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<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ali="http://www.niso.org/schemas/ali/1.0/" article-type="research-article" dtd-version="1.2" xml:lang="en"><front><journal-meta><journal-id journal-id-type="publisher-id">Russian Journal of Infection and Immunity</journal-id><journal-title-group><journal-title xml:lang="en">Russian Journal of Infection and Immunity</journal-title><trans-title-group xml:lang="ru"><trans-title>Инфекция и иммунитет</trans-title></trans-title-group></journal-title-group><issn publication-format="print">2220-7619</issn><issn publication-format="electronic">2313-7398</issn><publisher><publisher-name xml:lang="en">SPb RAACI</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="publisher-id">15624</article-id><article-id pub-id-type="doi">10.15789/2220-7619-DSA-15624</article-id><article-categories><subj-group subj-group-type="toc-heading" xml:lang="en"><subject>ORIGINAL ARTICLES</subject></subj-group><subj-group subj-group-type="toc-heading" xml:lang="ru"><subject>ОРИГИНАЛЬНЫЕ СТАТЬИ</subject></subj-group><subj-group subj-group-type="article-type"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title xml:lang="en">Designing structure and <italic>E. coli</italic> strain-producer bearing SARS-CoV-2 N, S, M, E protein-related sequence antigen</article-title><trans-title-group xml:lang="ru"><trans-title>Разработка структуры и штамма-продуцента <italic>E. coli</italic> для антигена, содержащего последовательности белков N, S, M, E коронавируса SARS-CоV-2</trans-title></trans-title-group></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-6573-6743</contrib-id><name-alternatives><name xml:lang="en"><surname>Kopat</surname><given-names>Vladimir V.</given-names></name><name xml:lang="ru"><surname>Копать</surname><given-names>Владимир Владиславович</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Development Director</p></bio><bio xml:lang="ru"><p>директор по развитию</p></bio><email>kopat@service-gene.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-9973-0753</contrib-id><name-alternatives><name xml:lang="en"><surname>Riabchenkova</surname><given-names>Anastasia A.</given-names></name><name xml:lang="ru"><surname>Рябченкова</surname><given-names>Анастасия Андреевна</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Researcher</p></bio><bio xml:lang="ru"><p>научный сотрудник</p></bio><email>riabchenkova@service-gene.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0001-9167-5000</contrib-id><name-alternatives><name xml:lang="en"><surname>Chirak</surname><given-names>Evgenii L.</given-names></name><name xml:lang="ru"><surname>Чирак</surname><given-names>Евгений Леонидович</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Researcher</p></bio><bio xml:lang="ru"><p>научный сотрудник</p></bio><email>chirak.evgenii@service-gene.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-1610-8935</contrib-id><name-alternatives><name xml:lang="en"><surname>Chirak</surname><given-names>Elizaveta R.</given-names></name><name xml:lang="ru"><surname>Чирак</surname><given-names>Елизавета Романовна</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Researcher</p></bio><bio xml:lang="ru"><p>научный сотрудник</p></bio><email>chirak.elizaveta@service-gene.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0009-0003-1059-1991</contrib-id><name-alternatives><name xml:lang="en"><surname>Saenko</surname><given-names>Anna I.</given-names></name><name xml:lang="ru"><surname>Саенко</surname><given-names>Анна Игоревна</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Chief Process Engineer</p></bio><bio xml:lang="ru"><p>главный технолог</p></bio><email>anna.saenko@gmail.com</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-4672-6208</contrib-id><name-alternatives><name xml:lang="en"><surname>Kolmakov</surname><given-names>Nikolai N.</given-names></name><name xml:lang="ru"><surname>Колмаков</surname><given-names>Николай Николаевич</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>Researcher, Department of Molecular Genetics</p></bio><bio xml:lang="ru"><p>научный сотрудник отдела молекулярной генетики</p></bio><email>kolmakov@service-gene.ru</email><xref ref-type="aff" rid="aff2"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-8228-4240</contrib-id><name-alternatives><name xml:lang="en"><surname>Simbirtsev</surname><given-names>Andrey S.</given-names></name><name xml:lang="ru"><surname>Симбирцев</surname><given-names>Андрей Семенович</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>RAS Corresponding Member, DSc (Medicine), Professor, Head of the Laboratory of Medical Biotechnology</p></bio><bio xml:lang="ru"><p>член-корреспондент РАН, доктор медицинских наук, профессор, зав. лабораторией медицинской биотехнологии</p></bio><email>simbas@mail.ru</email><xref ref-type="aff" rid="aff3"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0002-5268-9802</contrib-id><name-alternatives><name xml:lang="en"><surname>Dukhovlinov</surname><given-names>Ilya V.