Peptoid Oligomers with R-Chiral, Aromatic Side Chains: Effects of Chain Length on Secondary Structure Cindy W. Wu, ² Tracy J. Sanborn, ² Ronald N. Zuckermann, ‡ and Annelise E. Barron* ,² Contribution from the Department of Chemical Engineering, Northwestern UniVersity, EVanston, Illinois 60208, and Chiron Technologies, Chiron Corporation, 4560 Horton Street, EmeryVille, California 94608 ReceiVed August 23, 2000 Abstract: Oligomeric N-substituted glycines or “peptoids” with R-chiral, aromatic side chains can adopt stable helices in organic or aqueous solution, despite their lack of backbone chirality and their inability to form intrachain hydrogen bonds. Helical ordering appears to be stabilized by avoidance of steric clash as well as by electrostatic repulsion between backbone carbonyls and π clouds of aromatic rings in the side chains. Interestingly, these peptoid helices exhibit intense circular dichroism (CD) spectra that closely resemble those of peptide R-helices. Here, we have utilized CD to systematically study the effects of oligomer length, concentration, and temperature on the chiral secondary structure of organosoluble peptoid homooligomers ranging from 3 to 20 (R)-N-(1-phenylethyl)glycine (Nrpe) monomers in length. We find that a striking evolution in CD spectral features occurs for Nrpe oligomers between 4 and 12 residues in length, which we attribute to a chain length-dependent population of alternate structured conformers having cis versus trans amide bonds. No significant changes are observed in CD spectra of oligomers between 13 and 20 monomers in length, suggesting a minimal chain length of about 13 residues for the formation of stable poly(Nrpe) helices. Moreover, no dependence of circular dichroism on concentration is observed for an Nrpe hexamer, providing evidence that these helices remain monomeric in solution. In light of these new data, we discuss chain length-related factors that stabilize organosoluble peptoid helices of this class, which are important for the design of helical, biomimetic peptoids sharing this structural motif. Introduction Biological polymers such as DNA, RNA, and polypeptides have evolved to perform a myriad of interdependent structural and catalytic functions that together enable cellular life. These polymer systems are unique in their ability to fold and self- assemble into complex and specific structures. Inspired by natural polymer systems, organic and medicinal chemists have worked to develop non-natural oligomer systems that mimic some of the fundamental molecular features of proteins and DNA. Various groups have ventured into bioinspired molecular design to create novel oligomer scaffolds such as peptoids, 1,2 vinylogous polypeptides, 3 peptide nucleic acids, 4 oligoureas, 5 oligopyrrolinones, 6 -peptides, 7,8 and γ-peptides. 9,10 Others have created novel oligomers that include stiff, aromatic groups in the backbone that cause them to fold or pleat into ordered structures in polar solvents, including the oligo(phenylene ethynylenes) 11 and aedamers. 12 Non-natural oligomers generally are resistant to enzymatic degradation, increasing their potential for in ViVo stability as therapeutics or as biomaterials. The development of a man-made polymer system that captures the defining characteristics of natural polypeptides, including sequence and length specificity and the ability to fold into defined structures, will no doubt offer intriguing avenues for design of novel therapeutics and for the engineering of bio- compatible, nanostructured materials. 13,14 Fundamental studies of the folding propensities of novel, sequence-specific oligomers may also provide us with deeper insight into protein folding by better revealing the hierarchies of forces that enable mimicry of the natural protein paradigm, in which function derives from folded structure, and folded structure is derived from het- eropolymer sequence. Poly-N-substituted glycines or “peptoids” are a unique class of non-natural, sequence- and length-controlled polymers that * Address correspondence to this author. Phone: (847) 491-2778. Fax: (847) 491-3728. E-mail: a-barron@northwestern.edu. ² Northwestern University. ‡ Chiron Corporation. (1) Simon, R. J.; Kania, R. S.; Zuckermann, R. N.; Huebner, V. D.; Jewell, D. A.; Banville, S.; Ng, S.; Wang, L.; Rosenberg, S.; Marlowe, C. K.; Spellmeyer, D. C.; Tan, R.; Frankel, A. D.; Santi, D. V.; Cohen, F. E.; Bartlett, P. A. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 9367-9371. (2) Zuckermann, R. N.; Kerr, J. M.; Kent, S. B. H.; Moos, W. H. J. Am. Chem. Soc. 1992, 114, 10646-10647. (3) Hagihara, M.; Anthony, N. J.; Stout, T. J.; Clardy, J.; Schreiber, S. L. J. Am. Chem. Soc. 1992, 116, 6568-6570. (4) Nielsen, P. E. Acc. Chem. Res. 1999, 32, 624-630. (5) Burgess, K.; Linthicum, K. S.; Shin, H. Angew. Chem., Int. Ed. Engl. 1995, 34, 907-909. (6) Smith, A. B.; Favor, D. A.; Sprengeler, P. A.; Guzman, M. C.; Carroll, P. J.; Furst, G. T.; Hirschmann, R. Bioorg. Med. Chem. 1999, 7,9-22. (7) Appella, D. H.; Christianson, L. A.; Karle, I. L.; Powell, D. R.; Gellman, S. H. J. Am. Chem. Soc. 1996, 118, 13071-13072. (8) Seebach, D.; Overhand, M.; Kuhnle, F. N. M.; Martinoni, B. HelV. Chim. Acta 1996, 79, 913-941. (9) Hanessian, S.; Luo, X. H.; Schaum, R. Tetrahedron Lett. 1999, 40, 4925-4929. (10) Hintermann, T.; Gademann, K.; Jaun, B.; Seebach, D. HelV. Chim. Acta 1998, 81, 983-1002. (11) Prince, R. B.; Saven, J. G.; Wolynes, P. G.; Moore, J. S. J. Am. Chem. Soc. 1999, 121, 3114-3121. (12) Nguyen, J. Q.; Iverson, B. L. J. Am. Chem. Soc. 1999, 121, 2639- 2640. (13) Kirshenbaum, K.; Zuckermann, R. N.; Dill, K. A. Curr. Opin. Struct. Biol. 1999, 9, 530-535. (14) Barron, A. E.; Zuckermann, R. N. Curr. Opin. Chem. Biol. 1999, 3, 681-687. 2958 J. Am. Chem. Soc. 2001, 123, 2958-2963 10.1021/ja003153v CCC: $20.00 © 2001 American Chemical Society Published on Web 03/08/2001