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1.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Ozerskaya A. V., Zamay T. N., Kolovskaya O. S., Tokarev N. A., Belugin K. V., Chanchikova N. G., Badmaev O. N., Zamay G. S., Shchugoreva I. A., Moryachkov R. V., Zabluda V. N., Khorzhevskii V. A., Shepelevich N., Gappoev S. V., Karlova E. A., Saveleva A. S., Volzhentsev A. A., Blagodatova A. N., Lukyanenko K. A., Veprintsev D. V., Smolyarova T. E., Tomilin F. N., Zamay S. S., Silnikov V. N., Berezovski M. V., Kichkailo A. S.
Заглавие : 11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography-computed tomography
Место публикации : Mol. Ther. Nucl. Acids. - 2021. - Vol. 26. - P.1159-1172. - ISSN 21622531 (ISSN), DOI 10.1016/j.omtn.2021.10.020
Примечания : Cited References: 44
Аннотация: Identification of primary tumors and metastasis sites is an essential step in cancer diagnostics and the following treatment. Positron emission tomography-computed tomography (PET/CT) is one of the most reliable methods for scanning the whole organism for malignancies. In this work, we synthesized an 11C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer. The 11C-aptamer was applied for in vivo imaging of Ehrlich ascites carcinoma and its metastases in mice using PET/CT. The imaging experiments with the 11C-aptamer determined very small primary and secondary tumors of 3 mm2 and less. We also compared 11C imaging with the standard radiotracer, 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18F-FDG), and found better selectivity of the 11C-aptamer to metastatic lesions in the metabolically active organs than 18F-FDG. 11C radionuclide with an ultra-short (20.38 min) half-life is considered safest for PET/CT imaging and does not cause false-positive results in heart imaging. Its combination with aptamers gives us high-specificity and high-contrast imaging of cancer cells and can be applied for PET/CT-guided drug delivery in cancer therapies.
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2.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Moryachkov R. V., Zabluda V. N., Shchugoreva, Irina A., Artyushenko P. V., Kichkaylo A.S., Spiridonova V. A., Berlina A. N., Sokolov A. Е.
Заглавие : Investigation of the spatial structure of bionanoconjugates based on DNA aptamers by synchrotron methods
Коллективы : "Functional materials", International conference, Крымский федеральный университет имени В.И. Вернадского
Место публикации : Ovchinnikov S. G. International conference "Functional materials": book of abstracts/ ed. V. N. Berzhansky ; org. com. S. G. Ovchinnikov [et al.]. - Simferopol, 2021. - P.310
Примечания : Библиогр.: 3 назв. - The research was carried out with a grant from the Russian Science Foundation № 21-12-00226, https://rscf.ru/project/21-12-00226/
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3.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Mironov, Vladimir, Shchugoreva I. A., Artyushenko P. V., Morozov D. I., Borbone N., Oliviero G., Zamay T. N., Moryachkov R. V., Kolovskaya, ., Lukyanenko K. A., Song Y. L., Merkuleva I. A., Zabluda V. N., Peters G., Koroleva L. S., Veprintsev D. V., Glazyrin Y. E., Volosnikova E. A., Belenkaya S. V., Esina T. I., Isaeva A. A., Nesmeyanova, ., Shanshin D. V., Berlina A. N., Komova N. S., Svetlichnyi V. A., Silnikov V. N., Shcherbakov D. N., Zamay G. S., Zamay S. S., Smolyarova T. E., Tikhonova E. P., Chen U. S., Jeng G., Condorelli V., Franciscis G., Groenhof C. Y., Yang A. A., Moskovsky D. G., Fedorov F. N., Tomilin F. N., Tan Y., Alexeev M. V., Berezovski A. S., Kichkailo A.S.
