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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 The paper published in this journal implies that the work described has not been, and will not be published elsewhere, except in abstract, as part of a lecture, review or academic thesis.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 6 Documents
 1 
Search results for , issue "Vol 1, No 2 (2020)" : 6 Documents clear
IN SILICO STUDY OF CENTELLA ASIATICA ACTIVE COMPOUND AS BACE1 INHIBITOR IN ALZHEIMER’S DISEASE Mawaddani, Nala; Wibowo, Natalia RK; Nadhira, Qumaira HH; Pramifta, Ratih Ayu
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 2 (2020)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (464.148 KB) | DOI: 10.21776/ub.jsmartech.2020.001.02.3

Abstract

Alzheimer (AD) is a chronical neurodegenerative disease which is the 6th leading cause of death worldwide. About 36 million cases in the world and may increase to 115 million in 2050. The pathological cause of AD is the presence of residual A? peptides. A? peptides is produced in the cleavage process of the amyloid precursor protein (APP) sequentially by Beta amyloid precursor protein cleavage enzyme 1 (BACE1) and ?-secretase. Flavonol, germacrene B, and  sitosterol are compounds found in Centella asiatica which is has potential as BACE1 inhibitor. The aim of this study was to analyze the interaction between BACE1 with  flavonol, germacrene B and sitosterol  by molecular docking to predict the BACE1 inhibitor potent of those compound. We obtained BACE1 from RSCB database, flavonol, germacrene B  and  sitosterol from PubChem database. Molecular dockcing was done using Hex 8.0.0. The docking result were vizualized with Discovery Studio 3.5. Interaction of BACE1 resulted binding energy for sitosterol was-239,7 kcal/mol, flavonol was -188,1 kcal/mol, and germacrene B was -185,6 kcal/mol. Flavonol and sitosterol bound to the active site of BACE1 involving  Thr232 and Ile110 on flavonol,  while Tyr71 on sitosterol. All of the active compounds didn?t have the interaction at S1? subsite,which is the center of BACE1 active site which has become the key of APP activation from BACE1. This study has shown that flavonol  and sitosterol had potential to reduce BACE1 activity but not directly inhibit BACE1 activity.
IN-SILICO ANALYSIS OF METHOXYL PECTIN COMPOUNDS FROM BANANA PEELS AS HMG-COA REDUCTASE INHIBITOR COMPLEXES Tapiory, Adelia Adrianne; Pertiwi, Kadita Octavia; Fadilla, Khalisa; Reyhanditya, Davy; Fatchiyah, Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 2 (2020)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (360.419 KB) | DOI: 10.21776/ub.jsmartech.2020.001.02.5

Abstract

Cardiovascular disease (CVD) is one of the most important health problems that emerge in the last decade. The major factor of the disease is by the high level of cholesterol in blood. Several ways can be used to reduce the amount of cholesterol in blood, as using HMGR treatment. This enzyme acts as catalyst in the initial step and limits the cholesterol biosynthesis. Pectin is a polysaccharide compound that used as an agent to reduce the total cholesterol in bloods. In this research, we aim to analyze the function of methoxyl pectin in inhibiting excessive cholesterols in blood by binding with the HMGR. The method we used in this research, first step searching data mining from database and preparation of protein and ligands using discovery studio. Molecular docking analyzed via HEX software. The result of molecular docking is visualized using discovery studio to analyze the energy binding level, also the bonds that formed and the impact that comes from the bonds. The results show that HMGR binding energy for native ligand (HMGCoA) as control ligand was -450,2 kJ/mol, methoxyl pectin was -177,3 kJ/mol and atorvastatin, a group of drugs commonly used for CVD treatment was -386,6 kJ/mol. HMGR binds to HMGCoA with 7 hydrogen bonds and a hydrophobic bond. Methoxyl pectin binds to HMGR with residue Glu700 and His625. Atorvastatin binds to HMGR with residue Lys633 and Leu634. It is known that native ligands bind to HMGR when cholesterol goes down. Based on research, methoxyl pectin bond with HMGR is the same as the HMGCoA native ligand with HMGR, namely His635. This shows that methoxyl pectin is predicted to inhibit HMGR and resulting LDL cholesterol decrease. Methoxyl pectin is indicated to be an alternative drug for cardiovascular disease considering that atorvastatin has several side effects. While methoxyl pectin, which is derived from natural ingredients with minimum side effect.
FRONT MATTER JSMARTECH APRIL 2020, VOL 01 NO 02 Safitri, Anna
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 2 (2020)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (750.176 KB)

Abstract

MOLECULAR DOCKING APPROACH OF POTENTIAL ALPHA-GLUCOSIDASE INHIBITORS FROM EXTRACTS COMPOUNDS OF R. TUBEROSA L Safitri, Anna; Tirto Sari, Dewi Ratih; Roosdiana, Anna; Fatchiyah, Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 2 (2020)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (414.017 KB) | DOI: 10.21776/ub.jsmartech.2020.001.02.1

