PARISFOLDAMERS2013 SYMPOSIUM  Les Cordeliers ͼ Latin Quarter ͼ Paris ͼ France  10 Ͳ12 April 2013



  PARISFOLDAMERS2013 SYMPOSIUM  Les Cordeliers ͼ Latin Quarter ͼ Paris ͼ France  10 Ͳ12 April 2013 





 ORGANIZATION 

Co Ͳchairmen 

David J. Aitken (ICMMO Ͳ Université Paris Sud, Orsay)  Ivan Huc (IECB &CBMN, CNRS –Université de Bordeaux) 

Scientific Committee 

D. J. Aitken (Université Paris Sud), I. Huc (CNRS –Université de Bordeaux),  T. A. Martinek (University of Szeged), R. M. Ortuño (Universitat Autònoma de  Barcelona), A. J. Wilson (University of Leeds), F. Fülöp (University of Szeged) 

Symposium Management 

Lina Boitier (ICMMO Ͳ Université Paris Sud, Orsay)    

SPONSORS AND PARTNERS 





 

WELCOME



It is our pleasure to welcome all delegates to this three Ͳday scientific meeting devoted to  state Ͳof Ͳthe Ͳart foldamer science. Our symposium will focus on various aspects of the design  and preparation of foldamers, the structural characterization of their structures and folding  propensity,  and  their  properties  and  function.  A prime  objective  will  be  to  illustrate  the  multidisciplinary aspects of the field. 

In testimony to the tremendous developments in this emerging area, the symposium is held  under the joint European patronage of the COST Action CM0803 and the Marie Curie IAPP  FOLDAPPI  project  (FP7),  both  of  which  are  dedicated  to  the  advancement  of  foldamers.  However  with  speakers  and  participants  coming  from  more  than  20  different  countries  across Europe, Asia and America, this is the largest scientific meeting focussing on foldamer  science to date. 

The  European  networks  will  draw  to  a close  in  2013,  but  we  believe  that  they  will  have  served as aspringboard, for fostering future international cooperation and progress, and for  stimulating greater interest in neighbouring bioscience and therapeutics fields.  We sincerely  hope that this meeting will contribute towards those goals. 

We wish you avery warm welcome to Paris and we hope you will enjoy the symposium. 



David J. Aitken, Ivan Huc  Co Ͳchairmen  

THE CONFERENCE VENUE Ͳ LES CORDELIERS, PARIS



Les  Cordeliers  is  a refreshingly  peaceful  academic centre located in the heart of  the  Latin  Quartier,  surrounded  by  the  lively atmosphere of the Paris Left Bank.





Historically,  the  area  was  occupied  by  religious orders, and Les Cordeliers was  inhabited by Franciscan monks from as  early as the 13th Century. 





During  the  French  Revolution,  the  monks  were  expelled  and  the  site  became  famous  for  hosting  the  Society for Human and Citizen Rights,  and the Club des Cordeliers ,animated  by renowned revolutionaries including  Danton,  Desmoulins,  Hébert  and  Marat. 



Today,  the  campus  belongs  to  the  City  of  Paris  and  serves partly as aconference centre. It also plays host  to the Faculty of Medicine of Université Pierre &Marie  Curie  Ͳ Paris  Universitas,  as  well  as  the  Centre  de  Recherche  des  Cordeliers  (CRC),  a joint  university Ͳ hospital research unit. 

  SYMPOSIUM PROGRAMME 

TUESDAY 9APRIL 

14h00 Ͳ18h00  Arrival /Registration  16h00 Ͳ18h00  MC Meeting (COST only) 

WEDNESDAY 10 APRIL 

8h00 –9h00  Arrival /Registration  9h10 –9h25  Chairmen’s Welcome 

Session Chair: Andy Wilson  9h25 –10h15  PL1  Jean ͲMarie Lehn (Université de Strasbourg, France)  Controlled folding and motional dynamics of polyheterocyclic molecular  strands and their metallosupramolecular architectures 

10h15 –10h45  Coffee break 

Session Chair: Rosa Ortuño  10h45 –11h05  SL1  Young Kee Kang (Chungbuk National University, South Korea)  ɲͲ Peptide foldamers based on 2Ͳ(aminomethyl)cyclohexanecarboxylic acid  11h05 –11h25  SL2  Knud J. Jensen (University of Copenhagen, Denmark)  Higher Ͳorder self Ͳassembly of proteins  11h25 –11h55  KL1  James S. Nowick (University of California, Irvine, USA)  The supramolecular chemistry of EͲsheet foldamers  11h55 –12h25  KL2  Gangadhar J. Sanjayan (National Chemical Laboratory, Pune, India)  Diversifying the foldamer architecture: the aliphatic Ͳaromatic hybrid  foldamer approach 

12h25 –14h00  Lunch +poster viewing 

Session Chair: Luc Brunsveld  14h00 –14h50  PL2  Stephen Kent (University of Chicago, USA)  Chemical protein synthesis: racemic protein crystallography and DͲprotein  therapeutics  14h50 –15h20  KL3  Thomas R. Ward (University of Basel, Switzerland)  Artificial metalloenzymes based on the biotin Ͳavidin technology: recent  advances and challenges  15h20 –15h40  SL3  Miriam Royo (University of Barcelona, Spain)  Cis ͲɶͲ LͲproline peptides as multifunctional platforms scaffolds for diverse  therapeutic applications  15h40 –16h00  SL4  Jonathan Farjon (Université Paris Sud, France)  Anew NMR tool to probe hydrogen bonds in EͲpeptide foldamers 

16h00 –16h30  Coffee &refreshments break  Session Chair: Fernando Formaggio  16h30 –16h50  SL5  Aya Tanatani (Ochanomizu University, Tokyo, Japan)  Aromatic foldamers based on the cis conformational preference of  NͲalkylated aromatic amide and urea bonds  16h50 –17h10  SL6  Tamás A. Martinek (University of Szeged, Hungary)  Targeting solvent exposed protein surfaces with peptidic foldamers  17h10 –18h00  PL3  Stephen G. Davies (University of Oxford, UK)  Solid and solution phase conformational preferences of EͲpeptides derived  from transpentacin and 3Ͳalkyltranspentacin 

THURSDAY 11 APRIL 

Session Chair: Gilles Guichard  9h00 –9h50  PL4  Peter B. Dervan (California Institute of Technology, USA)  Is the DNA binding hairpin Py ͲIm ͲHp polyamide an archetypical foldamer?  9h50 –10h20  KL4  Oliver Reiser (Universität Regensburg, Germany)  Cyclic cis ͲEͲaminocarboxylic acids –versatile constituents in foldamers 

10h20 –10h50  Coffee break 

Session Chair: Claudia Tomasini  10h50 –11h10  SL7  Nozomi Saito (Tohoku University, Japan)  Synthesis and two Ͳcomponent lyotropic liquid crystal formation of  cyclobis(ethynylhelicene)oligomer  11h10 –11h30  SL8  Emeric Miclet (Université Pierre et Marie Curie, Paris, France)  How the helical fold of peptidomimetic urea oligomers behaves in aqueous  solution? New insights from the NMR spectroscopy of methylene groups  11h30 –12h00  KL5  Jonathan Clayden (University of Manchester, UK)  Torque talk: conformational communication through helical molecules  12h00 –12h30  KL6  Kent Kirshenbaum (New York University, USA)  From chaos to control: design of functional peptoid oligomers 

12h30 –14h00  Lunch +poster viewing 

Session Chair: Sven Mangelinckx  14h00 –14h50  PL5  Hiroaki Suga (University of Tokyo, Japan)  Non Ͳtraditional peptide “foldamer” discovery accelerated by the RaPID  system  14h50 –15h20  KL7  Helma Wennemers (ETH Zurich, Switzerland)  Peptides as Asymmetric Catalysts  15h20 –15h40  SL9  Aloysius Siriwardena (CNRS Laboratoire des Glucides, Amiens, France)  Effects of co Ͳ and post Ͳtranslational modification by sugars on peptide  folding: insights from astudy of afamily of “glyco”–foldamers  15h40 –16h00  SL10  Olga Iranzo (Universidade Nova de Lisboa, Portugal)  Harnessing the flexibility of peptidic scaffolds to control their copper(II)  coordination properties: apotentiometric and spectroscopic study  16h00 –16h30  Coffee &refreshments break 

Session Chair: Juha Rouvinen  16h30 –16h50  SL11  Alessandro Moretto (University of Padova, Italy)  Reversible chirality control in peptide Ͳfunctionalized gold nanoparticles  16h50 –17h10  SL12  Sophie Faure (Clermont Université, France)  Control of amide cis Ͳtrans isomerism in peptoid: “directing” side chains to  promote stable secondary structures  17h10 –18h00  PL6  Ferenc Fülöp (University of Szeged, Hungary)  Cyclic EͲamino acids: an unlimited field 

FRIDAY 12 APRIL 

Session Chair: Alison Edwards  9h00 –9h30  KL8  Bing Gong (State University of New York at Buffalo, USA)  Cavity Ͳcontaining aromatic oligoamide foldamers and macrocycles  9h30 –9h50  SL13  Ona Illa (Universitat Autónoma de Barcelona, Spain)  Hybrid cyclobutane peptides: influence of the spacer on their folding in  solution and on their gelation ability  9h50 –10h10  SL14  András Perczel (Eötvös L. University, Budapest, Hungary)  Foldamer stability coupled to aggregation propensity of elongated Trp Ͳcage  miniproteins 

10h10 –10h40  Coffee break 

Session Chair: Norbert Sewald  10h40 –11h10  KL9  Martin D. Smith (University of Oxford, UK)  Can aCͲH•••O interaction be adeterminant of conformation?  11h10 –12h00  PL7  Samuel H. Gellman (University of Wisconsin, USA)  Mimicry of protein recognition surfaces with peptidic foldamers 

12h00 –12h15  Concluding remarks 



  PROGRAMME AT AGLANCE 

     LECTURES

 Plenary Lecture PL1

Controlled Folding and Motional Dynamics of Polyheterocyclic Molecular Strands and their Metallosupramolecular Architectures

Jean-Marie Lehn

ISIS, Université de Strasbourg

Molecular self-organization is reflected in the ability to generate specific structural patterns by design. In particular, the folding of molecular strands may be controlled by the implementation of folding codons (foldons) , allowing for the control of molecular folding through structure enforcing subunits. Supramolecular self-organization explores systems capable of spontaneously generating well- defined functional supramolecular architectures by self-assembly from their components, on the basis of the molecular information stored in the covalent framework of the components and read out at the supramolecular level through specific interactional algorithms. At both levels, the processes represent the behaviour of programmed chemical systems . The broad case of polyheterocyclic strands and their interaction with metal cations will be presented, involving: - the powerful structure enforcing features of selected sequences of heterocylic groups, based on non-bonded intramolecular interactions; - the generation of given metallosupramolecular architectures by the complexation of these strands with metal cations presenting a specific coordination geometry; - the functional features of the parent strands and their metal complexes, in particular the dynamic structural changes involved in the strand/complex folding/unfolding interconversion, generating molecular mechanical motion. The three features, molecular design , selection of coordination processes and motional dynamics allow for a broad range of structural and functional features of interest in particular for nanoscience and nanotechnology.

References ¾ G.S. HANAN , J.-M. LEHN , N. KYRITSAKAS , J. FISCHER , “Molecular helicity: a general approach for helicity induction in a polyheterocyclic molecular strand ”, J. Chem. Soc., Chem. Commun., 765-766, 1995. ¾ M. OHKITA , J.-M. LEHN , G. BAUM , D. FENSKE , “Helicity coding: Programmed molecular self-organization of achiral nonbiological strands into multiturn helical superstructures: Synthesis and characterization of alternating pyridine - pyrimidine oligomers ”, Chem. Eur. J. 5, 3471-3481, 1999. ¾ M. BARBOIU , J.-M. LEHN , ”Dynamic chemical devices: Modulation of contraction/extension molecular motion by coupled-ion binding/pH change-induced structural switching ”, Proc. Natl. Acad. Sci. USA, 99 , 5201-5206, 2002. ¾ J.-L. SCHMITT , A.M. STADLER , N. KYRITSAKAS , J.-M. LEHN , “Helicity-encoded molecular strands: Efficient access by the hydrazone route and structural features ”, Helv. Chim. Acta, 86 , 1598-1624, 2003. ¾ A.-M. STADLER , N. KYRITSAKAS , R. GRAFF , J.-M. LEHN , “Formation of rack- and grid-type metallosupramolecular architectures and generation of molecular motion by reversible uncoiling of helical ligand strands ”, Chem. Eur. J., 12, 4503-4522, 2006.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL1

J-Peptide Foldamers Based on 2-(Aminomethyl)cyclohexanecarboxylic Acid

Young Kee Kang

Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea [email protected]

The conformational preferences of turn and helix foldamers of J-peptides of 2- D E (aminomethyl)cyclohexanecarboxylic acid ( JAmc 6) with a cyclohexyl constraint on the C C bond have been carried out using density functional methods in water. The chirospecific JAmc 6 dipeptide with the (2 S,3 S)-(2 R,3 R) configurations forms a stable turn structure in water, resembling a type II ' turn of D-peptides, which can be used as a E-turn motif in E-hairpins of Ala-based D- [1] peptides. The JAmc 6 dipeptide with homochiral (2 S,3 S)-(2 S,3 S) configurations but different cyclohexyl puckerings shows the capability to be incorporated into one of two E-turn motifs of gramicidin S. The helical structures of the JAmc 6 oligopeptides with homochiral configurations are known to be much stable than those with heterochiral configurations in the gas phase and in [2] solution (chloroform and water). In particular, it is found that the ( P/M)-2.5 14 -helices are most preferred in the gas phase and in chloroform, whereas the ( P/M)-2.3 12 -helices become most populated in water due to the larger helix dipole moments. As the peptide sequence becomes longer, the helix propensities of 14- and 12-helices are found to increase both in the gas phase and in solution. The JAmc 6 peptides longer than octapeptide are expected to exist as a mixture of 12- and 14-helices with the similar populations in water. The mean backbone torsion angles and helical parameters of the 14-helix foldamers of JAmc 6 oligopeptides are quite similar to those of 2- 2,3,4 aminocyclohexylacetic acid oligopeptides and J -aminobutyric acid tetrapeptide in the solid state, despite the different substituents on the backbone. Our calculated results and the recently observed results may imply the wider applicability of chirospecific J-peptides with a cyclohexyl constraint on the backbone to form various peptide foldamers.

Figure 1. Chemical structure of 2-(aminomethyl)cyclohexanecarboxylic acid ( JAmc 6).

References [1] Y. K. Kang, B. J. Byun, Biopolymers 2012 , 97 , 1018. [2] B. J. Byun, Y. K. Kang, Biopolymers 2013 , submitted to.

This research was supported by the National Research Foundation of Korea (NRF 2010-0021076).

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL2

Higher-order self-assembly of proteins

Henrik K. Munch, Leila Malik, Knud J. Jensen

Department of Chemistry, University of Copenhagen, Denmark [email protected]

The oligomeric state of peptides and proteins and proteins is central for their biological function and for the pharmaceutical efficacy of their therapeutic preparation. Here we present application of ligands for the control of peptide and protein self-assembly to form higher-order nano-scale assemblies. They utilize either selective complexation with di-valent metal ions or bio-orthogonal fluorous interactions [1,2] . Insulin, a small protein with three disulfide bridges, is a widely used biopharmaceutical drug for the management of glucose levels in diabetic patients. Human insulin forms a hexamer around a Zn(II) ion, as insulin has an inherent ability to form hexamers by combining three dimers, where each dimer has an antiparallel orientation. Several variants of insulin have been developed that are either fast- or long-acting, mainly by controlling the diffusion rates from subcutaneous depots via manipulations of insulin oligomer states. New methods to control insulin self-assembly and dissociation are thus highly relevant and could lead to new long-acting drugs. Here we describe the introduction of a second metal ion binding site in insulin for controlled nano-scale self-assembly and its characterization by UV-Vis and CD spectroscopy, and small angle X-ray scattering (SAXS). Furthermore, we report the synthesis and biophysical evaluation of a series of insulin variants with perfluoroalkyl substituents. Perfluorinated alkyl chains of varying length were attached by acylation of the İ-amino position of the side chain of LysB29. This surface exposed substituent enables intermolecular fluorous interactions leading to self-assembly, as a new and orthogonal approach to direct the self-assembly of proteins. The self-assembly was studied using SAXS and dynamic light scattering (DLS).

Figure 1. Human insulin forms stable hexamers in the presence of divalent cations such as zinc. Introduction of a metal ligand on each insulin monomer enables the combination of native and abiotic self-assembly. A: Human insulin - bipyridine forms hexamer in the presence of Zn 2+ , whereas Fe 2+ preferentially coordinates to bipyridine.

References [1] J. Nygaard, H. K. Munch, P. W. Thulstrup, N. J. Christensen, T. Hoeg-Jensen, K. J. Jensen, L. Arleth, Langmuir 2012 , 28, 12159-12170. [2] H. K. Munch, S. T. Heide, N. J. Christensen, T. Hoeg-Jensen, P. W. Thulstrup, K. J. Jensen , Chem. Eur. J. 2011, 17 , 7198-7204. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL1

The Supramolecular Chemistry of E-Sheet Foldamers

James S. Nowick

Department of Chemistry, University of California, Irvine, Irvine, California USA [email protected]

E-Sheets exhibit rich patterns of intermolecular interactions that are ubiquitous in peptide and protein aggregation, protein-protein interactions, and protein quaternary structure. Our laboratory is using foldamers that adopt E-sheet structures and participate in E-sheet interactions to understand and control the supramolecular chemistry of E-sheets. We have developed families of macrocyclic peptides containing unnatural turn and template units that fold into well-defined E-sheet structures. X-ray crystallography and 1H NMR spectroscopic studies in aqueous solution show that the macrocyclic E-sheets form well-defined hydrogen-bonded dimers that further assemble to form tetramers and other higher-order assemblies. We have used these folded macrocycles to inhibit the aggregation of peptides and proteins associated with Alzheimer's and other amyloid diseases and to gain insights into the aggregation processes. This talk will describe our studies of the folding and supramolecular chemistry of these macrocyclic E-sheet foldamers.

O R O R O R O R O R 1 H 3 H 5 H 7 H 9 H + H3N N N N N N N N N N N CH 2 H H H H H H2C O R2 O R4 O R6 O R8 O CH 2 H C O R O O R O O CH 2 H 11 H H 10 H H 2 H2C N N N N N + N N N N N NH 3 H H H H H R O O O O O 12 O O Me Me

Selected Relevant Publications 1. "An Unnatural Amino Acid that Mimics a Tripeptide E-Strand and Forms E-Sheetlike Hydrogen-Bonded Dimers" Nowick, J. S.; Chung, D. M.; Maitra, K.; Maitra, S.; Stigers, K. D.; Sun, Y. J. Am. Chem. Soc . 2000 , 122 , 7654- 7661. 2. "A New Turn Structure for the Formation of E-Hairpins in Peptides", Nowick, J. S.; Brower, J. O. J. Am. Chem. Soc . 2003 , 125 , 876-877. 3. "Cyclic Modular £-Sheets" Woods, R. J.; Brower, J. O.; Castellanos, E.; Hashemzadeh, M.; Khakshoor, O.; Russu, W. A.; Nowick, J. S. J. Am. Chem. Soc. 2007 , 129 , 2548-2558. 4. "Macrocyclic £-Sheet Peptides that Mimic Protein Quaternary Structure through Intermolecular £-Sheet Interactions" Khakshoor, O.; Demeler, B.; Nowick, J. S. J. Am. Chem. Soc. 2007 , 129 , 5558-5569. 5. "Exploring £-Sheet Structure and Interactions with Chemical Model Systems" Nowick, J. S. Acc. Chem. Res. 2008 , 41 , 1319-1330. 6. "X-ray Crystallographic Structure of an Artificial ȕ-Sheet Dimer" Khakshoor, O.; Lin, A. J.; Korman, T. P.; Sawaya, M. R.; Tsai, S.-C.; Eisenberg, D.; Nowick, J. S. J. Am. Chem. Soc. 2010 , 132 , 11622-11628. 7. "Macrocyclic ȕ-Sheet Peptides that Inhibit the Aggregation of a Tau-Protein-Derived Hexapeptide" Zheng, J.; Liu, C.; Sawaya, M. R.; Vadla, B.; Khan, S.; Woods, R. J.; Eisenberg, D.; Goux, W. J.; Nowick, J. S. J. Am. Chem. Soc. 2011 , 133 , 3144-3157. 8. "Characteristics of Amyloid-Related Oligomers Revealed by Crystal Structures of Macrocyclic ȕ-Sheet Mimics" Liu, C.; Sawaya, M. R.; Cheng, P.-N.; Zheng, J.; Nowick, J. S.; Eisenberg, D. J. Am. Chem. Soc. 2011 , 133 , 6736- 6744. 9. "Heterodivalent Linked Macrocyclic ȕ-Sheets with Enhanced Activity against A ȕ Aggregation: Two Sites are Better than One." Cheng, P.-N.; Spencer, R.; Woods, R. J.; Glabe, C. G.; Nowick, J. S. J. Am. Chem. Soc. 2012 , 133 , 14179-14184. 10. "Amyloid ȕ-Sheet Mimics that Antagonize Protein Aggregation and Reduce Amyloid Toxicity" Cheng, P.-N.; Liu, C.; Zhao, M.; Eisenberg, D.; Nowick, J. S. Nature Chemistry 2012 , 4, 927-933. doi:10.1038/nchem.1433. 11. "Out-of-Register ȕ-Sheets Suggest a Pathway to Toxic Amyloid Aggregates" Liu, C.; Zhao, M.; Jiang, L.; Cheng, P.-N.; Park, J.; Sawaya,. M. R.; Pensalfini, A.; Gou, D.; Berk, A. J.; Glabe, C. G.; Nowick, J. S.; Eisenberg, D. Proc. Natl. Acad. Sci. U. S. A. 2012 , 109 , 20913-20918 .

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL2

Diversifying the Foldamer Architecture: The Aliphatic-Aromatic Hybrid Foldamer Approach

Gangadhar J. Sanjayan

Division of Organic Chemistry, National Chemical Laboratory, Pune 411008, India [email protected]

The folding and assembly of biomolecules, by means of a collection of non-covalent interactions, are two of the most important events observed in the world of biomolecular science. In an attempt to mimic the bio-machineries, both structurally and functionally, synthetic oligomers were designed and developed. In this context, an area of research that has attained enormous attention in recent years is foldamers whose objective is the development of “conformationally ordered synthetic oligomers” mimicking the conformational features of biopolymers. [1]

The major thrust of our research focus is in the generation of conformationally ordered synthetic scaffolds capable of displaying diverse secondary structural features. Scaffolds with well-defined secondary structural preferences ( i.e. helices, sheets, or turns) could, for example, be used to create new types of tertiary structures, which in turn may have medicinal applications, e.g. for disruption of specific protein-protein interactions. Over the last few years, we have been able to develop and report diverse class of conformationally ordered synthetic peptide structures displaying remarkable conformational ordering, as would be evident from their biophysical studies. [2] This talk will cover our recent efforts directed towards the generation of novel conformationally ordered synthetic oligomers featuring aromatic-aliphatic backbones.

References [1] S. H. Gellman. Acc. Chem. Res ., 1998 , 31 , 173 [2] Sanjayan et al : Chem. Commun ., 2012 , 48 , 11205; Chem. Commun ., 2012 , 48 , 9747; Chem. Commun ., 2012 , 48 , 8922; Angew. Chem., Int. Ed . 2012 , 51 , 4006; Chem. Commun ., 2011 , 47, 11593; Chem. Commun ., 2009 , 3446; Chem. Commun ., 2008 , 712; Chem. Commun ., 2008 , 2541; J. Am. Chem. Soc ., 2008 , 130 , 17743.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Plenary Lecture PL2

Chemical Protein Synthesis: Racemic Protein Crystallography & D-Protein Therapeutics

Stephen Kent

Department of Chemistry, Department of Biochemistry & Molecular Biology, Institute for Biophysical Dynamics, University of Chicago, Chicago, USA [email protected]

The total synthesis of proteins & enzymes was one of the 'Grand Challenges' of 20th century chemistry. Despite decades of development by skilled organic chemists throughout the world, conventional synthetic methods were able to reproducibly make only the smallest protein molecules. To overcome this size limitation, in 1992 we introduced the 'chemical ligation’ concept: chemoselective reaction forming an analogue structure linking two unprotected synthetic peptide segments. [1] Then, in 1994 we introduced ‘native chemical ligation’: thioester-mediated chemoselective condensation of unprotected peptides to give a native peptide bond linking two peptide segments .[2] The chemical ligation concept as realized in native chemical ligation forms the basis of modern methods that enable the practical total chemical synthesis of a wide range of protein molecules, including enzymes. [3] Synthetic products are characterized at high resolution by LCMS for purity and covalent structure, by multidimensional NMR for unique fold, and by X-ray crystallography to reveal the tertiary structure of the synthetic protein molecule. Chemical protein synthesis gives precise, atom-by-atom control over the complete covalent structure of a protein molecule, and enables the incorporation of a wide range of non-coded building blocks and the introduction of isotope labels with single atom precision. Here I will present case studies to illustrate the application of chemical protein synthesis to the preparation of ‘mirror image’ D-protein molecules, to the use of racemic crystallography for protein structure determination, [4][5][6] and to the systematic creation of a potent D-protein antagonist of VEGF-A as a candidate human therapeutic. [7]

References [1] Constructing proteins by dovetailing unprotected synthetic peptides: backbone engineered HIV protease. Martina Schnölzer, Stephen B.H. Kent Science , 256 , 221-225 (1992). [2] Synthesis of proteins by native chemical ligation. Philip E. Dawson, Tom W. Muir, Ian Clark-Lewis, Stephen B.H. Kent, Science , 266 , 776-779 (1994). [3] Total chemical synthesis of proteins. Stephen B.H. Kent, Chemical Society Reviews , 38 , 338-51 (2009). [4] Racemic protein crystallography. Todd O. Yeates, Stephen B.H. Kent, Ann. Review Biophysics , 41 , 41–61 (2012). [5] Design, total chemical synthesis, and X-ray structure of a protein having a novel polypeptide chain topology. Kalyaneswar Mandal, Brad L. Pentelute, Duhee Bang, Zachary P. Gates, Vladimir Yu. Torbeev, Stephen B. H. Kent, Angewandte Chem Int Ed , 51 , 1481-1486 (2012). [6] Convergent chemical synthesis of ester insulin: determination of the high resolution X-ray structure by racemic protein crystallography. Michal Avital-Shmilovici, Kalyaneswar Mandal, Zachary P. Gates, Nelson Phillips, Michael A. Weiss, Stephen B.H. Kent, J Am Chem Soc, 135 , 3173–3185 (2013). [7] Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus VEGF-A} protein complex by racemic crystallography. Kalyaneswar Mandal, Maruti Uppalapati, Dana Ault-Riché, John Kenney, Joshua Lowitz, Sachdev Sidhu, Stephen B.H. Kent, Proc Natl Acad Sci USA, 109 , 14779-14784 (2012) .

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL3

Artificial Metalloenzymes Based on the Biotin-Avidin Technology: Recent Advances and Challenges

Thomas R. Ward

Department of Chemistry, University of Basel, Spitalstrasse 51, CH-4056 Basel, Switzerland [email protected]

Artificial metalloenzymes result from incorporation of a catalytically competent organometallic moiety within a host protein. We have been exploiting the potential of the biotin-avidin technology for the creation of artificial metalloenzymes. Thanks to the remarkable affinity of biotin for either avidin or streptavidin, covalent linking of a biotin anchor to a catalyst precursor ensures that, upon stoichiometric addition of (strept)avidin, the metal moiety is quantitatively incorporated within the host protein. Such artificial metalloenzymes are optimized either by chemical (variation of the biotin-spacer- ligand moiety) or genetic (mutation of (strept)avidin) means. Such chemogenetic optimization schemes were applied to various organic transformations. The reaction implemented thus far include: 1) The rhodium catalyzed hydrogenation of N- protected dehydroaminoacids (ee up to 95 %). 2) The palladium catalyzed allylic alkylation (ee up to 95%). 3) The ruthenium pianostool catalyzed transfer hydrogenation of prochiral ketones and imines (ee up to 97 %). 4) The vanadyl catalyzed oxidation of prochiral sulfides (ee up to 93 %). 5) The osmium catalyzed dihydroxylation of olefins (ee up to 97 %). 6) The ruthenium catalyzed oxidation of alcohol to ketones and the ruthenium catalyzed olefin metathesis. Noteworthy features, reminiscent of homogeneous catalysis include: the straightforward access to both enantiomers of the product; broad substrate scope; organic solvent tolerance and reactions typical of homogeneous catalysis. Enzyme-like features include: genetic optimization; aqueous medium as the preferred solvent; Michaelis-Menten behaviour; single substrate derivatization. X-ray characterization of artificial metalloenzymes provide a fascinating insight into possible enantioselection mechanism involving a well-defined second coordination sphere environment. Thus, such artificial metalloenzymes combine attractive features of both homogeneous and enzymatic kingdoms. After presenting an overview of recent results for the above reactions, the last part of the talk will outline our current efforts on performing catalysis on crude cell extracts, thus paving the way towards in vivo catalysis and directed evolution of artificial metalloenzymes.

