Judul: Active Compounds of Natural Products as Covid-19 Antivirus Candidates Using Molecular Docking and Dynamics Studies
Abstrak: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) adalah virus penyebab Coronavirus 2019 (COVID-19) yang menjadi pusat perhatian global pada tahun 2020. Hingga saat ini, belum ada obat yang terbukti efektif untuk pengobatan atau pencegahan COVID-19. Kajian pengembangan inhibitor virus dilakukan dengan metode virtual screening dan simulasi molecular docking. Enam protein esensial yang berperan dalam perkembangan virus, seperti protein 3CL-Pro, PL-Pro, Helikase, Protein N, E, dan M digunakan sebagai protein target. Tujuan dari penelitian ini adalah untuk mendapatkan model interaksi ligan senyawa alam aktif terhadap protein reseptor yang dikode oleh genom SARS-CoV-2 dan energi ikat bebasnya sehingga dapat mengusulkan senyawa aktif dari produk alam yang berpotensi sebagai obat untuk COVID-19. Autodock Vina, Autodock 4.2, PSOVina, dan Amber20 digunakan dalam penelitian ini. Berdasarkan nilai energi ikat bebas dan interaksi protein-ligan, diperoleh kandidat senyawa dengan nilai terbaik untuk setiap protein target. Korilagin (-14,42 kkal/mol), Skutelarein 7-rutinosida (-13,2 kkal/mol), Genistein 7-O-glukuronida (- 10,52 kkal/mol), Basa Biflavonoid-flavon + 3O dan basa flavanon + 2O + 1MeO (- 11 ,88 dan -9,61 kkal/mol), dan Enoksolon (-6,96 kkal/mol) memiliki nilai energi bebas terbaik pada setiap protein target yang menunjukkan bahwa senyawa tersebut berpotensi sebagai inhibitor protein virus untuk diteliti lebih lanjut. Penelitian ini terbatas pada simulasi komputer, dimana hasil yang diperoleh masih berupa prediksi. Diperlukan penelitian lebih lanjut untuk menguji aktivitas ligan terpilih yang memiliki nilai energi bebas terendah dari keenam protein target. Pada uji stabilitas dengan simulasi dinamika molekul, kompleks 3CL-Pro – Korilagin merupakan kompleks yang paling stabil dibandingkan kompleks lainnya, sehingga korilagin merupakan senyawa yang paling direkomendasikan untuk diteliti lebih lanjut., Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19) which has become the center of global attention in 2020. To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on the development of inhibitors for this virus is carried out using virtual screening and molecular docking simulation methods. Six essential proteins that play a role in virus development, such as 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. The purpose of this study was to obtain a model of ligands interactions of active natural compounds against the receptor protein encoded by the SARS-CoV- 2 genome and their free binding energy so that it can propose active compounds from natural products that have potential as a drug for COVID-19.Autodock Vina, Autodock 4.2, PSOVina, and Amber20 were used in this study. Based on the value of free binding energy and protein-ligand interactions, the candidate compounds with the best value are obtained for each target protein. Corilagin (-14,42 kcal/mol), Scutellarein 7-rutinoside (-13,2 kcal/mol), Genistein 7-O-glucuronide (-10,52 kcal/mol), Biflavonoid-flavone base + 3O and flavanone base + 2O + 1MeO (-11,88 and -9,61 kcal/mol), and Enoxolone (-6,96 kcal/mol) has the best free energy value at each protein target indicating that the compound has the potential as a viral protein inhibitor for further investigation. This research is limited to computer simulations, where the results obtained are still a prediction. Further research is needed to test the selected ligand activity, which has the lowest
Keyword: covid-19, molecular docking, molecular dynamic, natural compound, sars-cov-2, virtual screening

Judul: Analysis of Active Compounds in Phyllanthus niruri L. as  potential inhibitors to SARS-CoV-2 3CLpro EPI_ISL_576383 with Molecular  Docking
