Fig 1.
(A) CVA16 particle with capsid protein subunits VP1 (blue), VP2 (green), VP3 (red), VP4 (yellow) in surface representation. Inset in (A) shows the location of CVA16 inhibitor binding in the pocket (shown schematically in blue) lying below the canyon floor, here occupied by a natural pocket factor (magenta, in sticks representation). The VP1 subunits at the icosahedral five-fold axis are shown as a blue surface overlaid on a cartoon representation whereas the other subunits are in light gray. A segment around the five-fold axis is cut away to reveal two pockets. (B) A selection of 3-(4-pyridyl)-2-imidazolidinone derivative structures. The following chemical moieties are labeled in GPP3: A, pyridine ring; B, imidazole moiety; C, phenoxy group.
Table 1.
Data collection and refinement statistics.
Fig 2.
Real-space averaged OMIT |Fo| − |Fc| map (green mesh) of GPP3 inhibitor bound to CVA16.
VP1 residues within 3 Å of the ligand are colored in blue and shown as sticks; the side chain of Ile24 of VP3 is colored in orange.
Fig 3.
Comparison of complexes of CVA16 with sphingosine and GPP3.
Sphingosine (green)–CV16 VP1 (cyan), superimposed on GPP3 (magenta)–CVA16 VP1 (blue). The RMS difference between all Cα atoms of the icosahedral protomer is 0.2 Å.
Fig 4.
Molecular docking of GPP3 and NLD into the VP1 pocket.
Both ligands are shown as sticks. (A) Overlay of the docked ligand GPP3 (cyan) by QMPLD and the experimentally determined conformation of GPP3 (magenta) (RMSD between the experimentally observed pose and docked pose for all inhibitor atoms 0.5Å) (B) NLD hydrogen-bonds with main chain nitrogen of Gln202 (RMSD between the experimentally observed pose and docked pose for all inhibitor atoms 0.6Å). (C) Highest score docking pose of protonated form of NLD hydrogen-bonds with main chain nitrogen of Gln202 (RMSD between the experimentally observed pose and docked pose for all inhibitor atoms 0.4Å). (D) Second highest docking score of NLD, note hydrogen bonds with the side chain of Asp112.
Table 2.
Antiviral activity of the capsid binders NLD, ALD and GPP3 in virus-cell-based assays against a panel of enteroviruses.
Fig 5.
Superposition of VP1 structures of the 3 types of poliovirus (PDBid: 1HXS in green, 1EAH in light orange, 1PVC in blue).
All the ligands and side chains in the pocket are shown as sticks. Sphingosine is shown in pink, palmitate in green, inhibitor SCH48973 in gray. The residues shown are Tyr159, Phe134 and Leu134.
Fig 6.
(A) VP1 pocket of CVB3. Ligand and residues in the pocket are shown as sticks (PDBid:1COV). (B) Superposition of CVB3 (orange) on EV71 (blue) in complex with NLD (PDBid:4CEY), ligand and side chain residues are shown in sticks. Residues shown in EV71 are: Asp112, Thr114, Phe135, Phe155. Residues shown in CVB3 are: Thr93, Arg95, Leu116 and Tyr143.
Fig 7.
(A) VP1 pocket of echovirus11 (EV11). Ligand and residues side chains are shown in sticks (PDBid:1H8T). (B) Superposition of EV11 (cyan) on EV71 (blue) in complex with NLD (PDBid:4CEY) ligand and side chain residues are shown in sticks. Residues shown in EV71 are: Asp112, Thr114, Phe135, Phe155. Residues shown in EV11 are: Ser96, Arg98, Arg104, Val119, Tyr146 and Tyr210.
Fig 8.
(A) VP1 pocket of CVA9. Inhibitor (violet) and residues side chains (green) are shown in sticks (PDBid:1D4M). (B) Superposition of CVA9 (yellow) on EV71 (blue) in complex with NLD (PDBid:4CEY). Ligand (magenta) and side chain residues (green for CVA9, blue for EV71) are shown as sticks. The residues shown in EV71 are: Asp112, Thr114, Phe135, Phe155. Residues shown in CVA9 are: Arg96, Lys98, Val119, Tyr146 and Tyr210.
Fig 9.
Residue conservation mapped onto the VP1 subunit of CVA16 (residues 2:8 and 19:297 the disordered portion spanning these residues is shown by a dashed line) using Consurf (violet = invariant, white = conserved, blue = variable), based on the alignment of all the virus structures used in the inhibitor assays.
The N and C terimini are marked.