Publications

  1. Trimpin S., Yenchick F.S., Lee C., Hoang K., Pophristic M., Karki S., Marshall D.D., Lu I.C., Lutomski C.A., El-Baba T.J., Wang B., Pagnotti V.S., Meher A.K., Chakrabarty S., Imperial L.F., Madarshahian S., Richards A.L., Lietz C.B., Moreno-Pedraza A., Leach S.M., Gibson S.C., Elia E.A., Thawoos S.M., Woodall D.W., Jarois D.R., Davis E.T.J., Liao G., Muthunayake N.S., Redding M.J., Reynolds C.A., Anthony T.M., Vithanarachchi S.M., DeMent P., Adewale A.O., Yan L., Wager-Miller J., Ahn Y.H., Sanderson T.H., Przyklenk K., Greenberg M.L., Suits A.G., Allen M.J., Narayan S.B., Caruso J.A., Stemmer P.M., Nguyen H.M., Weidner S.M., Rackers K.J., Djuric A., Shulaev V., Hendrickson T.L., Chow C.S., Pflum M.K.H., Grayson S.M., Lobodin V.V., Guo Z., Ni C.K., Walker J.M., Mackie K., Inutan E.D., McEwen C.N., New Processes for Ionizing Nonvolatile Compounds in Mass Spectrometry: The Road of Discovery to Current State-of-the-Art, J. Am. Soc. Mass. Spectrom, 2024, 35, 2753-2784
  2. Bremer HJ, Herppich AA, Pflum MKH. Kinase-catalyzed crosslinking: A comparison of ATP-crosslinker analogs, Bioorg. Med. Chem. Lett., 2024, 109, 129841
  3. Gary C.R., Acharige N.P.N., Oyewumi T.O., Pflum M.K.H., Kinase-catalyzed biotinylation for discovery and validation of substrates to multispecificity kinases NME1 and NME2, J. Biol. Chem., 2024, 300, 107588
  4. Venkatesh J., Muthu M., Singaravelu I., Cheriyan V.T., Sekhar S.C., Acharige N.C.P.N., Levi E., Assad H., Pflum M.K.H., Rishi A.K. Phosphorylation of cell cycle and apoptosis regulatory protein-1 by stress activated protein kinase P38γ is a novel mechanism of apoptosis signaling by genotoxic chemotherapy, Front. Oncol., 2024, 14, 1378888
  5. Kang M., Senatore A.J., Naughton H., McTigue M., Beltman R.J., Herppich A.A., Pflum M.K.H., Howe A.K. Protein kinase A is a functional component of focal adhesions. J. Biol. Chem., 2024, 300, 107234
  6. Bremer, H.J. and Pflum, M.K.H, Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates (K-BIPS), Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates (K-BIPS). Methods Mol. Biol., 2024, 2743, 135-152
  7. Dedigama-Arachchige PM, Acharige NPN, Zhang X, Bremer HJ, Yi Z, Pflum MKH. Identification of PP1c-PPP1R12A Substrates Using Kinase-Catalyzed Biotinylation to Identify Phosphatase Substrates. ACS Omega. 2023, 8, 35628-35637
  8. Case K.C., Beltman R.J., Pflum M.K.H., Greenberg ML. Valproate regulates inositol synthesis by reducing expression of myo-inositol-3-phosphate synthase. Sci Rep. 2023, 13, 14844
  9. Gary C.R., Pflum M.K.H.., Kinase-catalyzed Biotinylation with Inactivated Lysates for Discovery of Substrates (K-BILDS), Curr Protoc. 2023, 3, e851
  10. Beltman R.J., Herppich A.A., Bremer H.J., Pflum, M.K.H., Affinity-Based Kinase-Catalyzed Crosslinking to Study Kinase-Substrate Pairs. Bioconjug Chem. 2023; 34,1054-1060
  11. Herath, K.E. and Pflum, M.K.H., Proteomics-based Trapping with Single or Multiple Inactive Mutants Reproducibly Profiles Histone Deacetylase 1 Substrates, J. Proteomics, 2023, 274, 104807.
