About

Daniel Bachovchin is an Associate Professor at the Graduate School of Medical Sciences at Weill Cornell Medicine, affiliated with the Sloan Kettering Institute. His research employs chemical and cell biology approaches to study proteins and pathways involved in innate immunity, with a particular focus on inflammasomes. His laboratory is especially interested in characterizing the molecular mechanisms controlling the formation of inflammasomes, which are multi-protein complexes that activate inflammatory caspases and trigger pyroptosis, a lytic and pro-inflammatory form of cell death. Bachovchin's work has significantly advanced understanding of the activation and regulation of inflammasomes, especially NLRP1 and CARD8, and their roles in immune responses and cancer immunotherapy. He received his Ph.D. in 2011 from The Scripps Research Institute under Dr. Benjamin F. Cravatt, where he developed activity-based protein profiling approaches for enzyme inhibitor discovery. Following his Ph.D., he was a postdoctoral fellow at The Broad Institute in Dr. Todd Golub’s laboratory, developing high-throughput methods for profiling inhibitor selectivity. His research at SKI has been driven by the investigation of the immunostimulatory activity of small molecules like Val-boroPro (VbP), which activates inflammasomes and induces immune-mediated tumor regressions. His lab has made notable progress in elucidating the mechanisms of NLRP1 and CARD8 inflammasomes and aims to harness these pathways for therapeutic purposes. Dr. Bachovchin has received numerous distinctions, including the Geoffrey Beene Junior Faculty Chair, the Louise and Allston Boyer Young Investigator Award, and the Pershing Square Sohn Prize for Young Investigators in Cancer Research.

Research topics

• Biology
• Cell biology
• Biochemistry
• Chemistry
• Computational biology
• Virology
• Genetics

Selected publications

• The hydrophobicity of the CARD8 N-terminus tunes inflammasome activation

  Cell chemical biology · 2024-07-10 · 2 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• The interaction between NLRP1 and oxidized TRX1 involves a transient disulfide bond

  Cell chemical biology · 2024-01-11 · 12 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Meet the authors: Lydia P. Tsamouri and Daniel A. Bachovchin

  Cell chemical biology · 2024-09-01

  articleSenior author
  PublisherDOI

• The serine protease DPP9 and the redox sensor KEAP1 form a mutually inhibitory complex

  Journal of Biological Chemistry · 2024-11-29 · 4 citations

  articleOpen accessSenior author

  Synthetic inhibitors of the serine protease DPP9 activate the related NLRP1 and CARD8 inflammasomes and stimulate powerful innate immune responses. Thus, it seems plausible that a biomolecule similarly inhibits DPP9 and triggers inflammasome activation during infection, but one has not yet been discovered. Here, we wanted to identify and characterize DPP9-binding proteins to potentially uncover physiologically relevant mechanisms that control DPP9's activity. Notably, we found that the redox sensor protein KEAP1 binds to DPP9 in an inactive conformation and stabilizes this non-native fold. At the same time, this inactive form of DPP9 reciprocally inhibits the ability of KEAP1 to bind to and degrade the transcription factor NRF2, thereby inducing an antioxidant response. Although we discovered several experimental conditions, for example new protein expression and chemical denaturation, that force DPP9 out of its folded dimeric state and into a KEAP1-binding state, the key danger-related stimulus that causes this critical DPP9 conformational change is not yet known. Regardless, our data now reveal that an endogenous DPP9 inhibition mechanism does in fact exist, and moreover that DPP9, like the other NLRP1 regulator thioredoxin-1, is directly coupled to the intracellular redox potential. Overall, we expect this work will provide the foundation to discover additional biomolecules that regulate DPP9's activity, the DPP9-KEAP1 interaction, the intracellular redox environment, and the NLRP1 and CARD8 inflammasomes.

  PublisherOA PDFDOI

• The NLRP1 and CARD8 inflammasomes detect reductive stress

  Cell Reports · 2023-01-01 · 37 citations

  articleOpen accessSenior authorCorresponding

  The danger signals that activate the related nucleotide-binding domain leucine-rich repeat pyrin domain-containing 1 (NLRP1) and caspase activation and recruitment domain-containing 8 (CARD8) inflammasomes have not been fully established. We recently reported that the oxidized form of TRX1 binds to NLRP1 and represses inflammasome activation. These findings suggested that intracellular reductive stress, which would reduce oxidized TRX1 and thereby abrogate the NLRP1-TRX1 interaction, is an NLRP1 inflammasome-activating danger signal. However, no agents that induce reductive stress were known to test this premise. Here, we identify and characterize several radical-trapping antioxidants, including JSH-23, that induce reductive stress. We show that these compounds accelerate the proteasome-mediated degradation of the repressive N-terminal fragments of both NLRP1 and CARD8, releasing the inflammasome-forming C-terminal fragments from autoinhibition. Overall, this work validates chemical probes that induce reductive stress and establishes reductive stress as a danger signal sensed by both the NLRP1 and CARD8 inflammasomes.

  PublisherOA PDFDOI

• The interaction between NLRP1 and oxidized TRX1 involves a transient disulfide bond

  bioRxiv (Cold Spring Harbor Laboratory) · 2023-09-28 · 1 citations

  preprintOpen accessSenior authorCorresponding

  NLRP1 is an innate immune receptor that detects pathogen-associated signals, assembles into a multiprotein structure called an inflammasome, and triggers a proinflammatory form of cell death called pyroptosis. We previously discovered that the oxidized, but not the reduced, form of thioredoxin-1 directly binds to NLRP1 and represses inflammasome formation. However, the molecular basis for NLRP1's selective association with only the oxidized form of TRX1 has not yet been established. Here, we leveraged Alphafold-Multimer, site-directed mutagenesis, thiol-trapping experiments, and mass spectrometry to reveal that a specific cysteine residue (C427 in humans) on NLRP1 forms a transient disulfide bond with oxidized TRX1. Overall, this work demonstrates how NLRP1 monitors the cellular redox state, further illuminating an unexpected connection between the intracellular redox potential and the innate immune system.