Figure 1.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL3

Cis- J-amino-L-proline peptides as multifunctional platforms scaffolds for diverse therapeutic applications

Daniel Carbajo, a Ximena Pulido, a Almudena López-Sánchez, b Josep Farrera-Sinfreu, c Elena Rebollo, d Luis Rivas, b Fernando Albericio, c Miriam Royo a

a Combinatorial Chemistry Unit, Barcelona Science Park-University of Barcelona, Barcelona, Spain, bCentro de Investigaciones Biológicas, CSIC, Madrid, cInstitute for Research in Biomedicine, Barcelona Science Park, Barcelona, Spain, dAdvanced Fluorescence Microscopy Unit Fluorescence, Molecular Biology Institute of Barcelona-CSIC, Barcelona, Spain. [email protected]

Foldamer chemistry has become a useful tool to develop new chemical entities with well-defined secondary structure that can mimic protein interactions and consequently to be applied to explore [1] their use on a variety of therapeutic applications. Our group has described a family of J-peptides based on (2S, 4S)-4-amino-L-proline with well-defined secondary structure amenable for solid- phase synthesis with just one type of protected monomer with easy functionalization by introduction of diverse side chain mimetics. [2] Members of these family showed cell-uptake properties, low cytoxicity and imperviousness to proteolytic attack. [3] Under these experimental premises we have designed and synthesized a discrete library of J- peptides with diverse functionalization pattern with the aim to improve their translocation across cell membranes in order to establish SAR relationships. The ability to cross cell membranes have been estimated by flow cytometry and confocal microscopy in two different systems: HeLa cells as model of mammalian cells and Leishmania as a protozoan parasite model with a challenging membrane system. In both cases cellular internalization of some J-peptides members of the library superseded Tat, a gold-standard for cell penetrating peptides The modulation of the cell entry by diverse factors, such as peptide concentration, time, cell type and temperature was also documented, The cellular internalization pathway for those peptides with the highest capacity to cross cell membranes was assessed by specific inhibitors for the different endocytosis pathways. A preferential localization of these peptides in lysosomes was assessed by colocalization with specific fluorescent probes for different subcellular organelles (nuclei, mitochondria, lysosome, endoplasmic reticulum and golgi apparatus). The capacity to transport cargo molecules of interest for diverse therapeutic applications was also studied. Altogether, the J-peptide scaffold based on (2S, 4S)-4- amino-L-proline demonstrated a high versatility and potential application in nanotechnological applications in biology and biomedicine. [4]

Figure 1. General structure of the J-peptides library studied.

References [1] W. Seth Horne, Expert Opin. Drug Discov. 2011 , 6, 1247. [2] J. Farrera-Sinfreu, E. Giralt, S. Castel, F. Albericio, M. Royo, J.Am. Chem. Soc. 2005 ,127, 9459. [3] J. Farrera-Sinfreu, L. Zaccaro, D. Vidal, X.Salvatella, E. Giralt, M. Pons, F. Albericio, M. Royo J. Am. Chem. Soc . 2004 , 126, 6048. [4] Financial support: PI09-01928, PI12-02706, RD12/0018/0007 (L.R.) and CTQ2008-00177, SAF2011-30508-C02- 01 (M.R.).

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL4

A new NMR tool to probe hydrogen bonds in E-peptide foldamers

Jonathan Farjon, a Valérie Declerck, b Amandine Altmayer-Henzien, b David J. Aitken, b Denis Merlet a

aEquipe de RMN en Milieu Orienté, bEquipe de Synthèse Organique et Méthodologie ICMMO, Université Paris Sud – CNRS, 15 rue Georges Clemenceau, 91400 Orsay, France. [email protected]

Hydrogen bonds (H bonds) are fundamental key features for the stability, structure, and dynamics of chemical and biological systems. In parallel, NMR spectroscopy has proved to be a suitable tool for probing structure and dynamics in a large range of molecules. In the field of biomolecules, H bonds have been detected on uniformly 13 C and 15 N labeled proteins, or nucleic acids. [1] In the field of natural and synthetic organic products, H bonds are less studied, since the heteronuclei usually involved, namely 13 C and 15 N, are of low naturally abundance (1.1% for 13 C and 0.36 % for 15 N). If the H bond is sufficiently stable, trans H bond scalar couplings occur and can be detected by NMR. However, their magnitude is often very small. For instance, values from 0.2 to 0.6 Hz have been reported for N-H …O=C H bonds. [2] Therefore small trans H bond couplings involve longer evolution time for which transversal relaxation tends to reduce again the sensitivity.

In order to compensate the low sensitivity inherent to the low gamma nuclei and to the small trans H bond couplings, a new methodology utilizing sensitivity optimized fast repetition NMR techniques have been developed. These new tools use band selective pulses [3,4,5] to speed up longitudinal relaxation rates in order to decrease the experimental time of multidimensional spectra. The time-gain can be converted into a higher number of accumulations in order to increase the sensitivity of 1H detected signals. With this aim, a new set of SOFAST HMBC sequences has been developed: H N-CO, and H N-N versions for detecting N-H …OC and N-H …N H bonds respectively. With the help of new SOFAST HMBC experiments, in combination with a 950 MHz spectrometer equipped with a cold probe, a sensitivity gain of 29 can be reached in theory, in comparison with the standard HMBC data acquired on a 400 MHz with a warm probe.

The Aitken research group works on foldamers based on the trans -2-aminocyclobutanecarboxylic acid (ACBC) building block. [6] Using SOFAST HMBC, it is possible to detect the network of intramolecular H N-CO H bonds in an ACBC octamer [7] and to confirm the conformational folding N N as a H 12 helix. The H -CO SOFAST sequence is the first experiment able to detect all H -CO H bonds at natural abundance in less than a day of data acquisition. The technique has now been used to probe the detailed folding behavior of an aza-analogue of an ACBC hexamer, in which the N- terminal is a 1-aminoazetidin-2-carboxylic acid (AAzC) residue, [8] known to induce formation of an 8-ring H bond.

References [1] I. Alkorta, J. Elguero, G. S. Denisov, Magn. Reson. Chem. 2008 , 46 , 599. [2] S. Grzesiek, F. Cordier, V. Jaravine, M. Barfield, Prog. Nuc. Magn. Reson. Spect. 2004 , 45 , 275. [3] J. Farjon, J. Boisbouvier, P. Schanda, A. Pardi, J-P. Simorre, B. Brutscher, J. Am Chem Soc . 2009 , 131 , 8571. [4] P. Schanda, B. Brutscher, J. Am. Chem. Soc. 2005 , 127 , 8014-8015. [5] C. Amero, P. Schanda, A. M. Dura, I. Ayala, D. Marion, B. Franzetti, B. Brutscher, J. Boisbouvier, J. Am. Chem. Soc. , 2009 , 131 , 10, 3448. [6] V. Declerck, D. Aitken, Amino Acids 2011 , 41 , 587. [7] C. Fernandes, S. Faure, E. Pereira,V. Théry, V. Declerck, R. Guillot, D. J. Aitken, Org. Lett. 2010, 12 , 16, 3606. [8] A. Altmayer-Henzien, V. Declerck, R. Guillot, D. J. Aitken, Tetrahedron Lett. 2013 , 54 , 802. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL5

Aromatic Foldamers Based on the Cis Conformational Preference of N-Alkylated Aromatic Amide and Urea Bonds

Aya Tanatani, a Mayumi Kudo, a Mio Matsumura, a Yukiko Tojo, a Tomoyo Kaneko, a Shizuka Nishiyama, a Hyuma Masu, b Isao Azumaya, c Hiroyuki Kagechika d

aDepartment of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, bChemical Analysis Center, Chiba University, Japan, cFaculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, Japan, dInstitute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Japan. [email protected]

Aromatic secondary amides such as benzanilide exist in trans form, whereas N-alkylated benzanilides exist in cis form in the crystal and predominantly in cis form in solution. The cis conformational preference is also observed in N, N' -dialkylated ureas and guanidines ( Fig 1a ). The folded structure of cis-amide and (cis, cis)-urea bonds can be applied to construct the aromatic foldamers with unique conformational properties, including helical structures ( Fig. 1b ), [1] aromatic multi-layered structures ( Fig. 1c ), [2] and chiral cyclic structures ( Fig. 1d ). [3] The cis conformational preference was also observed in the amide bond on the heterocyclic rings such as pyrroles and imidazoles. The oligomers that benzamide and heterocyclic amide are linked alternately were synthesized and their structures were investigated. The oligomers 2 with chiral substituents showed significant CD signals in CH 3CN. Aromatic multi-layered oligoureas 4 showed the helical structure in the crystal. The helical properties of the oilgoureas in solution have been studied systematically by synthesis and conformational analysis of the derivatives with chiral substituents, such as 5. The folded amide structure is useful to construct cyclic amides with chiral properties. The introduction of the functional groups on the cyclic amide skeleton caused unique properties such as chiral capsule-type dimer formation. The utilities of cis -amides and ureas in developing aromatic foldamers will be discussed.

Figure 1. Conformational properties of aromatic amides and related functional groups (a) and its applications to aromatic foldamers, such as oligoamides (b), oligoureas (c), and cyclic amides (d) References [1] A. Tanatani, A. Yokoyama, I. Azumaya, Y. Takakura, C. Mitsui, M. Shiro, M. Uchiyama, A. Muranaka, N. Kobayashi,; T. Yokozawa, J. Am. Chem. Soc. 2005 , 127 , 8553-8561. [2] M. Kudo, T. Hanashima, A. Muranaka, H. Sato, M. Uchiyama, I. Azumaya, T. Hirano, H. Kagechika, A. Tanatani, J. Org. Chem. 2009 , 74 , 8154-8163. [3] N. Fujimoto, M. Matsumura, I. Azumaya, S. Nishiyama, H. Masu, H. Kagechika, A. Tanatani, Chem. Commun. 2012 , 48 , 4809-4811.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL6

Targeting solvent exposed protein surfaces with peptidic foldamers

Tamás A. Martinek

Institute of Pharmaceutical Chemistry, University of Szeged, Hungary [email protected]

Solvent exposed flat regions are responsible for many of the known protein–protein interaction interfaces. 1 It is challenging however to construct artificial folded structures that are able to cover these relatively large flat surfaces, and have programmable anchor points to stabilize the interaction. Short peptidic foldamer helices have been shown to be good candidates to inhibit protein-protein interactions, 2 but their low radius of curvature is a limiting factor when a protein surface without pockets or protrusions is targeted. We addressed this problem in three ways (Figure 1). First, construction of multivalent foldameric helix arrays can provide large interaction surface by forming contiguous binding area or separated anchor patches ( A). We have successfully synthesized multivalent helical foldamer-dendrimer conjugates that recognize and inhibit the neurotoxic properties of ȕ-amyloid. 3 Second, we explored the possibilities of synthesizing foldamer helices with increased diameter ( B). This approach aims to increase the radius of curvature in a single helix approach. Two large-diameter helices, ȕ-H18 4 and ȕ-H18/20 have been discovered recently. Third, water soluble ȕ-sandwich mimicking foldamers would offer ligands with sufficiently flat surface, but their stabilization in water is a great current challenge ( C). Here we present the design, main structural features and biological effects of the foldameric analogs of anginex, a 33-mer antiangiogenic peptide with a tendency to form ȕ-sandwich. The effects of the ȕ3-amino acid substitutions in this ȕ-sandwich tertiary structure will be discussed.

Figure 1. Approaches to cover flat protein surface with peptidic foldamers

References (1) Li, B.; Turuvekere, S.; Agrawal, M.; La, D.; Ramani, K.; Kihara, D. Proteins 2008 , 71 , 670. (2) Wilson, A. J. Chem Soc Rev 2009 , 38 , 3289. (3) Fulop, L.; Mandity, I. M.; Juhasz, G.; Szegedi, V.; Hetenyi, A.; Weber, E.; Bozso, Z.; Simon, D.; Benko, R.; Kiraly, Z.; Martinek, T. A. Plos One 2012 , 7. (4) Szolnoki, E.; Hetenyi, A.; Martinek, T. A.; Szakonyi, Z.; Fulop, F. Org Biomol Chem 2012 , 10 , 255.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Pleanary Lecture PL3

Solid and Solution Phase Conformational Preferences of E-Peptides derived from Transpentacin and 3-Alkyltranspentacin

Steve Davies

University of Oxford, UK

Peptides comprised solely of E-amino acid residues (termed E-peptides) often display useful biological activities whilst offering increased metabolic stability due to inherent immunity against peptidases. As such, the development of an understanding of the factors that contribute to the folding preferences of E-peptides has been an active area of research: whilst an D-peptide typically requires the presence of ca 20 amino acid residues to elicit any secondary structural conformational preference, several E-peptides comprising ~6 amino acid residues have been shown to adopt stable secondary structures, even in aqueous solution. A systematic investigation into the effect of increasing the length of a E-peptide derived from residues of the E-amino acid transpentacin (2-aminocyclopentanecarboxylic acid) and 3- alkyltranspentacin derivatives will be presented. Efficient methods based upon application of kinetic and parallel kinetic resolution strategies were developed to facilitate the synthesis of the requisite monomeric building blocks, bearing orthogonal N- and O-protecting groups, which were subsequently converted to the corresponding oligomers (2-mer Æ 6-mer). The secondary structural preferences of each series, both in the solid state and solution phase, was comprehensively investigated using a range of analytical techniques, including single crystal X-ray diffraction analysis, NMR spectroscopy, IR spectroscopy and CD spectroscopy.

References

¾ S.G. DAVIES , O. ICHIHARA , I. LENOIR , I.A.S. WALTERS “Asymmetric synthesis of (-)-(1R,2S)-cispentacin and related cis- and trans-2-amino cyclopentane- and its cyclohexane-1-carboxylic acid” J. Chem. Soc., Perkin Trans. 1, 1411-1415, 1994. ¾ M.E. BUNNAGE , S.G. DAVIES , R.M. PARKIN , P.M. ROBERTS , A.D. SMITH , J.M. WITHEY “Kinetic resolution of tert-butyl (RS)-3-alkylcyclopentene-1-carboxylates for the synthesis of homochiral 3-alkyl- cispentacin and 3-alkyl-transpentacin derivatives” , Org. Biomol. Chem., 2, 3337-3354, 2004. ¾ S.G. DAVIES , A.C. GARNER , M.J.C. LONG , A.D. SMITH , M.J. SWEET , J.M. WITHEY “Parallel kinetic resolution of tert-butyl (RS)-3-alkylcyclopentene-1-carboxylates for the asymmetric synthesis of 3-alkylcispentacin derivatives” , Org. Biomol. Chem., 2, 3355-3362, 2004. ¾ E. ABRAHAM , C.W. BAILEY , T.D.W. CLARIDGE , S.G. DAVIES , K.B. LING , B. ODELL , T.L. REES , P.M. ROBERTS , A.J. RUSSELL , A.D. SMITH , L.J. SMITH , H.R. STORR , M.J. SWEET , A.L. THOMPSON , J.E. THOMSON , G.E. TRANTER , D.J. WATKIN “A systematic study of the solid state and solution phase conformational preferences of E-peptides derived from transpentacin” , Tetrahedron: Asymmetry, 21 , 1797-1815, 2010. ¾ E. ABRAHAM , T.D.W. CLARIDGE , S.G. DAVIES , B. ODELL , P.M. ROBERTS , A.J. RUSSELL , A.D. SMITH , L.J. SMITH , H.R. STORR , M.J. SWEET , A.L. THOMPSON , J.E. THOMSON , G.E. TRANTER , D.J. WATKIN “A systematic study of the solid state and solution phase conformational preferences of E-peptides derived from C(3)-alkyl substituted transpentacin derivatives” , Tetrahedron: Asymmetry, 22 , 69-100, 2011.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Pleanary Lecture PL4

Is the DNA Binding Hairpin Py-Im-Hp Polyamide an Archetypical Foldamer?

Peter B. Dervan

Division of Chemistry & Chemical Engineering California Institute of Technology [email protected]

Oligomers comprising three aromatic amino acid monomers (pyrrole, imidazole, hydroxypyrrole) and an aliphatic Ȗ amino acid turn unit fold into a U-shaped conformation and bind in the minor groove of DNA in a sequence specific manner by a set of well-defined intermolecular interactions between antiparallel ring pairs and the edges of the four Watson-Crick base pairs. [1-3] The structure and energetics of these interactions have been characterized by X-ray crystallography and quantitative footprint titrations, respectively. [4,5] The oligomers likely have no shape in the absence of DNA but like many biologically important peptides have a propensity to fold into a compact conformation in the presence of the macromolecular target. The Ȗ “turn” unit is strategically placed in the oligomer primary sequence to hold specific ring pairs in defined side-by-side positions. [1-3] Programmed in the primary sequence of the hairpin oligomer is the target DNA sequence according to the modular “pairing rules”: Im/Py targets GC, Py/Im targets CG, Hp/Py targets TA and Py/Hp targets AT. [3,4] When the hairpin folds in the presence of DNA it has multiple functions: sequence- specific recognition [1-3] , nucleosome core particle recognition, [6] and allosteric modulation which disrupts protein-DNA interfaces. [7] Substitution on the Ȗ turn unit controls gene regulation properties, [8] cell uptake, [9] toxicity and antitumor activity in mouse xenograft. [10]

References [1] M. Mrksich, M. E. Parks, P. B. Dervan, J. Am. Chem. Soc. 1994 , 116 , 7983. [2] J. W. Trauger, E. E. Baird, P. B. Dervan, Nature 1996 , 382 , 559. [3] S. White, J. W. Szewczyk, J. M. Turner, E. E. Baird, P. B. Dervan, Nature 1998 , 391 , 468. [4] C. L. Kielkopf, S. White, J. W. Szewczyk, J. M. Turner, E. E. Baird, P. B. Dervan, D. C. Rees, Science 1998 , 282 , 111. [5] C. F. Hsu, J. W. Phillips, J. W. Trauger, M. E. Farkas, J. M. Belitsky, A. Heckel, B. Z. Olenyuk, J. W. Puckett, C. C. C. Wang, P. B. Dervan, Tetrahedron 2007 , 63 , 6146. [6] R. K. Suto, R. S. Edayathumangalam, C. L. White, C. Melander, J. M. Gottesfeld, P. B. Dervan, K. Luger, J. Mol. Biol. 2003 , 326 , 371. [7] D. M. Chenoweth, P. B. Dervan, Proc. Natl. Acad. Sci. 2009 , USA , 106 , 13175. [8] N. G. Nickols, P. B. Dervan, Proc. Natl. Acad. Sci. USA 2007 , 104 , 10418. [9] J. Meier, D. Montgomery, P. B. Dervan, Nucleic Acids Res. 2012 , 40 , 2345. [10] F. Yang, N. G. Nickols, B. C. Li, G. K. Marinov, J. W. Said, P. B. Dervan, Proc. Natl. Acad. Sci. USA 2013 , 110, 1863. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL4

Cyclic Cis- E-aminocarboxylic acids – versatile constituents in foldamers

Oliver Reiser

Institut für Organische Chemie, Universität Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany [email protected]

Cyclic cis- E-amino acids have proved to be versatile constituents in peptide foldamers, giving rise to unique helical structures with good stability in aqueous environments as well as confer function, e.g. as selective ligands for neuropeptide Y receptors or as organocatalysts. Some recent examples from our laboratory in connection with collaborations within the COST-Foldamer network will be discussed. [1]

References [1] Leading reference: L. Berlicki, L. Pilsl, E. Weber, I. M. Mandity, C. Cabrele, T. A. Martink, F. Fülöp, O. Reiser, Angew. Chem. Int. Ed. Engl. 2012 , 51 , 2208.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL7

Synthesis and Two-Component Lyotropic Liquid Crystal Formation of Cyclobis(ethynylhelicene)oligomer

Nozomi Saito, a,b Masahiko Yamaguchi a

a Graduate School of Pharmaceutical Sciences, Tohoku University b Tohoku University International Advanced Research and Education Organization [email protected]

Lyotropic liquid crystals (LLCs), which are ordered fluid phases obtained by mixing mesogenic compounds and solvents, are unique materials in terms of both mobility and anisotropic order at molecular and bulk level. LLCs play crucial roles in biological systems, and the ordered assemblies have attracted attention as functional materials. [1] It is then considered interesting to develop new LLCs, which can respond to external stimuli. We previously reported that pseudoenantiomeric ethynylhelicene oligomers ( M)- 1/( P)- 1 form hetero-double-helices, [2] which aggregate to form higher assemblies such as gels in toluene and vesicles in diethyl ether. [2, 3] In this study, a cyclic derivative ( M)- 2 was synthesized to examine the effect of cyclized structure on the assembly formation, in which two ethynylhelicene tetramers were connected by hexadecamethylene linkers. ( M)- 2 formed an intra molecular homo-double-helix in organic solvents. When ( M)- 2 was mixed with ( P)- 1, CD spectra (toluene, 0.25 mM, 25 °C) showed enhanced Cotton effects, and UV-Vis spectra showed the red-shift of the absorption maxima. Job plots experiment indicated that they formed hetero-aggregate in 1:2 ratio. It was therefore concluded that inter molecular 1:2 hetero-double-helix was formed (Figure 1). It should be noted that the inter molecular complexation predominated over the intra molecular complexation. At a higher concentration of 10 mM, a 1:2 mixture of ( M)- 2/( P)- 1 formed a viscous fluid in toluene. Polarizing optical microscopy (POM) showed birefringence, which indicated LLC formation in toluene (Figure 1). Atomic force microscopy (AFM) showed that the mesogens of the LLC were fibrous assemblies. Although LLC formation of DNAs and RNAs, which are biological double- helix molecules, have been studied, [4] LLC-forming synthetic double-helix molecules have not been known before.

Figure 1. Hetero-double-helix and LLC formation of pseudoenantiomeric ethynylhelicene oligomers.

References [1] D. L. Gin, C. S. Pecinovsky, J. E. Bara, R. L. Kerr, Struct. Bond. , 2008 , 128 , 181. [2] R. Amemiya, M. Mizutani, M. Yamaguchi, Angew. Chem. Int. Ed. , 2010 , 49 , 1995. [3] N. Saito, M. Shigeno, M. Yamaguchi, Chem. Eur. J. 2012 , 18 , 8994. [4] M. Nakata, G. Zanchetta, B. D. Chapman, C. D. Jones, J. O. Cross, R. Pindak, T. Bellini, N. A. Clark, Science , 2007 , 318 , 1276.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL8

How the helical fold of peptidomimetic urea oligomers behaves in aqueous solution? New insights from the NMR spectroscopy of methylene groups

Emeric Miclet, a Paul Claudon, b Gilles Guichard b

aLaboratoire des Biomolécules, CNRS UMR 7203, Université Pierre et Marie Curie, 4 place Jussieu, 75005 Paris, France. bInstitut Européen de Chimie et Biologie, CNRS UMR 5248, Université de Bordeaux, 2 rue R. Escarpit, 33607 Pessac, France. [email protected]

Oligomers consisting of N,N’-linked urea bridging units represent a new family of peptidomimetic foldamers that is receiving increasing attention (Figure 1a). [1] This oligomeric backbone has been found to possess a remarkable propensity to fold into helical secondary structures in organic solvents and showed promise for interaction with biologically relevant [2] targets. Oligoureas share isosteric and isostructural relationship with J-peptides, another class of helical foldamers. Compared to J-peptides, helix stabilization in oligoureas is promoted by the presence of additional backbone conformational restriction and H-bond donor sites. In particular, three-centered H-bonding between C=O( i) and urea HN( i3) and HN’( i2) has been characterized in solution by NMR spectroscopy (MeOH and pyridine) as well as in the solid-state by X-ray crystallography. [3-5] a) b)

Figure 1. (a) Covalent structure of a monomer i within a N,N’ -linked oligourea. Backbone dihedral angles are marked by curved arrows. R denotes any proteinogenic side chain. (b) Structure of compound 1.

We were then interested in evaluating the stability of these 12- and 14-membered pseudo rings in aqueous solvent. A complete NMR study has been performed on compound 1 (a representative oligourea with antimicrobial properties) [2] in water (Figure 1b). Methylene NMR allowed the measurements of numerous scalar and dipolar couplings in weakly aligned samples. Restrained Molecular Dynamics has been performed, which highlights the dynamics and structural features of compound 1. Comparisons with the canonical oligourea X-ray structure will be discussed in details.

References [1] L. Fischer, G. Guichard, Org. Biomol. Chem. , 2010 , 8, 3101-3117. [2] P. Claudon, A. Violette, K. Lamour, M. Decossas, S. Fournel, B. Heurtault, J. Godet, Y. Mély, B. Jamart-Grégoire, M.-C. Averlant-Petit, J.-P. Briand, G. Duportail, H. Monteil, G. Guichard, Angew. Chem. Int. Ed. Engl. , 2010 , 49 , 333- 336. [3] L. Fischer, P. Claudon, N. Pendem, E. Miclet, C. Didierjean, E. Ennifar, G. Guichard, Angew. Chem. Int. Ed. Engl. , 2010 , 49 , 1067-1070. [4] B. Legrand, C. André, E. Wenger, C. Didierjean, M.-C. Averlant-Petit, J. Martinez, M. Calmes, M. Amblard, Angew. Chem. Int. Ed. , 2012 , 51 , 11267-11270. [5] G. Guichard, A. Violette, G. Chassaing, E. Miclet, Magn. Reson. Chem ., 2008 , 46 , 918-924.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL5

Torque Talk: Conformational Communication through Helical Molecules

Jonathan Clayden

School of Chemistry, University of Manchester, Oxford Rd., Manchester M13 9PL, UK [email protected]

While synthetic chemistry has made great progress in building the molecular structures of biology, the same is not yet true of the ability of synthetic molecules to communicate and process information in the manner of biological molecular devices such as the G-protein coupled receptor (GPCR). [1] This lecture will detail the design, synthesis and function of oligomeric structures (foldamers) whose conformational preferences may be dynamically controlled by a stereochemical influence located at one terminus. Inspired by the structures of fungal antibiotics such as the [2] cephaibols, oligomers of the achiral D-amino acid Aib (2-aminoisobutyric acid) are employed to build a racemic helical scaffold, in which we are able to induce from one end a screw-sense preference persisting over multi- Figure 1: The longest known crystallographic 3 10 helix: CbzPheAib GlyAib Ot-Bu nanometre distances (Fig. 1). [3] 8 8 These conformationally switchable molecular structures are able to mediate the communication of information, allowing remote control of spectroscopic or reactive properties. [4] The lecture will describe the use simple NMR techniques that allow detailed exploration of their conformational preferences, [5-7] and will show how these techniques have allowed us to maximize screw-sense control to a quantitative preference for a single helix handedness. The lecture will show how screw- sense induction in foldamers may be used to achieve by far the most remote asymmetric induction ever reported (Fig 2) and will detail progress towards the design of functional GPCR mimics. These include a synthetic purinergic receptor capable of relaying information about the identity and configuration of a reversibly bound nucleoside ligand over multi-nanometre distances commensurate with the thickness of a lipid bilayer membrane (Fig 3).

References [1] Rasmussen, S. G. F et al. , Nature (London) 2011, 477 , 549. [2] Bunkószi, G.; Schell, M.; Vértesy, L.; Sheldrake, G. M., J. Pept. Sci. 2003, 9, 745. [3] Clayden, J.; Castellanos, A.; Solà, J.; Morris, G. A., Angew. Chem. Int. Ed. 2009, 48 , 5962. [4] Solà, J.; Fletcher, S. P.; Castellanos, A.; Clayden, J., Angew. Chem. Int. Ed. 2010, 49 , 6836. [5] Solà, J.; Morris, G. A.; Clayden, J., J. Am. Chem. Soc. 2011, 133 , 3712. [6] Brown, R. A.; Marcelli, T.; De Poli, M.; Clayden, J., Angew. Chem. Int. Ed. 2012, 51 , 1395. [7] De Poli, M.; De Zotti, M.; Raftery, J.; Aguilar, J. A.; Morris, G. A.; Clayden, J. J. Org. Chem. 2013 , in press.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL6

From Chaos to Control: Design of Functional Peptoid Oligomers

Kent Kirshenbaum

Department of Chemistry, New York University, New York, NY USA 10003 [email protected]

Peptoids are peptidomimetic oligomers composed of highly diverse N-substituted glycine units. Due to their inability to establish backbone hydrogen bond networks, peptoids are anticipated to exhibit substantial conformational heterogeneity. A variety of strategies have now been described to identify peptoid side chains that can enforce local conformational ordering. Long-range conformational constraints can be established by macrocyclization. [1] These strategies are now permitting the elucidation of predictable sequence-structure-function relationships. Control of peptoid primary sequence permits the design of oligomers that function as antifreeze agents [2] and bioactive multivalent displays. [3,4] Control of peptoid secondary structure permits the design of potent antimicrobial agents, [5] along with supramolecular assemblies such as peptoid nanotubes that reversibly sequester water molecules. [6] A rudimentary peptoid tertiary structure has recently been attained by the tethered packing of peptoid macrocycles ( Figure 1 ). [7] Future rational design will increasingly be propelled by development of computational tools for accurate prediction of peptoid structure. [8,9] Advances in computer-assisted design of peptoid structures will be highlighted, including efforts to introduce non-natural monomer types into the Rosetta suite of protein design algorithms.

