1
|
Dymova MA, Malysheva DO, Popova VK, Dmitrienko EV, Endutkin AV, Drokov DV, Mukhanov VS, Byvakina AA, Kochneva GV, Artyushenko PV, Shchugoreva IA, Rogova AV, Tomilin FN, Kichkailo AS, Richter VA, Kuligina EV. Characterizing Aptamer Interaction with the Oncolytic Virus VV-GMCSF-Lact. Molecules 2024; 29:848. [PMID: 38398600 PMCID: PMC10892425 DOI: 10.3390/molecules29040848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/06/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Aptamers are currently being investigated for their potential to improve virotherapy. They offer several advantages, including the ability to prevent the aggregation of viral particles, enhance target specificity, and protect against the neutralizing effects of antibodies. The purpose of this study was to comprehensively investigate an aptamer capable of enhancing virotherapy. This involved characterizing the previously selected aptamer for vaccinia virus (VACV), evaluating the aggregation and molecular interaction of the optimized aptamers with the recombinant oncolytic virus VV-GMCSF-Lact, and estimating their immunoshielding properties in the presence of human blood serum. We chose one optimized aptamer, NV14t_56, with the highest affinity to the virus from the pool of several truncated aptamers and built its 3D model. The NV14t_56 remained stable in human blood serum for 1 h and bound to VV-GMCSF-Lact in the micromolar range (Kd ≈ 0.35 μM). Based on dynamic light scattering data, it has been demonstrated that aptamers surround viral particles and inhibit aggregate formation. In the presence of serum, the hydrodynamic diameter (by intensity) of the aptamer-virus complex did not change. Microscale thermophoresis (MST) experiments showed that NV14t_56 binds with virus (EC50 = 1.487 × 109 PFU/mL). The analysis of the amplitudes of MST curves reveals that the components of the serum bind to the aptamer-virus complex without disrupting it. In vitro experiments demonstrated the efficacy of VV-GMCSF-Lact in conjunction with the aptamer when exposed to human blood serum in the absence of neutralizing antibodies (Nabs). Thus, NV14t_56 has the ability to inhibit virus aggregation, allowing VV-GMCSF-Lact to maintain its effectiveness throughout the storage period and subsequent use. When employing aptamers as protective agents for oncolytic viruses, the presence of neutralizing antibodies should be taken into account.
Collapse
Affiliation(s)
- Maya A. Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
| | - Daria O. Malysheva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Victoria K. Popova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
| | - Elena V. Dmitrienko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
| | - Anton V. Endutkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
| | - Danil V. Drokov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Vladimir S. Mukhanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Arina A. Byvakina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova str. 1, 630090 Novosibirsk, Russia
| | - Galina V. Kochneva
- State Research Center of Virology and Biotechnology “Vector”, 630559 Koltsovo, Russia;
| | - Polina V. Artyushenko
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, Partizana Zheleznyaka str. 1, 660022 Krasnoyarsk, Russia; (P.V.A.); (I.A.S.); (A.V.R.); (A.S.K.)
- Federal Research Center KSC SB RAS, 50 Akademgorodok, 660036 Krasnoyarsk, Russia;
| | - Irina A. Shchugoreva
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, Partizana Zheleznyaka str. 1, 660022 Krasnoyarsk, Russia; (P.V.A.); (I.A.S.); (A.V.R.); (A.S.K.)
- Federal Research Center KSC SB RAS, 50 Akademgorodok, 660036 Krasnoyarsk, Russia;
| | - Anastasia V. Rogova
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, Partizana Zheleznyaka str. 1, 660022 Krasnoyarsk, Russia; (P.V.A.); (I.A.S.); (A.V.R.); (A.S.K.)
- Federal Research Center KSC SB RAS, 50 Akademgorodok, 660036 Krasnoyarsk, Russia;
| | - Felix N. Tomilin
- Federal Research Center KSC SB RAS, 50 Akademgorodok, 660036 Krasnoyarsk, Russia;
- Kirensky Institute of Physics, 50/38 Akademgorodok, 660012 Krasnoyarsk, Russia
| | - Anna S. Kichkailo
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, Partizana Zheleznyaka str. 1, 660022 Krasnoyarsk, Russia; (P.V.A.); (I.A.S.); (A.V.R.); (A.S.K.)
- Federal Research Center KSC SB RAS, 50 Akademgorodok, 660036 Krasnoyarsk, Russia;
| | - Vladimir A. Richter
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
| | - Elena V. Kuligina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (D.O.M.); (V.K.P.); (E.V.D.); (A.V.E.); (D.V.D.); (V.S.M.); (A.A.B.); (V.A.R.); (E.V.K.)
| |
Collapse
|
2
|
Stepin EA, Sushko ES, Vnukova NG, Churilov GN, Rogova AV, Tomilin FN, Kudryasheva NS. Effects of Endohedral Gd-Containing Fullerenols with a Different Number of Oxygen Substituents on Bacterial Bioluminescence. Int J Mol Sci 2024; 25:708. [PMID: 38255785 PMCID: PMC10815327 DOI: 10.3390/ijms25020708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Gadolinium (Gd)-containing fullerenols are perspective agents for magnetic resonance imaging and cancer research. They combine the unique paramagnetic properties of Gd with solubility in water, low toxicity and antiradical activity of fullerenols. We compared the bioeffects of two Gd-containing fullerenols with a different number of oxygen groups-20 and 42: Gd@C82O20H14 and Gd@C82O42H32. The bioluminescent bacteria-based assay was applied to monitor the toxicity of fullerenols, bioluminescence was applied as a signal physiological parameter, and bacterial enzyme-based assay was used to evaluate the fullerenol effects on enzymatic intracellular processes. Chemiluminescence luminol assay was applied to monitor the content of reactive oxygen species (ROS) in bacterial and enzymatic media. It was shown that Gd@C82O42H32 and Gd@C82O20H14 inhibited bacterial bioluminescence at >10-1 and >10-2 gL-1, respectively, revealing a lower toxicity of Gd@C82O42H32. Low-concentration (10-3-10-1 gL-1) bacterial bioluminescence activation by Gd@C82O42H32 was observed, while this activation was not found under exposure to Gd@C82O20H14. Additional carboxyl groups in the structure of Gd@C82O42H32 were determined by infrared spectroscopy and confirmed by quantum chemical calculations. The groups were supposed to endow Gd@C82O42H32 with higher penetration ability through the cellular membrane, activation ability, lower toxicity, balancing of the ROS content in the bacterial suspensions, and lower aggregation in aqueous media.
