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PDBsum entry 2op9
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References listed in PDB file
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Key reference
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Title
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Substrate specificity profiling and identification of a new class of inhibitor for the major protease of the sars coronavirus.
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Authors
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D.H.Goetz,
Y.Choe,
E.Hansell,
Y.T.Chen,
M.Mcdowell,
C.B.Jonsson,
W.R.Roush,
J.Mckerrow,
C.S.Craik.
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Ref.
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Biochemistry, 2007,
46,
8744-8752.
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PubMed id
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Abstract
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Severe acute respiratory syndrome (SARS) is an emerging infectious disease
associated with a high rate of mortality. The SARS-associated coronavirus
(SARS-CoV) has been identified as the etiological agent of the disease. Although
public health procedures have been effective in combating the spread of SARS,
concern remains about the possibility of a recurrence. Various approaches are
being pursued for the development of efficacious therapeutics. One promising
approach is to develop small molecule inhibitors of the essential major
polyprotein processing protease 3Clpro. Here we report a complete description of
the tetrapeptide substrate specificity of 3Clpro using fully degenerate peptide
libraries consisting of all 160,000 possible naturally occurring tetrapeptides.
The substrate specificity data show the expected P1-Gln P2-Leu specificity and
elucidate a novel preference for P1-His containing substrates equal to the
expected preference for P1-Gln. These data were then used to develop optimal
substrates for a high-throughput screen of a 2000 compound small-molecule
inhibitor library consisting of known cysteine protease inhibitor scaffolds. We
also report the 1.8 A X-ray crystal structure of 3Clpro bound to an irreversible
inhibitor. This inhibitor, an alpha,beta-epoxyketone, inhibits 3Clpro with a
k3/Ki of 0.002 microM(-1) s(-1) in a mode consistent with the substrate
specificity data. Finally, we report the successful rational improvement of this
scaffold with second generation inhibitors. These data provide the foundation
for a rational small-molecule inhibitor design effort based upon the inhibitor
scaffold identified, the crystal structure of the complex, and a more complete
understanding of P1-P4 substrate specificity.
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