Triangular prism-shaped β-peptoid helices as unique biomimetic scaffolds

Nature Communications

Volumn 6, Issue , 2015, Pages

  Laursen, Jonas S ^a,b   Harris, Pernille ^a   Fristrup, Peter ^a   Olsen, Christian A ^a,b  

^a TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BETA PEPTOID; BIOMIMETIC MATERIAL; MOLECULAR SCAFFOLD; OLIGOMER; ORGANIC SOLVENT; PEPTOID; UNCLASSIFIED DRUG;

CRYSTAL STRUCTURE; FUTURE PROSPECT; MOLECULAR ANALYSIS; PEPTIDE; RESOLUTION; SIMULATION; SOLVENT;

ARTICLE; BIOMIMETICS; CIRCULAR DICHROISM; CONFORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; PRISM; CHEMISTRY; DRUG DESIGN; ISOMERISM; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN SECONDARY STRUCTURE; SPECTROFLUOROMETRY; STRUCTURE ACTIVITY RELATION; TISSUE SCAFFOLD; X RAY CRYSTALLOGRAPHY;

BIOMIMETIC MATERIALS; CIRCULAR DICHROISM; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; ISOMERISM; MOLECULAR DYNAMICS SIMULATION; PEPTOIDS; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; SPECTROMETRY, FLUORESCENCE; STRUCTURE-ACTIVITY RELATIONSHIP; TISSUE SCAFFOLDS;

EID: 84928911841     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms8013     Document Type: Article

References (52)

