Kirshenbaum Research Lab - NYU Chemistry

NYU Chemistry

Publications

Journal Articles

 

  1. Mukudai, S.; Kraja, I.; Bing, R.; Nalband, D.M.; Tatikola, M.; Hiwatashi N.; Kirshenbaum, K.; Branski, R.C. (2019) Implementing Efficient Peptoid‐Mediated Delivery of RNA‐Based Therapeutics to the Vocal Folds. Laryngoscope Investigative Otolaryngology 4:640-644 Link
  2. Spencer, R.K.; Butterfoss, G.L.; Edison, J.R.; Eastwood, J.R.B.; Whitelam, S.; Kirshenbaum, K.; Zuckermann, R.N. (2019) Stereochemistry of Polypeptoid Chain Configurations. Biopolymers e23266 Link
  3. Schneider, J.A.; Craven, T.W.; Kasper, A.C.; Yun, C.; Haugbro, M.; Briggs, E.M.; Svetlov, V.; Nudler, E.; Knaut, H.; Bonneau, R.; Garabedian, M.J.; Kirshenbaum, K.; Logan, S.K. (2018) Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer. Nat. Commun. 9:4396-405 Link
  4. Battigelli, A.; Kim, J.H.; Dehigaspitiya, D.C.; Proulx, C.; Robertson, E.J.; Murray, D.J.; Rad, B.; Kirshenbaum, K.; Zuckermann, R.N. (2018) Glycosylated Peptoid Nanosheets as a Multivalent Scaffold for Protein Recognition. ACSNano. 12:2455−65 Link
  5. Kraja I.; Bing R.; Hiwatashi N.; Rousseau B.; Nalband D.; Kirshenbaum K.; Branski R.C. (2017) Preliminary study of a novel transfection modality for in vivo siRNA delivery to vocal fold fibroblasts. The Laryngoscope 127:E231–E237 Link
  6. Andreev, K.; Martynowycz, M.; Ivankin, A.; Huang, M.; Kuzmenko, I.; Meron, M.; Lin, B.; Kirshenbaum, K.; Gidalevitz, D. (2016) Cyclization Improves Membrane Permeation by Antimicrobial Peptoids. Langmuir 32(48):12905–12913. Link
  7. Wang, Y; Dehigaspitiya, D.C.; Levine, P.M.; Profit, A.A.; Haugbro, M; Imberg-Kazdan, K; Logan, S.K.; Kirshenbaum, K; Garabedian, M.J. (2016) Multivalent Peptoid Conjugates Which Overcome Enzalutamide Resistance in Prostate Cancer Cells. Cancer Res. 76(17): 5124-32. Link
  8. Craven, T.W.; Bonneau, R.; Kirshenbaum, K. (2016) PPII Helical Peptidomimetics Templated by Cation–π Interactions. ChemBioChem. 17(19): 1824-28 Link
  9. Bowling, H.; Bhattacharya, A.; Zhang, G.; Lebowitz, J. Z.; Alam, D.; Smith, P. T.; Kirshenbaum, K.; Neubert, T. A.; Vogel, C.; Chao, M. V.; Klann, E. (2016) BONLAC: A Combinatorial Proteomic Technique to Measure Stimulus-Induced Translational Profiles in Brain Slices. Neuropharmacology  100: 76-89. Link
  10. Craven, T. W.; Cho, M. K.;  Traaseth, N. J.; Bonneau, R.; Kirshenbaum, K. (2016) A Miniature Protein Stabilized by a Cation−π Interaction Network. J. Am. Chem. Soc. 138 (5): 1543-50. Link
  11. Smith, P. T.; Huang, M. L.; Kirshenbaum, K. (2015) Osmoprotective polymer additives attenuate the membrane pore-forming activity of antimicrobial peptoids. Biopolymers, 103: 227–36. Link
  12. Zhang, G.; Bowling, H.;  Hom, N.; Kirshenbaum, K.; Klann, E.; Chao, M. V.; Neubert, T. A. (2014) In-Depth Quantitative Proteomic Analysis of de Novo Protein Synthesis Induced by Brain-Derived Neurotrophic Factor. J Proteome Res., 13(12): 5707-14. Link
  13. Nalband, D. M.; Warner, B. P.; Zahler, N. H.; Kirshenbaum, K. (2014) Rapid identification of metal-binding peptoid oligomers by on-resin X-ray fluorescence screening. Biopolymers, 102: 407–415. Link
