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Article ; Online: New anticoagulant protein from medicinal leech.

Manuvera, Valentin A / Kharlampieva, Daria D / Bobrovsky, Pavel A / Grafskaia, Ekaterina N / Brovina, Ksenia A / Lazarev, Vassili N

Biochemical and biophysical research communications

2024 Volume 696, Page(s) 149473

Abstract: The saliva of the medicinal leech contains various anticoagulants. Some of them, such as hirudin, are well known. However, it is reasonable to believe that not all anticoagulant proteins from medicinal leech saliva have been identified. We previously ... ...

Abstract	The saliva of the medicinal leech contains various anticoagulants. Some of them, such as hirudin, are well known. However, it is reasonable to believe that not all anticoagulant proteins from medicinal leech saliva have been identified. We previously performed a comprehensive study of the transcriptome, genome, and proteome of leech salivary gland cells, which led to the discovery of several previously unknown hypothetical proteins that may have anticoagulant properties. Subsequently, we obtained a series of recombinant proteins and investigated their impact on coagulation in in vitro assays. We identified a previously undescribed protein that exhibited a high ability to suppress coagulation. The His-tagged recombinant protein was expressed in Escherichia coli and purified using metal chelate chromatography. To determine its activity, commonly used coagulation methods were used: activated partial thromboplastin time, prothrombin time, and thrombin inhibition clotting assay. Clotting and chromogenic assays for factor Xa inhibition were performed to evaluate anti-Xa activity. We used recombinant hirudin as a control anticoagulant protein in all experiments. The new protein showed significantly greater inhibition of coagulation than hirudin at the same molar concentrations in the activated partial thrombin time assay. However, hirudin demonstrated better results in the direct thrombin inhibition test, although the tested protein also exhibited the ability to inhibit thrombin. The chromogenic analysis of factor Xa inhibition revealed no activity, whereas the clotting test for factor Xa showed the opposite result. Thus, a new powerful anticoagulant protein has been discovered in the medicinal leech. This protein is homologous to antistatin, with 28 % identical amino acid residues. The recombinant protein was expressed in E. coli. This protein is capable of directly inhibiting thrombin, and based on indirect evidence, other proteases of the blood coagulation cascade have been identified.
MeSH term(s)	Anticoagulants/pharmacology ; Hirudins/pharmacology ; Hirudins/genetics ; Hirudins/metabolism ; Thrombin/metabolism ; Factor Xa ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Recombinant Proteins/metabolism
Chemical Substances	Anticoagulants ; Hirudins ; Thrombin (EC 3.4.21.5) ; Factor Xa (EC 3.4.21.6) ; Recombinant Proteins
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2024.149473
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Article ; Online: Upregulation of YciM Expression Reduces Endotoxin Contamination of Recombinant Proteins Produced in Escherichia coli Cells.

Bobrovsky, Pavel A / Kharlampieva, Daria D / Kirillin, Sergey A / Brovina, Ksenia A / Grafskaia, Ekaterina N / Lazarev, Vassili N / Manuvera, Valentin A

Biochemistry. Biokhimiia

2023 Volume 88, Issue 9, Page(s) 1318–1325

Abstract: Recombinant proteins produced in Escherichia coli are often contaminated with endotoxins, which can be a serious problem for their further application. One of the possible solutions is the use of modified strains with reduced lipopolysaccharide (LPS) ... ...

Abstract	Recombinant proteins produced in Escherichia coli are often contaminated with endotoxins, which can be a serious problem for their further application. One of the possible solutions is the use of modified strains with reduced lipopolysaccharide (LPS) levels. We compared two approaches to engineering such strains. The first commonly known approach was modification of LPS biosynthesis pathway by knocking out seven genes in the E. coli genome. The second approach, which has not been previously used, was to increase expression of E. coli protein YciM. According to the published data, elevated expression of YciM leads to the reduction in the amount of the LpxC enzyme involved in LPS biosynthesis. We investigated the impact of YciM coexpression with eGFP on the content of endotoxins in the purified recombinant eGFP samples. Both approaches provided similar outcomes, i.e., decreased the endotoxin levels in the purified protein samples.
MeSH term(s)	Escherichia coli/metabolism ; Lipopolysaccharides/metabolism ; Up-Regulation ; Endotoxins/genetics ; Endotoxins/metabolism ; Escherichia coli Proteins/metabolism ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Membrane Proteins/metabolism
Chemical Substances	Lipopolysaccharides ; Endotoxins ; Escherichia coli Proteins ; Recombinant Proteins ; YciM protein, E coli ; Membrane Proteins
Language	English
Publishing date	2023-09-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1109-5
ISSN	1608-3040 ; 0006-2979 ; 0320-9717
ISSN (online)	1608-3040
ISSN	0006-2979 ; 0320-9717
DOI	10.1134/S0006297923090110
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Article ; Online: iPSC-derived cells lack immune tolerance to autologous NK-cells due to imbalance in ligands for activating and inhibitory NK-cell receptors.

