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The Kodadek Lab

Publications

2012

Sarma, B.K. and Kodadek, T. (2012) “Sub-Monomer Synthesis of A Hybrid Peptoid-Azapeptoid Library” ACS Comb. Sci. 14, In press.

Liu, X. Dix, M., Speers, A.E., Bachovchin, D.A., Zuhl, A.M., Cravatt, B.F. and Kodadek, T. (2012) “Rapid Development of a Potent Photo-Triggered Inhibitor of the Serine Hydrolase RBBP9” ChemBioChem 13, In press.

Simpson, L. and Kodadek, T. (2012) “A cleavable scaffold strategy for the synthesis of one-bead one-compound cyclic peptoid libraries that can be sequenced by tandem mass spectrometry” Tet. Lett. 53, 2341-2344.

Aditya, A. and Kodadek, T. (2012) “Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries” ACS Comb. Sci. 14, 164-169.

2011

Aquino, C., Sarkar, M., Chalmers, M.J., Mendes, K., Kodadek, T. and Micalizio, G. (2011) “ A Biomimetic polyketide-inspired approach to small molecule ligand discovery” Nature Chemistry 4, 99-104.

Mendes, K. and Kodadek, T. (2011) “PDZ dimerization brings proteins together” Chem. & Biol. 18, 1071-1072.

Sarma, B.K., Yousufuddin, M. and Kodadek, T. (2011) “Acyl hydrazides as peptoid sub-monomers” Chem. Comm 47, 10590-10592.

Cai, D., Lee, A.Y., Chiang, C.-M. and Kodadek, T. (2011) “Peptoid ligands that bind selectively to phosphoproteins” Bioorg. Med. Chem. Lett. 21, 4960-4964.

Kodadek, T. (2011) “The rise, fall and reinvention of combinatorial chemistry” Chem. Comm. 47, 9757-9763.

Reddy, M.M., Wilson, R., Wilson, J., Connell, S., Gocke, A., Hynan, L., German, D. and Kodadek, T. (2011) Identification of candidate IgG biomarkers for Alzheimer’s disease via combinatorial library screening Cell 144, 132-142.

2010

Kodadek T, Cai D, (2010) "Chemistry and biology of orexin signaling." Mol Biosyst. 6(8):1366-75

Astle, JM, Simpson LS, Huang Y. Reddy, MM, Wilson, R, Connell S, Wilson J, Kodadek T., (2010)  "Seamless bead to microarray screening:  rapid identification of teh highest affinity protein ligands from large combinatorial librairies."  Chem Bio 17(1):38-45.

Lee, J., Reddy, M.M. and Kodadek, T. (2010)  "Discovery of an orexin receptor positive potentiator."  Chem Sci. 1, 48-54.

Lee, J., Udugamasooriya, D.G., Lim, H.-S. and Kodadek, T. (2010) “Potent and selective photo-inactivation of proteins with peptoid-ruthenium conjugates” Nature Chem. Biol. 6, 258-260.

Kodadek, T. (2010) “Rethinking screening” Nature Chem. Biol. 6, 162-165.

2009

Gocke, A. R., Udugamasooriya, D.G., Archer, C.T., Lee, J. and Kodadek, T. (2009) “Isolation of antagonists of antigen-specific autoimmune T cell proliferation” Chem. & Biol. 16, 1133-1139.

Chan, Y.-C., Wu, S.-Y., Lim, H.-S., Chiang, C.-M. and Kodadek, T. (2009) "Non-proteolytic regulation of p53-mediated transcription through destabilization of the activator-promoter complex by the proteasomal ATPases" J. Biol. Chem. 284, In press.

Qi, X., Astle, J. and Kodadek, T. (2009) "Rapid identification of orexin receptor ligands using cell-based screening accelerated with magnetic beads" Molecular BioSystems 5, In press.

Liu, B. and Kodadek, T. (2009) "Investigating the Cellular Permeability of DNA-binding Pyrrole-Imidazole Polyamides " J. Med. Chem. 52, 4604-4612.

