1
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Gushchina IV, Nilov DK, Shcherbakova TA, Baldin SM, Švedas VK. Search for Inhibitors of Mycobacterium tuberculosis Transketolase in a Series of Sulfo-Substituted Compounds. Acta Naturae 2023; 15:81-83. [PMID: 37538800 PMCID: PMC10395774 DOI: 10.32607/actanaturae.15709] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/12/2023] [Indexed: 08/05/2023] Open
Abstract
As a result of the computer screening of a library of sulfo-substituted compounds, molecules capable of binding to the active site of transketolase from Mycobacterium tuberculosis were identified. An experimental verification of the inhibitory activity of the most promising compound, STK045765, against a highly purified recombinant enzyme preparation was carried out. It was shown that the STK045765 molecule competes for the binding site of the pyrophosphate group of the thiamine diphosphate cofactor and, at a micromolar concentrations, is able to suppress the activity of mycobacterial transketolase. The discovered furansulfonate scaffold may serve as the basis for the creation of anti-tuberculosis drugs.
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Affiliation(s)
- I. V. Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234 Russian Federation
| | - D. K. Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
| | - T. A. Shcherbakova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
| | - S. M. Baldin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
| | - V. K. Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234 Russian Federation
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
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2
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Morozova IA, Guranda DT, Panin NV, Švedas VK. Specificity of Penicillin Acylases in Deprotection of N-Benzyloxycarbonyl Derivatives of Amino Acids. Acta Naturae 2023; 15:69-73. [PMID: 37153508 PMCID: PMC10154775 DOI: 10.32607/actanaturae.13703] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/16/2023] [Indexed: 05/09/2023] Open
Abstract
Changes in the structure of the N-acyl group in N-acylated amino acid derivatives significantly affect both the recognition and activity of penicillin acylases on this series of substrates. However, penicillin acylases from both Alcaligenes faecalis and Escherichia coli are capable of removing the N-benzyloxycarbonyl protecting group in amino acid derivatives under mild conditions without the use of toxic reagents. Efficiency in using penicillin acylases in preparative organic synthesis can be improved by utilizing modern rational enzyme design methods.
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Affiliation(s)
- I. A. Morozova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
| | - D. T. Guranda
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
| | - N. V. Panin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
- Lomonosov Moscow State University, Research Computing Center, Moscow, 119234 Russian Federation
| | - V. K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119234 Russian Federation
- Lomonosov Moscow State University, Research Computing Center, Moscow, 119234 Russian Federation
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234 Russian Federation
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3
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Shcherbakova TA, Baldin SM, Shumkov MS, Gushchina IV, Nilov DK, Švedas VK. Isolation and Biochemical Characterization of Recombinant Transketolase from Mycobacterium tuberculosis. Acta Naturae 2022; 14:93-97. [PMID: 35923567 PMCID: PMC9307985 DOI: 10.32607/actanaturae.11713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/25/2022] [Indexed: 11/20/2022] Open
Abstract
Transketolase, an enzyme of the pentose phosphate pathway, plays an important
role in the functioning of mycobacteria. Using plasmid pET-19b carrying the
Rv1449c gene of transketolase from Mycobacterium
tuberculosis and an additional histidine tag, we isolated and purified
recombinant transketolase and determined the conditions for obtaining the
apoform of the protein. The Michaelis constants were evaluated for the thiamine
diphosphate cofactor in the presence of magnesium and calcium ions. We found
that the affinity of mycobacterial transketolase for thiamine diphosphate is by
three orders of magnitude lower than that of the human enzyme. Analysis of the
structural organization of the active centers of homologous enzymes showed that
this difference is due to a replacement of lysine residues by less polar amino
acid residues.