Collapse
Affiliation(s)
- Evsei A. Stepin
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
| | - Ekaterina S. Sushko
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
- Institute of Biophysics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
| | - Natalia G. Vnukova
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Solid State Physics and Nanotechnology, School of Engineering Physics and Radioelectronics, Siberian Federal University, 660074 Krasnoyarsk, Russia
| | - Grigoriy N. Churilov
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Solid State Physics and Nanotechnology, School of Engineering Physics and Radioelectronics, Siberian Federal University, 660074 Krasnoyarsk, Russia
| | - Anastasia V. Rogova
- Department of Physical and Inorganic Chemistry, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660025 Krasnoyarsk, Russia;
- Laboratory for Digital Controlled Drugs and Theranostics, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - Felix N. Tomilin
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Physical and Inorganic Chemistry, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660025 Krasnoyarsk, Russia;
- Laboratory for Digital Controlled Drugs and Theranostics, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - Nadezhda S. Kudryasheva
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
- Institute of Biophysics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| |
Collapse
|
3
|
Yakimanskiy AA, Kaskevich KI, Zhukova EV, Berezin IA, Litvinova LS, Chulkova TG, Lypenko DA, Dmitriev AV, Pozin SI, Nekrasova NV, Tomilin FN, Ivanova DA, Yakimansky AV. Synthesis, Photo- and Electroluminescence of New Polyfluorene Copolymers Containing Dicyanostilbene and 9,10-Dicyanophenanthrene in the Main Chain. Materials (Basel) 2023; 16:5592. [PMID: 37629884 PMCID: PMC10456789 DOI: 10.3390/ma16165592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023]
Abstract
Using palladium-catalyzed Suzuki polycondensation, we synthesized new light-emitting fluorene copolymers containing the dicyano derivatives of stilbene and phenanthrene and characterized them by gel permeation chromatography, UV-vis absorption spectroscopy, spectrofluorimetry, and cyclic voltammetry. The photoluminescence spectra of the synthesized polymers show significant energy transfer from the fluorene segments to the dicyanostilbene and 9,10-dicyanophenanthrene units, which is in agreement with the data of theoretical calculations. OLEDs based on these polymers were fabricated with an ITO/PEDOT-PSS (35 nm)/p-TPD (30 nm)/PVK (5 nm)/light emitting layer (70-75 nm)/PF-PO (20 nm)/LiF (1 nm)/Al (80 nm) configuration. Examination of their electroluminescence revealed that copolymers of fluorene with dicyanostilbene show yellow-green luminescence, while polymers with 9,10-dicyanophenanthrene have a greenish-blue emission. The 9,10-dicyanophenanthrene units have a more rigid structure compared to dicyanostilbene and, in OLEDs based on them, an increase in maximum brightness is observed with an increase in the content of the additive to the polymer chain. In particular, the device using fluorene copolymer with 9,10-dicyanophenanthrene (2.5 mol%) exhibited a maximum brightness of 9230 cd/m2 and a maximum current efficiency of 3.33 cd/A.
Collapse
Affiliation(s)
- Anton A. Yakimanskiy
- Institute of Macromolecular Compounds RAS, Bolshoi Prospect of Vasilyevsky Island 31, St. Petersburg 199004, Russia; (A.A.Y.); (K.I.K.); (E.V.Z.); (I.A.B.); (L.S.L.); (T.G.C.)
| | - Ksenia I. Kaskevich
- Institute of Macromolecular Compounds RAS, Bolshoi Prospect of Vasilyevsky Island 31, St. Petersburg 199004, Russia; (A.A.Y.); (K.I.K.); (E.V.Z.); (I.A.B.); (L.S.L.); (T.G.C.)
| | - Elena V. Zhukova
- Institute of Macromolecular Compounds RAS, Bolshoi Prospect of Vasilyevsky Island 31, St. Petersburg 199004, Russia; (A.A.Y.); (K.I.K.); (E.V.Z.); (I.A.B.); (L.S.L.); (T.G.C.)
| | - Ivan A. Berezin
- Institute of Macromolecular Compounds RAS, Bolshoi Prospect of Vasilyevsky Island 31, St. Petersburg 199004, Russia; (A.A.Y.); (K.I.K.); (E.V.Z.); (I.A.B.); (L.S.L.); (T.G.C.)
| | - Larisa S. Litvinova
- Institute of Macromolecular Compounds RAS, Bolshoi Prospect of Vasilyevsky Island 31, St. Petersburg 199004, Russia; (A.A.Y.); (K.I.K.); (E.V.Z.); (I.A.B.); (L.S.L.); (T.G.C.)
| | - Tatiana G. Chulkova
- Institute of Macromolecular Compounds RAS, Bolshoi Prospect of Vasilyevsky Island 31, St. Petersburg 199004, Russia; (A.A.Y.); (K.I.K.); (E.V.Z.); (I.A.B.); (L.S.L.); (T.G.C.)
