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Article ; Online: Synthesis and antitumor activity of cyclopentane-fused anthraquinone derivatives.

Tikhomirov, Alexander S / Sinkevich, Yuri B / Dezhenkova, Lyubov G / Kaluzhny, Dmitry N / Ilyinsky, Nikolay S / Borshchevskiy, Valentin I / Schols, Dominique / Shchekotikhin, Andrey E

European journal of medicinal chemistry

2023 Volume 265, Page(s) 116103

Abstract: In our pursuit of developing novel analogs of anthracyclines with enhanced antitumor efficacy and safety, we have designed a synthesis scheme for 4,11-dihydroxy-5,10-dioxocyclopenta[b]anthracene-2-carboxamides. These newly synthesized compounds exhibit ... ...

Abstract	In our pursuit of developing novel analogs of anthracyclines with enhanced antitumor efficacy and safety, we have designed a synthesis scheme for 4,11-dihydroxy-5,10-dioxocyclopenta[b]anthracene-2-carboxamides. These newly synthesized compounds exhibit remarkable antiproliferative potency against various mammalian tumor cell lines, including those expressing activated mechanisms of multidrug resistance. The structure of the diamine moiety in the carboxamide side chain emerges as a critical determinant for anticancer activity and interaction with key targets such as DNA, topoisomerase 1, and ROS induction. Notably, the introduced modification to the doxorubicin structure results in significantly increased lipophilicity, cellular uptake, and preferential distribution in lysosomes. Consequently, while maintaining an impact on anthracyclines targets, these novel derivatives also demonstrate the potential to induce cytotoxicity through pathways associated with lysosomes. In summary, derivatives of cyclic diamines, particularly 3-aminopyrrolidine, can be considered a superior choice compared to aminosugars for incorporation into natural and semi-synthetic anthracyclines or new anthraquinone derivatives, aiming to circumvent efflux-mediated drug resistance.
MeSH term(s)	Animals ; Antineoplastic Agents/chemistry ; Anthraquinones/chemistry ; Cyclopentanes ; Drug Screening Assays, Antitumor ; Antibiotics, Antineoplastic/pharmacology ; Anthracyclines ; Topoisomerase II Inhibitors/pharmacology ; Structure-Activity Relationship ; Mammals/metabolism
Chemical Substances	Antineoplastic Agents ; Anthraquinones ; Cyclopentanes ; Antibiotics, Antineoplastic ; Anthracyclines ; Topoisomerase II Inhibitors
Language	English
Publishing date	2023-12-30
Publishing country	France
Document type	Journal Article
ZDB-ID	188597-2
ISSN	1768-3254 ; 0009-4374 ; 0223-5234
ISSN (online)	1768-3254
ISSN	0009-4374 ; 0223-5234
DOI	10.1016/j.ejmech.2023.116103
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Article ; Online: Short-Term Effect of SARS-CoV-2 Spike Protein Receptor-Binding Domain-Specific Antibody Induction on Neutrophil-Mediated Immune Response in Mice.

Bolkhovitina, Elena L / Vavilova, Julia D / Bogorodskiy, Andrey O / Zagryadskaya, Yuliya A / Okhrimenko, Ivan S / Sapozhnikov, Alexander M / Borshchevskiy, Valentin I / Shevchenko, Marina A

International journal of molecular sciences

2022 Volume 23, Issue 15

Abstract: Vaccination protects against COVID-19 via the spike protein receptor-binding domain (RBD)-specific antibody formation, but it also affects the innate immunity. The effects of specific antibody induction on neutrophils that can cause severe respiratory ... ...

Abstract	Vaccination protects against COVID-19 via the spike protein receptor-binding domain (RBD)-specific antibody formation, but it also affects the innate immunity. The effects of specific antibody induction on neutrophils that can cause severe respiratory inflammation are important, though not completely investigated. In the present study, using a mouse model mimicking SARS-CoV-2 virus particle inhalation, we investigated neutrophil phenotype and activity alterations in the presence of RBD-specific antibodies. Mice were immunized with RBD and a week after a strong antibody response establishment received 100 nm particles in the RBD solution. Control mice received injections of a phosphate buffer instead of RBD. We show that the application of 100 nm particles in the RBD solution elevates neutrophil recruitment to the blood and the airways of RBD-immunized mice rather than in control mice. Analysis of bone marrow cells of mice with induced RBD-specific antibodies revealed the increased population of CXCR2
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral ; Antibody Formation ; COVID-19 ; Humans ; Inflammation ; Neutrophils ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-07-26
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/ijms23158234
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Article ; Online: Intracellular microbial rhodopsin-based optogenetics to control metabolism and cell signaling.

