Independent Research (NCBI)

Members of the Woo lab in Bold. Undergraduates underlined. * equal contribution. # co-corresponding authors.

2024

  1. Cheng S. S.*, Mody A. C.*, Woo C. M. “Opportunities for Therapeutic Modulation of O-GlcNAc.” Chem Rev 2024, in press. Review

  2. Yvon R., Woo C. M. “Small molecules help misplaced proteins hitchhike around cells.” Nature 2024, 633, 773. Commentary

  3. Mody A. C., Woo C. M. “Ubiquitin gets sweet: Sugar-mediated ubiquitination regulates Nrf1 function.” Mol Cell 2024, 84, 3003. Commentary

  4. Xu W., Zhao Z., Su M., Jain A., Lloyd H. C., Feng E. Y., Cox N., Woo C. M. “Genesis and regulation of C-terminal cyclic imides from protein damage.” Proc Natl Acad Sci 2024, in press.

  5. Flaxman H. A., Chrysovergi M.-A., Han H., Kabir F., Lister R. T., Chang C.-F., Yvon R., Black K. E., Weigert A., Savai R., Egea-Zorrilla A., Pardo-Saganta A., Lagares D.#, Woo C. M.# “Sanglifehrin A mitigates multi-organ fibrosis by targeting the collagen chaperone cyclophilin B.” JCI Insight 2024, 9, e171162.

  6. Payne N. C.*, Ichikawa S.*, Woo C. M., Mazitschek R. “Protocol for the comprehensive biochemical and cellular profiling of small-molecule degraders using CoraFluor TR-FRET technology.” STAR Protocols 2024, 5, 103129.

  7. Homan R. A., Lapek J. D., Woo C. M., Niessen S., Jones L. H., Parker C. G. “Photoaffinity labelling with small molecules.” Nat Rev Methods Primers 2024, 4, 30. Review

  8. Ichikawa S.*, Payne N. C.*, Xu W., Chang C.-F., Vallavoju N., Frome S., Flaxman H. A., Mazitschek R.#, Woo C. M.# “The cyclimids: Degron-inspired cereblon binders for targeted protein degradation.” Cell Chem Biol 2024, 31, 1162.

  9. Leon Duque M. A.*, Vallavoju N.*, Zhang T., Yvon R., Pan Y.-X., Woo C. M. “Photo-affinity and Metabolic Labeling Probes Based on the Opioid Alkaloids.” ChemBioChem 2024, 25, e202300841.

    2023

  10. Miyamoto D. K., Curnutt N. M., Park S-M., Stavropoulos A., Kharas M. G., Woo C. M. “Design and Development of IKZF2 and CK1α Dual Degraders.” J Med Chem 2023, 66, 16953.

  11. Henry C. C., Kruell J. A., Wilson R. M., Chang C.-F., Woo C. M., Koehler A. N. “A versatile isocyanate-mediated strategy for appending chemical tags onto drug-like small molecules.” Bioconjugate Chem 2023, 34, 2181.

  12. Leon Duque M. A., Vallavoju N., Woo C. M. “Chemical tools for the opioids.” Mol Cell Neurosci 2023, 125, 103845. Review

  13. Park S-M.*, Miyamoto D. K.*, Han G., Chan M., Curnutt N. M., Tran N. L., Velleca A., Kim J. H., Schurer A., Chang K., Xu W., Kharas M. G.#, Woo C. M.# “Dual IKZF2 and CK1α degrader targets acute myeloid leukemia cells.” Cancer Cell 2023, 41, 726.

  14. Cheng S. S., Woo C. M. “Dual-specificity RNA aptamers: A sweet new tool for studying O-GlcNAc biology.” Mol Cell 2023, 83, 657. Commentary

  15. Ge Y.#, Lu H., Yang B., Woo C. M.# “Small Molecule-Activated O-GlcNAcase for Spatiotemporal Removal of O-GlcNAc in Live Cells.” ACS Chem Biol 2023, 18, 193.

    2022

  16. West A. V., Woo C. M. “Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions.” Isr J Chem 2022, 63, e202200081. Review

  17. West A. V., Amako Y., Woo C. M. “Design and Evaluation of a Cyclobutane Diazirine Alkyne Tag for Photoaffinity Labeling in Cells.” J Am Chem Soc 2022, 144, 21174.

  18. Lin Z., Shen D., Yang B., Woo C. M. “Molecular and structural characterization of lenalidomide-mediated sequestration of eIF3i.” ACS Chem Biol 2022, 17, 3229.

  19. Ichikawa S.*, Flaxman H. A.*, Xu W.*, Vallavoju N., Lloyd H. C., Wang B., Shen D., Pratt, M. R., Woo C. M. “The E3 ligase adapter cereblon targets the C-terminal cyclic imide degron.” Nature 2022, 610, 775.

