23 results on '"Veprintsev, Dmitry V."'
Search Results
2. Development of DNA aptamers for visualization of glial brain tumors and detection of circulating tumor cells
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Kichkailo, Anna S., Narodov, Andrey A., Komarova, Maria A., Zamay, Tatiana N., Zamay, Galina S., Kolovskaya, Olga S., Erakhtin, Evgeniy E., Glazyrin, Yury E., Veprintsev, Dmitry V., Moryachkov, Roman V., Zabluda, Vladimir V., Shchugoreva, Irina, Artyushenko, Polina, Mironov, Vladimir A., Morozov, Dmitry I., Khorzhevskii, Vladimir A., Gorbushin, Anton V., Koshmanova, Anastasia A., Nikolaeva, Elena D., Grinev, Igor P., Voronkovskii, Ivan I., Grek, Daniil S., Belugin, Kirill V., Volzhentsev, Alexander A., Badmaev, Oleg N., Luzan, Natalia A., Lukyanenko, Kirill A., Peters, Georgy, Lapin, Ivan N., Kirichenko, Andrey K., Konarev, Petr V., Morozov, Evgeny V., Mironov, Gleb G., Gargaun, Ana, Muharemagic, Darija, Zamay, Sergey S., Kochkina, Elena V., Dymova, Maya A., Smolyarova, Tatiana E., Sokolov, Alexey E., Modestov, Andrey A., Tokarev, Nikolay A., Shepelevich, Nikolay V., Ozerskaya, Anastasia V., Chanchikova, Natalia G., Krat, Alexey V., Zukov, Ruslan A., Bakhtina, Varvara I., Shnyakin, Pavel G., Shesternya, Pavel A., Svetlichnyi, Valery A., Petrova, Marina M., Artyukhov, Ivan P., Tomilin, Felix N., and Berezovski, Maxim V.
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- 2023
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3. Comparative Proteomic Profiling of Blood Plasma Revealed Marker Proteins Involved in Temporal Lobe Epilepsy.
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Glazyrin, Yury E., Veprintsev, Dmitry V., Timechko, Elena E., Minic, Zoran, Zamay, Tatiana N., Dmitrenko, Diana V., Berezovski, Maxim V., and Kichkailo, Anna S.
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TEMPORAL lobe epilepsy , *BLOOD plasma , *PROTEOMICS , *MAGNETIC resonance imaging , *COMPLEMENT (Immunology) , *PROTEINS - Abstract
Temporal lobe epilepsy has various origins, involving or not involving structural changes in brain tissue. The mechanisms of epileptogenesis are associated with cell regulation and signaling disruptions expressed in varied levels of proteins. The blood plasma proteomic profiling of temporal lobe epilepsy patients (including magnetic resonance imaging (MRI)-positive and MRI-negative ones) and healthy volunteers using mass spectrometry and label-free quantification revealed a list of differently expressed proteins. Several apolipoproteins (APOA1, APOD, and APOA4), serpin protease inhibitors (SERPINA3, SERPINF1, etc.), complement components (C9, C8, and C1R), and a total of 42 proteins were found to be significantly upregulated in the temporal lobe epilepsy group. A classification analysis of these proteins according to their biological functions, as well as a review of the published sources, disclosed the predominant involvement of the processes mostly affected during epilepsy such as neuroinflammation, intracellular signaling, lipid metabolism, and oxidative stress. The presence of several proteins related to the corresponding compensatory mechanisms has been noted. After further validation, the newly identified temporal lobe epilepsy biomarker candidates may be used as epilepsy diagnostic tools, in addition to other less specific methods such as electroencephalography or MRI. [ABSTRACT FROM AUTHOR]
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- 2024
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4. Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples
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Kolovskaya, Olga S., primary, Zyuzyukina, Alena V., additional, Dassie, Justin P., additional, Zamay, Galina S., additional, Zamay, Tatiana N., additional, Boyakova, Nina V., additional, Khorzhevskii, Vladimir A., additional, Kirichenko, Daria A., additional, Lapin, Ivan N., additional, Shchugoreva, Irina A., additional, Artyushenko, Polina V., additional, Tomilin, Felix N., additional, Veprintsev, Dmitry V., additional, Glazyrin, Yury E., additional, Minic, Zoran, additional, Bozhenko, Vladimir K., additional, Kudinova, Elena A., additional, Kiseleva, Yana Y., additional, Krat, Alexey V., additional, Slepov, Eugene V., additional, Bukatin, Anton S., additional, Zukov, Ruslan A., additional, Shesternya, Pavel A., additional, Berezovski, Maxim V., additional, Giangrande, Paloma H., additional, and Kichkailo, Anna S., additional