  14. Levine, P. M.; Garabedian, M. J.; Kirshenbaum, K. (2014) Targeting the Androgen Receptor with Steroid Conjugates. J. Med. Chem. 57 (20): 8224-8237. Link
  15. Butterfoss, G. L.; Drew, K.; Renfrew, P. D.; Kirshenbaum, K.; Bonneau, R. (2014) Conformational preferences of peptide–peptoid hybrid oligomers. Biopolymers , 102: 369–378.  Link
  16. Renfrew, P. D.; Craven, T. W.; Butterfoss, G. L.; Kirshenbaum, K.; Bonneau, R. (2014) A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers. J. Am. Chem. Soc. 136 (24): 8772–8782. Link
  17. Konca, Y. U.; Kirshenbaum, K.; Zuckermann, R. N. (2014) Nanometer-scale siRNA carriers incorporating peptidomimetic oligomers: Physical characterization and biological activity. Int. J. Nanomedicine. 9(1): 2271—2285 Link
  18. Levine, P. M.; Craven, T. W.; Bonneau, R.; Kirshenbaum, K. (2014) Intrinsic bioconjugation for site-specific protein PEGylation at N-terminal serine. Chem. Commun. 50: 6909-6912. Link
  19. Levine, P. M.; Craven, T. W.; Bonneau, R.; Kirshenbaum, K. (2014) Semisynthesis of Peptoid–Protein Hybrids by Chemical Ligation at Serine. Org. Lett. 16: 512–515. Link
  20. Drew, K.; Renfrew, P. D.; Craven, T. W.; Butterfoss, G. L.; Chou, F.; Lyskov, S.; Bullock, B. N.; Watkins, A.; Labonte, J. W.; Pacella, M.; Kilambi, K. P.; Leaver-Fay, A.; Kuhlman, B.; Gray, J. J.; Bradley, P.; Kirshenbaum, K.; Arora, P.S.; Das, R.; Bonneau R. (2013) Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. PloS One. e67051. Link
  21. Levine, P. M.; Craven, T. W.; Bonneau, R.; Kirshenbaum, K. (2013) Chemoselective Fragment Condensation Between Peptide and Peptidomimetic Oligomers. Org. Biomol. Chem. 11: 4142-4146. Link
  22. Huang, M. L., Benson, M. A., Shin, S. B. Y., Torres, V. J., & Kirshenbaum, K. (2013). Amphiphilic Cyclic Peptoids That Exhibit Antimicrobial Activity by Disrupting Staphylococcus aureus Membranes. EurJOC. (17), 3560-3566. Link
  23. Vollrath, S. B. L.; Hu, C.; Brase, S.; Kirshenbaum, K. (2013) Peptoid Nanotubes: An Oligomer Macrocycle that Reversibly Sequesters Water Via Single-Crystal-to-Single-Crystal Transformations. Chem. Commun. 49: 2317-2319. Link
  24. Levine, P. M.; Carberry, T.; Holub, J. M.; Kirshenbaum, K. (2013) Crafting Precise Multivalent Architectures. Med. Chem. Commun. 4: 493-509. Link
  25. Huang, M.; Ehre, D.; Jiang, Q.; Hu, C.; Kirshenbaum, K.; Ward. M. (2012) Biomimetic Peptoid Oligomers as Dual-Action Antifreeze Agents. Proc. Natl. Acad. Sci. USA. 109, 49: 19922-19927. Link
  26. Hom, N.; Mehta, K.; Chou, T.; Foraker, A.; Brodsky, F.; Kirshenbaum, K.; Montclare, J. (2012) Anisotropic Nanocrystal Arrays Organized on Protein Lattices Formed by Recombinant Clathrin Fragments. J. Mater. Chem. 22: 23335-23339. Link
  27. Butterfoss, G. L.; Yoo, B.; Jaworski, J. N.; Chorny, I.; Dill, K. A.; Zuckermann, R.; Bonneau, R.; Kirshenbaum, K.; Voelz, V. A. (2012) De novo Structure Prediction and Experimental Characterization of Folded Peptoid Oligomers. Proc. Natl. Acad. Sci. USA. 109(36): 14320-14325. Link
