retreat 22 & 23.06 2012

exchange ○ group meeting ○ presentations ○ CONVERSATIONS

POSTER SESSION ○ CONVIVIALITY ○ SHARING ○ LEARNING

jONGNYin

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FRIdAY 22.06

8:309:00

9:15

11:15

12:45

14:1514:45

16:45

18:00

19:0019:30

arrival and sign-in

Welcome and introductionKai Johnsson & Howard Riezman

project 7 - cellular uptake and membranesAndreas ZumbuehlCharlotte GehinEun-Kyoung BangMiwa UmebayashiAndrea FinRémi Vanel

project 2 - system level chemical interferenceRobbie LoewithKarolina Niewola-StaskowskaLudovic PineauManuele PiccolisAurélien RouxMichael Stahl

Lunch

poster session

project 3 - membrane localization and endocytosisChristine BissigDimitri MoreauGisou van der GootAsvin Lakkaraju

accessGerardo TurcattiRuud van DeursenAntoine Gibelin

speaker - Stephen Helliwell, Novartis Institute for BioMedical Research “Quality & Quantity – Mapping of Pathways and Targets using automated chemogenomic profiling”

apéroDinner

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SATuRdAY 23.06

7:30

8:30

10:00

11:30

12:30

14:00

15:30

17:30

Light breakfast and poster session

project 4- signal transduction Pierre GönczyKai JohnssonFalco Kilchmann

poster session

Lunch

project 6 - g-protein coupled receptor mediated signalingHorst VogelAleksandr (Sasha) BenkeLina CarliniJoachim Piguet

project 1-chemical interferenceKarl GademannJean-Louis ReymondPaul DysonJérôme WaserSimon SieberThomas Hannich

project 5 - notch signaling Freddy RadtkeChristian Heinis

Wrap-upKai Johnsson & Howard Riezman

iDentification of xanthurenic aciD, A mETAbOLITE IN THE kYNuRENINE PATHwAY,

AS AN INHIbITOR OF TETRAHYdRObIOPTERIN SYNTHESISHirohito Haruki, Miriam Grønlund Pedersen and Kai Johnsson

Tetrahydrobiopterin (BH4) is an essential cofactor for enzymes which are involved in synthesis of signaling molecules such as

dopamine, norepinephrine, serotonin and nitric oxide. Sepiapterin reductase (SPR) catalyzes the final step in BH4 synthesis.

We performed a small molecule screen in the BSF at EPFL to find new inhibitors of SPR, and identified xanthurenic acid (XA),

a metabolite in the kynurenine pathway. Cell based assays showed that 50% inhibition is observed at 10 μM.

We are currently investigating the hypothesis that XA is a missing factor which links inflammation and mental depression.

Small organic molecules serve as valuable tools in chemical biology and drug discovery. In order to interact with biological systems, increasingly complex molecules are constantly needed.In this context, the choice of structures is limited by the synthetic methods available.

In our laboratory, we develop new methods for the functionalization and synthesis of heterocycles, which are omnipresent in natural products and biomolecules. We focus especially on the introduction of alkynes in view of further functionalization (“Click chemistry”) and the synthesis of nitrogen-rich bioactive compounds.

Jonathan P. Brand, Stefano Nicolai, Florian de Nanteuil, Fides Benfatti, Jérôme Waser

NEw TOOLS FOR THE SYNTHESIS ANd FuNCTIONALIzATION OF bIOACTIVE COmPOuNdS

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Laboratory of Catalysis and Organic Synthesis, EPFL

Laboratory of Protein Engineering (LIP), EPFL

NPC is a disease characterized by the accumulation of cholesterol and other lipids in the endosomes. It is caused by mutations in the endosomal proteins NPC1 and NPC2, but the mechanism of cholesterol export from endosomes remains elusive.

We developed an in vitro assay to study cholesterol export from isolated organelles in order to characterize the direct involvement of proteins in the process. We integrate these studies with a general analysis of endo-somal lipid composition of NPC cells, with a special focus on lysobisphosphatidic acid (LBPA), an endosome-specific lipid linked to cholesterol traffic.

Fabrizio Vacca, Jean Gruenberg

ANALYSIS OF CHOLESTEROL ExPORT from purifieD enDosomes in niemann-PICk C CELLuLAR mOdELS

An intimate relationship links cholesterol with the atypical glycerophospholipid LBPA and thus the fate

of endocytic membranes.We carried out genome-wide, high-content imaging screens

by RNAi to identify the regulators of these lipids and to obtain a broader overview of the collective behavior of membrane

components.This analysis reveals the importance of individual gene

products, e.g. the LDL receptor in controlling LBPA, as well as the central role of the wnt signaling pathway in cholesterol

homeostasis. We are now analyzing the complete lipidome of candidates of interest.

