Encodable Activators of Src Family Kinases

Abstract

There is considerable current interest in the design of encodable molecules that regulate intracellular protein circuitry and/or activity, ideally with a high level of specificity. Src homology 3 (SH3) domains are ubiquitous components of multidomain signaling proteins, including many kinases, and are attractive drug targets because of the important role their interactions play in diseases as diverse as cancer, osteoporosis, and inflammation. Here we describe a set of miniature proteins that recognize distinct SH3 domains from Src family kinases with high affinity. Three of these molecules discriminate effectively between the SH3 domains of Src and Fyn, which are expressed ubiquitously, and two of these three activate Hck kinase with potencies that rival HIV Nef, one of the most potent kinase activators known. These results suggest that miniature proteins represent a viable, encodable strategy for selective activation of Src family kinases in a variety of cell types.

Arginine Mimetics Using α‐Guanidino Acids: Introduction of Functional Groups and Stereochemistry Adjacent to Recognition Guanidiniums in Peptides

“…Because of the importance of SH3 domains in cell signaling, there has been substantial interest in developing inhibitors of SH3 domain-mediated protein-protein interactions. [9] However, the inherent flatness of the recognition surface has resulted in significant problems in achieving paralog specificity, that is, achieving specific recognition of one SH3 domain among the approximately 300 SH3 domains in the human proteome. [9f, 10] Challenges in achieving paralog specificity have resulted in a significant reduction in pharmaceutical efforts to target SH3 domains, compared to the peak interest in the 1990s, despite potential applications as therapeutics in cancer and other diseases.…”

“…[8c, 9f, 11] Confounding attempts to achieve paralog specificity, it was recognized that a single SH3 domain could bind both type I and type II ligands, via a reversal of the orientation of ligand binding. Analysis of available high resolution structures of peptides bound to SH3 domains reveals that arginine recognition by SH3 domains involves a combination of electrostatic and hydrogen bonding interactions with the guanidinium and hydrophobic interactions with the arginine methylenes (Figure 2).…”

Arginine Topology Controls Escape of Minimally Cationic Proteins from Early Endosomes to the Cytoplasm

“…Miniature proteins are a family of small (36-aa), well-folded polypeptides that adopt a characteristic hairpin fold consisting of axially packed α- and PPII helices (Blundell et al, 1981; Hodges and Schepartz, 2007). Miniature proteins identified through both rational design (Zondlo and Schepartz, 1999; Zellefrow et al, 2006) and molecular evolution (Chin and Schepartz, 2001; Rutledge et al, 2003; Golemi-Kotra et al, 2004; Gemperli et al, 2005) can modulate protein function by inhibiting protein interactions (Rutledge et al, 2003; Gemperli et al, 2005); both loss of function and gain of function activities have been observed (Golemi-Kotra et al, 2004; Gemperli et al, 2005; Zellefrow et al, 2006). We reported previously that minimally cationic miniature proteins containing between 2 and 6 arginine residues embedded within the α- or PPII helix were taken up by mammalian cells in culture more efficiently than Tat or Arg 8 (Daniels and Schepartz, 2007; Smith et al, 2008).…”

Identification of Dual Natural Inhibitors for Chronic Myeloid Leukemia by Virtual Screening, Molecular Dynamics Simulation and ADMET Analysis

“…They are structurally different in C-terminal region but homologous in N-terminal region where SH2 and SH3 domains are present [17]. The SH2 and SH3 domains of the ABL protein play a significant regulatory role to activate it, and SH3 domain of ABL is homologous to SRC protein's SH3 domain [18]. SH2 domain of the SRC or ABL is interacting with the inhibitor and mediated the inhibitory reactions.…”