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.
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.
Sorghum [Sorghum bicolor (L.) Moench] is a multipurpose food crop that can adapt to climate change. Sorghum productivity can be increased by applying chemical fertilizers and arbuscular mycorrhiza fungi (AMF). This research aimed to assess the effect of AMF application and N and P concentration gradients to support Super 2 and KS sorghum accession growth. The plants were grown in a sterilized zeolite (coarse and fine) and inoculated with Glomus mosseae 40 spores per pot. The experimental design was a randomized complete block design with 40 treatments and three replications. N and P concentration gradient treatments were carried out using a dose level of fertilizer N (urea) and P (TSP) at 12,5%; 50%; 75%; 100%; and 125%. Analysis of variance was carried out using SAS 9.0 software at a level of 5%, and the results were significantly different, followed by DMRT. The application of AMF and urea 50% and TSP 75% in Super 2 accessions and urea 50% and TSP 50% in KS accessions gave the highest plant height and biomass. However, the increase in sorghum growth did not correlate with root colonization and root length, which could be seen that the highest in both accessions were obtained at urea 12,5% and TSP 12,5%. The application of AMF can significantly lower the use of urea and TSP fertilizers by up to 50% compared to a positive control (urea and TSP 100%) and support sorghum growth in both accessions. Keywords: Glomus mosseae, Konawe Selatan accession, Super 2 accession, TSP, urea
The majority of carbohydrates found in edible mushroom are in the form of polysaccharides, specifically beta-glucans. These beta-glucans have been reported as anticancer, antioxidant, and immunomodulator. This study aimed to investigate the potential of P. pulmonarius as functional food by comparing the carbohidrate content (total carbohydrate, beta-glucans, and reducing sugars) in P. pulmonarius extracted using microwave assisted extraction (MAE) at different temperatures: 60oC, 80oC and 100oC. Moreover, active compound screening was also conducted. MAE was chosen as the extraction method due to its short extraction time. The phenol-sulfiric acid method was used to measure total carbohydrates, while beta-glucan content was measured using the Megazyme Beta-Glucan Kit. Reducing sugar content was measured using the DNS (3,5-Di Nitro Salisilic Acid) and active compound screening was performed by qualitative method. The results showed that the highest total carbohydrates and beta-glucans were obtained at 60oC (75,089±0,012 mg/mL and 32,356±0,006% w/w respectively) while the highest reducing sugar content was obtained at 80oC (0,216±0,009 mg/mL). Active compound screening revealed the presence of flavonoids, saponins, and triterpenoids in each sample. These findings suggest that P. pulmonarius has potential as functional food since the rich content of beta-glucans and active compounds. The use of MAE at 60oC is more effective to extract P. pulmonarius compared with 80oC and 100oC.
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