Cameron Scott, Stefania Vossio, Nicolas Guex, Marc Chambon, Adrian Schmid, Fabrice David, Fabrizio Vacca, Marc Moniatte,

Gerardo Turcatti, Jean Gruenberg

ImAGEd-bASEd, HIGH-CONTENT ANALYSIS OF GENES CONTROLLING INTRACELLuLAR CHOLESTEROL

TRANSPORT ANd LIPId STORAGE dISEASES

Gruenberg Group, UniGE

Department of Biochemistry, UniGE

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Over-activation of Notch signaling has been linked to cancer. Recently, we identified the novel Notch inhibitor I3.

We aim to reveal the cellular target as well as the structure-activity relationship (SAR) of I3 and to optimize the molecular

structure to obtain a higher potency.

We synthesized and tested a systematic set of I3 derivatives, thus identifying further active molecules and receiving

information about the SAR. According to these results we will accomplish further chemical modifications on I3.

Target identification will be achieved using a pull-down assay and the yeast-3-hybrid system.

Viktoria Reinmüller, Rajwinder Lehal, Kai Johnsson, Jieping Zhu, Freddy Radtke

TARGET IdENTIFICATION ANd OPTImIzATION OF THE NOVEL NOTCH INHIbITOR I3

Cdc48 is essential for many cellular processes. Functional specificity is due to association with substrate adaptors. Depletion of UBXN-2, a Cdc48 adaptor, results in spindle positioning defects in the C. elegans embryo.

We find that UBXN-2 plays a role in the regulation of centrosome maturation timing, which in turn influences spindle alignment with the polarity axis. Our aim is to inhibit CDC48 with high temporal specificity to study its involvement in this process. We will present the development of drug screen strategies using yeast to identify CDC48 inhibitors.

Maria Papaserafeim, Karolina Niewola, Elsa Kress, Francoise Schwager, Robbie Loewith, Monica Gotta

iDentification of inhibitors OF THE TRIPLE A ATP CdC48/P97

Gotta Group, UniGELoewith Group, UniGE

Swiss Institute for Experimental Cancer Research, EPFL

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ase

By establishing a country-wide Academic Chemical Screening Platform for Switzerland (ACCESS) in the frame of the NCCR «Chemical Biology», a long-term strategy for compound management and analytical procedures was defined. We are currently validating the selected hardware infrastructure for hosting and handling the 150-200’000 compounds that will compose the chemical collection. Moreover, an analytical system for quality assessment of compounds has been acquired. This system will assist us to maintain the quality and the integrity of the screening collection.

Antoine Gibelin, Miquel Busquets Lopez, Ruud van Deursen, Manuel Bueno, Damiano Banfi, Gerardo Turcatti

managing, maintaining anD PRESERVING THE INTEGRITYOF THE ACCESS CHEmICAL COLLECTION

Though important for bioactivity, shape diversity of ligands is sparsely used to address a wide variety of biological targets.

For primary screening it is however desirable to identify multiple distinct chemical families to anticipate downstream issues that may arise in any family.

Whereas molecular shape descriptors have been merely used for analytical purposes, we herein describe the selection of a screening collection using these shape descriptors.

Ruud van Deursen, Gerardo TurcattiBiomolecular Screening Facility, EPFLNCCR Chemical Biology

ACCESS SCREENING COLLECTION: SELECTING A dIVERSE LIbRARY uSING mOLECuLAR SHAPE dESCRIPTORS

Biomolecular Screening Facility, EPFLNCCR Chemical Biology

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Our group has developed a series of stable carbocations part of the triangulenium family,

exhibiting good fluorescence properties.The side chains, along with the heteroatoms within the

triangulenium scaffold, can be modulated “at will”, influencing the physical, chemical and optical properties of these cations.

We are currently investigating the possible use of trianguleniums as pH sensitive dyes (project 7),

as fluorescent probes for cell membrane imaging (project 7) and as multipodal platforms (project 1).

Johann Bosson, Jérôme Gouin, Geraldine M. Labrador,Rémi Vanel, Antoine Wallabregue, Jérôme Lacour

STAbLE CARbOCATIONS AS FLuORESCENT dYES ANd muLTIPOdAL PLATFORmS

The library of amphiphilic compounds was developed on the basis of dynamic covalent bonds, and it was screened for transfection activity by using the ACCESS facility. The amphiphiles are expected to transport a polar molecule through a membrane because of their structure: presence of a charged group allows complexation with polar molecules (like DNA), while the presence of hydrophobic tails permits penetration into lipid bilayer.Obtained results showed that our amphiphiles are active both in lipid vesicles and in live cells. Importantly, new amphiphiles containing fullerene scaffolds were synthesized and their properties were investigated.

