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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 The paper published in this journal implies that the work described has not been, and will not be published elsewhere, except in abstract, as part of a lecture, review or academic thesis.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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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)
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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.
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)
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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.
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)
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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 OCTOBER 2019, VOL 01 NO 01 Suyanto, Eko
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 1 (2019)
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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)
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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.
FRONT MATTER JSMARTECH APRIL 2020, VOL 01 NO 02 Safitri, Anna
JSMARTech: Journal of Smart Bioprospecting and Technology Vol 1, No 2 (2020)
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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)
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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. 
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)
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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
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)
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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. 
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)
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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

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