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"Latar belakang: Proses pematangan spermatozoa membutuhkan interaksi antar protein yang disintesis dan disekresikan oleh epitel epdidimis ke lumen di area tertentu. Gen yang terekspresi secara spesifik di region-region tertentu akan menciptakan lingkungan mikro yang kondusif untuk proses pematangan spermatozoa. Spink2 adalah salah satu gen yang diketahui berperan dalam pematangan spermatozoa yang ekspresinya terdekteksi di epididimis. Studi peran SPINK2 membutuhkan protein yang cukup untuk karakterisasi. Tujuan penelitian ini adalah untuk mengklon, mengekspresikan, dan menguji aktivitas protein rekombinan SPINK2.Metode: Dalam penelitian ini gen mSpink2 dikonstruksikan secara sintetis. Plasmid pQE80L digunakan sebagai vektor ekspresi dan strain sel Escherichia coli yang digunakan adalah Top10 dan BL21. Proses pengklonaan diawali dengan transformasi plasmid pQE80L-mSpink2 ke E. coli Top10 kompeten menggunakan metode heatshock. Proses ekspresi dilakukan dengan penambahan agen induksi Isopropyl-1-Thio-d-Galactopyranoside (IPTG), dipurifikasi dengan kromatografi Ni-NTA. Kemudian dilakukan uji aktivitas protease dengan pembacaan panjang gelombang 660 nm.Hasil: Plasmid pQE80L-mSpink2 terkonfirmasi berhasil diklon dengan analisis enzim restriksi dan sekuensing. Hasil elekstroforesis menunjukan adanya fragmen DNA dengan panjang 4709 pb dan 258 pb. Hasil ekspresi SDS-PAGE dan western blot menunjukkan SPINK2 berhasil terekspresi pada waktu optimum induksi jam ke-4 dan terdapat pita tebal dengan ukuran 14 kDa. Protein rekombinan SPINK2 berhasil dipurifikasi dan ditunjukan dari hasil western blot pada elusi ke-1 hingga ke-4. Hasil uji aktivitas protease menunjukan terdapat penurunan aktivitas enzim tripsin setelah diberi protein rekombinan SPINK2 dengan konsentrasi optimum 0,6 mM.Kesimpulan: Protein rekombinan SPINK2 telah berhasil dikonstruksi secara sintetis, diklon pada vektor plasmid pQE80L, diekspresikan pada E.coli strain BL21 kompeten, dan diketahui dapat menghambat aktivitas enzim protease dengan konsentrasi 0,7 mM.

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Background: The process of spermatozoa maturation requires interaction between proteins synthesized and secreted by the epididymal epithelium to the lumen in a particular area. The interaction between these protein produces a microenvironment for maturation process of spermatozoa. In this condition, it takes genes that are specifically expressed. Spink2 in one of the genes known have a role in the maturation of spermatozoa and expressed in the epididymis. The SPINK2 role study requires sufficient protein for characterization. The aim of this study was to clone, express, and protease assay of the recombinant protein SPINK2.

Methods: In this study the mSpink2 gene was constructed synthetically. The plasmid pQE80L was used as an expression vector and the cell Escherichia coli strains used were Top10 and BL21. The cloning process begins with transformation of the plasmid pQE80L-mSpink2 to a competent E. coli Top10. The expression process was carried out by adding the induction agent Isopropyl-1-Thio-d-Galactopyranoside (IPTG), purified by Ni-NTA chromatography. Then the protease activity assay was carried out with a wavelength 660 nm.

Results: The plasmid pQE80L-mSpink2 was confirmed to be cloned by restriction enzyme and sequencing analysis. The result showed that is formation of DNA with a length of 4709 bp and 258 bp. The SDS-PAGE and western blot result showed that SPINK2 was successfully expressed at the optimum time is 4th hour. There was a thick band with a size of 14 kDa. The SPINK2 recombinant protein was successfully purified and shown form the western blot. The result of the protease activity assay showed that there was a decrease in trypsin enzyme activity after being given SPINK2 recombinant protein with an optimum concentration is 0,6 mM.

