Daniel Bachovchin: Publications

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Daniel Bachovchin: Publications

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51.  Tsamouri, L.P; Hsiao, J.C.; Wang, Q.; Geeson, M.B; Huang, H.-C.; Nambiar, D.R.; Zou, M.; Ball, D.P.; Chui, A.J.; Bachovchin, D. A.* “The hydrophobicity of the CARD8 N-terminus tunes inflammasome activation.” Cell Chem Biol, 2024, in press.

50.  Geeson, M.B*; Hsiao, J.C. *; Tsamouri, L.P; Ball, D.P.; Bachovchin, D. A. # “The interaction between NLRP1 and oxidized TRX1 involves a transient disulfide bond.” Cell Chem Biol. 2024, 31, 955-961.

49. Bhattacharjee, A.; Bachovchin, D. A.# “DPP8/9 are not required to cleave most proline containing peptides.” Israel Journal of Chemistry, 2023, e202200117.

48.  Chen, Q.; Wang, A.; Covelli, D.J.; Orth-He, E.L.; Rao, S.D.; Huang, H.C.; Ball, D.P.; Hsiao, J.C.; Bachovchin, D. A.# “Optimized M24B Aminopeptidase Inhibitors for CARD8 Inflammasome Activation.” J Med Chem, 2023, 66, 111965.

47.  Orth-He, E.L.*; Huang, H.C.*; Rao, S.D.; Wang, Q.; Chen, Q.; O’Mara, C.M.; Chui, A.J.; Saoi, M.; Griswold, A.R.; Bhattacharjee, A.; Ball, D.P.; Cross, J.R.; Bachovchin, D. A.# “Cytosolic peptide accumulation activates the NLRP1 and CARD8 inflammasomes.” Cell Reports, 2023, 42, 111965.

46.  Wang, Q. Hsiao, J.C.; Yardeny, N.; Huang, H.C.; O’Mara, C.M.; Orth-He, E.L.; Ball, D.P.; Zhang, Z.; Bachovchin, D. A.# “The NLRP1 and CARD8 inflammasomes detect reductive stress.” Cell Reports, 2023, 42, 111966.

45.  Ball, D.P.; Tsamouri, L.P.; Wang, A.E.; Warren, C.D.; Wang, Q.; Edmonson, I.H.; Griswold, A.R.; Rao, S.D.; Johnson, D.C.; Bachovchin, D. A.#; “Oxidized thioredoxin-1 restrains the NLRP1 inflammasome.” Science Immunol. 2022, 7, eabm7200.

44.  Volpe, M.R.; Velilla, J.A.; Daniel-Ivad, M; Yao, J.J.; Stornetta, A.; Villalta, P.W.; Huang, H.C.; Bachovchin, D.A.; Balbo, S.; Gaudet, R.; Balskus, E.P.# “A small molecule inhibitor prevents gut bacterial genotoxin production,” Nat Chem Biol. 2022, 19, 159-167.

43.  Hsiao, J.C.#; Neugroschl, A.R.; Chui, A.J.; Taabazuing, C.Y.; Griswold, A.R.; Wang, Q.; Huang, H.C.; Orth-He, E.L.; Ball, D.P.; Hiotis, G.; Bachovchin, D.A.# “A ubiquitin-independent proteasome pathway controls activation of the CARD8 inflammasome,” J Biol Chem. 2022, 298, 102032.

42.  Griswold, A.R.#; Huang, H.C.; Bachovchin, D.A.# “The NLRP1 Inflammasome induces pyroptosis in human corneal epithelial cells,” Invest Opthalmol Vis Sci. 2022, 63, 2.

41.  Rao, S.D.*; Chen, Q.*; Wang, Q.*; Orth-He, E.L.*; Saoi, M.; Griswold, A.R.; Bhattacharjee, A.; Ball, D.P.; Huang, H.-C.; Chui, A.J.; Covelli, D.J.; You, S.; Cross, J.R.; Bachovchin, D.A. # “M24B aminopeptidase inhibitors selectively activate the CARD8 inflammasome.” Nat Chem Biol. 2022, 18, 565-574.

40.  Sharif, H.*; Hollingsworth, R.L. *; Griswold, A.R.*; Hsiao, J.C.; Wang, Q.; Bachovchin, D.A. #; Wu, H. # “Structural mechanism of CARD8 regulation by DPP9.” Immunity, 2021, 54, 1392-1404.

39.  Hollingsworth, R.L. *; Sharif, H. *; Griswold, A.R. *; Fontana, P.; Mintseris, J.; Dagbay, K.B.; Paulo, J.A.; Gygi, S.P.; Bachovchin, D.A. #; Wu, H. # “DPP9 sequesters the NLRP1 C-terminus to repress inflammasome activation.” Nature, 2021, 592, 778-783.