Figure 1. X-ray crystal structure of a rudimentary peptoid tertiary structure assembled by covalent tethering of oligomer macrocycles. [7]

References [1] B. Yoo, S. B. Y. Shin, M. L. Huang, K. Kirshenbaum, Chem. Eur. J 2010, 16, 5528. [2] M. Huang, D. Ehre, Q. Jiang, C. Hu, K. Kirshenbaum, M. Ward, Proc. Natl. Acad. Sci. USA 2012 ,109, 49: 19922. [3] P. M. Levine, E. Lee, A. Greenfield, R. Bonneau, S. K. Logan, M. J. Garabedian, K. Kirshenbaum, ACS Chem. Biol . 2012 , 7, 1693. [4] P. M. Levine, K. Imberg, M. J. Garabedian, K. Kirshenbaum, J. Am. Chem. Soc. 2012 , 134, 6912. [5] M. L. Huang, S. B. Y. Shin, M. A. Benson, V. J. Torres, K. Kirshenbaum, ChemMedChem 2012, 7, 114. [6] S. B. L. Vollrath, C. Hu, S. Brase, K. Kirshenbaum, Chem. Commun. 2013, in print. [7] S. B. L. Vollrath, S. Brase, K. Kirshenbaum, Chem. Sci. 2012 , 3, 2726. [8] G. L. Butterfoss, P. D. Renfrew, B. Kuhlman, K. Kirshenbaum, R. Bonneau, J. Am. Chem. Soc. 2009 131, 16798. [9] G. L. Butterfoss, B. Yoo, J. N. Jaworski, I. Chorny, K. A. Dill, R. Zuckermann, R. Bonneau, K. Kirshenbaum, V. A. Voelz, Proc. Natl. Acad. Sci. USA 2012, 109, 14320.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Plenary Lecture PL5

Non-traditional Peptide “Foldamer” Discovery Accelerated by the RaPID System

Hiroaki Suga

Department of Chemistry, Graduate School of Science, The University of Tokyo 7-3-1 Hongo, Bunkyo-ku, 113-0033 Japan [email protected]

The genetic code is the law of translation, where genetic information encoded in RNA is translated to amino acid sequence. The code consists of tri-nucleotides, so-called codons, assigning to particular amino acids. In cells or in ordinary cell-free translation systems originating from prokaryotes, the usage of amino acids is generally restricted to 20 proteinogenic (standard) kinds, and thus the expressed peptides are composed of only such monomers. To overcome this limitation, we recently devised a new means to reprogram the genetic code, which allows us to express non- standard peptides containing multiple non-proteinogenic amino acids in vitro.

This lecture will describe the most recent development in the genetic code reprogramming technology that enables us to express natural product-like non-standard peptides. The technology involves (1) efficient macrocyclization of peptides, (2) incorporation of non-standard amino acids, such as N-methyl amino acids, and (3) reliable synthesis of libraries with the complexity of more than a trillion members. When the technology is coupled with an in vitro display system, referred to as RaPID (Random non-standard Peptide Integrated Discovery) system, the non-standard macrocyclic peptide libraries with a variety ring sizes and building blocks can be screened (selected) against various drug targets inexpensively, less laboriously, and very rapidly. The work represents a bridge between chemistry and biology, leading to the next generation of peptide drugs.

References • J. Morimoto, Y. Hayashi, H. Suga “ Discovery of macrocyclic peptides armed with a mechanism-based warhead that isoform-selectively inhibit a human deacetylase SIRT2” Angew. Chem. Int. Ed. 51 , 3423-3427 (2012). • Y. Hayashi, J. Morimoto, H. Suga “ In Vitro Selection of Anti-Akt2 Thioether-Macrocyclic Peptides Leading to Isoform-Selective Inhibitors” ACS Chem. Biol. 7, 607-613 (2012). • Y. Yamagishi, I. Shoji, S. Miyagawa, T. Kawakami, T. Katoh, Y. Goto, H. Suga "Natural product-like macrocyclic N- methyl-peptide inhibitors against a ubiquitin ligase uncovered from a ribosome-expressed de novo library" Chem. Biol. 18 , 1562-1570 (2011). • Y. Goto, T. Katoh, H. Suga “Flexizymes for genetic code reprogramming” Nature Protocols 6, 779-790 (2011) • T.-J. Kang, Y. Hayashi, H. Suga “Synthesis of a Backbone-cyclic Peptide SFTI-1 Promoted by the Induced Peptidyl- tRNA Drop-off" Angew. Chem. Int. Ed. 50 , 2159-2161 (2011). • T. Kawakami, A. Ohta, M. Ohuchi, H. Ashigai, H. Murakami, H. Suga “Diverse backbone-cyclized peptides via codon reprogramming” Nat. Chem. Biol. 5, 888-890 (2009) • H. Xiao, H. Murakami, H. Suga, A. R. Ferré-D'Amaré "Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme" Nature 454 , 358-361 (2008). • H. Murakami, A. Ohta, H. Ashigai, H. Suga "The fexizyme system: a highly flexible tRNA aminoacylation tool for the synthesis of nonnatural peptides" Nature Methods 3, 357-359 (2006). 

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL7

Peptides as Asymmetric Catalysts

Helma Wennemers

Laboratory of Organic Chemistry, ETH Zurich, Wolfgang-Pauli-Strasse 10, CH-8001 Zurich, Switzerland [email protected]

In Nature, proteins fulfill manifold different functions and are crucial as, for example, enzymes or templates for the controlled formation of structural components such as bones. The Wennemers group is intrigued by the question whether also peptides with significantly lower molecular weights compared to proteins can fulfill functions for which nature evolved large macromolecules. Specifically we ask whether peptides can serve as effective asymmetric catalysts, templates for the controlled formation of inorganic materials, or tumor targeting vectors.

The lecture will focus on the development of peptides as asymmetric catalysts. Tripeptides of the general type H-Pro-Pro-Xaa (Xaa = amino acid with a carboxylic acid) will be presented that are effective catalysts for aldol reactions and conjugate addition reactions between aldehydes and nitroolefins. [1] The peptides allow for enamine catalysis with catalyst loadings of as little as 0.1-1 mol% and provide synthetically versatile products in high stereoselectivities. Several synthetically valuable compounds such as J-amino acids, pyrrolidines, J-butyrolactones and J-butyrolactams are easily accessible using this methodology.

The scope of these peptide-catalyzed reactions will be discussed and recent insight into the mechanism as well as the importance of the conformational properties for effective catalysis will be discussed.

References [1] For a recent review, see: H. Wennemers, J. Pept. Sci. 2012 , 18 , 437.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL9

Effects of Co- and Post-translational Modification by Sugars on Peptide Folding: Insights from a Study of a Family of “Glyco”–Foldamers

Tushar K. Chakraborty, a Kirin Kumar, a Saumya Roy, b Omprakash Bande, b Subhash Ghosh, d Johannes W. Vad Pedersen, c Henrik Clausen, c Ravi S. Ampapathi, a Aloysius Siriwardena b

aCentral Drug Research Institute (CSIR), Chattar Manzil Palace, Lucknow - 226 001, UP, India bLaboratoire des Glucides, UMR 6912-CNRS, 33 Rue St Leu, 80039, Amiens, France cKøbenhavns Universitet, Det Sundhedsvidenskabelige Fakultet, Institut for Cellulær og Molekylær Medicin Blegdamsvej 3B, 2200 København, Denmark dIndian Institute of Chemical T echnology, Hyderabad – 500 007, India [email protected]

Interactions of glycoproteins with their cellular environments, impacts on a wide range of physiological phenomena. [1] Indeed, it is predicted that over half eukaryotic proteins are glycosylated and it is known that co- and post-translational modification of proteins with glycans has dramatic consequences on their folding, stability and ultimately, their function. Considerable effort has thus been invested in delineating and understanding the impact of carbohydrates on the conformational preferences of glycoproteins and glycopeptides in solution and also in manipulating their interactions with their cognate receptors. These endeavors have revealed themselves not to be straightforward and success in rationalizing or predicting such processes has been possible only in a handful of well-studied cases. Important insights into such questions have been gleaned from the study of glycopeptide- and oligosaccharide-mimetics and especially those that are structurally well defined. However, attempts to correlate secondary structures with the biological activities of non-multivalent glycopeptide mimetics have been relatively sparse despite the importance of such targets in the quest for carbohydrate-based therapeutics. In the present work we sought to examine the effects of appended sugar moieties on the [2] conformational behavior of a family of G!sugar amino acid ( G!SAA)-derived foldamers. Foldamers are synthetic oligomers able to adopt ordered conformations in solution and their study has helped enlighten our understanding of the origins of the preferred secondary structures and biological activities of polymers prevalent in Nature. [3] Considering the importance of glycoproteins we were struck by the absence of reports describing the impact of glycosylation or the absence thereof, on the preferred secondary structures of foldamers and how such preferences might impact on their biological activity.

We here examine the secondary structures adopted by various G-SAA-derived foldamer backbones either appended and not with selected sugar moieties. We also show the impact of the conformational preferences manifested in water by these G-glycofoldamers on their non - multivalent interactions with model protein targets.

References [1] (a) Larkin, A.; Imperiali, B., Biochemistry, 2011 , 50 , 4411; (b) Price, J. L.; Powers, D. L.; Powers, E. T.; Kelley, J. W., PNAS , 2011 , 108 , 14127. [2] Chakraborty, T. K.: Srinivasu, P.; Tapadar, S.; Mohan, B. K., Glycoconjug. J ., 2005 , 22 , 83. [3] (a) Gellman, S. H., Acc. Chem. Res ., 1998 , 31 , 173; (b) Goodman, C. A.; Choi, S.; Shandler, S.; DeGrado, W. F., Nature Chemical Biology 2007 , 3, 252; (c) Guichard, G.; Huc, I., Chem. Comm , 2011 , 47 , 5933 and references cited therein.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL10

Harnessing the flexibility of peptidic scaffolds to control their copper(II) coordination properties: a potentiometric and spectroscopic study

Ana Fragoso, a Pedro Lamosa, a Rita Delgado, a Olga Iranzo a,b

aInstituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal b Institut des Sciences Moléculaires de Marseille/BiosCiences UMR CNRS 7313, Aix-Marseille Université, Campus Scientifique de Saint Jérôme, F-13397 Marseille Cedex 20, France [email protected]

Designing small peptides capable of binding Cu(II) mainly by the side chain functionalities and forming single species in the neutral pH range is a hard task since the amide nitrogens strongly compete for Cu(II) coordination. [1] However, metalloproteins are proficient on this and generate the appropriated coordination pocket to avoid amide coordination. This exquisite control allows copper proteins to attain a myriad of catalytic activities and thus, biological functions. [2] Achieving this with short peptides will be very appealing to engineer miniaturized copper proteins with potential redox and hydrolytic activities.

In this presentation we will report our recent results on the design, synthesis and characterization of two His-containing decapeptides, a cyclic (C-Asp) and an open derivative (O-Asp), capable of coordinating Cu(II). [3] Detailed potentiometric, mass spectrometric and spectroscopic studies (UV- Vis, CD, NMR and EPR) were carried out. The results indicated that at 1:1 Cu(II)/peptide ratio these peptides formed single species (CuH(peptide), Figure 1) at close to neutral pH values and spectroscopic data were consistent with the coordination of the metal ion exclusively by the side chain functionalities. Additionally, these studies showed how cyclization and coordination to an Asp residue played an important role in determining the Cu(II) coordination properties of these peptides. Interestingly, different properties were observed for the similar [CuH(peptide)] species due to the distinct intrinsic nature of their peptidic scaffolds.

Figure 1. Species distribution diagrams for the Cu(II) complexes of C-Asp (blue) and O-Asp (green) peptides (aqueous solution, I = 0.1 M KNO 3, 298.2 K, [peptide] = [Cu(NO 3)2] = 1.0 mM).

References [1] a) H. Sigel; R. B. Martin Chem. Rev. 1982 , 82 , 385-426. b) H. Koz áowski; W. Bal; M. Dyba; T. Kowalik- Jankowska Coord. Chem. Rev. 1999 , 184 , 319-346. [2] a) R. H. Holm; P. Kennepohl; E. I. Solomon Chem. Rev. 1996 , 96 , 2239-2314; b) E. Gaggelli; H. Koz áowski; D. Valensin; G. Valensin Chem. Rev. 2006 , 106 , 1995-2044. [3] A. Fragoso; P. Lamosa; R. Delgado; O. Iranzo Chem. Eur. J. , 2013 , 19 , 2076-2088.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL11

Reversible chirality control in peptide-functionalized gold nanoparticles

Alessandro Moretto, Paolo Scrimin, Fabrizio Mancin, Andrea Orlandin, Edoardo Longo  Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy [email protected]

Nucleotides and D-amino acids are crucial building blocks for living organisms. These chiral molecules are the biosynthetically precursors of two of the most important classes of biopolymers, DNA and proteins, respectively. The 3D-structures of biomolecules are currently studied using a variety of techniques, while helical handedness is routinely detected by means of light pulses of opposite circular polarization. The difference in the UV absorption of these two circularly polarized pulses is called electronic circular dichroism (ECD). In Nature, biomolecules explore a wide range of conformations with intrinsically strong ECD signals in the 200-300 nm region, but these signals are essentially absent in the visible. Nanomaterials such as metallic nanoparticles (depending on their sizes) display absorptions in the visible region but are achiral. As a result, when biomolecules are co-assembled with nanomaterials their chirality is transferred to create a plasmon-induced ECD signal in the visible region. In this work, we present our results which underscore the occurrence of moderately strong ECD bands in the range 300-550 nm resulting from a series of appropriately thiol-functionalized peptide oligomers (based on alternating L-Ala and Aib residues) covalently anchored to 2-2.5 nm sized gold nanoparticles. We related the (positive or negative) signs of the ECD plasmonic signal with the oligopeptide length, that in turn is strictly associated with their secondary structure. This latter property was simultaneously monitored via ECD in the 200-250 nm range. We believe that in our systems a peptide-to-metallic surface chirality transfer would take place.

Figure 1. Peptide folding effect on the plasmonic ECD response.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL12

Control of amide cis-trans isomerism in peptoid: “directing” side chains to promote stable secondary structures

Cécile Caumes, a Thomas Hjelmgaard, b Olivier Roy, a Sophie Faure, a Claude Taillefumier a a Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP10448, F-63000 Clermont-Ferrand, and CNRS, UMR 6296, ICCF, BP 80026, F-63171 Aubière, France, b Department of Chemistry, Section for Chemical Biology and Nanoscience, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark. [email protected]

Peptoids developed in the early 1990s are structurally related to D-peptides with the side chains [1] located on the amide nitrogen rather than the D-carbon. A major advantage of peptoids is their ease of synthesis, particularly by the straightforward so-called submonomer method. The diversity, brought by primary amines, is virtually unlimited and peptoids possess other desirable advantages like proteolytic stability and greater cell permeability than peptides. [2] Peptoids are inherently more flexible than peptides due to the absence of internal hydrogen bonding and achiral backbones but the primary cause is the presence of N,N-disubstituted amides in the backbone which can populate both cis and trans conformations. However peptoids still retain propensities to adopt stable secondary structures, in particular PPI and PPII helical conformations, provided the cis/trans isomerism is optimally controlled. [3] To meet this challenge, the design of side chains that control the amide geometry in cis or trans by formation of local non-covalent interactions with the backbone is crucial. [4] In this communication, we introduce two novel side chains that force peptoid amides to adopt the cis conformation [5] and we present their use for the preparation of stable all- cis and alternated cis - trans peptoid sequences.

O O cis O N O N -amide inducer

N N trans -amide inducer

O O Figure 1. Conformation control of N,N -disubstituted amides

References [1] R. N. Zuckermann, Biopolymers 2011 , 96 , 545; R. J. Simon, R. S. Kania, R. N. Zuckermann, V. D. Huebner, D. A. Jewell, S. Banville, S. Ng, L. Wang, S. Rosenberg, D. C. Spellmeyer, R. Tan, A. D. Frankel, D. V. Santi, F. E. Cohen, and P. A. Bartlett, Proc. Natl. Acad. Sci. USA 1992 , 89 , 9367. [2] J. A. Patch, K. Kirshenbaum, S. L. Seurynck, R. N. Zuckermann, A. E. Barron, Versatile Oligo(N-Substituted) Glycines: The Many Roles of Peptoids in Drug Discovery ; Wiley-VCH Weinheim, Germany: 2004; pp 1-31. [3] C. W. Wu, K. Kirshenbaum, T. J. Sanborn, J. A. Patch, K. Huang, K. A. Dill, R. N. Zuckermann, A. E. Barron, J. Am. Chem. Soc. 2003 , 125 , 13525; N. H. Shah, G. L. Butterfoss, K. Nguyen, B. Yoo, R. Bonneau, D.L. Rabenstein, K. Kirshenbaum, J. Am. Chem. Soc. 2008 , 130 , 16622; J. R. Stringer, J. A. Crapster, I. A. Guzei, H. E. Blackwell, J. Am. Chem. Soc. 2011 , 133 , 15559. [4] C. Gorske, J. R. Stringer, B. L. Bastian, S. A. Fowler, and H. E. Blackwell, J. Am. Chem. Soc. 2009 , 131 , 16555. [5] C. Caumes, O. Roy, S. Faure, C. Taillefumier, J. Am. Chem. Soc. 2012 , 134 , 9553.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Plenary Lecture PL6

Cyclic E-amino acids: an unlimited field

Ferenc Fülöp

Institute of Pharmaceutical Chemistry, University of Szeged H-6720 Szeged, Eötvös u. 6, Hungary [email protected]

The alicyclic ȕ-amino acids have acquired great interest in recent years in view of their pharmacological potential. Cispentacin, an antifungal antibiotic with a cyclopentane skeleton, is one of the most important derivatives. (1 R,2 S)-2-Amino-4-methylenecyclopentanecarboxylic acid (Icofungipen) is a known antifungal agent, [1] and even higher activity was achieved when cyclic, conformationally rigid ȕ-amino acids were applied to create foldameric structures. [2] The present lecture will discuss out different strategies that result in the regio- and stereoselective functionalization of 2-aminocycloalkenecarboxylic acids to form exotic building blocks for the development of bioactive compounds and/or the construction of new units from which to prepare bioactive foldamers. [3]

HO CO 2R CO 2R CO R O 2 BocHN NHP N CO 2R NHP R2 NHP 2 R R1 HO ( ) n NHP O O N N CO 2R HO CO 2R N NH NH HO NHP HO ( ) n NHP

F CO 2R N3 CO 2R CO 2R CO 2R ( ) n NHP HO ( ) n NHP N F P2 NHP ( ) NHP F n

The lecture will also focus on E-amino acids with a norbornene skeleton, where new procedures involving retro Diels-Alder reactions, ring opening and subsequent ring closure strategies are applied. A safe and efficient flow chemistry-based procedure will be presented for 1,3-dipolar [4] cycloaddition reactions between E-amino acids with azide functions and acetylenes .

References [1] (a) F. Fülöp, Chem. Rev. 2001 , 101 , 2181. (b) F. Fülöp, T. A. Martinek, G. K. Tóth, Chem. Soc. Rev . 2006 , 35 , 323. (c) T. A. Martinek, F. Fülöp, Chem. Soc. Rev . 2012 , 41 , 687. [2] (a) D. H. Appella, L. A. Christianson, D. A. Klein, D. R. Powell, X. Huang, J. J. Barchi, S. H. Gellman, Nature 1997 , 387 , 381. (b) S. H. Gellman, Acc. Chem. Res. , 1998 , 31 , 173. [3] (a) L. Kiss, E. Forró, R. Sillanpää, F. Fülöp, Tetrahedron 2010 , 65 , 8021. (b) M. Nonn, L. Kiss, E. Forró, Z. Mucsi, F. Fülöp, Tetrahedron 2011 , 67 , 4079. (c) L. Kiss, E. Forró, S. Fustero, F. Fülöp, Org. Biomol. Chem . 2011 , 9, 6528. (d) M. Nonn, L. Kiss, R. Sillanpää, F. Fülöp, Beilstein J. Org. Chem ., 2012 , 8, 1000. (e) L. Kiss, M. Cherepanova, E. Forró, F, Fülöp, Chem. Eur. J . 2013 , 19 , 2102. [4] S. B. Ötvös, I. Mándity, L. Kiss, F. Fülöp, Chem. Asian J . DOI: 10.1002/asia.201201125.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL8

Cavity-Containing Aromatic Oligoamide Foldamers and Macrocycles

Bing Gong

Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY 14260, USA, and College of Chemistry, Beijing Normal University, Beijing, China. [email protected]

Based on highly favorable three-center intramolecular H-bonding interactions, we have developed backbone-rigidification strategy that is generally applicable to the generation of a host of porous folding oligomers. [1] The first series of such cavity-containing foldamers are aromatic oligoamide strands that adopt well-defined, crescent or helical conformations. The generality of this backbone- rigidification strategy has been demonstrated in other unnatural folding oligomers: oligoureas and oligo(phenylene ethynylenes). Large nanosized cavities have been created based on the folding of these helical foldamers. Tuning the size of the nanocavities has been achieved without changing the underlying helical topology. Attempts to extend the same folding principle for preparing helically folded polymers have instead led to the discovery of shape-persistent macrocycles that are formed in one-pot in very high yields. [2] The oligoamide macrocycles were found to have a high propensity for forming nanotubular assemblies [3] that act as highly conducting ion channels. [4] Recently, by equipping nanocavity-containing, rigid macrocycles with multiple directional non-covalent forces, organic nanotubes with non-collapsible internal pores have been obtained. [5] These nanotubes mimic pore- and channel-forming proteins and at the same time, offer more structural and functional tunability. These created porous structures are being used as novel platforms for the development of protein-like nanostructures.

Figure 1. Aromatic oligoamides are forced to adopt defined conformation by highly favorable intramolecular three-center hydrogen bonds. This back-rigidifying strategy has turned out to be effective for enforcing the folding of other oligomers and for forming a variety of rigid macrocycles in one pot.

References [1] B. Gong, Acc. Chem. Res . 2008 , 41 , 1376-1386. [2] W. Feng, K. Yamato, L. Q. Yang, J. Ferguson, L. J. Zhong, S. L. Zou, L. H. Yuan, X. C. Zeng, B. Gong, J. Am. Chem. Soc . 2009 , 131 , 2629–2637. [3] Y. A. Yang, W. Feng, J. C. Hu, S. L. Zou, R. Z. Gao, K. Yamato, M. Kline, Z. F. Cai, Y. Gao, Y. B. Wang, Y. B. Li, Y. L. Yang, L. H. Yuan, X. C. Zeng, B. Gong, J. Am. Chem. Soc. 2011 , 133 , 18590-18593. [4] A. J. Helsel, A. L. Brown, K. Yamato, W. Feng, L. H. Yuan, A. Clements, S. V. Harding, G. Szabo, Z. F. Shao, B. Gong, J. Am. Chem. Soc . 2008 , 130 , 15784-15785. [5] X. B. Zhou, G. D. Liu, K. Yamato, Y. Shen, R. X. Cheng, X. X. Wei, W. L. Bai, Y. Gao, H. Li, Y. Liu, F. T. Liu, D. M. Czajkowsky, J. F. Wang, M. J. Dabney, Z. H. Cai, J. Hu, F. V. Bright, L. He, X. C. Zeng, Z. F. Shao, B. Gong, Nature Commun . 2012 , 3, 949. DOI: 10.1038/ncomms1949 . PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL13

Hybrid cyclobutane peptides: influence of the spacer on their folding in solution and on their gelation ability

Sergi Celis, a Pau Nolis, b Ona Illa, a Vicenç Branchadell, a Rosa M. Ortuño a aDepartment de Química, Universitat Autònoma de Barcelona, 08193-Cerdanyola del Vallès, Spain bServei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, 08193-Cerdanyola del Vallès, Spain [email protected]

The use of carbocyclic amino acids to construct peptides confers rigidity to the corresponding oligomers. Alternation with linear residues results in new conformational bias in solution. Hybrid tetra-, hexa- and octapeptides that join in alternation glycine, ȕ-alanine or Ȗ-amino butyric acid (GABA), respectively, and an enantiopure cyclobutane ȕ-amino acid have been synthesized. Studies have been carried out by NMR, CD and theoretical calculations and results show that the spacer length has an effect on the folding pattern shown by these peptides. [1] This behaviour contrasts with that of oligomers consisting exclusively of cyclobutane residues. [2] The gelation ability of the tetrapeptides in various organic solvents has been studied by means of SEM, CD and NMR. Differences in the morphology of the gels have been observed ( Figure 1 ). A model for the gelation process has been proposed using NMR data together with theoretical calculations. [3]

Figure 1. Structures of tetrapeptides 1, 2 and 3; SEM images of xerogel samples of 1 (a), 2 (b), 3 (c) as on graphite at 70 Pa.

References [1] S. Celis, E. Gorrea, P. Nolis, O. Illa, R. M. Ortuño, Org. Biomol. Chem . 2012 , 10 , 861-868. [2] E. Torres, E. Gorrea, K. K. Burusco, E. Da Silva, P. Nolis, F. Rúa, S. Boussert, I. Díez-Pérez, S. Dannenberg, S. Izquierdo, E. Giralt, C. Jaime, V. Branchadell, R. M. Ortuño, Org. Biomol. Chem . 2010 , 8, 564-575. [3] S. Celis, P. Nolis, O. Illa, V. Branchadell, R. M. Ortuño, submitted .

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Short Lecture SL14

Foldamer stability coupled to aggregation propensity of elongated Trp-cage miniproteins

Viktor Farkas, a Barbara Csordás, a Orsolya Hegyi, b Gábor K. Tóth, b András Perczel a

aProtein Modeling Group HAS-ELTE and Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös L. University, Pázmány P. s. 1/A, Budapest, H-1117 Hungary. bDepartment of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged, H-6720 Hungary. [email protected]

Structure and aggregation propensity of se lected elongated “Trp-cage” foldamers were studied by NMR, ECD, VCD and FT-IR spectroscopy, namely the 20 amino acid long E0, the 25 residue containing E5 with its variant and the 30 amino acid incorporating E10. Backbone folding associated aggregation propensity of the three different model systems of comparable molecular properties were analyzed in a comprehensive manner. Spectroscopy measurements were used to monitor their concentration dependent, heat induced (5 °C ĺ 65 °C) Į-helix to ȕ-sheet fold transitions. While the ECD curves of E0 reflect to an ensemble of highly dynamic set of backbone structures, those of E5 and E10 foldamers show the expected Trp-cage fold, [1] dominated by Į- helical properties. At low molecular concentration (c < 1 mM), typically used for ECD measurements, no sign of ȕ-structures was revealed at any conditions (5 °C < T < 65 °C, 5 < pH < 7, c~30 ȝM) for any of these miniproteins. However, at higher concentration (c~1-30 mM) both VCD and FT-IR spectral features of E5 and E10 resemble to that of a ȕ-strand (~1615 cm -1 ), accompanied with “free ȕ-edges”, [2] or native ȕ-sheets (~1630 cm -1 ). E5 at lower (c~1-3 mM), while E10 at higher concentration (c~30 mM) witness the Įĺ native- ȕĺ ȕ-sheet folding transition pathway, effectively monitored by the characteristic C=O vibrational normal mode frequency shift as follows: ~1650 cm -1 ĺ ~1630 cm -1 ĺ ~1615 cm -1 . The latter folding path happens to be irreversible. The shortest polypeptide E0 has an unordered or very dynamic fold, while E10 presents the most tightly packed Trp-cage 3D-structure. We have found that both high dynamicity and/or tight molecular core packing are different in nature, but common in efficacy to prevent the polypeptide backbone chain against self-aggregation. However, E5 is intermediate in size and stability, and thus among these three it is the most “vulnerable” foldamer against aggregation. [3] The present foldamer triad, E0, E5 and E10, [4] serve as a good example of larger globular proteins for which, aggregation and amyloid-fiber like nano-particle formations is often associated with Alzheimer’s, Creutzfeldt–Jakob, or Prion diseases.

References [1] J. W. Neidigh, R. M. Fesinmeyer, N. H. Andersen, Nat. Struct. Biol. 2002, 9 , 425-430. [2] A. Perczel, P. Hudáky, V. K. Pálfi, J. Am. Chem. Soc. 2007 , 129 , 14959-14965. [3] J. Kardos, B. Kiss, A. Micsonai, J. Kovács, P. Rovó, Gy. Váradi, G. K. Tóth, A. Perczel, 2013 , submitted. [4] V. Farkas, B. Csordás, O. Hegyi, G. K. Tóth, A. Perczel, EurJOC 2013 , accepted.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Keynote Lecture KL9

Can a C-H•••O interaction be a determinant of conformation?

