A systematic methodology for proteome-wide identification of peptides inhibiting the proliferation and migration of endothelial cells

Abstract

We introduce a systematic computational methodology based on bioinformatics that has enabled us to identify and classify >120 endogenous peptide inhibitors of endothelial cell proliferation and migration. These peptides are derived from members of the type IV collagen, thrombospondin, and CXC chemokine protein families, as well as somatotropin hormones, serpins, and various kringlecontaining proteins. Their activity in suppressing the proliferation and migration of endothelial cells in vitro provides proof of principle for the validity of this computational method. Interestingly, some of the peptides are derived from proteins known to be proangiogenic. By performing receptor neutralization studies, we have identified receptors to which these peptides bind. On the basis of this receptor-binding information, we evaluated several examples of peptide-based combinatorial screening strategies. In some cases, this combinatorial screening identified strong synergism between peptides. The current work provides a guideline for a computational-based peptidomics approach for the discovery of endogenous bioactive peptides.angiogenesis ͉ bioinformatics ͉ extracellular matrix

Development of a biomimetic peptide derived from collagen IV with anti-angiogenic activity in breast cancer

“…Previously, in a preliminary investigation using neutralizing monoclonal antibodies against the α V β 1 and α V β 3 integrins we demonstrated a significant reduction in the in vitro activity of the parent peptide SP2000. 15 These results showed a significant reduction in the activity of the peptide; however function blocking antibodies experiments have their own limitations as the binding epitope might be different or the peptide which is much smaller in size and could perhaps still bind the receptor in spite of the antibody binding. Thus, in the present study using more specific assays we confirmed through specific pulldown of the β 1 integrin subunit from cell lysates that the modified peptide retained the β 1 integrin target.…”

“…15 It was demonstrated to have activity in vivo by inhibiting the growth of breast and lung cancer xenografts. 26,29 To facilitate translational applications of the compound, we substituted the cysteines in SP2000 by L-α-amino-n-butyric acid with the goal of developing a biomimetic peptide which retains biological activity with increased stability.…”

“…Previously, we have demonstrated via antibody neutralization studies that the activity of the parent compound SP2000 can be blocked by antibodies against the α V β 1 or α V β 3 integrins, and thus we hypothesized that this would be true for the new modified sequence, since the cysteines have been substituted by similar amino acids and the in vitro activity has not been compromised. 15 We now characterize the interaction in more depth using different methods since antibody neutralization has its limitations. First, receptor pulldown assays were performed with cellular extracts which where incubated and crosslinked with a custom probe to identify interacting proteins.…”

“…15 Considering the diversity of these endogenous peptides, we can envision a therapeutic approach based on a cocktail of peptides, which target different aspects containing multiple cysteines can be difficult to synthesize and are often unstable due to their ease of oxidation, thus they are replaced by other amino acids such as serine or by non-natural amino acids that are structurally similar but more stable such as L-α-amino-n-butyric acid. [19][20][21][22][23][24][25] In this study we present the biological activity of a biomimetic peptide modified from an endogenous sequence derived from the α5 fibril of collagen IV, whose anti-angiogenic activity was previously demonstrated in MDA-MB-231 ER/PR/HER2 triple negative breast cancer xenograft model.…”

Degradome Products of the Matricellular Protein CCN1 as Modulators of Pathological Angiogenesis in the Retina

“…The CT domain at the extreme C-terminal end is well exposed, which may facilitate the oligomerization of the CCN1 proteins and/or its interaction with other ECM proteins. Of particular interest is that the removal of the CT domain unmasked a short peptide sequence within the TSP1 domain, TSWSQCSKTCGTGISTRV, that computationally based peptidomics approaches have previously identified as cyrostatin, a potential suppressor of endothelial cell growth and migration (45). Moreover, further removal of the TSP1 domain resulted in a more compact molecule in which most residues were exposed and readily accessible to receptors and interacting partners (Fig.…”