Vlasova, Anastasiia D / Bukhalovich, Siarhei M / Bagaeva, Diana F / Polyakova, Aleksandra P / Ilyinsky, Nikolay S / Nesterov, Semen V / Tsybrov, Fedor M / Bogorodskiy, Andrey O / Zinovev, Egor V / Mikhailov, Anatolii E / Vlasov, Alexey V / Kuklin, Alexander I / Borshchevskiy, Valentin I / Bamberg, Ernst / Uversky, Vladimir N / Gordeliy, Valentin I

Chemical Society reviews

2024 Volume 53, Issue 7, Page(s) 3327–3349

Abstract: Microbial rhodopsin (MRs) ion channels and pumps have become invaluable optogenetic tools for neuroscience as well as biomedical applications. Recently, MR-optogenetics expanded towards subcellular organelles opening principally new opportunities in ... ...

Abstract	Microbial rhodopsin (MRs) ion channels and pumps have become invaluable optogenetic tools for neuroscience as well as biomedical applications. Recently, MR-optogenetics expanded towards subcellular organelles opening principally new opportunities in optogenetic control of intracellular metabolism and signaling
MeSH term(s)	Rhodopsins, Microbial/genetics ; Optogenetics ; Signal Transduction
Chemical Substances	Rhodopsins, Microbial
Language	English
Publishing date	2024-04-02
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1472875-8
ISSN	1460-4744 ; 0306-0012
ISSN (online)	1460-4744
ISSN	0306-0012
DOI	10.1039/d3cs00699a
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Article ; Online: The Role of Tyr-His-Trp Triad and Water Molecule Near the N1-Atom of 2-Hydroperoxycoelenterazine in Bioluminescence of Hydromedusan Photoproteins: Structural and Mutagenesis Study.

Natashin, Pavel V / Burakova, Ludmila P / Kovaleva, Margarita I / Shevtsov, Mikhail B / Dmitrieva, Daria A / Eremeeva, Elena V / Markova, Svetlana V / Mishin, Alexey V / Borshchevskiy, Valentin I / Vysotski, Eugene S

International journal of molecular sciences

2023 Volume 24, Issue 7

Abstract: Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which ... ...

Abstract	Hydromedusan photoproteins responsible for the bioluminescence of a variety of marine jellyfish and hydroids are a unique biochemical system recognized as a stable enzyme-substrate complex consisting of apoprotein and preoxygenated coelenterazine, which is tightly bound in the protein inner cavity. The binding of calcium ions to the photoprotein molecule is only required to initiate the light emission reaction. Although numerous experimental and theoretical studies on the bioluminescence of these photoproteins were performed, many features of their functioning are yet unclear. In particular, which ionic state of dioxetanone intermediate decomposes to yield a coelenteramide in an excited state and the role of the water molecule residing in a proximity to the N1 atom of 2-hydroperoxycoelenterazine in the bioluminescence reaction are still under discussion. With the aim to elucidate the function of this water molecule as well as to pinpoint the amino acid residues presumably involved in the protonation of the primarily formed dioxetanone anion, we constructed a set of single and double obelin and aequorin mutants with substitutions of His, Trp, Tyr, and Ser to residues with different properties of side chains and investigated their bioluminescence properties (specific activity, bioluminescence spectra, stopped-flow kinetics, and fluorescence spectra of Ca
MeSH term(s)	Aequorin/genetics ; Aequorin/chemistry ; Protons ; Water ; Protein Conformation ; Luminescent Proteins/metabolism ; Mutagenesis ; Calcium/metabolism ; Luminescent Measurements
Chemical Substances	Aequorin (50934-79-7) ; Protons ; Water (059QF0KO0R) ; Luminescent Proteins ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2023-04-06
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/ijms24076869
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Article ; Online: Confocal Laser Scanning Microscopy-Based Quantitative Analysis of Aspergillus fumigatus Conidia Distribution in Whole-Mount Optically Cleared Mouse Lung.