Oleksandr Kucherak, Charlotte Gehin, Eun-Kyoung Bang, Ana Caxaraville-Leiro, Javier Montenegro, Stefan Matile

dYNAmIC AmPHIPHILES FOR RNAdELIVERY IN CELLS

si

Lacour Group, UniGE

Matile Group, UniGERiezman Group, UniGE

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Direct SuPER-RESOLuTION ImAGING OF CELLuLAR dNA

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Laboratory of Experimental Biophysics, EPFLAlexander Benke, Suliana Manley

Higher-order chromatin structure determines the degree of local DNA condensation, which in turn influences gene accessibility and therefore the expression of particular genes. Conventional imaging methods lack the spatial resolution required for resolving higher-order chromatin structure and dynamics in intact cells.

Here we present a method to address this limitation: super-resolution imaging of directly labeled DNA. The combination of DNA and protein super-resolution imaging will allow us to study chromatin organization at previously inaccessible scales.

The possibility to visualize and investigate membrane domains and cellular uptake processes is one of the most

important biological research areas in the last years. Unfortunately most fluorescent probes are insensitive to their

local environment and most uptake mediators are invisible. Here new fluorescent probes are introduced as an innovative

methodology to label lipid bilayer membranes.

Lessons from nature suggest that the combination of fluorophore polarization and fluorophore planarization could provide an attractive approach to achieve high sensitivity to

membrane fluidity (microdomains), membrane potentialand membrane stretching.

David Alonso Doval, Marta Dal Molin, Andrea Fin, Naomi Sakai, Stefan Matile

PLANARIzAbLE PuSH-PuLL OLIGOTHIOPHENES AS NEw FLuORESCENT mEmbRANE PRObES

The objective of this study is to develop a conceptually new way toward the delivery of cargos into cells by growing poly(disulfide)s directly on a selected thiol-containing cargo.

We recently developed a method to obtain poly(disulfide)s by ring-opening disulfide-exchange polymerization.Our intention is to apply this technique in solution in order to covalently link the cargo and the carrier.This is expected to afford enhanced bioavailability since the cargo will be released in native form selectively inside the cell, where glutathione will be able to depolymerize the toxic carriers.

Giulio Gasparini, Eun-Kyoung Bang, Naomi Sakai, Stefan Matile

CARGO-INITIATEd CELL-PENETRATING POLY(dISuLFIdE)S

Department of Organic Chemistry, UniGE

Department of Organic Chemistry, UniGE

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Notch signalling is a means of inter-cellular communication regulating a wide range of processes such as stem cell division, cell fate determination and proliferation. It is also increasingly recognised as playing a key role in various cancers. The discovery of novel inhibitors of Notch signalling would thus provide new valuable tools for fundamental research, as well as represent putative new therapeutic agents. The Radtke lab has uncovered two such compounds,that we are currently testing and validating in a fruitfly model of Notch-regulated cell fate decision.

Sylvain Loubéry, Rajwinder Lehal, Freddy Radtke, Marcos González-Gaitán

VALIdATION ANd CHARACTERISATION OF NEw NOTCH SIGNALLING inhibitors in D. melanogaster

The Notch1 receptor is known to be mutated in more than 80% of patients suffering from T-cell acute lymphoblastic leukemia.The most frequent mutations arise in the negative regulatory region (NRR), which is normally in a stable and closed conformation, preventing the activation of the receptor.However mutations occurring in the NRR lead to the relaxation of this region and the constitutive activation of the receptor.

By using phage display, we want to select for bicyclic peptides that will keep the mutated NRR in its closed conformation in order to decrease or prevent the activation of the signaling pathway.

Charlotte Varenne, Rajwinder Lehal, Christian Heinis, Freddy Radtke

FINdING bICYCLIC PEPTIdE INHIbITORS to the notch1 receptor

Swiss Institute for Experimental Cancer Research, EPFL

Gonzáles-Gaitán Group, UniGESwiss Institute for Experimental Cancer Research, EPFL

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L-PBE is the second enzyme of the inducible peroxisomal β-oxidation pathway. We show that L-pbe-/- mice fed a diet rich in

coconut oil die from fulminant liver failure, with massive hepatic inflammation and fibrosis.

These events are caused by activation of the ω-oxidation and accumulation of dicarboxylic fatty acids (DCA). Inhibition of

ω-oxidation by the non-specific inhibitor ABT suppressed DCA production and protected L-pbe-/- mice against liver damage.

The primary goal of this project is to establish DCA as a new etiological factor of hepatitis and to develop new

inhibitors against ω-oxidation.

