Thomas Kodadek

Thomas Kodadek, Ph.D.

Professor Of Chemistry

Department: SR-CHEM-KODADEK LAB
Business Phone: (561) 228-2461
Business Email: kodadek@ufl.edu

About Thomas Kodadek

Accomplishments

Co-Founder
2022 · Triana Biosciences
Co-Founder
2017 · Deluge Biotechnologies
Makineni Award
2017 · American Peptide Society
Cope Scholar Award
2016 · American Chemical Society
Chemical Biology Faculty Member of the Year
2007 · Faculty of 1000
Pioneer Award
2006 · NIH
Elected Fellow
1999 · American Association for the Advancement of Science
Junior Faculty Research Award
1991 · American Cancer Society
Post-doctoral Fellowship
1985 · Jane Coffin Childs Foundation

Research Profile

The Kodadek laboratory works in the general area of chemical biology with an emphasis on translational research. The laboratory employs a broad spectrum of techniques that span organic chemistry to molecular genetics. Recently, significant effort has been focused on the development of novel strategies to tackle the “undraggable” proteome. We have developed DNA-encoded libraries of non-peptidic macrocycles and other novel molecular species that we believe will be better suitable to engage difficult protein targets than traditional drug candidates. We are also developing novel techniques to screen these libraries for molecules with novel functions, for example the ability to recruit to target proteins post-translational modifying enzymes that alter the levels or activity of the target.

Another focus is to use the chemical tools we have developed to monitor and manipulate the immune system. One goal of these efforts is to discover effective and early diagnostic tests for a variety of disease states, including cancers, autoimmune diseases and neurodegenerative conditions. Another is to identify compounds that act as “antigen surrogates” in that they have the ability to recognize the antigen-binding sites of antibodies and T cell receptors. These compounds are being developed as potential therapeutic agents to block autoimmune responses selectively without interfering with normal functions of the immune system.

Open Researcher and Contributor ID (ORCID)

