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"Neuraminidase (NA) memiliki peran penting dalam melepaskan virion yang menggantung pada sialic acid (SA) sel inang sehingga dapat menginfeksi sel inang lainnya dan meningkatkan pathogenisitas virus. Untuk dapat mengetahui lebih dalam tentang pengaruh kontribusi residu fungsional terhadap ikatan antara NA dengan SA dilakukan simulasi permodelan molekuler dengan membandingkan NA Low Paihogenic Avian Influenza (LPAI) A/Mallard/Pennsylvania/10218/84 dan High Paihogenic Avian Influenza (HPAI) A/Tokyo/3/67. Dari penelitian diperoleh energi bebas ikatan NA-SA HPAI dan LPAI sebesar -231.59 kcal/mol dan -350.62 kcal/mol. Analisis okupansi dan energi ikatan menunjukkan bahwa Asp151, Arg152, Glu276, Arg292 dan Arg371 merupakan residu fungsional yang berperan penting pada aktivitas enzimatik NA virus dan berperan besar dalam menentukan pathogenisitas virus. Kemudian dari analisis murasi dikerahui D147G, V1491, I194V, K19911, V2751, I290V, V3031, T346N, Q347P, L370S, S400N, D401N, R4o3W dan K431P memiliki pengamh yang signiikan terhadap kestabilan ikatan di wilayah aktif.

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Neurciminidcise (NA) has a significant role in releasing virions that are attached to the sialic acid (SA) of the host cells so that the new virions could infect other cells and increasing the virus pathogenicity. To gain insight on the effects of the contribution of the functional residues towards the binding of NA with SA, we conducted a molecular dynamics simulation and compared Low Pathogenic Avian Influenza (LPAI) NA A/Mallard/Pennsylvania/lO2l8/84[l] with High Pathogenic Avian Influenza (HPAI) NA A/Tokyo/3/67[2]. From this study we obtained the binding free energy of the NA-SA HPAI and LPAI with the value of -231.59 kcal/mol and -350.62 kcal/mol respectively. Hydrogen bond occupancy analysis and binding energy showed that Aspl5l, Argl52, Glu276, Arg292 and Arg37l are functional residues that have a significant role on the enzymatic activities of the NA and also have a big responsibility to detennine virus pathogenicity. And then from the mutation analysis it was observed that Dl47G, Vl49I, Il94V, K19911, v2751, 129ov, v3o31, T346N, Q347P, L370S, S400N, D40lN, R4o3w and K43 lP mutations has the most influence on bond stability at the active site."

"Currently, we reported results of a nested polymerase chain reaction (PCR) assay specific 5` untranslated region (UTR) region of hepatitis C virus (HCV) genome that showed three different patterns of deoxyribonucleic acid (DNA) fragments (single expected specific DNA band, single DNA band higher in size than an expected band, and multiple DNA bands). Three isolates (Isolate A, B, and C), representing all the three DNA bands, were analyzed by using phylogenetic trees. The results showed that the Isolate A, B, and C were classified into HCV genotypes 2, 1, and 3, respectively. The Isolate A and B were very closely related to viral isolates from Madagascar and Brazil, respectively and were not closely related to other Indonesia isolates. In contrast with the Isolate A and B, the Isolate C was very closely related to another Indonesia isolate. Among all there isolates, the Isolate C was very closely related to an Indonesia isolate detected from a cirrhosis patient, indicating that the Isolate C might be more virulence than the Isolate B and C. However, a complete genome-based comprehensive genetic characterization for all the three isolates needs to be conducted in future research to confirm all findings in this study."

"ABSTRAKTingginya angka infeksi virus dengue (DENV) di Indonesia merupakan masalahkesehatan yang masih belum tertangani. Pengobatan infeksi DENV hingga saat inimasih mengandalkan imunitas penderita. Berbagai jenis antiviral DENV sedangdikembangkan, salah satunya menggunakan rekayasa genetika berbasis sekuensuntranslated region (UTR). Namun data mengenai UTR DENV masih sedikit. Olehkarena itu, penulis melakukan penelitian untuk menganalisa sekuens danfilogenetik UTR DENV-1. Dalam penelitian ini, dua strain Indonesia dibandingkandengan 25 strain dari GenBank menggunakan program Genetyx 5.1. Hasilpenelitian ini menunjukan bahwa terdapat beberapa sekuens yang lestari, sehinggamemenuhi kriteria sebagai target siRNA, yaitu 3’UAR, CS1, CS2, dan RCS2.Sementara sekuens 5’ UTR tidak memenuhi syarat siRNA karena ditemukanperubahan pada beberapa strain, termasuk strain Indonesia. Filogenetikmenggunakan UTR tidak sesuai dengan filogenetik envelope dan tidak dapatdigunakan untuk menjelaskan pola penyebaran DENV-1.