  20. Lin Z., Woo C. M. “Methods to Characterize and Discover Molecular Degraders in Cells.” Chem Soc Rev 2022, 51, 7115. Review

  21. Schwein P., Ge Y., Yang B., D’Souza A. K., Mody A., Shen D., Woo C. M. “Writing and erasing O-GlcNAc on casein kinase 2 alpha alters the phosphoproteome.” ACS Chem Biol 2022, 17, 1111.

  22. Lim D., Zhou Q., Cox K. J., Law B. K., Lee M., Kokkonda P., Choudhary S. K., Pergu R., Sreekanth V., Gangopadhyay S. A., Maji B., Lai S., Amako Y., Thompson D. B., Subramanian H. K. K., Mesleh M. F., Dancik V., Clemons P. A., Wagner B. K., Woo C. M., Church G. M., Choudhary A. “A general approach to identify miniature cell-permeable and synthetic anti-CRISPRs.” Nat Cell Biol 2022, 24, 1766.

  23. Mealer R. G., Williams S. E., Noel M., Yang B., D’Souza A. K., Nakata T., Graham D. B., Creasey E. A., Cetinbas M., Sadreyev R., Scolnick E. M., Woo C. M., Smoller J. W., Xavier R. J., Cummings R. D. “The schizophrenia-associated variant in SLC39A8 alters N-glycosylation in the mouse brain.” Mol Psychiatry 2022, 27, 1405.

  24. Lin Z.*, Amako Y.*, Kabir F., Flaxman H. A., Budnik B., Woo C. M. “Development of photo-lenalidomide for cellular target identification.” J Am Chem Soc 2022, 144, 606.

  25. Jackson E. G., Cutolo G., Yang B., Yarravarapu N., Burns M. W. N., Bivena-Todd G., Roustan C., Thoden J. B., Lin-Jones H. M., van Kuppevelt T. H., Holden H. M., Schumann B., Kohler J. J., Woo C. M., Pratt M. R. "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.” ACS Chem Biol 2022, 17, 159.

  26. Yu W., Lin Z., Woo C. M., Baskin J. M. “A chemoproteomics approach to profile phospholipase D-derived phosphatidyl alcohol interactions.” ACS Chem Biol 2022, 17, 3276.

    2021

  27. Ge Y., Woo C. M. “Writing and erasing O-GlcNAc from target proteins in cells.” Biochem Soc Trans 2021, 49, 2891. Review

  28. Ramirez D. H., Yang B., D’Souza A. K., Shen D., Woo C. M. “Truncation of the TPR domain of OGT alters substrate and glycosite selection.” Anal Bioanal Chem 2021, 413, 7385.

  29. Kawahara R., Chernykh A., Alagesan K., Bern M., Cao W., Chalkley R. J., Cheng K., Choo M. S., Edwards N., Goldman R., Hoffmann M., Hu Y., Huang Y., Kim J. Y., Kletter D., Liquet-Weiland B., Liu M., Mechref Y., Meng B., Neelamegham S., Nguyen-Khuong T., Nilsson J., Pap A., Park G. W., Parker B. L., Pegg C. L., Penninger J. M., Phung T. K., Pioch M., Rapp E., Sakalli E., Sanda M., Schulz B. L., Scott N. E., Sofronov G., Stadlmann J., Vakhrushev S. Y., Woo C. M., Wu H. Y., Yang P., Ying W., Zhang H., Zhang Y., Zhao J., Zaia J., Haslam S. M., Palmisano G., Yoo J. S., Larson G., Khoo K.-H., Medzihradszky K. F., Kolarich D., Packer N. H., Thaysen-Andersen M. “Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies of glycopeptide data.” Nat Meth 2021, 18, 1304.

  30. McKitrick T., Ackerman M. E., Anthony R., Bennett C., Demitriou M., Hudulla G. A., Ribbeck K., Ruhl S., Woo C. M., Yang L., Zost S., Schnaar R. L., Doering T. L. “The crossroads of glycoscience, infection, and immunology.” Front Microbiol 2021, 12, 731008. Perspective

  31. Chang C., Flaxman H. A., Woo C. M. "Enantioselective Synthesis and Biological Evaluation of Sanglifehrin A and B and Analogs." Angew Chem Int Ed, 2021, 60, 31, 17045.

  32. Ramirez D. H., Ge Y., Woo C. M. “O-GlcNAc engineering on a target protein in cells with nanobody-OGT and nanobody-splitOGA.” Curr Protoc Chem Biol, 2021, 1, e117.

