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Polokhov D, Fedorova D, Ignatova A, Ponomarenko E, Rashevskaya E, Martyanov A, Podoplelova N, Aleksenko M, Mersiyanova I, Seregina E, Poletaev A, Truchina E, Raykina E, Plyasunova S, Novichkova G, Zharkov P, Panteleev M. Novel SLFN14 mutation associated with macrothrombocytopenia in a patient with severe haemorrhagic syndrome. Orphanet J Rare Dis 2023; 18:74. [PMID: 37041648 PMCID: PMC10091655 DOI: 10.1186/s13023-023-02675-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 03/11/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND Platelet-type bleeding disorder 20 (BDPLT20), as known as SLFN14-related thrombocytopenia, is a rare inherited thrombocytopenia (IT). Previously, only 5 heterozygous missense mutations in the SLFN14 gene have been reported. METHODS A comprehensive clinical and laboratory examination of a 17-year-old female patient with macrothrombocytopenia and severe mucocutaneous bleeding was performed. Examination was carried out using standardized questionnaires to assess bleeding, high-throughput sequencing (Next Generation Sequencing), optical and fluorescence microscopy, flow cytometry with activation and analysis of intracellular calcium signaling of platelets, light transmission aggregometry and thrombus growth in the flow chamber. RESULTS Analysis of the patient's genotype revealed a previously undescribed c.655 A > G (p.K219E) variant in the hotspot of the SLFN14 gene. Immunofluorescence and brightfield examination of platelets in the smear showed heterogeneity in cells size, including giant forms over 10 μm (normal size 1-5) in diameter, with vacuolization and diffuse distribution of β1-tubulin and CD63. Activated platelets showed impaired contraction and shedding/internalization of GPIb. GP IIb/IIIa clustering was increased at rest and attenuated upon activation. Intracellular signalling study revealed impaired calcium mobilization upon TRAP 35.97 nM (reference range 180 ± 44) and CRP-XL 10.08 nM (56 ± 30) stimulation. Aggregation with ADP, collagen, TRAP, arachidonic acid and epinephrine was impaired in light transmission aggregometry; agglutination with ristocetin persisted. In the flow chamber with a shear rate of 400 s-1 platelet adhesion to collagen and clot growth were impaired. CONCLUSION The revealed disorders of phenotype, cytoskeleton and intracellular signaling explain the nature of SLFN14 platelet dysfunction and the patient's severe hemorrhagic syndrome.
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Affiliation(s)
- Dmitrii Polokhov
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation.
| | - Daria Fedorova
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Anastasiya Ignatova
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Evgeniya Ponomarenko
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Elena Rashevskaya
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Alexey Martyanov
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Nadezhda Podoplelova
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Maxim Aleksenko
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Irina Mersiyanova
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Elena Seregina
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Aleksandr Poletaev
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Ekaterina Truchina
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Elena Raykina
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Svetlana Plyasunova
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Galina Novichkova
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Pavel Zharkov
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Mikhail Panteleev
- Dmitriy Rogachev National Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
- Center for Theoretical Problems of Physicochemical Pharmacology, Moscow, Russia
- Faculty of Physics, Moscow State University, Moscow, Russia
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Ilin I, Podoplelova N, Sulimov A, Kutov D, Tashchilova A, Panteleev M, Shikhaliev K, Krysin M, Stolpovskaya N, Potapov A, Sulimov V. Experimentally Validated Novel Factor XIIa Inhibitors Identified by Docking and Quantum Chemical Post-processing. Mol Inform 2023; 42:e2200205. [PMID: 36328974 DOI: 10.1002/minf.202200205] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 11/03/2022] [Indexed: 11/06/2022]
Abstract
Antithrombotic agents based on factor XIIa inhibitors can become a new class of drugs to manage conditions associated with thrombosis. Herein, we report identification of two novel classes of factor XIIa inhibitors. The first one is triazolopyrimidine derivatives designed on the basis of the literature aminotriazole hit and identified using virtual screening of the focused library. The second class is a spirocyclic furo[3,4-c]pyrrole derivatives identified by virtual screening of a large chemical library of drug-like compounds performed in a previous study but confirmed in vitro here. In both cases, the prediction of inhibitory activity is based on the score of the SOL docking program, which uses the MMFF94 force field to calculate the binding energy. For the best ligands selected in virtual screening of the large chemical library, postprocessing with the PM7 semiempirical quantum-chemical method was used to calculate the enthalpy of protein-ligand binding to prioritize 16 compounds for testing in enzymatic assay, and one of them demonstrated micromolar activity. For triazolopyrimidine library, 21 compounds were prioritized for the testing based on docking scores, and visual inspection of docking poses. Of these, 4 compounds showed inhibition of factor XIIa at 30 μM.
