Publications
2023
A Method to Monitor Activity of SARS-CoV-2 Nsp3 from Cells. Christopher Rainville, David E. Sterner and Kumar Suresh. Methods Mol. Biol., 2023;2591:269-282. doi: 10.1007/978-1-0716-2803-4_16. PMID: 36350554.
Potent and Selective Covalent Inhibition of the Papain-like Protease from SARS-CoV-2. Brian C. Sanders, Suman Pohkrel, Audrey D. Labbe, Irimpan I. Mathews, Connor J. Cooper, Russell B. Davidson, Gwyndalyn Phillips, Kevin L. Weiss, Qiu Zhang, Hugh O’Neill, Manat Kaur, Lori Ferrins, Jurgen G. Schmidt, Walter Reichard, Surekha Surendranathan, Jyothi Parvathareddy, Lexi Phillips, Christopher Rainville, David E. Sterner, Desigan Kumaran, Babak Andi, Gyorgy Babnigg, Nigel W. Moriarty, Paul D. Adams, Andrzej Joachimiak, Brett L. Hurst, Suresh Kumar, Tauseef R. Butt, Colleen B. Jonsson, Soichi Wakatsuki, Stephanie Galanie, Martha S. Head, and Jerry M. Parks. Nature Communications. 14, Article number: 1733 (2023)
The Ubiquitin Proteasome System as a Therapeutic Area in Parkinson’s Disease . Kumar Suresh, Michael Mattern, Matthew S. Goldberg, Tauseef R Butt. NeuroMolecular Medicine. 2023 (Manuscript accepted for publication).
2022
Combined deep learning and molecular docking simulations approach identifies potentially effective FDA approved drugs for repurposing against SARS-CoV-2. Muhammad U. Anwaar, Farjad Adnan, Asma Abro, Rayyan A. Khan, Asad U. Rehman, Muhammad Osama, Christopher Rainville, Suresh Kumar, David E. Sterner, Saad Javed, Syed B. Jamal, Ahmadullah Baig, Muhammad R. Shabbir, Waseh Ahsa, Tauseef R. Butt, Muhammad Z. Assir. Computers in Biology and Medicine. November 2021, 105049.
2021
The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22. Timothy J Stanek, Victoria J Gennaro, Mason A Tracewell, Daniela Di Marcantonio, Kristen L Pauley, Sabrina Butt, Christopher McNair, Feng Wang, Andrew V Kossenkov, Karen E Knudsen, Tauseef Butt, Stephen M Sykes, and Steven B McMahon. EMBO J (2021) 40:e102509.
2020
Advances in the Development of Deubiquitinase (DUB) Inhibitors. Jian Wu, Xu Wang, Kumar Suresh, 2019 Medicinal Chemistry Reviews. Volume 54, Chapter 17.
2019
TAM receptors attenuate murine NK-cell responses via E3 ubiquitin ligase Cbl-b. Chirino LM, Kumar S, Okumura M, et al. , 2019 Sep 17. Eur J Immunol. 2019;10.1002/eji.201948204. doi:10.1002/eji.201948204
Using Ubiquitin Binders to Decipher the Ubiquitin Code. Mattern M; Sutherland J; Kadimisetty K; Barrio R; Rodriguez M. Trends in Biochemical Sciences. 2019 Feb 25. doi: 10.1016/j.tibs.2019.01.011
USP7 Cooperates with NOTCH1 to Drive the Oncogenic Transcriptional Program in T-Cell Leukemia. Jin Q; Martinez C; Arcipowski K; Zhu Y; Gutierrez-Diaz B; Johnson M; Goo Y; Marshall S; Rendleman E; Takahashi Y; et al. Clinical Cancer Research- an official journal of the American Association for Cancer Research. 2019 Jan 1;25(1):222-239. doi: 10.1158/1078-0432.CCR-18-1740
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2018
Control of CCND1 ubiquitylation by the catalytic SAGA subunit USP22 is essential for cell cycle progression through G1 in cancer cells. Gennaro V; Stanek T; McMahon S; Peck A; Sun Y; Rui H; Wang F; Butt T; Qie S; Diehl A; et al. Proceedings of the National Academy of Sciences of the United States of America. 2018 Sep 7;115(40):e9298-e9307. https://doi.org/10.1073/pnas.1807704115
2017
Active site-targeted covalent irreversible inhibitors of USP7 impair the functions of Foxp3+ T-regulatory cells by promoting ubiquitination of Tip60 Wang F, Wang L, Wu J, Sokirniy I, Nguyen P, Bregnard T, Weinstock J, Mattern M, Bezsonova I, Hancock WW, Kumar S PLoS One. 2017 Dec 13;12(12):e0189744. doi: 10.1371/journal.pone.0189744.