Conclusion: Recombinant protein of SPINK2 has been successfully constructed synthetically, cloned, expressed, and tested for its protease inhibitor activity"

"Latar belakang: Beta defensin diekspresikan terutama oleh sel epitel pada permukaan mukosa berbagai organ seperti kulit, usus, mulut dan saluran genital. Studi sebelumnya menunjukkan bahwa Beta defensin 30 (Defb30) terekspresi spesifik di epididimis. Defb30 merupakan peptida kationik berukuran kecil yang diduga berperan penting pada proses pematangan spermatozoa di epididimis dan juga memiliki kemampuan untuk membunuh mikroba. Untuk mempelajari aktivitas antimikroba Defb30 ini diperlukan analisis pada tingkat protein dan hal tersebut memerlukan protein dalam jumlah yang cukup. Karena itu perlu dilakukan suatu rekayasa genetika berupa perancangan gen yang mengkode Defb30, pengklonaan dan ekspresi untuk pembuatan protein rekombinan DEFB30. Metode: Gen sintetik penyandi protein DEFB30 yang telah dioptimasi kodonnya diklona ke dalam vektor pQE-80L. Plasmid rekombinan yang mengandung sisipan gen target dikonfirmasi dengan analisis enzim restriksi dan sekuensing untuk selanjutnya diekpresikan ke dalam E. coli BL21 dan diinduksi menggunakan IPTG (Isopropyl-1-Thio-d-Galactopyranoside) dengan berbagai waktu inkubasi. Deteksi protein rekombinan dilakukan dengan SDS-PAGE dan westernblotting. IMAC (Immobilized Metal Affinity Chromatography) digunakan untuk mempurifikasi protein rekombinan. Uji antimikroba protein rekombinan dilakukan dengan cara pengukuran nilai optical density (OD) dan dianalisis hasilnya menggunakan uji one way anova. Hasil: Gen sintetik penyandi protein rekombinan DEFB30 berhasil dikonstruksi pada plasmid pQE-80L. Ekspresi ke dalam E. coli BL21 menghasilkan suatu protein fusi setelah diinduksi menggunakan IPTG selama 4 jam. Hasil analisis protein rekombinan dengan westernblotting menggunakan antibodi Anti-His G-HRP menunjukkan terbentuk pita tebal yang berukuran diatas 10 kDa (±12 kDa). Uji antimikroba protein rekombinan DEFB30 menunjukkan bahwa protein tersebut dapat menghambat pertumbuhan bakteri Eschericia coli dan Bacillus subtilis.Kesimpulan: Gen sintetik penyandi beta defensin 30 berhasil diklona ke dalam plasmid pQE-80L. Ekspresi protein rekombinan DEFB30 menghasilkan suatu protein fusi berukuran ±12kDa. Protein rekombinan DEFB30 terbukti memiliki sifat antimikroba terhadap Eschericia coli dan Bacillus subtilis.

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Background: Beta defensins are primarily expressed by epithelial cells at mucosal surfaces, such as those in skin, gut, mouth and genital tract. Previous studies have demonstrated that beta defensin 30 (Defb30) is exclusively expressed in the epididymis. Defb30 is known as a small cationic antimicrobial peptide which plays an important role in epididymal sperm maturation and also acts as a host defence against microbial infection. Study of Defb30 role in the antimicrobial activity requires generating DEFB30 protein for characterization. For the purpose of this study, Defb30 gene was designed, synthesized, cloned, and expressed for the manufacture of the DEFB30 recombinant protein. Method(s): In this study, according to the preferred codon in E. coli, the Defb30 gene was optimized and synthesized. The gene was cloned into pQE-80L vector and subsequently expressed in E. coli BL21; using IPTG (Isopropyl-1-Thio-d-Galactopyranoside) as an inducer. Detection of recombinant protein was carried out by using SDS-PAGE and westernblotting. IMAC (Immobilized Metal Affinity Chromatography) was used to purify recombinant protein. Optical density measurement was used to analyze antimicrobial property of the DEFB30 recombinant protein. Results: The synthetic gene was successfully constructed into pQE-80L plasmid and expression of the recombinant protein in E. coli BL21 produced a fusion protein after being induced by IPTG for 4 hours. Westernblotting analysis using Anti-His G-HRP antibody showed band above 10kDa (±12kDa). Antimicrobial assay for DEFB30 recombinant protein showed inhibition towards growth rates of Eschericia coli and Bacillus subtilis. Conclusion: Defb30 synthetic gene was succesfully cloned into pQE-80L plasmid. Expression of recombinant DEFB30 produced a fusion protein of ±12kDa. This recombinant protein has antimicrobial property towards Eschericia coli and Bacillus subtilis."

