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"Molecular dynamic simulation is one field of science that uses computer as a resource for computational methods to calculate the number of forces acting within a molecular system and analyzing its movement. This simulation is useful for the discovery of drug compounds from an illness. This study uses Gromacs as molecular dynamics application which is running on cluster computing environment. A significant speed up is obtained during the experiments. "

"ABSTRACTOne of the processes requiring HPC environments is Molecular Dynamics ( MD ) . In tropical countries, the MD process is very important in the preparation of virtual screening experiments for anti-malaria search. Previous works on the virtual screening project for anti-malaria search conducted by WISDOM project uses grid infrastructure with 1,700 CPUs of various infrastructure provided in 15 countries [13]. In silico anti malaria compounds searching from Indonesian medical plants using virtual screening methods are urgently required. This can reduce the cost and time required compared to the direct searching or examining each compound by in vitro and in vivo which will spend a lot of time and expense . However, the use of thousands of processors is difficult for the researchers with limited resources in developing countries such as Indonesia. Our of previous studies using MD with GROMACS shows the improvement of the simulation time using Cluster. But that is not the case for some of our previous works with AMBER on Cluster where we did not obtain significant speed up. However, our previous works running GROMACS on GPUs provided significant speed up about 12 times faster than that run on Cluster. In this study , we build a GPU -based computing environment and have some MD simulation with AMBER. We used several computing environments such as cluster with 16 cores , GPU Geforce GTX 465 , GTX 470 , GTX 560 , GTX 680 , and GTX 780 . In addition to PfENR ( Plasmodium falciparum Enoyl acyl Carrier Protein Reductase ) enzyme , as benchmark we also conducted MD experiments on Myoglobin protein , Dihydrofolate reductase (DHFR) protein, and Ras - Raf protein . All experimental results showed that the slowest MD processes occurred on Cluster, followed in increasing order by GTX 560, GTX 465, GTX 470, GTX 680 and GTX 780. While the GPU speed up relative to cluster is about 24 , 26 , 32 , 24 , 77 and 101, respectively. "

"As a prolactin antagonist, dopamine binds to its receptor D2 and suppresses the secretion of prolactinfrom the pituitary gland. Required ligand that can interact with receptor so that dopamine can nolonger bound to its receptor. Ligands empirically derived from plants and have been proven toincrease human lactation. In silico study using molecular docking technique to identify ligandinteraction with dopamine D2 receptor (PDB: 1I15). The best posing and binding energy (ΔG) wereanalyzed and ranked to get potential dopamine D2 receptor inhibitor. Binding energy of apigenin,luteolin, kaempferol, quercetin, and myricetin with PDB: 1I15 gives value respectively -5.90, -5.67, -5.64, -5.28, -4.36 kcal/mol. Interaction occurred between the ligand and amino acid residue ASN 192,PRO 204, SER 209 formed hydrogen bonding and hydrophobic interaction with HIS 189."

"ABSTRACTVirtual screening (VS) is a computational technique used in drug discovery. Virtual Screening process usually works by identifying structures that are most likely to bind the target of drug. Virtual screening is usually based on compound similarity or database docking. Thus, the identification for drugcompounds based on structure classification still remain as a challenging task. The purpose of this research is to find a new approach for ligand-based virtual screening using machine learning technique. In this paper, theclassification has been done by using Deep Belief Networks (DBN) method. The data from Nicotinamide Adenine Dinucleotide (NAD) protein target family were used for training and testing the model. This research used four protein target classes from literature and two protein target classes from DUD-E docking website. Feature were obtained from molecular fingerprint descriptor. The experiments result show that DBN method outperform the existing pharmacophore approach."

