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Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics / S. Poolsup, E. Zaripov, N. Huttmann [et al.] // Mol. Ther. Nucleic Acids. - 2023. - Vol. 31. - P. 731-743, DOI 10.1016/j.omtn.2023.02.010. - Cited References: 74. - M.V.B. thanks the Canadian Institutes of Health Research grant OV1-170353 for providing financial support. Molecular modeling and docking were supported by a grant from the Russian Science Foundation (project number 21-73-20240) for A.S.K. S.P. is thankful to Dr. Bob Dass, Dylan Tanner, and Dr. Degang Liu, Sartorius for generously providing excellent technical training and consumable support for binding assay on BLI, and Aldo Jordan for assisting with creating the figures. The authors also thank John L. Holmes’s mass spectrometry facility for providing access to perform nLC-MS/MS. Lastly, the authors thank the JCSS Joint Super Computer Center of the Russian Academy of Sciences for providing supercomputers for computer simulations . - ISSN 2162-2531
Кл.слова (ненормированные):
MT: Oligonucleotides: Diagnostics and Biosensors -- COVID-19 diagnosis -- SARS-CoV-2 nucleocapsid detection -- label-free optical aptasensor -- aptamer selection -- biolayer interferometry -- binding motif identification
Аннотация: The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6–3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.

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Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, Krasnoyarsk 660036, Russia
Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Poolsup, S.; Zaripov, E.; Huttmann, N.; Minic, Z.; Artyushenko, P. V.; Shchugoreva, I. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.; Berezovski, M. V.
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Core–shell Fe3O4@C nanoparticles for the organic dye adsorption and targeted magneto-mechanical destruction of Ehrlich ascites carcinoma cells / O. S. Ivanova, I. S. Edelman, Ch.-R. Lin [et al.] // Materials. - 2023. - Vol. 16, Is. 1. - Ст. 23, DOI 10.3390/ma16010023. - Cited References: 65. - This research was funded partly by the Ministry of Science and Higher Education of the Russian Federation, project FWES-2021-0035. C.-R.L., Y.-Z.C. and A.A.S. thank the National Science and Technology Council of Taiwan for the financial support, Grants NSTC № 108-2923-M-153-001-MY3 and № 110-2112-M-153-005-. Magnetic investigations were carried out in the Center for Collective Use of the Krasnoyarsk Regional Center of Research Equipment of Federal Research Center “Krasnoyarsk Science Center SB RAS” . - ISSN 1996-1944
Кл.слова (ненормированные):
magnetite nanoparticles -- adsorption -- organic dyes -- aptamers -- magnetically induced cell destruction
Аннотация: The morphology, structure, and magnetic properties of Fe3O4 and Fe3O4@C nanoparticles, as well their effectiveness for organic dye adsorption and targeted destruction of carcinoma cells, were studied. The nanoparticles exhibited a high magnetic saturation value (79.4 and 63.8 emu/g, correspondingly) to facilitate magnetic separation. It has been shown that surface properties play a key role in the adsorption process. Both types of organic dyes—cationic (Rhodomine C) and anionic (Congo Red and Eosine)—were well adsorbed by the Fe3O4 nanoparticles’ surface, and the adsorption process was described by the polymolecular adsorption model with a maximum adsorption capacity of 58, 22, and 14 mg/g for Congo Red, Eosine, and Rhodomine C, correspondingly. In this case, the kinetic data were described well by the pseudo-first-order model. Carbon-coated particles selectively adsorbed only cationic dyes, and the adsorption process for Methylene Blue was described by the Freundlich model, with a maximum adsorption capacity of 14 mg/g. For the case of Rhodomine C, the adsorption isotherm has a polymolecular character with a maximum adsorption capacity of 34 mg/g. To realize the targeted destruction of the carcinoma cells, the Fe3O4@C nanoparticles were functionalized with aptamers, and an experiment on the Ehrlich ascetic carcinoma cells’ destruction was carried out successively using a low-frequency alternating magnetic field. The number of cells destroyed as a result of their interaction with Fe3O4@C nanoparticles in an alternating magnetic field was 27%, compared with the number of naturally dead control cells of 6%.

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Kirensky Institute of Physics, Federal Research Center KSC Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Institute of Engineering Physics and Radioelectronics, Siberian Federal University, Krasnoyarsk 660041, Russia
Department of Applied Physics, National Pingtung University, Pingtung City 90003, Taiwan
Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk 660022, Russia
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center KSC Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia

