Judul: Dental Antibiofilm Potential of Ruku-Ruku Plant by In Silico Study of Glucosyltransferase Enzyme Inhibition
Abstrak: Biofilm gigi terbentuk akibat infeksi Streptococcus mutans yang memfermentasi karbohidrat menjadi asam. Bakteri tersebut memproduksi glukosiltransferase yang berperan dalam sintesis glukan enamel. Tanaman ruku-ruku memiliki senyawa aktif yang berpotensi sebagai antibiofilm. Penelitian ini bertujuan menguji potensi inhibisi senyawa aktif tanaman ruku-ruku terhadap glukosiltransferase serta menganalisis interaksinya. Penelitian dilakukan dengan metode penapisan virtual dan penambatan molekuler menggunakan perangkat lunak YASARA Structure. Hasil penelitian menunjukkan dari 40 senyawa aktif tanaman ruku-ruku, terdapat enam senyawa terbaik yang mampu menginhibisi glukosiltransferase serta memiliki interaksi dengan tiga residu penting pada enzim, yaitu Asn481, Glu515, dan Trp517. Senyawa tersebut adalah asam ursolat, asam olenolat, apigenin-7-glukuronida, orientin, isoorientin, dan isoviteksin yang memiliki konstanta disosiasi lebih rendah dibandingkan ligan alami dengan rentang 0.048 hingga 0.398 µM dan memiliki nilai energi bebas ikatan lebih negatif dari ligan alami dengan rentang -9979 hingga -8730 kal/mol., Dental biofilm is formed due to infection of Streptococcus mutans, which is able to ferment carbohydrates into acid. These bacteria produce glucosyltransferase which plays role in synthesizing glucan enamel. Ruku-ruku plant have active compounds that have potential as antibiofilm. This study aimed to examine the inhibition potential of active compounds from ruku-ruku plant against the glucosyltransferase and to analyze its interaction. The research was conducted using virtual screening molecular and docking methods with YASARA Structure software. The results showed that of 40 active compounds from ruku-ruku plant, there were six best compounds that could inhibit glucosyltransferase and interact with three important residues, namely Asn481, Glu515, and Trp517. These compounds are ursolic acid, oleanolic acid, apigenin-7-glucuronide, orientin, isoorientin, and isovitexin which have lower dissociation constants than natural ligands in range of 0.048 to 0.398 µM and have more negative free energy of binding values with range of -9979 to -8730 cal/mol.
Keyword: biofilm, glucosyltransferase, molecular docking, ruku-ruku, S. mutans

Judul: Molecular Docking of Flavonoid Compounds Against  Streptococcus mutans Glucosyltransferase Inhibition as Antibiofilm
Abstrak: Penyebab terjadinya karies gigi yaitu plak yang berada pada permukaan gigi dalam bentuk biofilm. Bakteri Streptococcus mutans berperan dalam pembentukan biofilm dan menghasilkan enzim glukosiltransferase yang dapat mengkatalisis pembentukan ekstra polisakarida. Beberapa senyawa flavonoid diketahui dapat menghambat sintesis biofilm. Oleh karena itu, senyawa flavonoid berpotensi untuk dikembangkan sebagai antibiofilm untuk pencegahan karies gigi. Penelitian ini bertujuan menentukan senyawa flavonoid dari penapisan virtual terhadap inhibisi glukosiltransferase pada S. mutans sebagai antibiofilm melalui penambatan molekuler dengan mempertimbangkan nilai energi bebas ikat, jenis pengikatan dan residu katalitik. Metode yang digunakan adalah preparasi ligan dan reseptor, penapisan virtual dan penambatan molekuler. Hasil penapisan virtual dari 87 senyawa flavonoid, diperoleh 36 senyawa yang dapat menginhibisi glukosiltansferase. Hasil penambatan molekuler menunjukkan 9 ligan yang dapat menghambat glukosiltransferase dengan nilai energi bebas ikat lebih negatif dari ligan alami (maltosa). Likuiritigenin memiliki ΔG paling negatif yaitu -7,0 kkal/mol dan nilai Ki 7,39 µM. 9 ligan memiliki jenis pengikatan terbaik pada enzim glukosiltransferase. Senyawa yang berikatan pada 3 residu katalitik enzim glukosiltransferase yaitu taksifolin, gallokatekin, sakuranetin sedangkan 6 senyawa lain berikatan pada 2 residu katalitik., The cause of dental caries is plaque that is on the dental surface in the form of a biofilm. Streptococcus mutans bacteria play role in the formation of biofilms and produce glucosyltransferase enzyme that can catalyze the formation of extra polysaccharides. Several flavonoid compounds are