Publications

Novel Chemistry for the Synthesis of DNA-Encoded Libraries

• Paciaroni, N.G., Ndungu, J.M. and Kodadek, T. (2020) “Solid-Phase Synthesis of DNA-Encoded Libraries Via An Aldehyde Explosion Strategy” Chem Comm. 56, 4656-4659.

• Dickson, P. and Kodadek, T. (2019) “Chemical Composition of DNA-Encoded Libraries, Past Present and Future” Org. Biomol. Chem. 17, 4676 – 4688.

• Shu, K. and Kodadek, T. (2018) “Solid-phase synthesis of b-hydroxyketones via DNA-compatible organocatalytic aldol reactions. ACS Comb. Sci. 20, 277-281.

• Pels, K., Dickson, P., An, H. and Kodadek, T. (2018) “DNA-compatible solid-phase combinatorial synthesis of b-cyanoacrylamides and related electrophiles” ACS Comb. Sci. 20, 61-69.

• Hoang, N.T. and Kodadek, T. (2018) “Solid-phase synthesis of -amino ketones via DNA-compatible organocatalytic Mannich reactions” ACS Comb. Sci. 20, 55-60.

• Wu, H., An, H., Mo, S. and Kodadek, T. (2017) “Asymmetric synthesis of vinylogous beta-amino acids and their incorporation into mixed backbone oligomers” Org. Biomol. Chem. 15, 3255-3264.

• Kodadek, T. and McEnaney, P. (2016) “Towards vast libraries of scaffold-diverse, conformationally constrained oligomers” Chem. Comm., 52, 6038-6059. Chosen as a Featured Article. Inside Cover Article.

• Morimoto, J. and Kodadek, T. (2015) “Synthesis of a large library of macrocyclic peptides containing multiple and diverse N-alkylated residues” Mol. Biosystems 11, 2770-2779.

• Sarma, B.K., Liu, X., Wu, H., Gao, Y. and Kodadek, T. (2015) “Solid Phase Synthesis of 1,3,4-oxadiazin- 5 (6R)-one and 1,3,4-oxadiazol- 2-one Scaffolds from Acyl Hydrazides” Org. Biomol. Chem. 12, 59-63.

• Suwal, S. and Kodadek, T. (2014) “Solid-phase synthesis of peptoid-like oligomers containing diverse diketopiperazine units” Org. Biomol. Chem. 12, 5831 – 5834.

• Suwal, S. and Kodadek, T. (2013) “Synthesis of Libraries of Peptidomimetic Compounds Containing A 2- Oxopiperazine Unit In The Main Chain” Org. Biomol. Chem. 11, 2088 – 2092.

• Gao, Y. and Kodadek, T. (2013) “Synthesis and Screening of Stereochemically Diverse Combinatorial Libraries of Conformationally Restrained Peptide Tertiary Amides” Chem. & Biol. 20, 360-369.

• Sarma, B.K. and Kodadek, T. (2012) “Sub-Monomer Synthesis of A Hybrid Peptoid-Azapeptoid Library” ACS Comb. Sci. 14, 558-564.

• 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.

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

Screening and Ligand Discovery

• McEnaney, P., Balzarini, M., Park, H. and Kodadek, T. (2020) “Structural characterization of peptoid-inspired conformationally constrained oligomer (PICCO) bound to Streptavidin” Chem Comm 56, 10560-10563.

• Kodadek, T., Paciaroni, N.G., Balzarini, M. and Dickson, P. (2019) “Beyond protein binding: Recent advances in screening DNA-encoded libraries” Chem. Comm. 55, 13330 – 13341.

• Kodadek, T., Paciaroni, N.G., Balzarini, M. and Dickson, P. (2019) “Beyond protein binding: Recent advances in screening DNA-encoded libraries” Chem. Comm. 55, 13330 – 13341.

• Erharuyi, O., Simanski, S., McEnaney, P. and Kodadek, T. (2018) “Screening One Bead One Compound Libraries Against Serum Using a Flow Cytometer: Determination of the Minimum Antibody Concentration Required For Ligand Discovery” Biorg. & Med. Chem. Lett. In press. Doi: 10.1016/j.bmcl.2018.01.033.