Доп.точки доступа:
Ivanova, O. S.; Иванова, Оксана Станиславовна; Edelman, I. S.; Эдельман, Ирина Самсоновна; Lin, Chun-Rong; Svetlitsky, E. S.; Светлицкий, Евгений Сергеевич; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Lukyanenko, Kirill A.; Sukhachev, A. L.; Сухачев, Александр Леонидович; Shestakov, N. P.; Шестаков, Николай Петрович; Chen, Ying-Zhen; Spivakov, Aleksandr A.
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Magnetic nanoscalpel for the effective treatment of ascites tumors / T. Zamay, S. Zamay, N. Luzan [et al.] // J. Funct. Biomater. - 2023. - Vol. 14, Is. 4. - Ст. 179, DOI 10.3390/jfb14040179. - 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» . - ISSN 2079-4983
Кл.слова (ненормированные):
magnetic nanodisks -- ascitic tumor -- magneto-mechanical therapy -- “smart nanoscalpel” -- DNA aptamers -- apoptosis -- necrosis
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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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center” of the Siberian Branch, Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
JSC «NPP «Radiosviaz», Krasnoyarsk 660021, Russia
Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk 634050, Russia
L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk 660036, Russia
Institute of Automation and Control Processes (IACP), Far Eastern Branch of the Russian Academy of Science, Vladivostok 690041, Russia
Far Eastern Federal University, Vladivostok 690950, Russia
V.P. Astafiev Krasnoyarsk State Pedagogical University, Krasnoyarsk 660049, Russia

Доп.точки доступа:
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.; Лукьяненко, Анна Витальевна; Borus, Andrey; Борус, Андрей Андреевич; Sukhachev, A. L.; Сухачев, Александр Леонидович; Volochaev, M. N.; Волочаев, Михаил Николаевич; Lukyanenko, Kirill; Shabanov, Alexandr; Zabluda, V. N.; Заблуда, Владимир Николаевич; Zhizhchenko, Alexey; Kuchmizhak, Aleksandr; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Narodov, Andrey; Prokopenko, Vladimir; Galeev, Rinat; Svetlichnyi, Valery; Kichkailo, Anna
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    Получение высокоселективных аптамеров к онколитическому вирусу VV-GMCSF-Lact. Теоретические и экспериментальные подходы / М. А. Дымова, Е. В. Кулигина, В. А. Рихтер [и др.] // Сиб. мед. обозрение. - 2023. - № 5. - С. 95-101 ; Sib. Med. Rev., DOI 10.20333/25000136-2023-5-95-101. - Библиогр.: 21. - Исследование выполнено за счет гранта Российского научного фонда № 22-64-00041, https://rscf.ru/project/22-64-00041/. Работа также поддержана в рамках государственного задания ИХБФМ СО РАН No121030200173-6 (наработка вируса). Авторы благодарят Межведомственный суперкомпьютерный центр Российской академии наук (МСЦ РАН) за предоставление вычислительных мощностей . - ISSN 1819-9496. - ISSN 2500-0136
   Перевод заглавия: Obtaining highly selective aptamers to the VV-GMCSF-Lact oncolytic virus. Theoretical and experimental approaches
Кл.слова (ненормированные):
аптамеры -- SELEX -- онколитический вирус VV-GMCSF-Lact -- цитофлуориметрия -- молекулярная динамика -- компьютерное моделирование -- aptamers -- SELEX -- VV-GMCSF-Lact oncolytic virus -- cytofluorimetry -- molecular dynamics -- computer modelling
Аннотация: Введение. Деструкция злокачественных опухолей с помощью онколитических вирусов – один из наиболее эффективных и безопасных способов противоопухолевой терапии. Для получения доступа к опухолевым клеткам вирус должен длительное время циркулировать в кровотоке, избегая действия иммунной системы. Однако при введении вируса в организм он провоцирует выработку вируснейтрализующих антител, снижающих его противоопухолевый эффект. Наиболее эффективным способом защиты вируса от нейтрализующих антител является его экранирование, в частности, с помощью селективных к нему ДНК-аптамеров. Цель исследования. С помощью экспериментальных методов и теоретических расчётов разработать подходящие для создания противоопухолевого препарата на основе онколитического вируса VV-GMCSF-Lact ДНК-аптамеры, эффективно экранирующие вирусы и способные защитить их от вируснейтрализующих антител. Материал и методы. Моделирование вторичных структур аптамеров выполнено в программе для фолдинга нуклеиновых кислот mFold, моделирование соответствующих пространственных полноатомных структур аптамеров – в программах SimRNA и VMD. Расчёты молекулярной динамики проведены в программном пакете GROMACS 2018.8. Кластерный анализ полученных молекулярно-динамических траекторий выполнен в программе VMD. Оценка связывания Cy5-модифицированных аптамеров с вирусом проведена с помощью проточной цитометрии на цитофлуориметре BD FACSCanto II (Becton Dickinson, г. Франклин Лейкс, Нью-Джерси, США). Результаты. Модификация аптамеров, экспериментально полученных с помощью технологии SELEX, позволила получить пять укороченных олигонуклеотидов NV1t_72, NV4t_64, NV4t_53, NV14t_41 и NV14t_57, экранирующих онколитический вирус VV-GMCSF-Lact, самым эффективным из которых оказался аптамер NV14t_57. Теоретические расчёты показали, что аффинность аптамеров определяется их трёхмерной структурой, зависящей от способа модификации. Заключение. Получен высокоселективный аптамер NV14t_57, который является наиболее перспективным кандидатом для дальнейшей работы по созданию препарата для противоопухолевой терапии онкологических заболеваний на основе онколитического вируса осповакцины VVGMCSF-Lact.
Introduction. Destruction of malignant tumours with oncolytic viruses is one of the most effective and safe methods of antitumor therapy. To gain access to tumour cells, the virus must circulate in the bloodstream for a long time, avoiding the action of the immune system. However, when a virus is introduced into the body, it provokes the production of virus-neutralising antibodies that reduce its antitumor effect. The most effective way to protect a virus from antibodies that neutralise it is to screen it: in particular, using selective DNA aptamers. The aim of the research. Using experimental methods and theoretical calculations, to develop DNA aptamers suitable for creating an antitumor drug based on the VV-GMCSF-Lact oncolytic virus, which effectively screen viruses and can protect them from virus-neutralising antibodies. Material and methods. Modelling of the secondary structures of aptamers was performed using the mFold program for nucleic acid folding, modelling of the corresponding spatial full-atom structures of aptamers was performed using the SimRNA and VMD programs. Molecular dynamics calculations were carried out using the GROMACS 2018.8 software package. Cluster analysis of the obtained molecular dynamic trajectories was performed using the VMD program. Binding of Cy5-modified aptamers to the virus was assessed using flow cytometry on a BD FACSCanto II cytometer (Becton Dickinson, Franklin Lakes, New Jersey, USA). Results. Modification of aptamers experimentally obtained using the SELEX technology made it possible to obtain five truncated oligonucleotides NV1t_72, NV4t_64, NV4t_53, NV14t_41, and NV14t_57, which screen the oncolytic virus VV-GMCSF-Lact, the most effective of which was the NV14t_57 aptamer. Theoretical calculations have shown that the affinity of aptamers is determined by their three-dimensional structure, which depends on the method of modification. Conclusion. A highly selective aptamer NV14t_57 has been obtained, which is the most promising candidate for further work on the creation of a drug for antitumor therapy of oncological diseases based on the VV-GMCSF-Lact oncolytic vaccinia virus.