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Affiliation(s)
- T. A. Shcherbakova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
| | - S. M. Baldin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
| | - M. S. Shumkov
- Federal Research Centre «Fundamentals of Biotechnology», Russian Academy of Sciences, Moscow, 119071 Russia
| | - I. V. Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991 Russia
| | - D. K. Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
| | - V. K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Moscow, 119991 Russia
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991 Russia
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4
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Nilov DK, Pushkarev SV, Gushchina IV, Manasaryan GA, Kirsanov KI, Švedas VK. Modeling of the Enzyme-Substrate Complexes of Human Poly(ADP-Ribose) Polymerase 1. Biochemistry (Mosc) 2020; 85:99-107. [PMID: 32079521 DOI: 10.1134/s0006297920010095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Poly(ADP-ribose) polymerase 1 (PARP-1) is a key DNA repair enzyme and an important target in cancer treatment. Conventional methods of studying the reaction mechanism of PARP-1 have limitations because of the complex structure of PARP-1 substrates; however, the necessary data can be obtained by molecular modeling. In this work, a molecular dynamics model for the PARP-1 enzyme-substrate complex containing NAD+ molecule and the end of the poly(ADP-ribose) chain in the form of ADP molecule was obtained for the first time. Interactions with the active site residues have been characterized where Gly863, Lys903, Glu988 play a crucial role, and the SN1-like mechanism for the enzymatic ADP-ribosylation reaction has been proposed. Models of PARP-1 complexes with more sophisticated two-unit fragments of the growing polymer chain as well as competitive inhibitors 3-aminobenzamide and 7-methylguanine have been obtained by molecular docking.
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Affiliation(s)
- D K Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - S V Pushkarev
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - I V Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - G A Manasaryan
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Moscow, 119991, Russia
| | - K I Kirsanov
- Blokhin National Medical Research Center of Oncology, Institute of Carcinogenesis, Moscow, 115478, Russia
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia. .,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
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5
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Kirilin EM, Švedas VK. Analysis of Glycosyl-Enzyme Intermediate Formation in the Catalytic Mechanism of Influenza Virus Neuraminidase Using Molecular Modeling. Biochemistry (Mosc) 2020; 85:490-498. [PMID: 32569556 DOI: 10.1134/s0006297920040094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Using classical molecular dynamics, constant-pH molecular dynamics simulation, metadynamics, and combined quantum mechanical and molecular mechanical approach, we identified an alternative pathway of glycosyl-enzyme intermediate formation during oligosaccharide substrate conversion by the influenza H5N1 neuraminidase. The Asp151 residue located in the enzyme mobile loop plays a key role in catalysis within a wide pH range due to the formation of a network of interactions with water molecules. Considering that propagation of influenza virus takes place in the digestive tract of birds at low pH values and in the human respiratory tract at pH values close to neutral, the existence of alternative reaction pathways functioning at different medium pH can explain the dual tropism of the virus and circulation of H5N1 viral strains capable of transmission from birds to humans.
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Affiliation(s)
- E M Kirilin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
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6
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Podshivalov DD, Kirilin EM, Konnov SI, Švedas VK. Structural Organization and Dynamic Characteristics of the Binding Site for Conformational Rearrangement Inhibitors in Hemagglutinins from H3N2 and H7N9 Influenza Viruses. Biochemistry (Mosc) 2020; 85:499-506. [PMID: 32569557 DOI: 10.1134/s0006297920040100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 06/11/2023]
Abstract
Computer models of hemagglutinins from the H3N2 and H7N9 influenza viruses were developed to study structural organization and dynamic characteristics of the binding site for the conformational rearrangement inhibitors. The metadynamics was used to map the binding site free energy and to define the volume of its most energetically favorable states. It was demonstrated by simulation of the umifenovir (Arbidol) interaction with hemagglutinin that ligand binding requires an increase in the binding site volume and deformation of its most energetically favorable state. We also identified amino acid residues directly involved in the ligand binding that determine the binding efficiency, as well as the dynamic behavior of the binding site. The revealed features of the binding site structural organization of the influenza virus hemagglutinin should be taken into account when searching for new antiviral drugs capable to modulate its functional properties.