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- 2023
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5. Nucleic Acid Aptamers Increase the Anticancer Efficiency and Reduce the Toxicity of Cisplatin-Arabinogalactan Conjugates In Vivo
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Zamay, Tatiana N., primary, Starkov, Alexander K., additional, Kolovskaya, Olga S., additional, Zamay, Galina S., additional, Veprintsev, Dmitry V., additional, Luzan, Natalia, additional, Nikolaeva, Elena D., additional, Lukyanenko, Kirill A., additional, Artyushenko, Polina V., additional, Shchugoreva, Irina A., additional, Glazyrin, Yury E., additional, Koshmanova, Anastasia A., additional, Krat, Alexey V., additional, Tereshina, Dariya S., additional, Zamay, Sergey S., additional, Pats, Yuriy S., additional, Zukov, Ruslan A., additional, Tomilin, Felix N., additional, Berezovski, Maxim V., additional, and Kichkailo, Anna S., additional
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- 2022
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6. Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers
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Mironov, Vladimir, primary, Shchugoreva, Irina A., additional, Artyushenko, Polina V., additional, Morozov, Dmitry, additional, Borbone, Nicola, additional, Oliviero, Giorgia, additional, Zamay, Tatiana N., additional, Moryachkov, Roman V., additional, Kolovskaya, Olga S., additional, Lukyanenko, Kirill A., additional, Song, Yanling, additional, Merkuleva, Iuliia A., additional, Zabluda, Vladimir N., additional, Peters, Georgy, additional, Koroleva, Lyudmila S., additional, Veprintsev, Dmitry V., additional, Glazyrin, Yury E., additional, Volosnikova, Ekaterina A., additional, Belenkaya, Svetlana V., additional, Esina, Tatiana I., additional, Isaeva, Anastasiya A., additional, Nesmeyanova, Valentina S., additional, Shanshin, Daniil V., additional, Berlina, Anna N., additional, Komova, Nadezhda S., additional, Svetlichnyi, Valery A., additional, Silnikov, Vladimir N., additional, Shcherbakov, Dmitriy N., additional, Zamay, Galina S., additional, Zamay, Sergey S., additional, Smolyarova, Tatyana, additional, Tikhonova, Elena P., additional, Chen, Kelvin H.‐C., additional, Jeng, U‐Ser, additional, Condorelli, Gerolama, additional, Franciscis, Vittorio, additional, Groenhof, Gerrit, additional, Yang, Chaoyong, additional, Moskovsky, Alexander A., additional, Fedorov, Dmitri G., additional, Tomilin, Felix N., additional, Tan, Weihong, additional, Alexeev, Yuri, additional, Berezovski, Maxim V., additional, and Kichkailo, Anna S., additional
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- 2022
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7. 11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography- computed tomography
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Ozerskaya, Anastasia V., primary, Zamay, Tatiana N., additional, Kolovskaya, Olga S., additional, Tokarev, Nikolay A., additional, Belugin, Kirill V., additional, Chanchikova, Natalia G., additional, Badmaev, Oleg N., additional, Zamay, Galina S., additional, Shchugoreva, Irina A., additional, Moryachkov, Roman V., additional, Zabluda, Vladimir N., additional, Khorzhevskii, Vladimir A., additional, Shepelevich, Nikolay, additional, Gappoev, Stanislav V., additional, Karlova, Elena A., additional, Saveleva, Anastasia S., additional, Volzhentsev, Alexander A., additional, Blagodatova, Anna N., additional, Lukyanenko, Kirill A., additional, Veprintsev, Dmitry V., additional, Smolyarova, Tatyana E., additional, Tomilin, Felix N., additional, Zamay, Sergey S., additional, Silnikov, Vladimir N., additional, Berezovski, Maxim V., additional, and Kichkailo, Anna S., additional
- Published
- 2021
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8. Development of Electrochemical Aptasensor for Lung Cancer Diagnostics in Human Blood
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Shabalina, Anastasiia V., primary, Sharko, Darya O., additional, Glazyrin, Yury E., additional, Bolshevich, Elena A., additional, Dubinina, Oksana V., additional, Kim, Anastasiia M., additional, Veprintsev, Dmitry V., additional, Lapin, Ivan N., additional, Zamay, Galina S., additional, Krat, Alexey V., additional, Zamay, Sergey S., additional, Svetlichnyi, Valery A., additional, Kichkailo, Anna S., additional, and Berezovski, Maxim V., additional
