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Abstrak :
Virus dengue merupakan virus kelas Flaviviridae yang ditularkan melalui gigitan nyamuk Aedes aegypti yang sebelumnya telah terinfeksi oleh virus dengue. Diagnostik dini dilakukan dalam upaya menekan penyebaran virus ini agar pasien yang terinfeksi bisa ditangani lebih cepat. NS1 merupakan protein yang terdapat pada virus dengue dapat ditemukan di darah pasien satu hari setelah gejala infeksi primer maupun sekunder. Hal ini menjadikan NS1 penanda biologis serta target nanobodi yang tepat dalam diagnosis infeksi virus dengue. Nanobodi yang mengenali antigen NS1 pada DENV menjadi potensi alat uji diagnostik dengue karena sifatnya yang lebih unggul daripada antibodi konvensional. Penelitian ini berfokus pada pembuatan prototipe tes diagnostik cepat berbasis uji aliran lateral untuk mendeteksi NS1 pada virus dengue menggunakan nanobodi anti-NS1. Pada penelitian ini, nanobodi anti-NS1 klon DD7 dan DD5 diekspresikan pada E. coli BL21(DE3). Dalam pembuatan prototipe, dilakukan optimasi formulasi konjugasi antara nanopartkel emas dengan nanobodi anti-NS1. Sebanyak tiga optimasi dilakukan dalam mendapatkan konjugasi nanopartikel emas dengan nanobodi yang optimal, yaitu optimasi pH buffer, konsentrasi nanobodi, dan diameter nanopartikel emas. pH buffer optimal untuk klon DD5 dan DD7 adalah buffer borat pH 9, konsentrasi nanobodi optimal untuk klon DD5 dan DD7 adalah 10 ng, dan diameter optimal nanopartikel emas untuk klon DD5 dan DD7 adalah 40 nm. Pada pembuatan prototipe, konjugasi antara nanopartikel emas dan nanobodi klon DD5 belum berhasil mendeteksi antigen yaitu berupa virus dengue pada bagian test line prototipe dan untuk konjugasi antara nanopartikel emas untuk klon DD7 menghasilkan reaksi false positive pada prototipe. ......Dengue virus is a class of Flaviviridae virus transmitted through the bite of Aedes aegypti mosquitoes that have previously been infected by the dengue virus. Early diagnostics are carried out in an effort to suppress the spread of this virus so that infected patients can be treated faster. NS1 is a protein found in the dengue virus that can be found in the patient's blood one day after symptoms of primary or secondary infection.This makes NS1 a biosensor as well as a precise target for nanobodies in the diagnosis of dengue virus infection. Nanobodies that recognize NS1 antigens in DENV are potential dengue diagnostic test kits because they are superior to conventional antibodies. This research focuses on making rapid diagnostic tests based on lateral flow assay to detect NS1 in dengue viruses using anti-NS1 nanobodies as an alternative diagnostic test on dengue virus. In this study, anti-NS1 nanobodies of DD7 and DD5 clones were expressed in E. coli BL21(DE3). In making prototypes, optimization of conjugate formulations between gold nanoparticles and anti-NS1 nanobodies was carried out. A total of three optimizations were carried out in obtaining the conjugation of gold nanoparticles with optimal nanobodies, namely optimization of buffer pH, nanobody concentration, and diameter of gold nanoparticles. The optimal buffer pH for DD5 and DD7 clones is pH 9 borate buffer, the optimal nanobody concentration for DD5 and DD7 clones is 10 ng, and the optimal diameter of gold nanoparticles for DD5 and DD7 clones is 40 nm. In making the prototype, the conjugation between gold nanoparticles and DD5 clone nanobodies has not succeeded in detecting antigens in the form of dengue virus in the prototype test line and for conjugation between gold nanoparticles for DD7 clones resulting in false positive reactions in the prototype.

Abstrak :
[ABSTRAK
Virus dengue terdiri atas 10 protein penyusun yang berbeda dan diklasifikasikan menjadi empat serotipe utama (DEN 1 ? DEN 4). Penelitian ini dirancang untuk melakukan pengelompokan terhadap 30 sekuens protein virus dengue yang diambil dari Virus Pathogen Database and Analysis Resource (ViPR) menggunakan metode Regularized Markov Clustering (R?MCL) dan untuk menganalisis hasilnya. Dengan menggunakan program Python 3.4, algoritma R-MCL diimplementasikan dan menghasilkan 8 kelompok dengan pusat kelompok lebih dari satu di beberapa kelompok. Banyaknya pusat kelompok menunjukkan tingkat kepadatan interaksi. Interaksi protein ? protein yang terhubung padat dalam jaringan cenderung membentuk kompleks protein yang berfungsi sebagai unit proses biologi tertentu. Hasil analisis menunjukkan hasil pengelompokan dengan R-MCL menghasilkan kelompok ? kelompok kekerabatan virus dengue berdasarkan peran yang sama dari protein penyusunnya, tanpa memperhatikan serotipenya.