Заглавие : Structure- and interaction-based design of anti-SARS-CoV-2 Aptamers
Коллективы : Aptamerlab LCC; U.S. Department of Energy, Office of ScienceUnited States Department of Energy (DOE) [DE-AC02-06CH11357]; European UnionEuropean Commission [H2020-INFRAEDI-02-2018-823830, H2020-EINFRA-2015-1-675728, 872391, PRISAR2 872860]; CSC-IT center in Espoo, Finland; PRACE; Russian Foundation for Basic ResearchRussian Foundation for Basic Research (RFBR) [19-03-00043]; Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS); Italian Ministry of Education and ResearchMinistry of Education, Universities and Research (MIUR) [FISR2020 _00177]; Canadian Institutes of Health ResearchCanadian Institutes of Health Research (CIHR) [OV1-170353]; Russian Science FoundationRussian Science Foundation (RSF) [21-73-20240]
Место публикации : Chem. - Eur. J. - 2022. - Vol. 28, Is. 12. - Ст.e202104481. - ISSN 0947-6539, DOI 10.1002/chem.202104481. - ISSN 1521-3765(eISSN)
Примечания : Cited References: 85. - The authors are grateful to JCSS Joint Super Computer Center of the Russian Academy of Sciences – Branch of Federal State Institution “Scientific Research Institute for System Analysis of the Russian Academy of Sciences” for providing supercomputers for computer simulations. The authors thank the RSC Group (www.rscgroup.ru) and personally Mr. Oleg Gorbachev for the constant support and establishment of “The Good Hope Net Project” (www.thegoodhope.net) multifunctional non-profit anti-CoVID research project. The authors also thank the Helicon Company (www.helicon.ru) and personally Olesya Kucenko, Alexander Kolobov, Leonid Klimov for instrumental support and help with conducting fluorescence polarization assays, which were performed on a demo instrument Clariostar Plus microplate reader (BMG LABTECH, Germany). We thank Dr. Yong-Zhen Zhang for providing the genome sequence of 2019-nCoV and Dr. Xinquan Wang for providing the crystal structure of the binding domain of the SARS-2 Spike protein. The authors are grateful to Aptamerlab LCC financial support (www.aptamerlab.com). Y.A.’s work at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, under contract DE-AC02-06CH11357. The work of D.M. and G.G. has been done as part of the BioExcel CoE (www.bioexcel.eu), a project funded by the European Union contracts H2020-INFRAEDI-02-2018-823830 and H2020-EINFRA-2015-1-675728. D.M. and G.G. also thank the CSC-IT center in Espoo, Finland, as well as PRACE for awarding access to resource Curie-Rome based in France at GENCI. V.M. thanks Russian Foundation for Basic Research (project number 19-03-00043). A.B.’s and N.K.’s work was supported by the Ministry of Science and Higher Education of Russian Federation (state assignment of the Research Center of Biotechnology RAS). V. deF. G.C., N.B and G.O. are grateful to FISR2020 _00177 Shield, Italian Ministry of Education and Research, for funding. GC is grateful to the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement: cONCReTE 872391; PRISAR2 872860. Use of the 13 A BioSAXS beamtime at the Taiwan Photon Source is acknowledged. The work of M.V.B was funded by the Canadian Institutes of Health Research grant OV1-170353. SAXS measurements and PIEDA analyses were funded by the Russian Science Foundation (project No 21-73-20240 for A.S.K.)
Предметные рубрики: BIOLOGICAL MACROMOLECULES
SOLUTION SCATTERING
BINDING
SPIKE
Аннотация: Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.
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4.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Moryachkov R. V., Nikolaeva P. A., Spiridonova V. A.
Заглавие : Structure approaches to study of DNA aptamers in solution
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.76-78. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-76-78; Сиб. мед. обозрение
Примечания : Cited References: 5. - The reported study was funded by RFBR, project number 19-32-90266
Аннотация: The high potential of aptamers – specific molecular agents based on short single-stranded nucleic acids – makes high demands on the molecules under development for the efficiency of interaction with target biomolecules. In this work, approaches are considered for studying the spatial structure of DNA aptamers in solution using various complementary methods, which make it possible to obtain a more complete picture of the formation of the structure and conformational changes, to track the interaction with the target protein, the tendency to oligomerization, and to characterize the spatial structure of both individual molecules and complexes.
