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JURNAL KIMIA SAINS DAN APLIKASI
Published by Universitas Diponegoro
ISSN : 14108917     EISSN : 25979914     DOI : -
Core Subject : Science, Engineering,
Chemical Engineering, Chemistry & Bioengineering Chemistry Engineering
urnal Kimia Sains dan Aplikasi (p-ISSN: 1410-8917) and e-ISSN: 2597-9914) is published by Department of Chemistry, Diponegoro University. This journal is published four times per year and publishes research, review and short communication in field of Chemistry.
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Articles 5 Documents
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Search results for , issue "Vol 24, No 5 (2021): Volume 24 Issue 5 Year 2021" : 5 Documents clear
Natural Compounds Activities against SARS-CoV-2 Mpro through Bioinformatics Approaches for Development of Antivirus Candidates Taufik Muhammad Fakih
Jurnal Kimia Sains dan Aplikasi Vol 24, No 5 (2021): Volume 24 Issue 5 Year 2021
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (2757.97 KB) | DOI: 10.14710/jksa.24.5.170-176

Abstract

Coronavirus infection (COVID-19) caused by SARS-CoV-2 appears as a pandemic that has spread to almost all countries in the world. Antiviral therapy using natural compounds is one alternative approach to overcome this infectious disease. The therapeutic mechanism is proven effective against the main protease (Mpro) of SARS-CoV-2. This research aims to perform bioinformatics studies, including ligand-docking simulations and protein-protein docking simulations, to identify, evaluate, and explore five compounds' activity on SARS-CoV-2 Mpro and their effects against Angiotensin-Converting Enzyme 2 (ACE-2). Protein-ligand docking simulations show kaempferol, flavonol, and their glycosides (Afzelin and Juglanin) and other flavonoids (Quercetin, Naringenin, and Genistein) have a high affinity towards SARS-CoV-2 Mpro. These results were then confirmed using protein-protein docking simulations to observe the ability of five compounds to prevent the attachment of ACE-2 to the active site. Based on the results of the bioinformatics studies, Quercetin has the best affinity, with a binding free energy value of −33.18 kJ/mol. The five compounds are predicted to be able to interact strongly with SARS-CoV-2. The results in this research are useful for further studies in the development of novel anti-infective drugs for COVID-19 that target SARS-CoV-2 Mpro.
Development of a Fast Simultaneous Analysis Method for Determination of Middle Rare-Earth Elements in Monazite Samples Heru Agung Saputra; Anni Anggraeni; Abdul Mutalib; Husein Hernandi Bahti
Jurnal Kimia Sains dan Aplikasi Vol 24, No 5 (2021): Volume 24 Issue 5 Year 2021
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (3346.792 KB) | DOI: 10.14710/jksa.24.5.177-184

Abstract

Rare earth elements are a set of seventeen metallic elements, which is an essential part of many high-tech devices. Hence, analysis and/or separation of the rare earth elements from their mineral become crucial. A novel analysis method combining ultraviolet-visible spectroscopic and multivariate analysis was developed to determine middle rare earth elements quickly and simultaneously. The data collected from ultraviolet-visible spectroscopic were analyzed by multivariate analysis. The results showed that the developed method has good accuracy and precision with a detection limit of 1.375 (± 0.012), 0.332 (± 0.004), 42.117 (± 0.200), 1.767 (± 0.011), and 0.576 (± 0.002) ppm, respectively for samarium, europium, gadolinium, terbium, and dysprosium. The interference effect of ammonium iron(II) sulfate hexahydrate, manganese(III) sulfate hydrate, calcium carbonate, sodium carbonate, and lead(II) nitrate were examined. The reliability of the proposed method was evaluated using monazite samples. Conclusively, the developed method was successfully applied to determine the middle rare earth elements in monazite samples.
Simultaneous Effect of Ultrasonic and Chemical Treatment on the Extraction of Nanocellulose From Sugarcane Bagasse A'yunil Hisbiyah; Lilik Nurfadlilah
Jurnal Kimia Sains dan Aplikasi Vol 24, No 5 (2021): Volume 24 Issue 5 Year 2021
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (34.666 KB) | DOI: 10.14710/jksa.24.5.146-151