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- 2021
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9. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer
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Morozov, Dmitry, primary, Mironov, Vladimir, additional, Moryachkov, Roman V., additional, Shchugoreva, Irina A., additional, Artyushenko, Polina V., additional, Zamay, Galina S., additional, Kolovskaya, Olga S., additional, Zamay, Tatiana N., additional, Krat, Alexey V., additional, Molodenskiy, Dmitry S., additional, Zabluda, Vladimir N., additional, Veprintsev, Dmitry V., additional, Sokolov, Alexey E., additional, Zukov, Ruslan A., additional, Berezovski, Maxim V., additional, Tomilin, Felix N., additional, Fedorov, Dmitri G., additional, Alexeev, Yuri, additional, and Kichkailo, Anna S., additional
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- 2021
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10. The Role of Small-Angle X-Ray Scattering and Molecular Simulations in 3D Structure Elucidation of a DNA Aptamer Against Lung Cancer
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Morozov, Dmitry, Mironov, Vladimir, Moryachkov, Roman V., Shchugoreva, Irina A., Artyushenko, Polina V., Zamay, Galina S., Kolovskaya, Olga S., Zamay, Tatiana N., Krat, Alexey V., Molodenskiy, Dmitry S., Zabluda, Vladimir N., Veprintsev, Dmitry V., Sokolov, Alexey E., Zukov, Ruslan A., Berezovski, Maxim V., Tomilin, Felix N., Fedorov, Dmitri G., Alexeev, Yuri, and Kichkailo, Anna S.
- Subjects
syöpäsolut ,oligonukleotidit ,immuunivaste ,nukleotidit ,vasta-aineet ,molekyylidynamiikka ,simulointi - Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here we present a general optimization procedure for finding most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated aptamer LC-18t was developed. A three-dimensional shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The truncated aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes. peerReviewed
- Published
- 2021
11. Proteomics-Based Regression Model for Assessing the Development of Chronic Lymphocytic Leukemia
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Bakhtina, Varvara I., primary, Veprintsev, Dmitry V., additional, Zamay, Tatiana N., additional, Demko, Irina V., additional, Mironov, Gleb G., additional, Berezovski, Maxim V., additional, Petrova, Marina M., additional, Kichkailo, Anna S., additional, and Glazyrin, Yury E., additional
- Published
- 2021
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12. Proteomics-Based Machine Learning Approach as an Alternative to Conventional Biomarkers for Differential Diagnosis of Chronic Kidney Diseases
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Glazyrin, Yury E., primary, Veprintsev, Dmitry V., additional, Ler, Irina A., additional, Rossovskaya, Maria L., additional, Varygina, Svetlana A., additional, Glizer, Sofia L., additional, Zamay, Tatiana N., additional, Petrova, Marina M., additional, Minic, Zoran, additional, Berezovski, Maxim V., additional, and Kichkailo, Anna S., additional
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- 2020
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13. Noninvasive Microsurgery Using Aptamer-Functionalized Magnetic Microdisks for Tumor Cell Eradication
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Zamay, Tatiana N., primary, Zamay, Galina S., additional, Belyanina, Irina V., additional, Zamay, Sergey S., additional, Denisenko, Valery V., additional, Kolovskaya, Olga S., additional, Ivanchenko, Tatiana I., additional, Grigorieva, Valentina L., additional, Garanzha, Irina V., additional, Veprintsev, Dmitry V., additional, Glazyrin, Yury E., additional, Shabanov, Alexandr V., additional, Prinz, Viktor Y., additional, Seleznev, Vladimir A., additional, Sokolov, Alexey E., additional, Prokopenko, Vladimir S., additional, Kim, Petr D., additional, Gargaun, Ana, additional, Berezovski, Maxim V., additional, and Zamay, Anna S., additional
- Published
- 2017
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14. DNA Aptamers for the Characterization of Histological Structure of Lung Adenocarcinoma
