Identification of Persuasive Antiviral Natural Compounds for COVID-19 by Targeting Endoribonuclease NSP15: A Structural-Bioinformatics Approach

Abstract

SARS-CoV-2 is a positive-stranded RNA virus that bundles its genomic material as messenger-sense RNA in infectious virions and replicates these genomes through RNA intermediates. Several virus-encoded nonstructural proteins play a key role during the viral life cycle. Endoribonuclease NSP15 is vital for the replication and life cycle of the virus, and is thus considered a compelling druggable target. Here, we performed a combination of multiscoring virtual screening and molecular docking of a library of 1624 natural compounds (Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products (NuBBE) database) on the active sites of NSP15 (PDB:6VWW). After sequential high-throughput screening by LibDock and GOLD, docking optimization by CDOCKER, and final scoring by calculating binding energies, top-ranked compounds NuBBE-1970 and NuBBE-242 were further investigated via an indepth molecular-docking and molecular-dynamics simulation of 60 ns, which revealed that the binding of these two compounds with active site residues of NSP15 was sufficiently strong and stable. The findings strongly suggest that further optimization and clinical investigations of these potent compounds may lead to effective SARS-CoV-2 treatment.

Keywords: NSP15; SARS-CoV-2; molecular dynamics; natural compounds; virtual screening.

Figure 1

Flow diagram of virtual-screening steps.

Figure 2

Complex structures of NuBBE-1970 and NuBBE-242 with active site of NSP15.

Figure 3

Root-mean-square deviations (RMSDs) of backbone atoms of each complex and of ligands (right plot). Black, NuBBE-1970–NSP15 complex; red plot, NuBBE-242–NSP15.

Figure 4

Representation of root mean square fluctuation (RMSF) of each complex. Black, NuBBE-1970–NSP15 complex fluctuations; red, NuBBE-242–NSP15 complex fluctuations.

Figure 5

Calculation of minimal distances from ligand within 0.4 nm to close residues. Black, NuBBE-1970–NSP15; red, NuBBE-242–NSP15.

Figure 6

Representation of H-bond calculation during simulation, signifying observation. Default cut-off of 0.35 nm was considered.

Figure 7

Cluster analysis of (a) NuBBE-1970–NSP15 and (b) NuBBE-242–NSP15 complexes by taking backbone for calculations. Descending blue and red lines indicate clusters of representation structures with respect to time. Subplots represent generated clusters during simulation. Cluster analysis was approximated using a cut-off of 0.15 nm.

Figure 8

Principal-component analysis of trajectories of both complexes (A) NuBBE-1970–NSP15 and (B) NuBBE-242–NSP15. Projections of all four eigenvectors during simulation. Calculation was considered for total of 60 ns of simulation.

Figure 9

Movement of backbone atoms during simulation by 100 collectively aligned frames. (b) NuBBE-1970–NSP15 complex; (a) NuBBE-242–NSP15. Motion of backbone atoms of NuBBE-1970–NSP15 and NuBBE-242–NSP15 is as calculated by principal-component analysis (PCA). Comparison of the wide and narrow sections shown by red and black ellipses, where red ellipses showed tendency towards active ligand site (arrow). Width of bands was proportional to amplitude, signifying that atoms moved in a similar direction.