"ABSTRAKLatar Belakang: Pematangan spermatozoa di epididimis terjadi melalui interaksi antara spermatozoa dengan protein yang disekresikan oleh sel epitel yang melapisi duktus epididimis. Sekresi protein tersebut menciptakan microenvironment yang diregulasi oleh gen-gen tertentu. Studi sebelumnya menunjukkan bahwa gen yang terlibat dalam pematangan spermatozoa pada umumnya terekspresi secara spesifik di epididimis dan dipengaruhi oleh androgen. Spink2 merupakan salah satu gen yang terekspresi di epididimis, namun regulasi ekspresinya masih belum diketahui. Tujuan penelitian ini adalah untuk mengkarakterisasi ekspresi dan regulasi gen Spink2 pada epididimis mencit jantan.Metode: Analisis secara in silico digunakan untuk mengetahui struktur gen dan prediksi sinyal peptida, serta domain fungsional gen Spink2. Quantitative real-time RT-PCR digunakan dalam mengukur ekspresi relatif gen Spink2 pada analisis spesifisitas jaringan, ketergantungan terhadap androgen dan faktor testikuler, serta post-natal development.Hasil: Spink2 termasuk dalam famili serine protease inhibitor yang ditandai dengan adanya domain Kazal type 2. Analisis signal peptide menunjukkan bahwa Spink2 merupakan protein sekretori. Spink2 terekspresi di testis dan epididimis, dengan ekspresi tertinggi berada di kaput epididimis. Ekspresi Spink2 pada mencit yang digonadektomi mengalami peningkatan setelah 6 jam, kemudian menurun mulai dari hari ke-1 hingga hari ke-5. Pemberian testosteron mampu mempertahankan ekspresi Spink2 pada 3 dan 5 hari setelah gonadektomi. Selain itu, pada analisis pengaruh faktor testikuler, ekspresi Spink2 menunjukkan adanya regulasi dari faktor testikuler pada semua kelompok setelah dilakukan efferent duct ligation EDL . Spink2 menujukkan regulasi post-natal yakni mulai terekspresi pada umur mendekati 22 hari.Kesimpulan: SPINK2 merupakan protein sekretori yang terekspresi pada kaput epididimis, serta diregulasi oleh androgen dan faktor testikuler. Spink2 tidak terekspresi secara konstitutif. Berdasarkan data tersebut Spink2 sangat berpotensi terlibat dalam proses pematangan spermatozoa di epididimis. Penelitian lebih lanjut diperlukan untuk mengkonfirmasi potensi tersebut.

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ABSTRACTBackground Sperm maturation in the epididymis occurs through interactions between sperm and proteins secreted by epithelium cells lining the epididymal duct. The secretion of these proteins creates a microenvironment that is regulated by certain genes. Previous studies showed that genes which are involved in sperm maturation process are expressed specifically in the epididymis and regulated by androgen. Spink2 is one of the epididymal genes, but the regulation of its expression is still unknown. Therefore, this study was aimed to characterize Spink2 expression and its regulation in the mouse epididymis.Method s In silico analysis was performed to determine the gene structure and identify the signal peptide, as well as the functional domain of Spink2. Quantitative real time RT PCR was performed to measure relative expression of Spink2 in the analyses of the tissue specificity, androgen dependency, testicular factor and post natal development.Result s Spink2 belongs to the serine protease inhibitor family which is characterized by the presence of Kazal type 2 domain. Signal peptide analysis showed that Spink2 amino acid sequence contains a signal peptide, indicating Spink2 is a secretory protein. Spink2 was expressed specifically in the testis and epididymis, with the highest level of its expression was in the epididymal caput. Spink2 expression increased after six hours and started to decrease on day 1 throughout day 5. Interestingly, administration of exogenous testosterone was able to maintain expression at the physiological level. In addition, Spink2 was slightly affected by testicular factors. During post natal development, Spink2 start to be expressed at day 22 before increased dramatically throughout day 60.Conclusion s Spink2 is a secretory protein that is expressed in caput region of the mouse epididymis and regulated by androgen. Spink2 is not constitutively expressed throughout development. Based on our data, may be involved in epididiymal sperm maturation process. Further studies are required to confirm its role. "

