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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 The paper published in this journal implies that the work described has not been, and will not be published elsewhere, except in abstract, as part of a lecture, review or academic thesis.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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Molecular Docking Analysis of α-Tomatine and Tomatidine to Inhibit Epidermal Growth Factor Receptor (EGFR) Activation in Non-Small-Cell Lung Cancer (NSCLC) Amalia, Intan Fitri; Sayyidah, Assyifa; Larasati, Kirana Aisyah; Budiarti, Sarah Fadilah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 1 (2020)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2020.002.01.1

Abstract

The use of chemical drugs is the most common option for NSCLC therapy but mostly it has side effects,suchasdiarrhea,skinproblems,excessivebodyfeeling,andmouthsores.Therefore,NSCLC therapy using herbal medicine from plant bioactive compound began to be developed to minimize the side effect of chemical drugs consumption. Tomato (Lycopersiconesculentum Mill.) is one of the herbal source which contains bioactive compounds such as α-tomatine and tomatidine. The aims of this study is to analyze the effectiveness of α-tomatine, tomatidine, and combination of both of them to inhibit EGFR activity by molecular docking. The ligand and protein preparations were done using Discovery Studio 2016 then Hex 8.0.0 is used for docking. Visualization were done using Discovery Studio 2016 as well. Alpha tomatine, tomatidine, and combination of both of them have potential as inhibitors of the interaction between EGFR and EGF as native ligands. Combination alpha tomatine and timitidine have the best results among other complex that has been tested with thread of alpha tomatine applied before tomatidine. Alpha tomatine and tomatidine can be considered as drugs that can control overexpression of EGFR and decrease activation of one of the lung cancer signaling pathways. 
Front Matter JSMartech Vol.02., No.02 Fatchiyah, Fatchiyah; Safitri, Anna
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 2 (2021)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.02.0

Abstract

Role of Mango Mistletoe on Superoxide Dismutase (SOD) in Hypertensive Rats Exposed to DOCA-Salt Suroyya, Mariyam; Sjakoer, Nour Athiroh Abdoes; Mubarakati, Nurul Jadid
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 2 (2021)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.02.61

Abstract

Abstract: Hypertension is a condition where there is an abnormal rise in blood pressure that may be the primary cause of cardiovascular disease. Hypertension induces the production of free radicals known as reactive oxygen species (ROS) and oxidative stress. The purpose of this study is to further examine the function of Dendropthoe pentandra as an endogenous antioxidant modulator in this case superoxide dismutase (SOD) in hypertensive rats.The testing approach used is experimental. Data were analyzed using the one-way ANOVA test and the Post Hoc test to see variations in SOD levels in different treatments. This research used a hypertensive rat model induced by deoxycorticosterone acetate (DOCA) and salt. The number of animals tested was 25 white male rats divided into 5 groups, each containing 5 rats.The group consisted of a control group, a group of non- Extract methanolic of mango mistletoe hypertensive rats, and three groups of hypertensive rats receiving mango mistletoe methanolic extract (EMBM) at dosages of 50 mg/kg, 100 mg/kg, and 200 mg/kg body weight. Based on the results of the study, it is known that the levels of increased lung SOD with extract methanolic of mango mistletoe dosage variations in all treatment groups were not different. The administration of mango parasite methanolic extract at a dose of 50 mg / kgBW was optimum in increasing lung SOD levels in hypertensive rats.
Developing Herbal Medicine, The Role of β-1,3/1,6-D-Glucan Forms of Polysaccharide Peptide (PsP) from Mycelia Ganoderma lucidum Extracts for Lowering Elevated Total Cholesterol Level in Patients with Heart Failure in Ischaemic Heart Disease Sargowo, Djanggan; Wihastuti, Titin Andri; Dewi, Elvira Sari; Saputri, Diana Nanda
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 1 (2020)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2020.002.01.40

Abstract

High levels of total cholesterol can worsen the condition of ischemic heart failure. Polysaccharide peptide (PsP) is a capsule of Ganoderma lucidum extract. This study aims to measure changes in total cholesterol levels in patients with ischemic heart failure before and after the administration of PSP and Placebo and to analyze differences in decreases in total cholesterol levels between PSP and Placebo group. This research is a true experiment with a prospective double-blind randomized control method through pre-post test design. The sample consisted of 26 patients, divided into 2 groups and given PSP or placebo capsules per oral interventions carried out every day for 90 days. Venipuncture blood was taken before and after the intervention to measure total cholesterol levels by spectrophotometry methods. Paired T Test was used to determine the average reduction in total cholesterol levels for each group. Independent T Test was used to determine the difference of reduction in total cholesterol average between the two groups. The decrease of total cholesterol average level in PsP group was 24.3 mg/dl (p value 0.001) and an increase of Placebo group was 8.3 mg/dl (p value 0.099). Comparison of the average reduction in total cholesterol levels in PsP : Placebo group was 24.31: -8.31 mg/dl (p value 0.000). There was significant decrease total cholesterol levels in PsP group and neither was of the Placebo group. In addition, there was significant difference in the reduction of total cholesterol levels between PSP and Placebo group.
Virtual Prediction of Lycopene and Quercetin Effects on Angiogenesis Through VEGFR-2 Pathway Samoedra, Rizky Senna; Sari, Fikriya Novita; Pratama, Setyaki Kevin
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 1 (2020)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2020.002.01.7