38. Bachovchin, D.A. # “NLRP1: A jack of all trades, or a master of one?” Mol. Cell, 2021, 81, 423-425.

37.  Hollingsworth, R.L. *; David, L.*; Li, Y.*; Griswold, A.R.; Ruan, J.; Sharif, H.; Fontana, P.; Orth-He, E.L.; Fu, T.M.; Bachovchin, D.A.; Wu, H. “Mechanism of filament formation in UPA-promoted CARD8 and NLRP1 inflammasomes” Nature Commun. 2021, 12, 189.

36.  Chui, A.C.; Griswold, A.R.; Taabazuing, C.Y.; Orth, E.L.; Gai, K.; Rao, S.D.; Ball, D.P.; Hsiao, J.C.; Bachovchin, D.A. # “Activation of the CARD8 inflammasome requires a disordered region.” Cell Reports. 2020, 33, 108264.

35.  Johnson, D.C.; Okondo, M.C.; Orth, E.L.; Rao, S.D.; Huang, H.C.; Ball, D.P.; Bachovchin, D.A. # “DPP8/9 inhibitors activate the CARD8 inflammasome in resting lymphocytes.” Cell Death Dis. 2020, 11, 628.

34.  Taabazuing, C.Y.; Griswold, A.R.; Bachovchin, D.A. # “The NLRP1 and CARD8 inflammasomes.” Immunological Reviews. 2020, doi: 10.1111/imr.12884.

33.  Ball, D.P.*; Taabazuing, C.Y.*; Griswold, A.R.; Orth, E.L.; Rao, S.D.; Kotliar, I.B.; Vostal, L.E.; Johnson, D.C.; Bachovchin, D.A. # “Caspase-1 interdomain linker cleavage is required for pyroptosis.” Life Sci Alliance. 2020, 3, e202000664­.

32.  Griswold, A.R.; Ball, D.P.; Bhattacharjee, A.; Chui, A.J.; Rao, S.D.; Taabazuing, C.Y.; Bachovchin, D.A. # “DPP9’s enzymatic activity and not its binding to CARD8 inhibits inflammasome activation.” ACS Chem Biol. 2019, 14, 2424-2429.

31.  Gai, K.*; Okondo, M.C.*; Rao, S.D.; Chui, A.J.; Ball, D.P.; Johnson, D.C.; Bachovchin, D.A. # “DPP8/9 Inhibitors are universal activators of functional NLRP1 alleles.” Cell Death Dis. 2019, 10, 587.

30. Griswold, A.R.; Cifani, P.; Rao, S.D.; Axelrod, A.J.; Miele, M.M.; Hendrickson, R.C.; Kensis, A.; Bachovchin, D.A. # “A chemical strategy for protease substrate profiling.” Cell Chem Biol. 2019, 26, 901-907.

29.  Chui, A.J*; Okondo, M.C.*; Rao, S.D.*; Gai, K.; Griswold, A.R.; Johnson, D.C.; Ball, D.P.; Taabazuing, C.Y.; Orth, E.L.; Vittimberga, B.A.; Bachovchin, D.A. # “N-terminal degradation activates the Nlrp1b inflammasome.” Science. 2019, 365, 82-85.

28.  Buckley B.J.; Aboelela, A.; Minaei, E.; Jiang, L.X.; Xu, Z.; Ali, U; Fildes, K; Cheung, C.Y.; Cook, S.M.; Johnson, D.C.; Bachovchin, D.A.; Cook, G.M.; Apte, M.; Huang, M.; Ranson, M.; Kelso, M.J. “6-Substituted Hexamethylene Amiloride (HMA) Derivatives as Potent and Selective Inhibitors of the Human Urokinase Plasminogen Activator for Use in Cancer.” J Med Chem. 2018, in press.

27.  Johnson, D. C. *; Taabazuing, C. Y. *; Okondo, M. C.; Chui, A. J.; Rao, S. D.; Brown, F. C; Reed, C.; Peguero, E.; de Stanchina, E.; Kentsis, A.; Bachovchin, D. A. # “DPP8/9 inhibitor-induced pyroptosis for treatment of acute myeloid leukemia.” Nat Med. 2018, 24, 1151-1156.

26.  Okondo, M. C.*; Rao, S. D.*; Taabazuing, C. Y.*; Chui, A. J.; Poplawski, S. E.; Johnson, D. C.; Bachovchin, D. A. # “Inhibition of Dpp8/9 Activates the Nlrp1b Inflammasome.” Cell Chem Biol. 2018, 25, 262-267.

25.  Goel, P.; Jumpertz, T.; Mikles, D.C.; Tichá, A.; Nguyen, M.T.N.; Verhelst, S.; Hubalek, M.; Johnson, D.C.; Bachovchin, D.A.; Ogorek, I.; Pietrzik, C.U.; Strisovsky, K.; Schmidt, B.; Weggen, S. “Discovery and Biological Evaluation of Potent and Selective N-Methylene Saccharin-Derived Inhibitors for Rhomboid Intramembrane Proteases.” Biochemistry. 2017, 56, 6713-6725.