Bogomiakova, Margarita E / Sekretova, Elizaveta K / Anufrieva, Ksenia S / Khabarova, Polina O / Kazakova, Anastasia N / Bobrovsky, Pavel A / Grigoryeva, Tatiana V / Eremeev, Artem V / Lebedeva, Olga S / Bogomazova, Alexandra N / Lagarkova, Maria A

Stem cell research & therapy

2023 Volume 14, Issue 1, Page(s) 77

Abstract: Background: Dozens of transplants generated from pluripotent stem cells are currently in clinical trials. The creation of patient-specific iPSCs makes personalized therapy possible due to their main advantage of immunotolerance. However, some reports ... ...

Abstract	Background: Dozens of transplants generated from pluripotent stem cells are currently in clinical trials. The creation of patient-specific iPSCs makes personalized therapy possible due to their main advantage of immunotolerance. However, some reports have claimed recently that aberrant gene expression followed by proteome alterations and neoantigen formation can result in iPSCs recognition by autologous T-cells. Meanwhile, the possibility of NK-cell activation has not been previously considered. This study focused on the comparison of autologous and allogeneic immune response to iPSC-derived cells and isogeneic parental somatic cells used for reprogramming. Methods: We established an isogeneic cell model consisting of parental dermal fibroblasts, fibroblast-like iPSC-derivatives (iPS-fibro) and iPS-fibro lacking beta-2-microglobulin (B2M). Using the cells obtained from two patients, we analyzed the activation of autologous and allogeneic T-lymphocytes and NK-cells co-cultured with target cells. Results: Here we report that cells differentiated from iPSCs can be recognized by NK-cells rather than by autologous T-cells. We observed that iPS-fibro elicited a high level of NK-cell degranulation and cytotoxicity, while isogeneic parental skin fibroblasts used to obtain iPSCs barely triggered an NK-cell response. iPSC-derivatives with B2M knockout did not cause an additional increase in NK-cell activation, although they were devoid of HLA-I, the major inhibitory molecules for NK-cells. Transcriptome analysis revealed a significant imbalance of ligands for activating and inhibitory NK-cell receptors in iPS-fibro. Compared to parental fibroblasts, iPSC-derivatives had a reduced expression of HLA-I simultaneously with an increased gene expression of major activating ligands, such as MICA, NECTIN2, and PVR. The lack of inhibitory signals might be due to insufficient maturity of cells differentiated from iPSCs. In addition, we showed that pretreatment of iPS-fibro with proinflammatory cytokine IFNγ restored the ligand imbalance, thereby reducing the degranulation and cytotoxicity of NK-cells. Conclusion: In summary, we showed that iPSC-derived cells can be sensitive to the cytotoxic potential of autologous NK-cells regardless of HLA-I status. Thus, the balance of ligands for NK-cell receptors should be considered prior to iPSC-based cell therapies. Trial registration Not applicable.
MeSH term(s)	Humans ; Induced Pluripotent Stem Cells/metabolism ; Receptors, Natural Killer Cell/metabolism ; Ligands ; Killer Cells, Natural ; Immune Tolerance
Chemical Substances	Receptors, Natural Killer Cell ; Ligands
Language	English
Publishing date	2023-04-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2548671-8
ISSN	1757-6512 ; 1757-6512
ISSN (online)	1757-6512
ISSN	1757-6512
DOI	10.1186/s13287-023-03308-5
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Article ; Online: Dual Adeno-Associated Virus 9 with Codon-Optimized DYSF Gene Promotes In Vivo Muscle Regeneration and May Decrease Inflammatory Response in Limb Girdle Muscular Dystrophy Type R2.

