Fragment-Based Discovery of Novel VE-PTP Inhibitors Using Orthogonal Biophysical Techniques

Poly-Dha Sequences as Pro-polypeptides: An Original Mechanistic Postulate Leads to the Discovery of a Long-Acting Vasodilator KU04212

The construction of polypeptides was revolutionized by Merrifield's solid-phase synthesis more than half a century ago. Herein, we explore a completely different approach to making peptides. We test an original mechanistic postulate wherein a single peptide made entirely of dehydroalanine (Dha) residues can give rise to regio- and stereodefined peptides by iterative conjugate addition of one- or two-electron nucleophiles. Each nucleophile appends a unique amino acid side chain to the peptide backbone. We show that side chain addition is not random. Side chains are added in one of two ways, in an electrophilicity-gated fashion (most cases) or in a substrate-directed manner, depending on the first nucleophile used in the synthesis. One peptide made in this series, KU04212, a first-in-class polyazole peptide, was found to reduce vascular length density (-17%; p < 0.05) and increase vessel diameter (124%; p < 0.001) in healthy day 6 chick embryos at 24 h post-single dose. It also rescued 75% of the embryos administered a 32-fold lethal dose of ischemia-inducing CoCl2 after 12 h and 12.5% of the embryos after 24 h. In comparison to three mechanistically distinct vasodilators, e.g., isosorbide mononitrate, amlodipine besylate, and prazosin, only KU04212 showed long-acting effects in vivo, making it an enticing lead for the treatment of ischemic disorders.

Fragment-Based Discovery of Allosteric Inhibitors of SH2 Domain-Containing Protein Tyrosine Phosphatase-2 (SHP2)

The ubiquitously expressed protein tyrosine phosphatase SHP2 is required for signaling downstream of receptor tyrosine kinases (RTKs) and plays a role in regulating many cellular processes. Genetic knockdown and pharmacological inhibition of SHP2 suppresses RAS/MAPK signaling and inhibit the proliferation of RTK-driven cancer cell lines. Here, we describe the first reported fragment-to-lead campaign against SHP2, where X-ray crystallography and biophysical techniques were used to identify fragments binding to multiple sites on SHP2. Structure-guided optimization, including several computational methods, led to the discovery of two structurally distinct series of SHP2 inhibitors binding to the previously reported allosteric tunnel binding site (Tunnel Site). One of these series was advanced to a low-nanomolar lead that inhibited tumor growth when dosed orally to mice bearing HCC827 xenografts. Furthermore, a third series of SHP2 inhibitors was discovered binding to a previously unreported site, lying at the interface of the C-terminal SH2 and catalytic domains.