  12. Beltman R., and Pflum M.K.H., Kinase-Catalyzed Crosslinking and Immunoprecipitation (K-CLIP) to Explore Kinase-Substrate Pairs, Curr. Protoc., 2022, 2, e539.
  13. Karaj E., Sindi S.H., Kuganesan N., Koranne R.A., Knoff J.R., James A.W., Fu Y., Kotsull L.N., Pflum MKH, Shah Z., Taylor W.R., Tillekeratne L.M.V. First-in-Class Dual Mechanism Ferroptosis-HDAC Inhibitor Hybrids, J. Med Chem, 2022, 65, 14764-14791
  14. Banerfee, R., Karaj E., Lamichhane S., Kotsull L.N., Kuganesan N., Dragan, I., Pflum MKH, Shah Z., Slama, J., Taylor W.R., Tillekeratne L.M.V. Rational Design of Metabolically Stable HDAC Inhibitors: An Overhaul of Trifluoromethyl Ketones, Eur. J. Med. Chem, 2022, 244, 114807.
  15. Zhang, Y, Andrade R., Hanna A.H., and Pflum, M.K.H., HDAC7 Acts as an Epigenetic “Reader” of AR Acetylation through NCoR-HDAC3 Dissociation, Cell Chem. Biol.,2022, 29, 1162-1173.e5.
  16. Al-Hamashi, A.A., Koranne, R., Dlamini, S., Alqahtani, A., Karaj, E., Rashi, M.S., Knoff J.R., Dunworth, M., Pflum, M.K.H., Casero, R.A. Jr., Perera, L., Taylor, W.R., and Tillekeratne, L.M.V. A new class of cytotoxic agents targets tubulin and disrupts microtubule dynamics, Bioorg Chem, 2021, 116, 105297.
  17. Ramanayake-Mudiyanselage V., Embogama D.M., and Pflum, M.K.H., Kinase-catalyzed Biotinylation to Map Cell Signaling Pathways (K-BMAPS): Application to Epidermal Growth Factor Signaling, J. Proteome Res. 2021, 20, 4852-4861.
  18. Gomes, I.D., Ariyaratne U.V., and Pflum, M.K.H, HDAC6 Substrate Discovery using Proteomics-Based Substrate Trapping: HDAC6 deacetylates PRMT5 to influence methyltransferase activity, ACS Chem. Biol., 2021, 16, 1435-1444.
  19. Bahl, S., Ling H., Acharige, N.P.N., Santos-Barriopedro I., Pflum, M.K.H., and Seto, E., EGFR phosphorylates HDAC1 to regulate its expression and anti-apoptotic function, Cell Death Dis., 2021, 12, 469.
  20. Zhang, Y, Nalawansha D. A., Herath, K.E., Andrade R., and Pflum, M.K.H, Breast Cancer Cells Maintain Different HDAC1 Substrate and Associated Protein Profiles, Mol. Omics 2021, 17, 544-553.
  21. Fouda, A. I.,* Gamage A.K.,* and Pflum, M.K.H, An affinity-based, cysteine-specific ATP analog for kinase-catalyzed crosslinking, Angewante Chemie, 2021, 60, 9859-9862.*co-first authors
  22. Acharige, N.P.N. and Pflum, M.K.H, l‐Lactate Dehydrogenase Identified as a Protein Tyrosine Phosphatase 1B Substrate by Using K‐BIPS, ChemBioChem, 2021, 22, 186-192.
  23. Gomes, I.D. and Pflum, M.K.H, Optimal substrate trapping mutants to discover substrates of HDAC1, ChemBioChem, 2019, 20, 1444-1449
  24. Nalawansha D.A., Y. Zhang, K. Herath, Pflum, M.K.H., HDAC1 Substrate Profiling Using Proteomics-Based Substrate Trapping, ACS Chem Biol. 2018, 13, 3315–3324.
  25. Garre, S., Gamage A.K.; Faner, T., Dedigama-Arachchige P, and Pflum, M.K.H., Identification of kinases and interactors of p53 using kinase-catalyzed crosslinking and immunoprecipitation (K-CLIP), J. Am. Chem. Soc., 2018, 140, 16299-16310
  26. Fouda, A.I., Embogama, D.M., Ramanayake-Mudiyanselage, V., and Pflum, M.K.H. Chitosan-assisted permeabilization of ATP-biotin for live cell kinase-catalyzed biotinylation, Biotechniques, 2018, 65, 143-148.
