spfpХранение и переработка сельхозсырьяStorage and Processing of Farm Products2072-96692658-767XРОСБИОТЕХ10.36107/spfp.2023.399spfp-399Research ArticleБИОТЕХНОЛОГИЧЕСКИЕ И МИКРОБИОЛОГИЧЕСКИЕ АСПЕКТЫBIOTECHNOLOGICAL AND MICROBIOLOGICAL ASPECTSМолекулярный in silico скрининг и докинг потенциальных ингибиторов активности ферментов растительного сырьяMolecular in Silico Screening and Docking of Potential Inhibitors of Enzyme Activity of Plant Raw Materialshttps://orcid.org/0000-0002-0532-9951ИвановНиколай ВикторовичIvanovNikolay V.nikolay.ivanov@rgau-msha.ruРоссийский государственный аграрный университет – МСХА им. К.А. ТимирязеваРоссияRussian State Agrarian University —Moscow Timiryazev Agricultural AcademyRussian Federation20233003202301117135Copyright © Иванов Н.В., 20232023Иванов Н.В.Ivanov N.V.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://www.spfp-mgupp.ru/jour/article/view/399Введение

Введение. Липолиз триацилглицеринов под действием собственной ферментативной системы в семенах подсолнечника является естественным биохимическим процессом, в рамках которого образуются моно- и диглицериды жирных кислот. Эти вещества являются предшественниками токсичных пищевых контаминантов - эфиров глицидола и монохлорпропандиола, которые образуются в технологии переработки жиров. Чтобы снизить вероятность их образования, представляет высокий практический интерес изучение влияния компонентов состава масличного сырья на естественные биохимические процессы в семенах подсолнечника в хранении.

Цель

Цель. Изучить механизмы влияния молекулярных взаимодействий минорных компонентов состава семян подсолнечника с ферментной системой на биохимический процесс распада триацилглицеринов.

Методы

Методы. В работе использовались моделирование трехмерной структуры липазы по гомологии, филогенетический анализ, множественное выравнивание аминокислотных последовательностей, анализ карт Раманчандрана, молекулярный докинг.

Результаты

Результаты. Наиболее близким к липазе семян подсолнечника по строению аминокислотной последовательности является панкреатическая липаза собаки (Canis lupus familiaris), кодируемая геном MPL1. Определено, что согласно множественному выравниванию аминокислотных последовательностей активные центры изучаемых липаз ATLIP1, LIPG, MPL1 не входят в консервативные участки, однако активные центры липазы подсолнечника MPL1 наиболее близки к консервативным участкам потенциального шаблона для моделирования.

Выводы

Выводы. По итогам множественного выравнивания аминокислотных последовательностей и филогенетического анализа было определено, что выбранные шаблоны для построения модели липаз подсолнечника являются близкородственными и могут быть использованы для гомологичного моделирования. Ингибиторы липазной активности микробиального происхождения показали устойчивую корреляционную зависимость со значениями концентрации полумаксимального ингибирования IC50. По результатам молекулярного докинга минорных компонентов масличного сырья показано, что наибольшим сродством к липазе обладают хлорогеновая и неохлорогеновая кислоты и даидзеин.

Introduction

Introduction. Lipolysis of triacylglycerols under the action of its own enzymatic system in sunflower seeds is a natural biochemical process in which mono- and diglycerides of fatty acids are formed. These substances are precursors of toxic food contaminants - glycidol and monochloropropanediol esters, which are formed in the technology of fat processing. In order to reduce the likelihood of their formation, it is of high practical interest to study the effect of the components of the composition of oilseed raw materials on the natural biochemical processes in sunflower seeds in storage.

Methods

Methods. The work used modeling of the three-dimensional structure of lipase by homology, phylogenetic analysis, multiple alignment of amino acid sequences, analysis of Ramanchandran maps, molecular docking.