"ABSTRACTXylitol is a five-carbon polyol sugar. It has many healthy benefits and is widely used in food, pharmaceutical, and healthcare. Natural sources with abundant carbon such as lignocellulose can be used for xylitol production. One of the potencial sources with high prevalency in Indonesia is water hyacinth. It is known as weeds and has not been fully utilized by people. The aim of this research was the utilization of water hyacinth which contains hemicellulose as a substrate in the bioconversion of xylose into xylitol by yeast cells Debaryomyces hansenii. Stages of processing include the optimization of water hyacinth hydrolysis using autohydrolysis method and optimization of fermentation conditions. Xylose and xylitol were determined by HPLC with RI detector and LiChrosorb® NH2 (4 mm x 125,00 mm, 5μm) column. Acetonitrile-water (90:10, v/v) was used as a solvent. 20 μL sample volume was injected at flow rate of 1.0 mL/min and room temperature. The results showed that optimum conditions for the acquisition of xylose were obtained through autohydrolysis methods for 75 minutes with 1:15 water hyacinth and water ratio and posthydrolysis for 45 min using 4% sulfuric acid. Xylose concentration in hydrolyzate obtained was 25.55 g/L. The optimum fermentation condition for xylitol production was achieved by four day cultivation, limited aeration condition, and addition of metal ions CaCl2.2H2O 0.01%. The yield of xylitol obtained using those conditions was 77.43 %. "

"ABSTRACTXylitol is five-carbon polyol sugar which widely used as a sweetener in food and pharmaceutical.Xylitol production by chemical procedures using high pressure and temperature also neededextensive purification are less cost-effective in production. Fermentation which has more advantageswith lower cost due tocheaper substrate and the non-necessity of xylose purification. The purposes ofthis research were to find optimum condition for xylitol production with particular variable such assubstrate concentration, aeration, methanol and nitrogen sources addition. Oil palm empty fruitbunch hydrolyzates containing xylose was fermented into xylitol by Debaryomyces hansenii UICC Y-276 at room temperature. Fermentation was carried out at 200 rpm for 72 hours. Then, xylose andxylitol were determined by HPLC with RI detector and LiChrosorb® NH2 (4 mm x 125,00 mm, 5μm)column. Acetonitrile-water was used as a solvent, 20 mL sample volume was injected at flow rate of1,0 mL/min at room temperature. The optimum fermentation conditions was obtained in a state ofsemi-anaerobic condition (1 : 2.5) with 10,0 % (w/v) xylose concentration. Meanwhile with theaddition of various concentration of methanol and nitrogen sources, it was obtained that 1,5 %methanol and 0,5 % ammonium sulfate gave high yield of xylitol production. The best result for yieldxylitol production was 31,83 %."

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Sirtuin 1 (SIRT1) adalah famili  kelas III dari protein histon deasetilasi (HDAC) dan reaksinya bergantung  dengan  NAD⁺. Aktivator SIRT1 menyerupai pembatasan kalori merupakan pendekatan terapi untuk diabetes mellitus tipe 2. Pencarian obat dapat dilakukan dengan metode  in silico untuk mempercepat dan memfasilitasi identifikasi kandidat senyawa terbaik dan karakteristik fisikokimia dan pemilihan hit-to-lead.

Penelitian ini bertujuan untuk mengeksplorasi dan mengidentifikasi senyawa tanaman obat yang menyerupai CR (calorie restriction mimetic) dari Basis Data Herbal Indonesia (HerbalDB) http://herbaldb.farmasi.ui.ac.id yang berpotensi sebagai kandidat untuk aktivator SIRT1  melalui kombinasi metode in silico dan in vitro. Pemodelan farmakofor diperoleh dengan dua cara yaitu  menggunakan ko-kristal yang terikat pada daerah allosterik SIRT1 dan senyawa-senyawa yang digunakan sebagai aktivator SIRT1. Kemudian, model ini digunakan untuk penapisan virtual dengan HerbalDB. Senyawa yang diperoleh diidentifikasi menggunakan penambatan molekul dengan program AutoDock4Zn dan simulasi dinamika molekul 50-ns menggunakan program Amber. Simulasi dinamika molekuler dianalisis menggunakan metode MM-GB(PB) SA. Senyawa yang terpilih diuji secara in vitro menggunakan uji luminesensi SIRT-Glo^TM.

