Chemical tools to monitor and manipulate the adaptive immune system

Chemistry and Biology

Volumn 21, Issue 9, 2014, Pages 1066-1074

  Kodadek, Thomas ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; B LYMPHOCYTE RECEPTOR; POLYCLONAL ANTIBODY; ANTIGEN; ANTIGEN ANTIBODY COMPLEX; MOLECULAR LIBRARY; MONOCLONAL ANTIBODY; QUANTUM DOT; RECOMBINANT PROTEIN;

ADAPTIVE IMMUNITY; ANTIBODY COMBINING SITE; ANTIGEN DETECTION; ANTIGEN SPECIFICITY; BINDING AFFINITY; BINDING SITE; COMBINATORIAL LIBRARY; HUMAN; IMMUNE RESPONSE; IMMUNOASSAY; NONHUMAN; QUANTITATIVE ANALYSIS; REVIEW; ANTIGEN ANTIBODY COMPLEX; B LYMPHOCYTE; BIOSYNTHESIS; CHEMISTRY; DIAGNOSTIC USE; GENETICS; IMMUNOLOGY; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; METABOLISM; MOLECULAR LIBRARY;

ADAPTIVE IMMUNITY; ANTIBODIES; ANTIBODIES, MONOCLONAL; ANTIGEN-ANTIBODY COMPLEX; ANTIGENS; B-LYMPHOCYTES; HUMANS; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; QUANTUM DOTS; RECOMBINANT PROTEINS; SMALL MOLECULE LIBRARIES;

EID: 84909586866     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2014.07.009     Document Type: Review

References (46)