| | - Dmitriy A. Lypenko
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy Prospect 31, bld.4, Moscow 119071, Russia; (D.A.L.); (A.V.D.); (S.I.P.); (N.V.N.)
| | - Artem V. Dmitriev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy Prospect 31, bld.4, Moscow 119071, Russia; (D.A.L.); (A.V.D.); (S.I.P.); (N.V.N.)
| | - Sergey I. Pozin
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy Prospect 31, bld.4, Moscow 119071, Russia; (D.A.L.); (A.V.D.); (S.I.P.); (N.V.N.)
| | - Natalia V. Nekrasova
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry RAS, Leninskiy Prospect 31, bld.4, Moscow 119071, Russia; (D.A.L.); (A.V.D.); (S.I.P.); (N.V.N.)
| | - Felix N. Tomilin
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk 660036, Russia;
- School of Non-Ferrous Metals and Material Science, Siberian Federal University, Krasnoyarsk 660041, Russia;
| | - Daria A. Ivanova
- School of Non-Ferrous Metals and Material Science, Siberian Federal University, Krasnoyarsk 660041, Russia;
| | - Alexander V. Yakimansky
- Institute of Macromolecular Compounds RAS, Bolshoi Prospect of Vasilyevsky Island 31, St. Petersburg 199004, Russia; (A.A.Y.); (K.I.K.); (E.V.Z.); (I.A.B.); (L.S.L.); (T.G.C.)
| |
Collapse
|
4
|
Kolovskaya OS, Zyuzyukina AV, Dassie JP, Zamay GS, Zamay TN, Boyakova NV, Khorzhevskii VA, Kirichenko DA, Lapin IN, Shchugoreva IA, Artyushenko PV, Tomilin FN, Veprintsev DV, Glazyrin YE, Minic Z, Bozhenko VK, Kudinova EA, Kiseleva YY, Krat AV, Slepov EV, Bukatin AS, Zukov RA, Shesternya PA, Berezovski MV, Giangrande PH, Kichkailo AS. Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples. Front Mol Biosci 2023; 10:1184285. [PMID: 37363395 PMCID: PMC10285395 DOI: 10.3389/fmolb.2023.1184285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: Breast cancer (BC) diagnostics lack noninvasive methods and procedures for screening and monitoring disease dynamics. Admitted CellSearch® is used for fluid biopsy and capture of circulating tumor cells of only epithelial origin. Here we describe an RNA aptamer (MDA231) for detecting BC cells in clinical samples, including blood. The MDA231 aptamer was originally selected against triple-negative breast cancer cell line MDA-MB-231 using cell-SELEX. Methods: The aptamer structure in solution was predicted using mFold program and molecular dynamic simulations. The affinity and specificity of the evolved aptamers were evaluated by flow cytometry and laser scanning microscopy on clinical tissues from breast cancer patients. CTCs were isolated form the patients' blood using the developed method of aptamer-based magnetic separation. Breast cancer origin of CTCs was confirmed by cytological, RT-qPCR and Immunocytochemical analyses. Results: MDA231 can specifically recognize breast cancer cells in surgically resected tissues from patients with different molecular subtypes: triple-negative, Luminal A, and Luminal B, but not in benign tumors, lung cancer, glial tumor and healthy epithelial from lungs and breast. This RNA aptamer can identify cancer cells in complex cellular environments, including tumor biopsies (e.g., tumor tissues vs. margins) and clinical blood samples (e.g., circulating tumor cells). Breast cancer origin of the aptamer-based magnetically separated CTCs has been proved by immunocytochemistry and mammaglobin mRNA expression. Discussion: We suggest a simple, minimally-invasive breast cancer diagnostic method based on non-epithelial MDA231 aptamer-specific magnetic isolation of circulating tumor cells. Isolated cells are intact and can be utilized for molecular diagnostics purposes.
Collapse
Affiliation(s)
- Olga S. Kolovskaya
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Alena V. Zyuzyukina
- Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Justin P. Dassie
- Department of Internal Medicine, University of Iowa, Iowa, IA, United States
| | - Galina S. Zamay
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Tatiana N. Zamay
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Nina V. Boyakova
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
- Department of General Surgery, Named After Prof. M.I. Gulman, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Vladimir A. Khorzhevskii
- Department of Pathological Anatomy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Daria A. Kirichenko
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Ivan N. Lapin
- Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk, Russia
| | - Irina A. Shchugoreva
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Polina V. Artyushenko
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, Russia
| | - Felix N. Tomilin
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, Russia
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, Russia
| | - Dmitry V. Veprintsev
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Yury E. Glazyrin
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Zoran Minic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | | | | | | | - Alexey V. Krat
- Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Eugene V. Slepov
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Anton S. Bukatin
- Alferov Federal State Budgetary Institution of Higher Education and Science, Saint Petersburg National Research Academic University of the Russian Academy of Sciences, Saint Petersburg, Russia
- Institute for Analytical Instrumentation of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Ruslan A. Zukov
- Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Pavel A. Shesternya
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Paloma H. Giangrande
- Department of Internal Medicine, University of Iowa, Iowa, IA, United States
- Platform Discovery Sciences, Biology, Wave Life Sciences, Cambridge, MA, United States
| | - Anna S. Kichkailo
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| |
Collapse
|
5
|
Poolsup S, Zaripov E, Hüttmann N, Minic Z, Artyushenko PV, Shchugoreva IA, Tomilin FN, Kichkailo AS, Berezovski MV. Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics. Mol Ther Nucleic Acids 2023; 31:731-743. [PMID: 36816615 PMCID: PMC9927813 DOI: 10.1016/j.omtn.2023.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
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.