Maslov, Ivan V / Bogorodskiy, Andrey O / Pavelchenko, Mariia V / Zykov, Ilia O / Troyanova, Natalya I / Borshchevskiy, Valentin I / Shevchenko, Marina A

Journal of visualized experiments : JoVE

2021 , Issue 175

Abstract: Aspergillus fumigatus conidia are airborne pathogens that can penetrate human airways. Immunocompetent people without allergies exhibit resistance and immunological tolerance, while in immunocompromised patients, conidia can colonize airways and cause ... ...

Abstract	Aspergillus fumigatus conidia are airborne pathogens that can penetrate human airways. Immunocompetent people without allergies exhibit resistance and immunological tolerance, while in immunocompromised patients, conidia can colonize airways and cause severe invasive respiratory disorders. Various cells in different airway compartments are involved in the immune response that prevents fungal invasion; however, the spatio-temporal aspects of pathogen elimination are still not completely understood. Three-dimensional (3D) imaging of optically cleared whole-mount organs, particularly the lungs of experimental mice, permits detection of fluorescently labeled pathogens in the airways at different time points after infection. In the present study, we describe an experimental setup to perform a quantitative analysis of A. fumigatus conidia distribution in the airways. Using fluorescent confocal laser scanning microscopy (CLSM), we traced the location of fluorescently labeled conidia in the bronchial branches and the alveolar compartment 6 hours after oropharyngeal application to mice. The approach described here was previously used for detection of the precise pathogen location and identification of the pathogen-interacting cells at different phases of the immune response. The experimental setup can be used to estimate the kinetics of the pathogen elimination in different pathological conditions.
MeSH term(s)	Animals ; Aspergillus fumigatus ; Bronchi ; Humans ; Lung ; Mice ; Microscopy, Confocal ; Spores, Fungal
Language	English
Publishing date	2021-09-18
Publishing country	United States
Document type	Journal Article ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/62436
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Article: Confocal laser scanning microscopy-based quantitative analysis of Aspergillus fumigatus conidia distribution in whole-mount optically cleared mouse lung

Maslov, Ivan V. / Bogorodskiy, Andrey O. / Pavelchenko, Mariia V. / Zykov, Ilia O. / Troyanova, Natalya I. / Borshchevskiy, Valentin I. / Shevchenko, Marina A.

Journal of visualized experiments. 2021 Sept. 18, , no. 175

2021

Abstract	Aspergillus fumigatus conidia are airborne pathogens that can penetrate human airways. Immunocompetent people without allergies exhibit resistance and immunological tolerance, while in immunocompromised patients, conidia can colonize airways and cause severe invasive respiratory disorders. Various cells in different airway compartments are involved in the immune response that prevents fungal invasion; however, the spatio-temporal aspects of pathogen elimination are still not completely understood. Three-dimensional (3D) imaging of optically cleared whole-mount organs, particularly the lungs of experimental mice, permits detection of fluorescently labeled pathogens in the airways at different time points after infection. In the present study, we describe an experimental setup to perform a quantitative analysis of A. fumigatus conidia distribution in the airways. Using fluorescent confocal laser scanning microscopy (CLSM), we traced the location of fluorescently labeled conidia in the bronchial branches and the alveolar compartment 6 hours after oropharyngeal application to mice. The approach described here was previously used for detection of the precise pathogen location and identification of the pathogen-interacting cells at different phases of the immune response. The experimental setup can be used to estimate the kinetics of the pathogen elimination in different pathological conditions.
Keywords	Aspergillus fumigatus ; conidia ; fluorescence ; fungi ; humans ; immune response ; lungs ; mice ; people ; quantitative analysis
Language	English
Dates of publication	2021-0918
Size	p. e62436.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/62436
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The SARS-CoV-2 receptor-binding domain facilitates neutrophil transepithelial migration and nanoparticle uptake in the mice airways

Bolkhovitina, Elena L / Vavilova, Julia D / Bogorodskiy, Andrey O / Zagryadskaya, Yuliya A / Okhrimenko, Ivan S / Sapozhnikov, Alexander M / Borshchevskiy, Valentin I / Shevchenko, Marina A

bioRxiv

Abstract: SARS-CoV-2-induced infection is still dangerous. Mouse models are convenient to the investigation of virus-activated immune response mechanisms. However, mice are not proper model organisms to study COVID-19 due to decreased interaction affinity between ... ...