0000-0003-1930-4795

Publications

2022
Applications and Limitations of Oxime‐Linked “Split PROTACs”
ChemBioChem. 23(18) [DOI] 10.1002/cbic.202200275. [PMID] 35802347.
2022
Synthesis and Screening of a DNA‐Encoded Library of Non‐Peptidic Macrocycles**
Angewandte Chemie International Edition. 61(18) [DOI] 10.1002/anie.202116999. [PMID] 35192245.
2022
Synthesis and Screening of a DNA‐Encoded Library of Non‐Peptidic Macrocycles**
Angewandte Chemie. 134(18) [DOI] 10.1002/ange.202116999.
2021
High‐Throughput Quality Control Assay for the Solid‐Phase Synthesis of DNA‐Encoded Libraries of Macrocycles**
Angewandte Chemie International Edition. 60(21):11983-11990 [DOI] 10.1002/anie.202100230. [PMID] 33682283.
2021
High‐Throughput Quality Control Assay for the Solid‐Phase Synthesis of DNA‐Encoded Libraries of Macrocycles**
Angewandte Chemie. 133(21):12090-12097 [DOI] 10.1002/ange.202100230.
2020
DELs Inside Cells.
Trends in pharmacological sciences. 41(4):225-227 [DOI] 10.1016/j.tips.2020.01.007. [PMID] 32033772.
2020
Mechanistic Studies of the Multiple Myeloma and Melanoma Cell-Selective Toxicity of the Rpn13-Binding Peptoid KDT-11.
Cell chemical biology. 27(11):1383-1395.e5 [DOI] 10.1016/j.chembiol.2020.08.008. [PMID] 32857986.
2020
Physical and Functional Analysis of the Putative Rpn13 Inhibitor RA190.
Cell chemical biology. 27(11):1371-1382.e6 [DOI] 10.1016/j.chembiol.2020.08.007. [PMID] 32857985.
2020
Solid-phase synthesis of DNA-encoded libraries via an “aldehyde explosion” strategy
Chemical Communications. 56(34):4656-4659 [DOI] 10.1039/d0cc01474e. [PMID] 32215395.
2020
Structural characterization of a peptoid-inspired conformationally constrained oligomer (PICCO) bound to streptavidin
Chemical Communications. 56(72):10560-10563 [DOI] 10.1039/d0cc02588g. [PMID] 32785302.
2019
Beyond protein binding: recent advances in screening DNA-encoded libraries
Chemical Communications. 55(89):13330-13341 [DOI] 10.1039/c9cc06256d. [PMID] 31633708.
2019
Chemical composition of DNA-encoded libraries, past present and future
Organic & Biomolecular Chemistry. 17(19):4676-4688 [DOI] 10.1039/c9ob00581a. [PMID] 31017595.
2019
Sweetening the Therapeutic Pot for Type 2 Diabetes with Long Noncoding RNAs.
Cell chemical biology. 26(3):311-313 [DOI] 10.1016/j.chembiol.2019.02.022. [PMID] 30901557.
2019
Synthesis and screening of bead-displayed combinatorial libraries.
Methods in enzymology. 622:91-127 [DOI] 10.1016/bs.mie.2019.02.005. [PMID] 31155067.
2018
A “Smart Lock” for Preventing Hepatitis B Entry into Cells.
Cell chemical biology. 25(7):804-806 [DOI] 10.1016/j.chembiol.2018.06.011. [PMID] 30028974.
2018
Another One (of the “Undruggable” Targets) Bites the Dust: Discovery of a Potent and Selective Inhibitor of the Histone Acetyl Transferase p300/CBP
Biochemistry. 57(6):899-900 [DOI] 10.1021/acs.biochem.7b01179.
2018
Antibody biomarker for de novo Parkinson disease: attempted validation.
NPJ Parkinson's disease. 4 [DOI] 10.1038/s41531-018-0064-2. [PMID] 30211310.
2018
DNA-Compatible Solid-Phase Combinatorial Synthesis of β-Cyanoacrylamides and Related Electrophiles
ACS Combinatorial Science. 20(2):61-69 [DOI] 10.1021/acscombsci.7b00169. [PMID] 29298042.
2018
Screening one bead one compound libraries against serum using a flow cytometer: Determination of the minimum antibody concentration required for ligand discovery.
Bioorganic & medicinal chemistry letters. 28(16):2773-2778 [DOI] 10.1016/j.bmcl.2018.01.033. [PMID] 29395976.
2018
Solid-Phase Synthesis of β-Amino Ketones Via DNA-Compatible Organocatalytic Mannich Reactions
ACS Combinatorial Science. 20(2):55-60 [DOI] 10.1021/acscombsci.7b00151. [PMID] 29316387.
2018
Solid-Phase Synthesis of β-Hydroxy Ketones Via DNA-Compatible Organocatalytic Aldol Reactions
ACS Combinatorial Science. 20(5):277-281 [DOI] 10.1021/acscombsci.8b00001. [PMID] 29578681.
2017
Asymmetric synthesis of vinylogous β-amino acids and their incorporation into mixed backbone oligomers
Organic & Biomolecular Chemistry. 15(15):3255-3264 [DOI] 10.1039/c7ob00333a. [PMID] 28346549.
2017
Establishment of a suite of assays that support the discovery of proteasome stimulators
Biochimica et Biophysica Acta (BBA) – General Subjects. 1861(4):892-899 [DOI] 10.1016/j.bbagen.2017.01.003. [PMID] 28065760.
2017
Global analysis of gene expression mediated by OX1 orexin receptor signaling in a hypothalamic cell line
PLOS ONE. 12(11) [DOI] 10.1371/journal.pone.0188082. [PMID] 29145494.
2017
High-throughput Identification of DNA-Encoded IgG Ligands that Distinguish Active and Latent Mycobacterium tuberculosis Infections
ACS Chemical Biology. 12(1):234-243 [DOI] 10.1021/acschembio.6b00855. [PMID] 27957856.
2016
BRD4 Phosphorylation Regulates HPV E2-Mediated Viral Transcription, Origin Replication, and Cellular MMP-9 Expression.
Cell reports. 16(6):1733-1748 [DOI] 10.1016/j.celrep.2016.07.001. [PMID] 27477287.
2016
Cell-Permeable Peptides Containing Cycloalanine Residues
Angewandte Chemie International Edition. 55(41):12637-12642 [DOI] 10.1002/anie.201605745. [PMID] 27529332.
2016
Cell-Permeable Peptides Containing Cycloalanine Residues
Angewandte Chemie. 128(41):12827-12832 [DOI] 10.1002/ange.201605745.
2016
Chemical Tools To Monitor and Manipulate Adaptive Immune Responses.
Journal of the American Chemical Society. 138(19):6076-94 [DOI] 10.1021/jacs.6b02954. [PMID] 27115249.
2016
Discovery of Phosphorylated Peripherin as a Major Humoral Autoantigen in Type 1 Diabetes Mellitus.
Cell chemical biology. 23(5):618-628 [DOI] 10.1016/j.chembiol.2016.04.006. [PMID] 27185639.
2016
Identification of selective covalent inhibitors of platelet activating factor acetylhydrolase 1B2 from the screening of an oxadiazolone-capped peptoid-azapeptoid hybrid library.