Collapse
Affiliation(s)
- Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Polina V Artyushenko
- 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
| | - Irina A Shchugoreva
- 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
| | - Felix N Tomilin
- Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia.,Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia
| | - Anna S Kichkailo
- 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
| | - Maxim V Berezovski
- 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
| |
Collapse
|
6
|
Kichkailo AS, Narodov AA, Komarova MA, Zamay TN, Zamay GS, Kolovskaya OS, Erakhtin EE, Glazyrin YE, Veprintsev DV, Moryachkov RV, Zabluda VV, Shchugoreva I, Artyushenko P, Mironov VA, Morozov DI, Khorzhevskii VA, Gorbushin AV, Koshmanova AA, Nikolaeva ED, Grinev IP, Voronkovskii II, Grek DS, Belugin KV, Volzhentsev AA, Badmaev ON, Luzan NA, Lukyanenko KA, Peters G, Lapin IN, Kirichenko AK, Konarev PV, Morozov EV, Mironov GG, Gargaun A, Muharemagic D, Zamay SS, Kochkina EV, Dymova MA, Smolyarova TE, Sokolov AE, Modestov AA, Tokarev NA, Shepelevich NV, Ozerskaya AV, Chanchikova NG, Krat AV, Zukov RA, Bakhtina VI, Shnyakin PG, Shesternya PA, Svetlichnyi VA, Petrova MM, Artyukhov IP, Tomilin FN, Berezovski MV. Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells. Molecular Therapy - Nucleic Acids 2023; 32:267-288. [PMID: 37090419 PMCID: PMC10119962 DOI: 10.1016/j.omtn.2023.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
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.
Collapse
Affiliation(s)
- Anna S. Kichkailo
- 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
- Corresponding author: Anna S. Kichkailo, Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia.
| | - Andrey A. Narodov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Maria A. Komarova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- 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
| | - Galina S. Zamay
- 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
| | - Olga S. Kolovskaya
- 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
| | - Evgeniy E. Erakhtin
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Yury E. Glazyrin
- 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
| | - Dmitry V. Veprintsev
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Roman V. Moryachkov
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Vladimir V. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina Shchugoreva
- 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
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina Artyushenko
- 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
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Vladimir A. Mironov
- Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, South Korea
| | - Dmitry I. Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
| | - Vladimir A. Khorzhevskii
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, 3d Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Anton V. Gorbushin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Anastasia A. Koshmanova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Elena D. Nikolaeva
- 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
| | - Igor P. Grinev
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Ivan I. Voronkovskii
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Daniil S. Grek
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Kirill V. Belugin
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexander A. Volzhentsev
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Oleg N. Badmaev
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia A. Luzan
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Kirill A. Lukyanenko
- 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
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Georgy Peters
- National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
| | - Ivan N. Lapin
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
| | - Andrey K. Kirichenko
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Petr V. Konarev
- National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” RAS, 59 Leninsky pr., Moscow 119333, Russia
| | - Evgeny V. Morozov
- 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”, Krasnoyarsk 660036, Russia
| | - Gleb G. Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Ana Gargaun
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Darija Muharemagic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Sergey S. Zamay
- 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
| | - Elena V. Kochkina
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Maya A. Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 8 Lavrentyev Avenue, Novosibirsk 630090, Russia
| | - Tatiana E. Smolyarova
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Alexey E. Sokolov
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Andrey A. Modestov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Nikolay A. Tokarev
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Nikolay V. Shepelevich
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anastasia V. Ozerskaya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia G. Chanchikova
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexey V. Krat
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
| | - Ruslan A. Zukov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
| | - Varvara I. Bakhtina
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Pavel G. Shnyakin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Pavel A. Shesternya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Valery A. Svetlichnyi
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
| | - Marina M. Petrova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Ivan P. Artyukhov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Felix N. Tomilin
- 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
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| |
Collapse
|
7
|
Kudryavtsev AN, Krasitskaya VV, Efremov MK, Zangeeva SV, Rogova AV, Tomilin FN, Frank LA. Ca 2+-Triggered Coelenterazine-Binding Protein Renilla: Expected and Unexpected Features. Int J Mol Sci 2023; 24:ijms24032144. [PMID: 36768474 PMCID: PMC9917264 DOI: 10.3390/ijms24032144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Ca2+-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay. In search of a similar substrate form for the luciferase NanoLuc, a furimazine-apoCBP complex was prepared and verified against furimazine, coelenterazine, and CBP. Furimazine-apoCBP is relatively stable in solution and in a frozen or lyophilized state, but as distinct from CBP, its bioluminescence reaction with NanoLuc is independent of Ca2+. NanoLuc turned out to utilize all the four substrates under consideration. The pairs of CBP-NanoLuc and coelenterazine-NanoLuc generate bioluminescence with close efficiency. As for furimazine-apoCBP-NanoLuc pair, the efficiency with which it generates bioluminescence is almost twice lower than that of the furimazine-NanoLuc. The integral signal of the CBP-NanoLuc pair is only 22% lower than that of furimazine-NanoLuc. Thus, along with furimazine as the most effective NanoLuc substrate, CBP can also be recommended as a substrate for in vitro analytical application in view of its water solubility, stability, and Ca2+-triggering "character".