USP7-Specific Inhibitors Target and Modify the Enzyme’s Active Site via Distinct Chemical Mechanisms. Pozhidaeva A, Valles G, Wang F, Wu J, Sterner DE, Nguyen P, Weinstock J, Kumar KGS, Kanyo J, Wright D, Bezsonova I. Cell Chem Biol. 2017 Dec 21;24(12):1501-1512.e5. doi: 10.1016/j.chembiol.2017.09.004.
Chemical Approaches to Intervening in Ubiquitin Specific Protease 7 (USP7) Function for Oncology and Immune Oncology Therapies. Wu, J., Kumar, S., Wang, F., Wang, H., Chen, L., Arsenault, P., Mattern, and, M., and Weinstock, J.J. Med. Chem. 2017, DOI: 1021/acs.jmedchem.7600498.
2016
HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma. Tavana, O., Li, D., Dai, C., Lopez, G., Banerjee, D., Kon, N., Chen, C., Califano, A., Yamashiro, D., Sun, H., and Gu, W. Nature Med 2016, Oct; 22(10):1180-1186.
Ubiquitin-specific Protease-7 Inhibition Impairs Tip60-dependent Foxp3+ T-regulatory Cell Function and Promotes Antitumor Immunity. Wang, L., Kumar, S., Dahiya, S., Wang, F., Wu, J., Newick, K., Han, R., Samanta, A., Beier, U.H., Akimova, T., Bhatti, T.R., Nicholson, B., Kodrasov, M.P., Agarwal, S., Sterner, D.E., Gu, W., Weinstock, J., Butt, T.R,, Albelda, S.M., Hancock, W.W. EBioMedicine 2016, Nov; 13: 99-112.
2015
Itch WW domains inhibit its E3 ubiquitin ligase activity by blocking E2-E3 transthiolation.
Riling, C., Kamadurai, H., Kumar, S., O’Leary, C.E., Wu, K.P., Manion, E.E., Ying, M., Schulman, B.A., and Oliver, P.M. J. Biol. Chem. 2015, August 5. (Epub ahead of print).
2014
Proteasome inhibitors vs. E3 ligase inhibitors for cancer therapy.
Mattern, M.R., Eddins, M.J., Agarwal, S., Sterner, D.E., Kodrasov, M.P., Suresh Kumar, K.G., Wu, J., and Nicholson, B. In: QP Dou, Ed., Resistance to proteasome inhibitors in cancer. New York, NY: Springer Publishing Co. 2014, August. 291-316.
Discovery of therapeutic deubiquitylase effector molecules: current perspectives.
Nicholson, B., Suresh Kumar, K.G., Agarwal, S., Eddins, M., Marblestone, J.G., Wu, J., Kodrasov, M.P., LaRocque, J.P., Sterner, D.E., and Mattern, M.R. J. Biomol. Screening. 2014, March.19(7):989-999 (Epub ahead of print).
2013
Comprehensive Ubiquitin E2 Profiling of Ten Ubiquitin E3 Ligases.
Marblestone J.G., Butt S., McKelvey D.M., Sterner D.E., Mattern M.R., Nicholson B., Eddins M.J. Cell Biochem Biophys. 2013 Sep;67(1):161-7.
Spongiacidin C, a pyrrole alkaloid from the marine spongeStylissa massa, functions as a USP7 inhibitor.
Yamaguchi, M., Miyazaki, M., Kodrasov, M.P., Rotinsulu, H., Losung, F., Mangindaan, R.E.P., de Voogd, N.J., Yokosawa, H., Nicholson, B., and Tsukamoto, S. Bioorganic & Medicinal Chemistry Letters. 2013 May 3. 23; 3884-3886.
2012
Bioluminescence Assay Platform for Selective and Sensitive Detection of Ub/Ubl Proteases.
Orcutt, S.J., Wu, J., Eddins, M.J., Leach, C.A., and Strickler, J.E. Biochim Biophys Acta. 2012 November; 1823(11): 2079-2086.
A Small Molecule Inhibitor of Ubiquitin-Specific Protease-7 Induces Apoptosis in Multiple Myeloma Cells and Overcomes Bortezomib Resistance.
Chauhan, D., Tian, Z., Nicholson, B., Kumar, K.G., Zhou, B., Carrasco, R., McDermott, J.L., Leach, C.A., Fulcinniti, M., Kodrasov, M.P., Weinstock, J., Kingsbury, W.D., Hideshima, T., Shah, P.K., Minvielle, S., Altun, M., Kessler, B.M., Orlowski, R., Richardson, P., Munshi, N., and Anderson, K.C. Cancer Cell. 2012 Sep 11;22(3):345-58.