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Affiliation(s)
- D D Podshivalov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.
| | - E M Kirilin
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - S I Konnov
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia
| | - V K Švedas
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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7
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Panin NV, Nikulin MV, Tiurin ES, Drobot VV, Morozova IA, Švedas VK. Studying the Possibilities of Using 2-Halogen-Substituted Acetamides As Acyl Donors in Penicillin Acylase-Catalyzed Reactions. Acta Naturae 2019; 11:77-81. [PMID: 31413883 PMCID: PMC6643344 DOI: 10.32607/20758251-2019-11-2-77-81] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The possibility of using amides of halogen-substituted acetic acids as acyl
donors in penicillin acylase-catalyzed reactions has been investigated, and the
ability of this group of compounds to inactivate enzymes in the course of the
catalytic conversion has been established. The strongest inactivating effect
was demonstrated by iodoacetamide and bromoacetamide. However, the negative
contribution of this side activity can be minimized by decreasing the
temperature, when the rate of acyl donor conversion by penicillin acylases is
still high enough, but the impact of enzyme inactivation becomes less
significant. The catalytic activity of penicillin acylase from
Alcaligenes faecalis in the conversion of 2-haloacetamides was
significantly (5–8 times) higher than that of penicillin acylase from
Escherichia coli.
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Affiliation(s)
- N V Panin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia
| | - M V Nikulin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia.,Lomonosov Moscow State University, Department of Chemistry, Lenin Hills 1, bldg. 3, Moscow, 119991 , Russia
| | - E S Tiurin
- Lomonosov Moscow State University, Department of Chemistry, Lenin Hills 1, bldg. 3, Moscow, 119991 , Russia
| | - V V Drobot
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia.,Lomonosov Moscow State University, Department of Chemistry, Lenin Hills 1, bldg. 3, Moscow, 119991 , Russia
| | - I A Morozova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia.,Lomonosov Moscow State University, Department of Chemistry, Lenin Hills 1, bldg. 3, Moscow, 119991 , Russia
| | - V K Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Lenin Hills 1 , bldg. 40, Moscow, 119991, Russia
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8
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Akparov VK, Timofeev VI, Khaliullin IG, Konstantinova GE, Kuranova IP, Rakitina TV, Švedas VK. Mobile Loop in the Active Site of Metallocarboxypeptidases as an Underestimated Determinant of Substrate Specificity. Biochemistry (Mosc) 2019; 83:1594-1602. [PMID: 30878033 DOI: 10.1134/s0006297918120167] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
It is generally accepted that the primary specificity of metallocarboxypeptidases is mainly determined by the structure of the so-called primary specificity pocket. However, the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT) with the primary specificity pocket fully reproducing the one in pancreatic carboxypeptidase B (CPB) retained the broad, mainly hydrophobic substrate specificity of the wild-type enzyme. In order to elucidate factors affecting substrate specificity of metallocarboxypeptidases and the reasons for the discrepancy with the established views, we have solved the structure of the complex of the CPT G215S/A251G/T257A/D260G/T262D mutant with the transition state analogue N-sulfamoyl-L-phenylalanine at a resolution of 1.35 Å and compared it with the structure of similar complex formed by CPB. The comparative study revealed a previously underestimated structural determinant of the substrate specificity of metallocarboxypeptidases and showed that even if substitution of five amino acid residues in the primary specificity pocket results in its almost complete structural correspondence to the analogous pocket in CPB, this does not lead to fundamental changes in the substrate specificity of the mutant enzyme due to the differences in the structure of the mobile loop located at the active site entrance that affects the substrate-induced conformational rearrangements of the active site.
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Affiliation(s)
- V Kh Akparov
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia.
| | - V I Timofeev
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Center, Russian Academy of Sciences, Moscow, 119333, Russia. .,Kurchatov Institute National Research Center, Moscow, 123098, Russia
| | - I G Khaliullin
- Laboratory of Ion and Molecular Physics, Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700, Russia.
