bioinformatics and experimental approaches to predict the functions and metabolic role of the new proteins. The main application of the work is to search, validate, and prioritize new targets for designing a new generation of drugs. Modern computer and experimental methods for discovery of new lead compounds have also expanded and integrated into the process referred to as rational drug design. They are directed to accelerate and optimize the drug discovery process using experimental and virtual (computer-aided drug discovery) methods. Recently, these methods and approaches have merged into a “from gene to lead” platform that includes the processes from new target discovery through obtaining highly effective lead compounds. This chapter describes the strategies as employed by the “From Gene to Lead” platform, including the major computer and experimental approaches and their interrelationship. The latter part of the chapter contains some examples of the steps required for implementing this platform. Key WordsRational drug design–bioinformatics–lead compound–computer-aided drug discovery–target discovery–database mining–target validation–structure-based drug design–ligand-based drug design– de novo design
  02/2008: pages 389-431;
• Article: Protein-protein interactions as new targets for drug design: virtual and experimental approaches.

  Alexis S Ivanov, Oksana V Gnedenko, Andrey A Molnar, Yury V Mezentsev, Andrey V Lisitsa, Alexander I Archakov
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  ABSTRACT: Protein-protein and protein-ligand interactions play a central role in biochemical reactions, and understanding these processes is an important task in different fields of biomedical science and drug discovery. Proteins often work in complex assemblies of several macromolecules and small ligands. The structural and functional description of protein-protein interactions (PPI) is very important for basic-, as well as applied research. The interface areas of protein complexes have unique structure and properties, so PPI represent prospective targets for a new generation of drugs. One of the key targets of PPI inhibitors are oligomeric enzymes. This report shows interactive links between virtual and experimental approaches in a total pipeline "from gene to drug" and using Surface Plasmon Resonance technology for experimentally assessing PPI. Our research is conducted on two oligomeric enzymes -- HIV-1 protease (HIVp) (homo-dimer) and bacterial L-asparaginase (homo-tetramer). Using methods of molecular modeling and computational alanine scanning we obtained structural and functional description of PPI in these two enzymes. We also presented a real example of application of integral approach in searching inhibitors of HIVp dimerization -- from virtual database mining up to experimental testing of lead compounds.
  Journal of Bioinformatics and Computational Biology 05/2007; 5(2B):579-92.
• Article: Bioinformatics platform development: from gene to lead compound.

  Alexis S Ivanov, Alexander V Veselovsky, Alexander V Dubanov, Vladlen S Skvortsov
  [show abstract] [hide abstract]
  ABSTRACT: In the past 10 yr, the field of bioinformatics has been characterized by the mapping of many genomes. These efforts have stimulated explosive development of novel bioinformatics and experimental approaches to predict the functions and metabolic role of the new proteins. The main application of the work is to search, validate, and prioritize new targets for designing a new generation of drugs. Modern computer and experimental methods for discovery of new lead compounds have also expanded and integrated into the process referred to as rational drug design. They are directed to accelerate and optimize the drug discovery process using experimental and virtual (computer-aided drug discovery) methods. Recently, these methods and approaches have merged into a "from gene to lead" platform that includes the processes from new target discovery through obtaining highly effective lead compounds. This chapter describes the strategies as employed by the "From Gene to Lead" platform, including the major computer and experimental approaches and their interrelationship. The latter part of the chapter contains some examples of the steps required for implementing this platform.
  Methods in molecular biology (Clifton, N.J.) 02/2006; 316:389-431.
• Article: Computer visualisation of the active site of monoamine oxidase-A by means of selective inhibitors.

  Alexei E Medvedev, Alexis S Ivanov, Alexander V Veselovsky
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  ABSTRACT: Computer visualisation of the active site of monoamine oxidase (MAO) is based on an assumption that the specific and reversible interaction of a ligand (substrate or inhibitor) with the substrate-binding region of the active site requires shape complementarity. The size of the ligand must allow its accommodation at the substrate-binding region. Analysis of the MAO-inhibitory activity of rigid analogues of isatin and pirlindole revealed a dependence between three-dimensional linear sizes of these molecules and the efficacy of inhibition of both MAO-A and MAO-B. However, flexible molecules did not exhibit any dependence between linear sizes and MAO-B inhibitory potency, possibly because they folded into compact structures could fit into the substrate-binding pocket of MAO-B. 'Moulding' of the substrate/inhibitor binding region by superposition of effective MAO-A inhibitors from various groups of chemicals allowed the shape of substrate/inhibitor binding region to be visualised. 'Removal of contents' from this mould yielded a cavity, which corresponded to the shape of substrate/inhibitor binding region. Such cavity can be used to evaluate the most probable positions known inhibitors take in binding to it. The docking procedure can also be used for searching molecular databases for new inhibitors. Pilot experiments revealed that relatively rigid compounds, which did not fit to this cavity, were poor inhibitors of MAO-A.
  Inflammopharmacology 02/2003; 11(2):135-43.
• Article: ONIX: an interactive PC program for the examination of protein 3D structure from PDB.

  Alexis S. Ivanov, Andrey B. Rumjantsev, Vladlen S. Skvortsov, Alexander I. Archakov
  Computer Applications in the Biosciences. 01/1997; 13:111-113.
• Article: QSAR Analysis of Indole Analogues as Monoamine Oxidase Inhibitors.

  A. E. Medvedev, Alexis S. Ivanov, A. V. Veselovsky, Vladlen S. Skvortsov, Alexander I. Archakov
  Journal of Chemical Information and Computer Sciences. 01/1996; 36:664-671.
• Article: Education Program for Macromolecules Structure Examination.

  Alexis S. Ivanov, Andrey B. Rumjantsev, Vladlen S. Skvortsov, Alexander I. Archakov
  Journal of Chemical Information and Computer Sciences. 01/1996; 36:660-663.