Molecular Docking Studies : Activity of Natural Compounds as SAR-CoV-2 Inhibitors in Papain-like protease (PL pro)

SARS-CoV-2 is a respiratory virus often referred to as COVID-19.   The challenge of finding SARS-CoV-2 antivirals also attracted many researchers, one of which was by utilizing natural compounds. The purpose of this study was to analyze the potential activity of herbal plants in Indonesia as anti-COVID-19, specifically tasked with inhibiting the target protein, PLpro using the in-silico method. This research is an insilico approach with molecular docking studies. Docking simulation in this study was used to analyze the activity of natural herbal plant compounds against the target protein, namely PLpro. In addition, the docking method is also able to examine the interaction of compounds contained in plants with target receptors seen from a computational-based visual approach. So, the results obtained in this study are that when viewed from the value of the gibbs energy produced, the compound that has the best activity to inhibit the PLpro target protein (SARS CoV-2) is Luteolin. The Gibbs energy generated in the Luteolin docking simulation is -7.3 kcal/mol. The Gibbs energy value produced by the Luteolin ligand is the most negative or the smallest value of the 14 tested ligands. This means that the bond formed between the Papain-like protease (PLpro) protein and the Luteolin ligand is the most stable among the others. In addition to the Luteonin compound, there are also several compounds that have quite good potential when viewed from the amount of gibbs energy owned, namely Mangostin, quercetin compounds and Myricetin compounds with gibbs energy values of -7.1 kcal / mol, -7.0 kcal / mol and -7.0 kcal / mol. Based on these results, it can be concluded that several compounds from typical Indonesian plants such as Luteolin compounds (Compounds found in Celery plants (Apium graveolens)), Mangostin compounds (Compounds found in Mangosteen plants (Garcinia mangostana)), Quercetin compounds (Compounds found in Citrus plants (Citrus aurantium)) and Myricetin compounds (Compounds found in Clove plants (Syzygium aromaticum)) have the potential to be developed as anti-COVID-19

The Effect of Calcination Time Variation on CaO Synthesa from Limestone

Abstract – Catalysts are needed in a chemical reaction. With a catalyst it will accelerate the rate of chemical reactions. This saves time and money compared to chemical reactions without a catalyst. Catalysts are classified into two types, namely homogeneous and heterogeneous catalysts. CaO is a compound classified as a heterogeneous catalyst. Limestone has the potential as a base for the synthesis of CaO compounds. There are 3 stages in the synthesis of CaO compounds. The first stage is the preparation of limestone. The second stage is limestone calcination with temperature variations. The third stage is the characterization of CaO using XRD. The result of CaO synthesis is that the compound formed from calcination for 6 hours and 10 hours in limestone is a CaO compound. This is indicated by the appearance of peaks on the graph that match the reference to the CaO compound in the database. From the COD database, information was obtained that the CaO compound formed was a CaO compound with a crystalline phase. The crystalline system formed is cubic. The space group for the CaO compound formed is Fm-3m. There was no significant difference in the XRD results of the 6 hours and 10 hours calcinations, the only difference was the variation in the intensity of the peaks formed. So it can be concluded that calcination at a temperature of 1000oC for 6 hours and 10 hours produces CaO crystals with a crystalline phase. Keywords – limestone, CaO, calsination, synthesis

Anti-Malarial Activity in Plasmepsin II Inhibitors Using Molecular Docking

Abstract – The biggest challenge for indonesians is finding more efficient malaria drugs to overcome malaria by utilizing indonesian medicinal plants. Nowadays, increased computing capabilities are the solution to finding new drugs that use the insilico approach. In this study will be conducted an analysis of antimalarial activity between plasmepsin II receptors and ligands that act as inhibitors through the method of study in silico. The ligands used are derived from the filtering of the Chemical Database namely Cyanidin 3,5-di-(6- malonylglucoside); Isoscutellarein 4'methyl ether 8-(6"-n-butylglucuronide); Cyanidin 3-(6"-malonylglucoside)- 5-glucoside; Delphinidin 3-(2-rhamnosyl-6-malonylglucoside); Cyanidin 3-[6-(6-sinapylglucosyl)-2-xylosylgalactoside; and Delphinidin 3-(6- malonylglucoside)- 3',5'-di-(6-p coumaroylglucoside). This research method is divided into three stages. The first is the preparatory stage, at this stage the downloaded plasmepsin II receptors are then prepared using Pymol software. The second stage is docking simulation. The software used in doing this simulation is autodock vina software. The third stage is the Analysis stage. The docking simulation results were then analyzed using Pymol and VMD software to see the activity resulting from docking simulations performed between receptors and ligands. The results of the study are among the six ligandssimulated in plasmepsin II receptors then the six ligands are stable if used as candidates for new drugs, this is because the free energy produced from docking is low and negative value. This means that the reaction that occurs is a spontaneous reaction. The free energy value between the six ligands is the difference between the smallest and the largest not too far in the range of only about -2 kcal/mol. This means the six could be used as drug candidates. Keywords – Malaria, Docking, Drug, Plasmepsin II, Ligand