Bioorganic & medicinal chemistry. 24(17):3953-3963 [DOI] 10.1016/j.bmc.2016.04.047. [PMID] 27160052.
2016
Selection of a potential diagnostic biomarker for HIV infection from a random library of non-biological synthetic peptoid oligomers.
Journal of immunological methods. 435:85-9 [DOI] 10.1016/j.jim.2016.05.001. [PMID] 27182050.
2016
Targeting Stereotyped B Cell Receptors from Chronic Lymphocytic Leukemia Patients with Synthetic Antigen Surrogates.
The Journal of biological chemistry. 291(14):7558-70 [DOI] 10.1074/jbc.M115.701656. [PMID] 26851280.
2016
The Immune System and Neuroinflammation as Potential Sources of Blood-Based Biomarkers for Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease.
ACS chemical neuroscience. 7(5):520-7 [DOI] 10.1021/acschemneuro.6b00042. [PMID] 27046268.
2016
Towards vast libraries of scaffold-diverse, conformationally constrained oligomers.
Chemical communications (Cambridge, England). 52(36):6038-59 [DOI] 10.1039/c6cc00617e. [PMID] 26996593.
2015
A reversible and highly selective inhibitor of the proteasomal ubiquitin receptor rpn13 is toxic to multiple myeloma cells.
Journal of the American Chemical Society. 137(19):6312-9 [DOI] 10.1021/jacs.5b02069. [PMID] 25914958.
2015
And then there were two.
eLife. 4 [DOI] 10.7554/eLife.12724. [PMID] 26716612.
2015
Direct comparison of linear and macrocyclic compound libraries as a source of protein ligands.
ACS combinatorial science. 17(3):190-5 [DOI] 10.1021/co500161c. [PMID] 25623285.
2015
Discovery of native autoantigens via antigen surrogate technology: application to type 1 diabetes.
ACS chemical biology. 10(2):401-12 [DOI] 10.1021/cb5007618. [PMID] 25474415.
2015
Editorial overview: Omics: Methods to monitor and manipulate biological systems: recent advances in ‘omics’.
Current opinion in chemical biology. 24:v-vii [DOI] 10.1016/j.cbpa.2014.12.023. [PMID] 25549533.
2015
High affinity binding of conformationally constrained synthetic oligomers to an antigen-specific antibody: Discovery of a diagnostically useful synthetic ligand for murine Type 1 diabetes autoantibodies.
Bioorganic & medicinal chemistry letters. 25(21):4910-4917 [DOI] 10.1016/j.bmcl.2015.05.046. [PMID] 26067174.
2015
Optimization of the Magnetic Recovery of Hits from One-Bead-One-Compound Library Screens.
ACS combinatorial science. 17(9):506-17 [DOI] 10.1021/acscombsci.5b00090. [PMID] 26221913.
2015
Rapid lead discovery through iterative screening of one bead one compound libraries.
ACS combinatorial science. 17(1):49-59 [DOI] 10.1021/co500154e. [PMID] 25434974.
2015
Reliable diagnosis of murine type 1 diabetes using a panel of autoantigens and “antigen surrogates” mounted onto a liquid array.
Molecular bioSystems. 11(11):3156-63 [DOI] 10.1039/c5mb00521c. [PMID] 26390856.
2015
Site-Specific Dual Antibody Conjugation via Engineered Cysteine and Selenocysteine Residues.
Bioconjugate chemistry. 26(11):2243-8 [DOI] 10.1021/acs.bioconjchem.5b00244. [PMID] 26161903.
2015
Solid phase synthesis of 1,3,4-oxadiazin-5 (6R)-one and 1,3,4-oxadiazol-2-one scaffolds from acyl hydrazides.
Organic & biomolecular chemistry. 13(1):59-63 [DOI] 10.1039/c4ob01883d. [PMID] 25354697.
2015
Solid-phase synthesis of diverse peptide tertiary amides by reductive amination.
ACS combinatorial science. 17(3):152-5 [DOI] 10.1021/acscombsci.5b00007. [PMID] 25695359.
2015
Synthesis of a large library of macrocyclic peptides containing multiple and diverse N-alkylated residues.
Molecular bioSystems. 11(10):2770-9 [DOI] 10.1039/c5mb00308c. [PMID] 26067000.
2014
A liquid array platform for the multiplexed analysis of synthetic molecule-protein interactions.
ACS chemical biology. 9(2):339-46 [DOI] 10.1021/cb400806r. [PMID] 24245981.
2014
Chemical tools to monitor and manipulate the adaptive immune system.
Chemistry & biology. 21(9):1066-74 [DOI] 10.1016/j.chembiol.2014.07.009. [PMID] 25237855.
2014
Dextran as a generally applicable multivalent scaffold for improving immunoglobulin-binding affinities of peptide and peptidomimetic ligands.
Bioconjugate chemistry. 25(8):1479-91 [DOI] 10.1021/bc500226j. [PMID] 25073654.
2014
Discovery of biomarkers for systemic lupus erythematosus using a library of synthetic autoantigen surrogates.
Journal of immunological methods. 402(1-2):23-34 [DOI] 10.1016/j.jim.2013.11.004. [PMID] 24269750.
2014
Recognition of antigen-specific B-cell receptors from chronic lymphocytic leukemia patients by synthetic antigen surrogates.
Chemistry & biology. 21(12):1670-9 [DOI] 10.1016/j.chembiol.2014.10.010. [PMID] 25467125.
2014
Roadblocks for integration of novel biomarker concepts into clinical routine: the peptoid approach.
Alzheimer's research & therapy. 6(2) [DOI] 10.1186/alzrt253. [PMID] 25031636.
2014
Solid-phase synthesis of peptoid-like oligomers containing diverse diketopiperazine units.
Organic & biomolecular chemistry. 12(31):5831-4 [DOI] 10.1039/c4ob00829d. [PMID] 24976298.
2014
Split-and-pool synthesis and characterization of peptide tertiary amide library.
Journal of visualized experiments : JoVE. (88) [DOI] 10.3791/51299. [PMID] 24998250.
2014
Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits.
ACS combinatorial science. 16(6):259-70 [DOI] 10.1021/co500030f. [PMID] 24749624.
2013
A jack of all trades to combat drug-resistant Gram-negative bacteria.
Chemistry & biology. 20(10):1202-3 [DOI] 10.1016/j.chembiol.2013.10.006. [PMID] 24210003.
2013
Advances in blood-based protein biomarkers for Alzheimer’s disease.
Alzheimer's research & therapy. 5(3) [DOI] 10.1186/alzrt172. [PMID] 23659521.
2013
Decoding split and pool combinatorial libraries with electron-transfer dissociation tandem mass spectrometry.
Journal of the American Society for Mass Spectrometry. 24(7):1026-36 [DOI] 10.1007/s13361-013-0633-x. [PMID] 23636859.
