ssmuБюллетень сибирской медициныBulletin of Siberian Medicine1682-03631819-3684Siberian State Medical University, the Ministry of Healthcare of the Russian Federation10.20538/1682-0363-2026-2-115-120ssmu-6540Research ArticleОРИГИНАЛЬНЫЕ СТАТЬИORIGINAL PAPERSКомпьютерное моделирование взаимодействия ксантотоксина с каспазой 3Computer simulation of xanthotoxin interaction with caspase 3https://orcid.org/0000-0001-6077-0347ЧасовскихН. Ю.ChasovskikhN. Yu.

Часовских Наталия Юрьевна – д-р мед. наук, доцент, зав. кафедрой медицинской и биологической кибернетики

Россия, 634050, г. Томск, Московский тракт, 2

2 Moskovsky trakt, 634050 Tomsk, Russian Federation

chasovskih.ny@ssmu.ruhttps://orcid.org/0000-0003-4731-8449ШестаковаЕ. Е.ShestakovaE. E.

Шестакова Евгения Евгеньевна – ассистент, кафедра медицинской и биологической кибернетики

Россия, 634050, г. Томск, Московский тракт, 2

2 Moskovsky trakt, 634050 Tomsk, Russian Federation

chizik.ee@ssmu.ruНовицкийД. Е.NovitskyD. E.

Новицкий Дмитрий Евгеньевич – студент 6-го курса

Россия, 634050, г. Томск, Московский тракт, 2

2 Moskovsky trakt, 634050 Tomsk, Russian Federation

novitskydima07@mail.ruСибирский государственный медицинский университет (СибГМУ)РоссияSiberian State Medical UniversityRussian Federation202623072026252115120Copyright © Часовских Н.Ю., Шестакова Е.Е., Новицкий Д.Е., 20262026Часовских Н.Ю., Шестакова Е.Е., Новицкий Д.Е.Chasovskikh N.Y., Shestakova E.E., Novitsky D.E.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://bulletin.ssmu.ru/jour/article/view/6540

Цель – провести компьютерное моделирование и оценить взаимодействие каспазы 3 с ксантотоксином.Материалы и методы. Структуры каспазы 3 и ксантотоксина извлечены из банка данных белков PDB (ID 2J31) и базы данных химических соединений и смесей PubChem (ID 4114) соответственно. Для подготовки структуры каспазы 3 к докингу применяли PyMOL v. 2.5, для конвертации ксантотоксина в формат .pdb использовали OpenBabel. Докинг проводили в AutoDock Vina. Молекулярно-динамическое моделирование выполняли с использованием GROMACS 2023.3. Для генерации топологии белка использовали силовое поле CHARMM 36, для топологии лиганда – сервер CHARMM General Force Field (CGenFF). Для анализа результатов применяли Xmgrace и PyMOL.Результаты. В результате проведенного молекулярного докинга каспазы 3 и ксантотоксина получен стабильный комплекс с энергией связывания –4,83 ккал/моль. Выявлены аминокислотные остатки каспазы 3, участвующие в межмолекулярном взаимодействии: тирозин 195 (TYR195), валин 266 (VAL266), лизин 137 (LYS137). Результаты проведенной симуляции молекулярной динамики подтвердили устойчивость комплекса, полученного в результате докинга.Заключение. Полученные данные свидетельствуют о возможной роли изучаемого фурокумарина в реализации программируемой гибели клеток и могут быть использованы для дальнейших экспериментальных исследований.

Aim. To perform computer modeling and evaluate the interactions between caspase 3 and xanthotoxin.Materials and methods. The structures of caspase 3 and xanthotoxin were extracted from the PDB protein database (ID 2J31) and the PubChem chemical compounds and mixtures database (ID 4114), respectively. PyMOL v. 2.5 was used to prepare the caspase 3 structure for docking, and OpenBabel was used to convert xanthotoxin to .pdb format. Molecular docking was performed in AutoDock Vina. Molecular dynamics was performed using GROMACS 2023.3. The CHARMM 36 force field was used to generate the protein topology, and the CHARMM General Force Field (CGenFF) server was used for the ligand topology. Xmgrace and PyMOL were used to analyze the results.Results. Molecular docking of caspase 3 and xanthotoxin resulted in a stable complex with binding energy of -4.83 kcal/mol. The amino acid residues of caspase 3 involved in intermolecular interaction were identified: tyrosine 195 (TYR195), valine 266 (VAL266), lysine 137 (LYS137). The results of the molecular dynamics simulation confirmed the stability of the complex obtained as a result of docking.Conclusion. The data obtained indicate the possible role of the studied furocoumarin in the implementation of programmed cell death and can be used for further experimental studies.

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The authors declare that there are no conflicts of interest present.