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Держатели документа:
Институт химической биологии и фундаментальной медицины СО РАН, Новосибирск 630090, Российская Федерация
Красноярский государственный медицинский университет имени профессора В. Ф. Войно-Ясенецкого, Красноярск 660022, Российская Федерация
Федеральный исследовательский центр «Красноярский научный центр» СО РАН, Красноярск 660036, Российская Федерация
Сибирский федеральный университет, Красноярск 660041, Российская Федерация
Институт физики им. Л. В. Киренского СО РАН, Красноярск 660036, Российская Федерация

Доп.точки доступа:
Дымова, М. А.; Кулигина, Е. В.; Рихтер, В. А.; Артюшенко, П. В.; Рогова, А. В.; Щугорева, И. А.; Томилин, Феликс Николаевич; Tomilin, F. N.; Кичкайло, А. С.; Замай, Т. Н.

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Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells / A. S. Kichkailo, A. A. Narodov, M. A. Komarova [et al.] // Mol. Ther. - Nucleic Acids. - 2023. - Vol. 32. - P. 267-288, DOI 10.1016/j.omtn.2023.03.015. - 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) . - ISSN 2162-2531
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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Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
Department of Molecular Electronics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 50 Akademgorodok, Krasnoyarsk 660036, Russia
National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
Krasnoyarsk Regional Pathology-Anatomic Bureau, 3d Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
Department of Chemistry, Lomonosov Moscow State University, 1/3 Leninskie gory, Moscow 119991, Russia
Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 702-701, South Korea
Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” RAS, 59 Leninsky pr., Moscow, 119333, Russia
Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
Institute of Chemistry and Chemical Technology SB RAS – The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, Ontario K1N6N5, Canada
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 8 Lavrentyev Avenue, 630090 Novosibirsk, Russia

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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.; Заблуда, Владимир Николаевич; 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.; Лапин, И. Н.; 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.; Соколов, Алексей Эдуардович; 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.; Томилин, Феликс Николаевич; Berezovski, Maxim V.
}
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Structural analysis of thrombin-binding G-aptamers in presence of bivalent ions / P. A. Nikolaeva, R. V. Moryachkov, V. N. Raldugina [et al.] // Sib. Med. Rev. - 2022. - Is. 5. - P. 111-113 ; Сиб. мед. обозрение, DOI 10.20333/25000136-2022-5-111-113. - Cited References: 4. - The study was supported by a grant from the Russian Science Foundation (project number 21-73-20240) . - ISSN 1819-9496
Кл.слова (ненормированные):
3D structures -- DNA aptamers -- thrombin inhibitors -- G-quadruplexes
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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Держатели документа:
Department bioimformatics and bioengineery, Lomonosov Moscow State University, Moscow, 119992, Russian Federation
Federal Research Center «Krasnoyarsk Science Center SB RAS», Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk, 660036, Russian Federation
Belozersky Institute of physical chemical biology, Lomonosov Moscow State University, Moscow, 119992, Russian Federation

Доп.точки доступа:
Nikolaeva, P. A.; Moryachkov, R. V.; Морячков, Роман Владимирович; Raldugina, V. N.; Naumova, Iu. O.; Novikova, T. M.; Spiridonova, V. A.