1. 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.
2. Agathangelidis, A., Darzentas, N., Hadzidimitriou, A., Brochet, X., Murray, F., Yan, X.J., Davis, Z., van Gastel-Mol, E.J., Tresoldi, C., Chu, C.C., et al. (2012). Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies. Blood 119, 4467-4475.
3. Anderson, K.S., and LaBaer, J. (2005). The sentinel within: exploiting the immune system for cancer biomarkers. J. Proteome Res. 4, 1123-1133.
4. Aquino, C., Sarkar, M., Chalmers, M.J., Mendes, K., Kodadek, T., and Micalizio, G.C. (2012). A biomimetic polyketide-inspired approach to small-molecule ligand discovery. Nat. Chem. 4, 99-104.
5. Barrett, D.M., Singh, N., Porter, D.L., Grupp, S.A., and June, C.H. (2014). Chimeric antigen receptor therapy for cancer. Annu. Rev. Med. 65, 333-347.
6. Boutz, D.R., Horton, A.P., Wine, Y., Lavinder, J.J., Georgiou, G., and Marcotte, E.M. (2014). Proteomic identification of monoclonal antibodies from serum. Anal. Chem. 86, 4758-4766.
7. Brenner, S., and Lerner, R.A. (1992). Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. USA 89, 5381-5383.
8. Caulfield, M.J., Dudkin, V.Y., Ottinger, E.A., Getty, K.L., Zuck, P.D., Kaufhold, R.M., Hepler, R.W., McGaughey, G.B., Citron, M., Hrin, R.C., et al. (2010). Small molecule mimetics of an HIV-1 gp41 fusion intermediate as vaccine leads. J. Biol. Chem. 285, 40604-40611.
9. Chiorazzi, N., Rai, K.R., and Ferrarini, M. (2005). Chronic lymphocytic leukemia. N. Engl. J. Med. 352, 804-815.
10. Chu, C.C., Catera, R., Zhang, L., Didier, S., Agagnina, B.M., Damle, R.N., Kaufman, M.S., Kolitz, J.E., Allen, S.L., Rai, K.R., and Chiorazzi, N. (2010). Many chronic lymphocytic leukemia antibodies recognize apoptotic cells with exposed nonmuscle myosin heavy chain IIA: implications for patient outcome and cell of origin. Blood 115, 3907-3915.
11. Clark, M.A. (2010). Selecting chemicals: the emerging utility of DNA-encoded libraries. Curr. Opin. Chem. Biol. 14, 396-403.
12. 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.
13. Doran, T.M., Gao, Y., Mendes, K., Dean, S., Simanski, S., and Kodadek, T. (2014). Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits. ACS Comb. Sci. 16, 259-270.
14. Edwards, J.C., Szczepanski, L., Szechinski, J., Filipowicz-Sosnowska, A., Emery, P., Close, D.R., Stevens, R.M., and Shaw, T. (2004). Efficacy of B-cell-targeted therapy with rituximab in patients with rheumatoid arthritis. N. Engl. J. Med. 350, 2572-2581.
15. Figliozzi, G.M., Goldsmith, R., Ng, S.C., Banville, S.C., and Zuckermann, R.N. (1996). Synthesis of N-substituted glycine peptoid libraries. Methods Enzymol. 267, 437-447.
16. Gao, Y., and Kodadek, T. (2013). Synthesis and screening of stereochemically diverse combinatorial libraries of peptide tertiary amides. Chem. Biol. 20, 360-369.
17. Georgiou, G., Ippolito, G.C., Beausang, J., Busse, C.E., Wardemann, H., and Quake, S.R. (2014). The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat. Biotechnol. 32, 158-168.
18. 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.
19. Handlogten, M.W., Kiziltepe, T., Moustakas, D.T., and Bilgic¸er, B. (2011). Design of a heterobivalent ligand to inhibit IgE clustering on mast cells. Chem. Biol. 18, 1179-1188.
20. Kanter, J.L., Narayana, S., Ho, P.P., Catz, I., Warren, K.G., Sobel, R.A., Steinman, L., and Robinson, W.H. (2006). Lipid microarrays identify key mediators of autoimmune brain inflammation. Nat. Med. 12, 138-143.
21. Knittelfelder, R., Riemer, A.B., and Jensen-Jarolim, E. (2009). Mimotope vaccination - from allergy to cancer. Expert Opin. Biol. Ther. 9, 493-506.
22. Laserson, U., Vigneault, F., Gadala-Maria, D., Yaari, G., Uduman, M., Vander Heiden, J.A., Kelton, W., Taek Jung, S., Liu, Y., Laserson, J., et al. (2014). High-resolution antibody dynamics of vaccine-induced immune responses. Proc. Natl. Acad. Sci. USA 111, 4928-4933.
23. Lennon, V.A., Kryzer, T.J., Pittock, S.J., Verkman, A.S., and Hinson, S.R. (2005). IgG marker of optic-spinal multiple sclerosis binds to the aquaporin-4 water channel. J. Exp. Med. 202, 473-477.
24. Lian, W., Upadhyaya, P., Rhodes, C.A., Liu, Y., and Pei, D. (2013). Screening bicyclic peptide libraries for protein-protein interaction inhibitors: discovery of a tumor necrosis factor-α antagonist. J. Am. Chem. Soc. 135, 11990-11995.