Collapse
Affiliation(s)
- Alexander N. Kudryavtsev
- Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
| | - Vasilisa V. Krasitskaya
- Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
| | - Maxim K. Efremov
- School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Sayana V. Zangeeva
- School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
| | - Anastasia V. Rogova
- School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
- Kirensky Institute of Physics, Federal Research Center “Krasnoyarsk Science Center SB”, 660036 Krasnoyarsk, Russia
| | - Felix N. Tomilin
- School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
- Kirensky Institute of Physics, Federal Research Center “Krasnoyarsk Science Center SB”, 660036 Krasnoyarsk, Russia
| | - Ludmila A. Frank
- Institute of Biophysics, Federal Research Center “Krasnoyarsk Science Center SB RAS”, 660036 Krasnoyarsk, Russia
- School of Fundamental Biology and Biotechnology, School of Non-Ferrous Metals and Material Science, Siberian Federal University, pr. Svobodny 79, 660041 Krasnoyarsk, Russia
- Correspondence:
| |
Collapse
|
8
|
Zamay TN, Starkov AK, Kolovskaya OS, Zamay GS, Veprintsev DV, Luzan N, Nikolaeva ED, Lukyanenko KA, Artyushenko PV, Shchugoreva IA, Glazyrin YE, Koshmanova AA, Krat AV, Tereshina DS, Zamay SS, Pats YS, Zukov RA, Tomilin FN, Berezovski MV, Kichkailo AS. Nucleic Acid Aptamers Increase the Anticancer Efficiency and Reduce the Toxicity of Cisplatin-Arabinogalactan Conjugates In Vivo. Nucleic Acid Ther 2022; 32:497-506. [PMID: 35921069 DOI: 10.1089/nat.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Tatiana N Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Alexander K Starkov
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS," Krasnoyarsk, 660036, Russia
| | - Olga S Kolovskaya
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Galina S Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Dmitry V Veprintsev
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia
| | - Natalia Luzan
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Elena D Nikolaeva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Kirill A Lukyanenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia
| | - Polina V Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia
| | - Irina A Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia
| | - Yury E Glazyrin
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Anastasia A Koshmanova
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Alexey V Krat
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Dariya S Tereshina
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Sergey S Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia
| | - Yuriy S Pats
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Ruslan A Zukov
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Felix N Tomilin
- Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia.,Laboratory for Physics of Magnetic Phenomena, Kirensky Institute of Physics, Federal Research Center Krasnoyarsk Science Center SB RAS, Krasnoyarsk, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Anna S Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| |
Collapse
|
9
|
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 U, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky AA, Fedorov DG, Tomilin FN, Tan W, Alexeev Y, Berezovski MV, Kichkailo AS. Cover Feature: Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers (Chem. Eur. J. 12/2022). Chemistry 2022. [PMCID: PMC9086947 DOI: 10.1002/chem.202200378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
10
|
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 U, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky AA, Fedorov DG, Tomilin FN, Tan W, Alexeev Y, Berezovski MV, Kichkailo AS. Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers. Chemistry 2022; 28:e202104481. [PMID: 35025110 PMCID: PMC9015568 DOI: 10.1002/chem.202104481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/10/2022]
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.
Collapse
|
11
|
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, Kichkailo AS. 11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography- computed tomography. Mol Ther Nucleic Acids 2021; 26:1159-1172. [PMID: 34853715 PMCID: PMC8601970 DOI: 10.1016/j.omtn.2021.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/30/2021] [Accepted: 10/19/2021] [Indexed: 11/25/2022]
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 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.
Collapse
Affiliation(s)
- Anastasia V. Ozerskaya
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Olga S. Kolovskaya
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Nikolay A. Tokarev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Kirill V. Belugin
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia G. Chanchikova
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Oleg N. Badmaev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Galina S. Zamay
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | | | - Roman V. Moryachkov
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
- Kirensky Institute of Physics, Krasnoyarsk, Russia
| | | | - Vladimir A. Khorzhevskii
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Nikolay Shepelevich
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Stanislav V. Gappoev
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Elena A. Karlova
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anastasia S. Saveleva
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexander A. Volzhentsev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anna N. Blagodatova
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
| | - Kirill A. Lukyanenko
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | | | - Tatyana E. Smolyarova
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
- Kirensky Institute of Physics, Krasnoyarsk, Russia
| | | | - Sergey S. Zamay
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Anna S. Kichkailo
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| |
Collapse
|
12
|
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, Kichkailo AS. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer. Mol Ther Nucleic Acids 2021; 25:316-327. [PMID: 34458013 PMCID: PMC8379633 DOI: 10.1016/j.omtn.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
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.
Collapse
Affiliation(s)
- Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Roman V. Moryachkov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina A. Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina V. Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Galina S. Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Olga S. Kolovskaya
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey V. Krat
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Vladimir N. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Dmitry V. Veprintsev
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey E. Sokolov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Ruslan A. Zukov
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Felix N. Tomilin
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anna S. Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| |
Collapse
|
13
|
Tomilin FN, Rogova AV, Burakova LP, Tchaikovskaya ON, Avramov PV, Fedorov DG, Vysotski ES. Unusual shift in the visible absorption spectrum of an active ctenophore photoprotein elucidated by time-dependent density functional theory. Photochem Photobiol Sci 2021; 20:10.1007/s43630-021-00039-5. [PMID: 33834429 DOI: 10.1007/s43630-021-00039-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/29/2021] [Indexed: 11/28/2022]
Abstract
Active hydromedusan and ctenophore Ca2+-regulated photoproteins form complexes consisting of apoprotein and strongly non-covalently bound 2-hydroperoxycoelenterazine (an oxygenated intermediate of coelenterazine). Whereas the absorption maximum of hydromedusan photoproteins is at 460-470 nm, ctenophore photoproteins absorb at 437 nm. Finding out a physical reason for this blue shift is the main objective of this work, and, to achieve it, the whole structure of the protein-substrate complex was optimized using a linear scaling quantum-mechanical method. Electronic excitations pertinent to the spectra of the 2-hydroperoxy adduct of coelenterazine were simulated with time-dependent density functional theory. The dihedral angle of 60° of the 6-(p-hydroxy)-phenyl group relative to the imidazopyrazinone core of 2-hydroperoxycoelenterazine molecule was found to be the key factor determining the absorption of ctenophore photoproteins at 437 nm. The residues relevant to binding of the substrate and its adopting the particular rotation were also identified.
