2. Results and Discussion
Several proteins have been identified for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may serve as potential targets for chemotherapeutic intervention in coronavirus disease 2019 (COVID-19). These protein targets include SARS-CoV-2 main protease (SARS-CoV-2 Mpro), SARS-CoV-2 endoribonucleoase (SARS-CoV-2 Nsp15/NendoU), SARS-CoV-2 ADP−ribose−1″−phosphatase (SARS-CoV-2 ADRP), SARS-CoV-2 RNA-dependent RNA polymerase (SARS-CoV-2 RdRp), the binding domain of the SARS-CoV-2 spike protein (SARS-CoV-2 rS), and human angiotensin−converting enzyme (hACE2). There have already been several molecular docking studies on these macromolecular targets. Several groups have carried out molecular docking of natural product libraries with SARS-CoV-2 Mpro [102,103,104,105]. Additionally, commercially available drugs have also been examined using in silico methods [106,107].
A molecular docking study was carried out with 171 essential oil components with SARS-CoV-2 Mpro (PDB: 5R7Z, 5R80, 5R81, 5R82, 5R83, 5R84, 6LU7, 6M03, and 6Y84), SARS-CoV-2 Nsp15/NendoU (PDB: 6VWW, 6W01, and 6W02), SARS-CoV-2 rS (PDB: 6M0J, 6M17, 6VX1, and 6VW1), and SARS-CoV-2 RdRp (PDB: 6M71). The best docking scores are summarized in Table 3.
The main protease, SARS-CoV-2 Mpro, is a cysteine protease that is essential for processing the polyproteins that are translated from the coronavirus RNA [108]. The substrate binding site of the enzyme is a cleft flanked by Gln189, Met49, Pro168, Glu166 and His41; the active site is Cys145 and His41. The compound with the best normalized docking score to SARS-CoV-2 Mpro was the sesquiterpene hydrocarbon (E)-β-farnesene (DSnorm = −115.4 kJ/mol). Other essential oil components showing good docking scores with SARS-CoV-2 Mpro were (E,E)-α-farnesene (DSnorm = −115.0 kJ/mol), (E,E)-farnesol (DSnorm = −112.4 kJ/mol), and (E)-nerolidol (DSnorm = −110.7 kJ/mol). The sesquiterpene hydrocarbons (E,E)-α-farnesene and (E)-β-farnesene occupy the substrate binding site, flanked by Gln189, Arg188, Met165, His41, and Asp 187 (Figure 1). The lowest-energy docked poses of both (E,E)-farnesol and (E)-nerolidol showed hydrogen bonding of the alcohol moiety to Gln192 and Thr190 and, in the case of (E)-nerolidol, also with GLN189 and ARG188 (Figure 2).
Non-structural protein 15 (Nsp15) of SARS-CoV-2 is an endoribonuclease that preferentially cleaves RNA at uridylate. Furthermore, it has been shown that SARS-CoV Nsp15/NendoU is required for successful viral infection [109]. The best docking ligands for SARS-CoV Nsp15/NendoU are (E,E)-α-farnesene (DSnorm = −107.5 kJ/mol), (E)-β-farnesene (DSnorm = −105.0 kJ/mol), (E,E)-farnesol (DSnorm = −104.6 kJ/mol), and (E)-nerolidol (DSnorm = −101.6 kJ/mol). All of these sesquiterpenoids preferentially docked into a binding site formed by amino acid residues Gln347, Ile328, Val276, Ser274, Thr275, Ser329, Asn74, Asn75, Glu327, and Lys71 (Figure 3). In addition to van der Waals interactions, (E,E)-farnesol showed hydrogen-bonding interactions with Ser329 and Glu327, while (E)-nerolidol hydrogen bonded with Asn75 and Lys71 (Figure 3). Unfortunately, the docking scores for these ligands as well as the scores of the other essential oil components with this protein are too low for it to be considered a viable target (see Table 3).
ADP ribose phosphatase (ADRP) serves to convert ADP-ribose 1″-monophosphate (Appr-1″-p) to ADP-ribose (Appr), which serves to regulate virus replication [110]. This enzyme may be dispensable in SARS-CoV-2, however [111]. Nevertheless, (E,E)-farnesol showed the most exothermic docking to SARS-CoV-2 ADRP with DSnorm = −121.4 kJ/mol. The binding site in SARS-CoV-2 ADRP is surrounded by Phe132, Asn40, Ile131, Ala38, and Ala39, with hydrogen-bonded interactions between the ligand alcohol and Asn40 (Figure 4). Additional essential oil components with good docking scores with SARS-CoV-2 ADRP include the sesquiterpene hydrocarbons (E)-β-farnesene (DSnorm = −116.3 kJ/mol), (E,E)-α-farnesene (DSnorm = −114.2 kJ/mol), β-sesquiphellandrene (DSnorm = −115.7 kJ/mol), and α-zingiberene (DSnorm = −115.4 kJ/mol); the diterpenoids phytol (DSnorm = −118.9 kJ/mol) and phytone (DSnorm = −116.9 kJ/mol); and the phenylpropanoid eugenyl acetate (DSnorm = −115.4 kJ/mol). Not surprisingly, β-sesquiphellandrene and α-zingiberene adopted the same docking orientation in the binding site of the enzyme (Figure 5A). Similarly, phytol and phytone occupy the same location in the binding site (Figure 5B).