2013
Discovery of peptoid ligands for anti-aquaporin 4 antibodies.
Chemistry & biology. 20(3):351-9 [DOI] 10.1016/j.chembiol.2012.12.009. [PMID] 23521793.
2013
Features of modularly assembled compounds that impart bioactivity against an RNA target.
ACS chemical biology. 8(10):2312-21 [DOI] 10.1021/cb400265y. [PMID] 24032410.
2013
Synthesis and screening of stereochemically diverse combinatorial libraries of peptide tertiary amides.
Chemistry & biology. 20(3):360-9 [DOI] 10.1016/j.chembiol.2013.01.013. [PMID] 23521794.
2013
Synthesis of libraries of peptidomimetic compounds containing a 2-oxopiperazine unit in the main chain.
Organic & biomolecular chemistry. 11(13):2088-92 [DOI] 10.1039/c3ob27476d. [PMID] 23440085.
2012
A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry.
Tetrahedron letters. 53(18):2341-2344 [PMID] 22736872.
2012
Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries.
ACS combinatorial science. 14(3):164-9 [DOI] 10.1021/co200195t. [PMID] 22320121.
2012
On-Bead Two-Color (OBTC) Cell Screen for Direct Identification of Highly Selective Cell Surface Receptor Ligands.
Current protocols in chemical biology. 4:35-48 [PMID] 22582145.
2012
Rapid development of a potent photo-triggered inhibitor of the serine hydrolase RBBP9.
Chembiochem : a European journal of chemical biology. 13(14):2082-93 [DOI] 10.1002/cbic.201200445. [PMID] 22907802.
2012
Submonomer synthesis of a hybrid peptoid-azapeptoid library.
ACS combinatorial science. 14(10):558-64 [DOI] 10.1021/co3000852. [PMID] 22958123.
2011
A biomimetic polyketide-inspired approach to small-molecule ligand discovery.
Nature chemistry. 4(2):99-104 [DOI] 10.1038/nchem.1200. [PMID] 22270625.
2011
Acyl hydrazides as peptoid sub-monomers.
Chemical communications (Cambridge, England). 47(38):10590-2 [DOI] 10.1039/c1cc12750k. [PMID] 21892506.
2011
Expanded polyglutamine-binding peptoid as a novel therapeutic agent for treatment of Huntington’s disease.
Chemistry & biology. 18(9):1113-25 [DOI] 10.1016/j.chembiol.2011.06.010. [PMID] 21944750.
2011
Identification of candidate IgG biomarkers for Alzheimer’s disease via combinatorial library screening.
Cell. 144(1):132-42 [DOI] 10.1016/j.cell.2010.11.054. [PMID] 21215375.
2011
PDZ dimerization brings proteins together.
Chemistry & biology. 18(9):1071-2 [DOI] 10.1016/j.chembiol.2011.09.001. [PMID] 21944744.
2011
Peptoid ligands that bind selectively to phosphoproteins.
Bioorganic & medicinal chemistry letters. 21(17):4960-4 [DOI] 10.1016/j.bmcl.2011.06.011. [PMID] 21742492.
2011
The rise, fall and reinvention of combinatorial chemistry.
Chemical communications (Cambridge, England). 47(35):9757-63 [DOI] 10.1039/c1cc12102b. [PMID] 21701754.
2010
Chemistry and biology of orexin signaling.
Molecular bioSystems. 6(8):1366-75 [DOI] 10.1039/c003468a. [PMID] 20532299.
2010
Development of antibody surrogates for the treatment of cancers and autoimmune disease.
Current opinion in chemical biology. 14(6):721-7 [DOI] 10.1016/j.cbpa.2010.07.002. [PMID] 20674470.
2010
Discovery Of An Orexin Receptor Positive Potentiator.
Chemical science. 1(1) [DOI] 10.1039/C0SC00197J. [PMID] 24409338.
2010
GU81, a VEGFR2 antagonist peptoid, enhances the anti-tumor activity of doxorubicin in the murine MMTV-PyMT transgenic model of breast cancer.
BMC cancer. 10 [DOI] 10.1186/1471-2407-10-397. [PMID] 20673348.
2010
MRI detection of VEGFR2 in vivo using a low molecular weight peptoid-(Gd)8-dendron for targeting.
Journal of the American Chemical Society. 132(37):12829-31 [DOI] 10.1021/ja105563a. [PMID] 20795620.
2010
No Splicing, no dicing: non-proteolytic roles of the ubiquitin-proteasome system in transcription.
The Journal of biological chemistry. 285(4):2221-6 [DOI] 10.1074/jbc.R109.077883. [PMID] 19955182.
2010
Potent and selective photo-inactivation of proteins with peptoid-ruthenium conjugates.
Nature chemical biology. 6(4):258-60 [DOI] 10.1038/nchembio.333. [PMID] 20228793.
2010
Rapid identification of orexin receptor binding ligands using cell-based screening accelerated with magnetic beads.
Molecular bioSystems. 6(1):102-7 [DOI] 10.1039/b915611a. [PMID] 20024071.
2010
Rethinking screening.
Nature chemical biology. 6(3):162-165 [PMID] 20154660.
2010
Seamless bead to microarray screening: rapid identification of the highest affinity protein ligands from large combinatorial libraries.
Chemistry & biology. 17(1):38-45 [DOI] 10.1016/j.chembiol.2009.12.015. [PMID] 20142039.
2010
Steroid receptor coactivator-3 expression in lung cancer and its role in the regulation of cancer cell survival and proliferation.
Cancer research. 70(16):6477-85 [DOI] 10.1158/0008-5472.CAN-10-0005. [PMID] 20663904.
2010
Synthetic receptors with antibody-like binding affinities.
Current opinion in chemical biology. 14(6):713-20 [DOI] 10.1016/j.cbpa.2010.07.001. [PMID] 20674471.
2010
The hydrophobic patch of ubiquitin is required to protect transactivator-promoter complexes from destabilization by the proteasomal ATPases.
Nucleic acids research. 38(3):789-96 [DOI] 10.1093/nar/gkp1066. [PMID] 19939937.
2010
The interface of chemical biology and the nervous system (related to the NIDA Chemical Genomics Symposium).
Molecular bioSystems. 6(8) [DOI] 10.1039/c0mb90009e. [PMID] 20582378.
2009
Genome-wide analysis of chromatin regulation by cocaine reveals a role for sirtuins.
Neuron. 62(3):335-48 [DOI] 10.1016/j.neuron.2009.03.026. [PMID] 19447090.
2009
Imipramine treatment and resiliency exhibit similar chromatin regulation in the mouse nucleus accumbens in depression models.
The Journal of neuroscience : the official journal of the Society for Neuroscience. 29(24):7820-32 [DOI] 10.1523/JNEUROSCI.0932-09.2009. [PMID] 19535594.
2009
Investigation of the relative cellular permeability of DNA-binding pyrrole-imidazole polyamides.