  33. West A. V., Muncipinto G., Wu H. Y., Huang A. C., Labenski M. T., Jones L. H., Woo C. M. “Labeling preferences of diazirines with protein biomolecules.” J Am Chem Soc, 2021, 143, 6691.

  34. Ge Y., Ramirez D. H., Yang B., D’Souza A. K., Aonbangkhen C., Wong S., Woo C. M. “Target protein deglycosylation in living cells by a nanobody-fused split O-GlcNAcase.” Nat Chem Biol, 2021, 17, 593.

  35. West A. V., Woo C. M. “First reactions: Ironing out New Antibiotic Mechanisms with Xanthocillin X” ACS Cent Sci, 2021, 7, 403. Commentary

    2020

  36. Darabedian N., Yang B., Ding R., Cutolo G., Zaro B. W., Woo C. M., Pratt M. R. “O-Acetylated chemical reporters of glycosylation can display metabolism-dependent background labeling of proteins but are generally reliable tools for the identification of glycoproteins.” Front Chem, 2020, 8, 318.

  37. Ramirez D. H., Aonbangkhen C., Wu H. Y., Naftaly J. A., Tang S., O’Meara T. R., Woo C. M. "Engineering a proximity-directed O-GlcNAc transferase for selective protein O-GlcNAcylation in cells." ACS Chem Biol, 2020, 15, 4, 1059.

  38. Schwein P. A., Woo C. M. "The O-GlcNAc Modification on Kinases." ACS Chem Biol, 2020, 15, 602. Review

    2019

  39. Amako Y., Woo C. M. “A chiral trick to map protein ligandability.” Nat Chem, 2019, 11, 1080. Commentary

  40. Miyamoto D. K., Flaxman H. A., Wu H. Y., Gao J., Woo C. M. “Discovery of a Celecoxib Binding Site on Prostaglandin E Synthase (PTGES) with a Cleavable Chelation-Assisted Biotin Probe.” ACS Chem Biol, 2019, 14, 2527.

  41. Flaxman H. A., Miyamoto D. K., Woo C. M. “Small molecule interactome mapping by photo-affinity labeling (SIM-PAL) to identify and map the interactions of small molecules on a proteome-wide scale.” Curr Protoc Chem Biol, 2019, 11, e75.

  42. Joiner C. M., Levine Z., Aonbangkhen C., Woo C. M., Walker S. “Aspartate residues within TPR lumen drive O-GlcNAc transferase substrate selection.” J Am Chem Soc, 2019, 141, 12974.

  43. Flaxman H. A., Chang C. F., Wu H. Y., Nakamoto C. H., Woo C. M. "A Binding Site Hotspot Map of the FKBP12–Rapamycin–FRB Ternary Complex by Photoaffinity Labeling and Mass Spectrometry-Based Proteomics." J Am Chem Soc, 2019, 141, 11759.

    2018

  44. Darabedian N., Gao J., Chuh K. N., Woo C. M., Pratt M. R. "The metabolic chemical reporter 6-azido-6-deoxy-glucose further reveals the substrate promiscuity of O-GlcNAc transferase and catalyzes the discovery of intracellular protein modification by O-glucose." J Am Chem Soc, 2018, 140, 7092.

  45. Chang C., Mfuh A., Gao J., Wu H., Woo C. M. "Synthesis of an electronically-tuned minimally interfering alkynyl photo-affinity label to measure small molecule–protein interactions." Tetrahedron, 2018, 74, 3273.

  46. Gao J., Mfuh A., Amako Y., Woo C. M. "Small molecule interactome mapping by photo-affinity labeling reveals binding site hotspots for the NSAIDs." J Am Chem Soc, 2018, 140, 4259.

  47. Woo C. M*., Lund P. J.*, Huang A. C., Davis M. M., Bertozzi C. R., Pitteri S. J. “Mapping and quantification of over 2,000 O-linked glycopeptides in activated human T cells with isotope-targeted glycoproteomics (IsoTaG).” Mol. Cell. Proteomics 2018, 17(4), 764.

  48. Flaxman H. A., Woo C. M. "Mapping the small molecule interactome by mass spectrometry." Biochemistry, 2018, 57, 186. Perspective

 

Prior Research

  1. Woo C. M., Felix A., Byrd W., Zuegel D., Ishihara M., Azadi P., Iavarone A., Pitteri S., Bertozzi C. R. “Development of IsoTaG, a chemical glycoproteomics technique for profiling intact N- and O-glycopeptides from whole cell proteomes.” J Prot Res 2017, 16, 1706.

  2. Woo C. M., Felix A., Zhang L., Elias J. E., Bertozzi C. R. “Isotope targeted glycoproteomics (IsoTaG) analysis of sialylated N- and O-glycopeptides on an Orbitrap Fusion Tribrid using azido and alkynyl sugars.” Anal Bioanal Chem 2017, 409, 579.

