Harnessing Brazilian biodiversity database: identification of flavonoids as potential inhibitors of SARS-CoV-2 main protease using computational approaches and all-atom molecular dynamics simulation

Abstract

SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the etiological agent responsible for the global outbreak of COVID-19 (Coronavirus Disease 2019). The main protease of SARS-CoV-2, Mpro, is a key enzyme that plays a vital role in mediating viral replication and transcription. In this study, a comprehensive computational approach was employed to investigate the binding affinity, selectivity, and stability of natural product candidates as potential new antivirals acting on the viral polyprotein processing mediated by SARS-CoV-2 Mpro. A library of 288 flavonoids extracted from Brazilian biodiversity was screened to select potential Mpro inhibitors. An initial filter based on Lipinski's rule of five was applied, and 204 compounds that did not violate any of the Lipinski rules were selected. The compounds were then docked into the active site of Mpro using the GOLD program, and the poses were subsequently re-scored using MM-GBSA (Molecular Mechanics Generalized Born Surface Area) binding free energy calculations performed by AmberTools23. The top five flavonoids with the best MM-GBSA binding free energy values were selected for analysis of their interactions with the active site residues of the protein. Next, we conducted a toxicity and drug-likeness analysis, and non-toxic compounds were subjected to molecular dynamics simulation and free energy calculation using the MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area) method. It was observed that the five selected flavonoids had lower MM-GBSA binding free energy with Mpro than the co-crystal ligand. Furthermore, these compounds also formed hydrogen bonds with two important residues, Cys145 and Glu166, in the active site of Mpro. Two compounds that passed the drug-likeness filter showed stable conformations during the molecular dynamics simulations. Among these, NuBBE_867 exhibited the best MM-PBSA binding free energy value compared to the crystallographic inhibitor. Therefore, this study suggests that NuBBE_867 could be a potential inhibitor against the main protease of SARS-CoV-2 and may be further examined to confirm our results.

Keywords: MMPBSA; SARS-CoV-2; drug-likeness; flavonoids; main protease; molecular docking; molecular dynamics; natural products.

FIGURE 1

Validation of molecular docking protocols using the GOLD program for the crystal structure of the COVID-19 main protease (Mpro) in complex with 3WL inhibitor. Blue is the co-crystal ligand and green is the docking pose.

FIGURE 2

Figure 1: (A) 3WL, (B) NuBBE_1884, (C) NuBBE_867, (D) NuBBE_1890, (E) NuBBE_1310, and (F) NuBBE_2328 binding interactions with Mpro. Dashed lines indicate hydrogen bonds between the ligands and interacting Mpro residues.

FIGURE 3

RMSD of the Apo form of Mpro and the Mpro complexes with 3WL, NuBBE_867, and NuBBE_1890 over a 100 ns MD simulation time.

FIGURE 4

Root Mean Square Fluctuations of the Apo protein and Mpro-ligand complexes’ residues.

FIGURE 5

Number of hydrogen bonds between the ligands and Mpro protein during the 100 ns MD simulation time.

FIGURE 6

Graphical representation of the interaction energy per residue.