1. Study compound The nine compounds tested are β-Sitosterol, Quercetin, Catechin, Lupeol, Rutin, Kaempferol, Gallic acid, Piperitone, and Limonene. They were isolated from three Djiboutian medicinal plants: Acacia seyal, Cymbopogon commutatus, and Indigofera caerulea. The extractions and isolations of these compounds are described in our previous publications (Elmi et al. 2018; Elmi 2018; Elmi et al. 2020). Two drugs against covid are used for comparison: Remdesivir and Hydrochloroquine.
2.1. Proteins and Chemical Compounds Studied In This Investigation Three proteins were selected for the purpose of this study; 1.SARS-CoV-2 main protease (PDB ID: 5R84) (Fearon et al. 2020), 2.Human furin protease (PDB ID:5MIM), and 3.SARS-CoV-2 receptor-binding domain (PDB ID: 6VW1)(Shang et al. 2020). Nine compounds were also selected; 1.β-Sitosterol (PubChem CID 222284), 2.Quercetin (PubChem CID 5280343), 3.Catechin (PubChem CID 9064), 4.Lupeol (PubChem CID 259846), 5.Rutin (PubChem CID 5280805), 6.Kaempferol (PubChem CID 5280863), 7.Gallic acid (PubChem CID 370), 8.piperitone (PubChem CID 6987), 9.Limonene (PubChem CID 22311), along with two reference drugs remdesivir (PubChem CID 121304016), and hydroxychloroquine (PubChem CID 3652).
2.2. Molecular Docking: Preparation of Ligand The chemical structures of eleven selected compounds were obtained from PubChem an online repository of chemical compounds (https://pubchem.ncbi.nlm.nih.gov/). The structures were obtained in 2D SDF format. A bioinformatics tool called LigPrep was used to perform ligand preparation. LigPrep is set in Schrödinger suite-Maestro (v 11.1). The following parameters were taken into consideration during this job: the structure was set as a project table, the force field was set at OPLS3, the target pH was 7.0 ± 2.0 using Epik and the output format was Maestro.
2.3. Molecular Docking: Preparation of Protein The desire proteins were taken from Protein Data Bank (PDB) an online database (https://www.rcsb.org/). The three-dimensional protein structures were downloaded in pdb format (Berman et al. 2002). The Resolution was 1.83 Å, 1.9 Å, and 2.68 Å of selected proteins with PDB ID: 5R84, 5MIM, and 5R84 respectively. Preprocessing, optimization, and minimization were done by using the Protein Preparation Wizard for preparing the proteins (Friesner et al. 2004). This wizard is also included in Schrödinger suite-Maestro (v 11.1). The following parameters were used in this job; the structures were optimized at pH 7.0, remove waters with less than 3 H-bond to non-waters, and minimized the proteins using OPLS3 force field. Then generate the receptor grid by using PockDrug an online tool for selecting the best docking site.
2.4. Molecular Docking: Glide Molecular Docking The molecular docking was performed to understand the possible mechanism of the selected compound comparing with two reference drugs against the receptors associate with COVID19 and human. The docking was completed by using the Ligand Docking tool attaches in Schrödinger suite-Maestro (v 11.1). Then the spreadsheet and 2d interaction figures were collected for further study. Discovery Studio (v 4.1) software was used for more understanding via 3d visualization (Discovery Studio 2008).
2.5. Prediction of the Pharmacokinetic Parameter (ADME) Several pharmacokinetic properties such as absorption, distribution, metabolism, excretion (ADME) are important to developing a drug. The following properties are investigated by SwissADME an online tool to determine various biochemical properties (http://www.swissadme.ch/). Some parameters were determined for evaluating the compounds from the SwissADME database based on Lipinski’s and Veber’s Rules. The following parameters were molecular weight, hydrogen bond acceptor, hydrogen bond donor, log P value, Lipinski’s Violations value, number of the rotatable bond (NRB), and topological polar surface area (TPSA).
2.6. Prediction of Toxicological Properties Toxicological determination is the most prime considerations in case of the development of new drugs. An online bioinformatics tool named AdmetSAR was used to evaluate the toxicological properties of desired compounds. The following parameters were counted in this study such as rat acute toxicity, acute oral toxicity, ames toxicity, and carcinogenic properties.