Laboratory of biocatalysis
Laboratory of biocatalysis was founded in 1997. Two major projects developing in the Laboratory that became a continuation of the Professor Gabibov’s pioneering work.
The first group that maintained by Ivan Smirnov continues to study a classic "abzimology" but a qualitatively new level. It is looking for a balance between combinatorial methods and rational design to create proteins with predetermined properties de novo. Recently the group developes the microfluidic technologies for multi-parameter screening of biocatalysts clones and cells in general.
The second team maintained by Alexey Belogurov studying the molecular basis of autoimmune processes with an emphasis in autoimmune neurodegeneration. Basically, on the agenda is a chronic demyelinating disease of the central nervous system — multiple sclerosis, and also a neurodegeneration and peripheral nervous system — Guillain-Barré syndrome. The Laboratory developes screening technology, such as yeast, phage and lentiviral displays (Tatyana Bobik participates in this work).
Early significant advances in biotechnology have been achieved in the laboratory such as expression of proteins, for example, blood factors, antibodies in prokaryotic systems and in cell line CHO. A huge contribution to the study made by professor Natalia Ponomarenko.
The laboratory has a wide range of partners both at the Institute and beyond. In collaboration with the Laboratory of Proteomics researchers study multiple sclerosis and Guillain-Barre syndrome, they workes on the creation of immunotoxins with the Laboratory of Protein Engineering and the Laboratory of Molecular Immunology, also they conduct the study of ion channels in autoreactive lymphocytes together with the Molecular Instruments for Neurobiology Group.
In addition, the Laboratory cooperates with the European Molecular Biology Laboratory in Hamburg, the Institute of Physical-Chemical Medicine, the Center of Nanotechnology of Russian Academy of Sciences, the Institute of Chemical Biology and Fundamental Medicine of Russian Academy of Sciences, SRP "Bioclinicum" and A.N. Belozersky Institute of Physico-Chemical Biology Moscow State University. The Laboratory keeps a good relationship with several prominent figures such as Nobel laureates Aaron Ciechanover and Sidney Altman, a former president of the Scripps Research Institute, and a father of modern abzimology Richard Lerner etc.
Liquid drop of DNA libraries reveals total genome information
In collaboration with Laboratory of hormonal regulation proteins,  Laboratory of proteolytic enzyme chemistry,  Laboratory of bioinformatics approaches in combinatorial chemistry and biology
Researchers from the Laboratory of biocatalysis, Laboratory of proteolytic enzyme chemistry, Laboratory of bioinformatics approaches in combinatorial chemistry and biology, Laboratory of hormonal regulation proteins IBCh RAS together with their Russian and foreign colleagues showed that amplification of single DNA molecules encapsulated in a myriad of emulsion droplets (emulsion PCR, ePCR) allows the mitigation of this problem. Different ePCR regimes were experimentally analyzed to identify the most robust techniques for enhanced amplification of DNA libraries. A phenomenological mathematical model that forms an essential basis for optimal use of ePCR for library amplification was developed. A detailed description by high-throughput sequencing of amplified DNA-encoded libraries highlights the principal advantages of ePCR over bulk PCR. ePCR outperforms PCR, reduces gross DNA errors, and provides a more uniform distribution of the amplified sequences. The quasi single-molecule amplification achieved via ePCR represents the fundamental requirement in case of complex DNA templates being prone to diversity degeneration and provides a way to preserve the quality of DNA libraries.
