Davide Bertoldo

Name

Name: Davide Bertoldo
Nationality: Italian

Ecole polytechnique fédérale de Lausanne (EPFL),
Institute of chemical sciences and engineering,
Laboratory of therapeutic proteins and peptides.
Mail address: EPFL SB ISIC LPPT BCH 5305 (Bâtochime)
CH-1015 Lausanne Switzerland

Contact details: davide.bertoldo@epfl.ch ;
+41 21 69 30551
Laboratory web site: http://lppt.epfl.ch/page-51014.html

Biosketch

Davide Bertoldo was born in Italy in 1987 and studied biotechnology at the University of Padova (Italy). He carried out his master thesis at the Center for Protein Engineering (CIP) at the University of Liège (Belgium) graduating in March 2012. He started in the same year the Ph.D. studies in the laboratory of Prof. Christian Heinis at the Ecole Polytechnique Fédérale de Lausanne (EPFL). He is currently working on the phage display selection of bicyclic peptide binders for sphingolipids and regulators of sphingolipids homeostasis.

Project title: Phage selection of bicyclic peptide binders to sphingolipids or regulators of sphingolipid homeostasis

Project summary:

The aim of the project is to develop peptide binders for i) sphingolipids and ii) regulators of sphingolipid homeostasis. Specifically, we want to generate binders to ceramide and sphingosine-1-phosphate and the GPCR S1PR1. Binders to the sphingolipids could be used as research tools to visualize the lipids in cell membranes. Antagonists of S1PR1 have potential application in anti-cancer therapy.

Phage display can be used to identify peptide ligands of a specific target1. Our laboratory is routinely developing bicyclic peptide ligands using a phage display-based approach. To select bicyclic peptides by phage display, peptides carrying three cysteine residues are displayed on the disulfide-free N-terminus of the filamentous phage coat protein pIII by genetic manipulation of the phage DNA. The phage-displayed peptides are then chemically modified via the cysteine side chains using a trivalent organic cyclization linker to obtain a bicyclic configuration. Bicyclic peptides with high affinity for the target of interest are isolated in affinity selections using immobilized antigen. The peptide identity is revealed by sequencing the encoding DNA1,2. Preliminary studies clearly showed the importance of the cyclization linker type, influencing the backbone conformation of the cyclized peptides, in the isolation of desired binders.

General strategy for the generation of specific bicyclic peptides. The peptide library is chemically modified with the cyclization linker (in this case tris(bromomethyl)benzene, TBMB). The specific binders are selected after incubating the library with the immobilized target protein while the non-binders phage are washed away. Finally, the specific phage are eluted from the target and used to infect bacteria. The sequence of the specific peptides is identified by sequencing the phage DNA.

Due to the small size of sphingolipids, potent binders to this class of molecules may not be isolatable from existing bicyclic peptide libraries. To increase the chances of isolating the desired binders, we propose to perform phage selections using a more structured peptide scaffold. For this purpose, we will generate bicyclic peptides with central structured cores to obtain bicyclic peptides with folded structure in solution.

References

1) Heinis, C., Rutherford, T., Freund, S., Winter, G. (2009) Phage-encoded combinatorial chemical libraries based on bicyclic peptides. Nature Chemical Biology; 5(7)502-507

2) Rentero Rebollo, I., Heinis, C. (2013) Phage selection of bicyclic peptides. Methods; 60(1)46-54

Supervisors

Christian Heinis (EPFL, Lausanne, Switzerland)
Stefan Hannus (Intana Bioscience GmbH, Munich, Germany)

Biosketch 1st scientific supervisor:

Christian Heinis was born in Aarberg (Switzerland) on July 18, 1975. He studied biochemistry at the ETH Zurich.

From 2000 to 2003 Christian Heinis did a Ph.D. in the research group of Prof. Dr. Dario Neri at the ETH Zurich where he worked on the in vitro evolution of enzymes with therapeutic applications in mind. In 2004, he joined the group of Prof. Dr. Kai Johnsson at the EPFL as a post-doctoral fellow. He was working on the directed evolution of an alkyltransferase for applications in molecular imaging. In 2006 Christian Heinis joined the group of Sir Greg Winter at the Laboratory of Molecular Biology (LMB) in Cambridge, UK. With Greg Winter, he had developed a novel method for the generation of chimeric peptide-small molecule macrocycles with tailored binding specificities for the use in therapeutic applications.

Since September 2008, Christian Heinis is a tenure-track Assistant Professor at the EPFL in Lausanne and since 2009, he is helding a professorship of the Swiss National Science Foundation.