Ursula Loizides-Mangold, Jun Ding, Gianpaolo Rando, Janardan K. Reddy, Walter Wahli, Howard Riezman, Bernard Thorens

dICARbOxYLIC FATTY ACId ACCumuLATIONIN L-PbE dEFICIENT mICE CAuSES

ACuTE LIVER INFLAmmATION ANd HEPATIC FAILuRE

Yvan Bouza, Elena A Dubikovskaya, Robbie J. Loewith

purification of torc1 from s. cerevisiae uSING A RAPAmYCIN ANALOG wITH A CHEmICAL TAG

In eukaryotes, the Target Of Rapamycin (TOR) protein kinase plays a central role in the regulation of cell growth. TOR protein kinase can form two complexes, TORC1 and TORC2, but only TORC1 is sensitive to the drug rapamycin. Here, we developed an analog of rapamycin bearing an azido moiety and we intend to conjugate it with a biotinylated alkyne in order to fish out TORC1 from cells and to perform structural studies on TORC1. Relative to genetically encoded protein tags, this approach doesn’t require gene manipulation and thus should enable us to obtain TORC1 from a variety of native sources.

Laboratory of Bioorganic Chemistry and Molecular Imaging, Institute of Chemical Sciences and Engineering, EPFLDepartment of Molecular Biology and NCCRs Frontiers in Genetics and Chemical Biology, UniGE

Center for Integrative Genomics, NCCR Frontiers in Genetics, UniLDepartment of Biochemistry, NCCR Chemical Biology, UniGEDepartment of Pathology, Northwestern University, Chicago, USA

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Bo Yao, Qian Wang, Jieping Zhu*

Pd(II)-CATALYzEd dOmINO REACTIONS OF ALkYNES TO FORm INdOLO[3,2-C]ISOquINOLINONES

Polyheterocycles with an embedded 3-aminoindole moiety are found in a number of natural products and bioactive synthetic compounds.Recently, indolo[3,2-c]isoquinolinones (see picture) were reported to have interesting biological activities.

As part of our ongoing research, which deals with palladium-catalyzed domino processes for the synthesis of hetero-cycles, we developed an efficient and practical synthesis of indolo[3,2-c]isoquinolinones. The biological activitiy of indolo[3,2-c]isoquinolinones will be investigated in the future.

A mild and general alumina-promoted hydrolysis of α-iminonitriles to amides was developed. In combination with the oxidative three-component Strecker reaction, a one-pot amidation of aldehydes and alcohols was documented.

We subsequently detailed an Yb(OTf)3-catalyzed Michael addition of thiols to α,β-unsaturated α-iminonitriles for the synthesis of β-mercapto-α-iminonitriles.Successful integration of both processes allowed us to develop a direct conversion of an amine, an aldehyde and a thiol to a β-mercaptoamide. All theses protocols were applicable to aromatic as well as aliphatic amines and aldehydes.

Jean-Baptiste Gualtierotti, Xavier Schumacher, Patrice Fontaine, Géraldine Masson, Qian Wang, Jieping Zhu*

CHEmISTRY OF α-ImINONITRILES

Institute of Chemical Sciences and Engineering, EPFLCentre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS

Laboratory of Synthesis and Natural Products, EPFL

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Don’t miss...

OuR NExT mONTHLY NCCR CHEmICAL bIOLOGY group meetings

We propose to increase communication across projects within the NCCR Chemical Biology through monthly gatherings.

We hope this will stimulate conversations and collaborations that take advantage of theNCCR network to achieve advances not possible through individual siloed research efforts.

oct 1816:00 - 17:30

sept 2016:00 - 17:30

NOV 14 & 15ALL dAY

Dec 1316:00 - 17:30

Project 6Project 3

Project 1Project 2

SNSF Site Review : Year 2all projects + poster session

Project 5Project 7

EPFL

UniGE

EPFL

UniGE

All Group Leaders and their lab are invited to each session.

The National Centre of Competence in Research (NCCR) «Chemical Biology » uses chemistry tools to obtain a better understanding of life at the molecular level.

Until now, few technologies could characterise in detail the countless biochemical activities that constitute a living cell.

In the NCCR Chemical Biology, chemists, biochemists, physicists and cell biologists develop innovative techniques based on small molecules and proteins to obtain new information about cellular processes and control them in situ.

The new tools will be applicable to various biological phenomena like visualising the activity of selected proteins during cell division and investigating how membranes control the activity of proteins in them.

THE NCCR CHEmICAL bIOLOGY

Co-directorsHoward Riezman (above)& Kai Johnsson (below)

NCCR Chemical BiologyUniversité de Genève

Faculté des Sciences, bur. 146Quai Ernest-Ansermet 30

1211 Genève 4 www.nccr-chembio.ch

+41 022 379 64 07

SuPPORTEd bY

contact us

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PRACTICAL INFORmATION

map of the seminar rooms

Hôtel du LémanChemin de la Fontaine 2, 1805 Jongny

Gare de Vevey

Gare de Jongny-village