Journal of medicinal chemistry. 52(15):4604-12 [DOI] 10.1021/jm9002999. [PMID] 19610652.
2009
Isolation of antagonists of antigen-specific autoimmune T cell proliferation.
Chemistry & biology. 16(11):1133-9 [DOI] 10.1016/j.chembiol.2009.10.011. [PMID] 19942136.
2009
Non-proteolytic regulation of p53-mediated transcription through destabilization of the activator.promoter complex by the proteasomal ATPases.
The Journal of biological chemistry. 284(50):34522-30 [DOI] 10.1074/jbc.M109.017277. [PMID] 19846554.
2009
Peptoids as potential therapeutics.
Current opinion in molecular therapeutics. 11(3):299-307 [PMID] 19479663.
2009
Protein binding: Antibody surrogates click into place.
Nature chemistry. 1(3):183-5 [DOI] 10.1038/nchem.228. [PMID] 21378844.
2009
Rapid identification of improved protein ligands using peptoid microarrays.
Bioorganic & medicinal chemistry letters. 19(14):3866-9 [DOI] 10.1016/j.bmcl.2009.03.153. [PMID] 19380225.
2009
Selective toxin sequestrants for the treatment of bacterial infections.
Journal of the American Chemical Society. 131(16):5760-2 [DOI] 10.1021/ja900852k. [PMID] 19351156.
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(1):59-65 [PMID] 18075676.
2008
A peptoid “antibody surrogate” that antagonizes VEGF receptor 2 activity.
Journal of the American Chemical Society. 130(17):5744-52 [DOI] 10.1021/ja711193x. [PMID] 18386897.
2008
A peptoid antagonist of VEGF receptor 2 recognizes a ‘hotspot’ in the extracellular domain distinct from the hormone-binding site.
Bioorganic & medicinal chemistry. 16(12):6338-43 [DOI] 10.1016/j.bmc.2008.05.015. [PMID] 18501615.
2008
Activation domain-dependent monoubiquitylation of Gal4 protein is essential for promoter binding in vivo.
The Journal of biological chemistry. 283(18):12614-23 [DOI] 10.1074/jbc.M801050200. [PMID] 18326036.
2008
Biochemistry: Molecular cloaking devices.
Nature. 453(7197):861-2 [DOI] 10.1038/453861a. [PMID] 18548057.
2008
Construction and evaluation of an automated light directed protein-detecting microarray synthesizer.
IEEE transactions on nanobioscience. 7(1):20-7 [DOI] 10.1109/TNB.2008.2000146. [PMID] 18334452.
2008
Encoded combinatorial libraries for the construction of cyclic peptoid microarrays.
Chemical communications (Cambridge, England). (44):5704-6 [DOI] 10.1039/b812735b. [PMID] 19009054.
2008
High-throughput evaluation of relative cell permeability between peptoids and peptides.
Bioorganic & medicinal chemistry. 16(11):5853-61 [DOI] 10.1016/j.bmc.2008.04.074. [PMID] 18490170.
2008
Phosphorylation of the Gal4 DNA-binding domain is essential for activator mono-ubiquitylation and efficient promoter occupancy.
Molecular bioSystems. 4(11):1116-25 [DOI] 10.1039/b809291e. [PMID] 18931787.
2008
Physical and functional interactions of monoubiquitylated transactivators with the proteasome.
The Journal of biological chemistry. 283(31):21789-98 [DOI] 10.1074/jbc.M803075200. [PMID] 18515799.
2008
Proteomes take the electrophilic bait.
Nature chemical biology. 4(7):387-8 [DOI] 10.1038/nchembio0708-387. [PMID] 18560426.
2008
Rapid identification of the pharmacophore in a peptoid inhibitor of the proteasome regulatory particle.
Chemical communications (Cambridge, England). (9):1064-6 [DOI] 10.1039/b717861a. [PMID] 18292891.
2008
Rise of the machines: Bruce Alberts and the biochemistry of multi-protein complexes.
Molecular bioSystems. 4(11):1043-5 [DOI] 10.1039/b815439b. [PMID] 18931779.
2008
The detection limit of a Gd3+-based T1 agent is substantially reduced when targeted to a protein microdomain.
Magnetic resonance imaging. 26(5):608-17 [DOI] 10.1016/j.mri.2007.11.002. [PMID] 18234462.
2008
The pharmacophore of a peptoid VEGF receptor 2 antagonist includes both side chain and main chain residues.
Bioorganic & medicinal chemistry letters. 18(22):5892-4 [DOI] 10.1016/j.bmcl.2008.07.023. [PMID] 18653335.
2008
Use of peptide analogue diversity library beads for increased depth of proteomic analysis: application to cerebrospinal fluid.
Journal of proteome research. 7(5):1922-31 [DOI] 10.1021/pr7006889. [PMID] 18357977.
2007
A cell-permeable synthetic transcription factor mimic.
Angewandte Chemie (International ed. in English). 46(16):2865-8 [PMID] 17351994.
2007
A convenient, high-throughput assay for measuring the relative cell permeability of synthetic compounds.
Nature protocols. 2(1):23-30 [PMID] 17401333.
2007
Characterization of proteomic and metabolomic responses to dietary factors and supplements.
The Journal of nutrition. 137(12):2787-93 [PMID] 18029500.
2007
Design and synthesis of a cell-permeable synthetic transcription factor mimic.
Journal of combinatorial chemistry. 9(4):592-600 [PMID] 17530904.
2007
Dynamics of the hypoxia-inducible factor-1-vascular endothelial growth factor promoter complex.
The Journal of biological chemistry. 282(48):35035-45 [PMID] 17916562.
2007
Identification of a peptoid inhibitor of the proteasome 19S regulatory particle.
Journal of the American Chemical Society. 129(25):7750-1 [PMID] 17536803.
2007
Label transfer chemistry for the characterization of protein-protein interactions.
Journal of the American Chemical Society. 129(41):12348-9 [PMID] 17894490.
2007
Periodate-triggered cross-linking reveals Sug2/Rpt4 as the molecular target of a peptoid inhibitor of the 19S proteasome regulatory particle.
Journal of the American Chemical Society. 129(43):12936-7 [PMID] 17929816.
2007
Quantitative comparison of the relative cell permeability of cyclic and linear peptides.
Chemistry & biology. 14(6):671-7 [PMID] 17584614.
2007
Quantitative evaluation of the relative cell permeability of peptoids and peptides.
Journal of the American Chemical Society. 129(6):1508-9 [PMID] 17283989.