Lim, H.-S., Reddy, M.M., Xiao, X., Wilson, J., Wilson, R., Connell, S. and Kodadek, T. (2009) "Rapid identification of improved protein ligands using peptoid microarrays" Bioorganic Med. Chem. Lett. 19, 3866-3869.

Zuckermann, R.N. and Kodadek, T. (2009) "Peptoids as potential therapeutics" Curr. Opin. Mol. Therapeutics 11, 299-307.

Simpson, L.S., Burdine, L., Dutta, A.K., Feranchak, A.P. and Kodadek, T. (2009) "Selective Toxin Sequestrants for the Treatment of Bacterial Infections" J. Amer. Chem. Soc. 131, 5760-5762.

Friedberg, E.C. and Kodadek, T. (2009) Nucleic Acids: Chemical Damage. Volume 3, 467-480 in Wiley Encyclopedia of Chemical Biology. John Wiley & Sons, Inc., Hoboken, N.J.

2008

Archer, C.T., Burdine, L., Liu, B., Ferdous, A., Johnston, S.A. and Kodadek, T. (2008) Physical and functional interaction of mono-ubiquitylated transactivators with the proteasome" J. Biol. Chem. 283, 21789-21798.

Kwon, Y.-U. and Kodadek, T. (2008) "Encoded combinatorial libraries for the construction of cyclic peptoid microarrays" Chem. Comm. 5704-5706.

Udugamasooriya, D.G., Dunham, G., Ritchie, C., Brekken, R.A. and Kodadek, T. (2008) "The pharmacophore of a peptoid VEGF Receptor antagonist includes both side chain and main chain residues" Bioorg, Med. Chem. Lett. 18, 5892-5894.

Kodadek, T. (2008) "Rise of the machines: Bruce Alberts and the biochemistry of multi-protein complexes" Mol. BioSystems 4, 1043-1045.

Ferdous, A., O'Neal, M., Nalley, K., Sikder, D., Kodadek, T. and Johnston, S.A. (2008) "Phosphorylation of the Gal4 DNA-binding domain is essential for activator mono-ubiquitylation and effeficient promoter occupancy" Mol. BioSystems 4, 1116-1125.

Archer, C.T., Burdine, L., Liu, B., Ferdous, A., Johnston, S.A. and Kodadek, T. (2008) Physical and functional interaction of mono-ubiquitylated transactivators with the proteasome" J. Biol. Chem. 283, 21789-21798.

Astle, J.M., Udugamasooriya, D.G., Smallshaw, J.E. and Kodadek, T. (2008) "A VEGFR2 antagonist and other peptoids evade immune recognition"Intl. J. Peptide Res. & Therapeutics 14, 223-227.

Kodadek, T. (2008) "Molecular cloaking devices" Nature 453, 861-862.

Tan, N.C., Yu, P., Kwon, Y.-U. and Kodadek, T. (2008) "High-throughput evaluation of relative cell permeability between peptoids and peptides" Bioorg. Med. Chem. 16, 5853-5861.

Kodadek, T. (2008) "Proteomes take the electrophilic bait" Nature Chem. Biol. 4, 387-388.

Udugamasooriya, D.G., Ritchie, C., Brekken, R.A. and Kodadek, T. (2008) A Peptoid Antagonist of VEGF Receptor 2 Recognizes A "Hotspot" In the Extracellular Domain Distinct From The Hormone-Binding Site" Bioorg. & Med. Chem. 16, 6338-6343.

Hanaoka, K., Lubag, A.J.M., Castillo-Muzquiz, A., Kodadek, T. and Sherry, A.D. (2008) "The detection limit of a Gd3+-based T1 agent is substantially reduced when targeted to a protein microdomain" Mag. Res. Imaging 26, 608-617.

Udugamasooriya, D.G., Dineen, S.P., Brekken, R.A. and Kodadek, T. (2008) "A peptoid "antibody surrogate" that antagonizes VEGF Receptor 2 activity" J. Amer. Chem. Soc. 130, 5744-52.