Abstract

Angiogenesis is a complex process that is required for cancer cells to perform metastasis. The binding of a growth factor such as VEGF to its receptor is one of the factors to trigger angiogenesis through VEGFR-2 pathway. This study is conducted to analyze the effect of lycopene and quercetin, which are compounds found in watermelon (Citrullus lanatus) on angiogenesis through VEGFR-2 pathway. The study was carried out in silico. Ligands were obtained from PubChem and prepared using PyRx while the protein was obtained from PDB and prepared using BIOVIA Discovery Studio 2019. The docking was done by using HEX 8.0.0 and the results were visualized using BIOVIA Discovery Studio 2019. Lycopene and quercetin were able to bind with VEGFR-2 to interrupt the binding of VEGFA. The presence of lycopene and quercetin also lowers the binding strength of VEGFA with VEGFR-2 as they can affect interactions between VEGFA and VEGFR-2 at 4 and 5 amino acid residues by changing the type of interactions to make the binding strength weaker. The binding of lycopene and quercetin have the potential to interrupt the downstream pathway of angiogenesis through VEGFR-2 pathway.
In Silico Analysis of rbcl Protein and D-Ribulose 1,5-bisphosphate Bond Ihwan, Ihwan; Sari, Dewi Ratih Tirto; Hakim, Luchman; Retnaningdyah, Catur; Arumingtyas, Estri Laras
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 2 (2021)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.02.65

Abstract

The aim of this study was to determine the bond between the protein rbcL and D-Ribulose 1,5-bisphosphate by insilico. DNA sequences of the Mangrove Rhizophora mucronate rbcL gene DNA sequences from 7 different sources were obtained from NCBI for further alignment analysis using BioEdit software, phylogeny analysis using Mega6 software, molecular docking using PyRx software, preparation and visualization of docking results using Biovia Discovery Studio Visualizer software and analysis of the protein model quality based on the number of amino acid residues (Ramachandran plot analysis). The results of the docking molecular analysis showed interaction of 9 hydrogen bonds namely Asp203, Thr173, His294, Glu204, His327, Ser379, His298, Arg295, and Asn123 and 2 unfavorable bonds namely Lys177 and Lys175. This ligand and protein interaction complex was of good quality because the presence of amino acid residues in the most favored regions was greater than the amino acid residues in the disallowed regions outcomes
In Silico Screening of Schleichera oleosa Phytocompounds as Estrogen Receptors Alpha Inhibitors for Breast Cancer Pratiwi, Radita Intan Aisyah; Rahayu, Tintrim; Mubarakati, Nurul Jadid
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 1 (2020)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2020.002.01.14

Abstract

Abstrak: This study aimed to predict the potential activity, toxicity, and interaction of fifteen bioactive compounds from Schleichera oleosa as estrogen receptors alpha inhibitors via in silico analysis. Active compound was downloaded from the PubChem database, and the 3D structure of the human estrogen receptor alpha (ERα) was obtained from the Protein Data Bank database with 4-Hydroxytamoxyfen as a positive control. The interaction of bioactive compounds with macromolecule was examined via a molecular specific docking using AutoDock Vina with PyRx 9.5 software. The protein was visualized using Discovery Studio 4.1. The drug-likeness property and human intestinal absorption of those fifteen bioactive compounds were evaluated through absorption, distribution, metabolism, and excretion (ADME) analysis using the pkCSM online tool program. The interactions between proteins and ligands are largely through the formation of hydrogen and van der Waals bonds. The binding energy of lupeol acetate, lupeol, schleicheol 1, betulinic acid, betulin, beta-sitosterol, schleicherastatin 7, schleicherastatin 2, schleicherastatin 4, scopoletin, schleicherastatin 3, schleicherastatin 1, schleicherastatin 6, schleicherastatin 5 alpha and schleicherastatin receptors including -8.3, -8.3, -7.1, -7.1, -6.7, -6.6, -6.6, -6.5, -6.5, -6.3, -6.2, -6.2 -6.1, -5.9 and -5.5 kcal / mol, respectively . The in silico ADME analysis also revealed that lupeol and lupeol acetate were the best active compound that passes the test based on the Lipinski rule, ADME, and toxicity. Therefore, it can be stated that Schleichera oleosa has potential as an inhibitor of alpha estrogen receptors. The inhibitory activity of alpha estrogen receptors has led to new breakthroughs in plant-based medicinal products, particularly for breast cancer. Keyword: Schleichera oleosa, alpha estrogen receptors, phytocompound, breast cancer and in silico
Molecular Docking Chlorogenic Acid and Isomer Compound as Cyclooxygenase-2 (COX-2) Inhibitor in Atherosclerosis Nurarifa, Ratna; Rachmawati, Devi Era; Utari, Dwi
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 1 (2020)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2020.002.01.22