2007
The neurohormone orexin stimulates hypoxia-inducible factor-1 activity.
Genes & development. 21(22):2995-3005 [PMID] 18006690.
2007
The role of the proteasomal ATPases and activator monoubiquitylation in regulating Gal4 binding to promoters.
Genes & development. 21(1):112-23 [PMID] 17167105.
2006
Chemistry of periodate-mediated cross-linking of 3,4-dihydroxylphenylalanine-containing molecules to proteins.
Journal of the American Chemical Society. 128(47):15228-35 [PMID] 17117875.
2006
Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival.
Molecular bioSystems. 2(12):627-39 [PMID] 17216044.
2006
Introduction to monitoring and manipulating signaling networks.
Molecular bioSystems. 2(12):603-4 [PMID] 17216040.
2006
Isolation and characterization of coactivator-binding peptoids from a combinatorial library.
Molecular bioSystems. 2(11):568-79 [PMID] 17216038.
2006
Keeping transcriptional activators under control.
Cell. 127(2):261-4 [PMID] 17055428.
2006
Optimized protocols for the isolation of specific protein-binding peptides or peptoids from combinatorial libraries displayed on beads.
Molecular bioSystems. 2(1):25-35 [PMID] 16880920.
2006
Proteolytic turnover of the Gal4 transcription factor is not required for function in vivo.
Nature. 442(7106):1054-7 [PMID] 16929306.
2006
The proteasomal ATPase complex is required for stress-induced transcription in yeast.
Nucleic acids research. 34(5):1351-7 [PMID] 16517940.
2006
Widespread, but non-identical, association of proteasomal 19 and 20 S proteins with yeast chromatin.
The Journal of biological chemistry. 281(37):27346-55 [PMID] 16837462.
2005
A high-throughput assay for assessing the cell permeability of combinatorial libraries.
Nature biotechnology. 23(6):746-51 [PMID] 15908941.
2005
A potent transactivation domain mimic with activity in living cells.
Journal of the American Chemical Society. 127(23):8254-5 [PMID] 15941237.
2005
Genomic studies of transcription factor-DNA interactions.
Current opinion in chemical biology. 9(1):38-45 [PMID] 15701451.
2005
Identification of Gal4 activation domain-binding proteins in the 26S proteasome by periodate-triggered cross-linking.
Molecular bioSystems. 1(5-6):366-72 [PMID] 16881005.
2005
NMR analyses of the activation of the Arp2/3 complex by neuronal Wiskott-Aldrich syndrome protein.
Biochemistry. 44(46):15247-56 [PMID] 16285728.
2005
Photo-induced oxidative cross-linking as a method to evaluate the specificity of protein-ligand interactions.
The journal of peptide research : official journal of the American Peptide Society. 65(2):221-8 [PMID] 15705166.
2005
Photolithographic synthesis of cyclic peptide arrays using a differential deprotection strategy.
Chemical communications (Cambridge, England). (5):581-3 [PMID] 15672142.
2005
Protein “fingerprinting” in complex mixtures with peptoid microarrays.
Proceedings of the National Academy of Sciences of the United States of America. 102(36):12672-7 [PMID] 16123137.
2005
Simple reporter gene-based assays for hairpin poly(amide) conjugate permeability and DNA-binding activity in living cells.
Molecular bioSystems. 1(4):307-17 [PMID] 16880996.
2005
Techniques: Oxidative cross-linking as an emergent tool for the analysis of receptor-mediated signalling events.
Trends in pharmacological sciences. 26(4):210-7 [PMID] 15808346.
2004
Peptides as modulators of enzymes and regulatory proteins.
Methods (San Diego, Calif.). 32(4):406-15 [PMID] 15003603.
2004
Periodate-triggered cross-linking of DOPA-containing peptide-protein complexes.
Journal of the American Chemical Society. 126(37):11442-3 [PMID] 15366882.
2004
Photolithographic synthesis of peptoids.
Journal of the American Chemical Society. 126(13):4088-9 [PMID] 15053581.
2004
Physical and functional association of RNA polymerase II and the proteasome.
Proceedings of the National Academy of Sciences of the United States of America. 101(16):5904-9 [PMID] 15069196.
2004
Synthetic molecules as antibody replacements.
Accounts of chemical research. 37(9):711-8 [PMID] 15379586.
2004
Target identification in chemical genetics: the (often) missing link.
Chemistry & biology. 11(5):593-7 [PMID] 15157870.
2004
The potential of protein-detecting microarrays for clinical diagnostics.
Advances in clinical chemistry. 38:217-38 [PMID] 15521193.
2004
Toward a general chemical method for rapidly mapping multi-protein complexes.
Journal of proteome research. 3(3):417-25 [PMID] 15253422.
2004
Transformation of low-affinity lead compounds into high-affinity protein capture agents.
Chemistry & biology. 11(8):1127-37 [PMID] 15324814.
2003
Immobilized peptides as high-affinity capture agents for self-associating proteins.
Chemistry & biology. 10(3):251-9 [PMID] 12670539.
2003
Isolation of protein ligands from large peptoid libraries.
Journal of the American Chemical Society. 125(46):13995-4004 [PMID] 14611236.
2003
Mixed-element capture agents: a simple strategy for the construction of synthetic, high-affinity protein capture ligands.
Journal of the American Chemical Society. 125(32):9550-1 [PMID] 12903996.
2003
Quantum dots as a visual aid for screening bead-bound combinatorial libraries.
Chembiochem : a European journal of chemical biology. 4(11):1242-5 [PMID] 14613120.
2003
Transcription activation by a PNA-peptide chimera in a mammalian cell extract.
Chemistry & biology. 10(10):909-16 [PMID] 14583257.
2003
Using oxidative crosslinking and proximity labeling to quantitatively characterize protein-protein and protein-Peptide complexes.
Chemistry & biology. 10(11):1115-27 [PMID] 14652079.
2002
A nonproteolytic function of the 19S regulatory subunit of the 26S proteasome is required for efficient activated transcription by human RNA polymerase II.
Biochemistry. 41(42):12798-805 [PMID] 12379122.