}
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Structure- and interaction-based design of anti-SARS-CoV-2 Aptamers / V. Mironov, I. A. Shchugoreva, P. V. Artyushenko [et al.] // Chem. - Eur. J. - 2022. - Vol. 28, Is. 12. - Ст. e202104481, DOI 10.1002/chem.202104481. - 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.) . - ISSN 0947-6539. - ISSN 1521-3765

РУБ Chemistry, Multidisciplinary
Рубрики:
BIOLOGICAL MACROMOLECULES
   SOLUTION SCATTERING
   BINDING
   SPIKE
Кл.слова (ненормированные):
aptamers -- fragment molecular orbitals method -- molecular dynamics -- SARS-CoV-2 -- SAXS
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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Держатели документа:
Lomonosov Moscow State Univ, Dept Chem, Moscow 119991, Russia.
Kyungpook Natl Univ, Dept Chem, Daegu 702701, South Korea.
Fed Res Ctr KSC SB RAS, Lab Digital Controlled Drugs & Theranost, Krasnoyarsk 660036, Russia.
Natl Tsing Hua Univ, Dept Chem Engn, Hsinchu 30013, Taiwan.
Siberian Fed Univ, Sch Nonferrous Met & Mat Sci, Krasnoyarsk 660041, Russia.
IRCCS Neuromed Ist Neurol Mediterraneo Pozzilli, Via Atinense 18, I-86077 Pozzilli, Italy.
Krasnoyarsk State Med Univ, Lab Biomol & Med Technol, Krasnoyarsk 660022, Russia.
Univ Jyvaskyla, Nanosci Ctr, Jyvaskyla 40014, Finland.
Univ Jyvaskyla, Dept Chem, Jyvaskyla 40014, Finland.
Univ Naples Federico II, Dept Pharm, I-80138 Naples, Italy.
Univ Naples Federico II, Dept Mol Med & Med Biotechnol, I-80131 Naples, Italy.
Kirensky Inst Phys, Lab Phys Magnet Phenomena, Krasnoyarsk 660012, Russia.
Siberian Fed Univ, Sch Fundamental Biol & Biotechnol, Krasnoyarsk 660041, Russia.
Xiamen Univ, Coll Chem & Chem Engn, Dept Chem Biol, Xiamen 361005, Peoples R China.
State Res Ctr Virol & Biotechnol Vector, Koltsov 630559, Russia.
NRC Kurchatov Inst, Moscow 117259, Russia.
Russian Acad Sci, Siberian Branch, Inst Chem Biol & Fundamental Med, Novosibirsk 630090, Russia.
Russian Acad Sci, Res Ctr Biotechnol, AN Bach Inst Biochem, Lab Immunobiochem, Moscow 119071, Russia.
Tomsk State Univ, Lab Adv Mat & Technol, Tomsk 634050, Russia.
Altai State Univ, Barnaul 656049, Russia.
Fed Res Ctr KSC SB RAS, Dept Mol Elect, Krasnoyarsk 660036, Russia.
Krasnoyarsk State Med Univ, Dept Infect Dis & Epidemiol, Krasnoyarsk 660022, Russia.
Natl Pingtung Univ, Dept Appl Chem, Pingtung 900391, Taiwan.
Natl Synchrotron Radiat Res Ctr, Hsinchu Sci Pk, Hsinchu 30076, Taiwan.
Res Natl Council CNR, Inst Genet & Biomed Res IRGB, I-09042 Milan, Italy.
Shanghai Jiao Tong Univ, Sch Med, Renji Hosp, Inst Mol Med, Shanghai 200127, Peoples R China.
Natl Inst Adv Ind Sci & Technol, Res Ctr Computat Design Adv Funct Mat, Tsukuba, Ibaraki 3058560, Japan.
Hunan Univ, Coll Chem & Chem Engn, Changsha 410082, Hunan, Peoples R China.
Argonne Natl Lab, Computat Sci Div, Lemont, IL 60439 USA.
Dept Chem & Biomol Sci, Ottawa, ON K1N 6N5, Canada.

Доп.точки доступа:
Mironov, Vladimir; Shchugoreva, I. A.; Artyushenko, P. V.; Артюшенко, Полина Владимировна; Morozov, D. I.; Морозов, Дмитрий И.; Borbone, N.; Oliviero, G.; Zamay, T. N.; Замай, Т. Н.; Moryachkov, R. V.; Морячков, Роман Владимирович; Kolovskaya, .; Коловская О. С.; Lukyanenko, K. A.; Лукьяненко Кирилл А.; Song, Y. L.; Merkuleva, I. A.; Zabluda, V. N.; Заблуда, Владимир Николаевич; 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.; Замай, Галина Сергеевна; Zamay, S. S.; Замай, С. С.; Smolyarova, T. E.; Смолярова, Татьяна Евгеньевна; 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.; Томилин, Феликс Николаевич; Tan, Y.; Alexeev, M. V.; Berezovski, A. S.; Kichkailo, A.S.; 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]
}
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Nucleic acid aptamers increase the anticancer efficiency and reduce the toxicity of cisplatin-arabinogalactan conjugates in vivo / T. N. Zamay, A. K. Starkov, O. S. Kolovskaya [et al.] // Nucleic Acid Ther. - 2022. - Vol. 32, Is. 6. - P. 497-506, DOI 10.1089/nat.2022.0024. - Cited References: 42 . - ISSN 2159-3337. - ISSN 2159-3345
Кл.слова (ненормированные):
cisplatin -- aptamer -- arabinogalactan -- cancer chemotherapy -- ascites carcinoma
Аннотация: Cisplatin is an effective drug for treating various cancer types. However, it is highly toxic for both healthy and tumor cells. Therefore, there is a need to reduce its therapeutic dose and increase targeted bioavailability. One of the ways to achieve this could be the coating of cisplatin with polysaccharides and specific carriers for targeted delivery. Nucleic acid aptamers could be used as carriers for the specific delivery of medicine to cancer cells. Cisplatin-arabinogalactan-aptamer (Cis-AG-Ap) conjugate was synthesized based on Cis-dichlorodiammineplatinum, Siberian larch arabinogalactan, and aptamer AS-42 specific to heat-shock proteins (HSP) 71?kDa (Hspa8) and HSP 90-beta (Hsp90ab1). The antitumor effect was estimated using ascites and metastatic Ehrlich tumor models. Cis-AG-Ap toxicity was assessed by blood biochemistry on healthy mice. Here, we demonstrated enhanced anticancer activity of Cis-AG-Ap and its specific accumulation in tumor foci. It was shown that targeted delivery allowed a 15-fold reduction in the therapeutic dose of cisplatin and its toxicity. Cis-AG-Ap sufficiently suppressed the growth of Ehrlich's ascites carcinoma, the mass and extent of tumor metastasis in vivo. Arabinogalactan and the aptamers promoted cisplatin efficiency by enhancing its bioavailability. The described strategy could be very promising for targeted anticancer therapy.