</given-names></name><name xml:lang="ru"><surname>Духовлинов</surname><given-names>Илья Владимирович</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>PhD (Biology), Director of Science</p></bio><bio xml:lang="ru"><p>кандидат биологических наук , директор по науке</p></bio><email>atg@service-gene.ru</email><xref ref-type="aff" rid="aff1"/></contrib><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">https://orcid.org/0000-0003-4571-8799</contrib-id><name-alternatives><name xml:lang="en"><surname>Totolian</surname><given-names>Areg A.</given-names></name><name xml:lang="ru"><surname>Тотолян</surname><given-names>Арег Артемович</given-names></name></name-alternatives><address><country country="RU">Russian Federation</country></address><bio xml:lang="en"><p>RAS Full Member, DSc (Medicine), Professor, Director</p></bio><bio xml:lang="ru"><p>академик РАН, доктор медицинских наук, профессор, директор</p></bio><email>totolian@spbraaci.ru</email><xref ref-type="aff" rid="aff3"/></contrib></contrib-group><aff-alternatives id="aff1"><aff><institution xml:lang="en">LLC “ATG Service Gene”</institution></aff><aff><institution xml:lang="ru">ООО «АТГ Сервис Ген»</institution></aff></aff-alternatives><aff-alternatives id="aff2"><aff><institution xml:lang="en">Institute of Experimental Medicine</institution></aff><aff><institution xml:lang="ru">ФГБНУ Институт экспериментальной медицины</institution></aff></aff-alternatives><aff-alternatives id="aff3"><aff><institution xml:lang="en">Saint Petersburg Pasteur Institute</institution></aff><aff><institution xml:lang="ru">ФБУН НИИ эпидемиологии и микробиологии имени Пастера</institution></aff></aff-alternatives><pub-date date-type="preprint" iso-8601-date="2023-08-17" publication-format="electronic"><day>17</day><month>08</month><year>2023</year></pub-date><pub-date date-type="pub" iso-8601-date="2023-10-24" publication-format="electronic"><day>24</day><month>10</month><year>2023</year></pub-date><volume>13</volume><issue>4</issue><issue-title xml:lang="en"/><issue-title xml:lang="ru"/><fpage>653</fpage><lpage>662</lpage><history><date date-type="received" iso-8601-date="2023-08-11"><day>11</day><month>08</month><year>2023</year></date><date date-type="accepted" iso-8601-date="2023-08-13"><day>13</day><month>08</month><year>2023</year></date></history><permissions><copyright-statement xml:lang="en">Copyright ©; 2023, Kopat V.V., Riabchenkova A.A., Chirak E.L., Chirak E.R., Saenko A.I., Kolmakov N.N., Simbirtsev A.S., Dukhovlinov I.V., Totolian A.A.</copyright-statement><copyright-statement xml:lang="ru">Copyright ©; 2023, Копать В.В., Рябченкова А.А., Чирак Е.Л., Чирак Е.Р., Саенко А.И., Колмаков Н.Н., Симбирцев А.С., Духовлинов И.В., Тотолян А.А.</copyright-statement><copyright-year>2023</copyright-year><copyright-holder xml:lang="en">Kopat V.V., Riabchenkova A.A., Chirak E.L., Chirak E.R., Saenko A.I., Kolmakov N.N., Simbirtsev A.S., Dukhovlinov I.V., Totolian A.A.</copyright-holder><copyright-holder xml:lang="ru">Копать В.В., Рябченкова А.А., Чирак Е.Л., Чирак Е.Р., Саенко А.И., Колмаков Н.Н., Симбирцев А.С., Духовлинов И.В., Тотолян А.А.</copyright-holder><ali:free_to_read xmlns:ali="http://www.niso.org/schemas/ali/1.0/"/><license><ali:license_ref xmlns:ali="http://www.niso.org/schemas/ali/1.0/">https://creativecommons.org/licenses/by/4.0</ali:license_ref></license></permissions><self-uri xlink:href="https://iimmun.ru/iimm/article/view/15624">https://iimmun.ru/iimm/article/view/15624</self-uri><abstract xml:lang="en"><p>T-cell immune response is extremely important in protecting human body from diverse viral infections. It is known that it can ensure viral clearance and complete recovery in patients with humoral immunodeficiency. COVID-19 patients were found to have T-cell response primarily directed against SARS-CoV-2 structural S, M, N, E proteins, with nucleocapsid protein being most conserved. To assess patients’ immunity against coronavirus infection and evaluate an effectiveness of vaccine candidates, it is necessary to develop an optimal diagnostic antigen to evaluate arising T-cell response against SARS-CoV-2 antigenic determinants. A diagnostic test to determine host specific susceptibility to SARS-CoV-2 infection should target conserved regions of global SARS-CoV-2 variants. The study was aimed to develop a structure of an antigen bearing conserved and immunogenic sequences derived from SARS-CoV-2 structural proteins and to obtain an Escherichia coli producer strain containing a recombinant protein to be subsequently used for assessing antiviral T-cell immunity. Developing of the antigen was performed in silico: TepiTool and NetMHCIIpan were used to predict and identify high affinity epitopes spanning SARS-CoV-2 E, M, N, S proteins and MHC II binding. Several variants of recombinant antigen proteins were constructed, from which one was