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All Journal JSMARTech : Journal of Smart Bioprospecting and Technology
Fatchiyah Fatchiyah
Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jalan Veteran, Malang, East Java, Indonesia, 65145
Biochemistry, Genetics & Molecular Biology Chemistry Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience

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In Silico Analysis of the Effectiveness of α-glucosidase Inhibitors (AGIs) on Phaseolus vulgaris L. as Antidiabetic Agents Alfi Tsuraya; Ainun Anugrah; Nur Aini; Salsabila Najah; Siti Sainidah; Yoravika Dwiwibangga; Nia Kurnawan; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 3 No. 2 (2022): JSMARTech Volume 3, No. 2, 2022
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2022.003.02.43

Abstract

Diabetes mellitus is a metabolic disorder characterized by high blood sugar levels accompanied by impaired carbohydrate, lipid, and protein metabolism. Alpha-glucosidase inhibitor is an agent that can inhibits the action of the α-glucosidase enzyme, but the synthetic α-glucosidase inhibitors caused various side effects, therefore the search for AGI from natural active compounds is needed. The objective of this study was to determine the effectiveness of the active compound α-glucosidase inhibitor contained in Phaseolus vulgaris as an antidiabetic agent by in silico methods. Flavonoid compounds such as rutin, isoquercitrin, hyperoside, isorhamnetin-3-glucoside, and acarbose (control), were downloaded from the NCBI PubChem database. Human α-glucosidase (PDB ID: 5KZW) 3D structure was obtained from RCSB PDB. Bioactivity predicted using PASSOnline. ADMET and Drug-Likeness with SwissADME and ProTox II. Molecular docking was conducted using HEX 8.0 and visualized with Discovery Studio. This study showed that all of these compounds have sites that interact with the active sites of the α-glucosidase enzyme, and have several similarities compared to acarbose. All compounds have good potential as α-glucosidase inhibitors.  Isorhamnetin-3-glucosidase is the most potential characteristic as an α-glucosidase inhibitor. It has amino acid residues HIS717 (hydrogen), TYR360 (hydrogen and hydrophobic), and ARG608 (hydrogen) which shows higher number of residues in common with acarbose and active sites that also shows fairly high stability. Based on ADME prediction, Isorhamnetin-3-glucoside most likely has the best characteristics based on LogS, %Abs, and also LogKp compared to the other compounds, and has much higher %Abs (40%) than acarbose (-1,8%). It even only has 2 violations of Lipinski rules compared to acarbose that has 3 violations. Thus, overall flavonoid group compounds in P. vulgaris, especially have good potential as a glucosidase inhibitors as antidiabetic agents.
An In Silico Evaluation of Flavonoids in Allium sp. as a Potent Anti-Acute Myeloid Leukemia (AML) Through FLT3 Inhibition Galuh Nafisah Diva; I Gusti Ngurah Agung Wiwekananda; Naila Salsabila Mawardi; Puspa Andhia Kemala Sari; Safira Aulia Rahma; Ichda Arini Dinana; Nia Kurniawan; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 3 No. 2 (2022): JSMARTech Volume 3, No. 2, 2022
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2022.003.02.63

Abstract

Acute Myeloid Leukemia (AML) is the most common leukemia caused by genetic abnormalities that affect the hematological proliferation and induce incomplete differentiation of myeloid cells in the peripheral blood and bone marrow. AML involving FLT3 gene mutation results in overexpression of FLT3 receptors. This study intended to predict the interaction between the FLT3 receptor in AML with flavonoids found in Allium sp. by a molecular docking method. Several 3D molecule structures of the highest flavonoids from Allium sp., including quercetin, kaempferol, isorhamnetin, myricetin, fisetin, morin, isoquercetin, quercitrin, spiraeoside, and quercetin-3,4-O-diglucoside were obtained from the PubChem database. Meanwhile, the FLT3 receptor complex with gilteritinib 3D structure was obtained from the RCSB PDB database. All compound properties were assessed using Swiss-ADME. FLT3 receptor prepared using Discovery Studio 2019. Meanwhile, all flavonoids' energy as ligands is minimized using PyRx 0.8 software. The specific docking was performed using Autodock Vina integrated with PyRyx v 0.8 software and visualized using Discovery Studio 2019, and several parameters of the docking data were analyzed. All flavonoids show favorable drug-likeness and pharmacokinetics properties apart from four quercetin derivatives. Meanwhile, the molecular docking result shows that Quercetin, kaempferol, isoquercetin, quercitrin, spiraeoside, and quercetin-3,4-O-diglucoside have inhibitory potential against FLT3 receptors because they share several same binding sites as control. They also have a fairly high binding affinity compared to the other compounds tested. Molecular dynamic simulation result demonstrates a considerably stable complex. It is estimated that quercetin and kaempferol from Allium sp. have the potential to be used as therapeutic drugs against AML.
In silico screening oil compounds of Nigella sativa L. as potential SARS-CoV-2 Omicron spike protein inhibitors Nadia Riqqah Nurlayla; Valenski Sicilia; Ananda Kautsar Nadia Faya; Michelle Fai; Peta Aurora Aga; Elsa Rahmania Criswahyudianti; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 3 No. 2 (2022): JSMARTech Volume 3, No. 2, 2022
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.54

Abstract

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has led to a global pandemic. Hence, identifying prospective inhibitors of spike protein SARS-CoV-2 drugs is urgently required for combatting SARS-CoV-2 entry by binding to human angiotensin-converting enzyme 2 (ACE-2). This study evaluated five Nigella sativa L. essential oil compounds as potential SARS-CoV-2 Omicron spike protein inhibitors. Its essential oil has a long history of traditional useas a natural treatment for numerous ailments and disorders. Five compounds of N. sativa essential oil, including thymoquinone, p-Cymene, dithymoquinone, thymohydroquinone, thymol, and bisoxatin as control, were downloaded from the PubChem database. The 3D structure of ACE-2 and spike proteins of the SARS-CoV-2 Omicron variant were retrieved from Protein Data Bank RCSB. The compounds and proteins were prepared by PyRx 0.8 version and Discovery Studio ver 21.1.1, then docked with Hex 8.0.0 and analyzed using Discovery Studio ver 21.1.1 and LigPlot+. According to Lipinski's five rules and Veber's rules, all compounds showed drug-likeness. ADMET evaluation implied five compounds of N. sativa essential oil are well absorbed with consideration of its potential hepatotoxicity. Molecular interactions showed that all compounds, including bisoxatin, have a higher affinity for the ACE-2 protein by thymohydroquinone and thymol are more likely to bind with ACE 2 as the binding energy is higher than control. Therefore, N. sativa L. essential oil compounds are potent to be the inhibitor of SARS-CoV-2 infections by blocking the binding of the spike protein to ACE-2.
Co-Authors Ainun Anugrah Alfi Tsuraya Ananda Kautsar Nadia Faya Elsa Rahmania Criswahyudianti Galuh Nafisah Diva I Gusti Ngurah Agung Wiwekananda Ichda Arini Dinana Michelle Fai Nadia Riqqah Nurlayla Naila Salsabila Mawardi Nia Kurnawan Nia Kurniawan Nur Aini Peta Aurora Aga Puspa Andhia Kemala Sari Safira Aulia Rahma Salsabila Najah Siti Sainidah Valenski Sicilia Yoravika Dwiwibangga