IN SILICO INVESTIGATION OF MOLECULAR INTERACTIONS BETWEEN INULOSUCRASE DERIVED FROM Aspergillus awamori AND EPE COMPOUNDS
DOI:
https://doi.org/10.26418/indonesian.v8i2.96978Abstract
Fructooligosaccharides (FOS) are important prebiotics synthesized by the enzymatic activity of inulosucrase, and understanding their molecular interactions is essential for exploring potential modulators. This study examined the interaction between inulosucrase from Aspergillus awamori (PDB ID: 1Y4W) and the compound EPE (4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid) using an in silico molecular docking approach. Since the 1Y4W structure lacks a co-crystallized ligand, EPE was selected as a surrogate ligand derived from PDB ID: 3SC7 and prepared for docking simulations. Docking with AutoDock Vina produced a best binding affinity of "“5.6 kcal/mol, with the strongest hydrogen bond observed with TRP305 (1.92 Ã…) and additional interactions with TYR279 (3.75 Ã…). These results indicate a moderate but stable interaction, weaker than the native substrate fructose reported in crystallographic studies. Overall, EPE shows potential as a modulatory compound of inulosucrase activity and provides a basis for further enzymological and biotechnological research.References
References
Natasya N.W.A., and Wikandari P.R. (2022). Pengaruh lama fermentasi umbi gembili (Dioscorea esculenta L.) dengan kultur starter Lactobacilus plantarum b1765 terhadap produksi fruktooligosakarida. Unesa Journal of Chemistry, 11(2):88-96. https://doi.org/10.26740/ujc.v11n2.p88-96
Kim W., Lee J., Singh B., Maharjan S., Hong L., Lee S., Cui L., Lee K., Kim G., Yun C., Kang S., Choi Y., and Cho C. (2018). A new way of producing pediocin in Pediococcus acidilacticit through intracellular stimulation by internalized inulin nanoparticles. Scientific reports, 8(1):58-78. https://doi.org/10.1038/s41598-018-24227-z
Nisa H.C., Jannah M., Ruhaiyah F., and Kurniasih E. (2021). Review sintesis fruktooligosakarida berbasis sukrosa jalur fermentasi: sinbiotic applied. Jurnal Teknik dan Teknologi, 16(31):22-27. https://www.neliti.com/id/publications/449850/review-sintesis-fruktooligosakarida-berbasis-sukrosa-jalur-fermentasi-sinbiotic
Aini D.M., and Balqis S. (2025). Halophilic bacteria as promising biocatalyst producers: a review on enzyme production. Jurnal Biologi Tropis, 25(2):2178-2186
Charoenwongpaiboon T., Klaewkla M., Chunsrivirot S., Wangpaiboon K., Pichyangkura R., Field R.A., and Prousoontorn M.H. (2019). Rational re-design of Lactobacillus reuteri 121 inulosucrasefor product chain length control. RSC Advances, 9(14957):14957–14965. https://doi.org/10.1039/C9RA02137J
Muhammed M. T., and Aki-Yalcin E. (2024). Molecular docking: principles, advances, and its applications in drug discovery. Letters in Drug Design & Discovery, 21(3):480-495. http://dx.doi.org/10.2174/1570180819666220922103109
Nagem, R. A., Rojas, A. L., Golubev, A. M., Korneeva, O. S., Eneyskaya, E. V., Kulminskaya, A. A., Neustroev, K. N., and Polikarpov, I. (2004). Crystal structure of exo-inulinase from Aspergillus awamori: the enzyme fold and structural determinants of substrate recognition. Journal of molecular biology, 344(2):471–480. https://doi.org/10.1016/j.jmb.2004.09.024
Pouyez, J., Mayard, A., Vandamme, A. M., Roussel, G., Perpète, E. A., Wouters, J., Housen, I., and Michaux, C. (2012). First crystal structure of an endo-inulinase, INU2, from Aspergillus ficuum: discovery of an extra-pocket in the catalytic domain responsible for its endo-activity. Biochimie, 94(11):2423–2430. https://doi.org/10.1016/j.biochi.2012.06.020
Prasetio, N. F., Kepel, B. J., Bodhi, W., Manampiring, A., & Budiarso, F. (2021). Molecular docking terhadap senyawa isoeleutherin dan isoeleutherol sebagai penghambat pertumbuhan SARS-CoV-2. eBiomedik, 9(1). https://doi.org/10.35790/ebm.9.1.2021.31809
Diedrich, K., Krause, B., Berg, O., & Rarey, M. (2023). PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. Journal of computer-aided molecular design, 37(10):491–503. https://doi.org/10.1007/s10822-023-00522-4
Makisake R.G., Montolalu R.I., Mewengkang H.W., Sanger G., Harikedua, S.D., Makapedua D.M., Salindeho N., Zagoto E.B.S., and Gumolung I.J.P.A. (2022). Studi in silico senyawa aktif daun tagalolo (Ficus septicaburm F) sebagai ligan uji pada enzim l-histidin decarboxylase. Media Teknologi Hasil Perikanan, 10(2):122-126. https://doi.org/10.35800/mthp.10.2.2022.40390
Makatita F.A,.Wardhani R., and Nuraini. (2020). Riset in silico dalam pengembangan sains di bidang pendidikan, studi kasus: analisis potensi cendana sebagai agen anti-aging. Jurnal ABDI (Sosial, Budaya dan Sains), 2(1):59-67. https://journal.unhas.ac.id/index.php/kpiunhas/article/view/9086
Sari I.W., Junaidin J., and Pratiwi D. (2020). Studi molecular docking senyawa flavonoid herba kumis kucing (Orthosiphon Stamineus B.) pada reseptor α-glukosidasebagai anti diabetes tipe 2. Jurnal Farmagazine, 7(2):54-60. http://dx.doi.org/10.47653/farm.v7i2.194
DÃaz-Cervantes E., Cortés-GarcÃa C.J., Chacón-GarcÃa L., and Suárez-Castro A. (2020) Molecular docking and pharmacophoric modelling of 1,5-disubstituted tetrazoles as inhibitors of two proteins present in cancer, the ABL and the mutated T315I kinase. In silico pharmacology, 8(1):6. https://doi.org/10.1007/s40203-020-00059-6
Hakiki A., Andika A., and Rahmawati R. (2024). Studi molecular docking dan prediksi admet senyawa turunan kurkumin sebagai inhibitor kasein kinase 2-α. Lumbung Farmasi: Jurnal Ilmu Kefarmasian, 5(2):195-212. https://doi.org/10.31764/lf.v5i2.22563
Endriyatno N.C., and Walid M. (2022). Studi in silico kandungan senyawa daun srikaya (Annona squamosa L.) terhadap protein dihydrofolate reductase pada mycobacterium tuberculosis. Pharmacon: Jurnal Farmasi Indonesia, 19(1):87-98. https://doi.org/10.23917/pharmacon.v19i1.18044
Tsujimura, M., Ishikita, H., & Saito, K. (2025). Determinants of hydrogen bond distances in proteins. Physical chemistry chemical physics : PCCP, 27(18):9794–9805. https://doi.org/10.1039/d5cp00511f
Laskowski RA, Swindells MB. (2011). LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery. J Chem Inf Model, (10):2778–86. https://doi.org/10.1021/ci200227u
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