| | - G E Konstantinova
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, 117545, Russia
| | - I P Kuranova
- Shubnikov Institute of Crystallography, Crystallography and Photonics Federal Scientific Research Center, Russian Academy of Sciences, Moscow, 119333, Russia. .,Kurchatov Institute National Research Center, Moscow, 123098, Russia
| | - T V Rakitina
- Kurchatov Institute National Research Center, Moscow, 123098, Russia. .,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Laboratory of Hormonal Regulation Proteins, Russian Academy of Sciences, Moscow, 117997, Russia
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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9
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Baldin SM, Shcherbakova TA, Švedas VK. Isolation, Purification and Characterization of L,D-transpeptidase 2 from Mycobacterium tuberculosis. Acta Naturae 2019. [DOI: 10.32607/20758251-2019-11-1-23-28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
L,D-transpeptidase 2 from Mycobacterium tuberculosis plays a key role in the formation of nonclassical 3-3 peptidoglycan cross-links in a pathogens cell wall making it resistant to a broad range of penicillin antibiotics. The conditions of cultivation, isolation, and purification of recombinant L,D-transpeptidase 2 from M. tuberculosis have been optimized in this study. Oxidation of the free SH groups of catalytic cysteine Cys354 is an important factor causing the inactivation of the enzyme, which occurs during both the expression and storage of enzyme preparations. The biochemical characteristics of purified L,D-transpeptidase 2 and L,D-transpeptidase 2 lacking domain A were determined; the kinetic constants of enzyme-catalyzed nitrocefin transformation were evaluated.
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10
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Schmalhausen EV, Shumkov MS, Muronetz VI, Švedas VK. Expression of glyceraldehyde-3-phosphate dehydrogenase from M. tuberculosis in E. coli. Purification and characteristics of the untagged recombinant enzyme. Protein Expr Purif 2019; 157:28-35. [PMID: 30710621 DOI: 10.1016/j.pep.2019.01.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/18/2019] [Accepted: 01/27/2019] [Indexed: 02/01/2023]
Abstract
The goal of the present work was to produce glyceraldehyde-3-phospate dehydrogenase from M. tuberculosis in E. coli cells in soluble and catalytically active form and to elaborate a method for the purification of the recombinant enzyme. The His-tagged recombinant enzyme (Mtb-GAPDH_His) was shown to be inactive and insoluble. The untagged enzyme (Mtb-GAPDH) was catalytically active and exhibited higher solubility. Mtb-GAPDH was purified from the cell extract using ammonium sulfate fractionation and ion-exchange chromatography. The presence of glycerol was necessary for isolation of Mtb-GAPDH, presumably, to facilitate folding of the recombinant enzyme. The yield of Mtb-GAPDH constituted 1.3 mg per 10 g of the cell biomass. The specific activity of the purified Mtb-GAPDH was 55 ± 5 μmol NADH/min per mg protein (pH 9.0, 22 °C) that exceeded the activity of the previously described preparation of His-tagged recombinant GAPDH from M. tuberculosis that was co-expressed with GroEL/ES chaperone by approximately 5-fold. The results suggest that the folding of the recombinant GAPDH is hindered by the His-tag, which may result in the production of insoluble protein or in isolation of the preparation with decreased specific activity.
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Affiliation(s)
- E V Schmalhausen
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Lenin's Hills 1 Bldg.40, Moscow, 119234, Russian Federation.
| | - M S Shumkov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Prospect, 33, Build. 2, Moscow, 119071, Russian Federation
| | - V I Muronetz
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Lenin's Hills 1 Bldg.40, Moscow, 119234, Russian Federation
| | - V K Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Lenin's Hills 1 Bldg.40, Moscow, 119234, Russian Federation
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11
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Baldin SM, Shcherbakova TA, Švedas VK. Isolation, Purification and Characterization of L,D-transpeptidase 2 from Mycobacterium tuberculosis. Acta Naturae 2019; 11:23-28. [PMID: 31024745 PMCID: PMC6475871] [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] [Indexed: 11/03/2022] Open
Abstract
L,D-transpeptidase 2 from Mycobacterium tuberculosis plays a key role in the formation of nonclassical 3-3 peptidoglycan cross-links in a pathogen's cell wall making it resistant to a broad range of penicillin antibiotics. The conditions of cultivation, isolation, and purification of recombinant L,D-transpeptidase 2 from M. tuberculosis have been optimized in this study. Oxidation of the free SH groups of catalytic cysteine Cys354 is an important factor causing the inactivation of the enzyme, which occurs during both the expression and storage of enzyme preparations. The biochemical characteristics of purified L,D-transpeptidase 2 and L,D-transpeptidase 2 lacking domain A were determined; the kinetic constants of enzyme-catalyzed nitrocefin transformation were evaluated.
