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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 The paper published in this journal implies that the work described has not been, and will not be published elsewhere, except in abstract, as part of a lecture, review or academic thesis.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 1 (2019)" : 6 Documents clear
COMPARISON OF VIRTUAL ANALYSIS OF DIOSGENIN AND TIGOGENIN WHICH HAS POTENTIAL DOWN-REGULATING ANDROGEN SIGNALING N., Shifaaun; Safitri, Erinda Hidayatus; R., Januar F.
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 1 (2019)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (291.234 KB) | DOI: 10.21776/ub.jsmartech.2019.001.01.5

Abstract

Costus speciosus contain several compounds that are important for fitocontraception, such as diosgenin and tigogenin. This study focused on analyzing the potential of diosgenin and tigogenin to down-regulate the androgen signaling with in silico. The androgen receptor (AR) was downloaded from the protein database with ID number 1A28. The diosgenin (CID: 119245) and tigogenin (CID: 99516) were obtained from Pubchem. Optimizing the energy of ligands was established using Pyrx. AR was docked with diosgenin and tigogenin using Hex 8.0.0. The interactions were visualized by Discovery Studio Client 3.5. The results showed that the interaction in the complex of Androgen receptor with diosgenin (ARD) and Androgen receptor with tigogenin (ART) occured in the ligand binding domain (LBD) area. ART had two hydrogen bonds (PRO817 and VAL818), while ARD had only one hydrogen bond (GLN798). There were 11 Van Der Walls bonds in ARD and 5 Van Der Walls bonds in ART. ARD still had unfavorable bump. ART had more hydrophobic bonds and alkyl groups than ARD. The energy binding of ART was also smaller than that of ARD, -264 kcal/mol compared to -249 kcal/mol. This study indicated that ART is more potential in the down-regulating mechanism of androgen signaling.
FRONT MATTER JSMARTECH OCTOBER 2019, VOL 01 NO 01 Suyanto, Eko
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 1 (2019)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (3388.461 KB)

Abstract

VIRTUAL PREDICTION OF THYMOQUINONE AND β-GLUCAN INTERACTION AS ESTROGEN RECEPTOR-ALPHA (ER-α RECEPTOR) MAY REDUCING ON THE BREAST CANCER SIGNALING PATHWAY Rachmawati, Farida; Zaidah, Laili Nur; Mardhiyah, Rihadatul Aisy; Fatchiyah, Fatchiyah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 1 (2019)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (469.081 KB) | DOI: 10.21776/ub.jsmartech.2019.001.01.1

Abstract

Many cases of chemical drug treatment in breast cancer patients result in a negative impact on drug resistance. Therefore the use of natural compounds such as ?-glucan on ajwa dates and thymoquinone on black cumin was expected to stop the process of cancer cell proliferation and to consume in long-term safety. This study aimed to predict the effect of thymoquinone and ?-glucan in reducing breast cancer cascade with molecular docking. This research was carried out in silico. The ligand and protein preparations were done using Discovery Studio 2016. We used Hex 8.0.0 for docking. Visualization was established using Discovery Studio 2016 as well. The results showed that thymoquinone and ?-glucan can undergo conformational changes in ligand binding domain (LBD) of ER-? receptor. The interaction between ER-? receptor with ?-estradiol (inhibited by thymoquinone-?-glucan) was suggested to be the best solution in downregulating breast cancer signaling pathway. This interaction showed more stable conformation with the smallest binding energy (-332,84 kcal/mol). The thymoquinone-?-glucan complex could block the His476 and Met438.
ANALYSIS OF ALLOPURINOL, CUCURBITACIN B, MORINDINE, AND PIPERINE AS XANTHINE OXIDASE INHIBITOR BY MOLECULAR DOCKING Fitria, Lailatul; Hermawan, Muhammad; Sakti, Sefihara Paramitha
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 1 (2019)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (360.5 KB) | DOI: 10.21776/ub.jsmartech.2019.001.01.2