"Spag11a diketahui terekspresi secara spesifik pada kaput epididimis sehingga dimungkinkan protein tersebut memiliki fungsi yang spesifik untuk maturasi spermatozoa. Studi peran SPAG11A dalam maturasi spermatozoa di epididimis memerlukan produksi protein SPAG11A untuk dikarakterisasi. Tujuan dari penelitian ini adalah untuk mengklon, mengekspreesikan, dan mengkarakterisasi sifat antimikroba dari protein rekombinan SPAG11A. Insert cDNA Spag11a yang dihasilkan melalui PCR diklon ke dalam vektor pET100/D-TOPO. Plasmid rekombinan kemudian diekspresikan ke Escherichia coli BL21 DE3 star. Deteksi dari fusi protein rekombinan dilakukan dengan SDS-PAGE dan Western Blotting. IMAC Immobilized Metal Affinity Chromatography digunakan untuk mempurifikasi protein rekombinan. Uji antimikroba protein rekombinan dianalisis melalui pengukuran Optical density.PCR amplifikasi dari cDNA kaput epididimis mencit menghasilkan insert Spag11a berukuran 210bp. Insert tersebut kemudian dikloning ke dalam pET100/D-TOPO menghasilkan 1 rekombinan plasmid dari 10 koloni yang diskrining. Ekspresi rekombinan klon ke dalam E.coli BL21 menghasilkan fusi protein setelah diinduksi IPTG selama 4 jam. Fusi protein dikonfirmasi menggunakan Western Blotting menggunakan antibodi yang mengenali N-terminal His-Tag 21kDa dan protein SPAG11A. Uji antimikroba protein rekombinan SPAG11A mununjukkan tidak ada inhibisi yang signifikan terhadap laju pertumbuhan E.coli dan Bacillus subtilis. Insert Spag11a yang berukuran 210bp berhasil diklon ke dalam vektor pET100/D-TOPO. Ekspresi rekombinan Spag11a menghasilkan fusi protein berukuran 21kDa. Protein rekombinan SPAG11A tidak membawa sifat antimikroba terhadap E.coli dan B. subtilis.

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Spag11a is known to be specifically expressed in the caput region of the epididymis suggesting a specific function for sperm maturation. Study of SPAG11A role in the epididymal sperm maturation requires generating SPAG11A protein for characterization. The objective of this study was to clone, express and characterize antimicrobial property of the recombinant SPAG11A. Spag11a cDNA insert was generated by PCR and cloned in TOPO vector. Recombinant DNA plasmid was subsequently expressed in E coli BL 21 star. Detection of recombinant fusion protein was carried out using SDS PAGE and western immunobloting. IMAC Immobilized Metal Affinity Chromatography was used to purify recombinant protein. Optical density measurement was used to analyse antimicrobial property of the recombinant protein. PCR amplification of mouse caput epididymis cDNA produced a 210 bp insert of Spag11a. Cloning of the insert into TOPO pET100 resulted in 2 recombinants out of 10 colonies that were screened. Expression of recombinant clones in the E coli BL21 produced a fusion protein after being induced IPTG for 4 hours. Fusion protein was confirmed by western immunobloting using two antibodies recognizing N terminal His Tag 21 kDa and SPAG11A protein. Antimicrobial assay for SPAG11A recombinant showed no significant inhibition towards growth rates of E coli and Bacillus subtilis. A 210 bp Spag11a insert was successfully cloned into TOPO pET100 vector. Expression of recombinant spag11a produced a fusion protein of 21 kDa. SPAG11A recombinant protein does not have antimicrobial property towards E coli and B subtilis."

"Lignoselulosa dapat dijadikan sebagai biomassa untuk menghasilkan produk bahan bakar. Hidrolisis biomassa lignoselulosa menggunakan enzim selulase. Selulase mengandung dari 3 komplek enzim yaitu, eksoglukanase, endoglukanase dan betaglukosidase Namun, betaglukosidase memiliki jumlah lebih sedikit daripada eksoglukanase dan endoglukanase. Semakin sedikit betaglukosidase dapat memicu proses hidrolisis selulosa terhambat, oleh karena itu pengembangan betaglukosida perlu dilakukan dengan diekpresikan ke dalam Pichia pastoris. Transformasi plasmid pLIPI-TnBgl1A dilakukan dengan metode elektroporasi, sedangkan ekspresi gen dan hasil purifikasi protein rekombinan dianalisis menggunakan SDS-PAGE dan Western blot. Gen betaglukosidase dari Thermotoga neapolitana berhasil ditransformasikan kedalam Pichia pastoris. Transforman yang telah diseleksi menghasilkan 2 koloni positif. Berat molekuler protein diperkirakan sekitar 53 kDa dan jumlah protein estimasi 1 mg/mL dan 1,4 mg/mL. Hasil analisis kemurnian protein rekombinan melalui SDS PAGE dan western blot memperlihatkan pita tepat di 53 kDa. Jumlah yield protein yang terpurifikasi didapatkan sekitar 21,4 % dan 24,1%. Hasil menunjukkan bahwa gen TnBgl1A telah berhasil ditransformasi dan terekspresikan dengan baik di Pichia pastoris dan protein rekombinan berhasil dipurifikasi dengan kemurnian yang cukup baik.

