Publications from NYU:

Sales, A.H.; Fu, I.; Durandin, A.; Ciervo, S.; Lupoli, T.J.; Shafirovich, V.; Broyde, S.; Geacintov, N.E. Variable Inhibition of DNA Unwinding Rates Catalyzed by the SARS-CoV-2 Helicase Nsp13 by Structurally Distinct Single DNA Lesions. Int. J. Mol. Sci. 2024, 25, 7930. DOI: https://doi.org/10.3390/ijms25147930 (formerly: bioRxiv. 2021, DOI: 10.1101/2021.10.13.464299).

Soper, N.; Yardumian, I.; Chen, E.; Yang, C.; Ciervo, S.; Oom, A. L.;  Desvignes, L.; Mulligan, M. J.; Zhang, Y.; Lupoli, T. J. A Repurposed Drug Interferes with Nucleic Acid to Inhibit the Dual Activities of Coronavirus Nsp13. ACS Chem. Biol. 2024, 19, 1593. DOI: 10.1021/acschembio.4c00244.

Nelson, B. N.; Soper, N.; Lupoli, T. J. Bacterial J-domains with C-terminal Tags Contact the Substrate Binding Domain of DnaK Sequester the Chaperone Activity. ChemBioChem 2023, 24, e202300261. DOI: 10.1002/cbic.202300261.

Richards, A.; Lupoli, T. J. Peptide-based Molecules for the Disruption of Bacterial Hsp70 Chaperones. Curr. Opin. Chem. Biol. 2023, 76, 102373. DOI: 10.1016/j.cbpa.2023.102373.

Harnagel, A.P.; Sheshova, M.; Zheng, M.; Zheng, M.; Skorupinska-Tudek, K.; Swiezewska, E.; Lupoli, T. J. Preference of Bacterial Rhamnosyltransferases for 6-Deoxysugars Reveals a Strategy To Deplete O-Antigens. J. Am. Chem. Soc. 2023, 145, 15639, DOI: 10.1021/jacs.3c03005.

Zheng, M.; Lupoli, T. J. Counteracting Antibiotic Resistance Enzymes and Efflux Pumps. Curr. Opin. Microbiol. 2023, 75, 102334. DOI: 10.1016/j.mib.2023.102334.

Zheng, M.; Zheng, M.; Kim, H.; Lupoli, T. J. Feedback Inhibition of Bacterial Nucleotidyltransferases by Rare Nucleotide L-Sugars Restricts Substrate Promiscuity. J. Am. Chem. Soc. 2023, 145, 15623. DOI: 10.1021/jacs.3c02319.

Zheng, M.; Zheng, M.; Lupoli, T. J. Expanding the substrate scope of a bacterial nucleotidyltransferase via allosteric mutations. ACS Infect. Dis. 2022, 8, 2035-44. DOI:10.1021/acsinfecdis.2c00402.

Richards, A.; Yawson, G. K.; Nelson, B.; Lupoli, T. J. Complementary Protocols to Evaluate Inhibitors Against the DnaK Chaperone Network. STAR Protoc. 2022, 3, 101381. DOI: 10.1016/j.xpro.2022.101381.

Nelson, B.; Hong, S. H.; Lupoli, T. J. Protein Cofactor Mimics Disrupt Essential Chaperone Function in Stressed Mycobacteria. ACS Infect. Dis. 2022, 8, 901. DOI: 10.1021/acsinfecdis.1c00651.

Hosfelt, J.; Richards, A.; Zheng, M.; Adura, C.; Nelson, B.; Yang, A.; Fay, A.; Resager, W.; Ueberheide, B.; Glickman, J.F.; Lupoli, T. J. An Allosteric Inhibitor of Bacterial Hsp70 Chaperone Potentiates Antibiotics and Mitigates Resistance. Cell Chem. Biol. 2022, 29, 854-869.e9. DOI: 10.1016/j.chembiol.2021.11.004.