Abstract

Xanthine oxidase (XO) is known to be involved in the mechanism of ROS and oxidants production.  XO inhibitor plays role in preventing changes in purines to uric acid so uric acid levels in serum and urine can be reduced. The aim of this study was to analyze the interactions between XO and allopurinol, cucurbitacin B, morindin, or piperine by molecular docking. We obtained XO (1FIQ), allopurinol (CID135401907), cucurbitacin B (CID5281316), morindin (CID151621), and piperine (CID638024) from the database.  Molecular docking was done using Hex 8.0. The docking results were visualized with Discovery Studio 3.5. The interaction of cucurbitacin B with XO and morindin with XO resulted in low docking energy, -375.08 kcal/mol and -377.4 kcal/mol. The docking energy of piperine with XO and allopurinol with XO was -163.32 kcal/mol and -281.4 kcal/mol. Cucurbitacin B and morindin bound to the active site of XO precisely on the FAD domain involving ARG426, ALA338, and ASP360. Both of the compounds established more than 10 bonds of van der waals when interacted with XO. Piperine and allopurinol bound to XO near the Fe2S cofactor. This study suggests that cucurbitacin B and morindin may have high potential as xanthine oxidase inhibitors.Keywords: allopurinol, cucurbitacine B, morindin, piperin, xanthine oxidase
MOLECULAR DOCKING OF POLYCYCLIC AROMATIC HYDROCARBONS AS POTENTIALLY CARCINOGENIC MOLECULES THROUGH BINDING WITH ARYL HYDROCARBON RECEPTOR Chaubah, Mas Adam Lukman; Bontes, Brenda Wilhelmina; Mulachelah, Naqiyah Afifah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 1 (2019)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (328.915 KB) | DOI: 10.21776/ub.jsmartech.2019.001.01.3

Abstract

Aryl hydrocarbon Receptor (AhR) can activate gene target regulation through transcription, activation, or deactivation. Ligands for the AhR are mostly aromatic hydrocarbons. One of them is Polycyclic Aromatic Hidrocarbons (PAHs). These compounds are naturally found everywhere and are strong carcinogens. The purpose of this study was to perform a molecular docking analysis of three PAHs compounds (BaA, BaP, and PA) towards AhR to observe the strongest interaction in which could potentially lead to carcinogenesis. In this research, we retrieved the strongest three of the PAHs types: Benz[a]Anthracene (BaA), Benzo[a]Pyrene (BaP), and Phenanthrene (PA) from PubChem database. PyRx was used to minimize the ligands energy. Protein model of AhR (ID: 5NJ8) was obtained from PDB database. Discovery Studio Client 3.5 was used to remove water molecules and ligands attached to AhR. We interacted each ligand to the receptor by HEX 8.0.0 and visualized using Discovery Studio Client 3.5. We found that BaP, followed by BaA and PA, had the strongest interaction towards AhR. It indicated that BaP had a higher risk leading to cancer with more adverse effects compared to the BaA and PA interaction to AhR
THE USE OF YELLOW KEPOK BANANA PEEL EXTRACT (MUSA PARADISIACA L. VAR BLUGGOE) AS AN ANTIBACTERIAL FOR CHRONIC PERIODONTITIS CAUSED BY PORPHYROMONAS GINGIVALIS Sutanti, Viranda; Destyawati, Arum Anugrah
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 1 (2019)
Publisher : JSMARTech

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (303.015 KB) | DOI: 10.21776/ub.jsmartech.2019.001.01.4

Abstract

Chronic periodontitis is the most common periodontal disease, and Porphyromonas gingivalis is its dominant causative microorganism. Yellow kepok banana peel (Musa Paradisiaca L. Var. Bluggoe) contains flavonoids, alkaloids, tannins, saponins and triterpenoids that can inhibit and kill Porphyromonas gingivalis. Purpose:  To reveal the antibacterial effectiveness of yellow kepok banana peel extract against Porphyromonas gingivalis. Method: This is true experimental research employing the post-test only control group approach. Preliminary research was conducted to determine the concentration of the sample group, 6 treatment groups (5%, 7.5%, 10%, 12.5%, 15%, 17.5%), and 2 control groups were involved. Yellow kepok banana peel extract was obtained through the maceration method using methanol as a solvent. The antibacterial activity was identified using the tube dilution method. Data analysis was conducted through the Kruskal Wallis test, the Mann Whitney test, and the Spearman correlation test. Result: Minimum Inhibitory Concentration (MIC) is obtained at a concentration of 10%, while the Minimum Bactericidal Concentration (MBC) is obtained at a concentration of 17.5%. The test results of tube turbidity statistics indicated that there were significant differences in each extract concentration and there was a relationship between the concentration variables and the turbidity of the tubes. The statistical test results of the colony growth revealed that there were significant differences in each extract concentration and there was a relationship between the concentration variables and the growth of bacterial colonies. Conclusion: Yellow kepok banana peel extract (Musa paradisiaca L. var. Bluggoe) is effective to use as antibacterial for chronic periodontitis caused by Porphyromonas gingivalis.

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