Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular Docking
Vernonia amygdalina was reported to be used as a therapy for Diabetes Mellitus (DM). One of the mechanisms of therapy DM was to inhibit the action of the α-amylase enzyme. This study aimed to prove the presence of compounds that could inhibit the action of α-amylase. Vernonia amygdalina leaves were...
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| Format: | Article |
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Department of Chemistry, Universitas Gadjah Mada
2022-03-01
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| Series: | Indonesian Journal of Chemistry |
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| Online Access: | https://jurnal.ugm.ac.id/ijc/article/view/71499 |
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| author | Norainny Yunitasari Tri Joko Raharjo Respati Tri Swasono Harno Dwi Pranowo |
| author_facet | Norainny Yunitasari Tri Joko Raharjo Respati Tri Swasono Harno Dwi Pranowo |
| author_sort | Norainny Yunitasari |
| collection | DOAJ |
| description | Vernonia amygdalina was reported to be used as a therapy for Diabetes Mellitus (DM). One of the mechanisms of therapy DM was to inhibit the action of the α-amylase enzyme. This study aimed to prove the presence of compounds that could inhibit the action of α-amylase. Vernonia amygdalina leaves were macerated with methanol and partitioned into n-hexane, dichloromethane (DCM), and ethyl acetate (EtOAc). Furthermore, they were tested for α-amylase inhibitory activity and analyzed using liquid chromatography-high resolutions mass spectrometry (LC-HRMS). Molecular docking and molecular dynamics simulation (MD simulation) examined unique compounds in the extract with good activity and chromatogram results. The EtOAc extracts showed potential as α-amylase inhibitors indicated by their IC50 values, namely 3.0 μg/mL. There are five unique compounds in the EtOAc extract predicted as 3-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-(2-phenylethyl)benzoic acid (compound 1), 2-hexylpentanedioic acid (compound 2), (2E,4E)-5-[1-hydroxy-2,6-dimethyl-4-oxo-6-({3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] oxy}methyl)cyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid (compound 3), 3,5,5-trimethyl-4-(3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-1-yl)oxy}butyl)cyclohex-2-en-1-one (compound 4), and 2-{[(6E)-2,10-dihydroxy-2,6,10-trimethyldodeca-6,11-dien-3-yl]oxy}-6-(hydroxymethyl)oxane-3, 4,5-triol (compound 5). The molecular docking analysis showed that compound 3 had better interaction energy (Ei) (-8.59 kcal/mol) and inhibition constant (Ki) values (0.503 μM) than acarbose. These data were supported by MD simulations based on the parameters of RMSD value, the radius of gyration, and protein-ligand interaction energy. |
| first_indexed | 2024-04-14T07:24:09Z |
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| publishDate | 2022-03-01 |
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| series | Indonesian Journal of Chemistry |
| spelling | doaj.art-0bcfd184832c4d8385431f5bc00af60f2022-12-22T02:06:04ZengDepartment of Chemistry, Universitas Gadjah MadaIndonesian Journal of Chemistry1411-94202460-15782022-03-0122252653810.22146/ijc.7149931471Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular DockingNorainny Yunitasari0Tri Joko Raharjo1Respati Tri Swasono2Harno Dwi Pranowo3Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, PO BOX BLS 21, Yogyakarta 55281, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, PO BOX BLS 21, Yogyakarta 55281, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, PO BOX BLS 21, Yogyakarta 55281, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara, PO BOX BLS 21, Yogyakarta 55281, IndonesiaVernonia amygdalina was reported to be used as a therapy for Diabetes Mellitus (DM). One of the mechanisms of therapy DM was to inhibit the action of the α-amylase enzyme. This study aimed to prove the presence of compounds that could inhibit the action of α-amylase. Vernonia amygdalina leaves were macerated with methanol and partitioned into n-hexane, dichloromethane (DCM), and ethyl acetate (EtOAc). Furthermore, they were tested for α-amylase inhibitory activity and analyzed using liquid chromatography-high resolutions mass spectrometry (LC-HRMS). Molecular docking and molecular dynamics simulation (MD simulation) examined unique compounds in the extract with good activity and chromatogram results. The EtOAc extracts showed potential as α-amylase inhibitors indicated by their IC50 values, namely 3.0 μg/mL. There are five unique compounds in the EtOAc extract predicted as 3-[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]-2,4-dihydroxy-6-(2-phenylethyl)benzoic acid (compound 1), 2-hexylpentanedioic acid (compound 2), (2E,4E)-5-[1-hydroxy-2,6-dimethyl-4-oxo-6-({3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl] oxy}methyl)cyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid (compound 3), 3,5,5-trimethyl-4-(3-{[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-1-yl)oxy}butyl)cyclohex-2-en-1-one (compound 4), and 2-{[(6E)-2,10-dihydroxy-2,6,10-trimethyldodeca-6,11-dien-3-yl]oxy}-6-(hydroxymethyl)oxane-3, 4,5-triol (compound 5). The molecular docking analysis showed that compound 3 had better interaction energy (Ei) (-8.59 kcal/mol) and inhibition constant (Ki) values (0.503 μM) than acarbose. These data were supported by MD simulations based on the parameters of RMSD value, the radius of gyration, and protein-ligand interaction energy.https://jurnal.ugm.ac.id/ijc/article/view/71499ethyl acetate extractdiabetes mellituslc-hrmsprotein 4gqrmolecular dynamic simulation |
| spellingShingle | Norainny Yunitasari Tri Joko Raharjo Respati Tri Swasono Harno Dwi Pranowo Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular Docking Indonesian Journal of Chemistry ethyl acetate extract diabetes mellitus lc-hrms protein 4gqr molecular dynamic simulation |
| title | Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular Docking |
| title_full | Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular Docking |
| title_fullStr | Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular Docking |
| title_full_unstemmed | Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular Docking |
| title_short | Identification α-Amylase Inhibitors of <i>Vernonia amygdalina</i> Leaves Extract Using Metabolite Profiling Combined with Molecular Docking |
| title_sort | identification α amylase inhibitors of i vernonia amygdalina i leaves extract using metabolite profiling combined with molecular docking |
| topic | ethyl acetate extract diabetes mellitus lc-hrms protein 4gqr molecular dynamic simulation |
| url | https://jurnal.ugm.ac.id/ijc/article/view/71499 |
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