Zheng, M.; Zheng, M.; Epstein, S.; Harnagel, A.P.; Kim, H.; Lupoli, T. J. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem. Biol. 2021, 16, 1841-1865. DOI: 10.1021/acschembio.1c00341.

Zheng, M.; Lupoli, T. J. Modulation of a Mycobacterial ADP-Ribosyltransferase to Augment Rifamycin Antibiotic Resistance. ACS Infect. Dis. 2021, 7, 2604-2611. DOI: 10.1021/acsinfecdis.1c00297.

Harnagel, A; Lopez Quezada, L; Park, S.W.; Baranowski, C.; Kieser, K.; Jiang, X.; Roberts, J.; Vaubourgeix, J.; Yang, A.; Nelson, B.; Fay, A.; Rubin, E.; Ehrt, S.; Nathan, C.; Lupoli, T. J. Non-Redundant Functions of Mycobacterium tuberculosis Chaperones Promote Survival Under Stress. Mol Microbiol. 2021, 115, 272-289. DOI: 10.1111/mmi.14615.

Krishna, K.; Lupoli, T.J. Exploiting Existing Molecular Scaffolds for Long-Term COVID Treatment. ACS Med. Chem. Lett. 2020, 11, 1357-1360. DOI: 10.1021/acsmedchemlett.0c00254. 

Publications from Graduate and Postdoctoral Training:

Quezada, L.L.; Smith, R.; Lupoli, T.J.; Edoo, Z.; Li, X.; Gold, B.; Roberts, J.; Ling, Y.; Park, S.W.; Nguyen, Q.; Schoenen, F.J.; Li, K.; Hugonnet, J.; Arthur, M.; Sacchettini, J.C.; Nathan, C.; Aubé, J. Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases. Front. Microbiol. 2020, 11, 1248. DOI: 10.3389/fmicb.2020.01248.

Yu, H.; Lupoli, T.J.; Kovach, A.; Meng, X.; Zhao, G.; Nathan, C.F.; Li, H. ATP hydrolysis-coupled peptide translocation mechanism of Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U.S.A.  2018, 115, E9560-E9569.

Lupoli, T.J.*; Vaubourgeix, J.*; Burns-Huang, K.*; Gold, B. Targeting the Proteostasis Network for Mycobacterial Drug Discovery.  ACS Infect. Dis., 2018, 4, 478–98.

Lupoli, T.J.; Fay, A.; Adura, C.; Glickman, M.; Nathan, C. Reconstitution of a Mycobacterium tuberculosis Proteostasis Network Highlights Essential Cofactor Interactions with Chaperone DnaK. Proc. Natl. Acad. Sci. U.S.A. 2016, 113, E7947-E7956.

Markovski, M.; Bohrhunter, J. L.; Lupoli, T. J.; Uehara, T.; Walker, S.; Kahne, D. E.; Bernhardt, T. G. Cofactor bypass variants reveal a conformational control mechanism governing cell wall polymerase activity. Proc. Natl. Acad. Sci. U.S.A. 2016, 113, 4788-93. 4

Vaubourgeix, J.; Lin, G.; Dhar, N.; Chenouard, N.; Jiang, X.; Botella, H.; Lupoli, T.; Mariani, O.; Yang,G.; Ouerfelli, O.; Unser, M.; Schnappinger, D.; McKinney, J.; Nathan, C. Stressed mycobacteria use the chaperone ClpB to sequester irreversibly oxidized proteins asymmetrically within and between cells. Cell Host Microbe 2015, 17, 178-90.

Lebar, M. D.; May, J. M.; Meeske, A. J.; Leiman, S. A.; Lupoli, T. J.; Tsukamoto, H.; Losick, R.; Rudner, D. Z.; Walker, S.; Kahne, D. Reconstitution of peptidoglycan cross-linking leads to improved fluorescent probes of cell wall synthesis. J. Am. Chem Soc. 2014, 136, 10874-7.