• Mendes, K., Malone, M.L., Ndungu, J.M., Suponitsky-Kroyter, I., Cavett, V., McEnaney, P.J., MacConnell, A.B., Doran, T.M., Ronacher, K., Stanley, K., Utset, O., Walzl, G., Paegel, B.M. and Kodadek, T. (2017) “High-
throughput identification of DNA-encoded IgG ligands that distinguish active and latent Mycobacterium Tuberculosis infections” ACS Chem. Biol. 12, 234-243.

• Gearhart, T., Montelaro, R.C., Schurdak, M.E., Picher, C.D., Rinaldo, C.R., Kodadek, T., Park, Y., Yurko, R., Marquest, E.T.A. Jr. and Burke, D.S. (2016) “Selection of a potential diagnostic biomarker for HIV infection
from a random library of non-biological synthetic peptoid oligomers”.  J. Immunol. Methods, 435, 85-89.

• Doran, T.M., Morimoto, J., Simanski S., Koesema, E, Clark, L.F., Pels, K., Stoops, S.L., Pugliese, A., Skyler, J. and Kodadek, T. (2016) “Discovery of phosphorylated peripherin as a major humoral autoantigen in type 1
diabetes mellitus using ‘epitope surrogate’ technology” Cell Chem. Biol. 23, 618-628.

• Doran, T.M., Sarkar, M. and Kodadek, T. (2016) “Chemical Tools To Monitor and Manipulate Adaptive Immune Responses” J. Amer. Chem. Soc. 138, 6076–6094.

• Sarkar, M., Liu, Y., Qi, J., Peng, H., Morimoto, J., Rader, C., Chiorazzi, N. and Kodadek, T. (2016) “Targeting stereotyped B cell receptors from chronic lymphocytic leukemia patients with synthetic antigen surrogates” J.
Biol. Chem. 291, 7558-7570.

• Doran, T.M., Morimoto, J. Simanski, S., McEnaney, P.J. and Kodadek, T. (2015) “Reliable Diagnosis of Murine Type 1 Diabetes Using A Panel of Autoantigens and “Antigen Surrogates” Mounted Onto A Liquid Array”
Molecular BioSystems 2015, 11, 3156 – 3163.

• Doran, T., Gao, Y., Simanski, S., McEnaney, P. and Kodadek, T. (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” Bioorg. Med. Chem. Lett. 25, 4910-4917.

• Trader, D.J., Simanski, S. and Kodadek, T. (2015) “A reversible and highly selective inhibitor of the Ubiquitin receptor Rpn13 is toxic to multiple myeloma cells” J. Amer. Chem. Soc. 137, 6312-6319.

• Doran, T.M., Simanski, S. and Kodadek, T. (2015) “Discovery of native autoantigens via antigen surrogate technology: Application to type 1 diabetes” ACS Chem. Biol. 10, 401-412. Highlighted by the ACS as an
Editor’s Choice article. Highlighted in the Jan. 12, 2015 issue of C&E News.

• Gao, Y. and Kodadek, T. (2015) “Direct comparison of linear and macrocyclic compounds as a source of protein ligands” ACS Comb. Sci. 17 190-195. Highlighted by the ACS as an Editor’s Choice article.

• Gao, Y., Amar, S., Pahwa, S., Fields, G. and Kodadek, T. (2015) “Rapid lead discovery through iterative screening of one bead one compound libraries” ACS Comb. Sci. 17, 49-59.

• Sarkar, M., Liu, Y., Morimoto, J., Peng, H., Aquino, C., Rader, C., Chiorazzi, N. and Kodadek, T. (2014) “Recognition of antigen-specific B cell receptors from chronic lymphocytic leukemia patients by synthetic “antigen surrogates” Chem & Biol. 21, 1-10.

• Kodadek, T. (2014) “Chemical tools to monitor and manipulate the adaptive immune system” Chem. & Biol. 21, 1066-1074.

• Doran, T.M. and Kodadek, T. (2014) “A liquid array platform for the multiplexed analysis of synthetic molecule- protein interactions” ACS Chem. Biol. 9, 339-346.

• Raveendra, B., Hao, W., Baccala, R., Reddy, M.M., Schilke, J., Bennett, J.L., Theofilopoulos, A.N. and Kodadek, T. (2013) “Discovery of peptoid ligands for anti-Aquaporin 4 antibodies” Chem. & Biol. 20, 351-359.

• 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.

• 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.