3.1 Molecular Docking: The highest binding affinity of ivermectin and levosalbutamoland at the interface of S protein were calculated − 9.0 and − 4.1 kcal/mol, respectively. Figure 2 shows the binding pocket of ivermectin with S protein. Here, residues GLN493 and LEU492 are involved in hydrogen bond (HB) formation with ivermectin. The hydrogen atom of NH2 group of GLN493 forms two HBs with the oxygen atom of -CO and oxygen atom of –OH groups in ivermectin and the oxygen atom of –CO group in LEU492 forms one HB with the hydrogen atom of –OH of ivermectin. The HB plays a vital role in stabilizing the protein-ligand complex. Besides these, oxygen atom of –CO groups in TYR505 and GLY496 form HBs with the hydrogen atom of alkyl group in ivermectin. GLU484, PHE497, ASN501, GLN498, TYR453, SER494, AGR403 and TYR495 interact with ivermectin through van der Waals interaction. Another stacking interaction between aromatic rings of residues (TYR449, TYR489, PHE456 and PHE490) and alkyl group of ivermectin plays a significant role to strengthen the binding of ivermectin with S protein, including hydrogen bonds and van der Waals interaction. Among all interacting residues, GLN493 and LEU455 residues which have favorable interactions with ACE2, can bind with ivermectin. Therefore, before the interaction between S protein and hACE2, it can block the S protein's binding pocket, which may inhibit SARS-CoV-2 binding with hACE2.
Figure 3 shows the interaction between S protein and levosalbutamol. TYR453 and TYR505 are involved to form two HBs with levosalbutamol. The oxygen atoms of –OH and –CO group in TYR453 and TYR505 form HBs with hydrogen atoms of –OH groups in levosalbutamol, respectively. Another stacking interaction is found between aromatic rings of residues (TYR453 and TYR505) and alkyl carbon of levosalbutamol. GLY496 residue interacts with levosalbutamol through the pi-donor hydrogen bond.
3.2 DFT Calculations: The initial geometries of ivermectin and levosalbutamol were optimized separately at the above mentioned level of theory. We considered only those amino acid residues of S protein that interact with either ivermectin or levosalbutamol through hydrogen bonds to reduce simulation time. Figure 4 shows the optimized configuration of four residues (GLN492, GLN493, GLY496 and TRY505), which interact with ivermectin through hydrogen bonds. The calculated binding energy of these four residues with ivermectin is -17.8 kcal/mol. Oxygen and hydrogen atoms of –CO and –OH groups of ivermectin form hydrogen bonds with –NH group of GLN493 and –OH group of LEU492, respectively. Alkyl hydrogens of ivermectin form two hydrogen bonds with GLY496 and TYR505. Hydrogen bonds (–CO- -NH-) and (–OH- -OC-) are shorter in distance compared to those forms with alkyl hydrogens of ivermectin. The hydrogen bond distances are shown in Fig. 4.
Similarly, two residues TYR453 and TYR505 with levosalbutamol were considered for DFT calculation because they formed hydrogen bonds with levosalbutamol. Their calculated binding energy is -20.08 kcal/mol. The hydrogen atom of –OH and the oxygen atom of –CO group of TYR453 and TYR505 form hydrogen bonds with –OH groups in levosalbutamol, respectively. Their hydrogen bond distances are 1.94 Å and 1.88 Å, respectively (Fig. 5).
The amount of charge transfers between two interacting species that occurs for electron transfer establishes the strength of the interaction between them. We have analyzed NBO charge transfer to compute the number of charges transferred by ivermectin and levosalbutamol from or to amino acid residues. Ivermectin donates 0.00845e− to four residues (GLN492, GLN493, GLY496 and TRY505) of S protein. On the other hand, levosalbutamol donates 0.01586e− to two residues (TYR453 and TYR505).
3.3 Stability of spike protein bound with ivermectin and levosalbutamol during MD simulation: To study the stability of the initial conformation of docked complex in an aqueous solution, the dynamics of the complex such as RMSD (root mean square deviation) and RMSFs (root mean square fluctuations) were examined. For this, a 100 ns long simulation was performed on the docked structure of the spike protein-ivermectin complex.
The RMSD computed for the backbone of protein (Fig. 6) shows the relative stability of the spike protein bound with ivermectin and levosalbutamol. The RMSD values for all structures were calculated using the mass-weighted least-squares fitting method. In Fig. 6, the black color represents the RMSD of the backbone of the protein bound with ivermectin, which reaches equilibrium within 2.0 ns and fluctuates between 0.9 nm to 0.12 nm up to 70 ns. During this period, the average RMSD value is ~ 0.11 nm. After 70 ns, the protein depicts a sudden drift towards a little higher deviation at ~ 0.18 nm. During this period, the RMSD fluctuates from 0.12 nm to 0.17 nm and the average RMSD is 0.15 nm. This lower deviation indicates the stability of protein bound with ivermectin in the active site throughout the simulation. On the other hand, the RMSD (red color) shows a large fluctuation for the protein bound with levosalbutamol. This is beacuse levosalbutamol moves away from the active site of the spike protein. Therefore, it confirms that ivermectin can bind strongly in the active site of spike protein than levosalbutamol.
To understand the dynamics in more details, we compute the time-averaged RMSF (Fig. 6) for the spike protein bound with ivermectin (black color) and levosalbutamol (red color) at 300 K. The RMSF is used to evaluate the flexibility of the residues of protein which reveals the extent to which fluctuations vary along the protein chain before and after binding with ivermectin. The RMSF values of GLN492, GLN493, GLY496 and TRY505 are found close to the baseline (~ 0.06 nm) except GLN493 and TRY505 (< 0.15 nm). This small fluctuation of these four important amino acids will be beneficial for binding ivermectin in S protein's active site. The large fluctuation (~ 0.45 nm) is found for amino acids 369–371 which are relatively far from the active site of ivermectin. In the case of spike protein bound with levosalbutamol, the RMSF values for TYR453 and TYR505 are found 0.06 and 0.1, respectively.