Martin D. Smith

Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK [email protected]

A range of noncovalent interactions, including hydrogen bonding and electrostatic repulsion, can significantly affect the conformations of small molecules. Nominally weak hydrogen bonds such as the C íH···O interaction are often overpowered by other effects, but their influence can be augmented by incorporation of electronegative substituents adjacent to the donor atom. [1] Whether these nonconventional hydrogen bonds are a consequence or a determinant of conformation is a long-running and unresolved issue. [2] In this lecture we outline an ongoing investigation combining a solid-state and quantum mechanical study designed to probe whether a C–H···O interaction can override the significant trans -planar conformational preferences of Į-fluoroamide substituents. A profound change in dihedral angle from trans -planar (OCCF) to cis -planar (OCCF) observed on introducing an acceptor group for a C–H···O hydrogen bond is consistent with this interaction functioning as a significant contributor to overall conformation in certain systems.

However, the study of non-covalent interactions is most relevant when examined in a dynamic environment and hence we decided to extend our investigations to encompass a solution- state investigation. Consequently, we decided to utilize our established E-turn scaffold stabilized by an intramolecular amide N-H···O hydrogen bond. [3,4] This parallel turn should allow us to determine the influence that a selection of C-H···O donors and acceptors would have on the rotation of a single bond within the confines of a conformationally well-defined system, using diastereotopic X and Y as reporter groups for rotation about the OCCH torsion. Our results in this endeavour and the potential for the application of the C-H···O interaction in a range fields will be discussed.

References [1] M. K. N. Qureshi, M. D. Smith, Chem. Commun., 2006 , 5006-5008. [2] C. R. Jones, P. K. Baruah, A. L. Thompson, S. Scheiner, M. D. Smith, J. Am. Chem. Soc., 2012 , 134 , 12064- 12071. [3] C. R. Jones, G. D. Pantos, A. J. Morrison, M. D Smith, Angew. Chem. Int. Ed., 2009 , 48 , 7391-7394. [4] C. R. Jones, M. K. N. Qureshi, F. R. Truscott, S.-Te D. Hsu, A. J. Morrison, M. D. Smith, Angew. Chem. Int. Ed., 2008 , 47 , 7099-7102.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Plenary Lecture PL7

Mimicry of Protein Recognition Surfaces with Peptidic Foldamers

Samuel H. Gellman

Department of Chemistry, University of Wisconsin, Madison, WI, USA [email protected]

Interactions between specific proteins are essential for life, with key roles in normal physiological signal transduction and disease-related processes. Many such interactions have proven recalcitrant to modulation with small molecules because the protein surface areas involved are large. In these cases, clinical modulation is generally achieved with large peptides or proteins. We are exploring an alternative approach to this fundamental challenge in molecular recognition, based on foldamers that adopt specific conformations and display protein-like surfaces. We have found that informational D-helices can be mimicked effectively with oligomers containing both D- and E- [1] amino acid residues (" D/E-peptides"). Placement of E residues throughout a sequence can confer substantial resistance to proteolysis. Successful D-helix mimicry has been demonstrated in the context of BH3 domain recognition by Bcl-2-family proteins and formation of CHR+NHR helix- bundles from gp41-derived segments (Figure 1). [2-4] Current efforts include expansion of protein- surface mimicry beyond isolated D-helices. 

Figure 1. Sequence of an D/E-peptide that mimics the D-helical CHR domain of HIV protein gp41 and inhibits HIV infection in cell-based assays, and a crystal structure of the D/E-peptide bound to a model protein.

References [1] L. M. Johnson, S. H. Gellman, Meth. Enzymol. 2013 , 253 , 407. [2] W. S. Horne, L. M. Johnson, T. J. Ketas, P. J. Klasse, M. Lu, J. P. Moore, S. H. Gellman, Proc. Natl. Acad. Sci. USA 2009 , 106 , 14751. [3] L. M. Johnson, S. H. Gellman, J. Am. Chem. Soc. 2011 , 133 , 10038. [4] M. D. Boersma, H. S. Haase, K. J. Peterson-Kaufman, E. F. Lee, O. B. Clarke, P. M. Colman, B. J. Smith, W. S. Horne, W. D. Fairle, S. H. Gellman, J. Am. Chem. Soc. 2012 , 134 , 315. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013

    POSTERS



Poster 1

Foldamer Chemistry Approach Towards Pro-apoptotic TRAIL mimetics

Karolina Pulka, a Neil Owens, a Katell Bathany, b Miriam Royo Expósito, c Jean-Marie Schmitter, b Gilles Guichard a

a European Institute of Chemistry and Biology, University of Bordeaux 1 – CNRS UMR 5248, Pessac, France b Functional Genomic Center of Bordeaux, University of Bordeaux 2 Victor Segalen - CNRS UMR 5248, Bordeaux, France cParc Cientific Barcelona, Combinatorial Chemistry Unit, Barcelona, Spain [email protected]

Death Receptors (DR), members of the tumor necrosis factor (TNF) receptor family, have come into focus as suitable targets for the selective activation of the cell death (apoptosis) pathway in tumors in vivo without causing toxicity to healthy cells. Current approaches in clinical development for replicating the function of the TNF-related apoptosis inducing ligand (TRAIL) are restricted to recombinant proteins which have poor pharmacokinetic properties due to their susceptibility to proteolytic degradation, and high production cost. In this context, the identification of small molecules that can both bind to TRAIL receptors (DR5 and/or DR4) and activate the TRAIL signaling pathway is of prime interest towards the development of new treatments complementary to conventional cancer therapy. The combinatorial approach is one of the most powerful tools for the discovery of new active [1] compounds. We created a library of urea/ J-amide foldamers aimed at replicating TRAIL activity in cancer cell lines. An one-bead-one-compound (OBOC) approach was used to generate such library. The urea/ J-amide hybrids were synthesized by the coupling of new azido succinimidyl [2] carbamates and Fmoc- J-AA (standard split-and-mix procedure). Microwave irradiation was used to accelerate the synthesis. To convert the azido function into amino group, Staudinger reaction was chosen with PMe 3 as a reducing agent. Fmoc- J-AA were coupled in the presence of HBTU/HOBt as a coupling reagent. The sublibraries of 8-mer with five variable (X) positions and three fixed were designed and prepared. Such length of the foldamers was chosen because it surpasses the minimum length required for helix formation (four residues). The X positions were varied by six of thirteen residues using a unique pairs method [3] , which reduces the number of redundant compounds, so the one sublibrary contains 31104 distinct foldamers. The difference between each sublibrary was the position of Trp- type residue. All the libraries were screened for binding affinity against DR5 labeled with the fluorescent dye (ATTO488) and the beads were analyzed by Complex Object Parametric Analyzer and Sorter (COPAS). The hit beads were manually chosen. MALDI analysis and sequencing is under investigation.

References [1] T. Kodadek Chem. Commun. , 2011 , 47 , 9757. [2] C. Douat-Casassus, K. Pulka, P. Claudon, G. Guichard Org. Lett. , 2012 , 14 , 3130. [3] J. Kofoed, J.-L. Reymond J. Comb. Chem., 2007 , 9, 1046.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 2

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry and its Application to Combinatorial Library Screening

Neil W. Owens, a,b Katell Bathany, b,c Karolina Pulka, a,b Jean-Marie Schmitter, b,c Gilles Guichard a,b

aInstitut Européen de Chimie et Biologie, 2 rue Robert Escarpit, 33607 Pessac, France. bCBMN, CNRS UMR 5248. cCentre de Génomique Fonctionnelle, Université Bordeaux 2 Victor Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France [email protected]

Synthetic oligomers with peptidomimetic helical folding properties have attracted considerable attention for use in biological and biomedical applications. Our work has focused on oligourea foldamers, which offer 2.5-helical scaffolds that are conformationally robust in solution, including aqueous environment. They are stabilized by regular bifurcated intramolecular hydrogen bonds between urea carbonyl groups ( i residue) and urea amide protons ( i-2 and i-3 residues). [1] The modular building blocks are readily accessible from Į-amino acids, thereby offering proteinogenic side chains.

The present work is focused on sequence analysis of oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. [2] A series of five model oligoureas has been synthesized in this view.

After evaluation of MS/MS spectra obtained for these model compounds with either MALDI or ESI sources, we found that the MALDI-ToF-ToF instrument gave the more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N’H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

Our most recent results include de novo sequencing from individual TentaGel beads isolated from combinatorial libraries.

References [1] L. Fischer and G. Guichard et al. Angew. Chem. Int. Ed. 2010 , 49 , 1067. [2] K. Bathany, N. W. Owens, G. Guichard, J.-M. Schmitter J. Am. Soc. Mass. Spec. 2013 , in press .

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 3

Left-handed helical preference in an achiral peptide chain is induced by an L-amino acid in an N-terminal Type II ȕ-turn

Matteo De Poli, a Marta De Zotti, b James Raftery, a Juan A. Aguilar, a Gareth A. Morris, a Jonathan Clayden a

aSchool of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, UK bDipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, 35131 Padova, Italy [email protected]

Oligomers of the achiral amino acid Aib (Aib = Į-aminoisobutyric acid) adopt helical [1] conformations known as 3 10 -helices, which display no screw-sense preference and undergo conformational inversion on a time scale of milliseconds. [2] We [3] and others [4] had previously shown that this dynamic equilibrium may be biased in favour of either left or right handed screw- sense by interaction of the helix with a chiral residue at the chain N-terminus. We also developed a simple NMR method to report on the degree of control obtained when different amino acids where used as well as their screw-sense induction to the rest of the Aib oligomer. [5] Using crystallographic and NMR techniques, we now show that the left- or right-handed sense of helical induction arises from the nature of the ȕ-turn at the N terminus: the tertiary amino acid L- Val induces a left handed Type II ȕ-turn in both the solid state and in solution, while the corresponding quaternary amino acid L- Į-methylvaline induces a right handed Type III ȕ-turn (Figure 1).

Figure 1. Newmann projection representing the two different types of ȕ-turns generating the observed left (a) and right handed (b) helical screw sense

References [1] Toniolo, C., Benedetti, E. Trends Biochem. Sci. 1991 , 16 , 350. [2] (a) Hummel, R. P., Toniolo, C., Jung, G. Angew. Chem., Int. Ed. Engl. 1987 , 99 , 1180. (b) Kubasik, M. A., Kotz, J., Szabo, C., Furlong, T., Stace, J. Biopolymers 2005 , 78 , 87. [3] Clayden, J., Castellanos, A., Solà, J., Morris, G. A. Angew. Chem., Int. Ed. 2009 , 48 , 5962. [4] Inai, Y., Tagawa, K., Takasu, A., Hirabayashi, T., Oshikawa, T., Yamashita, M. J. Am. Chem. Soc. 2000 , 122 , 11731. [5] Solà, J., Morris, G. A, Clayden, J. J. Am. Chem. Soc. 2011 , 133 , 3712.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 4

Strategies for Orthogonal Functionalisation of Į-Helix Mimetics

Anna Barnard, a,b Panchami Prabhakaran, a,b Thomas A. Edwards, a,b Andrew J. Wilson a,b

aSchool of Chemistry and bAstbury Centre for Structural and Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. [email protected] , [email protected]

Synthetic molecules that mimic the secondary elements of proteins, structurally and/or functionally, have received significant attention in recent years. [1] These de novo designed molecules with diverse backbones find applications in molecular recognition, drug design and material sciences. [2] Through proper design, these conformational mimetics can act as inhibitors of therapeutically relevant protein-protein interactions (PPIs). [3]  This poster describes the development of orthogonally functionalised variants on the original aromatic oligoamides reported in our group (Fig. 1a). [4] A method for the synthesis of an alternative di-hydroxylated monomer will be described along with the synthesis of a ‘clickable’ monomer; both can readily be incorporated into trimeric structures (Fig. 1b). The effect of these modifications on the inhibition activity in a fluorescence anisotropy assay will also be discussed. These initial results provide a promising starting point for the development of more elaborate, multifunctional PPI inhibitors and will be considered in our ongoing efforts towards the synthesis of Į-helix mimetics tailored to a range of biological targets.

Figure 1. Structures of (a) aromatic oligoamide trimer and (b) novel monomers designed as inhibitors of PPIs.

References [1] (a) C. M. Goodman, S.Choi, S. Shadler, W. F. DeGrado, Nat. Chem. Biol. , 2007, 3 , 252. (b) I. Saraogi, A. D. Hamilton, Biochem. Soc. Trans. , 2008, 36 , 1414. [2] W. S. Horne, M. D. Boersma, M. A. Windsor, S. H. Gellman, Angew. Chem. Int. Ed. , 2008, 47 , 2853. [3] A. J. Wilson, Chem. Soc. Rev. , 2009, 38 , 3289. [4] J. P. Plante, T. Burnley, B. Malkova, M. E. Webb, S. L. Warriner, T. A. Edwards, A. J. Wilson, Chem. Commun. , 2009, 5091.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 5

Synthesis and structural studies of J-peptides based on EJ-diaminoacids

Andrii Stanovych, Sophie Thétiot-Laurent, Emeric Miclet, Francelin Bouillère, Valérie Alezra, Cyrille Kouklovsky

Laboratoire des Procédés et Substances Naturelles, ICMMO, UMR 8182, Bât. 410, Université Paris Sud XI, 91405 Orsay France [email protected]  J-Peptides are a new class of peptides that share structural properties with D-peptides. The replacement of D-aminoacids by J-aminoacids in J-peptides can lead to the formation of interesting secondary structures starting from 4 residues. The aim of this work is both to allow the development of a new synthetic route to enantiopure EJ -diaminoacids and to use them to access to novel unnatural peptides having specific conformational properties.

Figure 1. Synthetic strategy

The synthetic strategy, developed in our laboratory, starts from natural enantiopure aminoacids and is based on two key-steps : a Blaise reaction followed by a diastereoselective [1-3] reduction. It gives access to enantio and diastereopure EJ -diaminoacids. The structural study of the synthetized peptides, realized in collaboration with Dr. E. Miclet (Paris 6), shows that hybrid DJ -peptides present stable extended helical conformation characterized [4] by the absence of any intramolecular hydrogen bond and a four-fold symmetry.  

 Figure 2. Hybride DJ -peptide

References [1] F. Bouillère, S. Thétiot-Laurent, C. Kouklovsky, V. Alezra Amino Acids 2011 , 41 , 687-707. [2] F. Bouillère, R. Guillot, C. Kouklovsky, V. Alezra Org. Biomol. Chem. 2011 , 9, 394-399. [3] C. T. Hoang, V. H. Nguyen, V. Alezra, C. Kouklovsky J. Org. Chem . 2009 , 73 , 1162. [4] F. Bouillère, D. Feytens, D. Gori, R. Guillot, C. Kouklovsky, E. Miclet, V. Alezra Chem. Commun ., 2012 , 48 , 1982- 1984.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 6

Synthesis of both enantiomers of a novel unsubstituted trans -E-amino- cyclopropanecarboxylic acid derivative using a chiral pool approach and their incorporation in dipeptides

Tamara Meiresonne, Sven Mangelinckx, Norbert De Kimpe

Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000 Ghent, Belgium [email protected]

Carbocyclic E-amino acid derivatives attract considerable attention because the incorporation of these non-proteinogenic amino acids in peptides can lead to a modification of their biological activity. For example, the ȕ-peptide bond is resistant to enzymatic degradation, which enhances the metabolic stability of a E-peptide. ȕ-Aminocyclopropanecarboxylic acid ( ȕ-ACC) is a carbocyclic analogue of ȕ-alanine which possesses severe ring strain. [1] To avoid spontaneous ring opening of the cyclopropane core via a push-pull mechanism, a suitable stabilizing group at nitrogen is essential, which complicates the synthesis of ȕ-ACC derivatives and their incorporation in peptides. Moreover, due to the presence of two stereogenic centres in the cyclopropane ring, ȕ-ACC exists as four stereoisomers. In this work, the stereoselective synthesis of a novel ȕ-aminocyclopropanecarboxylic acid, with no extra functionalization of the cyclopropane core, was developed. [2] (2 S)- N-( Tert - butoxycarbonyl)aspartic acid 4-benzyl ester 1a , a derivative of the naturally occuring ȕ-amino acid aspartic acid, was used as a chiral building block. Ph Ph O BnO (S) KHMDS N Ph N Ph BnO (S) I OH (R) (R) 4steps O N Ph THF, 78 °C 2steps H O NHBoc Ͳ  N COOMe (R) COOBn (R) Ph O 1a 2a 3a 4a Ph O N Ph (R) BnO (S) OH H 7steps N COOMe O NHBoc (S) O 1b 4b

The key-step in the reaction sequence is a stereoselective base-induced ring closure of ȕ-amino ester 2a towards (-)-benzyl ȕ-aminocyclopropanecarboxylate 3a with a good trans diastereoselectivity. Saponification of this ester and subsequent coupling with methyl glycinate led to the formation of the novel ȕ-ACC-containing dipeptide 4a . Starting from (2 R)- N-( tert - butoxycarbonyl)aspartic acid 4-benzyl ester 1b , the (+)-enantiomer of this ȕ-ACC derivative and the corresponding dipeptide 4b were prepared as well.

References [1] F. Gnad; O. Reiser, Chem. Rev. 2003 , 103 , 1603-1624. [2] T. Meiresonne, S. Mangelinckx, N. De Kimpe, Tetrahedron 2012 , 68 , 9566-9571.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 7

Polyproline II bio-inspired folded structures based on original spirolactam scaffolds

Guilhem Chaubet, a Thibault Coursindel, a Carine Baraguey, a Stéphane Betzi, b Nicolas Floquet, a Xavier Morelli, b Jean Martinez, a Isabelle Parrot a

aInstitut des Biomolécules Max Mousseron, UMR 5247-CNRS-IBMM Université Montpellier I, Université Montpellier II, bLaboratory of'integrative Structural & Chemical Biology (iSCB) & INT- 3D a Molecular Modeling Platform, Cancer Research Center of Marseille (CRCM), CNRS UMR 7258; INSERM U 1068; Université Aix-Marseille, Institut Paoli Calmettes, France [email protected]

Besides the two familiar secondary structures, Į-helices and ȕ-sheets, polyproline II helix is the architectural hallmark of many protein-protein interaction modules, playing a critical role in the coordination of different protein complexes. [1] The significance of this unique extended structure, its implication in various targets involved in crucial pathologies have stimulated chemists to synthesize PPII mimics over the past few years. However, compared to the ever-growing field of Į-helices or ȕ-turn mimics, only a few approaches have been described to emulate the PPII structure. Taking advantage of the highly stereoselective ring-contraction TRAL reaction, [2] followed by two unprecedented tandem reactions, we described here an efficient access to elegant spirocyclic scaffolds. After dimerization, structural analyses of our constructions highlighted an attractive edifice able to fold and behave as a PPII helix, in view of affording a contribution in the development of new tools to understand molecular basis in biological targets involving protein-rich domains.

Figure 1. Schematic analysis of the relative orientation of the spiro groups of the synthetic dimer (orange) with the N- and C- term Pro-Pro of a natural pentaproline (yellow)

References [1] B. Bochicchio, A. Tamburro, Chirality 2002 , 14 , 782. [2] D. Farran, I. Parrot, J. Martinez, G. Dewynter, Angew. Chem. Int. Edit. 2007 , 47 , 7488.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 8

Site specific anion recognition by urea foldamers

Lucile Fischer, Brice Kauffmann, Gilles Guichard

Institut Européen de Chimie et de Biologie, CBMN, Université de Bordeaux-CNRS UMR 5248, Pessac, France [email protected]

N,N’-linked oligoureas belong to the foldamer field based on amide bond surrogates and are extensively studied in the Guichard group. [1] They have shown a remarkable propensity to fold into well defined helical secondary structures in solution by remote intramolecular three-centred H-bond interactions between backbone ureas. [2] More recently, some of these helical urea oligomers have been characterized at atomic resolution. [3] Translating structure information into function certainly represents one of the most fascinating issues in the field of foldamers. Oligoureas have been shown to be very effective in terms of interaction with biomolecules and for possible biomedical applications. In particular, helices designed to mimic host-defense peptides disrupt bacterial cell membranes and display potent antimicrobial activities. [4] The importance of protein anion recognition processes in biology (anion channels/transporters, enzymatic reactions) and the role of H-bond mediated interactions in conferring selectivity led us to consider a new development of oligoureas in molecular recognition: the four urea NHs at the extremity of the helix are not involved into intramolecular interactions and build a cleft, intrinsically chiral, that could be suitable for binding anions or neutral protons acceptors. Different oligoureas have been tested with different anions by NMR titrations that gave us access to binding constants: the data suggest different binding modes depending on the anion and the terminal part of the oligourea helix. Overall, the results show that the interaction is site-specific and that the helicity of the foldamers is unaffected upon binding.

References [1] L. Fischer, G. Guichard, Org. Biomol. Chem. 2010 , 8, 3101-3017. [2] A. Violette, M. C. Averlant-Petit, V. Semetey, C. Hemmerlin, R. Casimir, R. Graff, M. Marraud, J. –P. Briand, D. Rognan, G. Guichard, J. Am. Chem. Soc. 2005 , 127 , 2156-2164; A. Violette, N. Lancelot, A. Poschalko, M. Piotto, J. P. Briand, J. Raya, K. Elbayed. A. Bianco, G. Guichard, Chem. Eur. J. 2008 , 14 , 3874-3882. [3] L. Fischer, P. Claudon, N. Pendem, E. Miclet, C. Didierjean, E. Ennifar, G. Guichard, Angew. Chem. Int. Ed. Engl. 2010 , 49 , 1067-1070. [4] A. Violette, S. Fournel, K. Lamour, O. Chaloin, B. Frisch, J.-P. Briand, H. Monteil, G. Guichard, Chem. Biol . 2006 , 13 , 531-538; P. Claudon, A. Violette, K. Lamour, M. Decossas, S. Fournel, B. Heurtault, J. Godet, Y. Mély, B. Jamart-Grégoire, M.-C. Averlant-Petit, J.-P. Briand, G. Duportail, H. Monteil, G. Guichard, Angew. Chem. Int. Ed. Engl. 2010 , 49 , 333-336.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 9

Development of ȕ-sheet-like aromatic amide-based foldamers

L. Sebaoun, V. Maurizot, B. Kauffmann, I. Huc

Institut Européen de Chimie et Biolog ie, Université de Bordeaux–CNRS UMR 5248, 2 rue Robert Escarpit, F-33607 Pessac, France. [email protected]

Foldamers, artificial oligomers with well-defined conformations, represent a new family of self- assembled supramolecular architectures that have developed rapidly in the last decade. Considerable advancements have been made in mimicking proteins architecture and fonction using foldamers that adopt helical conformations. However, foldamers do not yet span the same range of structural diversity that can be found in proteins. For example, foldamers with ȕ-sheet-like structures are very rare and most of them are of a peptidic nature.

Therefore, we have endeavored to expand foldamer diversity by developing a novel class of abiotic ȕ-sheet-like architectures. Our strategy is to use inter-strand ʌ-ʌ aromatic stacking between sequences of aromatic oligoamides and oligoamines to mimic the natural stabilization of ȕ-strands, which occurs through a network of regularly spaced hydrogen bonds. These oligamides and oligoamines sequences are connected by a rigid U-shaped moiety that will create a turn and initiate strand formation. These molecules are designed to adopt compact folded structures that can be studied in solution and in the solid state.

Figure 1. ȕ-sheet-like foldamers, from concept to crystal structure.

In this poster we report our stepwise approach in the development of ȕ-sheet-like aromatic amide- based foldamers: from the optimization of the design elements and the use of macrocycles, to the synthesis of multi-turn structures and curving strands ȕ-sheet-like foldamers.

References [1] S. Hecht and I. Huc, Foldamers : Structure, Properties and Applications, Wiley-VCH, Weinheim , 2007 . [2] G. Guichard, I. Huc, Chem. Comm . 2011 , 47 , 5933. [3] V. Maurizot, S. Massip, J-M. Léger, G. Déléris, Chem. Comm. 2009 , 38 , 5698. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 10

ȕ-Sandwich forming propensity and biological activity of foldameric anginex analogs

Zsófia Hegedüs, a Edit Wéber, a Éva Kriston-Pál, b Éva Monostori, b Tamás A. Martinek a

aInstitute of Pharmaceutical Chemistry, University of Szeged, Hungary bLymphocyte Signal Transduction Laboratory, Institue of Genetics Biological Research Center of the Hungarian Academy of Sciences, Hungary [email protected]

The 33mer peptide anginex is a potent antitumor agent with antiangiogenic and antiproliferative activity. Anginex forms E-sandwich with three antiparallel E-strands, associating into dimers, and tetramers. [1] Biological activity and binding to its main target protein galectin-1 [2] have been thoroughly studied, therefore anginex is a good model for investigating E-amino acid substitution effect on a E-sheet structure, along with its protein binding and biological activity. 3 Residue triplets were systematically replaced by E -amino acids in the sheet forming region 3 of anginex (Figure 1). This was expected to maintain the H-bonding network with one E -amino acid substitution in each E-strand. Structural analysis (CD measurements and NMR chemical shift difference analysis) showed that the sheet forming propensity of the analogs remains, but it is lower than the parent peptide anginex. Analysis of the effects of the substitution pattern revealed that the 3 E -amino acid substitution decreases the tightness of the hydrophobic side chain packing. Binding to galectin-1 was measured by using isothermal titration calorimetry, and one of the derivatives displayed affinity comparable to anginex. To investigate the biological activity of the foldameric ȕ-sandwiches, cell proliferation measurements were carried out with a brain endothelial cell line. The antiangiogenic effect showed correlation with the folding tendency.

Figure 1. Structure of anginex, and one letter code sequence with the substitution positions

References [1] Wang, J.; Wang, M.; Li, E.; Dong, D. Peptides 2012, 38, 457-462. [2] Thijssen, V.L.; Postel, R.; Brandwijk, R. J.; Dings, R. P.; Nesmelova, I.; Satijn, S.; Griffioen, A. W. Proc Natl Acad Sci . 2006 , 103 , 15975-15980. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 11

Peptide-Catalyzed Stereoselective Conjugate Addition Reactions Generating All-Carbon Quaternary Stereogenic Centers

Robert Kastl, Helma Wennemers

Laboratory of Organic Chemistry, ETH Zurich, Wolfgang Pauli-Strasse 10, 8093 Zurich, Switzerland [email protected]

The conjugate addition reaction of aldehydes to nitroolefins is an important reaction for the [1] synthesis of J-nitroaldehydes that can be readily converted into, for example, J-amino acids. Our group introduced tripeptides of the type Pro-Pro-Xaa (Xaa = acidic amino acid) as highly efficient catalysts for asymmetric conjugate addition reactions of aldehydes to E-mono- and D,E- [2,3] disubstituted nitroolefins. We now became interested in using E,E-disubstituted nitroolefins as electrophiles since they would afford J-nitroaldehydes with an all-carbon quaternary stereogenic center. Their stereoselective transformation is challenging due to the higher steric congestion at the electrophilic carbon of the E,E-disubstituted nitroolefin and consequently the difficulty of controlling the stereoselectivity compared to E-monosubstituted nitroolefins. The further transformation of such J-nitroaldehydes to J-amino acids bearing an all-carbon quaternary stereogenic center might not only be interesting for the development of therapeutics but also for foldamer research. Here, we show peptide-catalyzed stereoselective conjugate addition reactions of different aldehydes to E,E-disubstituted nitroolefins providing J-nitroaldehydes with an all-carbon quaternary stereogenic center in good yields and stereoselectivities.

Figure 1. 1,4-Addition reactions between aldehydes and E,E-disubstituted nitroolefins providing access to J-amino acids bearing an all-carbon quaternary stereogenic center.

References [1] D. Roca-Lopez, D. Sadaba, I. Delso, R. P. Herrera, T. Tejero, P. Merino, Tetrahedron: Asymmetry 2010 , 21 , 2561. [2] a) M. Wiesner, J. D. Revell, H. Wennemers, Angew. Chem. Int. Ed. 2008 , 47 , 1871. b) M. Wiesner, M. Neuburger, H. Wennemers, Chem. Eur. J. 2009 , 15 , 10103. c) M. Wiesner, G. Upert, G. Angelici, H. Wennemers, J. Am. Chem. Soc. 2010 , 132 , 6. [3] J. Duschmalé, H. Wennemers, Chem. Eur. J. 2012 , 18 , 1111 .