24.  Tichá, A.; Stanchev, S.; Vinothkumar, K.R.; Mikles, D.C.; Pachl, P.; Began, J.; Škerle, J.; Švehlová, K.; Nguyen, M.T.N.; Verhelst, S.H.L.; Johnson, D.C.; Bachovchin, D.A.; Lepšík, M.; Majer, P.; Strisovsky, K. “General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases.” Cell Chem Biol. 2017, 24, 1523-1536.

23.  Taabazuing, C. Y.; Okondo, M. C.; Bachovchin, D. A. # “Pyroptosis and apoptosis pathways engage in bidirectional crosstalk in monocytes and macrophages.” Cell Chem Biol. 2017, 24, 507-514.

22. Keckesova, Z.; Donaher, J.; DeCock, J.; Freinkman, E.; Lingrell, S.; Bachovchin, D. A.; Bierie, B.; Tischler, V.; Noske, A.; Reinhardt, F.; Thiru, P.; Golub, T.R.; Vance, J., Okondo, M.; Weinberg, R. “LACTB, a tumor suppressor that modulates lipid metabolism and differentiation.” Nature. 2017, 543, 681-686.

21. Okondo, M.C.; Johnson, D. C., Sridharan, R., Go, E. B., Chui, A. J., Wang, M. S., Poplawski, S. E., Wu, W., Liu, Y.; Lai, J. H.; Sanford, D. G.; Arciprete, M. O.; Golub, T. R.; Bachovchin, W. W.; Bachovchin, D. A.# “Inhibition of DPP8/9 induces pro-caspase-1-dependent pyroptosis in monocytes and macrophages.” Nat Chem Biol. 2017, 13, 46-53.

20.  Hatzios, S. K.; Abel, S.; Martell, J.; Hubbard, T.; Sasabe, J.; Munera, D.; Clark, L.; Bachovchin, D. A.; Qadri, F.; Ryan,  E. T.; Davis , B. M.; Weerapana, E.; Waldor, M. K. “Chemoproteomic profiling of host and pathogen enzymes active in cholera.” Nat Chem Biol. 2016, 12, 268-274.

19.  Zhao, N.; Darby, C.; Small, J.; Bachovchin, D. A.; Jiang, X.; Burns-Huang, K.; Botella, H.; Ehrt, S.; Boger, D.; Anderson, E.; Cravatt, B. F.; Speers, A.; Fernandez-Vega, V.; Rosen, H.; Spicer, T.; Nathan, C. “A target-based screen against mycobacterial acid resistance protease implicates an additional periplasmic serine protease in regulation of intrabacterial pH homeostasis in Mycobacterium tuberculosis.” ACS Chem Biol. 2015, 10, 364-371.

18.  Bachovchin, D. A.; Koblan, L. W.; Wu, W.; Liu, Y.; Li, Y.; Zhao, P.; Woznica, I.; Shu, Y.; Lai, J. H.; Poplawski, S. E.; Kiritsy, C. P.; Healey, S. E.; DiMare, M.; Sanford, D. G.; Munford, R. S.; Bachovchin, W. W.; Golub, T. R. “A high-throughput, multiplexed assay for superfamily-wide profiling of enzyme activity.” Nat Chem Biol. 2014, 10, 656-663.

17.  Liu, X.; Dix, M.; Speers, A.; Bachovchin, D. A.; Zuhl, A. M.; Cravatt, B. F.; Kodadek, T. “Rapid development of a potent photo-triggered inhibitor of the serine hydrolase RBBP9.” ChemBioChem. 2012, 13, 2082-2093.

16.  Adibekian, A.; Martin, B.; Chang, J. W.; Hsu, K. L.; Tsuboi, K.; Bachovchin, D. A.; Speers, A. E.; Brown, S. J.; Spicer, T.; Fernandez-Vega, V.; Rosen, H.; Cravatt, B. F. “Confirming target engagement of reversible inhibitors in vivo by kinetically tuned activity-based probes.” J Am Chem Soc. 2012, 134, 10345-10348.

15.  Dillon, M. B.; Bachovchin, D. A.; Brown, S. J.; Finn, M. J.; Rosen, H.; Cravatt, B. F.; Mowen, K. A. “Novel inhibitors for PRMT1 discovered by high-throughput screening using activity-based fluorescence polarization.” ACS Chem Biol. 2012, 7, 1198-1204.