  3. Sheta R., Woo C. M., Roux-Dalvai F., Fournier F., Bourassa S., Droit A., Bertozzi C. R., Bachvarov D. “A metabolic labeling approach for glycoproteomic analysis reveals altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells.” J Prot 2016, 145, 91.

  4. Sheta R., Roux-Dalvai F., Woo C. M., Fournier F., Bourassa S., Bertozzi C. R., Droit A., Bachvarov, D. “Proteomic dataset for altered glycoprotein expression upon GALNT3 knockdown in ovarian cancer cells” Data in Brief 2016, 8, 59.

  5. Woo C. M., Li Z., Paulson E., Herzon S. B. “Structural basis for DNA cleavage by the potent antiproliferative agent (–)-lomaiviticin A.” Proc Natl Acad Sci 2016, 11, 2851.

  6. Woo C. M., Bertozzi C. R. “Isotope targeted glycoproteomics (IsoTaG) to characterize intact, metabolically labeled glycopeptides from complex proteomes.” Curr Protoc Chem Bio 2016, 8, 59.

  7. Woo C. M., Iavarone A. T., Spiciarich D. R., Palaniappan K. K., Bertozzi C. R. “Isotope Targeted Glycoproteomics (IsoTaG): A mass independent platform for intact N- and O-glycopeptide discovery.” Nat Meth 2015, 12, 561.

  8. Woo C. M., Ranjan N., Arya D. P., Herzon S. B. “Analysis of diazofluorene DNA binding and damaging activity.  DNA cleavage by a synthetic monomeric diazofluorene.” Angew Chem Int Ed 2014, 53, 9325.

  9. Colis L. C., Woo C. M., Hegan D. C., Li Z., Glazer P. M., Herzon S. B. “The cytotoxicity of (–)-lomaiviticin A arises from induction of double-strand breaks in DNA.” Nat Chem 2014, 6, 504.

  10. Woo C. M., Gholap S. L., Herzon S. B. “Insights into lomaiviticin biosynthesis.  Isolation and structure elucidation of (–)-homoseongomycin.” J Nat Prod 2013, 76, 1238.

  11. Woo C. M., Gholap S. L., Lu L., Kaneko M., Li Z., Ravikumar P. C., Herzon S. B. “Development of enantioselective synthetic routes to (-)-kinamycin F and (-)-lomaiviticin aglycon.” J Am Chem Soc 2012, 134, 17262.

  12. Woo C. M., Beizer N. E., Janso J. E., Herzon S. B. “Isolation of lomaiviticins C-E.  Transformation of lomaiviticin C to lomaiviticin A, complete structure elucidation of lomaiviticin A, and structure-activity analyses.” J Am Chem Soc 2012, 134, 15285.

  13. Mulcahy S. P., Woo C. M., Ding W., Ellestad G. A., Herzon S. B. “Characterization of a reductively-activated elimination pathway relevant to the biological chemistry of the kinamycins and lomaiviticins.” Chem Sci 2012, 3, 1070.

  14. Herzon S. B., Woo C. M. “The diazofluorene antitumor antibiotics: Structural elucidation, biosynthetic, synthetic, and chemical biological studies.” Nat Prod Rep 2012, 29, 87.

  15. Herzon S. B., Lu L.*, Woo C. M.*, Gholap S. L. “11-Step enantioselective synthesis of (-)-lomaiviticin aglycon.” J Am Chem Soc 2011, 133, 7260.

  16. Woo C. M., Lu L., Gholap S. L., Smith D. R., Herzon S. B. “Development of a convergent entry to the diazofluorene antitumor antibiotics: Enantioselective synthesis of kinamycin F.” J Am Chem Soc 2010, 132, 2540.

  17. Gholap S. L., Woo C. M., Ravikumar P. C., Herzon S. B. “Synthesis of the fully glycosylated cyclohexenone core of lomaiviticin A.” Org Lett 2009, 11, 4322.

  18. Devji T., Reddy C., Woo C. M., Awale S., Kadota S., Carrico-Moniz D. “Pancreatic anticancer activity of a novel geranylgeranylated coumarin derivative.” Bioorg Med Chem Lett 2011, 21, 5770.

  19. Boonya-udtayan S., Yotapan N., Woo C. M., Bruns C. J., Ruchirawat S., Thasana N. “Synthesis and biological activities of azalamellarins.” Chem Asian J 2010, 5, 2113.

  20. Loehlin J. H., Lee M, Woo C. M. “Hydrogen-bond patterns and the structures of 1,4-cyclohexanediol: 2:1 cis:trans-1,4-cyclohexanediol.” Acta Cryst 2008, B64, 583.