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5.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Sokolov A. Е., Zabluda V. N., Sherepa A. V., Knyazev Yu. V., Volochaev M. N., Kurilina A., Velikanov D. A., Goncharova D. A., Shabalina A., Svetlichnyi V.
Заглавие : Magnetic properties of iron oxide nanoparticles to create aptamer bionanoconjugates
Коллективы : Aptamers in Russia, international conference
Место публикации : Aptamers in Russia, international conference (1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk). Molecular Therapy - Nucleic Acids: book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P.12
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6.

Вид документа : Статья из сборника (однотомник)
Шифр издания :
Автор(ы) : Denissenko P., Denisenko V. V., Denisov I., Kantsler V., Kolovskaya O. S., Lapin I. N., Sokolov A. Е., Svetlichnyi V., Zabluda V. N., Zamay S. S., Kichkailo A.S.
Заглавие : Magnetic sorting of tumor cells with attached magnetic nanoparticles in a microchannel
Коллективы : Aptamers in Russia, international conference
Место публикации : Aptamers in Russia, international conference (1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk). Molecular Therapy - Nucleic Acids: book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P.14
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7.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Artyushenko P. V., Mironov V. A., Morozov D. I., Shchugoreva I. A., Borbone N., Tomilin F. N., Kichkailo A. S.
Заглавие : Computational approach to design of aptamers to the receptor binding domain of sars-cov-2
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.66-67. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-66-67; Сиб. мед. обозрение
Примечания : Cited References: 5
Аннотация: The aim of the research. In this work, in silico selection of DNA-aptamers to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein was performed using molecular modeling methods. Material and methods. A new computational approach to aptamer in silico selection is based on a cycle of simulations, including the stages of molecular modeling, molecular docking, molecular dynamic simulations, and quantum chemical calculations. To verify the obtained calculated results flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods were applied. Results. An initial library consisted of 256 16-mer oligonucleotides was modeled. Based on molecular docking results, the only one aptamer (Apt16) was selected from the library as a starting aptamer to the RBD protein. For Apt16/RBD complex, molecular dynamic and quantum chemical calculations revealed the pairs of nucleotides and amino acids whose contribution to the binding between aptamer and RBD is the largest. Taking into account these data, Apt16 was subjected to the structure modifications in order to increase the binding with the RBD. Thus, a new aptamer Apt25 was designed. The procedure of 1) aptamer structure modeling/modification, 2) molecular docking, 3) molecular dynamic simulations, 4) quantum chemical calculations was performed sev-eral times. As a result, four aptamers (Apt16, Apt25, Apt27, Apt31) to the RBD were designed in silico without any preliminary experimental data. Binding of the each modeled aptamer to the RBD was studied in terms of interactions between residues in protein and nucleotides in the aptamers. Based on the simulation results, the strongest binding with the RBD was predicted for two Apt27 and Apt31aptamers. The calculated results are in good agreement with experimental data obtained by flow cytometry, fluorescence polarization, and small-angle X-ray scattering methods. Conclusion. The proposed computational approach to selection and refinement of aptamers is universal and can be used for wide range of molecular ligands and targets.
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8.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Nikolaeva P. A., Moryachkov R. V., Raldugina V. N., Naumova Iu. O., Novikova T. M., Spiridonova V. A.