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ABSTRACTHigh prevalence of dengue virus (DENV) infection still become an unresolved issuein Indonesia. Treatment for DENV infection relies heavily on natural immunity.Various DENV antivirals are on development, one of them is untranslated region(UTR)-sequence-based. However, there is only a few number of data available onUTR DENV. Therefore, this research was done to analyze the sequence andphylogenetic of UTR DENV-1. Two Indonesia strains were compared with 25strains from GenBank using the Genetyx 5.1 program. There are four conservedsequences that fill criteria as siRNA targets, which are 3’UAR, CS1, CS2, andRCS2. 5’UTR sequence does not fill the siRNA criteria because mutations werefound within some strains, including Indonesia strains. Phylogenetic using UTRdoes not fit envelope phylogenetic and can not be used to explain the DENV-1pattern."

"Sebagai upaya dalam memahami netralisasi virus H5N1 oleh antibodi manusia, simulasi dinamika molekuler dua kompleks antibodi-antigen dilakukan. Tiga struktur molekul yang membentuk dua kompleks tersbeut dibentuk termasuk antigen hemagglutinin Vietnam 2IBX, hemagglutinin Indonesia CDC, dan fragmen variabel dari antibodi 8H5 atau 8H5Fv.Dalam penelitian ini komplesks 8H5Fv-2IBX dan 8H5Fv-CDC diproduksi melalui pemodelan struktur molekul, homology modeling, dan molecular docking. Dua kompleks tersebut lalu melewati simulasi dinamika molekuler selama 2 nanosekon untuk menginvestigasi kestabilan struktur kompleks dan aktivitas netralisasi yang dapat diamati dengan berfokus pada epitope netralisasi masing ? masing hemagglutinin yang didapatkan hasil molecular docking.Didapatkan bahwa sifat dinamis atom ? atom pembentuk molekul tidak menihilkan aktivitas netralisasi. Dengan mengamati epitope netralisasi masing ? masing hemagglutinin juga didapatkan bahwa aktivitas netralisasi lebih efektif pada hemagglutinin 2IBX (Vietnam) dibandingkan dengan hemagglutinin Indonesia (CDC) berdasarkan kalkulasi solvent accessible surface (SAS), energi, root mean square displacement (RMSD), dan analisis okupansi ikatan hidrogen.

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In an effort to study the H5N1 virus neutralisation by a human antibody, molecular dynamics simulations on two antibody-antigen complexes were conducted. Three molecular structures were formed in this study including the Vietnamese hemagglutinin 2IBX, the Indonesian hemagglutinin CDC, and a variable fragment of the 8H5 antibody or 8H5Fv.

In this study the complexes 8H5Fv-2IBX and 8H5Fv-CDC, that were produced by molecular modeling, homology modeling and molecular docking, was subjected to a 2 nanosecond molecular dynamics simulation each to investigate the stability of such complexes and the maintenance of the neutralising activity that was observed by focusing on the neutralising epitopes that were predicted by molecular docking.

It is was found that the dynamic nature of the molecules in study did not negate the steric hindrance occuring from the antibody variable fragment 8H5Fv with the hemagglutinins, therefore suggesting that the 8H5 antibody should be able to neutralise these two hemagglutinins. By solvent accessible surface (SAS) calculations, energy analysis, root mean square displacement (RMSD) analysis, and also hydrogen bond occupance it was also found that the the 8H5Fv seem to be more effective against the 2IBX (Vietnamese) hemagglutinin than against the CDC (Indonesian) hemagglutinin."

"Delivering fundamental insights into the most popular methods of molecular analysis, this text is an invaluable resource for students and researchers. It encompasses an extensive range of spectroscopic and spectrometric techniques used for molecular analysis in the life sciences, especially in the elucidation of the structure and function of biological molecules. Covering the range of up-to-date methodologies from everyday mass spectrometry and centrifugation to the more probing X-ray crystallography and surface-sensitive techniques, the book is intended for undergraduates starting out in the laboratory and for more advanced postgraduates pursuing complex research goals. The comprehensive text provides strong emphasis on the background principles of each method, including equations where they are of integral importance to the individual techniques. With sections on all the major procedures for analysing biological molecules, this book will serve as a useful guide across a range of fields, from new drug discovery to forensics and environmental studies"--Provided by publisher"

