Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation

Abstract

Dynamic ligation screening is used to identify acylhydrazone-linked peptide-fragment hybrids which bind to the SHANK1 PDZ domain with comparable affinity to the native GKAP peptide as shown by biophysical and structural analyses.

Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling

“…On the other hand, PDZ domains have evolved to recognize a carboxyl group that is mostly derived from the C-terminus of natively binding proteins. Finally, the fact that PDZ can recognize internal motifs (Hillier et al, 1999), including KTXXXW of Frizzled-7 recognized by Dvl PDZ (Wong et al, 2003;Chandanamali et al, 2009), raises the question of what are key binding contributions with PDZ domains: negative charge, hydrogen bonding, or shape complementarity (Harris et al, 2003). For this reason, tangible compounds were preselected to have extensive hydrophobic contacts as well as chemical groups that mimic the carboxylic group.…”

Trimer-to-Monomer Disruption Mechanism for a Potent, Protease-Resistant Antagonist of Tumor Necrosis Factor-α Signaling

“…Excessive signaling mediated by cytokines, growth factors, and other proteins is associated with many human diseases. , These processes require that the soluble “message” protein engages with cell-surface receptors, and agents that block this engagement can be effective as drugs . Because contact between signaling proteins and their receptors usually involves large surfaces on each partner, therapeutically useful antagonists in current clinical use are themselves proteins, most commonly engineered antibodies. , Antagonists of lower molecular weight would be appealing because antibodies are challenging to produce and store, and sustained use of engineered proteins can lead to adverse immunological responses. , Efforts to inhibit protein–protein interactions with small molecules, however, have seldom led to clinical success, presumably because most small molecules cannot bind tightly enough to a target protein surface to prevent the engagement of a much larger partner protein. ,, This challenge has inspired many creative approaches involving peptides and related oligomers. − …”

Discovery of Internal Ligand Inhibitors Targeting SHANK1 PDZ Domain Guided by Dynamic Ligation Screening Strategy

“…Typically, SHANK PDZ binds to C-terminal PBMs in a β-strand conformation, such as the reported examples -βPIX/SHANK1 PDZ PPI (Figure 2A) [2] and GKAP/SHANK1 PDZ PPI (Figure 2B) [3]. Hegedüs et al used a dynamic ligation screening workflow (Figure 3) to identify peptide fragment hybrids bearing N-terminal modifications with strong affinity for SHANK1 PDZ (Figure 2C) [4], however no promising C-terminal fragments were identified. Internal ligands that bind PDZ domains have been identified as alternative motifs in modulating SHANK proteins in recent years (Figure 2D) [5] and may represent promising starting points for identification of C-terminal peptide-fragment hybrids.…”