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Держатели документа:
Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russian Federation
Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russian Federation
Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS, Krasnoyarsk660036, Russian Federation
Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russian Federation
Laboratory for Physics of Magnetic Phenomena, Kirensky Institute of Physics, Federal Research Center Krasnoyarsk Science Center SB RAS, Krasnoyarsk, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada

Доп.точки доступа:
Zamay, T. N.; Starkov, A. K.; Kolovskaya, O. S.; Zamay, G. S.; Veprintsev, D. V.; Luzan, N.; Nikolaeva, E. D.; Lukyanenko, K. A.; Artyushenko, P. V.; Shchugoreva, I. A.; Glazyrin, Y. E.; Koshmanova, A. A.; Krat, A. V.; Tereshina, D. S.; Zamay, S. S.; Pats, Y. S.; Zukov, R. A.; Tomilin, F. N.; Томилин, Феликс Николаевич; Berezovski, M. V.; Kichkailo, A. S.
}
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"Smart" nanoscalpel for microsurgery of glial tumors of the human brain / S. S. Zamay, A. A. Narodov, R. G. Galeev [et al.] // Sib. Med. Rev. - 2022. - Is. 5. - P. 109-110 ; Сиб. мед. обозрение, DOI 10.20333/25000136-2022-5-109-110. - Cited References: 2. - 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” № 2022060108781 and with the support of a partner company JSC «NPP «Radiosviaz» . - ISSN 1819-9496
Кл.слова (ненормированные):
aptamers -- glial tumor -- NMR tomography -- «smart» nanoscalpel -- nanodiscs -- magnetomechanical therapy
Аннотация: We studied the effectiveness of magnetomechanical therapy in the treatment of brain glial tumors using magnetic nanodiscs functionalized with DNA aptamers to human brain tumor glial cells. Materials and methods. The formation of a model of human glioblastoma was carried out by intracranial injection of tumor cells of glioblastoma obtained from a patient with glioblastoma. Antitumor therapy was carried out using nanodiscs modified with the Gli233 aptamer. The growth of the glial tumor was monitored using NMR tomography. Results and discussion. Therapy of a glial tumor during 4 sessions of magnetomechanical therapy using a "smart" nanoscalpel in MF (10Hz, 100Oe) led to a significant reduction in its size, while glial tumors in mice that were treated with nanodiscs modified with nonspecific aptamers continued to increase in size. Conclusion. Microsurgery using three-layer magnetic nanodisks with a quasi-dipole structure (Au/Ni/Au) modified with the specific for glial cells Gli233 aptamer (“smart” nanoscalpel) is effective for the treatment of human glial tumors in the brain.

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Держатели документа:
Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", Krasnoyarsk, 660036, Russian Federation
Prof. V. F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russian Federation
JSC «NPP «Radiosviaz», Krasnoyarsk, 660021, Russian Federation
V.P. Astafiev Krasnoyarsk State Pedagogical University, Krasnoyarsk, 660049, Russian Federation
L.V. Kirensky Institute of Physics, Siberian Branch of the Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Zamay, S. S.; Narodov, A. A.; Galeev, R. G.; Prokopenko, V. S.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Borus, A. A.; Борус, Андрей Андреевич; Zabluda, V. N.; Заблуда, Владимир Николаевич; Lukyanenko, A. V.; Лукьяненко, Анна Витальевна; Baron, F. A.; Барон, Филипп Алексеевич; Garifullin, V. F.; Masyugin, A. N.; Zelenov, F. V.; Grek, D. S.; Voronkovskii, I. I.; Gorbushin, A.; Kolovskaya, O. S.; Lukyanenko, K. A.; Nikolaeva, E. D.; Luzan, N. A.; Kichkailo, A. S.

}
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10.