Results

Results. It is shown that the closest to the lipase of sunflower seeds in the amino acid sequence is the pancreatic lipase of a dog (Canis lupus familiaris), encoded by the MPL1 gene. It was determined that according to the multiple alignment of amino acid sequences, the active centers of the studied sunflower lipases ATLIP1, LIPG, MPL1 are not included in the conservative sites, but the active centers of sunflower lipase MPL1 are closest to the conservative sites of a potential template for modeling.

Conclusions

Conclusions. Based on the results of multiple alignment of amino acid sequences and phylogenetic analysis, it was determined that the selected templates for constructing a model of sunflower lipases are closely related and can be used for homologous modeling. Inhibitors of lipase activity of microbial origin showed a stable correlation with the values of the concentration of semi-maximal inhibition of IC50. According to the results of molecular docking of minor components of oilseed raw materials, it was shown that chlorogenic and neochlorogenic acids and daidzein have the greatest affinity for lipase.

липаза подсолнечникагомологичное моделированиефилогенетический анализмолекулярный докингsunflower lipasehomologous modelingphylogenetic analysismolecular dockingReferencesCode of practice for the reduction of 3-monochloropropane-1,2- diol esters (3-mcpdes) and glycidyl esters (ges) in refined oils and food products made with refined oils. (2019). CXC 79-2019.Code of practice for the reduction of 3-monochloropropane-1,2- diol esters (3-mcpdes) and glycidyl esters (ges) in refined oils and food products made with refined oils. (2019). CXC 79-2019.Schultrich, K., Henderson, C. J., Braeuning, A., & Buhrke, T. (2020). Correlation between 3-MCPD-induced organ toxicity and oxidative stress response in male mice. Food and Chemical Toxicology, 136, 110957. https://doi.org/10.1016/j.fct.2019.110957Schultrich, K., Henderson, C. J., Braeuning, A., & Buhrke, T. (2020). Correlation between 3-MCPD-induced organ toxicity and oxidative stress response in male mice. Food and Chemical Toxicology, 136, 110957. https://doi.org/10.1016/j.fct.2019.110957Sagiroglu, A., Arabaci, N. (2005) Sunflower Seed Lipase: Extraction, Purification, and Characterization, Preparative Biochemistry and Biotechnology, 35:1, 37-51, DOI: https://doi.org/10.1081/PB-200041442Sagiroglu, A., Arabaci, N. (2005) Sunflower Seed Lipase: Extraction, Purification, and Characterization, Preparative Biochemistry and Biotechnology, 35:1, 37-51, DOI: https://doi.org/10.1081/PB-200041442Nebeg, H., Benarous, K., Serseg, T., Lazreg, A., Hassani, H., & Yousfi, M. (2019). Seeds, Leaves and Roots of Thapsia garganica as a Source of New Potent Lipases Inhibitors: In vitro and In silico Studies. Endocrine, Metabolic & Immune Disorders - Drug Targets, 19(5). https://doi.org/10.2174/1871530319666190128122211Nebeg, H., Benarous, K., Serseg, T., Lazreg, A., Hassani, H., & Yousfi, M. (2019). Seeds, Leaves and Roots of Thapsia garganica as a Source of New Potent Lipases Inhibitors: In vitro and In silico Studies. Endocrine, Metabolic & Immune Disorders - Drug Targets, 19(5). https://doi.org/10.2174/1871530319666190128122211Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6), 1547–1549. https://doi.org/10.1093/molbev/msy096Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.Jones D.T., Taylor W.R., and Thornton J.M. (1992). The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282.Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., & Schwede, T. (2018). SWISS-MODEL: Homology modelling of protein structures and complexes. Nucleic Acids Research, 46(W1), W296–W303. https://doi.org/10.1093/nar/gky427Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Gallo Cassarino, T., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Web Server Issue Published Online, 42. https://doi.org/10.1093/nar/gku340Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Gallo Cassarino, T., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Web Server Issue Published Online, 42. https://doi.org/10.1093/nar/gku340Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. In Nucleic Acids Research (Vol. 25, Issue 17). Oxford University Press. https://academic.oup.com/nar/article/25/17/3389/1061651Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. In Nucleic Acids Research (Vol. 25, Issue 17). Oxford University Press. https://academic.oup.com/nar/article/25/17/3389/1061651Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T. L. (2009). BLAST+: architecture and applications. https://doi.org/10.1186/1471-2105-10-421Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., Madden, T. L. (2009). BLAST+: architecture and applications. https://doi.org/10.1186/1471-2105-10-421Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. (2018). Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology OPEN. https://doi.org/10.1038/s41598-017-09654-8Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L., Schwede, T. (2018). Modeling protein quaternary structure of homo-and hetero-oligomers beyond binary interactions by homology OPEN. https://doi.org/10.1038/s41598-017-09654-8Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. 27(3), 343–350. https://doi.org/10.1093/bioinformatics/btq662Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. 27(3), 343–350. https://doi.org/10.1093/bioinformatics/btq662Bienert, S., Waterhouse, A., de Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. (2016). The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Research, 45, 313–319. https://doi.org/10.1093/nar/gkw1132Bienert, S., Waterhouse, A., de Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L., Schwede, T. (2016). The SWISS-MODEL Repository-new features and functionality. Nucleic Acids Research, 45, 313–319. https://doi.org/10.1093/nar/gkw1132Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084Meng, E. C., Pettersen, E. F., Couch, G. S., Huang, C. C., & Ferrin, T. E. (2006). Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics, 7, 1–10. https://doi.org/10.1186/1471-2105-7-339Meng, E. C., Pettersen, E. F., Couch, G. S., Huang, C. C., & Ferrin, T. E. (2006). Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics, 7, 1–10. https://doi.org/10.1186/1471-2105-7-339Trott, O., Olson A. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461. https://10.1002/jcc.21334Trott, O., Olson A. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461. https://10.1002/jcc.21334Schöning, K., Schöning-Stierand, S., Diedrich, K., Ahrrolfes, R. F. ¨, Flachsenberg, F., Meyder, A., Nittinger, E., Steinegger, R., & Rarey, M. (2020). ProteinsPlus: interactive analysis of protein-ligand binding interfaces. Web Server Issue Published Online, 48. https://doi.org/10.1093/nar/gkaa235Schöning, K., Schöning-Stierand, S., Diedrich, K., Ahrrolfes, R. F. ¨, Flachsenberg, F., Meyder, A., Nittinger, E., Steinegger, R., & Rarey, M. (2020). ProteinsPlus: interactive analysis of protein-ligand binding interfaces. Web Server Issue Published Online, 48. https://doi.org/10.1093/nar/gkaa235O’boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. https://doi.org/10.1186/1758-2946-3-33O’boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. https://doi.org/10.1186/1758-2946-3-33Wu, C. H., Nikolskaya, A., Huang, H., Yeh, L. S., Natale, D. A., Vinayaka, C. R., Hu, Z. Z., Mazumder, R., Kumar, S., Kourtesis, P., Ledley, R. S., Suzek, B. E., Arminski, L., Chen, Y., Zhang, J., Cardenas, J. L., Chung, S., Castro-Alvear, J., Dinkov, G., & Barker, W. C. (2004). PIRSF: Family classification system at the Protein Information Resource. Nucleic Acids Research, 32(DATABASE ISS.), 112–114. https://doi.org/10.1093/nar/gkh097Wu, C. H., Nikolskaya, A., Huang, H., Yeh, L. S., Natale, D. A., Vinayaka, C. R., Hu, Z. Z., Mazumder, R., Kumar, S., Kourtesis, P., Ledley, R. S., Suzek, B. E., Arminski, L., Chen, Y., Zhang, J., Cardenas, J. L., Chung, S., Castro-Alvear, J., Dinkov, G., & Barker, W. C. (2004). PIRSF: Family classification system at the Protein Information Resource. Nucleic Acids Research, 32(DATABASE ISS.), 112–114. https://doi.org/10.1093/nar/gkh097Ameis, D., Merkel, M., Eckerskornz, C., Greten, H. (1994). Purification, characterization and molecular cloning of human hepatic lysosomal acid lipase. In Eur. J. Biochem (Vol. 219).Ameis, D., Merkel, M., Eckerskornz, C., Greten, H. (1994). Purification, characterization and molecular cloning of human hepatic lysosomal acid lipase. In Eur. J. Biochem (Vol. 219).Warner TG, Dambach L M, Shin, J H, O'Brien, J S (1981). Purification of the lysosomal acid lipase from human liver and its role in lysosomal lipid hydrolysis. J Biol Chem 25; 256(6): 2952-7. PMID: 7204383Warner TG, Dambach L M, Shin, J H, O'Brien, J S (1981). Purification of the lysosomal acid lipase from human liver and its role in lysosomal lipid hydrolysis. J Biol Chem 25; 256(6): 2952-7. PMID: 7204383Ries, S., Büchler, C., Schindler, G., Aslanidis, C., Ameis, D., Gasche, C., Jung, N., Schambach, A., Fehringer, P., Vanier, M. T., Belli, D. C., Greten, H., & Schmitz, G. (1998). Different missense mutations in histidine-108 of lysosomal acid lipase cause cholesteryl ester storage disease in unrelated compound heterozygous and hemizygous individuals. Human Mutation, 12(1), 44–51. https://doi.org/10.1002/(SICI)1098-1004(1998)12:1<44::AID-HUMU7>3.0.CO;2-ORies, S., Büchler, C., Schindler, G., Aslanidis, C., Ameis, D., Gasche, C., Jung, N., Schambach, A., Fehringer, P., Vanier, M. T., Belli, D. C., Greten, H., & Schmitz, G. (1998). Different missense mutations in histidine-108 of lysosomal acid lipase cause cholesteryl ester storage disease in unrelated compound heterozygous and hemizygous individuals. Human Mutation, 12(1), 44–51. https://doi.org/10.1002/(SICI)1098-1004(1998)12:1<44::AID-HUMU7>3.0.CO;2-ORoussel, A., Canaan, S., Egloff, M. P., Rivière, M., Dupuis, L., Verger, R., & Cambillau, C. (1999). Crystal structure of human gastric lipase and model of lysosomal acid lipase, two lipolytic enzymes of medical interest. Journal of Biological Chemistry, 274(24), 16995–17002. https://doi.org/10.1074/jbc.274.24.16995Roussel, A., Canaan, S., Egloff, M. P., Rivière, M., Dupuis, L., Verger, R., & Cambillau, C. (1999). Crystal structure of human gastric lipase and model of lysosomal acid lipase, two lipolytic enzymes of medical interest. Journal of Biological Chemistry, 274(24), 16995–17002. https://doi.org/10.1074/jbc.274.24.16995Rogalska, E., Ransac, S., Verger, R. (1990) Stereoselectivity of lipases. II. Stereoselective hydrolysis of triglycerides by gastric and pancreatic lipases. J Biol Chem 25; 265(33): 20271-6. PMID: 2243091Rogalska, E., Ransac, S., Verger, R. (1990) Stereoselectivity of lipases. II. Stereoselective hydrolysis of triglycerides by gastric and pancreatic lipases. J Biol Chem 25; 265(33): 20271-6. PMID: 2243091Carriere, F., Moreau, H., Vhronique, R. R., Laugier, C. B., Junien, J.-L., Verger, R. (1991). Purification and biochemical characterization of dog gastric lipase. In Eur. J. Biochem (Vol. 202).Carriere, F., Moreau, H., Vhronique, R. R., Laugier, C. B., Junien, J.