Заглавие : Structural analysis of thrombin-binding G-aptamers in presence of bivalent ions
Место публикации : Sib. Med. Rev. - 2022. - Is. 5. - P.111-113. - ISSN 18199496 (ISSN), DOI 10.20333/25000136-2022-5-111-113; Сиб. мед. обозрение
Примечания : Cited References: 4. - The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240)
Аннотация: The aim of this study was to examine 3D structures of DNA aptamers, thrombin inhibitors. The main objective was to study 3D structure 15TBA, RE31, NU172 aptamers using the small-angle X-ray scattering method. The size of 15TBA was 4.5 nm, which corresponds to a partially unfolded conformation. The CD spectrum of Nu172 in the presence of 50 mM strontium ions indicates the presence of an antiparallel G-quadruplex, the concentration o f which drops at 50°C. NU172 does not have a rigid structure, apparently due to the presence of a guanine residue in the GT loop. The NU172 aptamer does not form a stable conformation in solution either without ions or with Ba2+ and Sr2+ ions. It was shown that there is possibility of aptamers transition from one conformation to another dependently on concentration and temperature confirms that the potassium ion is a unique stabilizing ion of natural molecules containing G-quadruplexes.
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9.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Zamay, Tatiana, Zamay, Sergey, Luzan, Natalia, Fedotovskaya, Victoriya, Masyugin, Albert, Zelenov F., Koshmanova, Anastasia, Nikolaeva, Elena, Kirichenko, Daria, Veprintsev, Dmitry, Kolovskaya, Olga, Shchugoreva, Irina, Zamay, Galina, Lapin I. N., Lukyanenko A. V., Borus, Andrey, Sukhachev A. L., Volochaev M. N., Lukyanenko, Kirill, Shabanov, Alexandr, Zabluda V. N., Zhizhchenko, Alexey, Kuchmizhak, Aleksandr, Sokolov A. Е., Narodov, Andrey, Prokopenko, Vladimir, Galeev, Rinat, Svetlichnyi, Valery, Kichkailo, Anna
Заглавие : Magnetic nanoscalpel for the effective treatment of ascites tumors
Место публикации : J. Funct. Biomater. - 2023. - Vol. 14, Is. 4. - Ст.179. - ISSN 20794983 (eISSN), DOI 10.3390/jfb14040179
Примечания : Cited References: 36. - This research was funded by the Regional State Autonomous Institution “Krasnoyarsk Regional Fund for Support of Scientific and Scientific and Technical Activities”, Competition of scientific, technical, and innovative projects in the interests of the first world-class climate scientific and educational center “Yenisei Siberia”, grant “Carrying out applied research and development aimed at creating technologies for the production of nanoscalpels based on magnetic nanodisks for microsurgery of glial brain tumors” No. 2022060108781 and with the support of a partner company JSC «NPP «Radiosviaz»
Аннотация: One of the promising novel methods for radical tumor resection at a single-cell level is magneto-mechanical microsurgery (MMM) with magnetic nano- or microdisks modified with cancer-recognizing molecules. A low-frequency alternating magnetic field (AMF) remotely drives and controls the procedure. Here, we present characterization and application of magnetic nanodisks (MNDs) as a surgical instrument (“smart nanoscalpel”) at a single-cell level. MNDs with a quasi-dipole three-layer structure (Au/Ni/Au) and DNA aptamer AS42 (AS42-MNDs) on the surface converted magnetic moment into mechanical and destroyed tumor cells. The effectiveness of MMM was analyzed on Ehrlich ascites carcinoma (EAC) cells in vitro and in vivo using sine and square-shaped AMF with frequencies from 1 to 50 Hz with 0.1 to 1 duty-cycle parameters. MMM with the “Nanoscalpel” in a sine-shaped 20 Hz AMF, a rectangular-shaped 10 Hz AMF, and a 0.5 duty cycle was the most effective. A sine-shaped field caused apoptosis, whereas a rectangular-shaped field caused necrosis. Four sessions of MMM with AS42-MNDs significantly reduced the number of cells in the tumor. In contrast, ascites tumors continued to grow in groups of mice and mice treated with MNDs with nonspecific oligonucleotide NO-MND. Thus, applying a “smart nanoscalpel” is practical for the microsurgery of malignant neoplasms.
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10.

