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: Approximation of the Median of Poisson Distribution Using the Relation of Poisson-Gamma Distribution
Abstrak: A major drawback of median is that median cannot usually be defined in closed form, even in the cases where their distribution functions are known. This study gives an approximation of the closed form for the median of the Poisson distribution by using the relation of Poisson-Gamma distribution. The approximation uses elementary techniques based on the monotonicity of certain sequences involving tail probabilities of the Poisson distribution and the Central Limit Theorem. Furthermore, a closed form expression for the mean absolute deviation 􀜧|􀜰􀰒 􀵆 􀜯􀝁􀝀􁈺􀜰􀰒􁈻| is also studied. The median is relevant because of the fact that it minimizes the mean absolute deviation of a Poisson random variable (􀜰􀰒􁈻 by considering median as central tendency.
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