Computational screening of known broad-spectrum antiviral small organic molecules for potential influenza HA stem inhibitors

Abstract

Background: With the emergence of new influenza virus strains that are resistant to current inhibitors such as oseltamivir (anti-neuraminidase (NA)) and amantadine (anti-M2 proton channel), influenza A viruses continue to be a serious threat to the public health worldwide. With this in view, there is a persistent need for the development of broader and more effective vaccines and therapeutics. Identification of broadly neutralizing antibodies (bNAbs) that recognize relatively invariant structures ‎on influenza haemagglutinin (HA) stem has invigorated efforts to develop universal influenza vaccines.

Aim: The current computational study is designed to identify potential flavonoid inhibitors that bind to the contact epitopes of HA stem that are targeted by broadly neutralizing antibodies (bNAb).

Method: In this study, we utilized the three-dimensional crystallographic structure of different HA subtypes (H1, H2, H5, H3, and H7) in complex with bNAb to screen for potential broadly reactive influenza inhibitors. We performed Quantitative Structure-Activity and Relationship (QSAR) for 100 natural compounds known for their antiviral activity and performed molecular docking using AutoDock 4.2 suite. Furthermore, we conducted virtual screening of 1413 bioassay hit compounds by using virtual lab bench CLC Drug Discovery.

Results: The results showed 18 lead flavonoids with strong binding abilities to bNAb epitopes of various HA subtypes. These 18 broadly reactive compounds exhibited significant interactions with an average of seven Hbonds, docking energy of -22.43 kcal·mol-1, and minimum interaction ‎ energy of -4.65 kcal·mol-1, with functional contact residues. Procyanidin depicted strong interactions with group 1 HAs, whereas both sorbitol and procyanidin exhibited significant interactions with group 2 HAs.

Conclusion: Using in silico docking analysis, we identified 18 bioactive flavonoids with potential strong binding cababilities to influenza HA-stems of various subtypes, which are the target for bNAb. The virtual screened bioassay hit compounds depicted a high number of Hbonds but low interaction and docking values compared to antiviral flavonoids. Using structure-based design and nanotechnology-based approaches, identified molecules could be modified to generate next generation anti-influenza drugs.

Fig 1. Computational docking of flavonoids on H1 stem.

Top five binders are shown: (a) Silybin, (b) Apigenin, (c) Morin, (d) Homoplantagnin and (e) Naringenin. H1 stem region is depicted in ribbon with yellow color. HB interaction are denoted in dashed blue color.

Fig 2. Docking of three main flavonoids (silybin, procyanidin and sorbitol) to group 1 HA-Stem (H1, H2 and H5).

Analysis was done with AutoDock 4.2 Software. Analysis was done by considering the important parameters including HB interaction, IE, and DE. A. Left panel shows H1 HA structure in light pink with CR6261 bNAb epitope shown in dark blue. Middle panel shows interaction of silybin denoted in orange color to the bNAb epitope and right panel shows anchoring residues between silybin molecule and stem epitope of bNAb. HB interaction is shown in black color. B. Left panel shows H2 HA structure in light pink with Fab C179 bnAb epitope shown in dark blue. Middle panel shows interaction of procyanidin to the bNAb epitope and right panel shows contact residues between procyanidin molecule and stem epitope of bNAb. C. Left panel shows H5 HA structure in light pink with F10 bNAb epitope shown in dark blue. Middle panel shows interaction of sorbitol to the bNAb epitope and right panel shows contact residues between sorbitol molecule and stem epitope of bNAb.

Fig 3. Computational docking of flavonoids on H2 stem.

Top five binders are shown: (a) Procyanidin, (b) EGCG, (c) Sorbitol, (d) Kuwanon L and (e) Morin. H2 stem region is depicted in ribbon with HA1 in pink and HA2 in yellow color. HB interaction are denoted in dashed blue color.

Fig 4. Computational docking study of flavonoids on H5 stem.

Top five binders are shown: (a) Salicin, (b) Scutellarin, (c) EGCG, (d) Quercetin and (e) Sorbitol. H5 stem region is depicted in ribbon with HA1 and HA2 in blue color. HB interaction are represented in dashed blue color.

Fig 5. Computational docking study of flavonoids on H3 stem.

Top five binders are shown: (a) Isorhamnetin, (b) EGCG, (c) Naringenin, (d) 7-O-galloytricetiflavon and (e) Sorbitol. H3 stem region is depicted in ribbon with HA1 and HA2 in shaded green color. HB interaction are represented in dashed blue color.

Fig 6. Docking of flavonoids sorbitol to group 2 HA structures, H3 and H7.

Analysis was done with AutoDock 4.2 Software. Analysis was done by considering the important parameters including HB interaction, IE, and DE. A. Left panel shows H3 HA structure in light green with CR8020 bNAb epitope shown in red. Middle panel shows interaction of sorbitol denoted to the bNAb epitope and right panel shows anchoring residues between sorbitol molecule and stem epitope of bNAb. HB interaction is shown in black color. B. Left panel shows H7 HA structure in green with CR9114 bNAb epitope in red. Middle panel shows interaction of sorbitol to the bNAb epitope and right panel shows contact residues between sorbitol molecule and stem epitope of bNAb.

Fig 7. Computational docking of flavonoids on H7 stem.

Top five binders are ‎shown: (a) Sorbitol, (b) Procyanidin, (c) 7-O-galloytricetiflavon, (d) Epicatechins and (e) Scutellarin. H7 stem region is depicted in ribbon with HA1 and HA2 in shaded pink color. HB interaction are represented in dashed blue color.

Fig 8. Heat map analysis of best 18 flavonoids binding to five HA subtypes while considering three main criteria: DE (Kcal/mol), HB and IE (Kcal/mol).

Fig 9. Virtual screening and molecular interaction with ten bioassay hit compounds on H1 stem region using CLC Drug Discovery Workbench.

This illustration shows interaction of ligands with maximum number of HB with the active site on the stem epitopes. H1 stem region is depicted in ribbon with HA1 and HA2 in pink color. HB interaction are represented in dashed black color. (A) SID:103512718 (blue color), (B) SID:160699960 (green color), (C) SID:103619997 (dark blue color), (D) SID:103217472 (light blue color), (E) SID:242620267 (dark pale green color), (F) SID:242620266 (red color), (G) SID:242620268 (magenta color), (H) SID:163315261 (pale blue color), (I) SID:163322216 (purple color), and (J) SID:160684110 (pale dark blue color).