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Zamay, Galina S., primary, Ivanchenko, Tatiana I., additional, Zamay, Tatiana N., additional, Grigorieva, Valentina L., additional, Glazyrin, Yury E., additional, Kolovskaya, Olga S., additional, Garanzha, Irina V., additional, Barinov, Andrey A., additional, Krat, Alexey V., additional, Mironov, Gleb G., additional, Gargaun, Ana, additional, Veprintsev, Dmitry V., additional, Bekuzarov, Sergey S., additional, Kirichenko, Andrey K., additional, Zukov, Ruslan A., additional, Petrova, Marina M., additional, Modestov, Andrey A., additional, Berezovski, Maxim V., additional, and Zamay, Anna S., additional
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- 2017
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15. In Vivo Cancer Cells Elimination Guided by Aptamer-Functionalized Gold-Coated Magnetic Nanoparticles and Controlled with Low Frequency Alternating Magnetic Field
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Belyanina, Irina V., primary, Zamay, Tatiana N., additional, Zamay, Galina S., additional, Zamay, Sergey S., additional, Kolovskaya, Olga S., additional, Ivanchenko, Tatiana I., additional, Denisenko, Valery V., additional, Kirichenko, Andrey K., additional, Glazyrin, Yury E., additional, Garanzha, Irina V., additional, Grigorieva, Valentina V., additional, Shabanov, Alexandr V., additional, Veprintsev, Dmitry V., additional, Sokolov, Alexey E., additional, Sadovskii, Vladimir M., additional, Gargaun, Ana, additional, Berezovski, Maxim V., additional, and Kichkailo, Anna S., additional
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- 2017
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16. Electrochemical aptasensor for lung cancer-related protein detection in crude blood plasma samples
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Zamay, Galina S., primary, Zamay, Tatiana N., additional, Kolovskii, Vasilii A., additional, Shabanov, Alexandr V., additional, Glazyrin, Yury E., additional, Veprintsev, Dmitry V., additional, Krat, Alexey V., additional, Zamay, Sergey S., additional, Kolovskaya, Olga S., additional, Gargaun, Ana, additional, Sokolov, Alexey E., additional, Modestov, Andrey A., additional, Artyukhov, Ivan P., additional, Chesnokov, Nikolay V., additional, Petrova, Marina M., additional, Berezovski, Maxim V., additional, and Zamay, Anna S., additional
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- 2016
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17. Cover Feature: Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers (Chem. Eur. J. 12/2022).
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Mironov, Vladimir, Shchugoreva, Irina A., Artyushenko, Polina V., Morozov, Dmitry, Borbone, Nicola, Oliviero, Giorgia, Zamay, Tatiana N., Moryachkov, Roman V., Kolovskaya, Olga S., Lukyanenko, Kirill A., Song, Yanling, Merkuleva, Iuliia A., Zabluda, Vladimir N., Peters, Georgy, Koroleva, Lyudmila S., Veprintsev, Dmitry V., Glazyrin, Yury E., Volosnikova, Ekaterina A., Belenkaya, Svetlana V., and Esina, Tatiana I.
- Subjects
MOLECULAR orbitals ,MOLECULAR dynamics ,APTAMERS ,SMALL-angle X-ray scattering - Abstract
Keywords: aptamers; fragment molecular orbitals method; molecular dynamics; SARS-CoV-2; SAXS EN aptamers fragment molecular orbitals method molecular dynamics SARS-CoV-2 SAXS 1 1 1 02/28/22 20220224 NES 220224 B Digital drug design reveals DNA aptamers binding SARS-CoV-2 b : A hybrid in silico et vitro approach, structure and interaction-based drug design, has been developed to create highly specific DNA aptamers for the receptor-binding domain of the SARS-CoV-2 spike protein. The structure and binding affinity of the aptamers were validated by small-angle X-ray scattering, flow cytometry, and fluorescence polarization. Cover Feature: Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers (Chem. Eur. J. 12/2022). [Extracted from the article]
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- 2022
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18. Development of DNA Aptamers to Native EpCAM for Isolation of Lung Circulating Tumor Cells from Human Blood.
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Zamay, Galina S., Kolovskaya, Olga S., Ivanchenko, Tatiana I., Zamay, Tatiana N., Veprintsev, Dmitry V., Grigorieva, Valentina L., Garanzha, Irina I., Krat, Alexey V., Glazyrin, Yury E., Gargaun, Ana, Lapin, Ivan N., Svetlichnyi, Valery A., Berezovski, Maxim V., and Kichkailo, Anna S.