Yakovlev, Ivan A / Emelin, Aleksei M / Slesarenko, Yana S / Limaev, Igor S / Vetrova, Iuliia A / Belikova, Liliya D / Grafskaia, Ekaterina N / Bobrovsky, Pavel A / Pokrovsky, Mikhail V / Kuzubova, Elena V / Pokrovsky, Vladimir M / Lebedev, Pyotr A / Bardakov, Sergei N / Isaev, Artur A / Deev, Roman V

International journal of molecular sciences

2023 Volume 24, Issue 17

Abstract: Dysferlinopathy treatment is an active area of investigation. Gene therapy is one potential approach. We studied muscle regeneration and inflammatory response after injection of an AAV-9 with a codon-optimized DYSF gene. A dual-vector system AAV.DYSF ... ...

Abstract	Dysferlinopathy treatment is an active area of investigation. Gene therapy is one potential approach. We studied muscle regeneration and inflammatory response after injection of an AAV-9 with a codon-optimized DYSF gene. A dual-vector system AAV.DYSF.OVERLAP with overlapping DYSF cDNA sequences was generated. Two AAV vectors were separately assembled by a standard triple-transfection protocol from plasmids carrying parts of the DYSF gene. Artificial myoblasts from dysferlin-deficient fibroblasts were obtained by MyoD overexpression. RT-PCR and Western blot were used for RNA and protein detection in vitro. A dysferlinopathy murine model (Bla/J) was used for in vivo studies. Histological assay, morphometry, and IHC were used for the muscle tissue analysis. Dysferlin was detected in vitro and in vivo at subphysiological levels. RT-PCR and Western Blot detected dysferlin mRNA and protein in AAV.DYSF.OVERLAP-transduced cells, and mRNA reached a 7-fold elevated level compared to the reference gene (GAPDH). In vivo, the experimental group showed intermediate median values for the proportion of necrotic muscle fibers, muscle fibers with internalized nuclei, and cross-sectional area of muscle fibers compared to the same parameters in the control groups of WT and Bla/J mice, although the differences were not statistically significant. The inverse relationship between the dosage and the severity of inflammatory changes in the muscles may be attributed to the decrease in the number of necrotic fibers. The share of transduced myofibers reached almost 35% in the group with the highest dose. The use of two-vector systems based on AAV is justified in terms of therapeutic efficacy. The expression of dysferlin at a subphysiological level, within a short observation period, is capable of inducing the restoration of muscle tissue structure, reducing inflammatory activity, and mitigating necrotic processes. Further research is needed to provide a more detailed assessment of the impact of the transgene and viral vector on the inflammatory component, including longer observation periods.
MeSH term(s)	Animals ; Mice ; Dependovirus/genetics ; Dysferlin/genetics ; Muscular Dystrophies, Limb-Girdle/genetics ; Muscular Dystrophies, Limb-Girdle/therapy ; Codon ; Muscle Fibers, Skeletal ; RNA, Messenger
Chemical Substances	Dysferlin ; Codon ; RNA, Messenger
Language	English
Publishing date	2023-08-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms241713551
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Article ; Online: Structural insights into thrombolytic activity of destabilase from medicinal leech.

Marin, Egor / Kornilov, Daniil A / Bukhdruker, Sergey S / Aleksenko, Vladimir A / Manuvera, Valentin A / Zinovev, Egor V / Kovalev, Kirill V / Shevtsov, Mikhail B / Talyzina, Anna A / Bobrovsky, Pavel A / Kuzmichev, Pavel K / Mishin, Alexey V / Gushchin, Ivan Y / Lazarev, Vassili N / Borshchevskiy, Valentin I

Scientific reports

2023 Volume 13, Issue 1, Page(s) 6641

Abstract: Destabilase from the medical leech Hirudo medicinalis belongs to the family of i-type lysozymes. It has two different enzymatic activities: microbial cell walls destruction (muramidase activity), and dissolution of the stabilized fibrin (isopeptidase ... ...

