Judul: Identification of Active Compounds in Black Tea and Turmeric to Increasing Activity of Superoxide Dismutase Enzymes Using In Silico Method
Abstrak: Superoksida dismutase (SOD) merupakan antioksidan penting dalam melindungi sel terhadap kerusakan yang timbul akibat stres oksidatif. Berbagai bahan alternatif telah terbukti meningkatkan aktivitas SOD sebagai agen antioksidan termasuk teh hitam dan kunyit, namun belum diketahui senyawa aktif yang berperan dalam meningkatkan aktivitas enzim SOD. Penelitian ini bertujuan menentukan senyawa aktif teh hitam dan kunyit yang berperan dalam meningkatkan aktivitas enzim superoksida dismutase dengan metode penapisan virtual dan penambatan molekuler terhadap reseptor Cu/Zn SOD (PDB ID: 1CB4). Penelitian dilakukan dengan analisis bioavaibilitas dan toksisitas 20 senyawa aktif teh hitam serta 29 senyawa aktif kunyit, dilanjutkan penapisan virtual dan penambatan molekuler. Hasil penambatan molekuler dianalisis melalui parameter energi bebas Gibbs (∆G) dan kesamaan situs ikat (BSS). Epicatechin gallate (teh hitam) dan curcumin (kunyit) memiliki potensi terbaik dalam meningkatkan aktivitas enzim Cu/Zn SOD dengan nilai energi afinitas masing-masing sebesar -9,5 dan -7,4 Kkal/mol serta nilai BSS yang sama besar yaitu 81,8% terhadap beta amyrin sebagai ligan pembanding. Epicatechin gallate dan curcumin diprediksi dapat diserap dengan baik oleh tubuh karena memenuhi aturan Lipinski dan aman dikonsumsi karena tidak bersifat toksik., Superoxide dismutase (SOD) a re regarded as important antioxidants for protecting cells against damage arising from oxidative stress. Various alternative materials have been shown to increase the activity of SOD as an antioxidant agent, including black tea and turmeric, but the active compounds that increasing the activity of the SOD enzyme is still unknwon. This study aims to determine the active compounds of black tea and turmeric that play a role in increasing the activity of the SOD enzyme by virtual screening methods and molecular docking of the Cu/Zn SOD receptor (ID: 1CB4). The study analyzes the bioavailability and toxicity of 20 active compounds of black tea and 29 active compounds of turmeric followed by virtual screening and molecular docking. The results were analyzed by Gibbs free energy (∆G) and binding site similarity (BSS) parameters. Epicatechin gallate (black tea) and curcumin (turmeric) are best potential compound to increase the activity of Cu/Zn SOD enzymes with ∆G values of -9.5 and -7.4 Kcal/mol and same BSS value that is 81.8% against beta amyrin as control ligand. Epicatechin gallate and curcumin can be well absorbed because comply with Lipinski’s rule and safe for consumption because they are not toxic.
Keyword: Antioksidan, Kunyit, Penambatan molekuler, Superoksida dismutase, Teh hitam, Antioxidants, Black tea, Molecular docking, Superoxide dismutase, Turm

Judul: Identification of Compounds in Purslane Stem (Portulaca oleracea L.) and Its Potential as Superoxide Dismutase Activator using In Silico Method
Abstrak: Superoksida dismutase (SOD) merupakan enzim yang berfungsi sebagai antioksidan dalam tubuh. Antioksidan dapat menangkal radikal bebas yang ada dalam tubuh. Krokot merupakan bahan alternatif yang telah terbukti memiliki sifat antioksidan, namun belum diketahui apakah batang krokot dapat meningkatkan aktivitas SOD dan jenis senyawa yang berperan dalam meningkatkan aktivitas tersebut. Penelitian ini bertujuan mengetahui potensi batang krokot terhadap aktivitas SOD dan jenis senyawa pada batang krokot yang berperan dalam meningkatkan aktivitas tersebut melalui penambatan molekuler terhadap reseptor SOD PDB ID 1CB4. Penelitian ini dilakukan dengan mengidentifikasi senyawa pada batang krokot menggunakan LC-MS/MS QTOF, kemudian memprediksi bioavailabilitas dan toksisitasnya, dan dilanjutkan dengan penambatan molekuler. Hasil penambatan molekuler diidentifikasi melalui parameter energi bebas Gibbs (∆G), konstanta disosiasi (Kd), dan residu yang berikatan antara reseptor dengan ligan. Xanthosine memiliki potensi terbaik dalam meningkatkan aktivitas SOD dengan nilai (∆G) sebesar -7.00 kkal/mol dan Kd sebesar 7.37 µM. Selain itu, hasil identifikasi residu yang berikatan antara reseptor dengan ligan menunjukkan bahwa xanthosine terikat pada situs aktivator alosterik enzim. Simpulan penelitian ini adalah batang krokot dapat menjadi aktivator superoksida dismutase secara in silico., Superoxide dismutase (SOD) is an enzyme that functions as an antioxidant in the body. Antioxidants can counteract free radicals in the body. Purslane is an alternative material that has been proven to have antioxidant properties, but it is not yet known whether purslane stems can increase SOD activity and the types of compounds that play a role in increasing this activity. This study aims to determine the potential of purslane stems on SOD activity and the types of compounds in purslane stems that play a role in increasing this activity through molecular binding to the SOD PDB ID 1CB4 receptor. This research was conducted by analyzing the compounds in purslane stems using LC-MS/MS QTOF, then predicting their bioavailability and toxicity, and followed by molecular docking. Molecular docking results were analyzed using Gibbs free energy (∆G), dissociation constant (Kd), and binding residue between the receptor and the ligand. Xanthosine has the best potential to increase SOD activity with a value (∆G) of -7.00 kcal/mol and a Kd of 7.37 µM. In addition, analysis of the residue binding between the receptor and the ligand shows that xanthosine binds to allosteric sites of the enzyme activator. The conclusion of this study is that purslane stems can be an activator of superoxide dismutase in silico.
Keyword: antioxidant, molecular docking, purslane stems, superoxide dismutase

Judul: Hamiltonian formulation for linear waves motion in two layers fluid
Abstrak: The surface wave could be considered as a wave that separates two fluids, namely water and air. Based on this assumption, it is introduced the interfacial wave, a wave between two layers of fluid with different density. The formulation of interfacial waves motion begins with deriving the base equation of irrotational ideal fluid. Furthermore, according to irrotational fluid assumption, the base equation can be stated in velocity potential. In this derivation, the fluids domain is assumed to be restricted by rigid lid boundary conditions, both at the upper and lower limit. Therefore, the interfacial waves motion can be explained in a hamiltonian formulation. In the hamiltonian formulation, total energy is defined as the sum of kinetic and potential energy. The hamiltonian system is obtained from reduction of kinetic energy by using the Dirichlet Neumann Operator. The resulted kinetic energy equation is nonlinear. Therefore, this form is linearized by first part of the Taylor expansion. This linearization gives a dispersion relation of linear wave. Based on this dispersion relation, the phase speed of the linear wave depends on the density ratio of the two layers fluid.
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