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Affiliation(s)
- Ivan Ilin
- Dimonta, Ltd., 117186, Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Nadezhda Podoplelova
- Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, 117997, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmakology, 119991, Moscow, Russia
| | - Alexey Sulimov
- Dimonta, Ltd., 117186, Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Danil Kutov
- Dimonta, Ltd., 117186, Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Anna Tashchilova
- Dimonta, Ltd., 117186, Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Mikhail Panteleev
- Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, 117997, Moscow, Russia
- Center for Theoretical Problems of Physicochemical Pharmakology, 119991, Moscow, Russia
| | - Khidmet Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018, Voronezh, Russia
| | - Mikhail Krysin
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018, Voronezh, Russia
| | - Nadezhda Stolpovskaya
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018, Voronezh, Russia
| | - Andrey Potapov
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018, Voronezh, Russia
| | - Vladimir Sulimov
- Dimonta, Ltd., 117186, Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, 119992, Moscow, Russia
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Podoplelova N, Soloveva P, Garzon Dasgupta A, Filkova A, Panteleev M. Analyzing the Interaction of Fluorescent-labeled Proteins with Artificial Phospholipid Microvesicles using Quantitative Flow Cytometry. J Vis Exp 2022. [DOI: 10.3791/63459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Tashchilova A, Podoplelova N, Sulimov A, Kutov D, Ilin I, Panteleev M, Shikhaliev K, Medvedeva S, Novichikhina N, Potapov A, Sulimov V. New Blood Coagulation Factor XIIa Inhibitors: Molecular Modeling, Synthesis, and Experimental Confirmation. Molecules 2022; 27:molecules27041234. [PMID: 35209023 PMCID: PMC8876603 DOI: 10.3390/molecules27041234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/06/2022] [Accepted: 02/08/2022] [Indexed: 12/02/2022] Open
Abstract
In the modern world, complications caused by disorders in the blood coagulation system are found in almost all areas of medicine. Thus, the development of new, more advanced drugs that can prevent pathological conditions without disrupting normal hemostasis is an urgent task. The blood coagulation factor XIIa is one of the most promising therapeutic targets for the development of anticoagulants based on its inhibitors. The initial stage of drug development is directly related to computational methods of searching for a lead compound. In this study, docking followed by quantum chemical calculations was used to search for noncovalent low-molecular-weight factor XIIa inhibitors in a focused library of druglike compounds. As a result of the study, four low-molecular-weight compounds were experimentally confirmed as factor XIIa inhibitors. Selectivity testing revealed that two of the identified factor XIIa inhibitors were selective over the coagulation factors Xa and XIa.
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Affiliation(s)
- Anna Tashchilova
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Nadezhda Podoplelova
- Russian Children’s Clinical Hospital of the Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 119571 Moscow, Russia; (N.P.); (M.P.)
- Center for Theoretical Problems of Physicochemical Pharmakology, 119991 Moscow, Russia
| | - Alexey Sulimov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Danil Kutov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
| | - Ivan Ilin
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Mikhail Panteleev
- Russian Children’s Clinical Hospital of the Pirogov Russian National Research Medical University of the Ministry of Healthcare of the Russian Federation, 119571 Moscow, Russia; (N.P.); (M.P.)
- Center for Theoretical Problems of Physicochemical Pharmakology, 119991 Moscow, Russia
| | - Khidmet Shikhaliev
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Svetlana Medvedeva
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Nadezhda Novichikhina
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Andrey Potapov
- Department of Organic Chemistry, Faculty of Chemistry, Voronezh State University, 1 Universitetskaya sq., 394018 Voronezh, Russia; (K.S.); (S.M.); (N.N.); (A.P.)
| | - Vladimir Sulimov
- Dimonta, Ltd., 117186 Moscow, Russia; (A.T.); (A.S.); (I.I.)
- Research Computing Center, Lomonosov Moscow State University, 119992 Moscow, Russia
- Correspondence: (D.K.); (V.S.)
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Ukrainskaya V, Rubtsov Y, Pershin D, Podoplelova N, Terekhov S, Yaroshevich I, Sokolova A, Bagrov D, Kulakovskaya E, Shipunova V, Deyev S, Ziganshin R, Chernov A, Telegin G, Maksimov E, Markov O, Oshchepkova A, Zenkova M, Xie J, Zhang H, Gabibov A, Maschan M, Stepanov A, Lerner R. Antigen-Specific Stimulation and Expansion of CAR-T Cells Using Membrane Vesicles as Target Cell Surrogates. Small 2021; 17:e2102643. [PMID: 34605165 DOI: 10.1002/smll.202102643] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Development of CAR-T therapy led to immediate success in the treatment of B cell leukemia. Manufacturing of therapy-competent functional CAR-T cells needs robust protocols for ex vivo/in vitro expansion of modified T-cells. This step is challenging, especially if non-viral low-efficiency delivery protocols are used to generate CAR-T cells. Modern protocols for CAR-T cell expansion are imperfect since non-specific stimulation results in rapid outgrowth of CAR-negative T cells, and removal of feeder cells from mixed cultures necessitates additional purification steps. To develop a specific and improved protocol for CAR-T cell expansion, cell-derived membrane vesicles are taken advantage of, and the simple structural demands of the CAR-antigen interaction. This novel approach is to make antigenic microcytospheres from common cell lines stably expressing surface-bound CAR antigens, and then use them for stimulation and expansion of CAR-T cells. The data presented in this article clearly demonstrate that this protocol produced antigen-specific vesicles with the capacity to induce stronger stimulation, proliferation, and functional activity of CAR-T cells than is possible with existing protocols. It is predicted that this new methodology will significantly advance the ability to obtain improved populations of functional CAR-T cells for therapy.
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Affiliation(s)
- Valeria Ukrainskaya
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Yuri Rubtsov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Dmitry Pershin
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Nadezhda Podoplelova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Stanislav Terekhov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Igor Yaroshevich
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - Anstasiia Sokolova
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Malaya Pirogovskaya, 1a, Moscow, 119435, Russia
| | - Dmitry Bagrov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - Elena Kulakovskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Victoria Shipunova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Sergey Deyev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Research Centrum for Oncotheranostics, Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk, 634050, Russia
| | - Rustam Ziganshin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Aleksandr Chernov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Georgii Telegin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Eugene Maksimov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia
| | - Oleg Markov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - Anastasiya Oshchepkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road MB-10, La Jolla, CA, 92037, USA
| | - Hongkai Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Alexander Gabibov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
| | - Alexey Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, 117997, Russia
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road MB-10, La Jolla, CA, 92037, USA
| | - Richard Lerner
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road MB-10, La Jolla, CA, 92037, USA
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