Part of the VP1 GH loop (residues 212 to 215)
that forms the entrance to the VP1 pocket had
become less ordered in the EV-D68-pleconaril
complex. The Ca atom of residue 211 had moved
1.2 Å toward the inside of the pocket relative to
that of the native structure, possibly blocking the
entrance to the pocket once pleconaril had entered
(Fig. 4C). Thus, the dynamics of the GH loop might
be a consideration for future structure-based design of EV-D68 capsid-binding inhibitors.
A comparison of the EV-D68–pleconaril, HRV14-
pleconaril, and HRV16-pleconaril structures showed
a similar binding mode for pleconaril in the VP1
pocket of these three viruses (fig. S4 and table
S3). This may explain why pleconaril is similarly
effective against these three EVs. To investigate
why pleconaril is more effective against EV-D68
than pirodavir or BTA-188, we performed in
silico docking experiments. The presence of a
trifluoromethyl-substituted oxadiazole moiety
in pleconaril, rather than a more hydrophilic
group in either pirodavir (ethyl carboxylate group)
or BTA-188 (O-ethyloxime group) at structurally
equivalent positions (fig. S5), probably contributes
to more favorable interactions of pleconaril with
the hydrophobic residues deep inside the VP1
pocket of EV-D68.
Our results show that the structure of EV-D68
has considerable similarities to those of the well-studied HRVs for which pleconaril was specifically designed. We also show that pleconaril
replaces the pocket factor and is a potent inhibitor of EV-D68, with an EC50 value of 430 nM.
The size and location of the pocket factor lodged
in the VP1 pocket are similar to those found in
other HRVs and different from those of the
pocket factors found in poliovirus 1 and EV-A71.
This correlates with the observation that pleconaril is far more active when the natural pocket
factor is short, as in the HRVs and in EV-D68.
Furthermore, sequence alignment of 188 EV-D68
strains found between 1962 and 2013 indicates
that residues in VP1 that interact with pleconaril,
as identified from the complex structure, are
completely conserved, with one exception. Therefore, pleconaril is likely to inhibit not only the
prototype strain examined here but also many
other strains. In view of the previous extensive
clinical trials that have established its safety,
pleconaril would be a possible drug candidate to
alleviate EV-D68 outbreaks.
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We thank M. Steven Oberste of the Centers for Disease Control
and Prevention for supplying us with the prototype strain of
EV-D68; M. A. McKinlay of the Task Force for Global Health for
helpful discussion and suggestions; S. Kelly for help with the
manuscript preparation; and V. Srajer, R. Henning, and the other
staff of the Advanced Photon Source BioCARS beamline 14 for
help with x-ray diffraction data collection. Use of BioCARS sector
14 was supported by the National Institutes of Health, National
Center for Research Resources (NIH/NCRR) grant RR007707.
Use of the Advanced Photon Source was supported by the U.S.
Department of Energy, Office of Science, Office of Basic Energy
Sciences, under contract DE-AC02-006CH11357. This study was
supported by NIH grant award AI11219 to M.G.R. Coordinates for
native EV-D68 and EV-D68–pleconaril structures were deposited
with the Protein Data Bank with accession numbers 4WM8
and 4WM7, respectively.
Materials and Methods
Figs. S1 to S5
Tables S1 to S3
References ( 34–49)
1 October 2014; accepted 25 November 2014
74 2 JANUARY 2015 • VOL 347 ISSUE 6217 sciencemag.org SCIENCE
Fig. 4. Structure of pleconaril bound into the VP1 pocket of EV-D68. (A) Pocket factor density (gray) compared to the pleconaril density (magenta). (B)
Pleconaril (green) fitted to density in the structure of the complex. (C) Conformational change of the VP1 GH loop as a consequence of the presence of pleconaril.
The native and complex structures are shown in marine blue and baby blue, respectively. Oxygen, nitrogen, sulfur, and fluorine atoms are shown in red, dark blue,
yellow, and light green, respectively.