Investigation of the spatial structure of bionanoconjugates based on DNA aptamers by synchrotron methods / R. V. Moryachkov, V. N. Zabluda, I. A. Shchugoreva [et al.] // International conference "Functional materials" : book of abstracts / ed. V. N. Berzhansky ; org. com. S. G. Ovchinnikov [et al.]. - Simferopol, 2021. - P. 310. - 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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Доп.точки доступа:
Berzhansky, V. N. \ed.\; Бержанский, Владимир Наумович; Ovchinnikov, S. G. \org. com.\; Овчинников, Сергей Геннадьевич; Moryachkov, R. V.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; Shchugoreva, Irina A.; Artyushenko, P. V.; Kichkaylo, A.S.; Spiridonova, V. A.; Berlina, A. N.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; "Functional materials", International conference(2021 ; Oct. 4-8 ; Alushta, Russia); Крымский федеральный университет имени В.И. Вернадского
}
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11.

11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography-computed tomography / A. V. Ozerskaya, T. N. Zamay, O. S. Kolovskaya [et al.] // Mol. Ther. Nucl. Acids. - 2021. - Vol. 26. - P. 1159-1172, DOI 10.1016/j.omtn.2021.10.020. - Cited References: 44 . - ISSN 2162-2531
Кл.слова (ненормированные):
11C radiolabeling -- radiopharmaceuticals -- PET/CT -- in vivo imaging -- DNA aptamers -- Ehrlich ascites carcinoma -- metastasis
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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Держатели документа:
Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russian Federation
Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russian Federation
Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russian Federation
Kirensky Institute of Physics, Krasnoyarsk, Russian Federation
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russian Federation

Доп.точки доступа:
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.; Морячков, Роман Владимирович; Zabluda, V. N.; Заблуда, Владимир Николаевич; 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.; Смолярова, Татьяна Евгеньевна; Tomilin, F. N.; Томилин, Феликс Николаевич; Zamay, S. S.; Silnikov, V. N.; Berezovski, M. V.; Kichkailo, A. S.
}
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12.

Computational approach to design of aptamers to the receptor binding domain of sars-cov-2 / P. V. Artyushenko, V. A. Mironov, D. I. Morozov [et al.] // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 66-67 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-66-67. - Cited References: 5 . - ISSN 1819-9496
Кл.слова (ненормированные):
selection -- aptamer -- receptor-binding domain -- SARS-CoV-2
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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Держатели документа:
Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Lomonosov Moscow State University, Moscow, 119991, Russian Federation
University of Jyvaskyla, Jyvaskyla, 40014, Finland
University of Naples Federico II, Naples, 80138, Italy
Kirensky Institute of Physics KSC SB RAS, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Artyushenko, P. V.; Mironov, V. A.; Morozov, D. I.; Shchugoreva, I. A.; Borbone, N.; Tomilin, F. N.; Томилин, Феликс Николаевич; Kichkailo, A. S.

}
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13.

Moryachkov, R. V.
Structure approaches to study of DNA aptamers in solution / R. V. Moryachkov, P. A. Nikolaeva, V. A. Spiridonova // Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P. 76-78 ; Сиб. мед. обозрение, DOI 10.20333/2500136-2021-2-76-78. - Cited References: 5. - The reported study was funded by RFBR, project number 19-32-90266 . - ISSN 1819-9496
Кл.слова (ненормированные):
biomolecules in solution -- tertiary structure -- small-angle X-ray scattering (SAXS) -- structure analysis
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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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center SB RAS”, 50, Akademgorodok St., Krasnoyarsk, 660036, Russian Federation
Kirensky Institute of Physics, Bld. 38, 50, Akademgorodok St., Krasnoyarsk, 660036, Russian Federation
Lomonosov Moscow State University, 1, Leninskie Gory St., Moscow, 119992, Russian Federation
A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Bld. 40, 1, Leninskie Gory St., Moscow, 119992, Russian Federation

Доп.точки доступа:
Nikolaeva, P. A.; Spiridonova, V. A.; Морячков, Роман Владимирович

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14.

Molecular epitope determination of aptamer complexes of the multidomain protein C-met by proteolytic affinity-mass spectrometry / L. Lupu, P. Wiegand, N. Huttmann [et al.] // ChemMedChem. - 2020. - Vol. 15, Is. 4. - P. 363-369, DOI 10.1002/cmdc.201900489. - Cited References: 40. - We gratefully acknowledge the advice and assistance of Prof. Friedemann Volklein and Oliver Muller, MSc in the preparation of chips for the SPR affinity determinations. We thank Dr. Stefan Maeser, Biogen GmbH, Munchen, for valuable advice and critical reading of the manuscript. This work has been partially funded (Chip-MS epitope analysis) by the LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany; Grant 696/19-16 . - ISSN 1860-7179. - ISSN 1860-7187

