Molecular modeling of spike glycoprotein
Fig. 2 shows the conformational structure of the models obtained by molecular modeling. The 6VXX-fill model is seen in the down conformation, and the up conformation is seen in the 6VYB- fill model.
Molecular docking and drug selection
Once the molecular docking was performed, the drugs with the highest affinity for the spike protein (mainly with amino acids belonging to the hinge site, the RBM and the FP) were selected. The drugs are listed in tables.The tables show the drug name, database Zinc identification number, use according to currently described pharmacological action, FDA approval number, inclusion in clinical studies related to COVID-19, affinity in kcal/mol (from highest to lowest affinity) and amino acid interactions from spike glycoprotein are indicated. The general scheme shows the possible sites of interaction (Fig.1).
Docking simulations on the hinge site
Docking simulations were performed on hinge sites (1 and 2), however only drug interactions were found at hinge site 1 (see table 1 and table 2). The affinity binding scores and molecular interactions of the drugs for down conformation are detailed in the Table1.
Fig. 3A shows Varenicline which binds to chain B and C in the hinge site 1, RBM and NTD with an affinity of -7. 6 kcal/mol in down conformation, interacting by Van der Waals forces (Pro230C, Lys458B and Arg466B), π-interactions (Ile231C and Tyr200C), alkyl Interactions (Trp353B and Arg355B), π-cation interactions (Asp467B and Arg355B) and finally forming hydrogen bonds (Gly232C, Glu465B, Asp198C and Gly199C).In addition Fig. 3B shows that Docosahexaenoic acid interacts by Van der Waals forces with the amino acids Pro230B, Val227B, His207B, Asp228B, Leu229B, Phe168B, Tyr170B, Ile128B, Ile203B, Phe194B, Ile119B, Phe192B, Trp104B and Asn121B, by an electrostatic interaction and a hydrogen bonds with Arg357B, and finally alkl interactions with Leu179B and Val126B. Other interesting drug was sulbactam (Fig. 3C) which interacts with in the hinge 1 site, the RBM and the NTD by Van der Waals forces with the amino acid Asp198C, Pro426B, Leu518B, Glu516B, Phe515B, Tyr396B and Ser514B, and two hydrogen bonds with the amino acids Arg466B and Arg355B.
The table 2 shows compounds that interact mainly with amino acids belonging to the hinge site 1, the RBM site and the NTD of the up conformation. In Fig. 4A and table 2 is show that Accolate binds to chain A and hinge 1 site (-10.3 kcal/mol) in the up conformation. Accolate make Van der Waals interactions (Phe168B, Arg357A, Ile128B, Leu176B, Ile119B, Asn121B, Arg102B, Phe175B, Phe192B, Ser172B and Gln173B), hydrogen bonds (Pro174B, Asp228B and Val227B), π-π interactions (Tyr170B), π-sigma interactions (Leu226B) and alkyl interactions (Pro174B, Leu226B, Val126B, Met177B and Pro230B). Tigecycline (Fig. 4B) joins the A-chain at the hinge 1 site with an affinity of -9.7 kcal/mol in the up conformation. The drug interacts through Van der Waals forces with the amino acids Glu516A, Tyr200B, Arg357A, Pro426A and Gly232B, hydrogen bonds with Pro230B, Gly199B, Ile231B, Phe429A, Phe515A, Thr430A, Phe464A and Asp198B, and π-π interactions with Tyr396A and π-Cation with Arg355A.
Docking simulations on the RBM
Table 3 and 4 show the drugs selected for the RBM in the down and up conformation, respectively.
The drug the highest binding score for the RBM site in down conformation is Naldemedine. Which (Fig. 5A) interacts by Van der Waals forces with Gln493C, NAG1303A, Leu492C, Gly476C, Ala475C, Tyr473C, Asp467C, Asp420C, Glu465C, Tyr453C, Phe456C and Arg457C; makes hydrogen bonds with Arg454C, Leu455C and Tyr421C; alkyl interactions with Pro491C and Lys458C and π-cation interactions with Lys417C and Arg454C. The second drug that showed the highest affinity was Conivaptan (Fig. 5B) which interacts in the chain C at RBM region by Van der Waals forces (Pro491C, Gln493C, Tyr453C, Lys458C, Ile472C, Asn422C and Asp420C), hydrogen bonds (Phe456C, Arg457C and Tyr421C) and π interactions (Asp467C, Leu455C, Lys417C and Tyr421C).