Analisis interaksi ikatan antara ligan dan reseptor SIRT1 (PDB ID 4zzj dan 5btr) menunjukkan selektivitas ligan adanya interaksi hidrofobik pada Leu206, Ile223, Ile227. Interaksi ikatan hidrogen antara [Glu230 dengan Arg446] dan Arg234 (daerah allosterik) dengan Arg446, Val459, His473, Asp475 (daerah katalitik), karena adanya interaksi ini menjadi dekat ke arah daerah substrat. Hasil penapisan virtual menggunakan model farmakofor berbasis struktur adalah mulberrin dan model farmakofor berbasis ligan adalah gartanin, kuinidin dan kuinina sebagai prediksi terbaik aktivator SIRT1. Analisis In silico, perhitungan MM-GB(PB)SA mengkonfirmasi bahwa mulberrin, gartanin, kuinidin, kuinina menunjukkan interaksi ikatan pada daerah allosterik dan uji in vitro nilai EC₅₀ masing-masing adalah 2,10; 1,79; 1,71; 1,14μM. Jadi, dari studi in silico dan in vitro senyawa mulberrin, gartanin. kuinidin, dan kuinina, menjadi kandidat potensial untuk aktivator SIRT1.

 

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Sirtuin 1 (SIRT1) is a class III family of protein histone deacetylases involved in NAD⁺-dependent deacetylation reactions. It has been suggested that SIRT1 activators, in a therapeutic approach for type 2 diabetes mellitus. Drug design can be performed in silico using molecular dynamic approaches to accelerate and facilitate identification of the best compound candidates and their physicochemical characteristics and hit-to-lead selection.

This study aimed to explore and identify medicinal plant compounds calorie restriction mimetic from Indonesian Herbal Database (HerbalDB) that might potentially become a candidate for SIRT1 activators through a combination of in silico and in vitro methods. Two pharmacophore models were developed using co-crystalized ligands that allosterically bind with SIRT1 similar to the putative ligands used by SIRT1 activators. Then, these were used for the virtual screening of HerbalDB. The identified compounds were subjected to molecular docking with the AutoDock4Zn program and 50-ns molecular dynamics simulation using the Amber program. Molecular dynamics simulation was analyzed using MM-GB(PB)SA methods.  The compounds identified by these methods were tested in an in vitro study using a SIRT-Glo^TM luminescence assay. Interaction analysis between activator ligand and the SIRT1 receptor (PDB IDs 4zzj and 5btr) revealed the ligand’s selectivity for hydrophobic interaction at Leu206, Ile223, Ile227. Hydrogen bond interactions between [Glu230 with Arg446] and Arg234 (allosteric region) with Val459, His473, and Asp475 (catalytic region) brought them close to the bounding substrate area. Virtual screening using structure-based pharmacophores predicted that mulberrin as the best candidate SIRT1 activator. Virtual screening using ligand-based pharmacophores predicted that gartanin, quinidine and quinine to be the best candidates as SIRT1 activators. The molecular docking studies showed the important residues involved were Ile223 and Ile227 at the allosteric region. The MM-GB(PB)SA calculations confirmed that mulberrin, gartanin, quinidine, quinine showed activity at allosteric region and their EC₅₀ in vitro values are 2.10; 1.79; 1.71; 1.14µM, respectively. Thus, mulberrin, gartanin, quinidine, and quinine, to be a potential candidate for SIRT1 activators.

