3.3. Molecular Docking
Each ligand structure was prepared using Spartan ’18 v. 1.4.4 (Wavefunction, Inc., Irvine, CA, USA). The lowest-energy conformations of the ligands were determined and used as starting structures in the molecular docking. This is particularly important to include all potential conformations in medium-sized rings where interconversion between conformations may be hindered (e.g., bicyclogermacrene, costunolide, curdione, germacrene D, germacrone, and α-humulene). A total of six protein targets of SARS-CoV-2 from the Protein Data Bank (PDB), represented by a total of 17 structures, were used in the molecular docking, including SARS-CoV-2 main protease (PDB: 5R7Z, 5R80, 5R81, 5R82, 5R83, 5R84, 6LU7, 6M03, and 6Y84), SARS-CoV-2 endoribonuclease (PDB: 6VWW), SARS-CoV-2 ADP ribose phosphatase (PDB: 6W01 and 6W02), SARS-CoV-2 RNA-dependent RNA polymerase (PDB: 6M71), SARS-CoV-2 spike protein binding domain (PDB: 6M0J, 6VX1, 6VW1, and 6M17), and the human angiotensin-converting enzyme (PDB: 6M0J, 6VX1, 6VW1, and 6M17). Molecular docking was carried out using Molegro Virtual Docker v. 6.0.1 (Aarhus, Denmark) as previously reported [128,129]. Briefly, a 15-Å radius sphere centered on the binding sites of each protein structure in order to permit each ligand to search. In the case of the spike protein and human ACE2, the docking sphere was located at the interface between the spike protein and ACE2. In one case, ACE2 was removed and docking was carried out with the spike protein, and in the other case, the spike protein was removed and docking was carried out with ACE2. Standard protonation states of each protein, based on neutral pH, were used, and charges were assigned based on standard templates as part of the Molegro Virtual Docker program. Each protein was used as a rigid model without protein relaxation. Flexible-ligand models were used in the docking optimizations. Different orientations of the ligands were searched and ranked based on their “rerank” energy scores. A minimum of 100 runs for each ligand was carried out. In analyzing the docking scores, we accounted for the recognized bias due to molecular weight [130,131,132] using the scheme: DSnorm = 7.2 × Edock/MW⅓, where DSnorm is the normalized docking score, Edock is the MolDock re-rank score, MW is the molecular weight, and 7.2 is a scaling constant to ensure the average DSnorm values are comparable to those of Edock [128]. The best docking results are summarized in Table 1.