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LUNG cancer diagnosis ,CANCER patients ,CELL adhesion molecules ,CELL lines ,DNA ,EPITHELIAL cells ,IMMUNOGLOBULINS ,METASTASIS ,MICROSCOPY ,STATISTICS ,DATA analysis - Abstract
We selected DNA aptamers to the epithelial cell adhesion molecule (EpCAM) expressed on primary lung cancer cells isolated from the tumors of patients with non-small cell lung cancer using competitive displacement of aptamers from EpCAM by a corresponding antibody. The resulting aptamers clones showed good nanomolar affinity to EpCAM-positive lung cancer cells. Confocal microscopy imaging and spectral profiling of lung cancer tissues confirmed the same protein target for the aptamers and anti-EpCAM antibodies. Furthermore, the resulted aptamers were successfully applied for isolation and detection of circulating tumor cells in clinical samples of peripheral blood of lung cancer patients. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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19. Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers
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Vladimir Mironov, Irina A. Shchugoreva, Polina V. Artyushenko, Dmitry Morozov, Nicola Borbone, Giorgia Oliviero, Tatiana N. Zamay, Roman V. Moryachkov, Olga S. Kolovskaya, Kirill A. Lukyanenko, Yanling Song, Iuliia A. Merkuleva, Vladimir N. Zabluda, Georgy Peters, Lyudmila S. Koroleva, Dmitry V. Veprintsev, Yury E. Glazyrin, Ekaterina A. Volosnikova, Svetlana V. Belenkaya, Tatiana I. Esina, Anastasiya A. Isaeva, Valentina S. Nesmeyanova, Daniil V. Shanshin, Anna N. Berlina, Nadezhda S. Komova, Valery A. Svetlichnyi, Vladimir N. Silnikov, Dmitriy N. Shcherbakov, Galina S. Zamay, Sergey S. Zamay, Tatyana Smolyarova, Elena P. Tikhonova, Kelvin H.‐C. Chen, U‐Ser Jeng, Gerolama Condorelli, Vittorio Franciscis, Gerrit Groenhof, Chaoyong Yang, Alexander A. Moskovsky, Dmitri G. Fedorov, Felix N. Tomilin, Weihong Tan, Yuri Alexeev, Maxim V. Berezovski, Anna S. Kichkailo, Mironov, Vladimir, Shchugoreva, Irina A., Artyushenko, Polina V., Morozov, Dmitry, Borbone, Nicola, Oliviero, Giorgia, Zamay, Tatiana N., Moryachkov, Roman V., Kolovskaya, Olga S., Lukyanenko, Kirill A., Song, Yangling, Merkuleva, Iuliia A., Zabluda, Vladimir N., Peters, Georgy, Koroleva, Lyudmila S., Veprintsev, Dmitry V., Glazyrin, Yury E., Volosnikova, Ekaterina A., Belenkaya, Svetlana V., Esina, Tatiana I., Isaeva, Anastasiya A., Nesmeyanova, Valentina S., Shanshin, Daniil V., Berlina, Anna N., Komova, Nadezhda S., Svetlichnyi, Valery A., Silnikov, Vladimir N., Shcherbakov, Dmitriy N., Zamay, Galina S., Zamay, Sergey S., Smolyarova, Tatyana, Tikhonova, Elena P., Chen, Kelvin H. -C., Jeng, U-Ser, Condorelli, Gerolama, de Franciscis, Vittorio, Groenhof, Gerrit, Yang, Chaoyong, Moskovsky, Alexander A., Fedorov, Dmitri G., Tomilin, Felix N., Tan, Weihong, Alexeev, Yuri, Berezovski, Maxim V., and Kichkailo, Anna S
- Subjects
oligonukleotidit ,aptamers, fragment molecular orbitals method, molecular dynamics, SARS-CoV-2, SAXS ,fragment molecular orbitals method ,SARS-CoV-2 ,SELEX Aptamer Technique ,Organic Chemistry ,aptamers ,SARS-CoV-2-virus ,COVID-19 ,SAXS ,General Chemistry ,Aptamers, Nucleotide ,Molecular Dynamics Simulation ,laskennallinen kemia ,molecular dynamics ,Catalysis ,lääkesuunnittelu ,Molecular Docking Simulation ,SARS-CoV-2, белки ,Spike Glycoprotein, Coronavirus ,Humans ,дизайн аптамеров ,molekyylidynamiikka ,proteiinit - Abstract
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.
- Published
- 2022
20. Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers.