 

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"Usaha para peneliti untuk menciptakan alat transportasi air (kapal) yang hemat energi terus dilakukan hingga saat ini. Modifikasi geometri, dimensi dan jumlah lambung merupakan suatu hal yang penting dalam usaha pengurangan hambatan kapal. Penggunaan Jenis kapal berlambung banyak katamaran dan trimaran mencapai angka 40% dari total kapal yang berlayar. Hambatan total kapal terdiri atas hambatan gesek dan hambatan sisa. Hambatan gesek merupakan fungsi dari geometris, perubahan tekanan, kekasaran permukaan dan coating pada permukaan lambung. Hambatan sisa fungsi dari gaya seret gelombang yang terbentuk oleh masing-masing lambung kapal. Dengan kemajuan ilmu material, diciptakan berbagai macam cat yang dapat berfungsi sebagai pelindung dinding kapal dan sebagai pengurang koefisien gesek. Kulit ikan belut yang mengandung lendir merupakan biopolimer yang ramah lingkungan dan tidak beracun. Tujuan dari penelitian ini yaitu mengetahui efek variasi pelekatan biopolimer kulit belut (Monopterus Albus) pada lambung model kapal monohull, katamaran asimetris dan trimaran asimetris terhadap hambatan total model kapal dengan variasi bilangan Froude. Model kapal monohull, katamaran dan trimaran dengan pendekatan displacement yang sama dan diberikan variasi posisi pelekatan kulit belut pada lambung model kapal ditarik dengan variasi kecepatan pada kolam percobaan. Variasi sarat dan trim digunakan pada percobaan ini. Pengukuran tegangan tali pada kecepatan kapal konstan (tercapainya terminal velocity) dilakukan dengan load cell transducer yang terhubung ke data akusisi. Percobaan dilakukan dengan teliti dan dilakukan pengulangan secepat mungkin untuk menghindari degradasi biopolimer lendir belut. Percobaan dilakukan pada air tawar dan perubahan temperatur seminimal mungkin (dijaga konstan). Hasil menunjukkan pelekatan biopolimer pada monohull menghasilkan drag reduction sebesar 8 % pada bilangan Re = 20.000. Pada kapal katamaran asimetris, S/L = 0,2 terjadi drag reduction sebesar 6 % pada bilangan Froude = 0,45. Pada kapal trimaran asimetris, S/L = 0,2 dan R/L = 0,0 terjadi drag reduction sebesar 10.4 % pada bilangan Froude = 0,35. Dimungkinkan efek biopolymer mempengaruhi distribusi kecepatan pada lapisan terluar (outer layer) sehingga laju kecepatan kapal bertambah.

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Up to present time researchers are still continuously attempting to create energy saving water transportation vehicles (ships). Geometry, dimensions and number of hulls modification is an important effort to reduce the resistance of ship. The use of multi-hull ships such as catamaran and trimaran has reached 40% of total sailing ships. Total ship resistance consists of frictional resistance and residual resistance. Frictional resistance is the function of geometrics, pressure changes, surface roughness and coating of the hull surface. Residual resistance is the function of wave dragging force created by individual hull. With the advancement of material science various kind of paints have been created that could act as hull protection and as frictional coefficient reducer. Eel skin contents mucus that is environmentally friendly and non-toxic.

The objective of the research is to investigate the effects of Monopterus Albus biopolymer attachment variations on monohull, asymmetric catamaran, and asymmetric trimaran model hulls to ship model total resistance with variation of Froude numbers. Monohull, catamaran, and trimaran ship models with same displacement approach were attached with eel skin at various positions on their hulls, the ship models were towed with various speeds on the test basin. Variation of drafts and trims were applied on the experiment. The tensions of the towing string at constant ship speed (at the terminal velocity) were measured using load cell transducer which was connected to data acquisition. The experiment was conducted very carefully and repetitions were carried out very quickly in order to avoid the degradation of Monopterus Albus biopolymer. The experiment was carried out on fresh water with very little changes of temperatures (kept constant).

The results showed the attachment of biopolymer on monohull produced 8% of drag reduction at Re number = 20.000. On asymmetric catamaran with S/L = 0.2 produced 6% drag reduction at Fr = 0.45. On asymmetric trimaran with S/L = 0.2, and R/L = 0.0 produced 10.4% drag reduction at Fr = 0.35. These results are due to the effect of biopolymer in distributing the velocity at the outer layers that increase the velocity of the ships."