netLibrary - eBook Summary Structure-based Drug Design by ...

Document
Page 617
Val (131) showed that the phophopeptide adopts a β-turn conformation about the P-P +3 residues and that
the P +2 Asn side chain carboxamide moiety is extensively hydrogen bonded to the protein. In contrast to
the well-defined binding pocket for the P +3 Ile of 127 to bind Src SH2, the P +3 Val of 131 engages in
limited surface hydrophobic interactions because the Trp121 residue of Grb2 SH2 sterically blocks the
phosphopeptide from attaining a similar binding mode. In the case of the SH3 domain, the binding of a
cognate Pro-rich peptide sequence ~Pro-Pro-Pro-Val-Pro-Pro-Arg-Arg~ shows distinct pockets which
recognize the Pro, Val, and Arg residues as illustrated in Figure 31. The peptide adopts a left-handed
polyproline type-II helical conformation which projects the three aforementioned residues to their
complementary binding pockets in the Grb2 SH3 domain.
Tyrosine Phosphatases and Phosphotyrosine Binding Domains
Two other types of signal-transduction proteins that recognize phosphotyrosine-containing sequences
are tyrosine phosphatases (e.g., PTP1B, Syp, and CD45) and proteins that contain a noncatalytic motif
referred to as a phosphotyrosine binding (PTB) domain. Although tyrosine phosphatases and PTB
domains are structurally quite different from each other they both are similar with respect to the binding
of pTyr-containing sequences with preference to the amino acids N-terminal to the pTyr residue. In
other words, the tyrosine phosphatase PTP1 binds EGF receptor (pTyr 992)-based phosphopeptide
substrates Asp-Ala-Asp-Glu-pTyr-Leu-NH 2 and Asp-Ala-Asp-Glu-pTyr-Leu-Ile-Pro-Gln-Gln-Gly
equally [272], and the substitution of pTyr by nonhydrolyzable F 2Pmp in the hexapeptide derivative has
been reported [273] to give a highly potent inhibitor (see compound 69, Figure 14). In the case of PTB
domains, ~Asn-Pro-Xxx-pTyr~ (where Xxx is variable) has been determined [274] as the cognate
sequence for several PTB-domain-containing proteins such as Shc and the insulin receptor substrate-1
(IRS-1). The preference for amino acids N-terminal to the pTyr residue in binding to either tyrosine
phosphatases or PTB domains is, therefore, opposite of that known for SH2 domains [275].
Among the tyrosine phosphatase superfamily, PTP1B was the first to be discovered and structurallydetermined
by x-ray crystallography, as the apoprotein catalytic domain [258b]. The first x-ray
crystallographic structure of PTP1B complexed with a phosphopeptide has also been very recently
determined [258c] using a catalytically inactive Cys215 rarrow.gif Ser PTP1B mutant and the
phosphopeptide Asp-Ala-Asp-Glu-pTyr-Leu-NH 2 (133). As illustrated in Figure 32, the molecular
interactions between the tyrosine phosphatase and the phosphopeptide are dominated by electrostatic
(i.e., the pTyr, P -1 Glu, and P -2 Asp residues) and hydrogen bonding contacts to key amide functionalities
of the backbone of 133. The P +1 Leu side chain forms hydrophobic contacts with
http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_617.html [4/9/2004 1:42:40 AM]