known to inhibit biofilm synthesis. Therfore, flavonoid compounds have the potential to be developed as antibiofims for the prevention of dental caries. This research aims to determine polyphenolic compounds from virtual screening against glucosyltransferase inhibition in S. mutans as an antibiofilm through molecular docking by considering the value of binding free energy, type of binding and catalytic residue. The methods used are ligand and receptor preparation, virtual screening and molecular docking. The results of virtual screening of 87 polyphenolic compounds, obtained 36 compounds that could inhibit glucosyltransferase. Molecular docking results showed 9 ligans that could inhibit glucosyltransferase with binding free energy value more negative than the native ligand (maltose). Liquiritigenin has the most negative ΔG which is -7,0 kkal/mol and Ki value of 7,39 µM. Compounds that bind to 3 catalytic residues of glucosyltransferase enzyme are taxifolin, gallocatechin, sakuranetin while 6 other compounds bind to 2 catalytic residues.
Keyword: biofilm, glucosyltransferase, molecular docking, S. mutans

Judul: Thermal Characteristics and Dynamics of Tropical Cyclone over Western North Pacific Ocean: A Case Study of Typhoon Songda (Chedeng) 2011
Abstrak: The frequent occasion of Tropical Cyclone (TC) over Western North Pacific (WNP) Ocean lies from 10˚N to 26˚N and 121˚E to 170˚E. Sources of TC development come from warm ocean temperature where latent heat is released during condensation processes and subsequently concentrated in the boundary layer. Relative humidity at 850-700 hPa is responsible to produce the most intense storm. Meanwhile, weak vertical wind shear between 850-200 hPa is one of the dynamical factors that lead to the development of TC. Pressure level of 850-200 hPa is chosen to minimize the thermodynamic effect in the lower troposphere. Typhoon Songda (Chedeng in the Philippines) or TSC lasted from May 18th to 30th, 2011 and strengthened into powerful Super Typhoon stage between May 24th and 27th. Long curving track and the exhibition of all sequences of TC life cycle, TSC is then considered as an ideal case of TC. The objective of the study with case of TSC is to investigate the role of thermal characteristics and dynamics on TC intensity. The research is carried out by using Advanced Research of Weather Research and Forecasting model (WRF ARW model) version 3.3. Two domains are employed in the model. The first domain situate from 02˚N to 40˚N and 118˚E to 149˚E and cover spatial resolution () of 33.1 km. The second domain situate from 09˚N to 27˚N and 119˚E to 132˚E with of 11 km. Timestep of the model () is 120 seconds. The model is supported by the following physical parameterization, i.e., Yonsei University Scheme (YSU) in the boundary layer, Kain-Fritsch scheme (KF) in the cumulus, and WRF Single-Moment 3-class scheme in the microphysics. Initial meteorological condition prior to the formation of the cyclone is generated using WRF ARW standard-release model. Sensitivity of the model output is obtained from a selected single-parameter change scenarios, namely, 10 % to 20 % decrease and increase of wind shear initial data at 850-200 hPa, and by 10 % to 20 % decrease of relative humidity initial data at 850-700 hPa. The result showed that the negative correlations between wind shear and intensity are found in wind shear scenarios. Wind shears of 10 ms-1 which lead to strengthening of the wind intensity in the early period of Typhoon development are found in wind shear scenarios. The effect of wind shear changes on wind intensity is statistically significant in the 20 % wind shear scenarios. During mature stage, weak wind intensity occurred when wind shear increase as given in the WRF standard-release and the 20 % decreasing scenario. Different situation is found in the 20 % increasing scenario where wind shear tend to weak and lead to strong wind intensity at this stage. Meanwhile, the reduction of moisture supply at 850-700 hPa resulting from 20 % decreasing relative humidity play a major role in the weakening of wind intensity and reduces mechanical energy of the cycle process as much as 300 J kg-1.
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