Judul: Analisis Potensi Daun Torbangun (Plectranthus amboinicus) sebagai Antibakteri terhadap Klebsiella pneumoniae secara in silico
Abstrak: Resistensi antibiotik adalah masalah global. Bakteri Klebsiella pneumoniae merupakan bakteri prioritas untuk ditemukan antibiotiknya karena adanya enzim extended spectrum beta-lactamase (ESBL) yang menyebabkan bakteri ini mudah mengalami resistensi. Daun torbangun diketahui memiliki banyak sekali kandungan flavonoid yang sering diteliti sebagai antibakteri. Penelitian ini bertujuan menganalisis potensi daun torbangun (Plectranthus amboinicus) sebagai antibakteri terhadap Klebsiella pneumoniae dengan metode in silico. Penelitian dilakukan dengan melakukan penambatan molekuler menggunakan aplikasi AutoDock Vina terhadap enzim dari bakteri Klebsiella pneumonia yaitu SHV (Sulfhydryl variable) dengan senyawa kimia yang diambil dari tanaman daun torbangun. Parameter yang digunakan adalah energi bebas ikatan, konstanta inhibisi, serta visualisasi ligan secara 3D dan 2D. Hasil yang diperoleh menunjukkan ligan alami memiliki energi bebas ikatan sebesar -6,7 kcal/mol dan konstanta inhibisi 12,11 µM. Nilai energi bebas ikatan dan konstanta inhibisi dari luteolin 3’Oglucuronide, apigenin 7-glucuronide, dan asam rosmarinat menunjukkan hasil yang lebih baik dibandingkan dengan ligan alami dari SHV-1 (1,4-thiazepine)., Antibiotic-resistant is a global issue. Klebsiella pneumoniae has high priority to find its antibiotic because it has extended-spectrum beta-lactamase (ESBL) enzyme that makes the bacteria easy to resist the antibiotic. Indian borage is one of the empirical medicinal plants that contain flavonoids being used for treating the disease. This research had the purpose of analyzing Indian borage potential as an antibacterial for Klebsiella pneumoniae in silico. Docking is the method for this research by using AutoDock Vina, an application to attach enzyme ESBL from Klebsiella pneumoniae which mention as SHV (Sulfhydryl variable) and metabolite seconders from the plant. The analyzed parameter was binding free energy, inhibition constant, and visualization in 3D and 2D. Binding free energy and inhibition constant of a native ligand is -6.7 kcal/mol and 12.11 µM. Binding free energy value of apigenin 7-glucuronide and rosmarinic acid perform higher potency than the native ligand of SHV-1 (1,4-thiazepine).
Keyword: Daun torbangun, Klebsiella pneumoniae, Resistensi antibiotik, Penambatan molekuler

Judul: Antibacterial Activity of Terpene Natural Compounds against Klebsiella pneumoniae: in silico study
Abstrak: Klebsiella pneumoniae, a Gram-negative, nonmotile, encapsulated rod-shaped bacterium has become an emerging nosocomial pathogen that can cause clinical infectious diseases. Through the years, frequent use and contact with antibiotics in hospitals have created antibiotic-resistant K. pneumoniae strains, limiting available treatment options for medical intervention against infections. Many proteins support the property of antibiotic resistance and one of these proteins found in Klebsiella bacteria is beta-lactamase SHV-1. Many terpenes are known to be active against a wide variety of microorganisms, including gram-positive and gram-negative bacteria and fungi. Toxic effects on membrane structure and function have been generally used to explain the antimicrobial action of essential oils and their monoterpenoid components. Monoterpene indole alkaloids (MIAs) are compounds that are identified from six genera of the Apocynaceae family. The following genera are Alstonia, Rauvolfia, Kopsia, Ervatamia, Tabernaemontana, and Rhazya. Traditionally, plant species of this family have been used for the treatment of fever, malaria, gastrointestinal ailments, diabetes, and pain. There are many terpenes natural compounds (>400 compounds). Thus, finding the terpene compounds that strongly interact with the targeted protein in K. pneumoniae would serve as a potential strategy to find the most potent compounds. The recent study examined the potential interactions between beta-lactamase (bla SHV-1), a protein that supports antibiotic resistance in Klebsiella, and MIAs from six genera of plants in the Apocynaceae family. The MIAs were used as ligands in this study. The PyRx program for molecular docking and other computer programs were used to assess the effectiveness of MIAs as inhibitors (PyMOL, LigPlot+, Discovery Studio, Notepad, Gimp 2.10). In this study, the initial molecular docking investigation identified several MIAs with potential as inhibitors. Paucidisine, (-)-19-Oxoisoeburnamine, and paucidactine A demonstrated the most promise. Ligand-protein interactions, such as hydrogen bonds and hydrophobic interactions, were also analyzed to determine the best terpenes. The most effective terpenes showed a higher percentage of similarity when compared to native ligands. It is important to note that these findings are based on an in silico study and require in vitro confirmation before being considered for future drug design. Overall, this study takes a significant step toward discovering alternative treatment options for antibiotic-resistant Klebsiella infections. By exploring the potential of MIAs as inhibitors, this research offers a promising avenue for combating antibiotic resistance and improving patient outcomes.
Keyword: Klebsiella pneumoniae, Antibiotic-resistant, Beta-lactamase, In silico, Monoterpene Indole Alkaloids

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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