COVID-19, caused by SARS-CoV-2, has become a massive worldwide concern of the 21st century. One potential strategy to block the biochemical pathway of SARS-CoV-2 was by inhibiting the main protease (Mpro), which is a key enzyme on viral replication. Black seed (Nigella sativa L.) has a long history for its use as a traditional medicine. Therefore, we hypothesised that the black seed contains numerous active compounds that could potentially confer inhibitory activity against SARS-CoV-2 viral Mpro. In this study, 24 active compounds from black seed were tested. Compounds were screened using Lipinski's Rules and admetSAR, then docked to viral Mpro 7BQY by AutoDockTools-1.5.6 and AutoDock Vina using a site directed docking approach resulting in affinity energy (∆G) and binding data. We found that the most potential active compound of N. sativa is 3-[(4-Methylphenyl)sulfanyl]-1,3-diphenyl-1-propanone, since its affinity energy was -7.6 kCal.mol-1. Its similarity to N3 inhibitor based on Ligplot analysis and DS were 86.7% and 76.19%, respectively, and the occupancy on binding site based on Ligplot analysis and DS were 90.91% and 81.82%, respectively. These findings can be used as a starting point for further investigation using in vitro and in vivo studies.
Elfirta RR, Falah S, Andrianto D, Lastini T. 2018. Identification of active compounds and antifungal activity of Toona sinensisleaves fractions against wood rot fungi. Biodiversitas 19: 1313-1318. Inhibitory activities of surian or toon (Toona sinensis) leavesfraction origin Sumedang, West Java, Indonesia against wood rot fungi (Ganoderma boninense IPBCC 10.658, Trametes versicolorInaCC F200, and Phanerochaete chrysosporium IPBCC 93.259) were studied. The samples were macerated using methanol andacetone. The results of brine shrimp lethality test (BSLT) showed that the methanol extract had the highest cytotoxicity of LC50 at 29.76μg/mL and inhibit the growth of G. boninense (27.78%), T. versicolor (79.26%) and P. chrysosporium (81.11%). The methanol extractwas then subsequently fractionated using n-hexane, diethyl ether, and ethyl acetate respectively. The diethyl ether fraction was found tohave the highest inhibitory activity against T. versicolor (46.30%) and P. chrysosporium (81.11%). This fraction was further separatedusing column chromatography and analyzed using thin layer chromatography (TLC), which gave six fractions. Antifungal test exhibitedthat fraction 5 had the highest antifungal properties against T. versicolor (74.07%) and P. chrysosporium (80.37%). Inhibition of P.chrysosporium resulted in abnormal growth of hyphae morphology as indicated by changes in its growth direction and excessive hyphaebranching. Additionally, the results of LC-MS/MS experiment indicated toon leaves fraction 5 which contains N-[2- (DGlucopyranosyloxy)ethyl]-2-hydroxy-N-[2hydroxy3 (octadecyloxy) propyl] butanamide dan Brucine compounds that were regarded as theantifungal compounds.
The food stuffs can be clasified as functional food since the foods can improve the human health. One of them are the food stuffs which have function as antioxidant and antibacterial. These activities were studied on crude polysaccharides from Auricularia auricula. The sample was subsequently isolated using hot water and 1 M NaOH to obtain water and alkali soluble of crude polysaccharides. The antioxidant activity was evaluated using β-caroten-linoleat assay. The results showed that the alkali soluble of crude polysaccharides had the highest antioxidant activity (85.82%) at 350 μg/ml. The water and alkali soluble of crude polysaccharides from A.auricula were evaluated for their antibacterial activity using disc diffusion method. The alkali soluble of crude polysaccharides was found to have the highest antibacterial activity at 100 mg/ml against Staphylococcus aureus InaCC B4 and Escherichia coli InaCC B5 with clear zone values of 3.18 mm and 5.10 mm, respectively. The findings indicated that the alkali soluble of crude polysaccharides from A. auricula could potentially be used in part of well-balanced diets and could be considered as a potential source of natural antioxidant and antibacterial products.
SARS-CoV-2 has caused a global COVID-19 pandemic since late 2019 and the reported cases have not ended until now. One way to overcome the Covid-19 pandemic is to find the main viral protease inhibitor (Mpro) SARS-CoV-2 which is a key enzyme of virus replication. Honey is a bee-derived product that contains various phenolic compounds and has antiviral activity. This study aimed to find candidate Mpro SARS-CoV-2 inhibitors from honey phenolic compounds using molecular docking simulations in a directed manner. A total of 27 test ligands (from honey’s phenolic compounds), 4 comparison ligands (from synthetic antiviral compounds), and reference ligands (N3 compound) were screened for their character as drug compounds by Lipinski’s rules and for their toxicity by admetSAR. All ligands were docked to the Mpro SARS-CoV-2 receptor code 7BQY using AutoDock Tools 1.5.6 and Autodock Vina with center of coordinates: X = 10,398; Y = -1,254; Z = 23.473 and grid size: X = 40; Y = 46; Z = 40. Molecular docking simulation produces affinity energy and molecular interactions data. The results showed that the best candidate for Mpro SARS-CoV-2 inhibitor from honey’s phenolic compounds was genistein because it complied with all Lipinski rules, was non-toxigenic, not a carcinogen, had an affinity energy of -7.6 kCal/mol, 80% similarity to the reference ligand N3, and occupies 63,64% of the tethercoverage area. The results of this study are expected to be used in further research, both in vitro and in vivo. Abstrak SARS-CoV-2 menyebabkan pandemi COVID-19 secara global sejak akhir 2019 dan kasusnya dilaporkan belum berakhir sampai saat ini. Salah satu cara untuk mengatasi pandemi COVID-19 diantaranya dengan menemukan inhibitor main viral protease (Mpro) SARS-CoV-2 yang merupakan enzim kunci pada replikasi virus. Madu merupakan produk turunan lebah yang mengandung berbagai senyawa fenolik dan memiliki aktivitas antivirus. Penelitian ini bertujuan untuk menemukan kandidat inhibitor Mpro SARS-CoV-2 dari senyawa fenolik madu menggunakan simulasi penambatan molekuler secara terarah. Sebanyak 27 ligan uji (dari senyawa fenolik madu), 4 ligan pembanding (dari senyawa antiviral sintetik), dan ligan acuan (senyawa N3) diskrining karakternya sebagai senyawa obat dengan aturan Lipinski dan toksisitasnya dengan admetSAR. Semua ligan ditambatkan ke reseptor Mpro SARS-CoV-2 kode 7BQY menggunakan AutoDock Tools 1.5.6 dan Autodock Vina dengan pusat koordinat: X= 10,398; Y= -1,254; Z= 23,473 dan ukuran kisi: X= 40; Y= 46; Z= 40. Simulasi penambatan molekuler menghasilkan data energi afinitas dan interaksi molekuler. Hasil penelitian menunjukkan kandidat inhibitor Mpro SARSCoV-2 terbaik dari senyawa fenolik madu adalah genistein karena memenuhi semua aturan Lipinski, tidak toksik, bukan karsinogen, memiliki energi afinitas -7,6 kKal/mol, kemiripan 80% dengan ligan acuan N3, dan menempati 63,64% area cakupan penambatan. Hasil penelitian ini diharapkan dapat digunakan dalam penelitian selanjutnya, baik secara in vitro maupun in vivo.
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