Judul: Molecular Docking of Turmeric (Curcuma longa L) and Black Tea (Camellia sinensis) Active Compound Against Asparagine Endopeptidase Enzyme
Abstrak: Asparagin Endopeptidase (AEP) memiliki peran dalam penyakit Alzheimer (PA) untuk membelah protein prekursor amiloid dan protein tau sehingga menyebabkan plak Aβ dan Tangels, keduanya merupakan penyebab utama PA. Penelitian ini bertujuan untuk menguji aktivitas senyawa aktif dari kunyit dan teh hitam pada AEP melalui penambatan molekuler. Bioavalibilitas ligan diprediksi berdasarkan karakteristik molekuler pada aturan Lipinski. Prediksi toksisitas ligan dilakukan pada laman ADMET properties. Reseptor diperoleh dari database PDB:5LUB. Ligan uji berasal dari senyawa aktif teh hitam dan kunyit. Hasil penambatan dengan binding energy tertinggi yang berasal dari teh hitam adalah asam galat (3,1330 kkal/mol), kaempferol (3,1800 kkal/mol) dan katekin (2,4170 kkal/mol), sementara itu ligan uji kunyit diantaranya, prokurkumadiol (4,0060 kkal/mol), epiprokurkumenol (2,3430 kkal/mol) dan dehidrokurdion (4,4560 kkal/mol). Kebanyakan ligan memiliki interaksi dengan residu sisi aktif, oleh karena itu, beberapa senyawa aktif tersebut diprediksi berpotensi besar menghambat AEP., Asparagine Endopeptidase (AEP) have a role in Alzheimer's disease (AD) which cleaves amyloid precursor protein (APP) and tau causing production of Aβ plaque and Tangels, which are main cause of AD. This study aims to examine the inhibition activity of the active compounds of turmeric and black in AEP through molecular docking. The bioavalibility of ligands is predicted based on the molecular characteristics of the Lipinski rule. The prediction of ligand toxicity was carried out on the ADMET properties. The receptors are obtained from the PDB:5LUB. The test ligands are derived from the active compounds of black tea and turmeric. The highest binding energy from black tea are (3,133gallic acid kcal/mol), kaempferol (3,1800 kcal/mol) and catechin (2,4170 kcal/mol), also ligans from turmeric are procurcumadiol (4,0060 kkal/mol), epiprocurcumenol (2,3430 kkal/mol) and dehydrocurcudione (4,4560 kkal/mol). Mostly ligands have interactions with active site residues, therefore, some of these active compounds are predicted to have great potential to inhibit AEP.
Keyword: Alzheimer, Asparagin Endopeptidase (AEP), kunyit, teh hitam, Alzheimer, Asparagine endopeptidase (AEP), black tea, turmeric

Judul: Molecular Docking of Black Cumin Active Compound to Inhibits Cholinesterase Enzyme in the Development of Alzheimer’s Therapy
Abstrak: Asetilkolinesterase (AChE) dan Butirilkolinesterase (BChE) merupakan dua jenis enzim kolinesterase yang berperan dalam penurunan kadar asetilkolin sebagai gejala khas penyakit alzheimer. Jintan hitam memiliki beragam senyawa aktif yang berpotensi menghambat aktivitas kedua enzim. Penelitian ini bertujuan menganalisis interaksi beberapa senyawa aktif penting dari jintan hitam dalam menghambat aktivitas kedua enzim. Senyawa uji terbaik dipilih berdasar analisis sifat kemiripan obat yang memenuhi kriteria dalam bioavailabilitas, toksisitas dan aspek farmakokinetik sebagai obat. Analisis penambatan molekul dilakukan dengan perangkat lunak komputer PyRx Virtual Screening dan YASARA Structure. Hasil penelitian menunjukkan 7 dari 25 senyawa uji diduga memiliki aktivitas penghambatan pada enzim AChE dan BChE. Senyawa nigelicin berpotensi sebagai inhibitor terbaik AChE (ΔG -7,74 kcal/mol; %BSS 69,23%). Senyawa nigelidin berpotensi sebagai inhibitor terbaik BChE (ΔG -6,73 kcal/mol; %BSS 33,33%). Ikatan inhibitor dan enzim pada keduanya didominasi interaksi hidrofobik dengan cincin aromatik berjajar. Kedua senyawa tergolong kelompok alkaloid jintan hitam yang berpotensi dikembangkan sebagai herbal terapi alzheimer., Acetylcholinesterase (AChE) and Butyrylcholinesterase (BChE) are two types of cholinesterase enzyme that plays important role in reducing acetylcholine as a symptom of alzheimer. Black cumin has a variety of active compounds and the potential to inhibit the activity of both enzymes. This study aims to analyze interaction of some crucial active compounds of black cumin in inhibiting AChE and BChE enzymes. Active compounds selected through drugs-likeness analysis that in compliance with bioavailability, toxicity and pharmacocinetics aspect. Docking simulation doing by the Pyrx Virtual Screening software and the YASARA Structure software. As a result, 7 of the 25 analyze compounds have the potential to inhibit activity of both enzymes. Nigelicin is the best compound that inhibits AChE (ΔG -7,74 kcal/mol; %BSS 69,23%). Nigelidin is the best compound that inhibits BChE (ΔG -6.73 kcal/mol; %BSS 33,33%). Both inhibitor and enzyme complex dominated by hydrophobic with lined aromatic structure. Both compounds are classified as alkaloid of black cumin that potential as alzheimer’s therapy.
Keyword: alzheimer’s disease, acetylcholinesterase, butyrylcholinesterase, black cumin, molecular docking

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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