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Lignocellulose can be used as biomass to produce fuel products. Hydrolysis of lignocellulosic biomass using the cellulase enzyme. Cellulase contains 3 enzyme complexes, there are exoglucanase, endoglucanase and betaglucosidase. However, betaglukosidase has less amount than exoglucanase and endoglucanase. The less betaglucosidase can trigger the cellulose hydrolysis process is inhibited, therefore the development of betaglucoside needs to be done by expressing it into Pichia pastoris. Transformation of the pLIPI-TnBgl1A plasmid was performed by electroporation method, while gene expression and recombinant protein purification results were analyzed using SDS-PAGE and Western blot. The betaglucosidase gene from Thermotoga neapolitana was successfully transformed into Pichia pastoris. Transformants that have been selected produce 2 positive colonies. The molecular weight of protein is estimated to be around 53 kDa and the estimated protein amount is 1 mg/mL and 1.4 mg/mL. The results of the analysis of recombinant protein purity through SDS PAGE and western blot show the right band at 53 kDa. The amount of purified protein yield was around 21.4% and 24.1%. The results showed that the TnBgl1A gene was successfully transformed and well expressed in Pichia pastoris and the recombinant protein was purified with good purity."

"COVID-19 yang disebabkan oleh SARS-CoV-2 telah menjadi isu global dan menimbulkan kasus infeksi dan korban jiwa diseluruh dunia. Penemuan obat sangat diperlukan untuk menghambat infeksi virus dan dampak yang ditimbulkannya. Namun, penelitian dan pengembangan molekul obat baru membutuhkan waktu yang sangat lama dan memakan biaya yang sangat besar.  Studi in silico merupakan salah satu alternatif solusi untuk mengatasi permasalahan tersebut. Dalam penelitian ini, uji in silico dilakukan untuk menentukan interaksi antara senyawa propolis dengan protease utama serta protein spike SARS-CoV-2 sebagai protein target. Protease utama berperan dalam replikasi virus sementara protein spike berperan penting dalam proses invasi virus ke dalam sel.  Kedua protein ini dijadikan target pengembangan obat dengan mencari inhibitor keduanya melalui proses penambatan molekuler terhadap 20 senyawa bioaktif propolis yang berasal dari lebah tanpa sengat Tetragonula sapiens. Senyawa propolis yang digunakan yaitu senyawa yang memenuhi aturan Lipinski’s Rule of Five. Adapun piranti lunak utama yang digunakan dalam metode penambatan molekuler pada penelitian ini yaitu AutoDock Vina. Hasil simulasi penambatan molekuler menunjukkan senyawa propolis yang berpotensi menghambat aktivitas protease utama adalah Sulabiroins A, Broussoflavonol F dan (2S)-5,7-dihydroxy-4'-methoxy-8-prenylflavanone dengan nilai penambatan masing-masing sebesar -8.1, -7.9, dan -7.9 kcal/mol. Sementara itu, Broussoflavonol F dan Glyasperin A merupakan senyawa propolis yang menunjukkan aktivitas inhibis terkuat terhadap protein spike SARS-CoV-2 dengan energi ikatan masing-masing sebesar -7.6 dan -7.3 kcal/mol. Senyawa-senyawa propolis tersebut juga terbukti dapat berikatan dengan asam amino kunci pada sisi aktif protein target sehingga berpotensi untuk dikembangkan lebih lanjut sebagai kandidat obat COVID-19.