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 12

1,4-Dihydropyridine carboxylic acids as biologically active building blocks

Gunars Duburs, Egils Bisenieks, Janis Uldrikis, Janis Poikans, Imants Bisenieks, Brigita Vigante

Latvian Institute of Organic Synthesis, Riga LV-1006, Latvia [email protected]

Bifunctional 1,4-dihydropyridine (1,4-DHP) derivatives comprising two or more functional groups suitable for condensation reactions (carboxylic acid, amino groups in side chains or in the 1,4-DHP nucleus) can be used for synthesis of oligomers and foldamers. 1,4-Dihydroisonicotinic acid monocyclic, bicyclic and tricyclic derivatives 1 could be mentioned as prototypes along with 1,4-DHP derivatives comprising carboxylic groups in position 3 and 5: attached to the DHP ring directly ( 3) or by a spacer ( e.g. carboxymethylene, 4). Compounds 1 can be further derivatized to obtain dipeptide type compounds 2. O R OH OH O NH O O O O O H H

N N H H 1 2

O H R O O H R O OH X X OH OH OH O O O O N N H H 3 4

Above mentioned 1,4-DHP derivatives possess mainly low toxicity, e.g. , monocyclic compound 2, R=CH 2CH 2CO 2H has LD 50 > 10,000 mg/kg p.o., rats. Monocyclic compound 1 (3,5-diethyl ester) possesses antimutagenic, DNA protective properties. It stimulates DNA repair and has dual effects on cellular defense systems against endogenously generated DNA damage. It reduces DNA strand breaks and stimulates apoptosis. After genotoxic stress it reduces DNA strand breaks and the number of apoptotic cells. The major target is DNA repair. [1] This compound significantly reduced DNA bare damage by treatment with X-irradiation and lowered mutation frequency. [2] [3] Compound 4 (X=CH 2, R=Et) stimulates anticancer activity of 5-fluorouracil and reveals antiviral activity. [4]

Acknowledgement. Study was supported by the State Research Program “Biomedicine”

References [1] N.I. Ryabokon, N.V. Nikitchenko, O.V. Dalivelya, R.I. Goncharova, G. Duburs, M. Konopacka, J. Rzeszowska- Wolny, Mut. Res. 2009 , 679 , 33-38. [2] M. Wojewodzka, I. Gradzka, I. Buraczewska, K. Brzoska, B. Sochanowicz, R. Goncharova, T. Kuzhir, I. Szumiel, Mut. Res. 2009 , 671 , 45-51. [3] E. Bisenieks, G. Duburs, I. Stonans, E. Jascenko, I. Domraceva, J. Poikans, I. Bruvere, I. Kalvins, I. Sestakova, J. Uldrikis, B.Vigante, K. Pubulis, I. Jonane-Osa, EP2406218(A1), 18.01.2012. [4] I. Stonans, I. Jansone, I. Jonane-Osa, E. Bisenieks, G. Duburs, I. Kalvins, B. Vigante, J. Uldrikis, I. Bruvere, L. Zuka, J. Poikans, Z. Neidere, WO/2012/010276, 26.01.2012.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 13

Conformational studies of DE-peptoids

Emiliana De Santis, a Bruce D. Alexander, b Sophie Faure, c,d Thomas Hjelmgaard, c,d Simon J. Holder, e Claude Taillefumier, c,d Alison A. Edwards a

aMedway School of Pharmacy, Universities of Kent and Greenwich at Medway, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK. bSchool of Science, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, UK. cClermont Université, Université Blaise Pascal, Laboratoire SEESIB, BP 10448, F-63000 Clermont-Ferrand, France. dCNRS, UMR 6504, Laboratoire SEESIB, F-63177 Aubière cedex, France. eSchool of Physical Sciences, University of Kent, Canterbury, CN2 7NZ, UK [email protected]

Į-Peptoids are a class of peptidomimetic foldamers structurally related to natural Į-peptides, in which the side chain is moved along the backbone from the C Į to the amide nitrogen. This determines favourable properties, such as greater flexibility, resistance to proteases and higher cell permeability. The E-homologues of Į-peptides, E-peptides, also have comparable E-peptoid counterparts. The study described herein examines the conformational preference of the hybrid ĮE - peptoid backbone, where Į- and E-residues are alternated along the backbone. A library of ĮE - peptoids with variability in the chain length, side chain patterns and terminal capping groups was designed to aid conformational investigation (Figure 1a). A comprehensive study of the library by circular dichroism (CD) has enabled us to identify a number of distinct conformational features and relate these to the primary structure using NMR, IR and X-ray crystallographic data. Further to this, a comprehensive binding study with a cyclic hexamer has enabled us to explore the binding selectivity of the hybrid architecture for a range of metal ions.

(a)  (b) 

Figure 1. (a) The ĮE -peptoid backbone and the side chains employed. (b) Several of the characteristic spectra observed for the cyclic ĮE -peptoid backbone in MeCN.

The work presented will focus on the most recent data obtained for the library of ĮE -peptoids where a distinct set of CD spectra were observed in MeCN (Figure 1b) and also in other solvents such as TFE. Six CD spectra have now been identified which are representative of all of the CD spectral features observed for the compound library. Therefore this set of spectra constitute the reference CD spectra for the conformations adopted by the novel backbone. Although molecular modeling is limited, due to the cis/trans isomerism of the amides, it is has been possible to propose (from literature and crystallographic data) what conformations these characteristic spectra may represent. The findings of this recent work will be presented alongside earlier achievements in the investigation of the DE -peptoid architecture to give a comprehensive overview of the current understanding of the conformational preferences of this hybrid architecture.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 14

Synthesis and structural study of aza -modified ACBC oligopeptides

Amandine Altmayer-Henzien, a Valérie Declerck, a Jonathan Farjon, b Jean-Pierre Baltaze, c Régis Guillot, c Denis Merlet, b David J. Aitken a

aLaboratoire de Synthèse Organique et Méthodologie, bLaboratoire de RMN en Milieu Orienté, cServices Communs, Institut de Chimie Moléculaire et des Matériaux d’Orsay (CNRS-UMR 8182), Université Paris-Sud, 15 rue Georges Clemenceau, 91405 Orsay, France [email protected]

E-Peptides are known for their resistance to enzymatic degradation and, like Į-peptides, they present multiple hydrogen bonding opportunities which can promote 3D structuration. In this respect, the use of cyclic ȕ-amino acids enhances foldamer propensity. Indeed, oligomers of 5- and 6-membered ring E-amino acids have been shown to adopt regular structures such as sheets or helices. Our interest focuses on 4-membered ring E-amino acids. It has been reported that oligomers [1] of cis -cyclobutane E-amino acid (ACBC) adopt a strand-type structure, whereas oligomers of trans -ACBC form a 12-helix. [2] In ACBC dipeptides, the predominance of eight-membered hydrogen-bonded rings have been reported for ( trans , trans ) and ( trans , cis ) configurations whereas six-membered rings are observed for ( cis , trans )-dimers. [3] These observations have prompted us to study N-aminoazetidinecarboxylic acid (AAzC), an aza -analogue of ACBC, which can potentially adopt either a cis or trans structure due to the configurational flexibility of the pyramidal nitrogen [4] atom that formally replaces the E-carbon of ACBC. Previous structural studies concerning three model cyclobutylamide derivatives containing ACBC or AAzC allowed us to conclude to a trans behaviour of AAzC, and a propensity to adopt an eight- membered hydrogen-bonded ring, stabilized by the formation of a hydrazinoturn. Moreover, the structural study of four hetero-dipeptides, each incorporating AAzC at the N-terminal position and a single stereoisomer of ACBC at the C-terminal position, revealed also the formation of the same hydrazinoturn, without any influence of the stereochemical pattern of ACBC.

Here, we will describe the synthesis of hetero-oligopeptides comprising a sequence of trans -ACBC residues bearing a single AAzC unit at the N-terminal position. The folding behaviour of these peptides will be examined on the basis of NMR studies, circular dichroism, X-ray diffraction and molecular modelling studies. We will demonstrate the influence of this single AAzC building block at the N-terminal position upon the structuration of an entire oligopeptide.

References [1] F. Rùa, S. Boussert, T. Parella, I. Díez-Pérez, V. Branchadell, E. Giralt, R. M. Ortuño, Org. Lett. 2007 , 9, 3643. [2] C. Fernandes, S. Faure, E. Pereira, V. Théry, V. Declerck, R. Guillot, D. J. Aitken, Org. Lett. 2010 , 12 , 3606. [3] E. Torres, E. Gorrea, E. Da Silva, P. Nolis, V. Branchadell, R. M. Ortuño, Org. Lett. 2009 , 11 , 2301. [4] V. Declerck, D. J. Aitken, J. Org. Chem. 2011 , 76 , 708. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 15

Helix Bundles of Aromatic Oligoamide Foldamers

Bo Chi, Sumito Tokuji, Ting Qi, Brice Kauffman, Victor Maurizot, Ivan Huc

Institut Européen de Chimie et Biolog ie, Université de Bordeaux–CNRS UMR 5248, 2 rue Robert Escarpit, F-33607 Pessac, France [email protected]

Over the last decades, strong efforts have been made to develop new molecular backbones for the construction of original, predictabable, and well defined molecular architectures: the foldamer chemistry. [1] These researches were mainly focused on the elaboration of architectures that mimic secondary structures of biomolecules (helices and sheets) and have lead to a wide variety of building blocks that can be used to build such molecular architectures. The second step in this process of biomolecular mimicking is the construction of more complex structures such as tertiary and quaternary structures which are key intermediates to reach functions. [2] Therefore some efforts have been done to design molecular architectures (mostly helices) that have specific side chains in their outer surface to specifically interact with biomolecules or other foldamers. [3]

In this context we have focused our attention into the design, the synthesis and the characterization of oligoamide-quinolines foldamers that have side chains designed to interact with each other and form specifically dimeric helix bundles. This study is the first step to learn how molecular recognition at the surface of this type of aromatic oligoamide foldamers could be design.

Figure : Schematic representation of the helix bundle formation.

References [1] (a) Foldamers: Structure, Properties and Applications S. Hecht, I. Huc, Eds. Wiley-VCH:Weinheim, 2007 ; (b) G. Guichard, I. Huc, Chem. Comm ., 2011 , 47 , 5933-5941. [2] (a) T. A. Martinek, F. Fülöp, Chem. Soc. Rev. , 2012 , 41 , 687-702. (b) J. L. Price, W. S. Horne, S. H. Gellman, J. Am. Chem. Soc. , 2010 , 132 , 12378-12387. [3] T. A. Edwards, A. J. Wilson , Amino Acids , 2011 , 41 , 743-754. (b) B. Baptiste, F. Godde, I. Huc, ChemBioChem 2009 , 10 , 1765-1767.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 16

Foldamers: new avenues towards protein-protein interactions (PPIs) disruptors

Marcella De Giorgi, Marie Jouanne, Anne Sophie Voisin-Chiret, Sylvain Rault

1-Univ, France; 2-UNICAEN, CERMN (Centre d’Etudes et de Recherche sur le Médicament de Normandie UPRES EA 4258-FR CNRS 3038 INC3M, Bd Becquerel), F-14032 Caen, France. [email protected]

Proteins modulate the majority of biological functions and are composed of highly organized secondary structural elements such as alpha helices, beta sheets and beta strands. These elements could represent attractive therapeutic targets. In the literature, numerous synthetic alpha- helix mimetic molecules have already been presented ranging from biotic to abiotic foldamers, that are, accordingly to Huc, [1] oligomeric compounds that adopt compact globular structure in solution stabilized through non covalent interactions between non adjacent monomer subunits. Our laboratory is interested for years in the synthesis of a large library of abiotic mixed aromatic oligopyridyl systems, [2] in the study of their conformational organization [3] and in their biological interest.

Figure 1

After describing general synthetic pathway, the poster will present possible biological applications. Alpha helices or beta sheets often facilitate protein-protein interactions (PPIs) which control numerous cellular processes. Therefore, PPIs misregulation can result in numerous disease states such as HIV, cancer, diabetes and neurodegenerative diseases. [4] Between them, in the last years, we have investigated the ability of our foldamers to restore apoptosis in cancer cells by inhibiting the function of pro-apoptotic members of Bcl-2 family proteins. To date, encouraging biological results show that these molecules are able to disturb these protein interactions.

References [1] Hecht, S.; Huc, I. Foldamers: Structure, Properties and Applications , Wiley-VCH: Weinheim, 2007 , 229. [2] (a) Burzicki, G.; Voisin-Chiret, A.S.; Sopková-de Oliveira Santos, J.; Rault, S . Tetrahedron 2009 , 65 , 5413-5417. (b) Burzicki, G.; Voisin-Chiret, A.S.; Sopková-de Oliveira Santos, J.; Rault, S. Synthesis 2010 , 16 , 2804-2810. (c) Voisin-Chiret, A.S.; Muraglia, M.; Burzicki, G.; Perato, S.; Corbo, F.; Sopková-de Oliveira Santos, J.; Franchini, C.; Rault, S. Tetrahedron 2010 , 66, 8000-8005. (d) Perato, S.; Voisin-Chiret, A.S.; Sopková-de Oliveira Santos, J.; Sebban, M.; Legay, R.; Oulyadi, H.; Rault, S. Tetrahedron 2012 , 68 , 1910-1917. (e) De Giorgi, M.; Voisin-Chiret, A.S.; Sopková-de Oliveira Santos, J.; Corbo, F.; Franchini, C.; Rault, S. Tetrahedron 2011 , 67 , 6145-6154. [3] (a) Sopková-de Oliveira Santos, J.; Voisin-Chiret, A.S.; Burzicki, G.; Sebaoun, L.; Sebban, M.; Lohier, J.F.; Legay, R.; Oulyadi, H.; Bureau, R.; Rault, S. J. Chem. Inf. Model. 2012 , 52 , 429-439. (b) Voisin-Chiret, A.S.; Burzicki, G.; Perato, S.; De Giorgi, M.; Franchini, C.; Sopková-de Oliveira Santos, J.; Rault, S. Tetrahedron 2012 , 68 , 4381- 4389. (c) Voisin-Chiret, A.S.; Rault, S. Pure Appl. Chem. 2012 , 84 , 2467-2478. [4] Davis, J. M.; Tsou, L. K.; Hamilton, A. D. Chem. Soc. Rev. 2007 , 36 , 326-334.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 17

Helix to Strand Transition in Rationally Designed DE-Hybrid Peptides and Their Self-Organization in Organic Media

Dhayalan Balamurugan, Kannoth M. Muraleedharan*

Department of Chemistry, Indian Institute of Technology Madras, Chennai, 600036 India [email protected]

Foldamers, molecules which adopts well-defined conformation in solution, [1] are receiving considerable attention because of their potential application in medicine and material design. [2] A number of building blocks of natural- and synthetic origin have been utilized in the synthesis of such molecular systems and a variety of conformations such as helix, E-sheets and turns have been [3] realized till date; hybrids of D-amino acids with E-amino acids are among one of the most [4] studied. We have recently shown that trans -E -amino acid residues in their D,E-hybrid peptides undergo anti- to gauche rotamer shift in response to intramolecular hydrogen bonding possibilities and facilitate formation of an 11-helix. [5] We have continued our studies in this direction and synthesized a new set of hybrid peptides which adopts helical structures in low polar solvents but change to extended conformation in polar ones (eg. peptide 1, Figure 1a). Such systems are ideal for studying conformational transition in peptides. Their synthetic details, along with results from NMR- and X-ray crystallographic studies will be presented here. [6] The peptide 1 from this group was found to aggregate and give nanometer-sized vesicles from isopropanol solution (Figure 1b). A discussion on the mode of self-organization that lead to spherical assemblies will also be a part of the presentation. [6]

a)  b) 

CHCl 3 iͲPrOH 

5

Figure 1. a) Solvent dependent conformational change of DE -hybrid peptide 1; b) SEM image showing the formation of vesicles from the peptide 1.

References [1] S. H. Gellman, Acc. Chem. Res. 1998 , 31 , 173. [2] (a) G. Guichard, I. Huc, Chem. Commun. 2011 , 47 , 5933. (b) T. A. Martinek, F. Fulop, Chem. Soc. Rev. 2012 , 41 , 687. [3] (a) D. J. Hill, M. J. Mio, R. B. Prince, T. S. Hughes, J. S. Moore, Chem. Rev. 2001 , 101 , 3893. (b) Foldamers: Structure, Properties and Applications ; S. Hecht, I. Huc, Eds.; Wiley-VCH:Weinheim, 2007 . [4] (a) W. S. Horne, S. H. Gellman, Acc. Chem. Res . 2008 , 41 , 1399. (b) L. K. A. Pilsl, O. Reiser, Amino Acids 2011 , 41 , 709. [5] D. Balamurugan, K. M. Muraleedharan, Chem. Eur. J. 2012 , 18 , 9516. [6] D. Balamurugan, K. M. Muraleedharan, Manuscript to be submitted.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 18

Foldaxanes: Helically Folded Oligomers around Dumbbell Molecules

Quan Gan, a Yann Ferrand, a Brice Kauffmann, a Hua Jiang, b Ivan Huc a

a Université de Bordeaux, CBMN, UMR5248 Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France and CNRS, CBMN, UMR5248, France b CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China [email protected]

Removing the peripheral subsituents from helical capsule sequences (these residues serve as end- caps of the helix hollow) allows the incoporation of guests that are longer than the hollow itself. Proof of concept was established by the crystal structure shown below which shows a dumbell- shape guest molecule threaded through a helix. The terminal diphenyl substituents of the guest are too large to go through the helix hollow, implying that the complex cannot form by a threading mechanism but through helix winding around the guest. The winding process requires helix unfolding and refolding, as well as a strict match between helix length and anchor points on the rods. The time scales of folding/unfolding being relatively slow, the helices can undergo some motions without dissociation, such as shuttling [1] or screwing, [2] on guest molecules having several binding sites. The strong analogy between this system and rotaxanes hints at possible applications of such constructs in the vast field of artificial molecular machines.





References [1] Q. Gan, Y. Ferrand, C. Bao, B. Kauffmann, A. Grélard, H. Jiang, I. Huc, Science 2011 , 331 , 1172-1175. [2] Y. Ferrand, Q. Gan, B. Kauffmann, H. Jiang, I. Huc , Angew. Chem. Int. Ed. 2011 , 50 ,7572-7575.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 19

Hydrophobic, Aib-rich peptides form nano-sized assemblies soluble in water

Edoardo Longo, Marco Crisma, Fernando Formaggio, Claudio Toniolo and Alessandro Moretto

ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy [email protected]

We recently reported that a series of helical Aib/Ala-containing peptides, lacking any charge or polar group, are soluble in water. [1,2] In this communication we present evidence of the formation of self-assembled structures in water, likewise responsible for the unexpected solubility properties. [3] Z-(Ala) 3-(Aib-Ala) 4-OMe forms spheres with diameters up to 100 nm (Figure 1), that can incorporate molecular systems of relevant size, such as Au nanoparticles. Our aggregates are larger than a typical micelle, although it is not clear yet if they form vesicles or a different type of supramolecular structure. To this aim, additional experiments are under way. In particular, we are investigating the role of (i) the non intramolecularly H-bonded amide N-H and C=O groups, (ii) the aromatic S-S interactions and (iii) the peptide helix dipole moment. Indeed, a few years ago Kimura and coworkers demonstrated that molecules with a large dipole moment are intrinsically hydrophilic. [4] We believe that our supramolecular systems may widen the number of applications currently accessible to self-assembled aggregates in the fields of biomedicine and materials science.

Figure 1. The hydrophobic, helical undecapeptide Z-(Ala) 3-(Aib-Ala) 4-OMe forms in water spherical aggregates as revealed by TEM (right image, uranyl acetate staining).

References [1] I. M. Rio-Echevarria, R. Tavano, V. Causin, E. Papini, F. Mancin, A. Moretto, J. Am. Chem. Soc. 2011 , 133 , 8-11. [2] E. Longo, A. Moretto, F. Formaggio, C. Toniolo, Chirality 2011 , 23 , 756-760. [3] E. Longo, M. Crisma, F. Formaggio, C. Toniolo, A. Moretto, Polym. J. 2013 , in press. [4] M. Fukuda, J. Sugiyama, T. Morita, S. Kimura, Polym. J. 2006 , 38 , 381-386.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 20

Designing beta-solenoid foldamers: stereochemistry, chain length and hydrophobic packing

Gábor Olajos, Edit Wéber, Lukács Németh, Tamás A. Martinek

University of Szeged, Institute of Pharmaceutical Chemistry, Hungary [email protected]

The study of water soluble ȕ-sandwich mimetic foldamer structures is challenging, because of the difficulties associated with the optimization of the long-range hydrophobic interactions. The larger surface of ȕ-sheets is however required in order to interact with solvent-exposed protein sites. To find a transition between ȕ-sandwiches and the thoroughly studied helices, we turned our attention to ȕ-solenoids, structures where parallel ȕ-strands are folded in an overall helical arrangement (Figure 1). Our de novo design consisted of two parts: short helical segments of cyclic beta amino acids, stabilized by stereochemical controlling effects, and ɲ/ȕ chimera strands with alternating polar and hydrophobic side-chains to create a hydrophobic core similar to ȕ-sandwiches. These strands connect the helix segments, resulting in a structure which can be de scribed as a “stretched helix”. We designed a number of peptide foldamers varying the number of strands and the hydrophobic core. The results of Molecular Dynamics (MD) modeling and Circular Dichroism (CD) measurements in water revealed that a minimal number of six strands is required for the folding. Unlike foldameric helices, these structures were not soluble in methanol. We were unable to get high-resolution NMR structural data, which indicates that stereochemical control on its own is not enough to ensure rigid folding. We assume that hydrophobic interactions need further optimization, and we aim to correct this by using cyclic ȕ-amino acids in the strands and less hydrophobic monomers in the helical segments.

Figure 1. Representaion of a soleonid structure

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 21

Structural Characterization of Heterogeneous Foldamers in the Ȗ-Peptide Superfamily

Nagendar Pendem, a Yella Reddy Nelli, a Céline Douat, a Gavin Collie, a Lucile Fischer, a Michel Laguerre, a Eric Ennifar, b Brice Kauffmann, c Gilles Guichard a aUniversité de Bordeaux CNRS UMR5248, Institut Européen de Chimie et Biologie, 33607 Pessac, France. bUniversité de Strasbourg-CNRS UPR9002, Architecture et Réactivité de l'ARN, IBMC, CNRS, 67084 Strasbourg,ԟ France. cUniversité de Bordeaux CNRS UMS3033, Institut Européen de Chimie et Biologie, 33607 Pessac, France. [email protected]ԟ

Aliphatic Ȗ-peptides, i.e. oligoamides consisting exclusively of Ȗ-amino acid residues, represent an interesting class of peptidomimetic foldamers that today still remains overlooked. [1] Compared to Į- amino acids, Ȗ-amino acids are characterized by a greater chemical diversity (seven substitution positions versus three for Į-amino acids) and conformational versatility. The Ȗ-peptide backbone can be seen as the prototypic member of a larger family (i.e. Ȗ-peptide superfamily or lineage) of peptidomimetic backbones and combinations thereof, all sharing an isosteric relationship ( e.g. oligocarbamates, [2] N,N’-linked oligo(thio)ureas, [3] oligoguanidines, [4] oligomers of ȕ-aminoxy acids, [5] sulfonamidopeptides [6] ). Although the constituent units in these backbones are endowed with different properties, their combination may represent an opportunity to generate new heterogeneous backbone oligomers with defined secondary structures, [7] thus further expanding the chemical space of foldamers in the Ȗ-peptide superfamily. Herein, we report the structural characterization of heterogeneous aliphatic oligomers containing different arrangements of isosteric amide, urea and carbamate units of general formula NH-CH(R)-CH 2-X-CO, X = CH 2, NH, O. Because these units display different helix folding propensities ( U (X = NH) > A (X = CH 2) > C (X = O), the stability of the resulting fold will be controlled by the ratio of A, U and C units and by their sequence distribution. We show that oligomers consisting of 1:1 alternation of U and C (or A) linkages and 2:2 alternations of U and A units retain the ability to fold into well defined helical structures. [8] We also provide evidence that high C to U ratio in U/C heterogeneous oligomers can cause local helix destabilization. [9] This study can be seen as the first step towards the introduction of a general folding code in the Ȗ-peptide foldamer superfamily.

References [1] See the following reviews : (a) D. Seebach, A. K. Beck, D. J. Bierbaum, Chem. Biodivers. 2004 , 1, 1111-1239. (b) F. Bouillère, S. Thétiot-Laurent, C. Kouklovsky, V. Alezra, Amino Acids 2011 , 41 , 687-707. [2] C. Cho, E. Moran, Cherry, J. Stephans, S. Fodor, C. Adams, A. Sundaram, J. Jacobs, P. Schultz, Science 1993 , 261 , 1303-1305. [3] L. Fischer, G. Guichard, Org. Biomol. Chem. 2010 , 8, 3101-3117. [4] Z. Zhang, E. Fan, J. Org. Chem. 2005 , 70 , 8801-8810. [5] X. Li, D. Yang, Chem. Commun. 2006 , 3367-3379. [6] C. Gennari, B. Salom, D. Potenza, A. Williams, Angew. Chem. Int. Ed. 1994 , 33 , 2067-2069. [7] For a review on heterogeneous foldamers, see : W. S. Horne, S. H. Gellman, Acc. Chem. Res. 2008 , 41 , 1399- 1408. [8] N. Pendem, Y. R. Nelli, C. Douat, L. Fischer, M. Laguerre, E. Ennifar, B. Kauffmann, G. Guichard, Angew. Chem. Int. Ed. 2013 , DOI: 10.1002/anie.201209838. [9] Y. R. Nelli, L. Fischer, G. Collie, W, B. Kauffmann, G. Guichard, submitted 2013 .

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 22

De novo design of a Cu(II) binding helix bundle

Henrique F. Carvalho, a Vanessa Miranda, a Anaïs M. Pujol, a Patrick Groves, a Olga Iranzo a,b

aInstituto de Tecnologia Química e Tecnológica, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal b Institut des Sciences Moléculaires de Marseille/BiosCiences UMR CNRS 7313, Aix-Marseille Université, Campus Scientifique de Saint Jérôme, F-13397 Marseille Cedex 20, France [email protected]

Metalloenzymes play crucial roles in biological systems and have great biotechnological potential. The design of suitable peptidic analogues is of great interest and has been an object of research to test our understanding of metal-protein interactions and catalysis. [1-3] Our work has the objective of constructing asymmetric metal ion binding pockets in the interior of de novo designed helical bundles to evolve artificial metalloenzymes.

[4] Starting from the de novo designed model peptide Į3D, we inserted the mutations L17H, L27D, F30H, L66H, and H71G to generate the mutant Į3DII_H71G which contains a metal ion binding pocket found in several enzymes, among them the Superoxide Dismutases. The mutated peptide was obtained by protein expression ( E. coli BL21*) and purified by reverse-phase HPLC. DOSY- NMR and Far-UV Circular Dichroism (CD) spectroscopies revealed a monomer Į-helical bundle structure in aqueous solution. However, the CD thermal denaturation studies indicated a significant loss of stability in comparison to the model peptide. UV-Vis and EPR spectroscopies showed the binding of 1 equivalent of Cu(II), a metal ion with interesting redox and hydrolytic properties. Far- UV CD spectroscopy indicated that upon Cu(II) binding, the Į-helical content of Į3DII_H71G increased. The same experiments carried out with the native Į3D peptide showed only unspecific Cu(II) binding.

Figure 1. Scheme of the Į3DII_H71G peptide showing the metal ion binding site.

References

[1] W. F. DeGrado, C. Summa, V. Pavone, F. Nastri, A. Lombardi, Annu. Rev. Biochem . 1999, 68, 779-819. [2] Lu Y. Lu, N. Yeung, N. Sieracki, and N. M. Marshall, Nature 2009 , 460 , 855–62. [3] (a) A. F. A. Peacock, O. Iranzo, V. L. Pecoraro, Dalton Trans. 2009 , 9226 , 2271–80. (b) M. L. Zastrow, A. F. A. Peacock, J. A. Stuckey, V. L. Pecoraro, Nature Chem. 2012 , 4, 118–23.  [4] Walsh S. T. Walsh, H. Cheng, J. W. Bryson, H. Roder, W. F. DeGrado, Proc . Natl . Acad . Sci . USA 1999 , 96 , 5486–91.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 23

Conformational study of the human urotensin-II and UII-related peptide

Jana Sopkova-de Oliveira Santos, a,b Alban Lepailleur, a,b Isabelle Milazzo-Segalas, c Ronan Bureau a,b

a Normandie Univ, France b UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie -FR CNRS INC3M - SF ICORE, Université de Caen Basse-Normandie, UFR des Sciences Pharmaceutiques Bd Becquerel) F-14032 Caen, France cUniversité de Rouen, Institut de Recherche en Chimie Organique Fine, UMR CNRS 6014, Laboratoire de RMN, Mont-Saint-Aignan, France [email protected]

Human urotensin-II (hU-II) is a cyclic peptide that plays a central role in cardiovascular homeostasis and is considered to be the most potent mammalian vasoconstrictor identified to date . It is a natural ligand of the human urotensin-II (hUT-II) receptor, a member of the family of rhodopsin-like G-protein-coupled receptors. hU-II is composed of 11 amino acids (ETPDCFWKYCV), generated by proteolytic cleavage from a precursor prohormone, with a conserved cysteine-linked macrocycle CFWKYC. The sequence WKY appears to be very important for the biological activities, whereas the disulfide bridge of U-II is of minor importance. A published report has demonstrated the existence, in mouse, rat and human, of a paralog of hU-II (ACFWKYCV for the sequence) named UII-related peptide (URP) suggesting that the biological effects previously attributed to hU-II could actually be exerted by URP.

From the structure-activity relationship studies of the reported ligands, a 3D pharmacophores for both non-peptide agonists and antagonists were previously built in our laboratory. We realized dynamic studies on hU-II and URP to check the conformation flexibilities of these peptides and established the relationships between their 3D structures and our pharmacophores.

