1
|
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.
Collapse
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
| | | | | |
Collapse
|
2
|
MacDonald JA, Wijekoon CP, Liao KC, Muruve DA. Biochemical and structural aspects of the ATP-binding domain in inflammasome-forming human NLRP proteins. IUBMB Life 2014; 65:851-62. [PMID: 24078393 DOI: 10.1002/iub.1210] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/22/2013] [Indexed: 01/01/2023]
Abstract
Nucleotide-binding domain and leucine-rich repeat-containing receptors (NLRs) regulate innate immunity by activating inflammatory responses in a variety of biological systems following the recognition of pathogen- or disease-associated molecular patterns. NLRs are characterized by a central nucleotide-binding and oligomerization (NACHT) domain found in P-loop NTPases. In this review, we detail the functional and structural properties of the NACHT domain of a subfamily of NLRs, the NLRPs (NLR containing a pyrin domain), based on previous studies, sequence analysis, homology modeling, and structure predictions. Several NLRPs have been found to regulate inflammatory responses through the assembly of oligomeric caspase 1-activating platforms known as inflammasomes, the 3-dimensional structure of the NLRP NACHT domain has still not been solved. Homology modeling suggests that sequence variability within the NACHT domains of different NLRP family members may alter the topology of the ATP-binding pocket. Based on this finding, we discuss the potential therapeutic prospects aligned with the NACHT domain and the development of selective inhibitors of inflammasome activity.
Collapse
Affiliation(s)
- Justin A MacDonald
- Libin Cardiovascular Institute and Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, T2N 4Z6, Canada
| | | | | | | |
Collapse
|