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COVID-19 caused by SARS-CoV-2 is a global health issue and resulting in morbidity and mortality across the world. There is an urgent need to find the treatments to inhibit the virus infections and its consequences. However, research and development of new drug molecules takes years and is very expensive. In silico research is an alternative solution to overcome these problems. Here we conducted in silico study to examine the interaction between propolis compounds with SARS-CoV-2 main protease and spike protein as target proteins. Main protease is responsible for the virus replication while spike protein mediates viral entry. Their important roles makes it an interesting target for developing SARS-CoV-2 potential drugs by developing the inhibitor using molecular docking toward 20 propolis active compounds from Tetragonula sapiens. Those propolis compounds then selected based on Lipinski’s Rule of Five (Lipinski’s RO5). The main software that used to conduct molecular docking in this research are AutoDock Vina. Docking results showed that propolis compound which has the high potential to inhibit SARS-CoV-2 main protease activity was Sulabiroins A, following by broussoflavonol F and (2S)-5,7-dihydroxy-4'-methoxy-8-prenylflavanone with docking score -8.1, -7.9, dan -7.9 kcal/mol, respectively. Broussoflavonol F and Glyasperin A were the most promising compounds that showed inhibition activity towards SARS-CoV-2 spike protein with binding affinity  -7.6 dan -7.3 kcal/mol. Those compounds were able to bind with the key residu on the active site of the target protein so that they could be potential to be further developed as COVID-19 drug candidates."

"COVID-19 yang disebabkan oleh virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) menjadi pandemi di seluruh dunia pada 2020 hingga 2022. Dari agen terapi yang direkomendasikan, nirmatrelvir dan ritonavir aktif bekerja langsung menargetkan virus. Kemudian berkembang berbagai peluang pengembangan obat yang menargetkan virus secara langsung, dan salah satu target yang menarik adalah papain-like protease (PLpro), yaitu proein yang berperan penting dalam replikasi virus. Beberapa bahan alam yang berpotensi diteliti aktivitas penghambatannya terhadap PLpro adalah bunga telang (Clitoria ternatea), daun belimbing manis (Averrhoa carambola L.), dan jamblang (Syzygium cumini). Tujuan dari penelitian ini ialah memprediksi aktivitas penghambatan PLpro kandungan bunga telang (Clitoria ternatea), daun belimbing manis (Averrhoa carambola L.), dan jamblang (Syzygium cumini) yang dilakukan dengan metode penambatan molekul (molecular docking) secara in silico, dan dilanjutkan dengan uji in vitro. Metode penambatan molekul divalidasi dengan metode redocking dan didapatkan nilai RMSD 0,728 Å yang berarti metode valid (RMSD<2,0 Å). Uji penambatan molekul ketiga tanaman tersebut menunjukkan hasil adanya kandungan senyawa yang berpotensi untuk menghambat aktivitas PLpro. Ligan dengan nilai afinitas ikatan ternegatif dari masing-masing tanaman adalah asam folat (jamblang) dengan nilai -8,3 kcal/mol; petunidin 3-glucoside (telang) dengan nilai -7,1 kcal/mol; dan (-)-Epicatechin 3-O-gallate (belimbing manis) dengan nilai -8,6 kcal/mol. Hasil uji in silico dikonfirmasi dengan uji in vitro yang dilakukan dengan fluorescence-based inhibitory assay menggunakan PLpro sebagai protein target, substrat Z-RLRGG-AMC, serta inhibitor kontrol GRL0617. Hasil uji in vitro mendapatkan nilai IC50 GRL0617 3,38 μM. Ekstrak herbal dengan persentase inhibisi terbaik adalah ekstrak tunggal jamblang dengan nilai 66,10%.

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COVID-19 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus became the cause of the global pandemic from 2020 until 2022. Among currently recommended therapeutic agents, nirmatrelvir and ritonavir actively works by directly targeting the virus. This leads to various opportunities for developing drugs that acts directly on the structure of the virus. One interesting target for such drugs is the papain-like protease (PLpro) which is a protein that plays a significant role in viral replication. Several natural sources which has potential for their inhibitory activity against PLpro to be studied are butterfly pea (Clitoria ternatea), star fruit (Averrhoa carambola L.) and Java plum (Syzygium cumini). This study aimed to predict the inhibitory activity against PLpro possessed by the chemical contents of butterfly pea (Clitoria ternatea), star fruit (Averrhoa carambola L.) and Java plum (Syzygium cumini) through molecular docking and in vitro assay. Prediction of inhibitory activity against PLpro was done using molecular docking. The molecular docking method was validated using redocking method and RMSD score of 0.728 Å was received. This indicated that the docking method was valid (RMSD<2.0 Å). Molecular docking result showed that all three plants contain chemicals that have potential to inhibit PLpro activity. Ligands with the lowest binding affinity from each plant are folic acid (Java plum) with a score of -8.3 kcal/mol; petunidin 3-glucoside (butterfly pea) with -7.1 kcal/mol; and (-)-Epicatechin 3-O-gallate (star fruit) with -8.6 kcal/mol. Results from in silico study were then confirmed through in vitro assay using fluorescence-based inhibitory assay using PLpro as target protein, Z-RLRGG-ACM as the substrate and GRL0617 as the control inhibitor. IC50 concentration result of GRL0617 was 3,38 μM. Herbal extract with the best inhibition percentage was found to be Java plum with an inhibition percentage of 66.10%."