Supported by: Interreg IV transmanche Program PERENE ( http://perene.univ-rouen.fr/ )

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 24

Stereoelectronic Effects on Cis-Trans Amide Bond Rotamers in Peptoids by Introduction of Surrogates of the Native Peptide Bonds

Jens Engel-Andressen, Jonas S. Laursen, Peter Fristrup, Pernille Harris, Christian A. Olsen *

Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800, Kongens Lyngby, Denmark [email protected]

Non-natural peptide analogs have significant potential for ̘the development of new materials and pharmacologically active ligands. ̘One such architecture, peptoids (N-alkyl-glycines), has found use in ̘a variety of biologically active compounds but has only been studied ̘to some extinct with respect to folding propensity. Thus, we here report an investigation of ̘the effect of structural variations on the cis-trans amide bond rotamer ̘equilibria in a selection of monomer model systems. We present the synthesis and investigation of cis-trans isomerism in the first ̘examples of peptoids containing thioamide bonds as well as ̘trifluoroacetylated peptoids. These systems revealed an  increase in the preference for cis -amides as compared to their parent ̘compounds and thus provide novel strategies for affecting the folding of peptoid constructs. By using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory calculations, we present evidence for the 2 presence of thioamide-aromatic interactions through Csp H···S amide hydrogen bonding, which stabilize certain peptoid conformations.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 25

Cis ŦTrans Amide Bond Rotamers in ȕ̂Peptoids and Peptoids: Evaluation of Stereoelectronic Effects in Backbone and Side Chains

Jonas Striegler Laursen, Christian A. Olsen *

Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800, Kongens Lyngby, Denmark [email protected]

Non-natural peptide analogs have significant potential for the development of new materials and pharmacologically active ligands. One such architecture, the ȕ-peptoids (N-alkyl- ȕ-alanines), has found use in a variety of biologically active compounds but has been sparsely studied with respect to folding propensity. We present an investigation of the effect of structural variations on the cis Ŧtrans amide bond rotamer equilibria in a selection of monomer model systems. In addition to various side chain effects, which correlated well with previous studies of Į-peptoids, we present the synthesis and investigation of cis Ŧtrans isomerism in the first examples of ȕ-peptoids containing thioamide bonds as well as trifluoroacetylated ȕ-peptoids. These systems revealed an increase in the preference for cis-amides as compared to their parent compounds and thus provide novel strategies for affecting the folding of peptoid constructs. By using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory calculations, we present evidence for the presence of 2 thioamide Ŧaromatic interactions through Csp ŦH···S amide hydrogen bonding, which stabilize certain peptoid conformations. [1]

References [1] Laursen, J. S.; Engel-Andreasen, J.; Fristrup, P.; Harris, P.; Olsen, C. A. J. Am. Chem. Soc. 2013 , 135 , 2835 Ŧ2844 .

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 26

Stability of oligourea helices containing achiral gem -dimethylated units

J. Fremaux, a C. Dolain, a B. Kauffmann, a J. Clayden, b G. Guichard a

aInstitut Européen de Chimie et Biologie, CBMN, Université de Bordeaux-CNRS UMR 5248, 2 rue Robert Escarpit, 33600 Pessac, France bSchool of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK [email protected]

N,N’-linked aliphatic oligoureas such as those developed in our laboratory are peptidomimetic foldamers that adopt well-defined helical secondary structures akin to that of Į- polypeptides [1] . In the past few years, we have investigated the rules that govern helix formation among oligoureas (chain length dependence, solvent effect, substitution pattern requirement, backbone isosteric replacements). This is of practical utility if one aims to elaborate functional helices. However, the possibility to use Thorpe-Ingold effects (i.e. introduction of a backbone quaternary carbons) to control conformation of oligoureas like with Aib ( Į-aminoisobutyric acid) in peptides, has not yet been studied. Aib is the simplest quaternary Į-amino acid well-known for its [2] ability to promote and stabilize 3 10 and Į-helical structures . Since it is achiral, (Aib) n homooligomers adopt both right- and left-handed helical conformations that interconvert rapidly in solution. It is nevertheless possible to control the helix screw sense by adding a chiral controller (covalently or non covalently) at either end of the helix [3] . Herein, we have tested whether the helix geometry of aliphatic oligoureas may accommodate the presence of achiral Aib-type units. Required activated monomers with gem - dimethyl substituents were prepared from 1,2-diamino-1,1-dimethylethane (DADME). Spectroscopic and X-ray diffraction studies have shown that the insertion of these units in the central region of an N,N’-linked Oligourea ( 1-4) does not impair 2.5 helical folding but may have a local destabilizing effect around the achiral residue depending on the position of the gem -dimethyl substituent (quaternary ĮC vs ȕC) and also induce some local conformational rearrangement [4] . This work is relevant to the design of oligourea helical structures made of contiguous gem -dimethylated units for studying helicity induction in the presence of a chiral controller.

References [1] (a) L. Fischer, G. Guichard, Org. Biomol. Chem. 2010 , 8, 3101-3117. (b) L. Fischer, P. Claudon, N. Pendem, E. Miclet, C. Didierjean, E. Ennifar, G. Guichard, Angew. Chem. Int. Ed. 2010 , 49 , 1067-1070. [2] C. Toniolo, E. Benedetti, Trends Biochem Sci. 1991 , 16 , 350-353. [3] (a) J. Solà, S. P. Fletcher, A. Castellanos, J. Clayden, Angew. Chem. Int. Ed. 2010 , 49 , 6836-6839. (b) R. A. Brown, T. Marcelli, M. De Poli, J. Solà, J. Clayden, Angew Chem Int Ed. 2012 , 51 , 1395-1399. [4] J. Fremaux, C. Dolain, B. Kauffmann, J. Clayden, G. Guichard, Submitted 2013  PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 27

Substituted prolines and E-prolines: tools for the design of foldamers targeting catalytic activity

Caumes Cécile, a Delsuc Nicolas, a Moumné Roba, a Beni Azza Redouane, b Chemla Fabrice, b Perez-Luna Alejandro, b Correia Isabelle, a Carlier Ludovic, a Sagan Sandrine, a Guianvarc'h Dominique, a Lequin Olivier, a Karoyan Philippe a*

aLaboratoire des Biomolécules (UMR 7203 CNRS-UPMC-ENS) Ecole Normale Supérieure - Département de Chimie, 24 rue Lhomond - 75252 Paris Cedex 05, France bUMR 7611, Institut Parisien de Chimie Moléculaire, UPMC-CNRS, 4 Place Jussieu, 75252 Paris Cedex 05, France [email protected]

Enzymes, built of Į-amino acids, are natural and powerful catalysts. They owe their remarkable efficiency to their tridimensional structure, which allows the formation of a specific and functionalized catalytic site stabilized by a large folded environment. Built of non-natural monomers, foldamers tend to mimic the folding ability of biopolymers along shorter sequences. A lot of foldamers families have been described in the literature, allowing access to a wide variety of stable secondary structures. [1] Nevertheless, the design of foldamers able to mimic the function of biopolymers remain a challenge and only a few examples have been described. [2] Our group has developed the synthesis of non-natural amino acids derived from proline which is well known to favor PPII helices and turn conformations in proteins. The synthetic pathway allows access to Į- and ȕ-proline derivatives substituted by a wide range of functional R groups including proteinogenic side chains. [3] These chimeras, combining conformational constraints together with natural amino acids side chains can be used to design functionalized foldamers targeting catalytic activity, we propose to call “ foldazymes ”.

The folding propensities of oligomers made of these proline chimeras have been investigated [4] with the aim of rationally design oligomers bearing side chains at predicted positions in order to mimic a catalytic site of an enzyme.

References [1] (a) Gellman S. H. ( 1998 ), Acc. Chem. Res. , 31:173-180. (b) Hill D. J., Mio M. J., Prince R. B., Hughes T. S., Moore J. S. ( 2001 ), Chem. Rev. , 101:3893-4012. (c) Hecht S., Huc I. in Foldamers: Structure, Properties and Applications , Wiley-VCH: Weinheim, 2007 . (d) Guichard G., Huc I. ( 2011 ), Chem. Commun. , 47:5933-5941. [2] (a) Müller M. M., Windsor M. A., Pomerantz W. C., Gellman S. H., Hilvert D. ( 2009 ), Angew. Chem. Int. Ed., 48:922-925. (b) Maayan G., Ward M. D., Kirshenbaum K. ( 2009 ), Proc. Natl. Acad. Sci. USA, 106(33):13679-13684. c) Araghi R. R., Koksch B. ( 2011 ) Chem. Commun. , 47:3544-3546. [3] (a) Mothes C., Lavielle S., Karoyan P. ( 2008 ) J. Org. Chem. , 73:6706. (b) Denes F., Pérez-Luna A., Chemla F. (2007), J. Org. Chem. 72:398. (c) Mothes C., Caumes C., Guez A., Boullet H., Gendrineau T., Darses S., Delsuc N., Moumné R., Oswald B., Lequin O., Karoyan P. ( 2013) , Molecules , 18 (2), 2307-2327. [4] Caumes C., Delsuc N., Beni Azza R., Chemla F., Ferreira F., Correia I., Carlier L., Perez Luna A., Lequin O., Moumné R., Karoyan P. ( 2013) New J. Chem , in press.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 28

Fluorinations around functionalized alicyclic beta-amino acids

Loránd Kiss, a Santos Fustero, c Ferenc Fülöp a,b

aInstitute of Pharmaceutical Chemistry, bStereochemistry Research Group of the Hungarian Academy of Sciences, University of Szeged, H-6720 Szeged, Eötvös u. 6, Hungary, cUniversidad de Valencia, Facultad de Farmàcia, Departamento de Química Orgánica, Valencia, Spain [email protected]

ȕ-Amino acids are of high relevance in pharmaceutical and medicinal chemistry. These compounds are key elements of bioactive substances and some derivatives are known to exhibit strong antifungal properties. [1-2] Fluorinated amino acids and peptides as a result of a series of interesting biological activities are considered valuable materials in pharmaceutical chemistry. These derivatives are known as enzyme inhibitors, antitumoural agents or antibiotics. [3-6] In the recent work several novel fluorination strategies will be discussed starting from 2-aminocyclohex-4- enecarboxylic esters. The syntheses were based on the selective transformations of the C-C ring double bond, via dihydroxylation, epoxidation-oxirane opening or oxidative olefinic bond cleavage, followed in each strategy by a hydroxyl-fluorine interconversion.

CO2Et F F HO CO Et CO 2Et NHBoc 2 H NHCOPh F NHBoc CO 2Et F CO 2Et CO 2Et NHCOPh F NHBoc NHBoc CO 2Et N3 CO 2Et O NC NHBoc F CO Et F NHBoc 2 O

O N NHCOPh F Ph

Figure 1. Fluorination of cyclohexene beta-aminocarboxylates

References [1] L. Kiss, E. Forró, F. Fülöp, Synthesis of carbocyclic ȕ-amino acids , In: Amino Acids, Peptides and Proteins in Organic Chemistry . Vol. 1, Ed. A. B. Hughes, Wiley: Weinheim, 2009 , 367. [2] L. Kiss, F. Fülöp, Synlett 2010 , 1302. [3] K. Mikami, S. Fustero, M. Sanchez-Rosello, J. L. Acena, V. Soloshonok, A. Sorochinsky, Synthesis 2011 , 304. [4] L. Kiss, E. Forró, S. Fustero, F. Fülöp, Eur J Org Chem 2011 , 4993. [5] L. Kiss, E. Forró, E.; S. Fustero, F. Fülöp, Org Biomol Chem 2011 , 9, 6528. [6] M. Nonn, L. Kiss, M. M. Hänninen, R. Sillanpää, F. Fülöp, Chem. Biodiv . 2012 , 9, 2571. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 29

Structure Elucidation of Host-Guest Complexes of Tartaric and Malic Acid by Quasi-Racemic Crystallography

a a a b a Guillaume Lautrette, Brice Kauffmann, Yann Ferrand, Christophe Aube, Nagula Chandramouli, Didier Dubreuil, b Ivan Huc a

a Université de Bordeaux, CBMN, UMR5248 Institut Européen de Chimie et Biologie 2 rue Escarpit, 33600 Pessac, France and CNRS, CBMN, UMR5248 bUniversité de Nantes, CEISAM, UMR6230 Faculté des Sciences et des Techniques 2 rue de la Houssinière, BP 92208 44322 Nantes Cedex 3, France and CNRS, CEISAM, UMR6230 [email protected]

The propensity of racemic solutions of organic molecules to frequently produce racemic crystals and to only rarely resolve into crystals containing exclusively one enantiomer (conglomerates) has been known for long. Over a decade of foldamer chemistry has provided strong empirical evidence that this observation also holds true in the case of helical aromatic foldamers. Racemic crystallography has been used to solve the structure of some proteins that can be produced by chemical synthesis and which were shown to crystallize more readily as a racemic pair than as a single enantiomer. [1] As an extension to racemic crystallography, quasi-racemates are sometimes found to co-crystallize, as was originally described by Pasteur for malate and tartrate salts. [2] A quasi-racemic crystal comprise a pair of molecules the structures of which are almost, but not exactly, mirror images. [3]

In this poster, we introduce the use of quasi-racemic crystallography as a method to elucidate the structures of host-guest foldamers complexes of tartaric and malic acid. We took advantage of the high propensity of enantiomeric P and M helices to co-crystallize, and demonstrated that co-crystals still form even when the guests introduced in the cavities are not mirror images.

References [1] (a) C. Toniolo, C. Peggion, M. Crisma, F. Formaggio, X. Shui, D.S. Eggleston, Nat. Struct. Biol . 1994 , 1, 908–914. (b) B. L. Pentelute, Z. P. Gates, V. Tereshko, J. L. Dashnau, J. M. Vanderkooi, A. Kossiakoff, S. B. H. Kent, J. Am. Chem. Soc. 2008 , 130 , 9695– 9701. [2] (a) L. Pasteur, Ann. Chim. Phys. 1853 , 28 , 437. (b) K. A. Wheeler, R. C. Grove, R. E. Davis, W. S. Kassel, Angew. Chem. 2008 , 120 , 84–87; Angew. Chem. Int. Ed. 2008 , 47 , 78–81. [3] (a) D. E. Mortenson, K. A. Satyshur, I. A. Guzei, K. T. Forest, S. H. Gellman, J. Am. Chem. Soc. 2012 , 134 , 2473. (b) K. Mandal, B. L. Pentelute, D. Bang, Z. P. Gates, V. Yu. Torbeev, S. B. H. Kent, Angew. Chem. 2012 , 124 , 1510–1515; Angew. Chem. Int. Ed. 2012 , 51 , 1481.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 30

Interactions of Biomimetic Oligomers with Metal Ions and Metal Nanparticles for Applications in Catalysis and Sensing

Galia Maayan

Schulich Faculty of Chemistry, Technion – Israel Institute of Technology, Haifa, Israel. [email protected]

The construction of synthetic materials that can mimic the unique structures and functions of natural biopolymers is an important goal in many fields of chemistry. Particularly interesting are (i) the ability to use biomimetic oligomers as recognition elements for selective catalysis and (ii) the interactions between biomimetic oligomers and metal ions, because the later are key elements both in the structure and function of natural biopolymers. Currently, there is a lack of knowledge regarding the structural organization of biomimetic oligomers, especially peptidomimetics, upon metal coordination. Therefore, the creation of functional materials based on such metallo- peptidomimetics is still a great challenge. We are studying (i) the interaction of peptidomimetic foldamers with metal ions and the properties of the new metallofoldamers with regard to coordination geometry and chirality for applications in biomimetic catalysis (Figure 1), and (ii) the aggregation of metal nanoparticles mediated by biomimetic oligomers (Figure 2) to be utilized for chemical and/or biological sensing and heterogeneous catalysis.



Figure 1: A peptidomimetic before (A) and after (B) metal coordination.



Figure 2: Ag(0) NPs (A) and their spherical assemblies (B) mediated by peptidomimetic oligomers. [1]

References [1] G. Maayan, L.-K. Liu, Pept. Sci., 2011 , 96 , 679.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 31

Synthesis and Structural Studies of Helical Oligomers of New Thiazole-Based J-Amino Acids (ATCs)

Loïc Mathieu, a Baptiste Legrand, a Jean Martinez, a Muriel Amblard, a Nicolas Masurier, a Vincent Lisowski, a Ludovic Maillard a

a IBMM UMR 5247 CNRS, UM1, UM2, ENSCM, Montpellier, France b LCPM, UMR 7568 CNRS-INPL, Nancy-Université, Nancy, France [email protected]

The ability of synthetic oligomers of ȕ- and Ȗ-amino acids to adopt protein-like secondary structures is of great interest to develop helical mimic with functional properties. Incorporation of constrained cyclic building blocks reducing the backbone flexibility has permitted to improve the stability of the folding and to substantially enlarge the helical foldamer realms. According to the results obtained with E-peptides, J-amino acids were expected to be valuable tools to design new scaffolds. Nevertheless, to date, only few Ȗ-subunits are available due to the difficulty to access stereochemically pure species and only few J-oligomers secondary structures have been described. [1] Additionally, while control of structure is crucial for biological function, access to foldamers bearing a wide variety of side chains and being soluble under physiological conditions is essential to purchase biological applications. Nevertheless the combination of these three criteria remains challenging. Herein, we report the design of a new family of highly constrained thiazole-based J-amino acids (ATC). The synthetic strategy for ATC residues is higly versatile allowing a straightforward modulation of the side chains. We demonstrate by NMR and X-ray crystallography studies that their ATC oligomers adopt a definite three-dimensional 9-helix structure thanks to periodic intramolecular hydrogen bonds in organic and aqueous solutions as well as at the solid state.

Figure 1. General structures of ATCs and of their corresponding oligomers

References [1] G. P. Dado, S. H. Gellman, J. Am. Chem. Soc. 1994 , 116 , 1054–1062.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 32

Novel cationic bola surfactants using difunctional cyclobutanes as scaffolds: synthesis and physicochemical behavior

Marta Sans, Alessandro Sorrenti, Ona Illa and Rosa M. Ortuño*

Departament de Química, Universitat Autonoma de Barcelona, 08193, Cerdanyola del Valles, Spain [email protected]

Cyclic 1,2-diamines and cyclic 1,2-dicarboxylic acids are versatile building blocks in organic chemistry. They have been used as scaffolds for the preparation of various derivatives ranging from hybrid materials [1] to ligands in catalyzed reactions [2] and self-assembling molecules (used as templates for inorganic nanostructures), [3] due to the possibility to control their stereochemistry, steric demand and rigidity. Herein we report on the stereoselective synthesis of new chiral bola surfactants derived from cyclobutane-1,2-diamine [4] and cyclobutane-1,2-dicarboxylic acid. Special attention has been focused on the study of the influence of the relative stereochemistry and the regiochemistry in their aggregation properties.

To the best of our knowledge, there are no reports concerning chiral surfactants derived from cyclobutane-1,2-dicarboxylic acid and cyclobutane-1,2-diamine, on their physicochemical characterization and on their aggregation properties so our aim is to investigate how the conformational constraints imposed by the rigid cyclobutane ring will affect their properties, aggregation behavior and the transfer of chirality from the monomers to the assemblies.

References [1] (a) J.J.E. Moreau, C. Vellutini, M. Bied, J. Wong Chi Man, J. Sol-Gel Sci Technolog . 2004 , 31 , 151-156. (b) I. Karatchevtseva, D. J. Cassidy, M. Wong Chi Man, D. R. G. Mitchell, J. V. Hanna, C. Carcel, J. J. E. Moreau, J. R. Barlet, Adv. Funct. Mater . 2007 , 17 , 3926-3932. [2] (a) D. Surry, S. Buchwald, Chem. Sci. 2010 , 1, 13-31. (b) S. Eyele-Mezui, E. Delahaye, G. Rogez, P. Rabu, Eur. J. Inorg. Chem. 2012 , 32 , 5225-5238. [3] Z. Dong, S. Bai, J. M. Fox, Chem. Commun. 2011 , 47 , 3781-3783. [4] M. Sans, O. Illa, R. M. Ortuño, Org. Lett. 2012 , 14 , 2431-2433 PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 33

PPII helix folding of silaproline oligomers

C. Martin a, A. Lebrun, b J. Martinez, a F. Cavelier a

aIBMM, UMR-CNRS-5247, Universités Montpellier I and II, Place Eugène Bataillon, 34095 Montpellier, France bLMP, IBMM, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier, France [email protected]

The importance of the left-handed polyproline II (PPII) helical conformation has recently become apparent. This conformation generally is involved in two important functions: protein-protein interactions and structural integrity. The PPII helix is believed to be the dominant conformation for many proline-rich regions of peptides and proteins. In particular PPII are major features of collagens. In our laboratory, an original proline analogue has been synthesized: the 4,4-dimethylsilaproline, denoted silaproline (Sip). [1] The presence of dimethylsilyl group confers to silaproline a higher lipophilicity as well as an improved resistance to biodegradation. Recently we developed a gram scale synthesis of enantiomerically pure Sip, requiring resolution of the racemate by chiral high performance liquid chromatography (HPLC). [2] With this new starting material, our aim was to construct polysilaproline polymers to investigate physico chemical properties and modifications of PPII structure. In this study monodisperses homopolypeptides have been synthesized by peptide coupling in solution, polydisperses homopolypeptides have been prepared by ring opening polymerization of N- carboxyanhydrides (ROP). These peptides have been characterized by NMR, MALDI-Tof and circular dichroism.

References [1] B. Vivet, F. Cavelier, J. Martinez, Eur. J. Org. Chem. 2000 , 5, 807-811. [2] C. Martin, N. Vanthuyne, H. Miramon, J. Martinez, F. Cavelier, Amino Acids 2012 , 43 , 649-655. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 34

Enhancement of the Į-helix stability induced by a double stapled, intersected bicycle-46-(E)ene motif

Daniela Mazzier, Cristina Peggion, Fernando Formaggio, Alessandro Moretto

Department of Chemical Science, University of Padova, Via Marzolo 1, 35131 Padova, Italy [email protected]

Protein-protein interactions form the basis of many cellular processes. Disruption or deregulation of these complex interactions is the main cause of a significant number of human ailments. Consequently, there is intense research effort to design inhibitors that target specific protein-protein interactions. Peptide drugs take benefit from the highly specific and selective interaction between proteins. An appealing approach to the modulation of protein-protein interactions is the use of “dominant-negative ” peptides representing only the fragment of a protein that engages a target. In practice, however, such dominant-negative peptide fragments rarely exhibit potent biologic activity, because their removal from the folded context of the parent protein tends to deprive them of conformational stability, leading to poor binding affinity, proteolytic instability, cell impermeability and rapid clearance in vivo by renal filtration. One approach toward circumventing this problem involves the introduction of synthetic cross-linking functionalities into the peptide, so as to restore and enforce its bioactive conformation. Given that the Į-helix is the most common secondary structural motif in proteins, it is not surprising that this particular folding motif has received the greatest deal of attention with respect to cross-link-induced stabilization. We have previously shown that an RCM-derived 18-membered macrocycle can be used to cross-link the side chains of i [1] and i + 3 amino acids in short 3 10 -helical peptide sequences. Recently, the meta xylyl group was carefully chosen as the optimal cysteine cross-linker from screening a library of potential cross- linkers. [2] In this work we present a dual set of intramolecular crossed-link reactions, accomplished on a Į-helical peptide, which results in a double stapled, intersected bicycle-46-(E)ene motif. The conformational studies revealed an enhancement effect of the original helical content.

Figure 1. Schematic representation of the linear, stapled and double stapled peptides discussed in this work.

References [1] A. K. Boal, I. Guryanov, A. Moretto, M. Crisma, E. L. Lanni, C. Toniolo, R. H. Grubbs, D. J. O’Leary, J. Am. Chem. Soc . 2007 , 129, 6986-6987. [2] H. Jo, N. Meinhardt, Y. Wu, S. Kulkarni, X. Hu, K. E. Low, P. L. Davies, W. F. DeGrado, D. C. Greenbaum, J. Am. Chem. Soc. 2012 , 134 , 17704 í17713.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 35

Synthesis and conformational studies of a new hybrid E-alanine-morpholine tetramer

Gloria Menchi a,b Andrea Trabocchi, a,b Antonio Guarna a,b a Department of Chemistry "Ugo Schiff”, University of Florence, Via della Lastruccia 13, I-50019 b Sesto Fiorentino, Florence, Italy. Interdepartmental Center for Preclinical Development of Molecular Imaging (CISPIM), University of Florence, Viale Morgagni 85, I-50134 Florence, Italy [email protected]

One of the relevant aspects in medicinal chemistry is related to the development of peptides and peptidomimetics as drugs, and to the comprehension of the role of small modified peptides in the development and cure of diseases and macromolecular systems gained interest to target extended peptide-protein and protein-protein interactions in biomedically relevant issues. Foldamers [1] have been proposed as a new promising class of macromolecues for the creation of unnatural oligomers able to mimic the structural features of biopolymers. In order to expand the conformational space available for foldamer design, synthetic oligomers based on the formation of special helix types in hybrid peptides derived from changing aliphatic amino acid residues have been proposed. [2] Recently, we reported on a new method for the synthesis of enantiopure Fmoc-protected morpholine-3-carboxylic acid from dimethoxyacetaldehyde and serine methyl ester through a practical synthetic route, [3] and we carried out the conformational analysis of model tetrapeptides containing L- or D-Mor at i+1 position of a model E-turn structure, with the aim to assess the role of such amino acids in determining the conformational preferences with respect to the parent peptide sequence bearing a proline residue at the same position. [4] We envisioned the possibility of applying this six-membered proline surrogate for the generation of D/E-hybrid peptide foldamers taking advantage of the folding propensity of the morpholine ring (Figure 1).

Figure 1. Morpholine-containing D/E-hybrid peptide.

In this work, we report the solution-phase synthesis of a model hybrid-peptide containing E-Ala and Mor residues using the Fmoc protocol. Such method, taking advantage of the corresponding activated acyl chlorides, enabled the facile preparation of a tetrameric structure. Such method may be easily translated to the synthesis of higher foldameric structures consisting of alternating E- and D-amino acid residues. The conformational analysis by NMR revealed the existence of a mixture of two rotamers, the major one possessing equilibrating intramolecular hydrogen-bonds for both amide protons. Moreover, molecular modeling calculations revealed a higher foldamer containing three E- Ala-Mor repeating units to fold in a compact Į-helix stabilized by J-turns and by the preferential trans geometry at the E-Ala-Mor amide bond. Thus, this study confirmed the possibility of using morpholine-3-COOH as a proline surrogate to generate higher D/E hybrid peptides.

References [1] R. P. Cheng, Curr. Opin. Struct. Biol. 2004 , 14 , 512–520. [2] C. Baldauf, R. Gunther, H.J. Hofmann, J. Org. Chem. 2006 , 71 , 1200–1208. [3] F. Sladojevich, A. Trabocchi, A. Guarna, J. Org. Chem. 2007 , 72 , 4254–4257. [4] F. Sladojevich, A. Trabocchi, A. Guarna, Chirality 2009 , 21 , 584–594.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 36

Preorganized Dipeptide Mimics as New Foldamer Building Blocks

Lorenzo Milli, a Nicola Castellucci, a Mattia Tedesco, b Claudia Tomasini a

aDipartimento di Chimica "G. Ciamician", Univ ersità di Bologna, Via Selmi, 2 – 40126 Bologna, Italy. bDipartimento di Chimica, Università di Torino, Via P. Giuria, 7 – 10125 Torino, Italy [email protected]

Preorganized dipeptide mimics, all containing a 1,2-disubstituted oxazolidin-2-one, a flexible methylene group and a 1,4-disubstituted triazole, have been prepared in few steps and high yield. The triazole ring may be easily prepared by Huisgen cycloaddition. [1] This reaction has been firstly developed by thermal addition, but generally mixtures of 1,4- and 1,5-substituted triazoles were obtained. Recently the copper-catalysed azide-alkyne cycloaddition (CuAAC) [2] has been reported: these approaches afford exclusively 1,5-disobstituted triazoles respectively in high yield. We have developed a general synthetic method that leads to the formation of both Oxd-Tri-CO- and Oxd-Tri-CH 2- moieties (Figure 1). These compounds contain two heterocyclic units, one oxazolidin-2-one (Oxd) and a triazole (Tri), connected by a methylene group, that is highly flexible and favours the formation of curves, needed for the formation of folded secondary structures, as we could demonstrate with ROESY and NOESY analysis of two derivatives containing some additional amino acids residues. [3]

Figure 1. General structure of the L-Oxd-Tri scaffolds.

References [1] R. Huisgen, Pure Appl. Chem. 1989 , 61 , 613-628. [2] L. Zhang, X. G. Chen, P. Xue, H. H. Y. Sun, I. D. Williams, K. B. Sharpless, V. V. Fokin, G. C. Jia, J. Am. Chem. Soc. 2005 , 127 , 15998–15999. [3] N. Castellucci, C. Tomasini, Eur. J. Org. Chem . submitted.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 37

Proline primed helix length as a modulator of the nuclear receptor-coactivator interaction

Sascha Fuchs, Hoang Duc Nguyen, Trang Phan, Matthew Burton, Lidia Nieto, Ingrid de Vries - van Leeuwen, Andrea Schmidt, Monireh Goodarzifard, Stijn Agten, Rolf Rose, Christian Ottmann, Lech-Gustav Milroy, Luc Brunsveld

Laboratory of Chemical Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands [email protected]

Nuclear receptor binding to coactivator proteins is an obligate first step in the regulation of gene transcription. Nuclear receptors preferentially bind to an LXXLL peptide motif which is highly conserved throughout the 300 or so natural coactivator proteins. This knowledge has shaped current understanding of this fundamental protein-protein interaction, and continues to inspire the search for new drug therapies. [1] However, sequence specificity beyond the LXXLL motif and the molecular functioning of flanking residues still requires urgent addressing. We have used ribosome display to reassess the estrogen receptor (ER) for new and enlarged peptide recognition motifs, leading to the discovery of a potent and highly evolved PXLXXLLXXP binding consensus (Figure 1, Left ). [2] Molecular modeling and X-ray crystallography studies have provided the molecular insights on the role of the flanking prolines in priming the length of the Į-helix and enabling optimal interactions of the Į-helix dipole and its surrounding amino acids with the surface charge clamp and the receptor activation function 2 (Figure 1, Right ). These findings represent new structural parameters for modulating the nuclear receptor-coactivator interaction based on linear sequences of proteinogenic amino acids and for the design of chemically modified inhibitors.