  28. Levine, P. M.; Lee, E.; Greenfield, A.; Bonneau, R.; Logan, S. K.; Garabedian, M. J.; Kirshenbaum, K. (2012) Androgen Receptor Antagonism by Divalent Ethisterone Conjugates in Castrate-Resistant Prostate Cancer Cells. ACS Chem. Biol. 7: 1693-1701. Link
  29. Vollrath, S. B. L.; Brase, S.; Kirshenbaum, K. (2012) Twice Tied Tight: Enforcing Conformational Order in Bicyclic Peptoid Oligomers. Chemical Science 3: 2726-2731. Link
  30. Levine, P. M.; Imberg. K; Garabedian, M. J.; Kirshenbaum, K. (2012) Multivalent Peptidomimetic Conjugates: A Versatile Platform For Modulating Androgen Receptor Activity. J. Am. Chem. Soc. 134: 6912-6915. Link
  31. Paul, B.; Butterfoss, G. L.; Boswell, M. G.; Huang, M. L.; Bonneau, R.; Wolf, C.; Kirshenbaum, K. (2012) N-Naphthyl Peptoid Foldamers Exhibiting Atropisomerism. Org. Lett. 14: 926-929. Link
  32. Huang, M. L.; Shin, S. B. Y.; Benson, M. A.; Torres, V. J.; Kirshenbaum, K. (2012) A Comparison of Linear and Cyclic Peptoid Oligomers as Potent Antimicrobial Agents. ChemMedChem 7: 114-122. Link
  33. Jordan, P. A.; Paul, B.; Butterfoss, G. L.; Renfrew, P. D.; Bonneau, R.; Kirshenbaum, K. (2011) Oligo(N-alkoxy glycines): Trans Substantiating Peptoid Conformations. Biopolymers (Pept. Sci.) 96: 617-626. Link
  34. Paul, B.; Butterfoss, G. L.; Boswell, M. G.; Renfrew, P. D.; Yeung, F. G.; Shah, N. H.; Wolf, C.; Bonneau, R.; Kirshenbaum, K. (2011) Peptoid Atropisomers. J. Am. Chem. Soc. 133: 10910-10919. Link
  35. Pohl, N. L. B.; Kirshenbaum, K.; Yoo, B.; Schulz, N.; Zea, C. J.; Streff, J. M.; Schwarz, K. L. (2011) Student-Driven Design of Peptide Mimetics: Microwave-Assisted Synthesis of Peptoid Oligomers. J. Chem. Ed. 88: 999-1001. Link
  36. Holub, J. M.; Garabedian, M. J.; Kirshenbaum, K. (2011) Modulation of Human Estrogen Receptor α Activity by Multivalent Estradiol-Peptidomimetic Conjugates. Mol. BioSyst. 7: 337-345. Link
  37. Yoo, B.; Shin, S. B. Y.; Huang, M. L.; Kirshenbaum, K. (2010) Peptoid Macrocycles: Making the Rounds with Peptidomimetic Oligomers. Chem. Eur. J. 16: 5528-5537. Link
  38. Holub, J. M.; Kirshenbaum, K. (2010) Tricks with Clicks: Modification of Peptidomimetic Oligomers via Copper-catalyzed Azide-alkyne [3+2] Cycloaddition. Chem. Soc. Rev. 39: 1325-1337. Link
  39. Utku, Y.; Rohatgi, A.; Yoo, B.; Zuckermann, R.; Pohl, N.; Kirshenbaum, K. (2010) Rapid Multistep Synthesis of a Bioactive Peptidomimetic Oliogomer for the Undergraduate Lab. J. Chem. Ed. 87: 637-639. Link
  40. Butterfoss, G. L.; Renfrew, P. D.; Kuhlman, B.; Kirshenbaum, K.; Bonneau, R. (2009) A Preliminary Survey of the Peptoid Folding Landscape. J. Am. Chem. Soc. 131: 16798- 16807. Link
  41. Maayan, G. Ward, M.; Kirshenbaum, K. (2009) Folded Biomimetic Oligomers for Enantioselective Catalysis. Proc. Natl. Acad. Sci. USA 106: 13679-13684. Link
  42. Jagasia, R.; Holub, J. M.; Bollinger, M.; Kirshenbaum, K.; Finn, M.G. (2009) Peptide Cyclization and Cyclodimerization by CuI-Mediated Azide-Alkyne Cycloaddition. J. Org. Chem. 74: 2964-2974. Link
  43. Maayan, G.; Ward, M.; Kirshenbaum, K. (2009) Metallopeptoids. Chem. Commun. 56-58. Link