-L., Verger, R. (1991). Purification and biochemical characterization of dog gastric lipase. In Eur. J. Biochem (Vol. 202).Carrière, F., Raphel, V., Moreau, H., Bernadac, A., Devaux, M. A., Grimaud, R., Barrowman, J. A., Bénicourt, C., Junien, J. L., Laugier, R., & Verger, R. (1992). Dog gastric lipase: Stimulation of its secretion in vivo and cytolocalization in mucous pit cells. Gastroenterology, 102(5), 1535–1545. https://doi.org/10.1016/0016-5085(92)91711-CCarrière, F., Raphel, V., Moreau, H., Bernadac, A., Devaux, M. A., Grimaud, R., Barrowman, J. A., Bénicourt, C., Junien, J. L., Laugier, R., & Verger, R. (1992). Dog gastric lipase: Stimulation of its secretion in vivo and cytolocalization in mucous pit cells. Gastroenterology, 102(5), 1535–1545. https://doi.org/10.1016/0016-5085(92)91711-CDavid, L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Sybille, M., Harel, M., James Remington, S., Silman, I., Schrag, J., Joel, L., Koen, H. G. V., & Goldman, A. (1992). The α/β hydrolase fold. Protein Engineering, Design and Selection, 5(3), 197–211. https://doi.org/10.1093/protein/5.3.197David, L., Cheah, E., Cygler, M., Dijkstra, B., Frolow, F., Sybille, M., Harel, M., James Remington, S., Silman, I., Schrag, J., Joel, L., Koen, H. G. V., & Goldman, A. (1992). The α/β hydrolase fold. Protein Engineering, Design and Selection, 5(3), 197–211. https://doi.org/10.1093/protein/5.3.197Selvan, A., Chandrabhan, S., Srinivas N.C., Nithyanand S., Sharmila A., Gautam, P. (2010) Molecular dynamics simulations of human and dog gastric lipases: Insightsinto domain movements. FEBS Letters. Vol. 584 (22) P. 4599-4605.Selvan, A., Chandrabhan, S., Srinivas N.C., Nithyanand S., Sharmila A., Gautam, P. (2010) Molecular dynamics simulations of human and dog gastric lipases: Insightsinto domain movements. FEBS Letters. Vol. 584 (22) P. 4599-4605.Messaoudi, A., Belguith, hatem, & ben hamida, J. (2011). Three-Dimensional structure of Arabidopsis thaliana Lipase predicted by Homology Modeling Method. Evolutionary Bioinformatics, 99–105. https://doi.org/10.4137/EBO.S7122Messaoudi, A., Belguith, hatem, & ben hamida, J. (2011). Three-Dimensional structure of Arabidopsis thaliana Lipase predicted by Homology Modeling Method. Evolutionary Bioinformatics, 99–105. https://doi.org/10.4137/EBO.S7122Wahab, H. A., Khairudin, N. B. A., Samian, M. R., & Najimudin, N. (2006). Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism. BMC Structural Biology, 6, 1–14. https://doi.org/10.1186/1472-6807-6-23Wahab, H. A., Khairudin, N. B. A., Samian, M. R., & Najimudin, N. (2006). Sequence analysis and structure prediction of type II Pseudomonas sp. USM 4-55 PHA synthase and an insight into its catalytic mechanism. BMC Structural Biology, 6, 1–14. https://doi.org/10.1186/1472-6807-6-23Birari, R. B., & Bhutani, K. K. (2007). Pancreatic lipase inhibitors from natural sources: unexplored potential. In Drug Discovery Today (Vol. 12, Issues 19–20, pp. 879–889). https://doi.org/10.1016/j.drudis.2007.07.024Birari, R. B., & Bhutani, K. K. (2007). Pancreatic lipase inhibitors from natural sources: unexplored potential. In Drug Discovery Today (Vol. 12, Issues 19–20, pp. 879–889). https://doi.org/10.1016/j.drudis.2007.07.024Tingli B., Daozhong Z., Shuangjun L., Qingshan L., Yemin W., Hongyu O., Qianjin K., Zixin D., Wen L. (2014) Operon for Biosynthesis of Lipstatin, the Beta-Lactone Inhibitor of Human Pancreatic Lipase. Appl Environmental Microbiology, 80 (24): 7473-83. doi: 10.1128/AEM.01765-14.Tingli B., Daozhong Z., Shuangjun L., Qingshan L., Yemin W., Hongyu O., Qianjin K., Zixin D., Wen L. (2014) Operon for Biosynthesis of Lipstatin, the Beta-Lactone Inhibitor of Human Pancreatic Lipase. Appl Environmental Microbiology, 80 (24): 7473-83. doi: 10.1128/AEM.01765-14.

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