Structure-Based Identification of Natural Products as SARS-CoV-2 Mpro Antagonist from Echinacea angustifolia Using Computational Approaches

Abstract

Coronavirus disease-19 (COVID-19) pandemic, caused by the novel SARS-CoV-2 virus, continues to be a global threat. The number of cases and deaths will remain escalating due to the lack of effective therapeutic agents. Several studies have established the importance of the viral main protease (M^pro) in the replication of SARS-CoV-2 which makes it an attractive target for antiviral drug development, including pharmaceutical repurposing and other medicinal chemistry approaches. Identification of natural products with considerable inhibitory potential against SARS-CoV-2 could be beneficial as a rapid and potent alternative with drug-likeness by comparison to de novo antiviral drug discovery approaches. Thereof, we carried out the structure-based screening of natural products from Echinacea-angustifolia, commonly used to prevent cold and other microbial respiratory infections, targeting SARS-CoV-2 M^pro. Four natural products namely, Echinacoside, Quercetagetin 7-glucoside, Levan N, Inulin from chicory, and 1,3-Dicaffeoylquinic acid, revealed significant docking energy (>-10 kcal/mol) in the SARS-CoV-2 M^pro catalytic pocket via substantial intermolecular contacts formation against co-crystallized ligand (<-4 kcal/mol). Furthermore, the docked poses of SARS-CoV-2 M^pro with selected natural products showed conformational stability through molecular dynamics. Exploring the end-point net binding energy exhibited substantial contribution of Coulomb and van der Waals interactions to the stability of respective docked conformations. These results advocated the natural products from Echinacea angustifolia for further experimental studies with an elevated probability to discover the potent SARS-CoV-2 M^pro antagonist with higher affinity and drug-likeness.

Keywords: COVID-19; Echinacea-angustifolia; Quercetagetin 7-glucoside; SARS-CoV-2; molecular dynamics simulation; natural products.

Figure 1

Computational assessment of natural products in E. angustifolia against SARS-CoV-2 M^pro. Herein, (i) 3D structures of natural products reported in E. angustifolia were retrieved from the PubChem database, (ii) these natural products were then screened into the active region of SARS-CoV-2 M^pro by XP docking, (iii) natural products with highest negative docking energy were collected and treated by DFT method for respective geometry optimization to calculate other molecular properties, (iv) these optimized geometries of natural products were re-docked with SARS-CoV-2 M^pro and studied for pose binding and molecular contacts formation, (v) best docked poses were further studied for stability and protein ligand contact formation as function of 100 ns interval, and (vi) frames were extracted from respective MD trajectories and used in binding free energy calculations.

Figure 2

2D structures and 3D optimized molecular geometries of natural products, viz. (a,b) Echinacoside, (c,d) Quercetagetin 7-glucoside, (e,f) Levan N, (g,h) Inulin from chicory, (i,j) 1,3-Dicaffeoylquinic acid, and (k,l) 6-(ethylamino) pyridine-3-carbonitrile as reference compound, were calculated using DFT/B3LYP/6-31G(d,p) level.

Figure 3

Molecular orbitals, i.e., highly occupied molecular orbital (HOMO) and lower unoccupied molecular orbitals (LUMO) of the optimized geometries of selected natural compounds, viz. (a) Echinacoside, (b) Quercetagetin 7-glucoside, (c) Levan N, (d) Inulin from chicory, and (e) 1,3-Dicaffeoylquinic acid, calculated using theoretical model B3LYP/6-31G** method.

Figure 4

3D and 2D interaction maps for the docked poses of SARS-CoV-2 M^pro with potent natural products, i.e., (a,b) Echinacoside, (c,d) Quercetagetin 7-glucoside, (e,f) Levan N, (g,h) Inulin from chicory, and (i,j) 1,3-Dicaffeoylquinic acid. In 3D interaction poses, the docked ligand surface was generated based on partial charge while protein surface was rendered based on secondary structure. In 2D maps, hydrogen bond formation (pink arrows), hydrophobic (green), polar (blue), red (negative), violet (positive), glycine (grey), π-π stacking (green line), π-cation stacking (red line), and salt bridge (red-blue line), interactions are logged for docked complexes of SARS-CoV-2 M^pro with selected natural products.

Figure 5

3D docked poses of SARS-CoV-2 M^pro-natural products, i.e., (a) Echinacoside, (b) Quercetagetin 7-glucoside, (c) Levan N, (d) Inulin from chicory, and (e) 1,3-Dicaffeoylquinic acid, and (f) 6-(ethylamino) pyridine-3-carbonitrile, exhibiting transition of docked poses through 100 ns MD simulation.

Figure 6

Root mean square deviation (RMSD) values plotted for alpha carbon atoms (blue curves) of SARS-CoV-2 M^pro and natural products (red curves), i.e., (a) Echinacoside, (b) Quercetagetin 7-glucoside, (c) Levan N, (d) Inulin from chicory, and (e) 1,3-Dicaffeoylquinic acid, were extracted from 100 ns MD simulation interval of respective docked complexes.

Figure 7

Protein-ligand interactions contact profiling for SARS-CoV-2 M^pro docked with potential natural products, viz. (a) Echinacoside, (b) Quercetagetin 7-glucoside, (c) Levan N, (d) Inulin from chicory, and (e) 1,3-Dicaffeoylquinica acid, computed from 100 ns MD simulation trajectories.

Figure 8

2D interaction diagrams for docked SARS-CoV-2 M^pro-potential natural products, i.e., (a) Echinacoside, (b) Quercetagetin 7-glucoside, (c) Levan N, (d) Inulin from chicory, and (e) 1,3-Dicaffeoylquinic acid, are generated at 30% of the total 100 ns MD simulation interaction interval.

Figure 9

Principal component analysis for SARS-CoV-2 docked complexes with natural products, i.e., (a) Echinacoside, (b) Quercetagetin 7-glucoside, (c) Levan N, (d) Inulin from chicory, and (e) 1,3-Dicaffeoylquinic acid. The change from blue to red through white color in respective scatter plots shows the periodic jumps in the different conformations of the viral protease during 100 ns MD simulation intervals.

Figure 10

Average binding free energy and their dissociation energy components calculated for the extracted poses of SARS-CoV-2 M^pro with potent natural products, i.e., (a) Echinacoside, (b) Quercetagetin 7-glucoside, (c) Levan N, (d) Inulin from chicory, and (e) 1,3-Dicaffeoylquinic acid, from respective 100 ns MD trajectories.