РУБ Chemistry, Medicinal + Pharmacology & Pharmacy
Рубрики:
DNA APTAMERS
ANTIBODIES
RECOGNITION
Кл.слова (ненормированные):
C-Met protein -- tumor biomarkers -- aptamer-C-Met complexes -- aptamer epitopes -- affinity-mass spectrometry -- epitope peptide analysis
Аннотация: C‐Met protein is a glycosylated receptor tyrosine kinase of the hepatocyte growth factor (HGF), composed of an α and a β chain. Upon ligand binding, C‐Met transmits intracellular signals by a unique multi‐substrate docking site. C‐Met can be aberrantly activated leading to tumorigenesis and other diseases, and has been recognized as a biomarker in cancer diagnosis. C‐Met aptamers have been recently considered a useful tool for detection of cancer biomarkers. Herein we report a molecular interaction study of human C‐Met expressed in kidney cells with two DNA aptamers of 60 and 64 bases (CLN0003 and CLN0004), obtained using the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Epitope peptides of aptamer‐C‐Met complexes were identified by proteolytic affinity‐mass spectrometry in combination with SPR biosensor analysis (PROTEX‐SPR‐MS), using high‐pressure proteolysis for efficient digestion. High affinities (KD, 80–510 nM) were determined for aptamer‐C‐Met complexes, with two‐step binding suggested by kinetic analysis. A linear epitope, C‐Met (381–393) was identified for CLN0004, while the CLN0003 aptamer revealed an assembled epitope comprised of two peptide sequences, C‐Met (524–543) and C‐Met (557–568). Structure modeling of C‐Met‐aptamers were consistent with the identified epitopes. Specificities and affinities were ascertained by SPR analysis of the synthetic epitope peptides. The high affinities of aptamers to C‐Met, and the specific epitopes revealed render them of high interest for cellular diagnostic studies.

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Steinbeis Ctr Biopolymer Anal & Biomed Mass Spect, Marktstr 29, D-65428 Russelsheim, Germany.
Univ Ottawa, Dept Chem & Biomol Sci, Ottawa, ON K1N 6N5, Canada.
Rhein Main Univ, Dept Engn Sci, D-65428 Russelsheim, Germany.
Russian Acad Sci, Siberian Branch, Kirensky Inst Phys, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Krasnoyarsk 66041, Russia.
Russian Acad Sci, Fed Res Ctr, Lab Digital Controlled Drugs & Theranost, Siberian Branch,Krasnoyarsk Sci Ctr, Krasnoyarsk 660036, Russia.
Pressure Biosci Inc, 14 Norfolk Ave, South Easton, MA 02375 USA.

Доп.точки доступа:
Lupu, Loredana; Wiegand, Pascal; Huttmann, N.; Rawer, Stephan; Kleinekofort, Wolfgang; Shugureva, Irina; Kichkailo, Anna S.; Tomilin, F. N.; Томилин, Феликс Николаевич; Lazarev, Alexander; Berezovski, Maxim V.; Przybylski, Michael; LOEWE-3 Funding Agency, Hessen-Agentur, Wiesbaden, Germany [696/19-16]
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15.

Aptamer-conjugated superparamagnetic ferroarabinogalactan nanoparticles for targeted magnetodynamic therapy of cancer / O. S. Kolovskaya, T. N. Zamay, G. S. Zamay [et al.] // Cancers. - 2020. - Vol. 12, Is. 1. - Ст. 216, DOI 10.3390/cancers12010216. - Cited References: 46. - This research was funded by the Ministry of Science and Higher Education of the Russian Federation; project 0287-2019-0007 . - ISSN 2072-6694
Кл.слова (ненормированные):
aptamers -- arabinogalactan -- superparamagnetic ferroarabinogalactans -- drug delivery -- magnetodynamic therapy -- magnetically induced cell disruption -- magnetic resonance imaging
Аннотация: Nanotechnologies involving physical methods of tumor destruction using functional oligonucleotides are promising for targeted cancer therapy. Our study presents magnetodynamic therapy for selective elimination of tumor cells in vivo using DNA aptamer-functionalized magnetic nanoparticles exposed to a low frequency alternating magnetic field. We developed an enhanced targeting approach of cancer cells with aptamers and arabinogalactan. Aptamers to fibronectin (AS-14) and heat shock cognate 71 kDa protein (AS-42) facilitated the delivery of the nanoparticles to Ehrlich carcinoma cells, and arabinogalactan (AG) promoted internalization through asialoglycoprotein receptors. Specific delivery of the aptamer-modified FeAG nanoparticles to the tumor site was confirmed by magnetic resonance imaging (MRI). After the following treatment with a low frequency alternating magnetic field, AS-FeAG caused cancer cell death in vitro and tumor reduction in vivo. Histological analyses showed mechanical disruption of tumor tissues, total necrosis, cell lysis, and disruption of the extracellular matrix. The enhanced targeted magnetic theranostics with the aptamer conjugated superparamagnetic ferroarabinogalactans opens up a new venue for making biocompatible contrasting agents for MRI imaging and performing non-invasive anti-cancer therapies with a deep penetrated magnetic field.