selected based on its physicochemical properties: isoelectric point, hydrophobicity index and aliphatic index, as well as 3D representation built by using the I-TASSER. The sequence was synthesized and cloned into the pET24a(+) vector. The resulting plasmid pCorD_PS was transformed into E. coli DH5α followed by Rosetta (DE3). The strain-producer of the recombinant E. coli protein CorD_PS was assessed for the presence and stability of IPTG-induced antigen protein expression and elimination of recombinant coronavirus antigen-bearing plasmid. Based on the study data, an antigen was developed consisting of conserved regions from SARS-CoV-2 S, M, N, E proteins. A 53 kDa recombinant protein was predicted to be stable in aqueous solutions with isoelectric point of 9.56 potentially allowing to simplify protein purification from E. coli cells. Plasmid DNA pCorD_PS (6695 bp) encoding final recombinant coronavirus antigen cloned into pET24a(+) vector was obtained. A stable, productive E. coli CorD_PS strain was obtained. The obtained strain-producer resulting in recombinant E. coli CorD_PS antigen is stable allowing to move on to design antigen purification technique and further develop SARS-CoV-2-specific diagnostic test system.</p></abstract><trans-abstract xml:lang="ru"><p>Т-клеточный иммунный ответ крайне важен при защите организма человека от многих вирусных инфекций. Известно, что он может обеспечить вирусный клиренс и полное выздоровление у пациентов с гуморальным иммунодефицитом. У пациентов с COVID-19 Т-клеточный ответ направлен в основном на структурные белки вируса S, M, N, E, из которых наиболее консервативным является белок нуклеокапсида. Для оценки иммунитета пациентов в отношении коронавирусной инфекции и определения эффективности вакцинных кандидатов необходима разработка оптимального диагностического антигена, используемого для оценки формирования Т-клеточной реакции против антигенных детерминант SARS-CoV-2. Диагностический тест для определения специфической чувствительности организма к инфекции, вызываемой SARS-CoV-2, должен быть нацелен на консервативные регионы глобальных вариантов SARS-CoV-2. Целью работы была разработка структуры антигена, содержащего консервативные и иммуногенные последовательности структурных белков коронавируса SARS-CoV-2, и получение штамма Escherichia coli — продуцента рекомбинантного белка для последующего использования белка в качестве антигена для оценки Т-клеточного противовирусного иммунитета. Создание последовательности антигена проводили in silico: TepiTool и NetMHCIIpan использовали для прогнозирования и идентификации высокоаффинных эпитопов, охватывающих белки E, M, N, S SARS-CoV-2 и связывающих MHC II. Было сконструировано несколько вариантов рекомбинантных белков-антигенов, из которых выбрали один на основании его физико-химических свойств: изоэлектрической точки, индекса гидрофобности и алифатического индекса, построенной с помощью I-TASSER 3D модели. Последовательность синтезировали и клонировали в вектор pET24a(+). Полученной плазмидой pCorD_PS последовательно трансформировали штаммы E. coli DH5α, затем Rosetta (DE3). Штамм-продуцент рекомбинантного белка E. coli CorD_PS проверяли на наличие и стабильность экспрессии белка-антигена индукцией ИПТГ, также оценивали элиминирование плазмиды, кодирующей синтез рекомбинантного коронавирусного антигена. В результате разработан антиген, включающий в себя консервативные участки белков S, M, N, E коронавируса SARS-CoV-2, на которые может формироваться Т-клеточный иммунный ответ. Для белка массой 53 kDa предсказана стабильность в водных растворах и изоэлектрическая точка 9,56, что потенциально позволит упростить процесс очистки белка от нативных белков E. coli. Получена плазмидная ДНК pCorD_PS (6695 п.о.), кодирующая клонированный в вектор pET24a(+) синтезированный антиген коронавирусный рекомбинантный. Получен стабильный, продуктивный по коронавирусному рекомбинантному антигену, штамм-продуцент E. coli CorD_PS. Полученный штамм — продуцент рекомбинантного антигена E. coli CorD_PS стабилен, что позволяет перейти к созданию методики очистки антигена и последующей разработке диагностической тест-системы.</p> <p> </p></trans-abstract><kwd-group xml:lang="en"><kwd>SARS-CoV-2</kwd><kwd>COVID-19</kwd><kwd>T cells</kwd><kwd>CD4+ T cells</kwd><kwd>CD8+ T cells</kwd><kwd>epitopes</kwd><kwd>HLA</kwd></kwd-group><kwd-group xml:lang="ru"><kwd>SARS-CoV-2</kwd><kwd>COVID-19</kwd><kwd>Т-клетки</kwd><kwd>CD4+ Т-клетки</kwd><kwd>CD8+ Т-клетки</kwd><kwd>эпитопы</kwd><kwd>HLA</kwd></kwd-group><funding-group/></article-meta></front><body></body><back><ref-list><ref id="B1"><label>1.</label><mixed-citation>Кудрявцев И.В., Головкин А.С., Тотолян А.А. Т-хелперы и их клетки-мишени при COVID-19 // Инфекция и иммунитет. 2022. Т. 12, № 3. C. 409–426. [Kudryavtsev I.V., Golovkin A.S., Totolian A.A. T helper cell subsets and related target cells in acute COVID-19. 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