Abstract

Atherosclerosis is an inflammatory disease caused by oxidized LDL. Chloroghenic acid (CGA) is a polyphenol compound and its isomers such as Caffeoylquinic acid (CQA) and Feruloylquinic acid (FQA) can increase the activity of antioxidant activity and can significantly reduce total cholesterol in the blood. Cyclooxygenase (COX) is an enzyme that correlates with the inflammatory process. COX is divided into two isoforms, COX-1 and COX-2. Prostanoid synthesis via the action of cyclooxygenase-2 (COX-2) is a component of the inflammatory response. All prepared compound of Chlorogenic acid (CGA) and its isomer, Caffeolycquinic acid (CQA) and Feruloylquinic acid (FQA) is used for molecular docking by using HEX 8.0.0. Visualization process is done by using Discovery Studio Client 4.1 software. The results showed docking between COX-2 with CGA compounds and its isomers also drug Ibuprofen shows energy binding COX-2 - CGA of -320 kcal / mol, COX-2 - CQA of -298 kcal / mol, COX-2 - FQA of -282 kcal / mol, and COX-2 - Ibuprofen of -230 kcal / mol. The docking results show the CGA compound and its isomers have smaller energy bindings than the drug Ibuprofen. This shows that the CGA compound and its isomers are better than the Ibuprofen drug so that it has the potential as an anti-inflammatory which can be used to prevent the formation of atherosclerosis.
Bilateral midbrain transection induced hyperphagia accelerates the development of diabetes in Spontaneously Diabetic Torii (SDT) rats Sasase, Tomohiko; Ito, Makoto; Ishii, Yukihito; Ohta, Takeshi
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 2, No 2 (2021)
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Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.21776/ub.jsmartech.2021.002.02.69

Abstract

Spontaneously Diabetic Torii (SDT) rat is a model of severe type 2 diabetes and its complications. These characteristics of SDT rat are very useful to research diseases; however, the slow onset of diabetes may limit the usefulness of this animal model. To solve this problem, we performed bilateral midbrain transection on SDT rats and evaluated whether hyperphagia accelerates the onset of diabetes. By severing ascending fibers from the nucleus tractus solitarius to limbic regions through ventral and dorsal tegmental regions, food consumption was significantly increased in SDT rats and the onset of diabetes was accelerated. Cumulative incidence of diabetes in midbrain transected SDT rats was 88.9% at 7 weeks after surgery (14 weeks of age), while sham operated rats was 20.0%. Increased food consumption was correlated to body weight, plasma glucose level, plasma triglyceride level, and plasma insulin level. In conclusion, the overeating caused by blocking anorexigenic signal in brain significantly accelerates the onset of diabetes in SDT rats. The early development of type 2 diabetes may accelerate microvascular complications and is considered useful in the study of the disease in SDT rats.
In-Silico Analysis of Procyanidin Type-A Extracted From Cinnamon for Diabetes Mellitus Type 2 Treatment Anandari, Risma Nila; Minnah, Siti Khaizatul; Widadni, Vidya Utami; Safira, Dona; 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.2021.002.03.92

Abstract

Type 2 diabetes mellitus (T2DM) is the most common disease in developing countries. People with type-2 diabetes are at high risk of complications leading to disability and premature death. Procyanidin compounds in cinnamon have an insulin-like activity that can regulate normal blood sugar levels. This research aimed to investigate the interaction between α-glucosidase and α-amylase with procyanidin A and their potential for diabetes treatment therapy. Data mining receptor was downloaded from RCSB PDB and ligands from PubChem. Drug likeness properties were evaluated using SwissADME, while toxicity analysis was assessed using metatox. Molecular docking between α-glucosidase and α-amylase with procyanidin A was performed using HEX 8.0.0 and was visualized by Discovery Studio. Procyanidin A showed interaction with α-glucosidase by non-bonds interaction, including hydrogen, hydrostatic and hydrophobic bonds, while procyanidin A and α-amylase formed hydrogen and hydrophobic bonds. Procyanidin A is an alternative treatment for T2DM with a variety of supportive chemical bonds. Procyanidin A has an excellent ability to inhibit activity α-glucosidase and α-amylase in the process of breaking down glucose in the intestines.

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