"Protein Transaktivator transkripsi (Tat) adalah protein regulator HIV-1 berfungsi sebagai aktivator transkripsi genom HIV-1. Varian protein Tat-Eli adalah aktivator transkripsi paling kuat daripada varian lain melalui induksi promotor LTR HVI-1. Kemampuan tersebut digunakan sebagai kontrol positif dalam pengembangan uji infeksitivitas HIV-1 berbasis gene reporter eGFP diregulasi LTR HIV-1. Pengembangan uji infeksivitas tersebut menawarkan waktu deteksi infeksi lebih singkat daripada uji p24 pada uji fenotipik. Penelitian ini bertujuan untuk mengekspresikan protein rekombinan Tat-Eli di sistem ekpresi prokariot dan mempurifikasinya sehingga dapat dijadikan kontrol positif penginduksi promotor. Pada penelitian ini dilakukan pengklonaan gen sintetik Tat-Eli ke vektor pQE80L. Protein rekombinan Tat-Eli dipurifikasi menggunakan Ni-NTA. Pengklonaan ulang gen reporter eGFP disisipkan setelah promotor LTR HIV-1. Aktivitas protein rekombinan Tat-Eli terhadap ekspresi eGFP di sel mamalia dinilai berdasarkan persentase sel pengekspresi eGFP dan intensitas cahaya eGFP.Konstruksi plasmid rekombinan membawa gen Tat-Eli, pQETat, berhasil dibuat, diekspresikan dan dipurifikasi kondisi native. Plasmid pengekspresi eGFP  dengan promoter HIV-1, pLTReGFP berhasil dikonstruksi. Penambahan Tat-Eli rekombinan pada sel mamalia yang ditransfeksi pLTReGFP menunjukkan perbedaan intensitas cahaya eGFP yang bermakna dan paling tinggi dari semua perlakuan. Protein rekombinan Tat-Eli dapat diekspresikan dan dipurifikasi secara optimal dari E.coli. Penambahan protein Tat-Eli pada sel yang ditransfeksi pLTReGFP meningkatkan intensistas cahaya eGFP.

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Transcriptional Transactivator Protein (Tat) is an HIV-1 regulatory protein functioning as an activator of HIV-1 genome transcription. The Tat-Eli protein variant was the most potent transcriptional activator than other variants through the induction of the HVI-1 LTR promoter. This ability was used as a positive control in the development of an HIV-1 infection test based on the eGFP reporter gene regulated by LTR HIV-1. The development of the infectiousness test offers a shorter infection detection time than the p24 test in the phenotypic test. This study aims to express Tat-Eli recombinant protein in the prokaryotic expression system and to purify it so that it can be used as a positive control inducer of the promoter. In this study, synthetic Tat-Eli gene was cloned into the pQE80L vector. Tat-Eli recombinant protein was purified using Ni-NTA. Recloning of the eGFP reporter gene was inserted after the HIV-1 LTR promoter. The activity of Tat-Eli recombinant protein on eGFP expression in mammalian cells was assessed based on the percentage of eGFP-expressing cells and eGFP light intensity. The recombinant plasmid construction carrying the Tat-Eli gene, pQETat was successfully generated, expressed and purified in native conditions. An eGFP-expressing plasmid with HIV-1 promoter, pLTReGFP was successfully constructed. The addition of recombinant Tat-Eli to mammalian cells transfected with pLTReGFP showed a significant difference in eGFP light intensity and was the highest of all treatments. Tat-Eli recombinant protein can be optimally expressed and purified from E. coli. The addition of Tat-Eli protein in pLTReGFP-transfected cells increased eGFP light intensity."