Abstract	Destabilase from the medical leech Hirudo medicinalis belongs to the family of i-type lysozymes. It has two different enzymatic activities: microbial cell walls destruction (muramidase activity), and dissolution of the stabilized fibrin (isopeptidase activity). Both activities are known to be inhibited by sodium chloride at near physiological concentrations, but the structural basis remains unknown. Here we present two crystal structures of destabilase, including a 1.1 Å-resolution structure in complex with sodium ion. Our structures reveal the location of sodium ion between Glu34/Asp46 residues, which were previously recognized as a glycosidase active site. While sodium coordination with these amino acids may explain inhibition of the muramidase activity, its influence on previously suggested Ser49/Lys58 isopeptidase activity dyad is unclear. We revise the Ser49/Lys58 hypothesis and compare sequences of i-type lysozymes with confirmed destabilase activity. We suggest that the general base for the isopeptidase activity is His112 rather than Lys58. pKa calculations of these amino acids, assessed through the 1 μs molecular dynamics simulation, confirm the hypothesis. Our findings highlight the ambiguity of destabilase catalytic residues identification and build foundations for further research of structure-activity relationship of isopeptidase activity as well as structure-based protein design for potential anticoagulant drug development.
MeSH term(s)	Animals ; Hirudo medicinalis/chemistry ; Muramidase/chemistry ; Endopeptidases/metabolism ; Leeches/metabolism ; Fibrinolytic Agents/therapeutic use
Chemical Substances	fibrin destabilase (EC 3.4.99.-) ; Muramidase (EC 3.2.1.17) ; Endopeptidases (EC 3.4.-) ; Fibrinolytic Agents
Language	English
Publishing date	2023-04-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-32459-x
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Article ; Online: Discovery of novel antimicrobial peptides: A transcriptomic study of the sea anemone Cnidopus japonicus.

Grafskaia, Ekaterina N / Polina, Nadezhda F / Babenko, Vladislav V / Kharlampieva, Daria D / Bobrovsky, Pavel A / Manuvera, Valentin A / Farafonova, Tatyana E / Anikanov, Nikolay A / Lazarev, Vassili N

Journal of bioinformatics and computational biology

2018 Volume 16, Issue 2, Page(s) 1840006

Abstract: As essential conservative component of the innate immune systems of living organisms, antimicrobial peptides (AMPs) could complement pharmaceuticals that increasingly fail to combat various pathogens exhibiting increased resistance to microbial ... ...

Abstract	As essential conservative component of the innate immune systems of living organisms, antimicrobial peptides (AMPs) could complement pharmaceuticals that increasingly fail to combat various pathogens exhibiting increased resistance to microbial antibiotics. Among the properties of AMPs that suggest their potential as therapeutic agents, diverse peptides in the venoms of various predators demonstrate antimicrobial activity and kill a wide range of microorganisms. To identify potent AMPs, the study reported here involved a transcriptomic profiling of the tentacle secretion of the sea anemone Cnidopus japonicus. An in silico search algorithm designed to discover toxin-like proteins containing AMPs was developed based on the evaluation of the properties and structural peculiarities of amino acid sequences. The algorithm revealed new proteins of the anemone containing antimicrobial candidate sequences, and 10 AMPs verified using high-throughput proteomics were synthesized. The antimicrobial activity of the candidate molecules was experimentally estimated against Gram-positive and -negative bacteria. Ultimately, three peptides exhibited antimicrobial activity against bacterial strains, which suggests that the method can be applied to reveal new AMPs in the venoms of other predators as well.
MeSH term(s)	Algorithms ; Animals ; Anti-Bacterial Agents/chemistry ; Anti-Bacterial Agents/pharmacology ; Computational Biology/methods ; Computer Simulation ; Drug Discovery/methods ; Drug Evaluation, Preclinical/methods ; Gene Expression Profiling ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Machine Learning ; Microbial Sensitivity Tests ; Peptides/chemistry ; Peptides/genetics ; Peptides/pharmacology ; Protein Structure, Secondary ; Proteomics ; Sea Anemones/chemistry ; Sea Anemones/genetics
Chemical Substances	Anti-Bacterial Agents ; Peptides
Language	English
Publishing date	2018-01-03
Publishing country	Singapore
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2115015-1
ISSN	1757-6334 ; 0219-7200
ISSN (online)	1757-6334
ISSN	0219-7200
DOI	10.1142/S0219720018400061
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Article ; Online: Manifestation of Huntington's disease pathology in human induced pluripotent stem cell-derived neurons.