1. Gellman, S. H. Foldamers: A manifesto. Acc. Chem. Res. 31, 173-180 (1998).
2. Goodman, C. M., Choi, S., Shandler, S. & DeGrado, W. F. Foldamers as versatile frameworks for the design and evolution of function. Nat. Chem. Biol. 3, 252-262 (2007).
3. Horne, W. S. & Gellman, S. H. Foldamers with heterogeneous backbones. Acc. Chem. Res. 41, 1399-1408 (2008).
4. Olsen, C. A. Peptoid-peptide hybrid backbone architectures. ChemBioChem. 11, 152-160 (2010).
5. Horne, W. S. Peptide and peptoid foldamers in medicinal chemistry. Exp. Opin. Drug Discov. 6, 1247-1262 (2011).
6. Cheng, R. P., Gellman, S. H. & DeGrado, W. F. beta-Peptides: from structure to function. Chem. Rev. 101, 3219-3232 (2001).
7. Seebach, D., Beck, A. K. & Bierbaum, D. J. The world of beta- and gammapeptides comprised of homologated proteinogenic amino acids and other components. Chem. Biodivers. 1, 1111-1239 (2004).
8. Seebach, D. & Gardiner, J. Beta-peptidic peptidomimetics. Acc. Chem. Res. 41, 1366-1375 (2008).
9. Simon, R. J. et al. Peptoids: a modular approach to drug discovery. Proc. Natl Acad. Sci. USA 89, 9367-9371 (1992).
10. Butterfoss, G. L., Renfrew, P. D., Kuhlman, B., Kirshenbaum, K. & Bonneau, R. A preliminary survey of the peptoid folding landscape. J. Am. Chem. Soc. 131, 16798-16807 (2009).
11. Hamper, B. C., Kolodziej, S. A., Scates, A. M., Smith, R. G. & Cortez, E. Solid phase synthesis of beta-peptoids: N-substituted beta-aminopropionic acid oligomers. J. Org. Chem. 63, 708-718 (1998).
12. Baldauf, C., Guenther, R. & Hofmann, H.-J. Helices in peptoids of alpha- and beta-peptides. Phys. Biol. 3, S1-S9 (2006).
13. Kirshenbaum, K. et al. Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure. Proc. Natl Acad. Sci. USA 95, 4303-4308 (1998).
14. Wu, C. W., Sanborn, T. J., Huang, K., Zuckermann, R. N. & Barron, A. E. Peptoid oligomers with alpha-chiral, aromatic side chains: sequence requirements for the formation of stable peptoid helices. J. Am. Chem. Soc. 123, 6778-6784 (2001).
15. Wu, C. W., Sanborn, T. J., Zuckermann, R. N. & Barron, A. E. Peptoid oligomers with alpha-chiral, aromatic side chains: effects of chain length on secondary structure. J. Am. Chem. Soc. 123, 2958-2963 (2001).
16. Tanatani, A. et al. Helical structures of N-alkylated poly(p-benzamide)s. J. Am. Chem. Soc. 127, 8553-8561 (2005).
17. Norgren, A. S., Zhang, S. & Arvidsson, P. I. Synthesis and circular dichroism spectroscopic investigations of oligomeric beta-peptoids with alpha-chiral side chains. Org. Lett. 8, 4533-4536 (2006).
18. Olsen, C. A., Lambert, M., Witt, M., Franzyk, H. & Jaroszewski, J. W. Solid-phase peptide synthesis and circular dichroism study of chiral beta-peptoid homooligomers. Amino Acids 34, 465-471 (2008).
19. Roy, O., Faure, S., Thery, V., Didierjean, C. & Taillefumier, C. Cyclic beta-peptoids. Org. Lett. 10, 921-924 (2008).
20. Shuey, S. W., Delaney, W. J., Shah, M. C. & Scialdone, M. A. Antimicrobial beta-peptoids by a block synthesis approach. Bioorg. Med. Chem. Lett. 16, 1245-1248 (2006).
21. Olsen, C. A. et al. Alpha-peptide/beta-peptoid chimeras. Org. Lett. 9, 1549-1552 (2007).
22. Olsen, C. A. et al. Antimicrobial, hemolytic, and cytotoxic activities of beta-peptoid-peptide hybrid oligomers: improved properties compared to natural AMPs. ChemBioChem. 11, 1356-1360 (2010).
23. Jahnsen, R. D., Frimodt-M?ller, N. & Franzyk, H. Antimicrobial activity of peptidomimetics against multidrug-resistant Escherichia coli: a comparative study of different backbones. J. Med. Chem. 55, 7253-7261 (2012).
24. Andreev, K. et al. Guanidino groups greatly enhance the action of antimicrobial peptidomimetics against bacterial cytoplasmic membranes. Biochim. Biophys. Acta Biomembr. 1838, 2492-2502 (2014).
25. Vedel, L. et al. Antiplasmodial and prehemolytic activities of alpha-peptidebeta- peptoid chimeras. ChemBioChem. 8, 1781-1784 (2007).
26. Foged, C. et al. Cellular uptake and membrane-destabilizing properties of alpha -peptide/beta -peptoid chimeras: lessons for the design of new cellpenetrating peptides. Biochim. Biophys. Acta Biomembr. 1778, 2487-2495 (2008).