Abstract	SARS-CoV-2-induced infection is still dangerous. Mouse models are convenient to the investigation of virus-activated immune response mechanisms. However, mice are not proper model organisms to study COVID-19 due to decreased interaction affinity between the SARS-CoV-2 receptor-binding domain (RBD) and mouse angiotensin-converting enzyme 2 (ACE2) compared with human ACE2. In the present study, we propose a mouse model that allows estimating the influence of SARS-CoV-2 on the immune system. To mimic the effects of RBD-ACE2 high-affinity interaction, mice received the ACE2 inhibitor MLN-4760. To simulate virus loading, we applied 100 nm particles suspended in the solution of RBD via the oropharyngeal route to mice. In this model, MLN-4760 application enhanced neutrophil egress from the bone marrow to the bloodstream and RBD attracted neutrophils to the luminal side of the conducting airway epithelium. By contrast, inert 100 nm particles were not potent to stimulate neutrophil recruitment to the conducting airway mucosa. Using this model, and by altering the dosage of the ACE2 inhibitor, nanoparticles, and RBD, one can adapt it to investigate different COVID-19 states characterized with mild or severe airway inflammation.
Keywords	covid19
Language	English
Publishing date	2022-04-12
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2022.04.12.488042
Database	COVID19

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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: Crystal structure of semi-synthetic obelin-v after calcium induced bioluminescence implies coelenteramine as the main reaction product.

Natashin, Pavel V / Eremeeva, Elena V / Shevtsov, Mikhail B / Kovaleva, Margarita I / Bukhdruker, Sergey S / Dmitrieva, Daria A / Gulnov, Dmitry V / Nemtseva, Elena V / Gordeliy, Valentin I / Mishin, Alexey V / Borshchevskiy, Valentin I / Vysotski, Eugene S

Scientific reports

2022 Volume 12, Issue 1, Page(s) 19613

Abstract: Coelenterazine-v (CTZ-v), a synthetic vinylene-bridged π-extended derivative, is able to significantly alter bioluminescence spectra of different CTZ-dependent luciferases and photoproteins by shifting them towards longer wavelengths. However, ... ...

Abstract	Coelenterazine-v (CTZ-v), a synthetic vinylene-bridged π-extended derivative, is able to significantly alter bioluminescence spectra of different CTZ-dependent luciferases and photoproteins by shifting them towards longer wavelengths. However, Ca
MeSH term(s)	Calcium/metabolism ; Protein Conformation ; Luminescent Proteins/metabolism ; Calcium, Dietary ; Luminescent Measurements
Chemical Substances	obelin ; Calcium (SY7Q814VUP) ; Luminescent Proteins ; Calcium, Dietary
Language	English
Publishing date	2022-11-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-24117-5
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Article ; Online: Structure-based rational design of an enhanced fluorogen-activating protein for fluorogens based on GFP chromophore.

Goncharuk, Marina V / Baleeva, Nadezhda S / Nolde, Dmitry E / Gavrikov, Alexey S / Mishin, Alexey V / Mishin, Alexander S / Sosorev, Andrey Y / Arseniev, Alexander S / Goncharuk, Sergey A / Borshchevskiy, Valentin I / Efremov, Roman G / Mineev, Konstantin S / Baranov, Mikhail S

Communications biology

2022 Volume 5, Issue 1, Page(s) 706

Abstract: Fluorescence-Activating and absorption-Shifting Tag" (FAST) is a well-studied fluorogen-activating protein with high brightness and low size, able to activate a wide range of fluorogens. This makes FAST a promising target for both protein and fluorogen ... ...

Abstract	"Fluorescence-Activating and absorption-Shifting Tag" (FAST) is a well-studied fluorogen-activating protein with high brightness and low size, able to activate a wide range of fluorogens. This makes FAST a promising target for both protein and fluorogen optimization. Here, we describe the structure-based rational design of the enhanced FAST mutants, optimized for the N871b fluorogen. Using the spatial structure of the FAST/N871b complex, NMR relaxation analysis, and computer simulations, we identify the mobile regions in the complex and suggest mutations that could stabilize both the protein and the ligand. Two of our mutants appear brighter than the wild-type FAST, and these mutants provide up to 35% enhancement for several other fluorogens of similar structure, both in vitro and in vivo. Analysis of the mutants by NMR reveals that brighter mutants demonstrate the highest stability and lowest length of intermolecular H-bonds. Computer simulations provide the structural basis for such stabilization.
MeSH term(s)	Fluorescence ; Fluorescent Dyes/chemistry ; Proteins
Chemical Substances	Fluorescent Dyes ; Proteins
Language	English
Publishing date	2022-07-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-022-03662-9
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