Regarding the up conformation the Fig. 6A shows that Tedizolid Phosphate binds to chain B in the RBM displays an affinity of -9.7 kcal/mol. The drug interacts through Van der Waals forces (Asp405, Gly416B, Ile402B, Ile418B, Gln493B, Ser494B, Tyr495B, Leu452B, Tyr451B and Tyr453B), π-cation interactions (Arg408B and Lys417B) and also forms hydrogen bonds with (Gln409B, Gln414B, Lys417B and Arg403B). The drug Atovaquone (Fig. 6B) binds to the B chain in the RBM interacting through Van der Waals forces (Leu455B, Ser494B, Ala352B, Asp467B, Phe456B, Asn450B, Pro491B, Thr478B, Gly476B and Ser477B), π-π interactions (Tyr351B), hydrophobic interactions (Leu492B and Leu452B) and hydrogen bonds (Arg454B and Pro479). This drug showed the second highest binding affinity as can be seen in Table 4.
Regarding the drug Cefotetan, although it did not show one of the highest affinities, this drug is the one that interacts with the most crucial amino acids for the formation of the spike-ACE2 complex. The drug Cefotetan (Fig. 6C) is bound in the up conformation by Van der Waals forces (Ser349B, Tyr489B, Leu455B, Pro491B, Gly476B, Ser477B, Phe490B, Gln493B, Leu492B, Tyr351B, Tyr449B and Asp467B), forms hydrogen bonds (Tyr449B, Asn450B, Arg454B and Thr478B), alkyl interactions (Pro479B and Leu452B) and π-sulfur interactions (Phe456B and Tyr449B).
Docking simulations on the FP
The drugs which displayed the highest affinity for the fusion peptide in both the down and up conformation are summarized in tables 5 and 6 respectively. Results from the docking analyses are ordered from highest to lowest affinity. Some representative drug interactions are described below.
The drug Saquinavir (Table 5 and Fig. 7A) shows the highest affinity to the FP site (-11. 1 kcal/mol), binding to the amino acids Cys851A and Leu849A in the down conformation. Saquinavir interacts through Van der Waals forces (Lys835A, Cys851A, Ala852A, Leu828A, Gly832A, Ile834A, Pro862A, Pro863A, Lys854A, Arg646C, Ile850A, Glu619C, Ser591C and NAG1309C), forms hydrogen bonds (Asp843A, Tyr837A, Asp614C, Asn616C, Val615C, Gln644C, Gly648C and Thr645C), π-Alkyl Interactions (Val860A and Tyr837A), π-Sigma Interactions (Leu849A) and π-Cation Interactions with (Tyr837A). While the drug Difluprednate showed less affinity to the same site (-8.9 Kcal/mol) (Table 5 and Fig. 7B) and in the down conformation, with Van der Waals interactions in amino acids Ala829A, Leu849A, Lys835A, Ala852A, Gly832A, Ile834A, Val860A, Asp614C, Ala668C, Thr866A, Ala647C and Cys840C, forms hydrogen bonds with amino acids Phe833A and Arg646C, halogen interactions with Ile850A and finally π-Alkyl interactions (Cys851A, Leu828A and Tyr837A).
Additionally Saquinavir (table 6 and Fig. 8A) show the highest affinity in the up conformation. Saquinavir interacts by Van der Waals forces (Asn856C, Asn960C, Gln853C, Leu858C, Ala852C, Thr859C, Asp614B Leu959C, Thr732C, Phe833C, Val952C, Asn955C, Ile834C, Gly832C, Ala831C, Arg646B, Leu849C, Gln836C, Ala570B and Tyr837C), forming hydrogen bonds with the following residues Arg847C, Asp848C anThr732C; alkyl interactions (Lys854C, Val860C, Ala956C, Lys835C and Cys851C) and π-sulfur interactions (Cys851C and Cys840C). Other drug that reach the up conformation was Maraviroc (Fig. 8B) which interacts through Van der Waals forces with the amino acids Val952C, Asn955C, Leu959C, Thr732C, Leu858C, Ala570B, Asn856C, Val860C, Asp848C, Arg847C, Tyr837C and Gln836C through Van der Waals forces, forming hydrogen bonds with the amino acids Arg646B and Gln836C and Alkyl interactions with amino acids the Lys835C, Ala956C, Phe833C, Val963C, Ala852C, Cys851C, Leu849C and Cys840C.