- Author
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Mironov V, Shchugoreva IA, Artyushenko PV, Morozov D, Borbone N, Oliviero G, Zamay TN, Moryachkov RV, Kolovskaya OS, Lukyanenko KA, Song Y, Merkuleva IA, Zabluda VN, Peters G, Koroleva LS, Veprintsev DV, Glazyrin YE, Volosnikova EA, Belenkaya SV, Esina TI, Isaeva AA, Nesmeyanova VS, Shanshin DV, Berlina AN, Komova NS, Svetlichnyi VA, Silnikov VN, Shcherbakov DN, Zamay GS, Zamay SS, Smolyarova T, Tikhonova EP, Chen KH, Jeng US, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky AA, Fedorov DG, Tomilin FN, Tan W, Alexeev Y, Berezovski MV, and Kichkailo AS
- Subjects
- Humans, Molecular Docking Simulation, Molecular Dynamics Simulation, SARS-CoV-2, SELEX Aptamer Technique, Spike Glycoprotein, Coronavirus, Aptamers, Nucleotide chemistry, COVID-19
- Abstract
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., (© 2022 Wiley-VCH GmbH.)
- Published
- 2022
- Full Text
- View/download PDF
21. 11 C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography- computed tomography.
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Ozerskaya AV, Zamay TN, Kolovskaya OS, Tokarev NA, Belugin KV, Chanchikova NG, Badmaev ON, Zamay GS, Shchugoreva IA, Moryachkov RV, Zabluda VN, Khorzhevskii VA, Shepelevich N, Gappoev SV, Karlova EA, Saveleva AS, Volzhentsev AA, Blagodatova AN, Lukyanenko KA, Veprintsev DV, Smolyarova TE, Tomilin FN, Zamay SS, Silnikov VN, Berezovski MV, and Kichkailo AS
- Abstract
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
11 C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer. The11 C-aptamer was applied for in vivo imaging of Ehrlich ascites carcinoma and its metastases in mice using PET/CT. The imaging experiments with the11 C-aptamer determined very small primary and secondary tumors of 3 mm2 and less. We also compared11 C imaging with the standard radiotracer, 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18 F-FDG), and found better selectivity of the11 C-aptamer to metastatic lesions in the metabolically active organs than18 F-FDG.11 C 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., Competing Interests: Authors declare no competing interests., (© 2021 The Author(s).)- Published
- 2021
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22. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer.
- Author
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Morozov D, Mironov V, Moryachkov RV, Shchugoreva IA, Artyushenko PV, Zamay GS, Kolovskaya OS, Zamay TN, Krat AV, Molodenskiy DS, Zabluda VN, Veprintsev DV, Sokolov AE, Zukov RA, Berezovski MV, Tomilin FN, Fedorov DG, Alexeev Y, and Kichkailo AS
- Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes., Competing Interests: The authors declare no competing interests., (© 2021.)
- Published
- 2021
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23. DNA Aptamers for the Characterization of Histological Structure of Lung Adenocarcinoma.
- Author
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Zamay GS, Ivanchenko TI, Zamay TN, Grigorieva VL, Glazyrin YE, Kolovskaya OS, Garanzha IV, Barinov AA, Krat AV, Mironov GG, Gargaun A, Veprintsev DV, Bekuzarov SS, Kirichenko AK, Zukov RA, Petrova MM, Modestov AA, Berezovski MV, and Zamay AS
- Abstract
Nucleic acid aptamers are becoming popular as molecular probes for identification and imaging pathology and, at the same time, as a convenient platform for targeted therapy. Recent studies have shown that aptamers may be effectively used for tumor characterization and as commercially available monoclonal antibodies. Here we present three DNA aptamers binding to whole transformed lung cancer tissues, including tumor cells, connective tissues, and blood vessels. Protein targets have been revealed using affinity purification followed by mass spectrometry analyses, and they have been validated using a panel of correspondent antibodies and 3D imaging of tumor tissues. Each of the proteins targeted by the aptamers is involved in cancer progression and most of them are crucial for lung adenocarcinoma. We propose the use of these aptamers in aptahistochemistry for the characterization of the histological structure of lung adenocarcinoma. The value of the presented aptamers is their application together or separately for indicating the spread of neoplastic transformation, for complex differential diagnostics, and for targeted therapy of the tumor itself as well as all transformed structures of the adjacent tissues. Moreover, it has been demonstrated that these aptamers could be used for intraoperative tumor visualization and margin assessment., (Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2017
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