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Affiliation(s)
- S. M. Baldin
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie gory 1, bldg. 40, 119991, Moscow, Russia ,Lomonosov Moscow State University, Faculty of Chemistry, Leninskie gory 1, bldg. 3, 119991, Moscow, Russia
| | - T. A. Shcherbakova
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie gory 1, bldg. 40, 119991, Moscow, Russia
| | - V. K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie gory 1, bldg. 40, 119991, Moscow, Russia
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12
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Sharapova YA, Švedas VK. Molecular Modeling of the Binding of the Allosteric Inhibitor Optactin at a New Binding Site in Neuraminidase A from Streptococcus pneumoniae. ACTA ACUST UNITED AC 2018. [DOI: 10.3103/s0027131418050097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Nilov DK, Yashina KI, Gushchina IV, Zakharenko AL, Sukhanova MV, Lavrik OI, Švedas VK. 2,5-Diketopiperazines: A New Class of Poly(ADP-ribose)polymerase Inhibitors. Biochemistry Moscow 2018; 83:152-158. [DOI: 10.1134/s0006297918020074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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14
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Gushchina IV, Nilov DK, Zakharenko AL, Lavrik OI, Švedas VK. Structure Modeling of Human TyrosylDNA Phosphodiesterase 1 and Screening for Its Inhibitors. Acta Naturae 2017. [DOI: 10.32607/20758251-2017-9-2-59-66] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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
The DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (Tdp1) represents a potential molecular target for anticancer therapy. A human Tdp1 model has been constructed using the methods of quantum and molecular mechanics, taking into account the ionization states of the amino acid residues in the active site and their interactions with the substrate and competitive inhibitors. The oligonucleotide- and phosphotyrosine-binding cavities important for the inhibitor design have been identified in the enzymes active site. The developed molecular model allowed us to uncover new Tdp1 inhibitors whose sulfo group is capable of occupying the position of the 3-phosphate group of the substrate and forming hydrogen bonds with Lys265, Lys495, and other amino acid residues in the phosphotyrosine binding site.
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15
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Baldin SM, Misiura NM, Švedas VK. Building a Full-Atom Model of L,Dtranspeptidase 2 from Mycobacterium tuberculosis for Screening New Inhibitors. Acta Naturae 2017. [DOI: 10.32607/20758251-2017-9-1-44-51] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [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
L,D-transpeptidase 2 from Mycobacterium tuberculosis plays a key role in the formation of the cell wall of a pathogen and catalyzes the cross-linking of growing peptidoglycan chains by non-classical 3-3 bonds, which causes resistance to a broad spectrum of penicillins. Molecular modeling of enzyme interactions with the N- and C-terminal tetrapeptide fragments of growing peptidoglycan chains has been performed for the first time and has allowed us to highlight the peculiarities of their binding at the formation of 3-3 cross-linkages, as well as to build a full-atom model of L,D-transpeptidase 2 for the screening and optimizing of inhibitors structures.
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16
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Nilov DK, Kulikov AV, Prokhorova EA, Švedas VK. Identification of New Structural Fragments for the Design of Lactate Dehydrogenase A Inhibitors. Acta Naturae 2016. [DOI: 10.32607/20758251-2016-8-3-118-122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
Human lactate dehydrogenase A plays an important role in the glucose metabolism of tumor cells and constitutes an attractive target for chemotherapy. Molecular fragments able to bind in the active site of this enzyme and form hydrogen bonds with the Arg168 guanidinium group, as well as additional interactions with the loop 96-111 in the closed conformation, have been identified by virtual screening of sulfonates and experimental testing of their inhibitory effect. The sulfo group can occupy a similar position as the carboxyl group of the substrate and its structural analogs, whereas the benzothiazole group attached via a linker can be located in the coenzyme (NADH) binding site. Thus, the value of merging individual structural elements of the inhibitor by a linker was demonstrated and ways of further structural modification for the design of more effective inhibitors of lactate dehydrogenase A were established.