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ABSTRACT
Dengue virus consists 10 different constituent proteins and are classified into four major serotypes (DEN 1 - DEN 4). This study was designed to perform clustering against 30 protein sequences of dengue virus taken from Virus Pathogen Database and Analysis Resource (VIPR) using Regularized Markov Clustering (R-MCL) algorithm and tp analyze the result. By using Python program 3.4, R-MCL algorithm produces 8 clusters with more than one centroid in several clusters. The number of centroid shows the density level of interaction. The density of interactions protein - protein connected in a network tend to form a protein complex that serves as the unit of specific biological processes. The analyzing result shows the R-MCL clustering produces clusters of dengue virus family based on the similirity role of their constituent protein, regardless serotypes;Dengue virus consists 10 different constituent proteins and are classified into four major serotypes (DEN 1 - DEN 4). This study was designed to perform clustering against 30 protein sequences of dengue virus taken from Virus Pathogen Database and Analysis Resource (VIPR) using Regularized Markov Clustering (R-MCL) algorithm and tp analyze the result. By using Python program 3.4, R-MCL algorithm produces 8 clusters with more than one centroid in several clusters. The number of centroid shows the density level of interaction. The density of interactions protein - protein connected in a network tend to form a protein complex that serves as the unit of specific biological processes. The analyzing result shows the R-MCL clustering produces clusters of dengue virus family based on the similirity role of their constituent protein, regardless serotypes;Dengue virus consists 10 different constituent proteins and are classified into four major serotypes (DEN 1 - DEN 4). This study was designed to perform clustering against 30 protein sequences of dengue virus taken from Virus Pathogen Database and Analysis Resource (VIPR) using Regularized Markov Clustering (R-MCL) algorithm and tp analyze the result. By using Python program 3.4, R-MCL algorithm produces 8 clusters with more than one centroid in several clusters. The number of centroid shows the density level of interaction. The density of interactions protein - protein connected in a network tend to form a protein complex that serves as the unit of specific biological processes. The analyzing result shows the R-MCL clustering produces clusters of dengue virus family based on the similirity role of their constituent protein, regardless serotypes, Dengue virus consists 10 different constituent proteins and are classified into four major serotypes (DEN 1 - DEN 4). This study was designed to perform clustering against 30 protein sequences of dengue virus taken from Virus Pathogen Database and Analysis Resource (VIPR) using Regularized Markov Clustering (R-MCL) algorithm and tp analyze the result. By using Python program 3.4, R-MCL algorithm produces 8 clusters with more than one centroid in several clusters. The number of centroid shows the density level of interaction. The density of interactions protein - protein connected in a network tend to form a protein complex that serves as the unit of specific biological processes. The analyzing result shows the R-MCL clustering produces clusters of dengue virus family based on the similirity role of their constituent protein, regardless serotypes]

Abstrak :
[ABSTRAK Virus Dengue (DENV) menyebabkan infeksi penyakit yang mengancam sekitar 40% populasi dunia. Hingga saat ini belum tersedia obat antiviral yang dapat digunakan sebagai upaya pengobatan penyakit yang disebabkan infeksi DENV. Dengan melakukan virtual screening terhadap 308 peptida siklis komersial, dicari kandidat obat yang mampu menginhibisi sebuah situs pengikatan β-OG yang terdapat pada protein envelope DENV. Melalui metode simulasi penambatan dan dinamika molekul serta analisis terhadap sifat farmakologi dan toksisitas dari senyawa-senyawa peptida yang ditapis, diketahui ligan Cyclo(-D-Trp-Tyr) memiliki afinitas yang baik dengan situs pengikatan β-OG binding pocket serta diprediksi memiliki sifat sebagai obat yang relatif baik. Ligan tersebut juga membentuk kompleks yang stabil dengan protein envelope pada temperatur 310 K dan 312 K. Ligan Cyclo(-D-Trp-Tyr) memiliki potensi sebagai inhibitor β-OG binding pocket untuk selanjutnya dikembangkan menjadi obat antiviral terhadap infeksi DENV.

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ABSTRACT , Dengue Virus (DENV) has caused infectious disease which put roughly 40% of world population at risk. Antiviral drug against DENV infection remains unavailable up until now. By screening to 308 commercial cyclic peptides virtually, this research aims to find drug candidate which can inhibit β-OG binding site. Through molecular docking and molecular dynamics simulation, along with pharmacology and toxicity analyzing, it is discovered that Cyclo(-D-Trp-Tyr) ligand has good affinity with β-OG binding pocket and is predicted to has relatively acceptable drug properties. Ligand forms stabile complexity with nvelope protein in 310 K and 312 K. Cyclo(-D-Trp-Tyr) ligand is revealed to be potential inhibitor of β-OG binding pocket. Thus, it is feasible for furher development as antiviral drug against DENV infection.]