Human
osteoclast-stimulating factor (hOSF) is an intracellular
protein produced by osteoclasts that induces osteoclast formation and
bone resorption. The
protein contains a modular Src homology 3 (SH3) domain that mediates the intermolecular recognition and interaction of hOSF with its biological partners. Here, we proposed targeting the hOSF SH3 domain to disrupt hOSF-partner interactions for
bone disease therapy by using SH3 inhibitors. In the procedure, the primary sequences of three known hOSF-interacting
proteins (c-Src, SMN and Sam68) were parsed, from which totally 31 octapeptide segments that contain the core SH3-binding motif PXXP were extracted, and their binding behavior to hOSF SH3 domain was investigated at structural level using a biomolecular modeling protocol. Several SH3-binding candidates were identified theoretically and then determined to have high or moderate affinity for the domain using fluorescence spectroscopy assays. One potent
peptide (425) APPARPVK(432) (Kd = 3.2 μM), which corresponds to the residues 425-432 of Sam68
protein, was used as template to derive N substitution of
peptides (
peptoids). Considering that
proline is the only endogenous N-substituted
amino acid that plays a critical role in SH3-peptide binding, the substitution was addressed at the two key
proline residues (Pro427 and Pro430) of the template
peptide with nine N-substituted
amino acid types. By systematically evaluating the structural and energetic effects of different N-substituted
amino acids presenting at the two
proline sites on
peptide binding, we rationally designed five
peptoid inhibitors and then determined in vitro their binding affinity to hOSF SH3 domain. Consequently, two designed
peptoids APPAR(N-Clp)VK and APPAR(N-Ffa)VK with Pro430 replaced by N-Clp and N-Ffa were confirmed to have increased (Kd = 0.87 μM) and comparable (Kd = 2.9 μM) affinities relative to the template, respectively. In addition, we also found that the Pro427 residue plays an essential role in restricting
peptide/
peptoid conformations to
polyproline II (PPII) helix as the basic requirement of SH3 binding so that the residue cannot be modified. Copyright © 2016 European
Peptide Society and John Wiley & Sons, Ltd.