RNA-dependent RNA polymerase catalyzes RNA replication from an RNA template and is an essential enzyme in RNA viruses. Because these enzymes are crucial in viral replication, they are viable targets in antiviral chemotherapy [112]. Molecular docking of essential oil components with SARS-CoV-2 RdRp showed only weak docking with this enzyme target (Table 3). The ligand with the best docking score was (E,E)-farnesol, with DSnorm = −89.6 kJ/mol.
The SARS-CoV-2 spike protein serves to attach to angiotensin-converting enzyme 2 (ACE2) of the human cell to be invaded. The interface between SARS-CoV-2 rS and human ACE2 would be a promising target to prevent binding of SARS-CoV-2 rS to human ACE2 [113,114]. The best docking ligands with human ACE2, i.e., normalized docking scores < -100 kJ/mol (α-bulnesene, eremanthin, (E,E)-α-farnesene, (E)-β-farnesene, (E,E)-farnesol, (E)-nerolidol, β-sesquiphellandrene, and (Z)-spiroether), all show docking preference to a cavity removed from the interaction interface between the SARS-CoV-2 spike protein and ACE2 (Figure 6). This cavity is a pocket surrounded by residues Pro565, Leu95, Val209, Asn210, Leu91, Lys94, Glu208, and Glu564. Because of the remote location of docking with ACE2, it is predicted that interaction of essential oil components with ACE2 will not prevent protein–protein interaction between the SARS-CoV-2 spike protein and human ACE2.
On the other hand, the lowest energy poses of essential oil components showing the strongest docking (<−80 kJ/mol; (E)-cinnamyl acetate, eremanthin, (E,E)-α-farnesene, (E)-β-farnesene, (E,E)-farnesol, and geranyl formate) with the binding domain of the SARS-CoV-2 spike protein do lie at the interface between the SARS-CoV-2 spike protein and human ACE2 (Figure 6). This docking site is a hydrophobic pocket formed by Tyr505, Tyr495, Asn501, Arg403, Tyr453, and Gly502. Unfortunately, the docking energies at this site are too weak and are unlikely, therefore, to disrupt binding between SARS-CoV-2 rS and human ACE2.
In order to compare docking scores of the essential oil components with other proteins, docking was also carried out with six randomly selected non-virus proteins: Bovine odorant binding protein (BtOBP, PDB: 1GT3), cruzain (PDB: 1ME3), torpedo acetylcholinesterase (TcAChE, PDB: 6G1U), Bacillus anthracis nicotinate mononucleotide adenylytransferase (BaNadD, PDB: 3HFJ), Russell’s viper phospholipase A2 (DrPLA2, PDB: 1FV0), and Escherichia coli l-aspartate aminotransferase (EcAspTA, PDB: 2Q7W). Docking scores for these proteins are summarized in Table 4.
The docking results of the essential oil components with the six randomly selected proteins indicate the best docking ligands to SARS-CoV-2 targets (i.e., (E,E)-α-farnesene, (E)-β-farnesene, and (E,E)-farnesol) have better docking energies with other proteins. These three sesquiterpenes have docking energies of −129.8, −122.7, and −133.0 kJ/mol with TcAChE, respectively, and −131.8, −131.8, and −135.6 kJ/mol, respectively, with BaNadD. Indeed, most of the essential oil ligands have better docking properties with one or more of the random proteins compared to the SARS-CoV-2 proteins.
Based on the docking energies of essential oil components with key protein targets of SARS-CoV-2, the individual essential oil components cannot be considered viable chemotherapeutic agents for interaction with the SARS-CoV-2 target proteins. However, essential oils are complex mixtures of compounds and several essential oil components may act synergistically to inhibit the virus. Astani and co-workers have shown, for example, that the antiviral activity (HSV-1) of Eucalyptus oil is much greater than the major component 1,8-cineole, and that tea tree oil has a greater antiviral activity than its components terpinen-4-ol, γ-terpinene, and α-terpinene [52].
Synergistic effects have also been observed between essential oils and synthetic antiviral agents. Civitelli and co-workers observed an antiviral synergism between Mentha suaveolens essential oil and acyclovir on HSV-1 [64]. Likewise, Melissa officinalis essential oil potentiated the activity of oseltamivir against avian influenza virus H9N2 [115]. Furthermore, essential oils are lipophilic and therefore may also serve to disintegrate viral membranes [116].
Outside of antiviral activity, there may be some relief of symptoms of COVID-19 provided by essential oils. For example, linalool [117,118], β-caryophyllene [119,120], and 1,8-cineole [121,122] have both anti-inflammatory and antinociceptive activity; menthol [123,124], camphor [125,126], and thymol [127] have antitussive activities.