Archer, C.T., Delahodde, A., Gonzalez, F., Johnston, S.A. and Kodadek, T. (2008) "Activation domain-dependent mono-ubiquitylation of Gal4 protein is essential for promoter binding in vivo" J. Biol. Chem. 283, 12614-12623.

Shores, K.S., Udugamasooriya, D.G., Kodadek, T. and Knapp, D.R. (2008) "Use of peptide analog diversity library beads for increased depth of proteomic analysis: Application to cerebrospinal fluid" J. Proteome Res. 7, 1922-1931.

Marthandan, N., Klyza, S., Li, S., Kodadek, T. and Garner, H.R. (2008) "Construction and evaluation of an automated light directed protein-detecting microarray synthesizer" IEEE Transactions in NanoBioscience 7, 20-27.

Lim, H.-S., Archer, C.T., Kim, Y.-C., Hutchens, T. and Kodadek, T. (2008) "Rapid identification of the pharmacophore in a peptoid inhibitor of the proteasome regulatory particle" Chem. Comm. 1064-1066.

Lee, J., Yu, P., Xiao, X. and Kodadek, T. (2008) "A General System for Evaluating the Efficiency of Chromophore-Assisted Light Inactivation (CALI) of Proteins Reveals Ru(II) tris-bipyridyl As An Unusually Efficient "Warhead" Molecular BioSystems 4, 59-65.

2007

Astle, J. Ferguson, JT. German, JB. Harrigan, GG. Kelleher, NL. Kodadek, T. Parks, BA. Roth, MJ. Singletary, KW. Wenger, CD. Mahady, G.B. (2007) "Characterization of proteomic and metabolomic responses to dietary factors and supplements" J. of Nutrition 137, 2787-2793.

Yu, P. and Kodadek, T. (2007) "Dynamics of the Hypoxia-Inducible Factor-1-VEGF promoter complex" J. Biol. Chem. 282, 35035 – 35045.

Lim, H.-S., Cai, D. and Kodadek, T. (2007) "Chemical cross-linking reveals Sug2/Rpt4 as the molecular target of a peptoid inhibitor of the 19S proteasome regulatory particle" J. Amer. Chem. Soc. 129, 12936-12937.

Sikder, D. and Kodadek, T. (2007) "The neurohormone orexin stimulates hypoxia-inducible factor-1 activity" Genes & Devel. 21, 2995-3005

Liu, B., Archer, C.T., Burdine, L., Gillette, T.G. and Kodadek, T. (2007) "Label transfer chemistry for the characterization of protein-protein interactions" J. Amer. Chem. Soc. 129, 12348-12349.

Kwon, Y.-U. and Kodadek, T. (2007) "Quantitative comparison of the relative cell permeability of cyclic and linear peptides" Chem. & Biol. 14, 671-677.

Lim, H.-Y., Archer, C.T. and Kodadek, T. (2007) "Identification of a peptoid inhibitor of the proteasome 19S regulatory particle" J. Amer. Chem. Soc. 129, 7750-7751.

Xiao, X., Yu, P., Lim, H.-Y., Sikder, S. and Kodadek, T. (2007) "Design and synthesis of a cell permeable transcription factor mimic" J. Comb. Chem. 9, 592-600.

Xiao, X., Yu, P., Lim, H.-S., Sikder, D. and Kodadek, T. (2007) "A cell permeable transcription factor mimic" Angew. Chem. Intl. Ed. 46, 2865-2868.

Yu, P. and Kodadek, T. (2007) "A convenient, high-throughput strategy for measuring the relative cell permeability of synthetic compounds" Nature Protocols 2, 23-30.

Kwon, Y.-U. and Kodadek, T. (2007) "Quantitative evaluation of the relative cell permeability of peptoids and peptides"J. Amer. Chem. Soc. 129, 1508-1509.

