WNT-mediated signaling relay in stem cells and oncogenesis - from basic biology to applications

Development of bicyclic peptides with WNT modulating activity

Experienced researcher 2 (ER2) project

Supervision: Peter Timmerman

Lab webpage:  http://www.pepscan.com

To develop potent agonist or antagonists for key WNT pathway target proteins using 2-CLIPS technology

ER2 will develop bicyclic peptides (‘2-CLIPS’), a novel type of conformationally restricted peptides developed at Pepscan. Pepscan developed the 2-CLIPS technology in particular for application in their proprietary surface-immobilized peptide-array platform (named ‘PEPSCAN’). Combining this platform with Isogenica CIS display allows systematic screening  by ER2 (private sector secondment) of large arrays of replacement variants, enabling the precise identification of the core binding site (“epitope mapping”) and thus also sub-optimal ’spots’ in the binding site that are amenable for affinity optimization, e.g. by substitution for a variety of non-natural, D-, NMe, a-Me, etc. The activity of de novo peptides on FZD function and turnover will be analysed in cells, organoid cultures and mouse models (collaboration Schulte, Maurice, international secondment: Koo).

Maurice, Schulte, Koo, Isogenica

Project goals:
ER2 will generate and optimize bicyclic peptides with agonistic and/or antagonistic activity for FZD5, FZD7 and the E3 ligase RNF43.

Risk assessment and contingency plans:
Pepscan proved this concept in a pilot-study, where lead inhibitors identified by PDL-screening were affinity-optimized from KD ~ 60 to 8 nM using the 2-CLIPS array platform.

Key publications:

1.  Timmerman P, Shochat SG, Desmet J, Barderas R, Casal JI, Meloen RH, Altschuh D. Binding of CDR-derived peptides is mechanistically different from that of high-affinity parental antibodies J Mol Recognit. 2010;23(6):559-68.

2.  Timmerman P, Barderas R, Desmet J, Altschuh D, Shochat S, Hollestelle MJ, Höppener JW, Monasterio A, Casal JI, Meloen RH. A combinatorial approach for the design of complementarity-determining region-derived peptidomimetics with in vitro anti-tumoral activity. J Biol Chem. 2009;284(49):34126-34.

3.  Timmerman P, Puijk WC, Meloen RH. Functional reconstruction and synthetic mimicry of a conformational epitope using CLIPS technology. J Mol Recognit. 2007;20(5):283-99.