  27. Anthony, T.M. and Pflum, M.K.H. Kinase-catalyzed biotinylation of DNA. Bioorg Med Chem, 2018, 15, 2331-2336.
  28. Dedigama-Arachchige, P.M., Acharige, N.P.N., and Pflum, M.K.H, Identification of PP1-Gadd34 substrates involved in the unfolded protein response using K-BIPS, a method for phosphatase substrate identification, Molecular Omics, 2018, 14, 121–133.
  29. Negmeldin A.T., Knoff, J.R., Pflum, M.K.H. The structural requirements of histone deacetylase inhibitors: C4-modified SAHA analogs display dual HDAC6/HDAC8 selectivity. Eur J Med Chem. 2018, 143, 1790-1806.
  30. Negmeldin A.T., Pflum, M.K.H. The structural requirements of histone deacetylase inhibitors: SAHA analogs modified at the C5 position display dual HDAC6/8 selectivity. Bioorg Med Chem Lett. 2017, 27, 3254-3258
  31. Nalawansha D.A., Gomes, I.; Wambua, M., and Pflum, M.K.H., HDAC inhibitor-induced mitotic arrest is mediated by Eg5/KIF11 acetylation, Cell Chem Biol. 2017, 24, 481-492
  32. Negmeldin, A.E.; Padige, G.; Bieliauskas, A.V., and Pflum, M.K.H., The structural requirements of HDAC inhibitors: SAHA analogs modified at the C2 position display HDAC6/8 selectivity, ACS Med Chem Lett., 2017, 8, 281-286.
  33. Nalawansha, D.A. and Pflum, M.K.H., LSD1 substrate binding and gene expression are affected by HDAC1-mediated deacetylation, ACS Chem. Biol. 2017, 12, 254-264.
  34. Embogama, D.M. and Pflum, M.K.H., K-BILDS: A kinase substrate discovery tool, ChemBioChem, 2017, 18, 136-141.
  35. Dedigama-Arachchige, P. and Pflum, M.K.H., K-CLASP: A phosphosite-specific kinase and interactome identification tool, ACS Chem. Biol., 2016, 11, 3251-3255.
  36. Bieliauskas A.V., Weerasinghe, S.V.W., Negmeldin, A., and Pflum, M.K.H., The structural requirements of histone deacetylase inhibitors: SAHA analogs modified on the hydroxamic acid, Arch de Pharm, 2016, 349, 373-382.
  37. Almaliti, J., Hanigan, C.L., Negmeldin, A.T., L. Perera, M.K.H. Pflum, R. A. Casero, Jr., and L.M.V. Tillekeratne, Synthesis and Biological Activity of Largazole Analogues Incorporating Major Changes in the Depsipeptide Ring, J. Med. Chem., 2016, 59, 10642-10660.
  38. Senevirathne, C., Embogama D.M., Anthony, T.M., Fouda A.E., and Pflum, M.K.H, The Generality of Kinase-Catalyzed Labeling, Bioorg Med Chem, 2016, 24, 12-19.
  39. Fouda, A.E, and Pflum, M.K.H, A Cell Permeable ATP analog, Angewante Chemie. 2015, 54, 9618-9621.
  40. Padige G., Negmeldin A.T., and Pflum, M.K.H, Development of an ELISA-based HDAC Activity Assay for Characterization of Isoform-Selective Inhibitors, J. Biomolecular Screening, 2015, 20, 1277-1285.
  41. Garre, S., Senevirathne, C., Pflum, M.K.H, A comparative study of ATP analogs for phosphorylation-dependent kinase–substrate crosslinking, Bioorg. Med. Chem. 2014, 22, 1620-1625.
  42. Wambua, M., Nalawansha, D., Negmeldin, A., and Pflum, M.K.H, Mutagenesis Studies of the 14 Å Internal Cavity of Histone Deacetylase 1: Insights towards the Acetate Escape Hypothesis and Selective Inhibitor Design, J. Med. Chem. 2014, 57, 642–650.