"ABSTRAKProtease (PR) pada HIV berperan dalam proses maturasi virus agar dapatmenginfeksi sel inang. Proses tersebut berlangsung dalam sisi aktif PR denganmemotong poliprotein virus. Banyaknya ragam mutasi residu PR membuatinteraksi PR dengan obat yang diberikan dapat berbeda. Pasien dari Indonesiasendiri memiliki karakteristik galur tipe AE yang berbeda dengan galur B yangbanyak ditemukan di negara-negara barat. Dua PR pasien dari Indonesia dengankode RY1 (10 mutasi) dan DY1 (12 mutasi) disimulasikan dengan metodesimulasi dinamika molekuler untuk meninjau interaksi antara kedua PR denganobat amprenavir (APV). Berdasarkan hasil energinya, interaksi RY1-APV lebihkuat bila dibandingkan dengan DY1-APV. Hasil tersebut diperkuat dengan tinjuanstruktural dan ikatan hidrogen terhadap residu mutasi yang dimiliki kedua pasien.Model pasien RY1 memiliki mutasi di residu ke-45 yang diketahui membantumempertahankan interaksi PR-APV, sedangkan model pasien DY1 memilikimutasi pada residu ke-10 yang diketahui mengurangi interaksinya dengan obat.

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ABSTRACTProtease (PR) on the HIV virus plays a role in the maturation process in order to

infect host cells. The process takes place in the active site PR by cutting viral

polyprotein. Many kinds of mutated residues at PR makes interaction with the

drug can vary. Patients from Indonesia itself has AE type strain that has different

characteristic with B type strain which are found in western countries. Two PR

patients from Indonesia with RY1 code (10 mutations) and DY1 code (12

mutations) is simulated by molecular dynamics simulation methods to evaluate

the interaction between two PR with amprenavir (APV). Based on the energy,

RY1-APV interaction is stronger when compared to DY1-APV. These results are

supported by structural insights and hydrogen bonding to residue mutations that

occur in both patients. RY1 patient model have mutations in 45th residue, that is

known to help maintain the interaction of PR-APV. While the DY1 patient model

have mutations in the 10th residue, that is known to reduce the interaction with

the drug."

"ABSTRAKSalah satu permasalahan yang dihadapi oleh pengobatan regeneratif menggunakan sel punca adalah metode verifikasi sifat pluripotensi terhadap sel punca yang telah diperoleh. Verifikasi sifat pluripotensi dilakukan dengan menggunakan antibodi untuk mengenali protein marka sel punca yang dihasilkan oleh sel tersebut. Penelitian ini bertujuan untuk mengekspresikan dan mempurifikasi salah satu protein marka sel punca, yaitu SOX2 sehingga dapat digunakan untuk memproduksi antibodi yang dapat digunakan untuk proses verifikasi tersebut. Ekspresi protein SOX2 dilakukan pada sistem ekspresi Escherichia coli BL21 codon plus dengan menggunakan plasmid rekombinan pQE-80L Sox2, kemudian protein SOX2 diverifikasi secara kualitatif dengan menggunakan SDS-PAGE dan Western blot. Hasil menunjukkan bahwa SOX2 telah berhasil diekspresikan pada sistem ekspresi yang digunakan, namun kodon gen sintetik Sox2 yang belum teroptimasi untuk beradaptasi pada sistem ekspresi menyebabkan jumlah protein yang dihasilkan sedikit. Purifikasi SOX2 juga telah berhasil dilakukan dengan menggunakan sistem purifikasi Ni-NTA dalam keadaan terdenaturasi.

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ABSTRACTOne of the problems faced by the use of stem cells in regenerative medicine is to find a proper method for verifying the pluripotency of a stem cell obtained. Verification of the cell pluripotency can be accomplished by using an antibody to identify the stem cell protein marker produced by the cell. The purpose of this research is to express and purify one of the stem cell marker protein, SOX2, in order to produce the antibody that can be used in the verification process. SOX2 protein expression was acomplished by using Escherichia coli BL21 codon plus expression system as host with pQE 80L Sox2 recombinant plasmid. The protein SOX2 obtained then was qualitatively verified by using SDS PAGE and Western blotting. Result showed that SOX2 has been successfully expressed by the expression system used. However, the unoptimized codon of the synthetic Sox2 gene causing the codon unable to adapt properly to the expression system, therefore may affect the translation process and lower the protein yield. Purification of SOX2 protein was also has been successfully conducted by using Ni NTA purification system in denatured protein condition."