Ferdous, A., Sikder, D., Gillette, T., Nalley, K., Kodadek, T. and Johnston, S.A. (2007) "The Role of the Proteasomal ATPases and Activator Mono-Ubiquitylation in Regulating Gal4 Binding to Promoters" Genes & Dev. 21, 112-123.

2006

Liu, B., Burdine, L. and Kodadek, T. (2006) "Chemistry of periodate-mediated cross-linking of 3,4-dihydroxyphenlalanine (DOPA)-containing molecules to proteins" J. Amer. Chem. Soc. 128, 15228-15235.

Page, T., Sikder, D. Yang, L. Pluta, L., Wolfinger, R.D., Kodadek, T. and Thomas, R.S. (2006) Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival" Molecular BioSystems 2, 627-639.

Kodadek, T., Sikder, D. and Nalley, K. (2006) "Keeping transcriptional activators under control" Cell 127, 261-264.

Sikder, D., Johnston, S.A. and Kodadek, T. (2006) "Widespread, but non-identical, association of proteasomal 19S and 20S proteins with yeast chromatin" J. Biol. Chem. 281, 27346-27355.

Nalley, K., Johnston, S.A. and Kodadek, T. (2006) "Proteolytic turnover of Gal4 is not required for function in vivo" Nature, 442, 1054-1057.

Alluri, P., Liu, B., Yu, P., Xiao, X. and Kodadek, T. (2006) "isolation and chearacterization of coactivator-binding peptoids from a combinatorial library" Molecular Biosystems 2, 568-579.

Sulahian, R., Sikder, D., Johnston, S.A. and Kodadek, T. (2006) "The Proteasomal ATPase Complex Is Required For Stressed-Induced Trasncription in Yeast" Nucl. Acids Res. 34, 1351-1357.

Sikder, K. and Kodadek, T. (2006) "Optimized protocols for the isolation of specific protein-binding peptides or peptoids from combinatorial libraries displayed on beads" Molecular BioSystems 2, 25-35.

2005

Archer, C., Burdine, L. and Kodadek, T. (2005) "Identification of Gal4 transactivation domain binding proteins in the 26S proteasome by perioddate-triggered cross-linking" Molecular BioSystems 1, 366-372.

Liu, B., Yu, P., Alluri, P.G. and Kodadek, T. (2005) "Simple reporter gene-based assays for hairpin polyamide conjugate permeability and DNA-binding activity in living cells" Molecular BioSystems 1, 307-317.

Reddy, M.M. and Kodadek, T. (2005) "Protein 'fingerprinting' in complex mixtures using peptoid microarrays" Proc. Natl. Acad. Sci. USA 102, 12672-12677.

Liu, B., Alluri, P., Yu, P. and Kodadek, T. (2005) "A KIX-binding peptoid functions as a transactivation domain in mammalian cells" J. Amer. Chem. Soc. 127, 8254-8255.

Yu, P., Liu, B. and Kodadek, T. (2005) "A high-throughput assay for assessing the cell permeability of combinatorial libraries" Nature Biotechnol. 23, 746-751.

Li, S., Marthandan, N., Bowerman, D., Garner, H.R. and Kodadek, T. (2005) Photolithographic synthesis of cyclic peptide arrays using a differential deprotection strategy" Chem. Comm., 581-583.

2004

Gillette, T., Gonzalez, F.G., Delahodde, A., Johnston, S.A. and Kodadek, T. (2004) "Physical and Functional Association of RNA Polymerase II and the Proteasome" Proc. Natl. Acad. Sci. USA 101, 5904-5909.

2002

Gonzalez, F., Delahoude, A., Kodadek, T. and Johnston, S.A. (2002)" A sub-complex of the 19S proteasome regulatory complex is recruited to an activated promoter" Science, 296, 548-550.

2001

Ferdous, A., Gonzalez, F., Sun, L., Kodadek, T. and Johnston, S.A. (2001) "The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II" Mol. Cell 7, 981-991.