2002
Development of protein-detecting microarrays and related devices.
Trends in biochemical sciences. 27(6):295-300 [PMID] 12069789.
2002
Inhibition of proteolysis and other posttranslational modifications with substrate-targeted inhibitors.
Biopolymers. 66(2):134-40 [PMID] 12325163.
2002
Magnetic resonance imaging detects a specific peptide-protein binding event.
Journal of the American Chemical Society. 124(14):3514-5 [PMID] 11929234.
2002
Microwave-assisted solid-phase synthesis of peptoids.
Organic letters. 4(23):4057-9 [PMID] 12423085.
2002
Physical association of the APIS complex and general transcription factors.
Biochemical and biophysical research communications. 296(4):991-9 [PMID] 12200147.
2002
Protein affinity labeling mediated by genetically encoded peptide tags.
Angewandte Chemie (International ed. in English). 41(2):356-9 [PMID] 12491432.
2002
Recruitment of a 19S proteasome subcomplex to an activated promoter.
Science (New York, N.Y.). 296(5567):548-50 [PMID] 11964484.
2002
Removal of impurities from transcription factor preparations that alter their DNA-binding properties.
Nucleic acids research. 30(16) [PMID] 12177316.
2002
Toward synthetic transcription activators: recruitment of transcription factors to DNA by a PNA-peptide chimera.
Journal of the American Chemical Society. 124(9):1838-9 [PMID] 11866581.
2001
An inhibitor of sequence-specific proteolysis that targets the substrate rather than the enzyme.
Chemistry & biology. 8(4):391-7 [PMID] 11325594.
2001
Evidence that Gal11 protein is a target of the Gal4 activation domain in the mediator.
Biochemistry. 40(31):9421-7 [PMID] 11478912.
2001
Protein cross-linking mediated by metal ion complexes.
Metal ions in biological systems. 38:351-84 [PMID] 11219015.
2001
Protein microarrays: prospects and problems.
Chemistry & biology. 8(2):105-15 [PMID] 11251285.
2001
The 19S regulatory particle of the proteasome is required for efficient transcription elongation by RNA polymerase II.
Molecular cell. 7(5):981-91 [PMID] 11389845.
2001
The Gal4 activation domain binds Sug2 protein, a proteasome component, in vivo and in vitro.
The Journal of biological chemistry. 276(33):30956-63 [PMID] 11418596.
2000
A CDC6 protein-binding peptide selected using a bacterial two-hybrid-like system is a cell cycle inhibitor.
The Journal of biological chemistry. 275(41):32098-105 [PMID] 10896933.
2000
Biochemical characterization of the TATA-binding protein-Gal4 activation domain complex.
The Journal of biological chemistry. 275(41):31914-20 [PMID] 10931832.
2000
Peptides selected to bind the Gal80 repressor are potent transcriptional activation domains in yeast.
The Journal of biological chemistry. 275(20):14979-84 [PMID] 10809742.
2000
Scope, limitations and mechanistic aspects of the photo-induced cross-linking of proteins by water-soluble metal complexes.
Chemistry & biology. 7(9):697-708 [PMID] 10980450.
2000
Selection and application of peptide-binding peptides.
Nature biotechnology. 18(1):71-4 [PMID] 10625395.
2000
TATA-binding protein and the Gal4 transactivator do not bind to promoters cooperatively.
The Journal of biological chemistry. 275(52):40797-803 [PMID] 11006288.
1999
Chemistry for the analysis of protein-protein interactions: rapid and efficient cross-linking triggered by long wavelength light.
Proceedings of the National Academy of Sciences of the United States of America. 96(11):6020-4 [PMID] 10339534.
1999
Genetic selection of short peptides that support protein oligomerization in vivo.
Current biology : CB. 9(8):417-20 [PMID] 10226028.
1999
TATA element recognition by the TATA box-binding protein has been conserved throughout evolution.
Genes & development. 13(24):3217-30 [PMID] 10617571.
1998
A critical role for tyrosine residues in His6Ni-mediated protein cross-linking.
Biochemical and biophysical research communications. 247(2):420-6 [PMID] 9642143.
1998
Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein-protein interactions.
Current biology : CB. 8(8):452-8 [PMID] 9550700.
1998
Mechanistic parallels between DNA replication, recombination and transcription.
Trends in biochemical sciences. 23(2):79-83 [PMID] 9538694.
1998
Protein cross-linking mediated by metalloporphyrins.
Bioorganic & medicinal chemistry. 6(8):1301-7 [PMID] 9784871.
1998
Small-molecule-based strategies for controlling gene expression.
Chemistry & biology. 5(6):R129-45 [PMID] 9653545.
1998
Synergistic activation of transcription by physiologically unrelated transcription factors through cooperative DNA-binding.
Biochemical and biophysical research communications. 247(2):530-5 [PMID] 9642164.
1997
DMC1 functions in a Saccharomyces cerevisiae meiotic pathway that is largely independent of the RAD51 pathway.
Genetics. 147(2):533-44 [PMID] 9335591.
1997
The gene 32 single-stranded DNA-binding protein is not bound stably to the phage T4 presynaptic filament.
Biochemical and biophysical research communications. 231(3):600-5 [PMID] 9070854.
1996
Direct association between the yeast Rad51 and Rad54 recombination proteins.
The Journal of biological chemistry. 271(52):33181-6 [PMID] 8969173.
1996
New chemistry for the study of multiprotein complexes: the six-histidine tag as a receptor for a protein crosslinking reagent.
Chemistry & biology. 3(7):551-9 [PMID] 8807887.
1995
A single GAL4 dimer can maximally activate transcription under physiological conditions.
Proceedings of the National Academy of Sciences of the United States of America. 92(17):7677-80 [PMID] 7644476.
1995
From carpet bombing to cruise missiles: the ‘second-order’ mechanisms used by transcription factors to ensure specific DNA binding in vivo.
Chemistry & biology. 2(5):267-79 [PMID] 9383429.
1995
