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Anna Safitri
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Research Center for Smart Molecule of Natural Genetics Resources (SMONAGENES) office: 2nd floor MIPA Building, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Jl. Veteran Malang, East Java, Indonesia – 65145
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JSMARTech : Journal of Smart Bioprospecting and Technology
Published by Universitas Brawijaya
ISSN : 26860805     EISSN : 27147894     DOI : https://doi.org/10.21776/ub.jsmartech.2020.001.02.
Core Subject : Health, Science,
Biochemistry, Genetics & Molecular Biology Chemistry Materials Science & Nanotechnology Medicine & Pharmacology Neuroscience
JSMARTech : Journal of Smart Bioprospecting and Technology (p-ISSN: 2686-0805, e-ISSN : 2714-7894) is an Open Access Scientific Journal published by Research Center of Smart Molecule and Natural Genetics Resources (SMONAGENES), Universitas Brawijaya, Malang, East Java, Indonesia, since 2019. It is a journal covering of bioprospecting, biochemical, biotechnology, bioinformatics, natural product, pharmaceuticals, biomedical, genetics engineering, nutrigenomic, and nanotechnology. The journal publishes a manuscript written in English for original research papers, short communications, and review articles. The paper published in this journal implies that the work described has not been, and will not be published elsewhere, except in abstract, as part of a lecture, review or academic thesis.
Arjuna Subject : Biokimia, Genetika dan Biologi Molekuler - Biokimia, Genetika dan Biologi Molekuler (Lain-Lain)
Articles 54 Documents
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Virtual Screening of Mimosa pudica Secondary Metabolites as Hyaluronidase B Potential Inhibitor to Prevent Vespa velutina Venom Spreading Rijalullah, Muhammad Asyraf; Pramudya, Muhammad Alif Imam; Maisuroh, Dalilatul; Zain, Dhiyaa Syahlaa Bianca Febrinnisa; Kurniawan, Nia; Fatchiyah, Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 3 (2021)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.96

Abstract

Vespa velutina, also known as the Yellow-legged hornet, is a wasp species native to Asia with a large distribution area in Indonesia. Hyaluronidase B in a wasp venom acts as a "spreading factor", which is the key at the beginning of envenomation. Shameplant (Mimosa pudica), a common plant in Indonesia, has shown the potential to be a hyaluronidase B inhibitor. This study aimed to analyze the potential of secondary metabolites in Shameplant as an inhibitor of V. velutina Hyaluronidase B base on their molecular interactions and as a topical drug base on physicochemical characteristics. In silico computational studies is performed to predict the binding modes of M. pudica compounds and hyaluronidase B enzyme. The secondary metabolites were retrieved from the PubChem database and screened using SwissADME. The seven metabolite compounds were docked with Hyaluronidase B and hyaluronan by HEX Cuda 8.0.0 program. Hyaluronidase B was also docked with its native ligand (hyaluronan) to validate the docking study. Three dimensional and 2D views were then evaluated using Discovery Studio 2016. Results of this study are all compounds do not have the same molecular interaction with the control. It defines no inhibition of the interaction on the active side. Mimopudine is the most potent inhibitor of hyaluronidase B based on its binding energy. While, jasmonic acid is the only compound that meets the physicochemical parameter of the topical drug.
Anti-Obesity Properties of Black Pepper (Piper nigrum): Completing Puzzle using Computational Analysis Lailiyah, Nurun Nafi'atul; Ibrahim, Mutiara Dwirosita; Fitriani, Chunafa Ayu; Hermanto, Feri Eko
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 3 (2021)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.101