  44. Yoo, B.; Kirshenbaum, K. (2008) Peptoid Architectures: Elaboration, Actuation, and Application. Curr. Opin. Chem. Biol. 12: 714-721. Link
  45. Shah, N. H.; Butterfoss, G. L.; Nguyen, K.; Yoo, B.; Bonneau, R.; Rabenstein, D. L.; Kirshenbaum, K. (2008) Oligo(N-aryl glycines): A New Twist on Structured Peptoids. J. Am. Chem. Soc. 130: 166222-16632. Link
  46. Shah, N.H.; Kirshenbaum, K. (2008) Direct Generation of Polymer Films on Copper Surfaces Through Azide-Alkyne Cycloaddition Reactions Between Peptidomimetic Oligomers. Macromol. Rapid Commun. 29: 1134-1139. Link
  47. Shah, N.H.; Kirshenbaum, K. (2008) Photoresponsive Peptoid Oligomers Bearing Azobenzene Side Chains. Org. Biomol. Chem. 6: 2516-2521. Link
  48. Maayan, G.; Yoo, B.; Kirshenbaum, K. (2008) Heterocyclic Amines for the Construction of Peptoid Oligomers Bearing Multi-Dentate Ligands. Tet. Lett. 49: 335-338. Link
  49. Shin, S.-B.Y.; Kirshenbaum, K. (2007) Conformational Rearrangements by Water-Soluble Peptoid Foldamers. Org. Lett. 9: 5003-5006. Link
  50. Holub, J. M., Garabedian, M.J., Kirshenbaum, K. (2007) Peptoids on Steroids: Precise Multivalent Estradiol-Peptidomimetic Conjugates Generated via Azide-Alkyne [3+2] Cycloaddition Reactions. QSAR & Comb. Sci. 26: 1175-1180. Link
  51. Holub, J.M., Jang, H., Kirshenbaum, K. (2007) Fit To Be Tied: Conformation-Directed Macrocyclization of Peptoid Foldamers. Org. Lett. 9: 3275-3278. Link
  52. Shin, S.-B.Y., Yoo, B., Todaro, L., Kirshenbaum, K. (2007) Cyclic Peptoids. J. Am. Chem. Soc. 129: 3218-3225. Link
  53. Fafarman, A.T., Borbat, P.P., Freed, J.H., Kirshenbaum, K. (2007) Characterizing the structure and dynamics of folded oligomers: Pulsed ESR studies of peptoid helices. Chem. Commun. 2: 377-379. Link
  54. Utku, Y., Dehan, E., Ouerfelli, O., Piano, F., Zuckermann, R.N., Pagano, M., Kirshenbaum, K. (2006) A peptidomimetic siRNA transfection reagent for highly effective gene silencing. Mol. BioSystems. 2: 312-317. Link
  55. Spencer, T., Yoo, B., Kirshenbaum, K. (2006) Purification and modification of fullerene C60 in the undergraduate laboratory. J. Chem. Ed. 83: 1218-1220. Link
  56. Anderson, E.A., Isaacman, S., Peabody, D.S., Wang, E.Y., Canary, J.W., Kirshenbaum, K. (2006) Viral nanoparticles donning a paramagnetic coat: conjugation of MRI contrast agents to the MS2 capsid. NanoLetters. 6: 1160-1164. Link
  57. Holub, J.M., Jang, H., Kirshenbaum, K. (2006) Clickity-click: Highly functionalized peptoid oligomers generated by sequential conjugation reactions on solid-phase support. Org. Biomol. Chem. 4: 1497-1502. Link
  58. Huang, K., Wu, C.W., Sanborn, T.J., Patch, J.A., Kirshenbaum, K., Zuckermann, R.N., Barron, A.E., Radhakrishnan, I. (2006) A threaded loop conformation adopted by a family of peptoid nonamers. J. Am. Chem. Soc. 128: 1733-1738. Link
  59. Yoo, B., Kirshenbaum, K. (2005) Protease-mediated ligation of abiotic oligomers. J. Am. Chem. Soc. 127: 17132-17133. Link
  60. Jang, H.J., Fafarman, A., Holub, J.M., Kirshenbaum, K. (2005) Click to fit: Versatile polyvalent display on a peptidomimetic scaffold. Org. Let. 7: 1951-1954. Link