Abstract

The focus of this study was the simultaneous effect of ultrasonic and chemical treatment on the extraction of nanocellulose from sugarcane bagasse. Ultrasonic waves can accelerate the dispersion process of nanocellulose particles so that extraction runs faster and is environmentally friendly. The bagasse was treated by chemical treatment with ultrasonic waves, and then the nanocellulose was prepared using acid hydrolysis with ultrasonic waves. The effect of ultrasonication was investigated. The crystallinity of sugarcane bagasse, cellulose, and nanocellulose was analyzed by X-ray diffraction. Based on the diffractogram, there was an increase in the crystallinity of nanocellulose. The chemical composition of extracted cellulose and nanocellulose was analyzed by Fourier-transformed infrared spectroscopy. The results of the analysis showed that lignin and hemicellulose were removed from the bagasse during the extraction process. The analysis results also showed that the breaking of intramolecular hydrogen and glycosidic bonds occurred during the hydrolysis process. The morphology of bagasse, cellulose, and nanocellulose was analyzed by Scanning electron microscopy. While the particle size of nanocellulose was analyzed by the Particle Size Analysis instrument. The average size of nanocellulose particles was 132.67 nm.
Molecular Cloning and Expression of Haloacid Dehalogenase Gene from a Local Pseudomonas aeruginosa ITB1 Strain and Tertiary Structure Prediction of the Produced Enzyme Enny Ratnaningsih; Lousiana Dwinta Utami; Nurlaida Nurlaida; Rindia Maharani Putri
Jurnal Kimia Sains dan Aplikasi Vol 24, No 5 (2021): Volume 24 Issue 5 Year 2021
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (3416.342 KB) | DOI: 10.14710/jksa.24.5.161-169

Abstract

Organohalogens are widely utilized as pesticides, herbicides, solvents, and for many other industrial purposes. However, the use of these compounds caused some negative impacts to the environment due to their toxicity and persistency. In the light of this, some microbes have been identified and employed to perform dehalogenation, converting halogenated organic compounds to non-toxic materials. In this research, we successfully cloned and sequenced the haloacid dehalogenase gene from a local Pseudomonas aeruginosa ITB1 strain, which is involved in the degradation of monochloroacetate. First, the haloacid dehalogenase gene was amplified by PCR using a pair of primers designed from the same gene sequences of other P. aeruginosa strains available in the GenBank. The cloned gene in pGEM-T in E. coli TOP10 was sequenced, analyzed, and then sub-cloned into pET-30a(+) for expression in E. coli BL21 (DE3). To facilitate direct sub-cloning, restriction sequences of EcoRI (G/AATTC) and HindIII (A/AGCTT) were added to the forward and reversed primers, respectively. The expressed protein in E. coli BL21 (DE3) appeared as a 26-kDa protein in SDS-PAGE analysis, which is in good agreement with the size predicted by ExPASy Protparam. We obtained that the best expression in LB liquid medium was achieved with 0.01 mM IPTG induction at 30°C incubation for 3 hours. We also found that the enzyme is more concentrated in the pellet cells as inclusion bodies. Furthermore, the in-silico analysis revealed that this enzyme consists of 233 amino acid residues. This enzyme’s predicted tertiary structure shows six β-sheets flanked by α-helixes and thus belongs to Group II haloacid dehalogenase. Based on the structural prediction, amino acid residues of Asp7, Ser121, and Asn122 are present in the active site and might play essential roles in catalysis. The presented study laid the foundation for recombinant haloacid dehalogenase production from P. aeruginosa local strains. It provided an insight into the utilization of recombinant local strains to remediate environmental problems caused by organohalogens.
An Insight of Co-Encapsulation Nigella sativa and Cosmos caudatus Kunth Extracts as Anti-Inflammatory Agent Through In Silico Study Nadiyah Zuhroh; Zubaidah Ningsih; Anna Safitri
Jurnal Kimia Sains dan Aplikasi Vol 24, No 5 (2021): Volume 24 Issue 5 Year 2021
Publisher : Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (3757.909 KB) | DOI: 10.14710/jksa.24.5.152-160

Abstract

This study analyzes anti-inflammatory activity from extracts of Nigella sativa and Cosmos caudatus Kunth co-encapsulated through in silico molecular docking. The LC-MS results revealed that extracts of N. sativa mostly contained thymoquinone and alpha-hederin, whereas quercetin and kaempferol were the major compounds in C. caudatus K. Nevertheless, the bioactive compounds are usually susceptible to degradation by exposure to light, heat, oxygen, which may limit its biological activity. Therefore, encapsulation is one of the promising techniques to protect bioactive compounds. Ligands were encapsulated with chitosan and sodium tripolyphosphate as wall materials. Cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) as the target enzymes were docked with a combination of these active compounds (non-encapsulated and encapsulated), using the HEX 8.0 program, and visualized using the Discovery studio visualizer software v16.1.0.15350. Interestingly, docking results of the combination of encapsulated ligands showed no interactions to COX-1 but interacted with COX-2. Therefore, co-encapsulation of extracts combinations has been suggested to act as anti-inflammatory agents targeted specifically to the COX-2 enzyme. The total energy of the encapsulated of combination of extract compounds to COX-2 were -1425.88 (mol/cal) for thymoquinone + quercetin; -1435.87 (mol/cal) for thymoquinone + kaempferol; 1175.97 (mol/cal) for quercetin + alpha hederin; -957.74 (mol/cal) for kaempferol + alpha hederin; and -283.3 (mol/cal) for diclofenac sodium, as a control NSAID drug. These suggest that encapsulated active compounds in N. sativa and C. caudatus K. have potency as a drug candidate for the selective NSAIDs category, which can be subjected to further in vitro and in vivo studies.

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