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Nilov DK, Tararov VI, Kulikov AV, Zakharenko AL, Gushchina IV, Mikhailov SN, Lavrik OI, Švedas VK. Inhibition of Poly(ADP-Ribose) Polymerase by Nucleic Acid Metabolite 7-Methylguanine. Acta Naturae 2016. [DOI: 10.32607/20758251-2016-8-2-108-115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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
The ability of 7-methylguanine, a nucleic acid metabolite, to inhibit poly (ADP-ribose) polymerase-1 (PARP-1) and poly(ADP-ribose)polymerase-2 (PARP-2) has been identified in silico and studied experimentally.The amino group at position 2 and the methyl group at position 7 were shown to be important substituents for the efficient binding of purine derivatives to PARPs. The activity of both tested enzymes, PARP-1 and PARP-2, was suppressed by 7-methylguanine with IC50 values of 150 and 50 M, respectively. At the PARP inhibitory concentration, 7-methylguanine itself was not cytotoxic, but it was able to accelerate apoptotic death of BRCA1-deficient breast cancer cells induced by cisplatin and doxorubicin, the widely used DNA-damaging chemotherapeutic agents. 7-Methylguanine possesses attractive predictable pharmacokinetics and an adverse-effect profile and may be considered as a new additive to chemotherapeutic treatment.
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Nilov DK, Tararov VI, Kulikov AV, Zakharenko AL, Gushchina IV, Mikhailov SN, Lavrik OI, Švedas VK. Inhibition of Poly(ADP-Ribose) Polymerase by Nucleic Acid Metabolite 7-Methylguanine. Acta Naturae 2016; 8:108-15. [PMID: 27437145 PMCID: PMC4947994] [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: 12/01/2015] [Indexed: 11/30/2022] Open
Abstract
The ability of 7-methylguanine, a nucleic acid metabolite, to inhibit poly(ADP-ribose)polymerase-1 (PARP-1) and poly(ADP-ribose)polymerase-2 (PARP-2) has been identified in silico and studied experimentally. The amino group at position 2 and the methyl group at position 7 were shown to be important substituents for the efficient binding of purine derivatives to PARPs. The activity of both tested enzymes, PARP-1 and PARP-2, was suppressed by 7-methylguanine with IC50 values of 150 and 50 μM, respectively. At the PARP inhibitory concentration, 7-methylguanine itself was not cytotoxic, but it was able to accelerate apoptotic death of BRCA1-deficient breast cancer cells induced by cisplatin and doxorubicin, the widely used DNA-damaging chemotherapeutic agents. 7-Methylguanine possesses attractive predictable pharmacokinetics and an adverse-effect profile and may be considered as a new additive to chemotherapeutic treatment.
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Affiliation(s)
- D. K. Nilov
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie Gory 1, bldg. 40, Moscow, 119991, Russia
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Leninskie Gory 1, bldg. 73, Moscow, 119991, Russia
| | - V. I. Tararov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991 , Russia
| | - A. V. Kulikov
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Lomonosovsky avenue 31 -5, Moscow, 119192, Russia
| | - A. L. Zakharenko
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Lavrentiev avenue 8, Novosibirsk, 630090, Russia
| | - I. V. Gushchina
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Leninskie Gory 1, bldg. 73, Moscow, 119991, Russia
| | - S. N. Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow, 119991 , Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Lavrentiev avenue 8, Novosibirsk, 630090, Russia
| | - V. K. Švedas
- Lomonosov Moscow State University, Belozersky Institute of Physicochemical Biology, Leninskie Gory 1, bldg. 40, Moscow, 119991, Russia
- Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Leninskie Gory 1, bldg. 73, Moscow, 119991, Russia
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Nilov DK, Prokhorova EA, Švedas VK. Search for Human Lactate Dehydrogenase A Inhibitors Using Structure-Based Modeling. Acta Naturae 2015; 7:57-63. [PMID: 26085945 PMCID: PMC4463413] [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] [Indexed: 11/13/2022] Open
Abstract
The human lactate dehydrogenase isoform A plays an important role in the anaerobic metabolism of tumour cells and therefore constitutes an attractive target in the oncology field. Full-atom models of lactate dehydrogenase A (in complex with NADH and in the apo form) have been generated to enable structure-based design of novel inhibitors competing with pyruvate and NADH. The structural criteria for the selection of potential inhibitors were established, and virtual screening of a library of low-molecular-weight compounds was performed. A potential inhibitor, STK381370, was identified whose docking pose was stabilized through additional interactions with the loop 96-111 providing for the transition from the open to the closed conformation.