Abstrak: Coronavirus disease 2019 (COVID- 19) merupakan penyakit yang disebabkan oleh infeksi virus corona SARS-CoV-2. Enzim 3-Chymotrypsin-Like Protease (3CLpro) berperan dalam siklus hidup SARS-CoV-2 sebagai enzim kunci dalam replikasi dan transkripsi virus. Penelitian ini bertujuan menganalisis interaksi molekuler senyawa aktif meniran terhadap reseptor 3CLpro dari SARS-CoV-2 asal Indonesia EPI_ISL_576383 dan menentukan senyawa aktif meniran sebagai inhibitor enzim 3CLpro SARS-CoV-2. Metode yang digunakan dalam penelitian ini yaitu penambatan molekuler menggunakan aplikasi YASARA Structure. Hasil penelitian menunjukkan dari 49 senyawa aktif meniran terdapat tujuh senyawa aktif yang memiliki afinitas pengikatan terhadap 3CLpro antara lain ellagic acid, lupeol, hinokinin, hypophyllanthin, methyl brevifolincarboxylate, quercetin dan niranthin. Senyawa aktif ellagic acid menjadi ligan terbaik dengan energi bebas ikatan (∆G) -4.296 kkal/mol yang berinteraksi dengan 13 residu asam amino. Hasil penelitian dapat digunakan sebagai acauan dalam studi in vitro dan in vivo terhadap enzim 3- Chymotrypsin-Like Protease (3CLpro) SARS-CoV-2., Coronavirus disease 2019 (COVID-19) is a disease caused by infection of coronavirus, SARS-CoV-2. The 3-Chymotrypsin-Like Protease (3CLpro) acts as a key enzyme in the replication and transcription of SARS-CoV-2 virus life cycle. This study aims to analyze the molecular interaction and determine the best ligand from the active compounds in Phyllanthus niruri L. against the 3CLpro receptor from Indonesian EPI_ISL_576383 in SARS-CoV-2 coronavirus. Molecular docking was conducted using YASARA Structure application. The results from 49 active compounds showed seven active compounds that exhibit affinity binding to 3CLpro, such as ellagic acid, lupeol, hinokinin, hypophyllanthin, methyl brevifolincarboxylate, quercetin and niranthin. Ellagic acid is determined as the best ligand out of all the active compounds with free energies of binding (∆G) - 4,296 kcal/mol and shown interaction with 13 amino acid residues. These results can be further used as a reference for in vitro and in vivo studies of SARS-CoV-2 3-Chymotrypsin-Like Protease (3CLpro).
Keyword: 3CLpro inhibitor, molecular docking, Phyllanthus niruri L

Judul: Etno-ornitologi Burung Kancilan Flores (Pachycephala nudigula nudigula Hartert 1897) pada Masyarakat Lio di Taman Nasional Kelimutu
Abstrak: Bare-throathed whistler is one of several wild birds in Kelimutu National Park (TNKL) that is believed to have correlation with Lio Community‟s belief. The estimation of Bare-throated whistler‟s population in Kelimutu National Park was about 186.41-1668.07 individual by the density about 0.0389-0.3481 ind/ha with the sex ratio 6.2:1 that spreaded on area with height of 1100 – 1600 masl. The characteristic of Bare-throated whistler‟s habitat is a natural forest with various canopy level, high plant species diversity and high density. The habitat characteristics related to the availability of food in the form of insects, cover, safety and a nesting site. Generally the most of Lio community knew the existence of Bare-throated whistler directly or from their parents‟ stories. The perceptions of Lio Community to the Bare-throated whistler‟s existence is generally support the conservation efforts. The perceptions construct the Lio Community‟s atitude that tend to be conservative to the existence of Bare-throated whistler. The attitude shown by their behavior that not cathing the Bare-throated whistler from the TNKL‟s area or the outside. The attitude have an important role to the existence of Bare-throated whistler in Kelimutu National Park‟s area.
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