25. Liu, R., Marik, J., and Lam, K.S. (2002). A novel peptide-based encoding system for "one-bead one-compound" peptidomimetic and small molecule combinatorial libraries. J. Am. Chem. Soc. 124, 7678-7680.
26. Lueking, A., Possling, A., Huber, O., Beveridge, A., Horn, M., Eickhoff, H., Schuchardt, J., Lehrach, H., and Cahill, D.J. (2003). A nonredundant human protein chip for antibody screening and serum profiling. Mol. Cell. Proteomics 2, 1342-1349.
27. MacBeath, G., Koehler, A.N., and Schreiber, S.L. (1999). Printing small molecules as microarrays and detecting protein-ligand interactions en masse. J. Am. Chem. Soc. 121, 7967-7968.
28. Murelli, R.P., Zhang, A.X., Michel, J., Jorgensen, W.L., and Spiegel, D.A. (2009). Chemical control over immune recognition: a class of antibody-recruiting small molecules that target prostate cancer. J. Am. Chem. Soc. 131, 17090-17092.
29. Nagele, E., Han, M., Demarshall, C., Belinka, B., and Nagele, R. (2011). Diagnosis of Alzheimer's disease based on disease-specific autoantibody profiles in human sera. PLoS ONE 6, e23112.
30. Palucka, K., and Banchereau, J. (2014). SnapShot: cancer vaccines. Cell 157, 516-516.e1.
31. Qiu, J., Madoz-Gurpide, J., Misek, D.E., Kuick, R., Brenner, D.E., Michailidis, G., Haab, B.B., Omenn, G.S., and Hanash, S. (2004). Development of natural protein microarrays for diagnosing cancer based on an antibody response to tumor antigens. J. Proteome Res. 3, 261-267.
32. Raveendra, B.L., Wu, H., 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.
33. 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.
34. Restrepo, L., Stafford, P., Magee, D.M., and Johnston, S.A. (2011). Application of immunosignatures to the assessment of Alzheimer's disease. Ann. Neurol. 70, 286-295.
35. Robinson, W.H., DiGennaro, C., Hueber, W., Haab, B.B., Kamachi, M., Dean, E.J., Fournel, S., Fong, D., Genovese, M.C., de Vegvar, H.E., et al. (2002). Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat. Med. 8, 295-301.
36. Robinson, W.H., Steinman, L., and Utz, P.J. (2003). Protein arrays for autoantibody profiling and fine-specificity mapping. Proteomics 3, 2077-2084.
37. Roep, B.O., Solvason, N., Gottlieb, P.A., Abreu, J.R., Harrison, L.C., Eisenbarth, G.S., Yu, L., Leviten, M., Hagopian, W.A., Buse, J.B., et al. (2013). Plasmid-encoded proinsulin preserves C-peptide while specifically reducing proinsulin-specific CD8(+) T cells in type 1 diabetes. Sci. Transl. Med. 5, 191ra182.
38. Sarkar, M., Pascal, B.D., Steckler, C., Aquino, C., Micalizio, G.C., Kodadek, T., and Chalmers, M.J. (2013). Decoding split and pool combinatorial libraries with electron-transfer dissociation tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 24 (7, Spec.), 1026-1036.
39. Sarma, B.K., Yousufuddin, M., and Kodadek, T. (2011). Acyl hydrazides as peptoid sub-monomers. Chem. Commun. (Camb.) 47, 10590-10592.
40. Scheuermann, J., and Neri, D. (2010). DNA-encoded chemical libraries: a tool for drug discovery and for chemical biology. ChemBioChem 11, 931-937.
41. Seiler, T., Woelfle, M., Yancopoulos, S., Catera, R., Li, W., Hatzi, K., Moreno, C., Torres, M., Paul, S., Dohner, H., et al. (2009). Characterization of structurally defined epitopes recognized by monoclonal antibodies produced by chronic lymphocytic leukemia B cells. Blood 114, 3615-3624.
42. 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.
43. Tan, Y.C., Blum, L.K., Kongpachith, S., Ju, C.H., Cai, X., Lindstrom, T.M., Sokolove, J., and Robinson, W.H. (2014). High-throughput sequencing of natively paired antibody chains provides evidence for original antigenic sin shaping the antibody response to influenza vaccination. Clin. Immunol. 151, 55-65.
44. Vignali, D.A. (2000). Multiplexed particle-based flow cytometric assays. J. Immunol. Methods 243, 243-255.
45. Wang, X., Yu, J., Sreekumar, A., Varambally, S., Shen, R., Giacherio, D., Mehra, R., Montie, J.E., Pienta, K.J., Sanda, M.G., et al. (2005). Autoantibody signatures in prostate cancer. N. Engl. J. Med. 353, 1224-1235.
46. Zuckermann, R.N., Kerr, J.M., Kent, S.B.H., and Moos, W.H. (1992). Efficient method for the preparation of peptoids [Oligo(N-substituted glycines)] by submonomer solid-phase synthesis. J. Am. Chem. Soc. 114, 10646-10647.