27. Gorske, B. C., Bastian, B. L., Geske, G. D. & Blackwell, H. E. Local and tunable n-4pi∗interactions regulate amide isomerism in the peptoid backbone. J. Am. Chem. Soc. 129, 8928-8929 (2007).
28. Gorske, B. C., Stringer, J. R., Bastian, B. L., Fowler, S. A. & Blackwell, H. E. New strategies for the design of folded peptoids revealed by a survey of noncovalent interactions in model systems. J. Am. Chem. Soc. 131, 16555-16567 (2009).
29. Caumes, C., Roy, O., Faure, S. & Taillefumier, C. The click triazolium peptoid side chain: a strong cis-amide inducer enabling chemical diversity. J. Am. Chem. Soc. 134, 9553-9556 (2012).
30. Laursen, J. S., Engel-Andreasen, J., Fristrup, P., Harris, P. & Olsen, C. A. Cis-trans amide bond rotamers in beta-peptoids and peptoids: evaluation of stereoelectronic effects in backbone and side chains. J. Am. Chem. Soc. 135, 2835-2844 (2013).
31. Stringer, J. R., Crapster, J. A., Guzei, I. A. & Blackwell, H. E. Extraordinarily robust polyproline type I peptoid helices generated via the incorporation of alpha-chiral aromatic N-1-naphthylethyl side chains. J. Am. Chem. Soc. 133, 15559-15567 (2011).
32. Armand, P. et al. NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. Proc. Natl Acad. Sci. USA 95, 4309-4314 (1998).
33. Bonke, G. et al. Dimeric building blocks for solid-phase synthesis of alpha-peptide-beta-peptoid chimeras. Synthesis 15, 2381-2390 (2008).
34. Crapster, J. A., Guzei, I. A. & Blackwell, H. E. A peptoid ribbon secondary structure. Angew. Chem. Int. Ed. 52, 5079-5084 (2013).
35. Hjelmgaard, T. et al. Convenient solution-phase synthesis and conformational studies of novel linear and cyclic alpha,beta-alternating peptoids. Org. Lett. 11, 4100-4103 (2009).
36. Abele, S., Vogtli, K. & Seebach, D. Oligomers of beta(2)- and of beta(3)- homoproline: What are the secondary structures of beta-peptides lacking H-bonds? Helv. Chim. Acta 82, 1539-1558 (1999).
37. Gorske, B. C., Nelson, R. C., Bowden, Z. S., Kufe, T. A. & Childs, A. M. "Bridged" n-4pi∗ interactions can stabilize peptoid helices. J. Org. Chem. 78, 11172-11183 (2013).
38. Fuller, A. A., Yurash, B. A., Schaumann, E. N. & Seidl, F. J. Self-association of water-soluble peptoids comprising (S)-N-1-(naphthylethyl)glycine residues. Org. Lett. 15, 5118-5121 (2013).
39. Torn?e, C. W., Christensen, C. & Meldal, M. Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67, 3057-3064 (2002).
40. Rostovtsev, V. V., Green, L. G., Fokin, V. V. & Sharpless, K. B. A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes. Angew. Chem. Int. Ed. 41, 2596-2599 (2002).
41. Glattli, A., Daura, X., Seebach, D. & van Gunsteren, W. F. Can one derive the conformational preference of a beta-peptide from its CD spectrum? J. Am. Chem. Soc. 124, 12972-12978 (2002).
42. Wixe, T., Christensen, N. J., Lidin, S., Fristrup, P. & Warnmark, K. A short designed semi-aromatic organic nanotube-synthesis, chiroptical characterization, and host properties. Org. Biomol. Chem. 12, 8930-8941 (2014).
43. Sheldrick, G. M. A short history of SHELX. Acta Crystallogr. A 64, 112-122 (2008).
44. Berendsen, H. J. C., Postma, J. P. M., Vangunsteren, W. F., Dinola, A. & Haak, J. R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690 (1984).
45. Nose, S. A unified formulation of the constant temperature moleculardynamics methods. J. Chem. Phys. 81, 511-519 (1984).
46. Hoover, W. G. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 31, 1695-1697 (1985).
47. Martyna, G. J., Tobias, D. J. & Klein, M. L. Constant-pressure moleculardynamics algorithms. J. Chem. Phys. 101, 4177-4189 (1994).
48. Tuckerman, M., Berne, B. J. & Martyna, G. J. Reversible multiple time scale molecular-dynamics. J. Chem. Phys. 97, 1990-2001 (1992).
49. Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8593 (1995).
50. Tiradorives, J. & Jorgensen, W. L. Molecular-dynamics of proteins with the Opls potential functions - simulation of the 3rd domain of silver pheasant ovomucoid in water. J. Am. Chem. Soc. 112, 2773-2781 (1990).
51. Banks, J. L. et al. Integrated modeling program, applied chemical theory (IMPACT). J. Comput. Chem. 26, 1752-1780 (2005).
52. Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38 (1996).