  43. Senevirathne, C. and Pflum, M.K.H, Biotinylated phosphoproteins from kinase-catalyzed biotinylation are stable to phosphatases: Implications for phosphoproteomics, ChemBioChem, 2013, 14, 381-387.
  44. Choi, S. E., and Pflum, M.K.H, The structural requirements of histone deacetylase inhibitors: Suberoylanilide hydroxamic acid analogs modified at the C6 position, Bioorg. Med. Chem. Lett. 2012, 22, 7084-7086.
  45. Suwal, S, Senevirathne, C., Garre S., and Pflum, M.K.H, Structural Analysis of ATP Analogs Compatible with Kinase-Catalyzed Labeling, Bioconjugate Chem. 2012, 23, 2386-2391.
  46. Senevirathne, C and Pflum, M.K.H, Kinase-catalyzed biotinylation of peptides, proteins, and lysates, Protocols in Chem. Biol., 2012, 4, 1.
  47. Choi, S.E., Weerasinghe, S.V.W., Pflum, M.K.H, The structural requirements of histone deacetylase inhibitors: Suberoylanilide hydroxamic acid analogs modified at the C3 position display isoform selectivity, 2011, 21, 6139-42.
  48. Weerasinghe S. V., Wambua M., Pflum, M. K. H, A histone deacetylase-dependent screen in yeast, Bioorg. Med. Chem. Lett., 2010, 18 (21), 7586-7592.
  49. Suwal S., and Pflum, M. K. H, Phosphorylation-Dependent Kinase-Substrate Cross-Linking, Angew. Chem. Int. Ed., 2010, 49 (9), 1627-1630.
  50. Article highlighted in: Chem & Eng News, 2010, 88, 48.           
  51. Green KD. and Pflum, M.K.H, Exploring Kinase Cosubstrate Promiscuity: Monitoring kinase activity through dansylation, ChemBioChem. 2009, 10, 234-237.
  52. Weerasinghe S. V., Estui G., Wiest O., and Pflum, M.K.H, Residues in the 11Å channel of histone deacetylase 1 promote catalytic activity, J. Med. Chem. 2008, 1 (18), 5542-5551.
  53. Singh E.K., Ravula S., Pan C., Pan P., Vasko R.C., Lapera S.A., Pflum, M.K.H, S. R. McAlpine, Synthesis and biological evaluation of histone deacetylase inhibitors that are based on the FR235222 scaffold, Bioorg. Med Chem Lett.  2008, 18, 2549-2554.
  54. Karwowska-Desaulniers P., Ketko A., Kamath N., and Pflum, M.K.H., Histone Deacetylase 1 phosphorylation at S421 and S423 is constitutive in vivo, but dispensable in vitro, Biochem. Biophys. Res. Comm., 2007, 361, 349-355.
  55. Bieliauskas A.V., Weerasinghe S.V., Pflum, M.K.H., Structural Requirements of HDAC Inhibitors: SAHA Analogs Functionalized Adjacent to the Hydroxamic Acid, Bioorg. Med. Chem. Lett. 2007, 17, 2216-2219.
  56. Green K.D. and Pflum, M.K.H., Kinase-Catalyzed Biotinylation for Phosphoprotein Detection, J. Am. Chem. Soc., 2007, 129, 10-11. Article highlighted in: ACS Chemical Biology, 2007, 2, 85. Journal of Proteome Research, 2007, 6, 931
  57. Warthaka M., Karwowska-Desaulniers P., and Pflum, M.K.H., Phosphopeptide Modification and Enrichment By Oxidation-Reduction Condensation, ACS Chemical Biology, 2006, 1, 697-701.
  58. Kamath N., Karwowska-Desaulniers P., Pflum, M.K.H., Limited Proteolysis of Histone Deacetylase 1, BMC Biochemistry, 2006, 7, 22.
  59. Flammer J., Popova K., and Pflum, M.K.H., Cyclic AMP Response Element-Binding Protein (CREB) and CAAT/Enhancer-Binding Protein beta (C/EBPbeta) Bind Chimeric DNA Sites with High Affinity, Biochemistry, 2006, 45, 9615-23.