Highly specific oxidative cross-linking of proteins mediated by a nickel-peptide complex.
Biochemistry. 34(14):4733-9 [PMID] 7718579.
1995
Homology dependence of UvsX protein-catalyzed joint molecule formation.
The Journal of biological chemistry. 270(10):5181-6 [PMID] 7890628.
1995
Phage T4 homologous strand exchange: a DNA helicase, not the strand transferase, drives polar branch migration.
Cell. 82(1):111-9 [PMID] 7606776.
1995
The activation domain of GAL4 protein mediates cooperative promoter binding with general transcription factors in vivo.
Proceedings of the National Academy of Sciences of the United States of America. 92(23):10683-7 [PMID] 7479865.
1995
The dangers of ‘splicing and dicing’: on the use of chimeric transcriptional activators in vitro.
Chemistry & biology. 2(4):187-94 [PMID] 9383420.
1994
Efficient unwinding of triplex DNA by a DNA helicase.
Biochemical and biophysical research communications. 204(3):1119-24 [PMID] 7980585.
1994
Inhibition of the DNA unwinding and ATP hydrolysis activities of the bacteriophage T4 DDA helicase by a sequence specific DNA-protein complex.
Biochemical and biophysical research communications. 198(3):1070-7 [PMID] 8117263.
1994
Spectrophotometric assay for enzyme-mediated unwinding of double-stranded DNA.
Proceedings of the National Academy of Sciences of the United States of America. 91(12):5471-4 [PMID] 8202510.
1994
Strand exchange through a DNA-protein complex requires a DNA helicase.
Biochemical and biophysical research communications. 205(2):1004-9 [PMID] 7802625.
1994
Zinc-free and reduced T4 gene 32 protein binds single-stranded DNA weakly and fails to stimulate UvsX-catalyzed homologous pairing.
The Journal of biological chemistry. 269(4):2773-81 [PMID] 8300610.
1993
How do “Zn2 cys6” proteins distinguish between similar upstream activation sites? Comparison of the DNA-binding specificity of the GAL4 protein in vitro and in vivo.
The Journal of biological chemistry. 268(33):24699-706 [PMID] 8227030.
1993
How does the GAL4 transcription factor recognize the appropriate DNA binding sites in vivo?
Cellular & molecular biology research. 39(4):355-60 [PMID] 8312971.
1993
The acidic activation domains of the GCN4 and GAL4 proteins are not alpha helical but form beta sheets.
Cell. 72(4):587-94 [PMID] 8440022.
1993
The role of protein-protein interactions in the assembly of the presynaptic filament for T4 homologous recombination.
The Journal of biological chemistry. 268(11):7904-11 [PMID] 8385125.
1992
Mechanism of the rhodium porphyrin-catalyzed cyclopropanation of alkenes.
Science (New York, N.Y.). 256(5063):1544-7 [PMID] 17836323.
1992
The antitumor agent CC-1065 inhibits helicase-catalyzed unwinding of duplex DNA.
Biochemistry. 31(16):3968-75 [PMID] 1314652.
1991
Inhibition of protein-mediated homologous pairing by a DNA helicase.
The Journal of biological chemistry. 266(15):9712-8 [PMID] 1851754.
1991
Spectroscopic studies of the DNA binding site of the GAL4 “zinc finger” protein.
Biochemical and biophysical research communications. 175(2):492-9 [PMID] 2018497.
1990
Cleavage of DNA by electrochemically activated MnIII and FeIII complexes of meso-tetrakis (N-methyl-4-pyridiniumyl)porphine.
Bioconjugate chemistry. 1(2):123-31 [PMID] 2095210.
1990
Functional interactions between phage T4 and E. coli DNA-binding proteins during the presynapsis phase of homologous recombination.
Biochemical and biophysical research communications. 172(2):804-10 [PMID] 2241970.
1990
Homologous pairing in vitro initiated by DNA synthesis.
Biochemical and biophysical research communications. 169(1):302-9 [PMID] 2350351.
1990
The role of the bacteriophage T4 gene 32 protein in homologous pairing.
The Journal of biological chemistry. 265(34):20966-9 [PMID] 2250001.
1989
The phage T4 uvs Y recombination protein stabilizes presynaptic filaments.
The Journal of biological chemistry. 264(28):16451-7 [PMID] 2550444.
1988
Efficient synthesis of a supercoiled M13 DNA molecule containing a site specifically placed psoralen adduct and its use as a substrate for DNA replication.
Biochemistry. 27(9):3210-5 [PMID] 3291944.
1988
The mechanism of homologous DNA strand exchange catalyzed by the bacteriophage T4 uvsX and gene 32 proteins.
The Journal of biological chemistry. 263(19):9427-36 [PMID] 2967823.
1987
Stimulation of protein-directed strand exchange by a DNA helicase.
Nature. 326(6110):312-4 [PMID] 2950327.
1984
Epoxidation of olefins by cytochrome P-450 model compounds: mechanism of oxygen atom transfer.
Proceedings of the National Academy of Sciences of the United States of America. 81(10):3245-8 [PMID] 6587349.
1983
Oxygenation of hydrocarbons by cytochrome P-450 model compounds: modification of reactivity by axial ligands.
Proceedings of the National Academy of Sciences of the United States of America. 80(22):7039-41 [PMID] 6580626.
High-Throughput Quality Control Assay for the Solid-Phase Syn-thesis of DNA-Encoded Libraries of Macrocycles
. [DOI] 10.26434/chemrxiv.13491312.v1.
Self-Assembly of Proteolysis Targeting Chimeras Via Reversible Bioorthogonal Reactions
. [DOI] 10.26434/chemrxiv-2022-1g1p4.
Synthesis and Screening of A DNA-Encoded Library of Non-Peptidic Macrocycles
. [DOI] 10.26434/chemrxiv.13490151.v1.

Grants

Apr 2022 – Aug 2022
Phenotypic screening using DNA-encoded libraries
Role: Principal Investigator
Funding: NATL INST OF HLTH NIGMS

Education

Jane Coffin Childs Post-doctoral Scholar
1985-1987 · UCSF
Ph.D. in Chemistry
1985 · Stanford University
Bachelor's of Science in Chemistry
1981 · University of Miami

Contact Details

Phones:
Business:
(561) 228-2461
Emails:
Business:
kodadek@ufl.edu
Laboratory Administrative Coordinator:
Addresses:
Business Mailing:
Location A335
130 SCRIPPS WAY BLDG 3A2
JUPITER FL 33458