Manufacture And Characterization Of Hydroxyapatite From Quail Eggshell Using Precipitation Methods

Abstract— Hydroxyapatite (HA) is a biomaterial used to treat bone defects. The utilization of HA in medicine is currently significantly increased this is because HA has high biocompatibility properties when used as a bone graft. Various kinds of bone grafts from HA are currently available in the market. However, its use is often bumped at a high price and is an imported product. This will ultimately increase the burden of financing that must be borne by hospitals and the government. HA sources can be obtained through extraction from natural products, such as eggshells. The purpose of this study was the creation and characterization of hydroxyapatite from quail egg shells using precipitation methods. The research stage consists of 4 stages, Stage 1 is the calcination of quail egg shells so that CaO compounds are obtained. Stage 2 is the synthesis of HA compounds from CaO compounds produced in the previous stage using wet precipitation or deposition methods. Stage 3 is sintering HA compounds produced in the previous stage using a furnace for five hours at a temperature of 900 oC. Stage 4 is the characterization of the HA compounds produced. The characterization is done using XRD and SEM. Hasil yang diperoleh yaitu Efisiensi dari senyawa HA yang dihasilkan sebesar 52,34%. Based on the characterization carried out using XRD it was obtained that the HA compound was successfully synthesized this is characterized by the peak of the quail eggshell difaktogram that is the same as the peak of the standard HA difractogram which is found at an angle of 2θ: 26.00oC, 31.90oC, 32.31oC, 33.02oC, 34.19oC, 46.81oC, 49.59oC with the crystal phase and the size of the lattice parameters, namely the lattice a = b = 9.4234 Å and c = 6.8801 Å. But in addition to the peak of HA there are also other peaks that show the existence of the impurities phase at 2θ : 10.01°, 21.85°, and 53.01°. Based on SEM characterization found that the size of the resulting HA particles is not homogeneous, meaning that there is a difference in the smallest particles with a size of 1,497 μm and there are the largest particles with a size of 60.98 μm. If observed the shape of a single particle tends to be round (Shperical). Thus it was concluded that the manufacture and characterization of hydroxyapatite from quail egg shells using precipitation methods has been successfully carried out. Keywords— hydroxyapatite; quail egg shell; precipitation; bone defect

Molecular Docking Studies of Potential Multifloroside and Trimyristin as Inhibitor for Anti Malaria

This study aims to analyze the potential of Multifloroside and Trimyristin as inhibitors of plasmepsin compounds as anti-malaria. The method used in analyzing the potential of Multifloroside and Trimyristin ligands as antimalarials is by insilico approach through tethering using Autodock Vina. Based on the free energy parameters of the Multifloroside molecular tethering, a value of -9.0 was obtained and for the Trimyristin molecule a value of -6.4 was obtained with 5 replications each. The free energy value of Multifloroside and Trimyristin ligands is negative, this means that Multifloroside and Trimyristin ligands are stable for use as Plasmepsin inhibitors. Because the lower the free energy of a molecule, the more stable the molecule is. But if you see the most potential between Multifloroside and Trimyristin, Multifloroside is better than Trimyristin ligands. Analysis based on hydrogen bonding parameters contained 1 hydrogen bond each showed that the stronger the Multifloroside and Trimyristin inhibitors bind to the receptors. For the Multifloroside ligand, the hydrogen bond formed is UNK-H ligand, whereas for Trimyristin ligand, the hydrogen bond formed is SER218-HN residue. The small number of hydrogen bonds does not affect the stability of the ligand and receptor bonds