Abstract

Pepper (Piper nigrum) is one of the most common spices found in almost every food. Current knowledge informed that pepper regulates physiological activity in obesity. However, the exact mechanism is still poorly understood. This study determined the potential of piperine and piperidine as major compounds in pepper as GHSR-Ghrelin inhibitors due to over-activity of Ghrelin as appetite hormone in obesity. Molecular docking was performed to simulate the binding pattern of piperine and piperidine as GHSR-Ghrelin antagonist. The result showed that piperidine has a lower potential as GHSR-Ghrelin antagonist than piperine based on binding energy calculation and amino acid interaction. Further, piperine binding to GHSR could shift the Ghrelin binding site to the GHSR. In conclusion, piperine may act as an inhibitor of GHSR-Ghrelin interaction to prevent appetite behavior resulting in bodyweight loss in obesity.  
In Silico Study of Vacuolin-1 as an Inhibitor of HSP27 for Precancerous Treatment of Breast Cancer Agustin, Diah Eka; Ulfah, Mumtaz Nabila; Aisyah, Siti Nur; Arumsari, Pamuji Lestari; Pertiwi, Kadita Octavia; Fatchiyah, Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 3 (2021)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.107

Abstract

Breast cancer has a great chance of being cured if it is diagnosed and treated properly in its early stage. The pre-cancer stage is an early stage of cancer development characterized by the overexpression of HSP27. Therefore, HSP27 can be a therapeutic target of cancer. This study aims to analyze whether vacuolin-1, a small drug compound known for its ability to inhibit metastasis, can inhibit HSP27 to prevent precancerous development in breast cancer, as well as its ADME and biosafety aspects. Protein & ligand structures were obtained from RCSB PDB and PubChem database. Preparation was performed with Discovery Studio and PyRx. Drug-likeness/ADME analysis was performed in Swiss-ADME web server. Biosafety analysis was performed in MetaTox web server. Molecular docking was performed using PyRx. The visualization of docking results was performed using Discovery Studio. The docking result between vacuolin-1 and HSP27 showed that vacuolin-1 can act as an HSP27 inhibitor by interacting with S78 residue of HSP27 and blocking its phosphorylation as well as depolymerization process. The drug-likeness characterization result of this compound showed that vacuolin-1 violates one of the four Lipinski's Rule of Five. Biosafety analysis showed that vacuolin-1 has a low toxicity level with an estimated LD50 around 13,016.65 mg/kg.
In-Silico Screening Compounds of Brassica rapa ssp. chinensis as Potential Inhibitor of Neutral Amino Acid Transporter B0AT1 as an Alternative Phenylketonuria Treatment Nathania, Nina Regina; Mantow, Jellyta Pricilla; Criswahyudianti, Elsa Rahmania; Atamimi, Fachrur Rozi; Fatchiyah, Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 3 (2021)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.113

Abstract

Phenylketonuria (PKU) is known as a severe autosomal recessive disease caused by mutations in the expression enzyme, namely the PAH (Phenylalanine Hydroxylase) enzyme that causes the build-up of phenylalanine in the body. Untreated PKU affected brain damage and developmental problems. One of the strategies to reduce phenylalanine in the body is inhibiting B0AT1 activity using carotenoid and terpenoids compounds from Bok choy (Brassica rapa ssp.chinensis). In this study, we evaluated the nine carotenoid and terpenoid compounds from Bok choy as B0AT1 inhibitors. Nine Bok choy compounds, including alpha-carotene, beta-carotene, dimethylallyl pyrophosphate, isopentenyl pyrophosphate, lutein, neoxanthin, violaxanthin, geranylgeranyl diphosphate, and zeaxanthin were downloaded from PubChem database, while the 3D structure of B0AT1 was retrieved from Protein Data Bank RCSB. The compounds and B0AT1 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. This screening implies that three terpenoid compounds dimethylallyl pyrophosphate, isopentenyl pyrophosphate, and geranylgeranyl diphosphate interacts in C domain of B0AT1 while six carotenoid compounds, alpha carotene, beta-carotene, lutein, neoxanthin, violaxanthin, and zeaxanthin interacts in A domain and have possibility to inhibit B0AT1, because it interact with same A domain and have a stronger binding energy than phenylalanine. Alpha carotene has a same residue with phenylalanine, Phe144, making it potentially greater than other compound as inhibitors. Brassica rapa ssp. chinensis is indeed good for consumption by people with phenylketonuria, but it is also necessary to do a further compound screening in other low-phenylalanine diet foods to know which one is better as alternative phenylketonuria treatment.
Spirulina platensis’s phycocyanobilin as an antiangiogenesis by inhibiting VEGFR2-VEGFA pathway in breast cancer: in silico study Jayanti, Dewa Ayu Putu Ismartati Sukma; Abimanyu, I Gede Agni Marwan; Azzamudin, Haidar
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 3 (2021)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.87