Nekrasov, Evgeny D / Vigont, Vladimir A / Klyushnikov, Sergey A / Lebedeva, Olga S / Vassina, Ekaterina M / Bogomazova, Alexandra N / Chestkov, Ilya V / Semashko, Tatiana A / Kiseleva, Elena / Suldina, Lyubov A / Bobrovsky, Pavel A / Zimina, Olga A / Ryazantseva, Maria A / Skopin, Anton Yu / Illarioshkin, Sergey N / Kaznacheyeva, Elena V / Lagarkova, Maria A / Kiselev, Sergey L

Molecular neurodegeneration

2016 Volume 11, Page(s) 27

Abstract: Background: Huntington's disease (HD) is an incurable hereditary neurodegenerative disorder, which manifests itself as a loss of GABAergic medium spiny (GABA MS) neurons in the striatum and caused by an expansion of the CAG repeat in exon 1 of the ... ...

Abstract	Background: Huntington's disease (HD) is an incurable hereditary neurodegenerative disorder, which manifests itself as a loss of GABAergic medium spiny (GABA MS) neurons in the striatum and caused by an expansion of the CAG repeat in exon 1 of the huntingtin gene. There is no cure for HD, existing pharmaceutical can only relieve its symptoms. Results: Here, induced pluripotent stem cells were established from patients with low CAG repeat expansion in the huntingtin gene, and were then efficiently differentiated into GABA MS-like neurons (GMSLNs) under defined culture conditions. The generated HD GMSLNs recapitulated disease pathology in vitro, as evidenced by mutant huntingtin protein aggregation, increased number of lysosomes/autophagosomes, nuclear indentations, and enhanced neuronal death during cell aging. Moreover, store-operated channel (SOC) currents were detected in the differentiated neurons, and enhanced calcium entry was reproducibly demonstrated in all HD GMSLNs genotypes. Additionally, the quinazoline derivative, EVP4593, reduced the number of lysosomes/autophagosomes and SOC currents in HD GMSLNs and exerted neuroprotective effects during cell aging. Conclusions: Our data is the first to demonstrate the direct link of nuclear morphology and SOC calcium deregulation to mutant huntingtin protein expression in iPSCs-derived neurons with disease-mimetic hallmarks, providing a valuable tool for identification of candidate anti-HD drugs. Our experiments demonstrated that EVP4593 may be a promising anti-HD drug.
MeSH term(s)	Calcium/metabolism ; Cell Differentiation ; Cell Line ; Corpus Striatum/metabolism ; Humans ; Huntington Disease/metabolism ; Huntington Disease/pathology ; Induced Pluripotent Stem Cells/cytology ; Lysosomes/metabolism ; Mutant Proteins/metabolism ; Neurons/cytology ; Nuclear Proteins/metabolism
Chemical Substances	Mutant Proteins ; Nuclear Proteins ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2016-04-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1750-1326
ISSN (online)	1750-1326
DOI	10.1186/s13024-016-0092-5
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Article ; Online: New anticoagulant protein from medicinal leech.

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Article ; Online: Upregulation of YciM Expression Reduces Endotoxin Contamination of Recombinant Proteins Produced in Escherichia coli Cells.

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Article ; Online: iPSC-derived cells lack immune tolerance to autologous NK-cells due to imbalance in ligands for activating and inhibitory NK-cell receptors.

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Article ; Online: Dual Adeno-Associated Virus 9 with Codon-Optimized DYSF Gene Promotes In Vivo Muscle Regeneration and May Decrease Inflammatory Response in Limb Girdle Muscular Dystrophy Type R2.

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Article ; Online: Structural insights into thrombolytic activity of destabilase from medicinal leech.

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Article ; Online: Discovery of novel antimicrobial peptides: A transcriptomic study of the sea anemone Cnidopus japonicus.

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Article ; Online: Manifestation of Huntington's disease pathology in human induced pluripotent stem cell-derived neurons.

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