In Silico Comparative Analysis of Ivermectin and Nirmatrelvir Inhibitors Interacting with the SARS-CoV-2 Main Protease

Abstract

Exploring therapeutic options is crucial in the ongoing COVID-19 pandemic caused by SARS-CoV-2. Nirmatrelvir, which is a potent inhibitor that targets the SARS-CoV-2 M^pro, shows promise as an antiviral treatment. Additionally, Ivermectin, which is a broad-spectrum antiparasitic drug, has demonstrated effectiveness against the virus in laboratory settings. However, its clinical implications are still debated. Using computational methods, such as molecular docking and 100 ns molecular dynamics simulations, we investigated how Nirmatrelvir and Ivermectin interacted with SARS-CoV-2 M^pro(A). Calculations using density functional theory were instrumental in elucidating the behavior of isolated molecules, primarily by analyzing the frontier molecular orbitals. Our analysis revealed distinct binding patterns: Nirmatrelvir formed strong interactions with amino acids, like MET49, MET165, HIS41, HIS163, HIS164, PHE140, CYS145, GLU166, and ASN142, showing stable binding, with a root-mean-square deviation (RMSD) of around 2.0 Å. On the other hand, Ivermectin interacted with THR237, THR239, LEU271, LEU272, and LEU287, displaying an RMSD of 1.87 Å, indicating enduring interactions. Both ligands stabilized M^pro(A), with Ivermectin showing stability and persistent interactions despite forming fewer hydrogen bonds. These findings offer detailed insights into how Nirmatrelvir and Ivermectin bind to the SARS-CoV-2 main protease, providing valuable information for potential therapeutic strategies against COVID-19.

Keywords: Ivermectin; Nirmatrelvir; SARS-CoV-2; main protease (Mpro); molecular docking; molecular dynamics.

Figure 1

Analysis of the frontier molecular orbitals (FMOs) of Ivermectin and Nirmatrelvir, depicting their LUMOs and HOMOs, and the energy GAPs (eV) between them.

Figure 2

Crystal structure of Nirmatrelvir and M^pro(A) from RCSB PDB Protein Data Bank (up) and structure of Ivermectin and M^pro(A) from molecular docking (down). The blue-to-red color band represents the orientation from the N-terminus to the C-terminus of M^pro(A).

Figure 3

Root-mean-square deviation (a), root-mean-square fluctuation (b), radius of gyration (c), binding free energy (d), and number of hydrogen bonds (e,f) of M^pro(A) in the Apo form and complex with Nirmatrelvir and Ivermectin throughout the 100 ns simulation.

Figure 4

By employing the optimal docking pose (see Figure 2), we examined snapshots at 0 ns (a,b), 50 ns (c,d), and 100 ns (e,f). These depictions reveal a significant disparity in the conformational flexibility: while both ligands consistently maintained their binding to M^pro(A) throughout the simulations, Nirmatrelvir exhibited a markedly more pronounced conformational variation compared with Ivermectin. The red, black, cyan, blue, and grey spheres represent the oxygen, carbon, fluorine, nitrogen, and hydrogen atoms, respectively.

Figure 5

Interactions of Nirmatrelvir and Ivermectin with M^pro(A) at 0 ns (a,b), 50 ns (c,d), and 100 ns (e,f). The red, black, cyan, and blue spheres represent the oxygen, carbon, fluorine, and nitrogen atoms, respectively.