Collapse
Affiliation(s)
- Felix N Tomilin
- Kirensky Institute of Physics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/38, Krasnoyarsk, 660036, Russia
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
- National Research Tomsk State University, Lenin Avenue 36, Tomsk, 634050, Russia
| | - Anastasia V Rogova
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
| | - Ludmila P Burakova
- Siberian Federal University, Svobodny 79 pr., Krasnoyarsk, 660041, Russia
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk, 660036, Russia
| | - Olga N Tchaikovskaya
- National Research Tomsk State University, Lenin Avenue 36, Tomsk, 634050, Russia
| | - Pavel V Avramov
- Kyungpook National University, 80 Daehakro, Bukgu, Daegu, 41566, South Korea
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan.
| | - Eugene S Vysotski
- Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, Krasnoyarsk, 660036, Russia.
| |
Collapse
|
14
|
Kazachenko AS, Tomilin FN, Pozdnyakova AA, Vasilyeva NY, Malyar YN, Kuznetsova SA, Avramov PV. Theoretical DFT interpretation of infrared spectra of biologically active arabinogalactan sulphated derivatives. Chem Pap 2020. [DOI: 10.1007/s11696-020-01220-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
15
|
Lupu L, Wiegand P, Hüttmann N, Rawer S, Kleinekofort W, Shugureva I, Kichkailo AS, Tomilin FN, Lazarev A, Berezovski MV, Przybylski M. Front Cover: Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C‐Met by Proteolytic Affinity‐Mass Spectrometry (ChemMedChem 4/2020). ChemMedChem 2020. [DOI: 10.1002/cmdc.202000050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Loredana Lupu
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
| | - Pascal Wiegand
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
| | - Nico Hüttmann
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa Ottawa, ON K1N 6N5 Canada
| | - Stephan Rawer
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
| | - Wolfgang Kleinekofort
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
- Dept. of Engineering SciencesRhein Main University 65428 Rüsselsheim am Main Germany
| | - Irina Shugureva
- Siberian Federal University Krasnoyarsk 66041 Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”Laboratory for Digital Controlled Drugs and Theranostics Krasnoyarsk 660036 Russia
| | - Anna S. Kichkailo
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”Laboratory for Digital Controlled Drugs and Theranostics Krasnoyarsk 660036 Russia
| | - Felix N. Tomilin
- Kirensky Institute of PhysicsRussian Academy of Sciences Siberian Branch Krasnoyarsk 660036 Russia
- Siberian Federal University Krasnoyarsk 66041 Russia
| | - Alexander Lazarev
- Pressure Biosciences Inc. 14 Norfolk Ave. South Easton, MA 02375 USA
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa Ottawa, ON K1N 6N5 Canada
| | - Michael Przybylski
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
| |
Collapse
|
16
|
Lupu L, Wiegand P, Hüttmann N, Rawer S, Kleinekofort W, Shugureva I, Kichkailo AS, Tomilin FN, Lazarev A, Berezovski MV, Przybylski M. Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C-Met by Proteolytic Affinity-Mass Spectrometry. ChemMedChem 2020; 15:363-369. [PMID: 31825565 DOI: 10.1002/cmdc.201900489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/29/2019] [Indexed: 12/21/2022]
Abstract
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.
Collapse
Affiliation(s)
- Loredana Lupu
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
| | - Pascal Wiegand
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
| | - Nico Hüttmann
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Stephan Rawer
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
| | - Wolfgang Kleinekofort
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany.,Dept. of Engineering Sciences, Rhein Main University, 65428, Rüsselsheim am Main, Germany
| | - Irina Shugureva
- Siberian Federal University, Krasnoyarsk, 66041, Russia.,Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Laboratory for Digital Controlled Drugs and Theranostics, Krasnoyarsk, 660036, Russia
| | - Anna S Kichkailo
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Laboratory for Digital Controlled Drugs and Theranostics, Krasnoyarsk, 660036, Russia
| | - Felix N Tomilin
- Kirensky Institute of Physics, Russian Academy of Sciences Siberian Branch, Krasnoyarsk, 660036, Russia.,Siberian Federal University, Krasnoyarsk, 66041, Russia
| | - Alexander Lazarev
- Pressure Biosciences Inc., 14 Norfolk Ave., South Easton, MA, 02375, USA
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Michael Przybylski
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
| |
Collapse
|
17
|
Kolovskaya OS, Zamay TN, Zamay GS, Babkin VA, Medvedeva EN, Neverova NA, Kirichenko AK, Zamay SS, Lapin IN, Morozov EV, Sokolov AE, Narodov AA, Fedorov DG, Tomilin FN, Zabluda VN, Alekhina Y, Lukyanenko KA, Glazyrin YE, Svetlichnyi VA, Berezovski MV, Kichkailo AS. Aptamer-Conjugated Superparamagnetic Ferroarabinogalactan Nanoparticles for Targeted Magnetodynamic Therapy of Cancer. Cancers (Basel) 2020; 12:cancers12010216. [PMID: 31952299 PMCID: PMC7017168 DOI: 10.3390/cancers12010216] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/02/2020] [Accepted: 01/10/2020] [Indexed: 11/16/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Olga S Kolovskaya
- 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
| | - Tatiana N Zamay
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Galina S Zamay
- 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
| | - Vasily A Babkin
- Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Elena N Medvedeva
- Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Nadezhda A Neverova
- Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Andrey K Kirichenko
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Sergey S Zamay
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, 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
| | - Ivan N Lapin
- Laboratory of Advanced Materials and Technology, Tomsk State University, 634050 Tomsk, Russia
| | - Evgeny V Morozov
- 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
- 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
| | - Alexey E Sokolov
- 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
- School of Engineering Physics and Radio Electronics, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Andrey A Narodov
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Felix N Tomilin
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, 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
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Vladimir N Zabluda
- 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