- (2020). Liquid drop of DNA libraries reveals total genome information. Proc Natl Acad Sci U S A 117 (44), 27300–27306
Protective allele for multiple sclerosis HLA-DRB1*0101 provides kinetic discrimination of myelin and exogenous antigenic peptides
Risk of the development of multiple sclerosis (MS) is known to be increased in individuals bearing distinct class II human leukocyte antigen (HLA) variants, whereas some of them may have a protective effect. Here we analyzed distribution of a highly polymorphous HLA-DRB1 locus in more than one thousand relapsing-remitting MS patients and healthy individuals of Russian ethnicity. Carriage of HLA-DRB1*15 and HLA-DRB1*03 alleles was associated with MS risk, whereas carriage of HLA-DRB1*01 and HLA-DRB1*11 was found to be protective. Analysis of genotypes revealed the compensatory effect of risk and resistance alleles in trans. We have identified previously unknown MBP153-161 peptide located at the C-terminus of MBP protein and MBP90-98 peptide that bound to recombinant HLA-DRB1*01:01 protein with affinity comparable to that of classical antigenic peptide 306–318 from the hemagglutinin (HA) of the influenza virus demonstrating the ability of HLA-DRB1*01:01 to present newly identified MBP153-161 and MBP90-98 peptides. Measurements of kinetic parameters of MBP and HA peptides binding to HLA-DRB1*01:01 catalyzed by HLA-DM revealed a significantly lower rate of CLIP exchange for MBP153-161 and MBP90-98 peptides as opposed to HA peptide. Analysis of the binding of chimeric MBP-HA peptides demonstrated that the observed difference between MBP153-161, MBP90-98 and HA peptide epitopes is caused by the lack of anchor residues in the C-terminal part of the MBP peptides resulting in a moderate occupation of P6/7 and P9 pockets of HLA-DRB1*01:01 by MBP153-161 and MBP90-98 peptides in contrast to HA308-316 peptide. This leads to the P1 and P4 docking failure and rapid peptide dissociation and release of empty HLA-DM–HLA-DR complex. We would like to propose that protective properties of the HLA-DRB1*01 allele could be directly linked to the ability of HLA-DRB1*01:01 to kinetically discriminate between antigenic exogenous peptides and endogenous MBP derived peptides.
A personalised approach for treating T-cell malignancies
Efficient and specific removal of malignant cells is the ultimate goal of cancer therapy. The current rapid development of chimeric antigen receptor T cell (CAR-T cell or CART) therapy potentially provides high efficiency and allows long-term surveillance, which have greatly extended the frontier of leukemia treatment. We validated the idea of using CARTs as targeting agents and observed excellent continuous efficacy as well as specificity. Combining CDR3 targeting with the CART approach provides a solution for a substantial portion of patients with T cell leukemia and lymphoma, with supposedly minimized side effects. After validation of this strategy to eliminate pathological T cells ex vivo and in vivo, we envisage this approach as a generally useful alternative and supplement to the popular approach of common antigen targeting to treat T cell malignancies, especially considering its safety.
- (2019). Unique CDR3 epitope targeting by CAR-T cells is a viable approach for treating T-cell malignancies. Leukemia 33 (9), 2315–2319
Oral microbiome of Siberian bear as a source of new antibiotics c
A new pipeline for antibiotic discovery using microfluidic screening technologies has been proposed. The biosynthetic pathways of the new antibiotic amicoumacin has been discovered. Specific enzymes: kinase and phosphatase, responsible for the inactivation and activation of the antibiotic were found
- (2018). Ultrahigh-throughput functional profiling of microbiota communities. Proc Natl Acad Sci U S A 115 (38), 9551–9556
Personalized therapy of B-cell lymphomas
We report the development of a novel platform to significantly enhance the efficacy and safety of Follicular lymphoma treatment. Since lymphoma is a clonal malignancy of a diversity system every tumor has a different antibody on its cell surface. Combinatorial autocrine-based selection is used to rapidly identify specific ligands for these B cell receptors on the surface of FL tumor cells. The selected ligands are used in a CAR-T format for redirection of human CTLs. Science Advances 2018. Stepanov AV,...,Gabibov AG, Lerner RA
- (2018). Autocrine-based selection of ligands for personalized CAR-T therapy of lymphoma. Sci Adv 4 (11), eaau4580
Development of ultrahigh-throughput method for screening of catalytic activity. Validation.
In collaboration with Group of combinatorial methods for constructing biocatalysts
The research is aimed at the search and creation of catalytic biological antidotes. To find new catalytic antidotes based on butyrylcholinesterase, a panel of libraries of the active center of BuChE was created. The library of 284-288 loop was successfully used to validate the method of ultrahigh-throughput screening of biocatalytic activity in droplets of a microfluidic emulsion. The obtained results, together with the developed quantum-mechanical algorithm for calculating the dephosphorylation step of covalent BChE-paraoxon complex, made it possible to create an optimized library for the BChE RKH-4 yeast display, representing 1 * 10 ^ 6 variants.
- (2017). Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity. Proc Natl Acad Sci U S A 114 (10), 2550–2555
Generation of enantioselective bioscavengers based on antibodies.
In collaboration with Group of combinatorial methods for constructing biocatalysts
In the framework of the study of catalytic antidotes based on antibodies, an algorithm for predicting mutants capable of selectively interacting with (R) and (S) isomers of PCT was proposed.
- (2017). Evolution of catalytic centers of antibodies by virtual screening of broad repertoire of mutants using supercomputer. Dokl Biochem Biophys 475 (1), 245–249