"Currently, we reported results of a nested polymerase chain reaction (PCR) assay specific 5` untranslated region (UTR)region of hepatitis C virus (HCV) genome that showed three different patterns of deoxyribonucleic acid (DNA)fragments (single expected specific DNA band, single DNA band higher in size than an expected band, and multipleDNA bands). Three isolates (Isolate A, B, and C), representing all the three DNA bands, were analyzed by usingphylogenetic trees. The results showed that the Isolate A, B, and C were classified into HCV genotypes 2, 1, and 3,respectively. The Isolate A and B were very closely related to viral isolates from Madagascar and Brazil, respectivelyand were not closely related to other Indonesia isolates. In contrast with the Isolate A and B, the Isolate C was veryclosely related to another Indonesia isolate. Among all there isolates, the Isolate C was very closely related to anIndonesia isolate detected from a cirrhosis patient, indicating that the Isolate C might be more virulence than the IsolateB and C. However, a complete genome-based comprehensive genetic characterization for all the three isolates needs tobe conducted in future research to confirm all findings in this study.Analisis Filogenetik Berbasis Region5` yang Tidak Ditranslasikan Sebagian (Partly 5` UTR) terhadap Tiga IsolatVirus Hepatitis C di Jakarta, Indonesia: Kajian Pendahuluan. Makalah ini adalah laporan hasil pengujian genomHCV dengan metode nested PCR 5` UTR spesifik yang menunjukkan adanya tiga pola fragmen DNA yang berbeda(untai DNA spesifik yang diekspektasi tunggal, untai DNA tunggal yang berukuran lebih tinggi daripada untai yangdiekspektasi, dan untai DNA majemuk). Tiga isolat (Isolat A, B, dan C) yang mewakili tiga berkas DNA itu dianalisisdengan pohon filogenetik. Hasil penelitian menunjukkan bahwa Isolat A, B, dan C tergolong genotipe HCV 2, 1, dan 3secara berturut-turut. Isolat A dan B masing-masing berhubungan erat dengan isolat virus dari Madagaskar dan Brazil,meskipun keduanya tidak berhubungan erat dengan isolat dari Indonesia. Berbeda dengan isolat A dan B, Isolat Cberhubungan erat dengan isolat dari Indonesia. Di antara ketiga isolat, Isolat C memiliki hubungan paling erat denganisolat Indonesia yang ditemukan pada seorang pasien kirosis. Hal ini menunjukkan adanya kemungkinan bahwa Isolat Clebih berbahaya daripada Isolat B dan C. Bagaimanapun, karakterisasi genetis komprehensif berbasis genom yanglengkap terhadap ketiga isolat perlu dilaksanakan pada kajian-kajian berikutnya untuk mendukung hasil penelitian ini."

"Penyakit yang disebabkan oleh infeksi virus dengue telah menjadi masalah kesehatan utama di dunia. Pengobatan baru bersifat antiviral yang menghambat aktivitas enzim yang berperan dalam replikasi di dalam tubuh sangat dibutuhkan saat ini. NS5 metiltransferase merupakan salah satu protein non struktural virus dengue yang diketahui dapat menjadi target inhibitor antiviral. Penelitian ini bertujuan menapis peptida siklis komersial yang dapat digunakan sebagai inhibitor NS5 metiltransferase virus dengue melalui molecular docking dan simulasi molecular dynamics. Screening dilakukan melalui metode molecular docking berdasarkan nilai ΔGbinding. Stabilitas kompleks enzim-ligan dianalisis dengan simulasi molecular dynamics. Screening 300 peptida siklis komersial didapatkan ligan terbaik untuk masing-masing sisi ikatan SAM dan RNA-cap NS5 metiltransferase yaitu [Tyr123] Prepro Endothelin (110-130),amide,human dan Urotensin II, human berdasarkan nilai ΔGbinding, molecular weight (MW) dan uji ADME-Tox. Hasil simulasi molecular dynamics menunjukan bahwa kedua ligan dapat mempertahankan interaksi dengan residu sisi aktif target. Ligan [Tyr123] Prepro Endothelin (110-130),amide,human dapat mempertahankan kestabilan konformasi kompleks enzim-ligan pada 310 K dan 312 K. Sedangkan ligan Urotensin II, human lebih reaktif pada 312 K dibandingkan pada 310 K. Oleh karena itu, kedua ligan dapat dijadikan kandidat inhibitor potensial untuk NS5 metiltransferase virus dengue.

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Disease caused by dengue virus infection has become a major health problem in the world. New treatment is antiviral which inhibits the activity of enzymes that play a role in replication in the body is needed at this time. NS5 methyltransferase was one of dengue virus non-structural proteins which were known to be a target of antiviral inhibitors. This research aims to screen commercial cyclic peptides that was used as inhibitors of dengue virus NS5 methyltransferase by molecular docking and molecular dynamics simulation.

Screening was done through molecular docking method based on the value of ΔGbinding. Stability of complex enzyme-ligand were analyzed by molecular dynamics simulation. Screening of 300 commercial cyclic peptide obtained best ligand for SAM and RNA-cap binding site of NS5 methyltransferase recpectively based on ΔGbinding value, molecular weight (MW) and ADME-Tox test.

Result of molecular dynamics simulation show that both of the ligand can maintain interaction with the active site residues of target. Ligand [Tyr123] Prepro Endothelin (110- 130),amide,human can maintain stable conformation of complex enzyme-ligand at 310 K and 312 K. Meanwhile, ligand Urotensin II,human more reactive at 312 K than at 310 K. Therefore, both ligands can be used as a potential inhibitor candidates for NS5 methyltransferase of dengue virus."