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Держатели документа:
Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia
Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
L.V. Kirensky Institute of Physics SB RAS—The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
Laboratory of Advanced Materials and Technology, Tomsk State University, 634050 Tomsk, Russia
Institute of Chemistry and Chemical Technology SB RAS—The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 660036 Krasnoyarsk, Russia
School of Engineering Physics and Radio Electronics, Siberian Federal University, 660041 Krasnoyarsk, Russia
Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660041 Krasnoyarsk, Russia
Faculty of Physics, Department of Magnetism, Lomonosov Moscow State University, 119991 Moscow, Russia
School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada

Доп.точки доступа:
Kolovskaya, O. S.; Коловская, О. С.; Zamay, T. N.; Замай, Т. Н.; Zamay, G. S.; Замай, Галина Сергеевна; Babkin, V. A.; Medvedeva, E. N.; Neverova, N. A.; Kirichenko, A. K.; Zamay, S. S.; Замай, С. С.; Lapin, I. N.; Morozov, E. V.; Морозов, Евгений Владимирович; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Narodov, A. A.; Fedorov, D. G.; Tomilin, F. N.; Томилин, Феликс Николаевич; Zabluda, V. N.; Заблуда, Владимир Николаевич; Alekhina, Yu.; Lukyanenko, K. A.; Glazyrin, Yu. E.; Svetlichnyi, V. A.; Berezovski, M. V.; Kichkailo, A. S.
}
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16.

Conformational changes in DNA aptamers upon binding to Pb ions / R. V. Moryachkov, A. N. Berlina, P. V. Artyushenko [et al.] // The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials : Proceedings. - VLadivostok : Dalnauka Publishing, 2020. - Ст. VII.31.01p. - P. 193. - The reported study was funded by RFBR, project number 19-32-90266. . - ISBN 978-5-8044-1698-1

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Доп.точки доступа:
Moryachkov, R. V.; Морячков, Роман Владимирович; Berlina, A. N.; Artyushenko, P. V.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Peters, G. S.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Asian School-Conference on Physics and Technology of Nanostructured Materials(5 ; 2020 ; 30 Jul - 3 Aug ; Vladivostok); Азиатская школа-конференция по физике и технологии наноструктурированных материалов(5 ; 2013 ; 30 июля - 3 авг. ; Владивосток)
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17.

Obtaining and properties of biomagnetic nanoconjugates based on DNA aptamers and magnetic nanoparticles for magnetodynamic cell therapy / A. Е. Sokolov, A. V. Kurilova, V. A. Svetlichniy [et al.] // The Fifth Asian School-Conference on Physics and Technology of Nanostructured Materials : Proceedings. - VLadivostok : Dalnauka Publishing, 2020. - Ст. V.01.17o. - P. 147 . - ISBN 978-5-8044-1698-1

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Доп.точки доступа:
Sokolov, A. Е.; Соколов, Алексей Эдуардович; Kurilova, A. V.; Svetlichniy, V. A.; Velikanov, D. A.; Великанов, Дмитрий Анатольевич; Sherepa, A. V.; Volochaev, M. N.; Волочаев, Михаил Николаевич; Goncharova, D. A.; Shabalina, A. V.; Asian School-Conference on Physics and Technology of Nanostructured Materials(5 ; 2020 ; 30 Jul - 3 Aug ; Vladivostok); Азиатская школа-конференция по физике и технологии наноструктурированных материалов(5 ; 2013 ; 30 июля - 3 авг. ; Владивосток)
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18.

Magnetic sorting of tumor cells with attached magnetic nanoparticles in a microchannel / P. Denissenko, V. V. Denisenko, I. Denisov [et al.] // 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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Доп.точки доступа:
Denissenko, P.; Denisenko, V. V.; Denisov, I.; Kantsler, V.; Kolovskaya, O. S.; Коловская, О. С.; Lapin, I. N.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Svetlichnyi, V.; Светличный, В. А.; Zabluda, V. N.; Заблуда, Владимир Николаевич; Zamay, S. S.; Замай, С. С.; Kichkailo, A.S.; Кичкайло, Анна Сергеевна; Aptamers in Russia, international conference(1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk)
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19.

Silicon nanowire based biosensor for detection of organic molecules / A. S. Tarasov, A. V. Lukyanenko, T. E. Smolyarova [et al.] // Molecular Therapy - Nucleic Acids : book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P. 4-5

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Tarasov, A. S.; Тарасов, Антон Сергеевич; Lukyanenko, A. V.; Лукьяненко, Анна Витальевна; Smolyarova, T. E.; Смолярова, Татьяна Евгеньевна; Shanidze, L. V.; Шанидзе, Лев Викторович; Yakovlev, I. A.; Яковлев, Иван Александрович; Volkov, N. V.; Волков, Никита Валентинович; Aptamers in Russia, international conference(1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk)
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20.

Molecular structure restoration of aptamers by small angle X-ray scattering and computer simulation / F. N. Tomilin, R. V. Moryachkov, I. A. Shchugoreva [et al.] // Molecular Therapy - Nucleic Acids : book of abstracts of the 1st Int. conf. "Aptamers in Russia 2019". - 2019. - Vol. 17, Suppl. 1. - P. 4

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Доп.точки доступа:
Tomilin, F. N.; Томилин, Феликс Николаевич; Moryachkov, R. V.; Морячков, Роман Владимирович; Shchugoreva, I. A.; Kaufman, E.; Drevolsky, A.; Sokolov, A. Е.; Соколов, Алексей Эдуардович; Aptamers in Russia, international conference(1 ; 2019 ; Aug. 27-30 ; Krasnoyarsk)
}
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