Abstract

Breast cancer is a cancer type that leads to many women deaths. The causes are from the primary tumour and other progressions such as metastatic and angiogenesis. Some therapy strategies have been developed to treat breast cancer, but they are not good enough for treating breast cancer progressions. Spirulina platensis has a phycocyanin and a phycocyanobilin, known as antioxidant and antiinflammatory bioactivities. This study identified anticancer activity of phycocyanobilin from Spirulina platensis. We also investigated the phycocyanobilin mechanism in breast cancer inhibition through VEGFR2-VEGFA pathway. In silico analysis was conducted the inhibition modelling of phycocyanobilin to the VEGF-VEGFR pathway. The VEGF and VEGFR proteins were taken out from Protein Data Bank (PDB) database and were prepared with BIOVIA Discovery Studio 2019. Phycocyanobilin as a ligand was obtained from PubChem and prepared with PyRx. The molecular docking was conducted using HEX 8.0.0 CUDA and the last step is the protein-ligand complexes were visualized and analyzed using BIOVIA Discovery Studio 2019. It results in five protein-ligand complexes in which the receptor-ligand complex VEGFR2-[VEGFA-phycocyanobilin] can inhibit the angiogenesis process by phycocyanobilin binds to VEGFA, and it prevents the angiogenesis process by blocks the VEGFR2 and stops VEGFA to bind with VEGFR2. Thus phycocyanobilin has potential as an anticancer agent especially in  breast cancer as an antiangiogenesis.
Front Matter Volume 2 No.3 Fatchiyah, Fatchiyah; Safitri, Anna; Sari, Dewi Ratih Tirto
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 3 (2021)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.03.0

Abstract

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
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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
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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 Study of Bioactive Compounds from Tangerines (Citrus reticulata) as Protein Inhibitor for 3CLpro SARS-CoV-2 : Omicron Variant Victor Alvianoes Guterez Hose; Shella Zahra Kumala Azmi; Muhammad Faiz Maulana; Daniel Tumbur Hamonangan Sirait; Ailsa Calista Salsabila; Rahmat Grahadi; Fatchiyah Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol. 3 No. 2 (2022): JSMARTech Volume 3, No. 2, 2022
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2022.003.02.38

Abstract

COVID-19 is a disease caused by coronavirus that was identified as a new strain of coronavirus last December 2019. Coronavirus disease can be handled by blocking its protein using bioactive compounds, it is known that there are compounds from Citrus reticulata that have potential as antiviral. An in silico evaluation of the active compounds available in Citrus reticulata was carried out to compare their anti-inflammatory effects based on the molecular characteristics of docking with nirmatrelvir as a control compound. In addition, analysis of binding affinity, binding site, ADME prediction, and molecular dynamics simulation was also carried out. The results obtained indicate that neohesperidin compounds can bind to receptors that bind to catalytic sites on Cys145 and His41 as well as nirmatrelvir. In addition, there is also phlorin which can bind to the catalytic site of the His41 receptor. Active site analysis of the interaction suggests neohesperidin and phlorin compounds may have a therapeutic effect against COVID-19. However, from the results of ADME predictions, not all of these compounds qualify Lipinski's rule criteria such as neohesperidin and diosmin.
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.

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