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Hartman G, Humphries P, Hughes R, Ho A, Montgomery R, Deshpande A, Mahanta M, Tronnes S, Cowdin S, He X, Liu F, Zhang L, Liu C, Dou D, Li J, Spasic A, Coll R, Marleaux M, Hochheiser IV, Geyer M, Rubin P, Fortney K, Wilhelmsen K. The discovery of novel and potent indazole NLRP3 inhibitors enabled by DNA-encoded library screening. Bioorg Med Chem Lett 2024; 102:129675. [PMID: 38417632 DOI: 10.1016/j.bmcl.2024.129675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 03/01/2024]
Abstract
NLRP3 is an intracellular sensor protein that detects a broad range of danger signals and environmental insults. Its activation results in a protective pro-inflammatory response designed to impair pathogens and repair tissue damage via the formation of the NLRP3 inflammasome. Assembly of the NLRP3 inflammasome leads to caspase 1-dependent secretory release of the pro-inflammatory cytokines IL-1β and IL-18 as well as to gasdermin d-mediated pyroptotic cell death. Herein, we describe the discovery of a novel indazole series of high affinity, reversible inhibitors of NLRP3 activation through screening of DNA-encoded libraries and the potent lead compound 3 (BAL-0028, IC50 = 25 nM) that was identified directly from the screen. SPR studies showed that compound 3 binds tightly (KD range 104-123 nM) to the NACHT domain of NLRP3. A CADD analysis of the interaction of compound 3 with the NLRP3 NACHT domain proposes a binding site that is distinct from those of ADP and MCC950 and includes specific site interactions. We anticipate that compound 3 (BAL-0028) and other members of this novel indazole class of neutral inhibitors will demonstrate significantly different physical, biochemical, and biological properties compared to NLRP3 inhibitors previously identified.
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Affiliation(s)
- George Hartman
- BioAge Labs, 1445 S. 50(th) St. Richmond, CA 94804, USA.
| | | | - Robert Hughes
- BioAge Labs, 1445 S. 50(th) St. Richmond, CA 94804, USA
| | - Andrew Ho
- BioAge Labs, 1445 S. 50(th) St. Richmond, CA 94804, USA
| | | | | | | | - Sarah Tronnes
- BioAge Labs, 1445 S. 50(th) St. Richmond, CA 94804, USA
| | | | - Xu He
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610000, China
| | - Fangchao Liu
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610000, China
| | - Lifang Zhang
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610000, China
| | - Chuan Liu
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610000, China
| | - Dengfeng Dou
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610000, China
| | - Jin Li
- HitGen Inc., Shuangliu District, Chengdu, Sichuan 610000, China
| | | | - Rebecca Coll
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast BT9 7BL, UK
| | - Michael Marleaux
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Inga V Hochheiser
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Paul Rubin
- BioAge Labs, 1445 S. 50(th) St. Richmond, CA 94804, USA
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Keuler T, Ferber D, Marleaux M, Geyer M, Gütschow M. Structure-Stability Relationship of NLRP3 Inflammasome-Inhibiting Sulfonylureas. ACS Omega 2022; 7:8158-8162. [PMID: 35284735 PMCID: PMC8908490 DOI: 10.1021/acsomega.2c00125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
In recent drug development efforts, particular emphasis has been devoted to the chemical interference with the NLRP3 inflammasome. A series of 12 tailored sulfonylureas was designed, prepared through convergent syntheses with a final sodium hydride-promoted reaction of isocyanates and sulfonamides, and subjected to a systematic, high-performance liquid chromatography-based survey of the chemical stability, a critical issue of sulfonylureas in terms of preparation, storage, and application. NLRP3 binding was determined by surface plasmon resonance spectroscopy. Sulfonylurea 2 was identified to be equipotent and similarly stable compared to the prototypical NLRP3 inhibitor MCC950.
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Affiliation(s)
- Tim Keuler
- Pharmaceutical
Institute, University of Bonn, 53121 Bonn, Germany
| | - Dominic Ferber
- Pharmaceutical
Institute, University of Bonn, 53121 Bonn, Germany
| | - Michael Marleaux
- Institute
of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Matthias Geyer
- Institute
of Structural Biology, University of Bonn, 53127 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, University of Bonn, 53121 Bonn, Germany
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Keuler T, Gatterdam K, Akbal A, Lovotti M, Marleaux M, Geyer M, Latz E, Gütschow M. Development of Fluorescent and Biotin Probes Targeting NLRP3. Front Chem 2021; 9:642273. [PMID: 33996748 PMCID: PMC8115122 DOI: 10.3389/fchem.2021.642273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Extracellular signals drive the nucleation of the NLRP3 inflammasome which leads to the release of cytokines and causes inflammatory events. Hence, the inflammasome has gained enormous momentum in biomedical basic research. The detailed mechanisms of inflammasome generation and regulation remain to be elucidated. Our study was directed toward the design, convergent synthesis, and initial biochemical evaluation of activity-based probes addressing NLRP3. For this purpose, probes were assembled from a CRID3/MCC950-related NLRP3-binding unit, a linker portion and a coumarin 343 fluorophore or biotin. The affinity of our probes to NLRP3 was demonstrated through SPR measurements and their cellular activity was confirmed by reduction of the interleukin 1β release from stimulated bone marrow-derived macrophages. The initial characterizations of NLRP3-targeting probes highlighted the coumarin probe 2 as a suitable tool compound for the cellular and biochemical analysis of the NLRP3 inflammasome.
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Affiliation(s)
- Tim Keuler
- Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Karl Gatterdam
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Anil Akbal
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Marta Lovotti
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Michael Marleaux
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
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Marleaux M, Anand K, Latz E, Geyer M. Crystal structure of the human NLRP9 pyrin domain suggests a distinct mode of inflammasome assembly. FEBS Lett 2020; 594:2383-2395. [PMID: 32542665 DOI: 10.1002/1873-3468.13865] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/17/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Inflammasomes are cytosolic multimeric signaling complexes of the innate immune system that induce activation of caspases. The NOD-like receptor NLRP9 recruits the adaptor protein ASC to form an ASC-dependent inflammasome to limit rotaviral replication in intestinal epithelial cells, but only little is known about the molecular mechanisms regulating and driving its assembly. Here, we present the crystal structure of the human NLRP9 pyrin domain (PYD). We show that NLRP9PYD is not able to self-polymerize nor to nucleate ASC specks in HEK293T cells. A comparison with filament-forming PYDs revealed that NLRP9PYD adopts a conformation compatible with filament formation, but several charge inversions of interfacing residues might cause repulsive effects that prohibit self-oligomerization. These results propose that inflammasome assembly of NLRP9 might differ largely from what we know of other inflammasomes.
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Affiliation(s)
- Michael Marleaux
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Kanchan Anand
- Institute of Structural Biology, University of Bonn, Bonn, Germany
| | - Eicke Latz
- Institute of Innate Immunity, University of Bonn, Bonn, Germany
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, Bonn, Germany
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