Ivan Smirnov

Publications (3)15.68 Total impact

• Article: Strategies for the selection of catalytic antibodies against organophosphorus nerve agents.

  Ivan Smirnov, Alexey Belogurov, Alain Friboulet, Patrick Masson, Alexander Gabibov, Pierre-Yves Renard
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  ABSTRACT: Among the strategies aimed at biocompatible means for organophosphorus nerve agents neutralization, immunoglobulins have attracted attention in the 1990's and 2000's both for their ability to immobilize the toxicants, but also for their ability to be turned into enzymatically active antibodies known as catalytic antibodies or abzymes (antibodies - enzymes). We will present here a critical review of the successive strategies used for the selection of these nerve agent-hydrolyzing abzymes, based on hapten design, namely antibodies raised against a wide variety of transition state analogues, and eventually the strategies based on anti-idiotypic antibodies and reactibodies.
  Chemico-biological interactions 11/2012; · 2.46 Impact Factor
• Article: Antibody-antigen pair probed by combinatorial approach and rational design: bringing together structural insights, directed evolution, and novel functionality.

  Alexey Belogurov, Ivan Smirnov, Natalya Ponomarenko, Alexander Gabibov
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  ABSTRACT: The unique hypervariability of the immunoglobulin (Ig) superfamily provides a means to create both binding and catalytic antibodies with almost any desired specificity and activity. The diversity of antigens and concept of adaptive response suggest that it is possible to find an antigen pair to any raised Ig. In the current review we discuss combinatorial approaches, which makes it possible to obtain an antibody with predefined properties, followed by 3D structure-based rational design to enhance or dramatically change its characteristics. A similar strategy, but applied to the second partner of the antibody-antigen pair, may result in selection of complementary substrates to the chosen Ig. Finally, 2D screening may be performed solving the "Chicken and Egg" problem when neither antibody nor antigen is known.
  FEBS letters 07/2012; 586(18):2966-73. · 3.54 Impact Factor
• Source

  Available from: Alexey A Belogurov Jr.

  Article: Reactibodies generated by kinetic selection couple chemical reactivity with favorable protein dynamics.

  Ivan Smirnov, Eugénie Carletti, Inna Kurkova, Florian Nachon, Yvain Nicolet, Vladimir A Mitkevich, Hélène Débat, Bérangère Avalle, Alexey A Belogurov, Nikita Kuznetsov, Andrey Reshetnyak, Patrick Masson, Alexander G Tonevitsky, Natalia Ponomarenko, Alexander A Makarov, Alain Friboulet, Alfonso Tramontano, Alexander Gabibov
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  ABSTRACT: Igs offer a versatile template for combinatorial and rational design approaches to the de novo creation of catalytically active proteins. We have used a covalent capture selection strategy to identify biocatalysts from within a human semisynthetic antibody variable fragment library that uses a nucleophilic mechanism. Specific phosphonylation at a single tyrosine within the variable light-chain framework was confirmed in a recombinant IgG construct. High-resolution crystallographic structures of unmodified and phosphonylated Fabs display a 15-Å-deep two-chamber cavity at the interface of variable light (V(L)) and variable heavy (V(H)) fragments having a nucleophilic tyrosine at the base of the site. The depth and structure of the pocket are atypical of antibodies in general but can be compared qualitatively with the catalytic site of cholinesterases. A structurally disordered heavy chain complementary determining region 3 loop, constituting a wall of the cleft, is stabilized after covalent modification by hydrogen bonding to the phosphonate tropinol moiety. These features and presteady state kinetics analysis indicate that an induced fit mechanism operates in this reaction. Mutations of residues located in this stabilized loop do not interfere with direct contacts to the organophosphate ligand but can interrogate second shell interactions, because the H3 loop has a conformation adjusted for binding. Kinetic and thermodynamic parameters along with computational docking support the active site model, including plasticity and simple catalytic components. Although relatively uncomplicated, this catalytic machinery displays both stereo- and chemical selectivity. The organophosphate pesticide paraoxon is hydrolyzed by covalent catalysis with rate-limiting dephosphorylation. This reactibody is, therefore, a kinetically selected protein template that has enzyme-like catalytic attributes.
  Proceedings of the National Academy of Sciences 09/2011; 108(38):15954-9. · 9.68 Impact Factor