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kichkailo A. S., Narodov A. A., Komarova M. A., Zamay T. N., Zamay G. S., Kolovskaya O. S., Erakhtin E. E., Glazyrin Y. E., Veprintsev D. V., Moryachkov R. V., Zabluda V. N., Shchugoreva I., Artyushenko P., Mironov V. A., Morozov D. I., Gorbushin A. V., Khorzhevskii V. A., Koshmanova A. A., Nikolaeva E. D., Grinev I. P., Voronkovskii I. I., Grek D. S., Belugin K. V., Volzhentsev A. A., Badmaev O. N., Luzan N., Lukyanenko K. A., Peters G., Lapin I. N., Kirichenko A. K., Konarev P. V., Morozov E. V, Mironov G. G., Gargaun A., Muharemagic D., Zamay S. S., Kochkina E. V., Dymova M. A., Smolyarova T. E., Sokolov A. Е., Modestov A. A., Tokarev N. A., Shepelevich N., Ozerskaya A. V., Chanchikova N. G., Krat A. V., Zukov R. A., Bakhtina V. I., Shnyakin P. G., Shesternya P. A., Svetlichnyi V. A., Petrova M. M., Artyukhov I. P., Tomilin F. N., Berezovski, Maxim V.
Заглавие : Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells
Место публикации : Mol. Ther. - Nucleic Acids. - 2023. - Vol. 32. - P.267-288. - ISSN 21622531 (eISSN), DOI 10.1016/j.omtn.2023.03.015
Примечания : Cited References: 69. - The authors are grateful to all the patients and hospital staff participating in this research. We acknowledge the assistance of the AptamerLab LCC (www.aptamerlab.com) and personally Mr. Vasily Mezko for the aptamer 3D structure optimization and financial and technical support. The authors thank Mr. Alexey Kichkailo, Dr. Arkady B. Kogan, and Dr. Rinat G. Galeev for their general support. Mrs. Valentina L. Grigoreva, and Irina V. Gildebrand for the help with histological staining. Technical and instrumental support was provided by the Multiple-Access Center at Tomsk State University; the Krasnoyarsk Inter-District Ambulance Hospital, named after N.S. Karpovich; John L. Holmes Mass Spectrometry Facility at the University of Ottawa; Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency; Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University and Krasnoyarsk Regional Centre for Collective Use at the Federal Research Centre “KSC SB RAS”. The confocal fluorescence microscopy research was carried out with the equipment of the Tomsk Regional Core Shared Research Facilities Center of the National Research Tomsk State University. The Center was supported by the Ministry of Science and Higher Education of the Russian Federation, grant no. 075-15-2021-693 (no. 13.RFC.21.0012). Acute toxicity studies were performed in a laboratory certified for preclinical studies, Laboratory of Biological Testing, Institute of Bioorganic Chemistry named after academics M.M. Shemyakin and Y.A. Ovchinnikov Russian Academy of Sciences. The authors are grateful to the Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations. Development of the glioma tumor model in immunosuppressed mice was supported by the Russian Science Foundation grant No. 22-64-00041 (M.A.D.), https://rscf.ru/en/project/22-64-00041/. Synthesis of 11C-aptamer and PET/CT visualization was funded by the Federal Medical Biological Agency; project 122041800132-2 (A.V.O.). Aptamer selection and their clinical applications were funded by the Ministry of Healthcare of the Russian Federation; project АААА-Б19-219090690032-5 (T.N.Z.). The Ministry of Science and Higher Education of the Russian Federation project FWES-2022-0005 (A.S.K.) supported aptamer characterization, molecular modelling, and in vivo experiments. Mass spectrometry analyses, DNA sequencing, and synthesis were supported by NSERC Discovery Grant (M.V.B.). We acknowledge the European Synchrotron Radiation Facility for SAXS experiments and thank Dr. Bart Van Laer for assistance in using a beamline BM29. SAXS measurements were supported by RFBR № 18-32-00478 for young scientists (R.V.M.). The synchrotron SEC-SAXS data for Gli-55 aptamer were also collected at beamline P12 operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany)
Аннотация: Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.
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