Lupoli, T. J.; Lebar, M. D.; Markovski, M.; Bernhardt, T.; Kahne, D.; Walker, S. Lipoprotein activators stimulate Escherichia coli penicillin-binding proteins by different mechanisms. J. Am. Chem Soc. 2014, 136, 52-5.

Rebets, Y.; Lupoli, T.; Qiao, Y.; Schirner, K.; Villet, R.; Hooper, D.; Kahne, D.; Walker, S. Moenomycin resistance mutations in Staphylococcus aureus reduce peptidoglycan chain length and cause aberrant cell division. ACS Chem. Biol. 2014, 9, 459-67.

Lebar, M. D.; Lupoli, T. J.; Tsukamoto, H.; May, J. M.; Walker, S.; Kahne, D. Forming crosslinked peptidoglycan from synthetic gram-negative Lipid II. J. Am. Chem. Soc. 2013, 12, 4632-5.

Knerr, P. J.; Oman, T. J.; Garcia De Gonzalo, C. V.; Lupoli, T. J.; Walker, S.; van der Donk, W. A. Non-proteinogenic Amino Acids in Lacticin 481 Analogues Result in More Potent Inhibition of Peptidoglycan Transglycosylation. ACS Chem. Biol. 2012, 7, 1791-5.

Lupoli, T.; Hooper, D. C.; Arnaout, R. A.; Kahne, D.; Walker, S. Pharmacology of Bacterial and Mycobacterial
Infections: Cell Wall Synthesis. In Principles of Pharmacology; 3rd Ed. Golan, D.E. Ed. Lippincott Williams & Wilkins: Philadelphia, 2012; pp 599-617.

Oman, T. J.; Lupoli, T. J.; Wang, T. S. A.; Kahne, D.; Walker, S.; van der Donk, W. A. Haloduracin α Binds the Peptidoglycan Precursor Lipid II with 2:1 Stoichiometry. J. Am. Chem. Soc. 2011, 133, 17544-47.

Lupoli, T. J.; Tsukamoto, H.; Doud, E. H.; Wang, T. S.; Walker, S.; Kahne, D. Transpeptidase-Mediated Incorporation of D-Amino Acids into Bacterial Peptidoglycan. J. Am. Chem. Soc. 2011, 133, 10748-51.

Wang, T. S.; Lupoli, T. J.; Sumida, Y.; Tsukamoto, H.; Wu, Y.; Rebets, Y.; Kahne, D. E.; Walker, S. Primer Preactivation of Peptidoglycan Polymerases. J. Am. Chem. Soc. 2011, 133, 8528-30.

Paradis-Bleau, C.; Markovski, M.; Uehara, T.; Lupoli, T. J.; Walker, S.; Kahne, D. E.; Bernhardt, T. G. Lipoprotein Cofactors Located in the Outer Membrane Activate Bacterial Cell Wall Polymerases. Cell 2010, 143, 1110-20.

Lupoli, T. J.; Taniguchi, T.; Wang, T. S.; Perlstein, D. L.; Walker, S.; Kahne, D. Studying a Cell Division Amidase Using Defined Peptidoglycan Substrates. J. Am. Chem. Soc. 2009, 131, 18230-1.

Fridman, M.; Balibar, C. J.; Lupoli, T.; Kahne, D.; Walsh, C. T.; Garneau-Tsodikova, S., Chemoenzymatic Formation of Novel Aminocoumarin Antibiotics by the Enzymes CouN1 and CouN7. Biochemistry 2007, 46, 8462-71.

Leimkuhler, C.; Fridman, M.; Lupoli, T.; Walker, S.; Walsh, C. T.; Kahne, D., Characterization of Rhodosaminyl Transfer by the AknS/AknT Glycosylation Complex and Its Use in Reconstituting the Biosynthetic Pathway of Aclacinomycin A. J. Am. Chem. Soc. 2007, 129, 10546-50.