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Affiliation(s)
- D. K. Nilov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, bldg. 40, 119991 Moscow, Russia,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, bldg. 73, 119991, Moscow, Russia
| | - E. A. Prokhorova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, bldg. 73, 119991, Moscow, Russia
| | - V. K. Švedas
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, bldg. 40, 119991 Moscow, Russia,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskie Gory 1, bldg. 73, 119991, Moscow, Russia
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Khaliullin IG, Nilov DK, Shapovalova IV, Švedas VK. Construction of a Full-Atomic Mechanistic Model of Human Apurinic/Apyrimidinic Endonuclease APE1 for Virtual Screening of Novel Inhibitors. Acta Naturae 2012. [DOI: 10.32607/actanaturae.10648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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
A full-atomic molecular model of human apurinic/apyrimidinic endonuclease APE1, an important enzyme in the DNA repair system, has been constructed. The research consisted of hybrid quantum mechanics/ molecular mechanics modeling of the enzyme-substrate interactions, as well as calculations of the ionization states of the amino acid residues of the active site of the enzyme. The choice of the APE1 mechanism with an Asp210 residue as a proton acceptor was validated by means of a generalization of modeling and experimental data. Interactions were revealed in the active site that are of greatest significance for binding the substrate and potential APE1 inhibitors (potential co-drugs of interest in the chemo- and radiotherapy of oncological diseases).
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Khaliullin IG, Nilov DK, Shapovalova IV, Švedas VK. Construction of a Full-Atomic Mechanistic Model of Human Apurinic/Apyrimidinic Endonuclease APE1 for Virtual Screening of Novel Inhibitors. Acta Naturae 2012. [DOI: 10.32607/20758251-2012-4-2-80-86] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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
A full-atomic molecular model of human apurinic/apyrimidinic endonuclease APE1, an important enzyme in the DNA repair system, has been constructed. The research consisted of hybrid quantum mechanics/ molecular mechanics modeling of the enzyme-substrate interactions, as well as calculations of the ionization states of the amino acid residues of the active site of the enzyme. The choice of the APE1 mechanism with an Asp210 residue as a proton acceptor was validated by means of a generalization of modeling and experimental data. Interactions were revealed in the active site that are of greatest significance for binding the substrate and potential APE1 inhibitors (potential co-drugs of interest in the chemo- and radiotherapy of oncological diseases).
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Romanova NN, Rybalko II, Tallo TG, Zyk NV, Švedas VK. Synthesis of Schiff bases from 3-amino-3-arylpropionic acid esters in aqueous medium. Russ J Org Chem 2012. [DOI: 10.1134/s107042801206019x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chilov GG, Stroganov OV, Švedas VK. Molecular modeling studies of substrate binding by penicillin acylase. Biochemistry Moscow 2011; 73:56-64. [DOI: 10.1134/s0006297908010082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Chernorizov KA, Švedas VK. Modeling of the Full-Size 3D Structure of Human Chaperone Hsp70 and Study of Its Interdomain Interactions. Acta Naturae 2010. [DOI: 10.32607/20758251-2010-2-4-66-71] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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Shapovalova IV, Alkema WBL, Jamskova OV, De Vries E, Guranda DT, Janssen DB, Švedas VK. Mutation of Residue βF71 of Escherichia coli Penicillin Acylase Results in Enhanced Enantioselectivity and Improved Catalytic Properties. Acta Naturae 2009. [DOI: 10.32607/actanaturae.10786] [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: 11/20/2022] Open
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Shapovalova IV, Alkema WBL, Jamskova OV, De Vries E, Guranda DT, Janssen DB, Švedas VK. Mutation of Residue βF71 of Escherichia coli Penicillin Acylase Results in Enhanced Enantioselectivity and Improved Catalytic Properties. Acta Naturae 2009. [DOI: 10.32607/20758251-2009-1-3-94-98] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [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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