Abstract

The present study investigates anti-diabetic capacity of compounds enclosed in the R. tuberosa L. root extracts by molecular simulation approach to examine the potential of those compounds acting as alpha-glucosidase inhibitors. Compounds chosen were cirsimarin, cirsimaritin, and sorbifolin; quercetin was used for the reference. Those compounds were downloaded from PubChem database, and human alpha-glucosidase 3D structure was obtained from Protein Data Bank. The protein was docked to the flavonoid compounds using HEX 8.0 software and visualized using Discovery Studio 4.1. The interactions of cirsimarin, cirsimaritin, sorbifolin, and quercetin on alpha-glucosidase showed similar binding patterns. They interacted with the active sites of the enzyme, causing inhibition on enzyme activity. The interactions between proteins and ligands were mostly through formation of hydrogen bonds and Van der Waals forces. The binding energy of cirsimarin cirsimaritin, sorbifolin, and quercetin to alpha glucosidase were comparable at -323.3, -279.4, -256.8, and -241.5 cal/mol, respectively. These confirm that compounds contained in the extracts of R. tuberosa L have capacity to be used as inhibitor for alpha glucosidase. 
A COMPARATIVE STUDY OF GALLIC ACID, ELLAGIC ACID, UROLITHIN A, AND UROLITHIN B WITH NF-κB PROTEIN AS ANTI TYPE 2 DIABETES MELLITUS BY IN SILICO Hikmaranti, Maulida; Astiyani, Ajeng Mareta; Hasanah, Khairul M.; Maghfiroh, Nuril M.
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 2 (2020)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (462.596 KB) | DOI: 10.21776/ub.jsmartech.2020.001.02.2

Abstract

Abstract: Diabaetes type 2 is a common disease with clinical symptoms of abnormal insulin secretion. One of the pathways involved in the pathogenic mechanism of Type 2 Diabetes Mellitus (T2DM) is NF-?B pathway. Walnuts contain natural compounds such as gallic acid, ellagic acid, urolithin A, urolithin B and its potential to be antioxidants and anti-inflammatory. In this research, we focus on the comparative study of 4 compounds as inhibitor of NF-?B complex by molecular docking interactions between NF-?B and these ligands as a anti-T2DM compounds. The method is preparation of NF-?B protein using Discovery Studio 4.1, preparation of ligan: gallic acid, ellagic acid, urolithin, and urolithin B using Pyrx software. After that, docking protein-ligand was done by using Hex 8.0.0 software, visualized with Discovery Studio 2019 and then analyzed the bioactivity of compound through web mollinspiration, respectively. The result of mollinspiration show that 4 compounds have good quality as a drug based on the lipinski 5 rules. The docking results show that four compounds can actively bind to the active site of NF-?B with the different bond energies. Ellagic acid is the most stable compound and the highest activity to inhibition of the NF-?B pathway because its have highest binding energy than other (-228,9kcal/mol). Ellagic acid is an active polyphenol compound which is good to use as an antidepressant. Based on these comparative studies, ellagic acid has the best potential among the three other compounds in inhibiting NF-?B activity. Beside that, all compounds can effectively inhibit the activation and translocation of NF-kB from the cytoplasm to the nucleus so the NF-?B is unable to regulate DNA sequences that encode proinflammatory proteins and then be able to reduce the pathophysiological effects of type 2 diabetes mellitus. 
EFFECTIVENESS OF USING TRICHODERMA VIRIDE AS BIOSORBENT FOR REMAZOL BRILLIANT PURPLE IN BATIK WASTEWATER TREATMENT Safitri, Anna; Febrianti, Wiwin Dwi; Rahmaniah, Galuh
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 2 (2020)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (309.634 KB) | DOI: 10.21776/ub.jsmartech.2020.001.02.4

Abstract

Synthetic dyes used in the batik industry cause negative impacts to the environment. One type of synthetic dyes used in batik industry is remazol brilliant violet. This synthetic dye is reactive, carcinogenic, and non-biodegradable. Therefore, a strategy to degrade this synthetic dye is needed. In this study, the potential application of Trichoderma viride for biosorption of remazol brilliant violet (RBZ) in batik wastewater was investigated. The current work aimed on determination of the optimum biosorption conditions, including pH, contact time, and  RBZ concentration. Biosorption of RBZ were carried out at pH 4 to 9; with contact times of 12, 24, 30, 36, and 42 h, with concentrations of dye solutions were 40, 60, 70, 80, and 90 mg/L. Results showed that the optimum biosorption of RBZ was obtained at pH 4, for 30 h, and optimum concentration of RBZ at 60 mg/L, with the RBZ absorbed was 79.27%. The FTIR analysis suggested that RBZ biosorption changed the chemical functional groups in the T. viride. The FTIR spectra revealed that the biomolecules that are affected during the process of biosorption were mainly lipids and proteins, and slightly from nucleic acids and carbohydrates.

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