Figure 1. Left : a. Peptide library design; b. sequence cluster analysis of peptide sequences identified through rounds 4, 6 and 8 of ribosome display screening against ER Į and ER ȕ; c. PXLXXLLXXP peptides selected for biochemical and cellular evaluation. Right : a-d. Structural basis for the potent binding of proline flanked peptides to ER provided by X-ray co-crystallography studies.

References [1] P. Huang, V. Chandra, F. Rastinejad, Ann. Rev. Physiol . 2010 , 72 , 247–272. [2] S. Fuchs, H. D. Nguyen, T. Phan, M. Burton, L. Nieto, I. de Vries - van Leeuwen, A. Schmidt, M. Goodarzifard, S. Agten, R. Rose, C. Ottmann, L.-G. Milroy, L. Brunsveld J. Am. Chem. Soc. 2013 , DOI: 10.1021/ja311748r.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 38

An unusual interstrand H-bond stabilizes the hetero-assembly of helical DEJ-chimeras with natural peptides

Elisabeth K. Nyakatura, Raheleh Rezaei Araghi, Jeremie Mortier, Sebastian Wieczorek, Carsten Baldauf, Gerhard Wolber, Beate Koksch*

Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 3, 14195 Berlin, Germany [email protected]

The substitution of Į-amino acids by ȕ/Ȗ-amino acids has a strong impact on a peptides overall structure and topology, and thus on the stability of interhelical interactions. The tetrameric Acid- pp/B3 ȕ2Ȗ coiled-coil system, which comprises a pentad of alternating ȕ- and Ȗ-amino acids, is known to tolerate this modification while a loss in thermal stability is observed compared to its parental system Acid-pp/Base-pp. [1] To this end, we applied phage display in search for preferred Acid-pp interaction partners of B3 ȕ2Ȗ. The predefined secondary and tertiary structure of the Į-helical coiled coil allows to randomize the direct interaction partners of the ȕ/Ȗ-amino acids and therefore to select specific binders out of the pool of Acid-pp mutants that contain every possible combination of the 20 canonical amino acids in four randomized positions. This screen lead to consensus sequences bearing a cysteine in combination with an aromatic residue. Molecular dynamic simulations confirm ideal core-packing as well as the formation of an interhelical H-bond between the cysteine and a non-H-bonded backbone carbonyl of the ȕ/Ȗ- segment. Moreover, selected peptides are able to form tetrametric assemblies with B3 ȕ2Ȗ and possess thermal stabilities that are similar to that of its parental system.

References [1] (a) R. Rezaei Araghi, C. Mahrenholz, R. Volkmer, B. Koksch, BJOC , 2012 , 8, 640. (b) R. Rezaei Araghi, B. Koksch, Chem. Commun., 2011 , 47 , 3544. (c) R. Rezaei Araghi, C. Jäckel, H. Cölfen, M. Salwiczek, A. Völkel, S. C. Wagner, S. Wieczorek, C. Baldauf, B. Koksch, ChemBioChem , 2010 , 11 , 335.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 39

Asymmetric modular synthesis of semi-rigid Pro-Gly dipeptide mimetic, as ȕ turn inducer

Sara Pellegrino, Alessandro Contini, Maria Luisa Gelmi, Emanuela Erba

DISFARM - Sez. Chimica Generale e Organica “A. Marchesini”- Università degli Studi di Milano- via Venezian 21, 20133 Milano, Italy [email protected]

An important challenge for chemical biology and medicinal chemistry is the development small synthetic molecules able to selectively perturb protein–protein interactions (PPI). [1] Researches in this field have been intensively carried out in the early 21th century, allowing the design and preparation of peptidomimetics, molecules that mimic peptides and protein-fragments. The most prevalent non repetitive motif observed in protein is the four residue ȕ turn, in which proline and glycine residues are generally found in the i+1 and i+2 positions. Many rigid scaffolds mimicking this structural motif have been developed during the years, while the Pro-D-Pro or D- Pro-Pro sequences have been demonstrated effective semi-rigid reverse turn nucleators. [2] Continuing our long time researches on multicomponent reaction between sulfonylazides and amidines, we recently developed the click reaction between the morpholino enamine of N-alkyl piperidone and tosyl azide, affording azacycloalkene monosulfonyl diamine 1, through a 5-amino- 1,2,3-triazoline decomposition rearrangement. [3] (Scheme 1)

O R N O O N O N N RN RN + + ArSO 2N3 N RN SO 2Ar N N H N NSO 2Ar NHSO 2Ar O 1

Scheme 1

Considering the biological importance of proline and its involvement in ȕ turn induction, we envisioned the possibility to apply our synthetic methodology for the preparation of compound 2. (Fig 1) The multicomponent reaction was carried out using proline as the secondary amine and, in order to obtain compound 2 in enantiopure form, we studied the selective reduction of the double bond of obtained intermediate like 1. Finally, we evaluated the possibility to use 2 as a semi-rigid ȕ turn inducer in peptide models. HO 2C

N HN

NHSO 2Ar 2 Figure 1

References [1] O. Keskin, A. Gursoy, B. Ma, R. Nussinov, Chem. Rev. 2008 , 108 , 1225-1244. [2] (a) A. Fuller, D. Du, F. liu, J. E. Davoren, G. Bhabha, G. Kroon, D. A. Case, H. J. Dyson, E. T. Powers, P. Wipf, M. Gruebele, J. W. Kelly PNAS , 2009 , 106 , 11067-11072. (b) J. A. Feng, L. A. Tessler, G. R. Marshall Int. J. Pep. Res. Ther. 2007 , 13 , 151-160. [3] A. Contini, E. Erba RSC Advances 2012 , 2, 10652-10660.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 40

Approaches to new foldamer manifolds based on cyclobutane amino acids: studies on J-peptides and EJ-peptides

Hawraà Awada, Claire Grison, Virginie André, Sylvie Robin, David J. Aitken

Université Paris-Sud, ICMMO, 15 rue George Clemenceau, 91405 Orsay, France [email protected] , [email protected]

It is widely established that oligomers of E-aminoacids can present a large variety of secondary structures including reverse-turns, sheets or helices. Studies of oligomers containing J-aminoacids are also potentially capable of adopting well-defined secondary structure: several stable helical conformers are predicted for J-peptides and EJ -peptides, including a 14-helix and a 13-helix, respectively. [1] The conformational restrictions imposed by the presence of a cyclobutane ring are expected to favor particular secondary structures in such peptides, and to this end our group [2] embarked on the expedient preparation of all possible stereoisomers of cyclobutane E-aminoacids [3] and cyclobutane J -aminoacids using a [2+2] photocycloaddition strategy.

O COOH O NH * * COOH N N O * NHBoc Ph * NHBoc Boc

Figure 1. Cyclobutane aminoacid building blocks.

In this contribution, we will present and discuss these syntheses, as well as our recent results regarding the preparation and study of short J-peptide and alternating EJ -peptide sequences which contain selected cyclobutane aminoacid residues, in the search for new foldamer manifolds.

O O H N N N N H O H H O

Figure 2. J-Peptides (left) and EJ -peptides (right), indicating the positions of cyclobutane residues.

References [1] (a) C. Baldauf, R. Günther, H.-J. Hofmann Helv. Chim. Acta 2003 , 86 , 2573. (b) C. Baldauf, R. Günther, H.-J. Hofmann J. Org. Chem . 2006 , 71 , 1200. [2] V. Declerck, D. J. Aitken Amino Acids , 2011 , 41 , 587. [3] (a) V. André, A. Vidal, J. Ollivier, S. Robin, D. J. Aitken Tetrahedron Lett. 2011 , 52 , 1253. (b) V. André, M. Gras, H. Awadaà, R. Guillot, S. Robin, D. J. Aitken Tetrahedron 2013 , 69 , 3571.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 41

Functionalizable Collagen Model Peptides

Christiane Siebler, Helma Wennemers*

ETH Zürich, Laboratory of Organic Chemistry, Wolfgang Pauli-Strasse 10, 8093 Zürich, Switzerland [email protected]

Collagen is the most abundant protein in mammals. [1] It is not only the most prevalent constituent of the extracellular matrix, but also providing for stability in disparate tissues and organs. [2] Furthermore, collagens play a crucial role in the modulation of cellular activities. [3] Due to its biocompatibility collagen based materials are interesting matrices in different medicinal applications, e. g. tissue engineering and delivery of proteins, drugs and genes. [4] Making collagen based materials more applicable is therefore an important objective. A promising approach towards this goal are short synthetically accessible collagen model peptides (CMPs).

N3 Amidation “Click” ͲChemistry H N N N 1) Staudinger Reduction O O O 2) coupling reagent, base (3 eq)

[Cu(MeCN) 4]PF 6 (0.5 eq) TBTA, DMF (0.5 eq) O OH

N N O NH N

H H N N N N N N

O O O O O O

=

= H, Me,  tBu

Figure 1. Functionalization of CMPs using the reductio n/amidation or “Click”Chemistry approach.

We have shown that (4 R)- and (4 S)-azidoprolines can be incorporated in CMPs as conformation directing amino acids and sites for functionalization. [5],[6],[7],[8] Furthermore, the functionalization of CMPs is possible keeping some structural characteristics in mind. After introducing (4 R)- azidoprolines to the CMP, both, functionalization via triazole formation and Staudinger reduction/Amidation procedures are feasible without disturbing the basic structure. We are now developing these CMPs further towards a biomimetic material for medicinal applications.

References [1] (a) J. Brinckmann, Top. Curr. Chem. 2005 , 247 , 1. (b) J. Myllyharju, K. Kivirikko, Ann. Med. 2001 , 33 , 7. (c) G.Veit, B. Kobbe, D.R. Keene, M. Paulsson, M. Koch, R. Wagener, J. Biol. Chem. 2006 , 281 , 3494. [2] M. D. Shoulders, R. T. Raines, Ann. Rev. Biochem. 2009 , 78 , 929. [3] T. Aigner, J. Stove, Adv. Drug Delivery Rev. 2003 , 55 , 1569. [4] (a) A. M. Jonker, D. W. P. M. Löwik, J. C. M. van Hest, Chem. Mater. 2012 , 24, 759. (b) C. H. Lee, A. Singla, Y. Lee, Int. J. Pharm. 2001 , 221 , 1. [5] R. S. Erdmann, M. Kümin, H. Wennemers, Chimia 2009 , 63 , 197. [6 ] R. S. Erdmann, H. Wennemers, J. Am. Chem. Soc. 2010 , 132 , 13957. [7] R. S. Erdmann , H. Wennemers, Org. Biomol. Chem. 2012 , 10, 1982. [8] R. S. Erdmann, H. Wennemers, Angew. Chem. Int. Ed. 2011 , 50 , 6835.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 42

Helical Aromatic Oligoamide Foldamers as Synthetic Second Coordination Spheres for Biologically Inspired Hydrogen Production Catalysts

Michael L. Singleton, Guillaume Lautrette, Yann Ferrand, Brice Kauffman, Ivan Huc

Institut Européen de Chimie et Biologie, Université de Bordeaux, CNRS UMR 5248 et UMS 3033, 2 Rue Robert Escarpit, 33607 Pessac, France [email protected]; [email protected]

It is becoming increasingly apparent that, in order to create a sustainable future, methods for efficiently activating/producing economically important small molecules (H 2, N 2, H 2O, CO 2, etc…) must be developed. Nature has evolved numerous metalloenzymes capable of performing such transformations as part of cellular processes. That it can do so with high turn-over frequencies and under physiological conditions is the result of active metal centers whose properties are specifically tuned through interactions with an assortment of functional groups in the protein. It would be ideal to replicate these interactions in synthetic systems in order to study how well-ordered functional groups arrays can improve the capabilities of synthetic catalysts. In the current work, aromatic oligoamide foldamers have been used to synthesize a helical scaffold around a tethered, [FeFe]- Hydrogenase inspired, 2Fe2S cluster, Figure 1. The interactions between the scaffold and the metal complex and their effect on the fluxional and catalytic properties of the system have been studied. Oligomers of several different lengths containing a ( ʅ-SCH 2NRCH 2S)[Fe(CO) 3]2 unit have been synthesized and characterized by X-ray crystallography. While there is little effect on the ground state structure of the diiron moiety in the solid state, further spectroscopic studies (NMR and IR) have shown that, depending on the oligomer used, the rotational/translational degrees of freedom afforded to the metal center can be limited with respect to the scaffold. Additionally, electrochemical studies of the foldamer/metal conjugates have shown that the organic scaffold is capable of inducing moderate shifts in the redox properties of the metal site. The implications of these results for the electrochemical reduction of protons to H 2 and application of helical aromatic oligoamides as synthetic second coordination spheres for biologically inspired catalysts are discussed.

Figure 1. Pictorial overview of the project showing the goal of the project (top) and a general scheme of the aromatic oligoamide foldamer scaffold that has been synthesized (bottom).

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 43

Exploiting Ion Pair Interactions to Induce Helicity in Aib Peptides

Sarah J. Pike, S. J. Webb,* Jonathan Clayden*

School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK [email protected]

In Nature, conformational changes in proteins are extensively used to relay and process information in biological systems; for example the G-protein coupled receptors. Whilst these natural switches are of immense conformational complexity, synthetically we are not constrained by evolutionarily- imposed structural requirements and as such can employ much simpler structures. Aib ( Į- [1] aminoisobutyric acid) peptides are known to adopt 3 10 helical structures. Since Aib is an achiral residue, the helices adopted show no intrinsic preference for left- or right-handedness ( M or P helicity respectively) and so its two enantiomeric conformations rapidly interconvert at ambient temperature. [2] Whilst the covalent attachment of chiral auxiliaries has been shown to induce high levels of helical conformational control [3] such that the equilibrium is perturbed to favour M or P helicity, reported examples of the exploitation of non-covalent interactions in the same context are surprisingly rare. [4] We wished to explore the use of ion pair interactions between chiral additives and Aib-based peptides as a means of realizing intermolecular communication and the transfer of stereochemical information. A series of achiral Aib oligopeptides with a cationic centre incorporated at the N terminus of the peptide have been synthesised. Ion pair interactions between chiral anions, such as TRISPHAT, and the charged peptides have been successfully exploited to realize intermolecular communication. Propagation of stereochemical information along the helix has been verified through detection of helical excess using NMR spectroscopy techniques (Figure 1). Control experiments undertaken with neutral analogues of the oligopeptides have established that the non-covalent ion-pair interaction is essential for the intermolecular communication of information.

Figure 1 : (a) Achiral helix which displays rapid interconversion between the M and P enantiomeric conformations in the absence of a chiral auxiliary (b) The introduction of a chiral anion induces the preference of one conformer through intermolecular communication of the stereochemical information via ion pair interactions.

References 1. I. Venkatraman, S. C., Shankaramma, P. Balaram, Chem. Rev., 2001, 101, 3131. 2. M. Kubasik, A. Blom, ChemBioChem., 2005, 6, 1187. (b) J. Clayden, A. Castellanos, J. Sola, G. A. Morris, Angew. Chem. Int. Ed., 2009 , 48 , 5962. 3. Y. Inai, Y. Kurokawa, T. Hirabashi, Biopolymers, 1999 , 49 , 551. 4. Y. Inai, K. Tagawa, A. Takasu, T. Hirabashi, T. Oshikawa, M. Yamashita, J. Am. Chem. Soc., 2000 , 122 , 11731.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 44

Combined computational and experimental approach for structure prediction of foldamers

Eduardo M. Sproviero, a Zhiwei Liu, a Jhenny Galan, a Ara Abramyan, a Jessica Geer, a Shubhashis Chakrabarty, a Guillermo Moyna, b Vojislava Pophristic. a

aWest Center for Computational Chemistry and Drug Design, and Department of Chemistry & Biochemistry, University of the Sciences in Philadelphia, 600 South 43rd Street, Philadelphia, Pennsylvania 19104-4495, USA. bCentro Universitario de Paysandú–UdeLaR, Departamento de Química, Polo Agroalimentario y Agroindutrial, EEMAC, Ruta 3 Km 363 / 60000 / Paysandú, Uruguay. [email protected]

Foldamers, synthetic oligomers that adopt defined, stable secondary structures in solution, have been the focus of intense research efforts. Arylamide oligomers constitute one of the most important foldamer classes. The main objective of this project is to establish information transferability between the oligoamide foldamer building blocks and the final oligoamide foldamer structure. Our goal is to develop a methodology and an associated library that will allow for rational design of aryl amide foldamers. To date, we have carried out a systematic computational and experimental study of arylamide building blocks and oligomers of varying types and sizes. Specifically, we used quantum mechanical calculations and NMR conformational studies of appropriate model compounds to reparameterize and validate critical torsional parameters. Using the improved parameters, we carried out molecular dynamics simulations of both building blocks and oligomers, in environments of varying polarities. [1,2] Our group also contributed developmental approaches, including a methodology aimed to quantify intramolecular interactions. The method allows identification of influences between different molecular fragments, including electrostatic interactions, charge delocalization pathways, core repulsions, and their relative importance. With that information it is possible to determine how far conformational or substituent information may travel along an oligomer chain and thus influence overall oligomer shape. [3] We also developed a methodology for determining oligomer structures. The method uses full quantum mechanics (QM) at short distances, and effective fragment potentials (EFP) at longer distances to model non-bonded interactions. This methodology allows the treatment of large systems without using fitted parameters. This approach gives descriptions of QM quality with computational demands closer to empirical methods. It also allows identification of different energy terms that contribute to the final conformations. [4] Using thus obtained structural and dynamical features; we establish information transferability between the small oligomer segments and the final folded structure.

References [1] J. F. Galan, J. Brown, J. Wildin, Z. Liu, D. Liu, G. Moyna, V. Pophristic, J. Phys. Chem. B 2009 , 113 , 12809. [2] Z. Liu, A. Teslja, V. Pophristic, J. Comp. Chem. 2011 , 32 , 1846. [3] E. M. Sproviero, V. Pophristic, Intramolecular Natural Energy Decomposition Analysis. Application to transmission of information between intramolecular fragments , in preparation. [4] E. M. Sproviero, V. Pophristic, A QM-based approach to modeling foldamer structure , in preparation.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 45

Synthesis and study of model peptides containing 2-(aminomethyl)-1- aminocyclopropane carboxylic acid derivatives

Stijn De Brabandere, a Sven Mangelinckx, a Alessandro Moretto, b Cristina Peggion, b Fernando Formaggio, b Norbert De Kimpe a

aDepartment of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium bICB, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy [email protected]

The recently synthesized conformationally constrained 2-(aminomethyl)-1- aminocyclopropanecarboxylic acid derivatives 1 and 2 are non-proteinogenic Į,Ȗ-diamino acid derivatives belonging to a class of versatile building blocks which can be used for the preparation of biologically active compounds and peptide design. The conformational preferences of peptides containing a cycloaliphatic residue Ac nc (n = 3–8) have already been investigated, [1] but the influence of an extra substituent on this cycloaliphatic moiety has not been fully studied so far. Furthermore, previous research has shown that the oxygen atoms of the 1,3-dioxane system of residue 3 may act as H-bond acceptors for amide NHs. [2] These main- chain to side-chain intramolecular H-bonds destabilize the 3 10 -helical structures, typically adopted by the related Ac 6c 4 homopeptides. Based on these findings, model peptides containing these substituted carbocyclic amino acids were synthesized to study the conformational bias imparted to a peptide chain and to assess whether the insertion of the aminomethyl substituent, as present in residues 1 and 2, affects the E-turn/helix induction tendency of the parent Ac 3c residue.

Figure 1. Relevant cycloaliphatic residues

References [1] C. Toniolo, M. Crisma, F. Formaggio, C. Peggion, Biopolymers (Pept. Sci.) 2001 , 60 , 396. [2] W. M. Wolf, M. Stasiak, M. T. Leplawy, A. Bianco, F. Formaggio, M. Crisma, C. Toniolo, J. Am. Chem. Soc. 1998 , 120 , 11558.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 46

beta,gamma-diamino acid as a gamma-turn inducer in short peptides

Sophie Thétiot-Laurent, a Francelin Bouillère, a Emeric Miclet, b Cyrille Kouklovsky, a Valérie Alezra a

aLaboratoire des Procédés et Substances Naturelles ICMMO, Bât. 410, Université Paris-Sud, 91405 Orsay, France bLaboratoire des Biomolécules, UPMC, Université Paris 6, 4 Place Jussieu, 75005 Paris, France [email protected]

A strategy aiming the stereoselective synthesis of EJ -diaminoacids has been developed in our laboratory. [1] Key steps in this sequence are a Blaise reaction followed by the reduction of the enaminoester giving access to enantiomerically and diastereomerically pure EJ -diaminoacids or 4- aminopyrrolidinones. Such synthetic aminoacids are interesting compounds, as they can either be [2] used in E- and/or J-peptides synthesis.

Generation of this EJ -diaminoacid moiety starting from ( L)-valine, as well as its utilization in the [3] synthesis of DJD tripeptides will be presented.

Cbz Cbz R NH O H2N CO 2H NH O H BocHN N OMe OH BocHN N H O O

(L)-valine -diamino acid -tripeptides R = Me, iBu, Bn

Conformation adopted by these short peptides, determined by extensive NMR and simulated annealing under NMR restraints, using vicinal coupling constants and NOE distance restraints, will be described. [4] To get further insights into the NMR structure stabilities, molecular dynamics calculations in chloroform solvent boxes have been performed and will be presented.

The capacity of these short DJD tripeptides to form a J-turn mimic, depending on the steric hindrance of the first residue of the peptidic chain, will be detailed.

References [1] (a) C.T. Hoang, V. Alezra, R. Guillot, C. Kouklovsky, Org. Lett . 2007 , 9, 2521. (b) C.T. Hoang, V.H. Nguyen, V. Alezra, C. Kouklovsky, J. Org. Chem . 2008 , 73 , 1162. (c) C.T. Hong, F. Bouillère, S. Johannessen, A. Zulauf, C. Panel, A. Pouilhès, D. Gori, V. Alezra, C. Kouklovsky, J. Org. Chem . 2009 , 74 , 4177. [2] F. Bouillère, S. Thétiot-Laurent, C. Kouklovsky, V. Alezra, Amino Acids 2011 , 41 , 687. [3] F. Bouillère, R. Guillot, C. Kouklovsky, V. Alezra, Org. Biomol. Chem . 2011 , 9, 394. [4] S. Thétiot-Laurent, F. Bouillère, J.-P. Baltaze, D. Feytens, C. Kouklovsky, E. Miclet, V. Alezra, Org. Biomol. Chem . 2012 , 10 , 9660. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 47

Alternated Hybrid Foldamers Containing the Oxd Unit

Claudia Tomasini, Nicola Castellucci, Lorenzo Milli

Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi, 2, 40126 Bologna, Italy [email protected]

Hybrid foldamers, containing the oxazolidin-2-one (Oxd) unit alternated with an D- or a E-amino acid, have been extensively studied by our group. [1] The relative configuration of the Oxd and the alternated amino acid is very important, since the L- [2] Ala-D-Oxd series tend to form E-bend ribbon spirals, while the L-Ala-L-Oxd series do not. Furthermore the insertion of the L-Phe residue alternated with the D-Oxd moiety allows us to obtain interesting compounds that behave as supramolecular materials, [3] while the L-Phe-L-Oxd oligomers tend to form PPII helixes, [4] as we could demonstrate by VCD analysis. In contrast, the formation of a H 11 helix was obtained, alternating an Oxd and a E-amino acid moiety in the chain and interesting cyclic pseudopeptides were prepared alternating these groups. Finally, more complex oligomers have been recently obtained by introducing, besides the Oxd group, a triazole ring, that may be easily prepared by Huisgen cycloaddition. [5]

Figure 1. Alternated hybrid foldamers containing the Oxd unit.

References [1] C. Tomasini, G. Angelici, N. Castellucci, Eur. J. Org. Chem. 2011 , 3648–3669. [2] C. Tomasini, G. Luppi, M. Monari, J. Am. Chem. Soc. 2006 , 128 , 2410-2420. [3] G. Angelici, G. Falini, H.-J. Hofmann, D. Huster, M. Monari, C. Tomasini, Chem. Eur. J. 2009 , 15 , 8037-8048. [4] G. Longhi, S. Abbate, F. Lebon, N. Castellucci, P. Sabatino, C. Tomasini, J. Org. Chem. 2012 , 77 , 6033–6042. [5] N. Castellucci, C. Tomasini, Eur. J. Org. Chem. submitted.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 48

Constrained 3,4-dihydro-2H-[1,4]oxazine scaffold as a building block for peptidomimetic hybrid foldamers: a modeling study

Andrea Trabocchi, Antonio Guarna

Department of Chemistry “Ugo Schiff”, University of Florence, via della Lastruccia 13, 50019 Sesto Fiorentino, Florence, Italy [email protected]

The role of alternating proline residues in nucleating novel folded structures has been widely demonstrated in the literature, because of the disruption of conventional hydrogen-bonding schemes found in helices. As an additional unexplored proline analogue, morpholine-3-carboxylic acid (Mor) is of interest due to the oxygen atom in the ring, which can modulate the polarity and the conformation profile. Accordingly, we recently reported on a new morpholine-containing foldameric hybrid peptide, and preliminary conformational preferences assessed by means of NMR and molecular modeling calculations. [1] We were also interested in applying constrained 3,4-dihydro-2H-[1,4]oxazine scaffolds as building blocks for hybrid peptidomimetic foldamers, as previous conformational studies on model tetrapeptides containing such scaffold at i+1 position of a model E-turn structure suggested a role of dihydro-oxazine in nucleating a well-defined compact structure of the peptide. [2] Preliminary synthetic studies revealed the application of primary amino acids as appendages at the nitrogen atom of the dihydro-oxazine scaffold to induce some skeletal diversity. Successful achievement of the title building block useful for hybrid foldamers was applicable only by using proline or E/J- amino acids, which impaired any skeletal rearrangements, and these molecules were taken into account for modelling studies to design an array of model foldameric structures.

Figure 1. Ser/Thr-derived scaffolds from primary amino acids or proline, and designed monomeric dipeptide scaffolds containing 3,4-dihydro-2 H-[1,4]oxazine.

References [1] A. Trabocchi, A. Krachmalnicoff, G. Menchi, A. Guarna, Tetrahedron 2012 , 68 , 9701–9705. [2] F. Sladojevich, A. Guarna, A. Trabocchi, Org. Biomol. Chem. 2010 , 7, 916–924.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 49

Aromatic composition and helical stability

Christos Tsiamantas, a Victor Maurizot, a Brice Kaufmann, a Matthias Kamuf, b Oliver Trapp, b Ivan Huc a

a IECB, CBMN, Université de Bordeaux, Bordeaux, France b Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Heidelberg, Germany [email protected]

Foldamers are artificial folded molecular architectures inspired by the structures and functions of biopolymers. [1] In the case of helical aromatic oligoamides, [2] folding is mainly due to local conformational preferences induced by endocyclic or exocyclic moieties on each aromatic monomer at the ortho positions of the amide bonds, for example, endocyclic nitrogen atoms and exocyclic fluorine, chlorine and methyl groups. [3] Studies have been carried out to determine the stability of helical aromatic oligoamides depending on their length, [4] the solvent [5] and the helix propensity of the monomers. [6] A series of 5 compounds were synthesized in order to study how certain functionalities located on a central unit influence the helical conformations and the resulting helical stability. The rate of interconversion of the P and M helical enantiomers was assessed to quantify the stability of the helices. [4] The dynamics and kinetics of this interconversion were determined using chiral HPLC, assisted by NMR spectroscopy.