Book Chapters

  1. Johnson, A. ; Kirshenbaum, K.; McBride, A. E. “Designing a Sustainable and Stretchable ‘Fox Testicle’ Ice Cream”, invited chapter in The Kitchen as Laboratory; Vega, C.; Ubbink, J; van der Linden, E.; Columbia University Press, New York, 2012.
  2. Patch, J.A., Kirshenbaum, K., Seurynck, S.L., Zuckermann, R.N., Barron, A.E. “Versatile Oligo(N-substituted) Glycines: The Many Roles of Peptoids in Drug Discovery”, invited chapter in Pseudo-peptides in Drug Development; Nielsen, P.E., Ed.; Wiley-VCH, Weinheim, Germany, 2004.

News and Views

  1. Carrico, I. S.; Kirshenbaum, K. (2009) Nanoparticles: Designer Labels for Virus Coats. (News and Views) Nature Nanotech. 4:14-15. Link
  2. Kirshenbaum, K. and Arora, P. S. (2008) Cross-dressing Proteins by Olefin Metathesis. (News and Views) Nat. Chem. Biol. 4:527-528. Link
  3. Arora, P.S., Kirshenbaum, K. (2004) Nano-tailoring: Stitching alterations on viral coats. Chem. Biol. 11: 418-420. Link

Publications Prior to NYU

  1. Wu, C.W., Kirshenbaum, K., Sanborn, T.J., Patch, J.A., Huang, K., Dill, K.A., Zuckermann, R.N., Barron, A.E. (2003) Structural and spectroscopic studies of peptoid oligomers with a-chiral aliphatic side chains. J. Am. Chem. Soc. 125: 13525-13530. Link
  2. Kwon, I., Kirshenbaum, K., Tirrell, D.A. (2003) Breaking the degeneracy of the genetic code. J. Am. Chem. Soc. 125: 7512-7513. Link
  3. Kirshenbaum, K., Carrico, I.S., Tirrell, D.A. (2002) Biosynthesis of proteins incorporating a versatile set of phenylalanine analogs. ChemBioChem 3: 235-237. Link
  4. Kirshenbaum, K., Zuckermann, R.N., Dill, K.A. (1999) Designing polymers that mimic biomolecules. Curr. Opin. Struc. Biol. 9: 530-535. Link
  5. Kirshenbaum, K., Young, M., Highsmith, S. (1999) Predicting allosteric switches in myosins. Protein Sci. 8: 1806-1815. Link
  6. Young, M., Kirshenbaum, K., Dill, K.A., Highsmith, S. (1999) Predicting conformational switches in proteins. Protein Sci. 8: 1752-1764. Link
  7. Armand, P., Kirshenbaum, K., Goldsmith, R.A., Farr-Jones, S., Barron, A.E., Truong, K.T.V., Dill, K.A., Mierke, D.F., Cohen, F.E., Zuckermann, R.N., Bradley, E.K. (1998) NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. Proc. Natl. Acad. Sci. USA 95: 4309-4314. Link
  8. Kirshenbaum, K., Barron, A.E., Goldsmith, R.A., Armand, P., Bradley, E.K., Truong, K.T.V., Dill, K.A., Cohen, F.E., Zuckermann, R.N. (1998) Sequence-specific polypeptoids: A diverse family of heteropolymers with stable secondary structure. Proc. Natl. Acad. Sci. USA 95: 4303-4308. Link
  9. Armand, P., Kirshenbaum, K., Falicov, A., Dunbrack, R.L., Dill, K.A., Zuckermann, R.N., Cohen, F.E. (1997) Chiral N-substituted glycines can form stable helical conformations. Folding & Design 2: 369-375. Link
  10. Kirshenbaum, K., Daggett, V. (1995) Sequence effects on conformational properties of the Amyloid b(1-28) Peptide: Testing a proposed mechanism for the α→β transition. Biochemistry 34: 7640-7647. Link
  11. Kirshenbaum, K., Daggett, V. (1995) pH-Dependent conformations of the amyloid b(1-28) peptide fragment explored using molecular dynamics. Biochemistry 34: 7629-7639. Link
  12. Kirshenbaum, K., Papp, S., Highsmith, S. (1993) Cross-linking myosin subfragment 1 Cys-697 and Cys-707 modifies ATP and actin binding site interactions. Biophys. J. 65: 1121-1129. Link