  PublisherOA PDFDOI

• Protein folding stress potentiates NLRP1 and CARD8 inflammasome activation

  Cell Reports · 2023-01-01 · 36 citations

  articleOpen accessSenior authorCorresponding

  NLRP1 and CARD8 are related pattern-recognition receptors (PRRs) that detect intracellular danger signals and form inflammasomes. Both undergo autoproteolysis, generating N-terminal (NT) and C-terminal (CT) fragments. The proteasome-mediated degradation of the NT releases the CT from autoinhibition, but the stimuli that trigger NT degradation have not been fully elucidated. Here, we show that several distinct agents that interfere with protein folding, including aminopeptidase inhibitors, chaperone inhibitors, and inducers of the unfolded protein response, accelerate NT degradation. However, these agents alone do not trigger inflammasome formation because the released CT fragments are physically sequestered by the serine dipeptidase DPP9. We show that DPP9-binding ligands must also be present to disrupt these complexes and allow the CT fragments to oligomerize into inflammasomes. Overall, these results indicate that NLRP1 and CARD8 detect a specific perturbation that induces both protein folding stress and DPP9 ligand accumulation.

  PublisherOA PDFDOI

• DPP8/9 are not Required to Cleave Most Proline‐Containing Peptides

  Israel Journal of Chemistry · 2023-02-14 · 2 citations

  articleOpen accessSenior authorCorresponding

  Small molecule inhibitors of the intracellular serine peptidases DPP8 and DPP9 (DPP8/9) activate the NLRP1 and CARD8 inflammasomes, but the key DPP8/9 substrates have not yet been identified. DPP8/9 cleave after proline to remove N-terminal dipeptides from peptides or proteins, and studies using pseudo-peptide reporter substrates have suggested that these enzymes may play key roles in the catabolism of many proline-containing peptides generated by the proteasome. Here, we evaluated the degradation of a wide array of actual peptides in cell lysates, and discovered that DPP8/9 are not in fact involved in the processing of the vast majority of proline-containing peptides. Overall, these results indicate that DPP8/9 have a much more limited substrate scope than previously thought, and likely specifically cleave some critically important, but as yet unknown, intracellular peptide or protein that regulates inflammasome activation.

  PublisherOA PDFDOI

• Optimized M24B Aminopeptidase Inhibitors for CARD8 Inflammasome Activation

  Journal of Medicinal Chemistry · 2023-02-01 · 2 citations

  articleOpen accessSenior authorCorresponding

  Inflammasomes are innate immune signaling platforms that trigger pyroptotic cell death. NLRP1 and CARD8 are related human inflammasomes that detect similar danger signals, but NLRP1 has a higher activation threshold and triggers a more inflammatory form of pyroptosis. Both sense the accumulation of intracellular peptides with Xaa-Pro N-termini, but Xaa-Pro peptides on their own without a second danger signal only activate the CARD8 inflammasome. We recently reported that a dual inhibitor of the Xaa-Pro-cleaving M24B aminopeptidases PEPD and XPNPEP1 called CQ31 selectively activates the CARD8 inflammasome by inducing the build-up of Xaa-Pro peptides. Here, we performed structure-activity relationship studies on CQ31 to develop the optimized dual PEPD/XPNPEP1 inhibitor CQ80 that more effectively induces CARD8 inflammasome activation. We anticipate that CQ80 will become a valuable tool to study the basic biology and therapeutic potential of selective CARD8 inflammasome activation.

  PublisherOA PDFDOI

• M24B aminopeptidase inhibitors selectively activate the CARD8 inflammasome

  Nature Chemical Biology · 2022-02-14 · 36 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

Recent grants

• Prolidase Inhibitors as Therapeutic Agents for Acute Myeloid Leukemia

  NIH · $3.1M · 2022–2027

• Redox control of the NLRP1 inflammasome

  NIH · $2.6M · 2021–2026

• Characterizing the Mechanism of DPP8/9 Inhibitor-Induced Pyroptosis

  NIH · $3.8M · 2018–2028

Frequent coauthors

• Andrew R. Griswold

  Tri-Institutional PhD Program in Chemical Biology

  168 shared

• Sahana D. Rao

  Tri-Institutional PhD Program in Chemical Biology

  88 shared

• Elizabeth L. Orth-He

  Tri-Institutional PhD Program in Chemical Biology

  86 shared

• Ashley J. Chui

  Tri-Institutional PhD Program in Chemical Biology

  80 shared

• Hsin‐Che Huang

  Tri-Institutional PhD Program in Chemical Biology

  77 shared

• Jeffrey C. Hsiao

  Cornell University

  72 shared

• Daniel P. Ball

  Memorial Sloan Kettering Cancer Center

  57 shared

• Darren C. Johnson

  Pfizer (United States)

  48 shared

Labs

• Daniel Bachovchin LabPI

Awards & honors

• David P. Hajjar Excellence in Teaching and Mentoring Award,…
• Geoffrey Beene Junior Faculty Chair (March 2022-March 2026)
• Louise and Allston Boyer Young Investigator Award for Distin…
• Pershing Square Sohn Prize for Young Investigators in Cancer…
• Alfred P. Sloan Foundation Fellow in Chemistry (February 201…