| | - Yulia Alekhina
- Faculty of Physics, Department of Magnetism, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kirill A Lukyanenko
- 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
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Yury E Glazyrin
- 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
| | - Valery A Svetlichnyi
- Laboratory of Advanced Materials and Technology, Tomsk State University, 634050 Tomsk, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Anna S Kichkailo
- 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
| |
Collapse
|
18
|
Fedorov AS, Krasnov PO, Visotin MA, Tomilin FN, Polyutov SP, Ågren H. Charge-transfer plasmons with narrow conductive molecular bridges: A quantum-classical theory. J Chem Phys 2019; 151:244125. [PMID: 31893913 DOI: 10.1063/1.5131734] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We analyze a new type of plasmon system arising from small metal nanoparticles linked by narrow conductive molecular bridges. In contrast to the well-known charge-transfer plasmons, the bridge in these systems consists only of a narrow conductive molecule or polymer in which the electrons move in a ballistic mode, showing quantum effects. The plasmonic system is studied by an original hybrid quantum-classical model accounting for the quantum effects, with the main parameters obtained from first-principles density functional theory simulations. We have derived a general analytical expression for the modified frequency of the plasmons and have shown that its frequency lies in the near-infrared (IR) region and strongly depends on the conductivity of the molecule, on the nanoparticle-molecule interface, and on the size of the system. As illustrated, we explored the plasmons in a system consisting of two small gold nanoparticles linked by a conjugated polyacetylene molecule terminated by sulfur atoms. It is argued that applications of this novel type of plasmon may have wide ramifications in the areas of chemical sensing and IR deep tissue imaging.
Collapse
Affiliation(s)
- A S Fedorov
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - P O Krasnov
- Federal Siberian Research Clinical Center under FMBA of Russia, 660037 Krasnoyarsk, Russia
| | - M A Visotin
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - F N Tomilin
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - S P Polyutov
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - H Ågren
- Federal Siberian Research Clinical Center under FMBA of Russia, 660037 Krasnoyarsk, Russia
| |
Collapse
|
19
|
Smyslov RY, Tomilin FN, Shchugoreva IA, Nosova GI, Zhukova EV, Litvinova LS, Yakimansky AV, Kolesnikov I, Abramov IG, Ovchinnikov SG, Avramov PV. Synthesis and photophysical properties of copolyfluorenes for light-emitting applications: Spectroscopic experimental study and theoretical DFT consideration. POLYMER 2019. [DOI: 10.1016/j.polymer.2019.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
|
20
|
Tomilin FN, Fedorov AS, Artyushenko PV, Ovchinnikov SG, Ovchinnikova TM, Tsikalova PE, Soukhovolsky VG. Estimation of the thermal and photochemical stabilities of pheromones. J Mol Model 2018; 24:323. [PMID: 30357483 DOI: 10.1007/s00894-018-3859-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/05/2018] [Indexed: 10/28/2022]
Abstract
The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value Lмах corresponding to the breaking of the bond under temperature excitation. The kinetic stability calculation only requires the eigenfrequencies and vibrational mode vectors in the molecule ground state to be calculated, without determining the transition states. The weakest bonds in molecules determined by the kinetic stability method are compared with the bond length variations in molecules in the excited state upon absorption of light by a molecule. Good agreement between the results obtained is demonstrated and the difference between them is discussed. The universality of formulations within both approaches used to estimate the stability of different pheromone molecules containing strained cycles and conjugated, double, and single bonds allows these approaches to be applied for studying other molecules. Graphical Abstract Estimation of the thermal and photochemical stabilities of pheromones.
Collapse
Affiliation(s)
- F N Tomilin
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia. .,Siberian Federal University, Krasnoyarsk, 660041, Russia.
| | - A S Fedorov
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia.,Siberian Federal University, Krasnoyarsk, 660041, Russia
| | - P V Artyushenko
- Federal Research Center KSC SB RAS, International Scientific Center for Extreme Organism States Research, Krasnoyarsk, 660036, Russia
| | - S G Ovchinnikov
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia.,Siberian Federal University, Krasnoyarsk, 660041, Russia
| | - T M Ovchinnikova
- Sukachev Institute of Forest, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia
| | - P E Tsikalova
- Federal Research Center KSC SB RAS, International Scientific Center for Extreme Organism States Research, Krasnoyarsk, 660036, Russia
| | - V G Soukhovolsky
- Sukachev Institute of Forest, Federal Research Center KSC SB RAS, Krasnoyarsk, 660036, Russia
| |
Collapse
|
21
|
Kuklin AV, Kuzubov AA, Kovaleva EA, Mikhaleva NS, Tomilin FN, Lee H, Avramov PV. Two-dimensional hexagonal CrN with promising magnetic and optical properties: A theoretical prediction. Nanoscale 2017; 9:621-630. [PMID: 27942666 DOI: 10.1039/c6nr07790k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Half-metallic ferromagnetic materials with planar forms are promising for spintronics applications. A wide range of 2D lattices like graphene, h-BN, transition metal dichalcogenides, etc. are non-magnetic or weakly magnetic. Using first principles calculations, the existence of graphene-like hexagonal chromium nitride (h-CrN) with an almost flat atomically thin structure is predicted. We find that freestanding h-CrN has a 100% spin-polarized half-metallic nature with possible ferromagnetic ordering and a high rate of optical transparency. As a possible method for stabilization and synthesis, deposition of h-CrN on 2D MoSe2 or on MoS2 is proposed. The formation of composites retains the half-metallic properties and leads to the reduction of spin-down band gaps to 1.43 and 1.71 eV for energetically favorable h-CrN/MoSe2 and h-CrN/MoS2 configurations, respectively. Calculation of the dielectric functions of h-CrN, h-CrN/MoSe2 and h-CrN/MoS2 exhibit the high transparency of all three low-dimensional nanomaterials. The honeycomb CrN may be considered as a promising fundamental 2D material for a variety of potential applications of critical importance.