Selective Dual Inhibitors of the Cancer-Related Deubiquitylating Proteases USP7 and USP47.
Weinstock, J., Wu, J., Cao, P., Kingsbury, W.D., McDermott, J.L., Kodrasov, M.P., McKelvey, D.M., Suresh Kumar, K.G., Goldenberg S.J., Mattern, M.R., and Nicholson, B. ACS Medicinal Chemistry Letters. 2012 Sep. 3(10);789–792.
Analysis of ubiquitin E3 ligase activity using selective polyubiquitinbinding proteins.
Marblestone, J.G., LaRocque J.P., Mattern, M.R., and Leach, C.A., Biochimica et Biophysica Acta. 2012 June 18. 1823; 2094-2097.
Ubiquitin-based anticancer therapy: Carpet bombing with proteasome inhibitors vs surgical strikes with E1, E2, E3, or DUB inhibitors.
Mattern, M.R., Wu, J., and Nicholson, B. Biochimica et Biophysica Acta. 2012 May 17; 1823. 2014-2021
2011
Activity-Based Chemical Proteomics Accelerates Inhibitor Development for Deubiquitylating Enzymes.
Altun, M., Kramer, H.B., Willems, L.I., McDermott, J.L., Leach, C.A., Goldenberg, S.J., Kumar, K.G.S., Konietzny, R., Fischer, R., Kogan, E., Mackeen, M.M., McGouran, J., Khoronenkova, S.V., Parsons, J.L., Dianov, G.L., Nicholson, B.,Kessler, B.M. Chemistry & Biology, 2011 Nov 23;18(11):1401-12
Pharmacological targets in the ubiquitin system offer new ways of treating cancer, neurodegenerative disorders and infectious diseases.
Edelmann, M.J., Nicholson, B., Kessler, B.M., Expert Review Mol Med. 2011 Nov 17;13:e35.
Tissue-specific expression and post-translational modifications of plant- and bacterial-type phosphoenolpyruvate carboxylase isozymes of the castor oil plant, Ricinus communis L.
O’Leary, B., Fedosejevs, E.T., Hill, A.T., Bettridge, J., Park, J., Rao, S.K., Leach, C.A., Plaxton, W.C. J Exp Bot. 2011 Nov;62(15):5485-95
A baker’s dozen of ubiquitin.
Haas, A.L., Leach, C.A. Cell Biochem Biophys. 2011 Jun;60(1-2):1
The Multifaceted Roles of USP7: New Therapeutic Opportunities.
Nicholson, B., and Suresh Kumar, K.G., Cell Biochem Biophys. 2011 Jun;60(1-2):61-8.
Targeting the Ubiquitin E3 Ligase MuRF1 to Inhibit Muscle Atrophy.
Eddins, M.J., Marblestone, J.G., Suresh Kumar, K.G., Leach, C.A., Sterner, D.E., Mattern, M.R., and Nicholson, B. Cell Biochem Biophys. 2011 Jun;60(1-2):113-8.
The Ubiquitin specific protease USP34 regulates Axin stability and Wnt/β-catenin signaling.
Lui, T.T., Lacroix, C., Ahmed, S.M., Goldenberg, S.J., Leach, C.A., Daulat, A.M., Angers, S. Mol. Cell Biol. 2011 May;31(10):2053-65.
Characterization of selective ubiquitin and ubiquitin-like protease inhibitors using a fluorescence-based multiplex assay format.
Tian, X., Isamiddinova, N.S., Peroutka, R.J., Goldenberg, S.J., Mattern, M.R., Nicholson, B., Leach, C..Assay Drug Dev Technol. 2011 Apr;9(2):165-73.
2010
Novel Approach for Characterizing Ubiquitin E3 Ligase Function.
Marblestone, J.G., Suresh Kumar, K.G., Eddins, M.J., Leach, C.A., Sterner, D.E., Mattern, M.R., and Nicholson, B. (2010). J Biomol Screening. Dec;15(10):1220-8
Ubiquitin Drug Discovery and Diagnostics 2009 – First Annual Conference.
Marblestone, J,G,. (2010). IDrugs, (12): 750-753
Strategies for the Identification of Ubiquitin Ligase Inhibitors.
Goldenberg, S.J., Marblestone, J.G., Mattern, M.R. and Nicholson, B. (2010). Biochemical Society Transactions, 38: 132-6
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