14.  Zuhl, A. M.; Mohr, J. T.; Bachovchin, D. A.; Niessen, S.; Hsu, K. L.; Berlin, J. M.; Dochnahl, M.; Lopez-Alberca, M. P.; Fu, G. C.; Cravatt, B. F. “Competitive activity-based protein profiling identifies aza-b-lactams as a versatile chemotype for serine hydrolase inhibition.” J Am Chem Soc. 2012, 134, 5068-5071.

13.  Bachovchin, D. A.; Cravatt, B. F. “The pharmacological landscape and therapeutic potential of serine hydrolases.” Nat Rev Drug Discov. 2012, 11, 52-68.

12.  Tsuboi, K.; Bachovchin, D. A.; Speers, A. E.; Spicer, T. P.; Fernandez-Vega, V.; Hodder, P.; Rosen, H.; Cravatt, B. F. “Potent and selective inhibitors of glutathione S-transferase omega 1 that impair cancer drug resistance.” J Am Chem Soc. 2011, 133, 16605-16616.

11.  Lone, A. M.; Bachovchin, D. A.; Westwood, D.; Speers, A. E.; Spicer, T. P.; Fernandez-Vega, V.; Chase, P.; Hodder, P. S.; Rosen, H.; Cravatt, B. F.; Saghatelian, A. “A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors.” J Am Chem Soc. 2011, 133, 11665-11674.

10.  Bachovchin, D. A.*; Zuhl, A. M.*; Speers, A. E.; Wolfe, M. R.; Weerapana, E.; Brown, S. J.; Rosen, H.; Cravatt, B. F. “Discovery and optimization of sulfonyl acrylonitriles as selective, covalent inhibitors of protein phosphatase methylesterase-1.” J Med Chem. 2011, 54, 5229-5226.

9.  Adibekian, A.; Martin, B. R.; Wang, C.; Hsu, K.; Bachovchin, D. A.; Niessen, S.; Hoover, H.; Cravatt, B. F. “Click-generated triazole ureas as a versatile scaffold for ultrapotent in vivo-active serine hydrolase inhibitors.” Nat Chem Biol. 2011, 7, 469-478.

8.  Bachovchin, D. A.; Mohr, J. T.; Speers, A. E.; Wang, C.; Berlin, J. M.; Spicer, T. P.; Fernandez-Vega, V.; Chase, P.; Hodder, P. S.; Schürer, S. C.; Nomura, D. K.; Rosen, H.; Fu, G. C.; Cravatt, B. F. “Academic cross-fertilization by public screening yields a remarkable class of protein phosphatase methylesterase-1 inhibitors.” Proc Natl Acad Sci. 2011, 108, 6811-6816.

7.  Weerapana, E.*; Wang, C.*; Simon, G. M.; Khare, S.; Richter, F.; Dillon, M. B.; Bachovchin, D. A.; Mowen, K.; Baker, D.; Cravatt, B. F. “Quantitative reactivity profiling predicts functional cysteines in native and designed proteins.” Nature. 2010, 468, 790-795.

6.  Bachovchin, D. A.*;  Ji, T.*; Li, W.*; Simon, G. M.; Hoover, H.; Niessen, S.; Cravatt, B. F. “A superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening.” Proc Natl Acad Sci. 2010, 107, 20941-20946. 

5.  Knuckley, B.; Jones, J. E.; Bachovchin, D. A.; Slack, J.; Causey, C. P.; Brown, S. J.; Rosen, H.; Cravatt, B. F.; Thompson, P. R. “A Fluopol-ABPP HTS Assay to Identify PAD Inhibitors.” Chem Comm. 2010, 46, 7175-7177.

4.  Bachovchin, D. A.; Wolfe, M. R.; Masuda, K.; Brown, S. J.; Spicer, T. P.; Fernandez-Vega, V.; Chase, P.; Hodder, P.S.; Rosen, H.; Cravatt, B. F. “Oxime esters as selective, covalent inhibitors of the serine hydrolase retinoblastoma-binding protein 9 (RBBP9).” Bioorg Med Chem Lett. 2010, 20, 2254-2258.

3.  Bachovchin, D. A.; Brown, S. J.; Rosen, H.; Cravatt, B. F.; “Identification of selective inhibitors of uncharacterized enzymes by high-throughput screening with fluorescent activity-based probes.” Nat. Biotechnol. 2009, 27, 387-394.

2.  Fraunhoffer, K. J.; Bachovchin, D. A.; White, M.C. “Hydrocarbon oxidation vs. C-C Bond forming approaches for efficient syntheses of oxygenated molecules.” Org Lett. 2005, 7, 223-226.

1.  Haddad, K. C.; Sudmeier, J. L.; Bachovchin, D. A.; Bachovchin, W.W.; “a-lytic protease can exist in two separately stable conformations with different His57 mobilities and catalytic activities.” Proc Natl Acad Sci. 2005, 102, 1006-1011.

 

*Equal contribution

# Corresponding author