Collapse
Affiliation(s)
- Artem V Kuklin
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia. and Department of Chemistry, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Alexander A Kuzubov
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia. and L.V. Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Evgenia A Kovaleva
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia.
| | | | - Felix N Tomilin
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia. and L.V. Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Hyosun Lee
- Department of Chemistry, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| | - Pavel V Avramov
- Department of Chemistry, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea
| |
Collapse
|
22
|
Alieva RR, Tomilin FN, Kuzubov AA, Ovchinnikov SG, Kudryasheva NS. Ultraviolet fluorescence of coelenteramide and coelenteramide-containing fluorescent proteins. Experimental and theoretical study. J Photochem Photobiol B 2016; 162:318-323. [PMID: 27400455 DOI: 10.1016/j.jphotobiol.2016.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/29/2016] [Accepted: 07/02/2016] [Indexed: 10/21/2022]
Abstract
Coelenteramide-containing fluorescent proteins are products of bioluminescent reactions of marine coelenterates. They are called 'discharged photoproteins'. Their light-induced fluorescence spectra are variable, depending considerably on external conditions. Current work studies a dependence of light-induced fluorescence spectra of discharged photoproteins obelin, aequorin, and clytin on excitation energy. It was demonstrated that photoexcitation to the upper electron-excited states (260-300nm) of the discharged photoproteins initiates a fluorescence peak in the near UV region, in addition to the blue-green emission. To characterize the UV fluorescence, the light-induced fluorescence spectra of coelenteramide (CLM), fluorophore of the discharged photoproteins, were studied in methanol solution. Similar to photoproteins, the CLM spectra depended on photoexcitation energy; the additional peak (330nm) in the near UV region was observed in CLM fluorescence at higher excitation energy (260-300nm). Quantum chemical calculations by time depending method with B3LYP/cc-pVDZ showed that the conjugated pyrazine-phenolic fragment and benzene moiety of CLM molecule are responsible for the additional UV fluorescence peak. Quantum yields of CLM fluorescence in methanol were 0.028±0.005 at 270-340nm photoexcitation. A conclusion was made that the UV emission of CLM might contribute to the UV fluorescence of the discharged photoproteins. The study develops knowledge on internal energy transfer in biological structures - complexes of proteins with low-weight aromatic molecules.
Collapse
Affiliation(s)
- Roza R Alieva
- Institute of Biophysics SB RAS, Akademgorodok 50/50, Krasnoyarsk 660036, Russia
| | - Felix N Tomilin
- Institute of Physics SB RAS, Akademgorodok 50/38, Krasnoyarsk, 660036, Russia; Siberian Federal University, Svobodny Prospect 79, Krasnoyarsk 660041, Russia
| | - Alexander A Kuzubov
- Siberian Federal University, Svobodny Prospect 79, Krasnoyarsk 660041, Russia
| | - Sergey G Ovchinnikov
- Institute of Physics SB RAS, Akademgorodok 50/38, Krasnoyarsk, 660036, Russia; Siberian Federal University, Svobodny Prospect 79, Krasnoyarsk 660041, Russia
| | - Nadezhda S Kudryasheva
- Institute of Biophysics SB RAS, Akademgorodok 50/50, Krasnoyarsk 660036, Russia; Siberian Federal University, Svobodny Prospect 79, Krasnoyarsk 660041, Russia.
| |
Collapse
|
23
|
Tomilin FN, Osina OV, Kuzubov AA, Ovchinnikov SG, Volkova PE, Ovchinnikova TM, Sukhovol'skiĭ VG. [Stability of lepidopterous pheromone molecules of forest insects to environmental factors]. Biofizika 2011; 56:714-722. [PMID: 21950075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The interactions of the pheromones of some representatives of the Lepidoptera order with each other and with materials contained in the forest air, as well as the effect of electromagnetic radiation on pheromone have been studied. It was found that the reactions of pheromones with substances contained in the forest air are irreversible and proceed with the liberation of heat. Electromagnetic radiation affects very strongly the structure of pheromones. In this case, a pheromone molecule is activated and can readily enter into reaction.
Collapse
|
24
|
Tomilin FN, Antipina LI, Vysotskiĭ ES, Ovchinnikov SG, Gitel'zon II. [The mechanism of formation of emitter by fluorescence of calcium-discharged obelin]. Biofizika 2009; 54:630-637. [PMID: 19795783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
It is known that bioluminescence of obelin is triggered by Ca2+ the binding of which to the protein induces the decarboxylation of 2-hydroperoxycoelenterazine. The molecular mechanism of fluorescence of obelin, which determines the fluorescence of see hydroid Obelia Longissima, has been investigated with the use of quantum chemical calculations. According to quantum chemical calculations, the emitter of the reaction is the ion-pair state of phenolate-anion of coelenteramide. It has been shown that the fluorescence spectrum of this state depends on the position of the proton between the oxygen atoms of the phenol group of coelenteramide and the nitrogen atom of His22. The agreement of the calculated absorption and fluorescence spectra with the experimental spectrum shows the accuracy of the quantum chemical calculations and conclusions.
Collapse
|