Appeal No. 2002-0796 Page 11
Application No. 09/110,994
up on this result by screening GenBank for proteins containing
EPFP and discovered that the aryl hydrocarbon receptor (AhR),
known to bind dioxin, has a motif with a similar sequence. The
applicants have further shown that the sequence EPFP allows the
identification of leukemia inhibitory factor (LIF) as a potential target
of dioxin, and have now demonstrated that dioxin does indeed bind
to LIF with at least micromolar affinity.
Id. at 31 (emphasis added).
Appellants also argue that the combination provides no reasonable
expectation of success at arriving at the method of claim 1. Specifically,
appellants argue that Sparks and Ivanenkov disclose methods for identifying
proteins based on protein-protein interaction, which are different from protein-
ligand interactions as instantly claimed. Appellants contend that the amino acids
which form the binding sites for small ligands must often be presented as a
“scaffold,” and one of ordinary skill in the art would have no reason to expect that
“a peptide library could sufficiently present binding site amino acids in the correct
scaffold,” while appellants assert that they have demonstrated that such correct
presentation does occur. Appeal Brief, page 11. Appellants urge that, thus, “one
of ordinary skill in the art would expect that any consensus binding sequence
derived from such peptide libraries would be highly artificial and specific to the
presentation system used, rather than similar to a binding site occurring on a
natural protein target of the small organic ligand.” Id. Appellants argue further
that one of ordinary skill in the art would not expect that the library data
generated by Petrenko to be amenable to the analysis of Ivanenkov and Sparks
to find natural protein targets of biologically active small molecules. See id.
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