References [1] G. Guichard, I. Huc, Chem. Commun . 2011 , 47 , 5933. [2] I. Huc, Eur. J. Org. Chem . 2004 , 1, 17-29. [3] (a) C. Li, S.-F. Ren, J.-L. Hou, H.-P. Yi, S.-Z. Zhu, X. K. Jiang and Z.-T. Li, Angew. Chem., Int. Ed . 2005 , 44 , 5725. (b) J. J. Mousseau, L. Xing, N. Tang and L. A. Cuccia, Chem. Eur. J . 2009 , 15 , 10030. [4] N. Delsuc, T. Kawanami, J. Lefeuvre, A. Shundo, H. Ihara, M. Takafuji, I. Huc, ChemPhysChem 2008 , 9, 1882. [5] T. Qi, V. Maurizot, H. Noguchi, T. Charoenraks, B. Kauffmann, M. Takafuji, H. Iharac, I. Huc, Chem. Commun. 2012 , 48 , 6337. [6] (a) C. Dolain, J.-M. Léger, N. Delsuc, H. Gornitzka, I. Huc, Proc. Natl. Acad. Sci. (USA) 2005 , 102 , 16146. (b) N. Delsuc, L. Poniman, J.-M. Léger, I. Huc, Tetrahedron 2012 , 68 , 4464. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 50

Antibacterial alfa-peptides and dendrimers covalently bound to textiles

Andrea Orlandin, Fernando Formaggio, Cristina Peggion

University of Padova, via Marzolo 1, 35131, Padova, Italy [email protected]

In the last decade the increasing resistance of bacteria and fungi against available antibiotics led to the development of a new way to fight against these species. Several recent works demonstrate that the best candidates for this aim are antimicrobial peptides (AMPs) and lipopeptides (LPs) based on cationic and nonionic aminoacids, as lysine (K). [1] AMPs and LPs are able to disrupt bacteria cell membrane by peptide-membrane interactions from outside the cell. Such mechanism suggests that these peptides can be immobilized on a solid support by covalent bonds producing surfaces (metals, polymers, fibers…) able to reduce bacterial adhesion and to prevent their proliferation. In this framework, our group is working with the aim at creating antibacterial textiles for medical devices and food packaging. [2-5] In the present work we have used cotton fibers as solid support. Several methods to functionalize the fibers were tested in order to found the most environmentally friendly technique. The first approach converted utilities fibers as a solid phase synthesis resin, on which we built short peptide sequences with known antimicrobial activity. [6] The second way tested refers to the “thiol-ene” click-chemistry. This method needs the use of a small amount of solvent and allows to bound the peptide on the fibers without activating agents (as HOAt or HATU). The linking process is activated via UV irradiation at 320 nm. The third methodology allows to convert the fiber in a thiolated support and on this surface build gold nanoparticles covalently linked to the textile and covered by peptides with antibacterial activity. The last methodology applied is based on several studies published in recent years [7] . The possibility to prepare peptides in bulk water is a new green approach that promise to offer a useful and cheap method to prepare these molecules. This approach uses 4-(4,6-Dimetoxy-1,3,5-triazin-2- yl)-4-methyl-morpholinium chloride (DMTMM) as activating agent of the carboxylic group [8] in alkaline conditions. In order to increase the reaction rate, relying on recent work, [9] we used a microwave assisted method, using a power of 70 W and a reaction temperature of 50°C. The peptides chosen are short (4-10 amino acid). We also built dendrimers covalently bound to textiles in order to favor aggregation and cooperation between the peptides. We will present the synthesis and chemical characterization of a series of antimicrobial peptides both free in solution and covalently linked to cotton fibres. To evaluate the effective link to the cotton surface, we employed UV absorption spectroscopy (of the removed Fmoc protecting group), and quantitative EPR spectroscopy. For this last kind of measurements, we prepared an analogue of the peptides containing a nitroxyl-probe in the place of aliphatic chain at N-terminal end of the peptide sequence.

References [1] A. Makovitziki, J. Baram, Y. Shai. Biochemistry 2008 , 47 , 10630-10636. [2] Darouiche, R. O. Clin. Infect. Dis. 2003 , 36 , 1284–1289. [3] Samuel, U.; Guggenbichler, J. P. Int. J. Antimicrob. Agents 2004 , 23 , 75–78. [4] Lee, S. B., Koepsel, R. R. Morley, S. W. Matyjaszewski, K. Sun, Y. Russell, A. J. Biomacromolecules 2004 , 5, 877–882. [4] Hu, F. X. Neoh, K. G. Cen, L. Kang, E. T. Biotechnol. Bioeng . 2005 , 89 , 474–484. [5] A. Makovitziki, D. Avrahami and Y. Shai. PNAS , 2006 , 103, 43, 15997-16002. [6] Int J Pept Res Ther 2008 , 14 ,373–380. [7] Tetrahedron 1999 , 55 ,13159-13170. [8] Tetrahedron Lett. 2012, 53 , 6931–6935. PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 51

Novel chiral and non chiral hydrazido foldamers displaying 8-helicity

Annafelicia Civitavecchia, Gianluca Martelli, Mario Orena, Samuele Rinaldi

Dipartimento di Scienze della Vita e dell’Ambiente - Università Politecnica delle Marche Via Brecce Bianche - I-60131 Ancona, Italy [email protected]

In our laboratory, starting from the chiral aziridine 1, we synthesized a new isostere of aspartic acid where a nitrogen atom occurs in place of the C-3 of the ring, leading to the imidazolidinone 2.

Starting from hydrazido oligomer 2, dimer, trimer, tetramer and eventually hexamer were obtained by homogeneous phase methods and on the basis of NMR and CD data we found a novel 8-helix. In the event, we focused again our attention towards foldamers obtained starting from linear monomers where C ȕ atom of ȕ-amino acid residues is replaced with a nitrogen atom. Thus, the monomer 3, obtained through simple steps, was reacted leading to corresponding trimer, tetramer and heptamer whose structure was assigned as 8-helix on the basis of 1H NMR spectra.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 52

Design and Synthesis of oligourea foldamers with multiple imidazole side-chains for gene transfer applications

Céline Douat, a Stéphanie Antunes, a Burkhard Bechinger, b Antoine Kichler, c Gilles Guichard a

a Université de Bordeaux CNRS UMR5248, Institut Européen de Chimie et Biologie, CBMN, 2 rue Robert Escarpit, Pessac 33607, France b Chemistry Institute – Universityԟ of Strasbourg – 8, rue Blaise Pascal, 67100, Strasbourg, France c Laboratoire de Chimie Génétique – UMR 7199 CNRS – Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin F -67401 Illkirch cedex, France [email protected]

One primary requirement for developing effective gene therapy systems to treat cancer and other diseases is the efficient delivery of the therapeutic macromolecule to the target cells. LAH4 is a synthetic amphipathic cationic peptide that efficiently transfers genes. The presence of histidine and lysine residues at specific positions in the sequence ensure a good transmembrane positioning and a pH sensitiveness. 1 From a structural standpoint, this peptide has a strong propensity to fold into an D-helical conformation with all His residues located on one face of the helix. Mimicking this peptide architecture with synthetic folded oligomers constitutes a valuable approach towards the design of novel agents for gene transfer with improved enzymatic stability. N,N’ -linked oligourea are aliphatic peptidomimetic foldamers that adopt well-defined 2.5- helical structures stabilized by three-centered hydrogen bonds in solution and solid state. 2 These oligoureas are routinely prepared either in solution or on solid support by iterative coupling of ethylene diamine type building blocks. Recent developments have allowed the preparation of a new challenging monomer: the His-derived building block 1.3 With this activated monomer in hand, we set out to prepare a series of amphipathic oligourea foldamers resembling the LAH4 peptide, with multiple His-type units at selected positions. Their synthesis and the evaluation of their gene transfer efficiency is reported.

References [1] A. Kichler, C. Leborgne, J. März, O. Danos, B. Bechinger, Proc. Natl. Acad. Sci. USA , 2003 , 100, 1564. [2] (a) N. Pendem, Y. R. Nelli, C. Douat, L. Fischer, M. Laguerre, E. Ennifar, B. Kauffmann, G. Guichard, Angew. Chem. Int. Ed. 2013 , DOI: 10.1002/anie.201209838. (b) J. Fremaux, L. Fischer, T. Arbogast, B. Kauffmann, G. Guichard, Angew. Chem. Int. Ed. 2011 , 50 , 11382. (c) L. Fischer, P. Claudon, N. Pendem, E. Miclet, C. Didierjean, E.Ennifar, G. Guichard, Angew. Chem. Int. Ed. 2010 , 49 , 1067. [3] Y-R. Nelli, C. Douat, P. Claudon, B. Kauffmann, C. Didierjean, G. Guichard, Tetrahedron , 2012 , 68 , 4492.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 53

Conformation Control of Į-helical abiotic Foldamers

Fogha Jade, a,b Perato Serge, a,b Sebban Muriel, c Voisin-Chiret Anne Sophie, a,b Oulyadi Hassan, c Sopková-de Oliveira Santos Jana, a,b Rault Sylvain a,b aNormandie Univ, France b UNICAEN, CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie -FR CNRS INC3M - SF ICORE, Université de Caen Basse-Normandie, UFR des Sciences Pharmaceutiques Bd Becquerel), F-14032 Caen, France c L.C.O.B.S., I.R.C.O.F., UMR 6014 CNRS C.O.B.R.A., rue Tesnière, F-76821 Mont Saint-Aignan, France [email protected] Protein-Protein Interactions (PPIs) play a central role in essential cellular processes and their misregulation may be involved in several diseases. As the fundamental recognition element in many PPIs, Į-helix motif contributes to a significant and specific recognition through a small subset of their residues. [1] To date, different approaches have been established to mimic side chains distribution of an Į-helix and then targeted PPIs by a diverse array of mimetics based on foldamers. Hamilton and co-workers, for instance, have designed a non-peptidic preorganized Į-helix mimetic terphenyl as 3,2 ƍ,2 Ǝ-trisubstituted terphenyl derivative where methyl groups mimic positions ith , i + 3rd , and i + 7 th[2] and few years later, they have provided terpyridyl scaffolds using sequential Bohlmann-Rahtz heteroannulation reactions. [3] However, due to the difficulty to prepare such compounds, our laboratory has described a methodology to design new foldamers, such as oligophenylpyridines, using as structural chemical units, pyridyl, thiophenyl and phenyl rings: the Garlanding concept. [4-6] Thus we were interested in the evaluation of the ability of oligophenylpyridyl scaffolds to mimic D-helix side chains. In this study, a three part methodology was applied. [7] Firstly, the preferential twist angle in biphenylpyridine was predicted from theoretical simulations in function of methyl substituent position and/or nitrogen position in the pyridyl ring. The latter have suggested a possible similitude with the geometry of side chain distribution of an D-helix. Then, suitable crystals for X-ray diffraction study were obtained for some synthesized oligophenylpyridyl compounds and the 3D structures were solved. Finally, molecular dynamic simulations under the NMR constraints from a NOESY experience were performed. The experimental results have fully confirmed that the theoretical predictions from the biphenylpyridyl models are reproduced in longer models in a solid state (crystal structures) as well as in a liquid state (NMR structures). Moreover, the superposition of oligophenylpyridyl along a helix axis has showed that the methyl substituants can successfully mimic certain side chains of an D-helix.

References [1] T. A. Edwards, A. J. Wilson, Amino Acids, 2011 , 41 , 743-754. [2] B. P. Orner, J. T. Ernst, A. D. Hamilton, J. Am. Chem. Soc. 2001 , 123 , 5382-5383. [3] J. M. Davis, A. Truong, A. D. Hamilton, Org. Lett . 2005 , 24 , 5405-5408. [4] A.-S. Voisin, A. Bouillon, G. Burzicki, M. Célant, R. Legay, H. El-Kashef, S. Rault, Tetrahedron 2009 , 65 , 607- 612. [5] S. Perato, A.-S. Voisin-Chiret, J. Sopková-de Oliveira Santos, M. Sebban, R. Legay, H. Oulyadi, S. Rault, Tetrahedron 2012 , 68 , 1910-1917. [6] M. De Giorgi, A.-S. Voisin-Chiret, J. Sopková-de Oliveira Santos, F. Corbo, C. Franchini, S. Rault, Tetrahedron 2011 , 67 , 6145-6154. [7] J. Sopková-de Oliveira Santos, A. S. Voisin-Chiret, G. Burzicki, L. Sebaoun, M. Sebban, J.- F. Lohier, R. Legay, H. Oulyadi, R. Bureau, S. Rault, J. Chem. Inf. Model . 2012 , 52 , 429-439.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 54

1,46-Asymmetric induction through an achiral monomer mediated by quantitative control of screw-sense preference

Liam Byrne, a Jordi Solà, a Tommaso Marcelli, b Jonathan Clayden a

aSchool of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK bDipartimento di Chimica, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy [email protected]

The controlled formation of a new chiral centre under the influence of a pre-existing stereochemical feature (asymmetric induction) typically requires close proximity of the controlling functionality and the prochiral reactive site. Remote asymmetric induction (over 3 or more bonds) invariably necessitates some degree of conformational organisation of the molecular architecture that connects the two. Oligomers of the achiral, non-proteinogenic amino acid 2-aminoisobutyric acid (Aib) adopt well-defined 3 10 helices which, in the absence of a stereochemical influence, rapidly interconvert between equally populated left- ( M) and right- ( P) handed conformations. [1] The introduction of an N-terminal chiral amino acid is sufficient to bias this equilibrium and induce preferential adoption of one of the two screw-sense conformers. [2] Given that helix fidelity persists over at least 20 Aib residues, [3] this constitutes a mechanism by which stereochemical information can be relayed over nanometre distances.

Herein, we describe how 13 C VT-NMR studies, in conjunction with Density Functional Theory calculations, have identified that Cbz- L-aMv 2 (aMv = D-methylvaline) at the N-terminus exerts quantitative screw-sense control ( P helix favoured). Subsequent work has exploited this for the installation of a new chiral centre 45 bonds (approx. 2.9 nm) away from the nearest source of stereochemical information (Figure 1).

Figure 1. Ultra-remote stereocontrol through a configurationally achiral oligomer

References [1] R.-P. Hummel, C. Toniolo, G. Jung, Angew. Chem. Int. Ed. 1987 , 26 , 1150. [2] J. Solà, M. Helliwell, J. Clayden, J. Am. Chem. Soc. 2010 , 132 , 4548; R. A. Brown, T. Marcelli, M. De Poli, J. Solà, J. Clayden, Angew. Chem. Int. Ed. 2012 , 51 , 1395. [3] J. Clayden, A. Castellanos, J. Solà, G. A. Morris, Angew. Chem. Int. Ed. 2009 , 48 , 5962.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 55

Synthesis and Evaluation of Foldamers as Inhibitors of Carbonic Anhydrase II

Cinzia Colombo, a Jérémie Buratto, b Lucile Fischer, a Bernard Gallois, b Ivan Huc a

aInstitut Européen de Chimie et Biologie, CBMN, CNRS UMR 5248, 2, rue Robert Escarpit, 33607 Pessac, France. bCBMN, 14 allée Geoffroy St Hilaire, 33600 Pessac, France. [email protected]

Protein-protein interactions play crucial roles in many biological processes and diseases, as the understanding of these interactions could lead to the development of new therapeutic approaches. [1] Recently, our laboratory has developed methodologies for the synthesis of aromatic amide foldamers resulting in highly functionalized, predictable, stable and well defined helical structures. [2] The application of these molecules as objects that could bind selectively to a given protein is a remarkable challenge and there is an urgent need for progress in this area. Hence, functionalized foldamers, if able to bind to the protein surface, can help to interfere with the molecular recognition events in which proteins participate and/or elucidate the mechanism of protein-protein interactions.

The target protein we chose is the human carbonic anhydrase II (HCAII) . It represents a model widely used by the scientific community for structural studies of enzymes. Indeed, its structural properties were extensively described, thanks to its high propensity to crystallize. [3] We decided to anchor the natural arylsulfonamide inhibitor, which has a very high affinity for HCAII, [4] to some different functionalized foldamers with the addition of a spacer (Figure 1). The challenge is to develop a foldamer able to interact with the surface of HCAII in a specific manner.

The synthesis of these compounds will be described and biochemical and biophysical evaluation of these molecules will be discussed.

Figure 1. Model of the proposed strategy: Arylsulfonamide inhibitor of the target protein (HCAII) is linked to different foldamers decorated with functional groups (R), with the aim of interacting with the protein surface.

References [1] A. G. Cochran, Chemistry & Biology 2000 , 7 , R85-R94. [2] G. Guichard, I. Huc, Chem. Commun ., 2011 , 47 , 5933-5941. [3] (a) V. M. Krishnamurthy, G. K. Kaufman, A. R. Urbach et al ., Chem.Rev. 2008 , 108 , 946-1051. (b) A. Di Fiore, A. Maresca, V. Alterio, C. T. Supuran, G. De Simone, Chem. Commun., 2011 , 47 , 11636-11638. [4] G. A. Papalia et al., Anal. Biochem. 2006 , 359, 94-105.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 56

Microwave-assisted solid phase synthesis of quinoline oligoamide foldamers

Simon J. Dawson, Ivan Huc

Institut Européen de Chimie et Biologie, 2 Rue Robert Escarpit, 33607 Pessac, France [email protected]

Foldamers are defined as artificial folded molecular architectures .[1] Work in the Huc group has shown that the introduction of side-chains bearing polar groups onto quinoline-based oligoamide foldamers endows them with good water solubility. [2] This, coupled with their resistance to proteases and high structural stability makes them ideal candidates for investigation as medicinal compounds.

The advantage of a solid phase strategy for oligomer synthesis is that it potentially allows rapid access to diverse analogues, since functionalised monomer units can be incorporated individually. Following on from initial studies by our group, [3] this work describes a highly reproducible and efficient methodology for the microwave-assisted solid phase synthesis of quinoline-based oligoamide foldamers. Using a variety of orthogonally protected quinoline units ( Figure 1 ) bearing peptide-like side-chain functionalities, foldamers up to 24 units in length have been synthesised.

Figure 1. Orthogonally protected quinoline units for Fmoc SPS of oligoamide foldamers.

References [1] G. Guichard, I. Huc, Chem. Commun. 2011 , 47 , 5933. [2] E. Gillies, C. Dolain, J.-M. Léger, I. Huc, J. Org. Chem. 2006 , 71 , 7931. [3] B. Baptiste, C. Douat-Casassus, K. Laxmi-Reddy, F. Godde, I. Huc, J. Org. Chem. 2010 , 75 , 7175.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 57

Encapsulation of ȕ-D-fructopyranose by a Helical Aromatic Oligoamide

Nagula Chandramouli, a Yann Ferrand, a Guillaume Lautrette, a Brice Kauffmann, a Mackereth C.D., a Christophe Aube, b Didier Dubreuil, b Ivan Huc a

aUniversité de Bordeaux and CNRS, CBMN, UMR 5248, IECB, 2 Rue Robert Escarpit, 33607 Pessac, France and CNRS, CBMN, UMR 5248 bUniversité de Nantes and CNRS, CEISAM, UMR 6230, Faculté des sciences et des Techniques, 2 rue de la Houssiniére, BP 92208 44322 Nantes Cedex 3, France and CNRS, CEISAM, UMR 6230 [email protected]

During the last decade major breakthroughs have been made in the recognition of carbohydrates by synthetic receptors both in organic solvents and water. [1] However, practical applications ( e.g. tools for glycobiology, sensor s…) are still premature at this stage and there is still a need for new receptor architectures. [2] Our group has developed helical foldamers – oligomers that adopt stable helical folded conformations – derived from aromatic amino acids. [3] Some of these folded objects have shown unprecedented conformational stability even in water, and constitute convenient building blocks to elaborate synthetic, very large (protein-sized) folded architectures. Cavities can be designed within such synthetic molecules that enable them to act as artificial receptors for chiral polar guests including carbohydrates (Fig. 1). This design offers unmatched modularity in that each and every monomer may be varied in order to tune the structure, the dynamics and host-guest properties. In this poster, we show how we use iterative evolution of oligoamide sequences to develop a receptor that can bind ȕ-D-fructopyranose with high affinity and selectivity. Rounds of selection have been made possible through the extensive use of crystallography, NMR and circular dichroism.

Figure 1 . Schematic representation of the capture and release of a guest molecule by a capsule consisting of a helix whose diameter is wider in the center than at the ends.

References [1] A. P. Davis, Nature 2010 , 464 , 169. [2] (a) Gabius, H. J.; Siebert, H. C.; Andre, S.; Jiménez-Barbero, J.; Rudiger, H. ChemBioChem 2004 , 5, 740. (b) Dwek, R. A.; Butters, T. D. Chem. Rev. 2002 , 102 , 283. (c) Bertozzi, C. R.; Kiessling, L. L. Science 2001 , 291 , 2357. [3] Y. Ferrand, N. Chandramouli, A. M. Kendhale, C. Aube, B. Kauffmann, A. lard, M. Laguerre, D. Dubreuil, I. Huc J. Am. Chem. Soc . 2012 , 134 , 11282.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 58

Controlling Molecular Helicity from the C-terminus of Aib-based Peptides

Bryden A F Le Bailly, Jonathan Clayden

School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL, UK [email protected]

Homopeptides of the unnatural amino acid 2-aminoisobutyric acid (Aib) have a strong propensity [1] for adopting 3 10 helical conformations. As with other dynamic helical foldamers, Aib is achiral and so its oligomers exist as isoenergetic left- ( M) and right-handed ( P) helices which rapidly interconvert at ambient temperatures. A screw-sense bias can be induced by a single chiral amino acid at the N-terminus. [2] Whilst C-terminal control of helicity has been briefly studied, [3] its mechanism of action is not well understood.

Figure 1. Phe-NH tBu controlled peptide and its 13 C VT-NMR spectrum (Aib methyl region)

This work describes the use of an N-terminal enantioenriched 13 C-labelled probe ( Figure 1 , blue) to study the level of screw-sense control that a chiral amino acid ( Figure 1 , green) exerts when placed at the C-terminus of an otherwise achiral peptide. Variable-temperature (VT) NMR studies were used to quantify the degree of helical bias induced by a variety of amino acid derivatives. A correlation was found between the position of the major peak (shown here on the right ) in the NMR and the preferred helical conformer ( right -handed). The identity and terminal functionality of the controlling amino acid were found to be important in both the level and direction of screw-sense preference.

References [1] R.-P. Hummel, C. Toniolo, G. Jung, Angew. Chem. Int. Ed. 1987 , 26 , 1150. [2] J. Clayden, A. Castellanos, J. Solà, G. A. Morris, Angew. Chem. Int. Ed. 2009 , 48 , 5962. [3] J. Solà, M. Helliwell, J. Clayden, J. Am. Chem. Soc. 2010 , 132 , 4548.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 59

Conformational Studies of Arylopeptoids

Soumya Sasi, a Bruce. D. Alexander, b Alison. A. Edwards a

aMedway School of Pharmacy, Universities of Kent & Greenwich, Central Avenue, Chatham Maritime, Kent, UK. bSchool of Science, University of Greenwich, Central Avenue, Chatham Maritime, Kent, UK [email protected]

Arylopeptoids (oligomeric N-substituted amino methyl benzamides) are entirely new backbones for aromatic oligoamides (Fig. 1a). These synthetic oligomers are only distantly related to D-peptides because they lack any amide hydrogen and possess aromatic rings in the backbone. Thus they may have altered folding of their backbone relative to D-peptides. However, studies have shown that N- alkylated aromatic backbones can adopt stable secondary structures by the use of solvophobic/or aromatic interactions. [1] A series of ortho, meta and para (o/m/p) substituted arylopeptoids with different side chains, were synthesized by solution and solid phase using sub monomer methods (Fig. 1b). [1-3] They differ from other synthetic aromatic oligoamides in that the presence of an additional aliphatic carbon provides the potential to sample a larger range of conformations. This also allows increased diversity and also facile synthesis. [1-3] The conformational studies of o/m/p arylopeptoids by NMR, demonstrates their folding propensity as tert -butyl and phenyl side chains are able to direct 100% adoption of cis and trans amide conformations respectively. [2,3]

O 300000300000 (a)  (c)  250000 N 200000200000 o3 - TH 167 N ) 150000 m3 - TH 111 R R= -1 100000100000 p3 - TH 109 n 50000 dmol n=1,3,6,9  2 00 -50000

-100000-100000 O O O -150000 N N OH cm (deg ] -200000-200000 T (b)  [ -250000 Ph Ph -300000-300000 180180 190 200200 210 220220 230 240240 250 260260 270 280280 290 300300 wavelength(nm) Figure 1. (a) General structure of arylopeptoids, (b) an example structure: meta dimer, and (c) the molar ellipticity CD spectra of the o/m/p trimers.

By contrast, arylopeptoids with chiral ( S)- N-(1-phenylethyl) (spe) side chain showed broader, and partly overlapping NMR signals which indicates the presence of cis/trans amide isomers. Conformational information was therefore difficult to obtain from NMR data. [1-3] Hence, current studies have focused on investigation of the influence of chiral spe side chains on the conformation and cis/trans isomerisation of arylopeptoids using circular dichroism (CD). This study has investigated: (i) the effect of ortho, meta and para substitution on conformation (Fig. 1c), (ii) effect of different protecting groups at the C and N termini, (iii) solvent interactions and (iv) cooperative folding within the series. The initial conformational information deduced by CD for these novel spe aromatic foldamers will be presented.

References [1] T. Hjelmgaard, et al. ,Tetrahedron 2012 , 68 , 4444-4454. [2] T. Hjelmgaard, et al. , European Journal of Organic Chemistry 2011 , 4121-4132. [3] T. Hjelmgaard, et al ., Organic & Biomolecular Chemistry 2011, 9, 6832-6843.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 60

Foldamers under pressure

Ludwig Pilsl, a Werner Kremer, b Hans Robert Kalbitzer, b Roland Winter, c Oliver Reiser a

aInstitute of Organic Chemistry, University of Regensburg, 93053 Regensburg, Germany, b Institute of Biophysics und Physical Biochemistry, University of Regensburg, 93053 Regensburg, Germany, cInstitute of Biophysical Chemistry, TU Dortmund University, 44227 Dortmund, Germany [email protected]

High pressure is known to accelerate a broad scope of different chemical reactions. [1] It has been shown that short DE -peptide foldamers ( 1) containing E-aminocyclopropanecarboxylic acid (E-ACC, Ÿ/ź) as a rigidifying element are highly efficient catalysts for various transformations. [2,3] In order to investigate the conformational behavior of such molecules under the influence of pressure we conducted high-pressure NMR (up to 2 kbar) and IR (up to 7 kbar) experiments. Furthermore, organocatalytic reactions under high pressure (4-5 kbar) applying 1 as catalyst were carried out. In addition to these short tripeptides, longer DDEE -peptide foldamers were investigated with high-pressure NMR/IR spectroscopy, and pressure-dependent conformational changes were detected and analyzed. [4,5]

Figure 1. Bifunctional tripeptide organocatalyst H-Pro- Ÿ-Pro-OH ( 1) in its two major conformations.

References [1] L. W. A. van Berkom, G. J. T. Kuster, H. W. Scheeren, Mol. Diversity 2003 , 6, 271. [2] V. D’Elia, H. Zwicknagl, O. Reiser, J. Org. Chem. 2008 , 73 , 3262. [3] M. Schmid, M. Fleischmann, V. D'Elia, O. Reiser, W. Gronwald, R. Gschwind, ChemBioChem 2009 , 10 , 440. [4] L. Pilsl, O. Reiser, Amino Acids 2011 , 41 , 709. [5] à. Berlicki, L. Pilsl, E. Wéber, I. M. Mándity, C. Cabrele, T. A. Martinek, F. Fülöp, O. Reiser, Angew. Chem. Int. Ed. 2012 , 51 , 2208.

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013 Poster 61

Towards a new conformationally constrained Ȗ-amino dicarboxylic acid: synthesis of 2-(aminomethyl)cyclopropane-1,1-dicarboxylic acid

Sven Mangelinckx, a,† Marina Rvovi ü,b Stijn De Brabandere, a Biljana Petrovi ü,b Živadin D. Bugar þiü,b Dieter Enders, c Norbert De Kimpe a

aDepartment of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium. b Department of Chemistry, Faculty of Sciences, University of Kragujevac, Radoja Domanovi üa 12, P.O. Box 60, 34000 Kragujevac, Serbia. cInstitute of Organic Chemistry, RWTH Aachen University,Landoltweg 1, D-52074 Aachen, Germany. [email protected]

Unlike 2-(aminomethyl)cyclopropane-1-carboxylic acid derivatives, which are biologically and synthetically important Ȗ-amino acid derivatives, the corresponding 2-(aminomethyl)cyclopropane- 1,1-dicarboxylic acid derivatives 1 have received far less attention. Only a few syntheses of bicyclic 3-aza-2-oxobicyclo[3.1.0]hexane-1-carboxylic acid derivatives 2 have been reported.

NR 2R3 NR 2 COOR 1 1 O COOR COOR 1 1 2

In the present disclosure, the first synthesis of 2-(aminomethyl)cyclopropane-1,1-dicarboxylic acid 5 is described, involving sequential iodocarbocyclization, azidation, saponification and reduction of dimethyl 2-allylmalonate 3. This new carbocyclic Ȗ-amino dicarboxylic acid could have a potential as a bidentate or tridentate ligand of metals due to the presence of both the cyclopropane-1,1- dicarboxylic acid (CPDCA) moiety and the amino group. Efforts towards the development of an asymmetric synthesis of these functionalized cyclopropanes via Michael-induced ring closure (MIRC) of formaldehyde N,N-dialkylhydrazones with halogenated alkylidenemalonates will be presented as well.

N3 NH 2 COOMe 2 steps 2 steps COOMe COOMe COOH COOMe COOH 3 4 5

† Postdoctoral Fellow of the Research Foundation – Flanders (FWO).

PARIS FOLDAMERS 2013 SYMPOSIUM 10-12 April 2013