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Gomez EB, Ebata K, Randeria HS, Rosendahl MS, Cedervall EP, Morales TH, Hanson LM, Brown NE, Gong X, Stephens J, Wu W, Lippincott I, Ku KS, Walgren RA, Abada PB, Ballard JA, Allerston CK, Brandhuber BJ. Preclinical characterization of pirtobrutinib, a highly selective, noncovalent (reversible) BTK inhibitor. Blood 2023; 142:62-72. [PMID: 36796019 PMCID: PMC10651869 DOI: 10.1182/blood.2022018674] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Bruton tyrosine kinase (BTK), a nonreceptor tyrosine kinase, is a major therapeutic target for B-cell-driven malignancies. However, approved covalent BTK inhibitors (cBTKis) are associated with treatment limitations because of off-target side effects, suboptimal oral pharmacology, and development of resistance mutations (eg, C481) that prevent inhibitor binding. Here, we describe the preclinical profile of pirtobrutinib, a potent, highly selective, noncovalent (reversible) BTK inhibitor. Pirtobrutinib binds BTK with an extensive network of interactions to BTK and water molecules in the adenosine triphosphate binding region and shows no direct interaction with C481. Consequently, pirtobrutinib inhibits both BTK and BTK C481 substitution mutants in enzymatic and cell-based assays with similar potencies. In differential scanning fluorimetry studies, BTK bound to pirtobrutinib exhibited a higher melting temperature than cBTKi-bound BTK. Pirtobrutinib, but not cBTKis, prevented Y551 phosphorylation in the activation loop. These data suggest that pirtobrutinib uniquely stabilizes BTK in a closed, inactive conformation. Pirtobrutinib inhibits BTK signaling and cell proliferation in multiple B-cell lymphoma cell lines, and significantly inhibits tumor growth in human lymphoma xenografts in vivo. Enzymatic profiling showed that pirtobrutinib was highly selective for BTK in >98% of the human kinome, and in follow-up cellular studies pirtobrutinib retained >100-fold selectivity over other tested kinases. Collectively, these findings suggest that pirtobrutinib represents a novel BTK inhibitor with improved selectivity and unique pharmacologic, biophysical, and structural attributes with the potential to treat B-cell-driven cancers with improved precision and tolerability. Pirtobrutinib is being tested in phase 3 clinical studies for a variety of B-cell malignancies.
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Ballard JA, Ebata K, Randeria HS, Tinline G, Lee T, Hanson LM, Latham JA, Cedervall EP, Chong J, Valle KBD, Collins BC, Morales TH, Benedict TC, Schureck MA, Bender ET, Mendoza C, Molina D, Nakamoto M, Shiah HC, Xu H, Espada A, Cano L, Allerston CK, Schnier P, Brandhuber BJ. Abstract 2780: Unique pharmacodynamic properties conferred by differential binding to BTK, pirtobrutinib vs covalent inhibitors. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Covalent Bruton tyrosine kinase inhibitors (cBTKi) have transformed the treatment of B cell malignancies. Despite the efficacy of cBTKi, treatment failure often occurs through development of resistance or intolerance. Pirtobrutinib, a highly selective, non-covalent BTKi, potently inhibits both WT and C481 mutant BTK. Pirtobrutinib has favorable oral pharmacology, is well tolerated, and has shown promising efficacy in patients with poor prognosis B cell malignancies following prior therapy, including prior cBTKi. Here we report in vitro BTK binding, conformation, and activation differences between cBTKi and pirtobrutinib. Cellular studies showed pirtobrutinib inhibited BTK phosphorylation at both Y223 and Y551 in REC-1 and Ramos A1 human lymphoma cell lines. In contrast, despite inhibition of Y223 phosphorylation, both cell lines treated with cBTKi, ibrutinib, acalabrutinib or zanubrutinib, retained Y551 phosphorylation. The differential effects on Y551 were also observed in PBMC isolated from treatment naïve human CLL donors treated in vitro with pirtobrutinib or ibrutinib. To investigate the binding effects of cBTKi and pirtobrutinib on BTK stability and conformation, a series of biophysical and structural studies were performed. In a hydrogen/deuterium exchange mass spectrometry study using full length BTK, all compounds significantly inhibited exchange in regions surrounding the ATP binding site in the kinase domain. While cBTKi induced significantly increased exchange for peptides in the SH3 and SH2 domains, pirtobrutinib significantly reduced exchange in a portion of the SH3 domain, nearly the entire SH2 domain, and SH2 linker, suggesting that pirtobrutinib uniquely stabilizes BTK in a closed/inactive conformation. Consistent with this proposed model, crosslinking mass spectrometry results of inhibitor bound BTK showed that pirtobrutinib promoted different interactions between the SH2 domain and kinase domain than cBTKi. To confirm that pirtobrutinib promotes greater stabilization of BTK, a mass spectrometry based cellular thermal shift assay was performed in both Ramos and BTK overexpressing HEK293 cells. In both cell lines, pirtobrutinib showed significantly greater stabilization of BTK compared to cBTKi. In addition, crystallographic studies of BTK in complex with pirtobrutinib revealed domain organization consistent with stabilized SH2-SH3 interactions with the kinase domain. These data suggest pirtobrutinib may differentially impact BTK stability and conformation compared to cBTKi. The cellular and biophysical data are consistent with a model in which cBTKi shift BTK toward an open conformation, whereas pirtobrutinib allosterically stabilizes a closed BTK conformation, preventing activation by upstream kinases. Additional studies are underway to further characterize the differential effects of pirtobrutinib on BTK conformation.
Citation Format: Joshua A. Ballard, Kevin Ebata, Hetal S. Randeria, Garrett Tinline, Thomas Lee, Lauren M. Hanson, John A. Latham, E. Peder Cedervall, Jenny Chong, Kyle B. Del Valle, Bernard C. Collins, Tony H. Morales, Thomas C. Benedict, Marc A. Schureck, Ethan T. Bender, Christopher Mendoza, David Molina, Meagan Nakamoto, Hsiao-Chiao Shiah, Hao Xu, Alfonso Espada, Leticia Cano, Charles K. Allerston, Paul Schnier, Barbara J. Brandhuber. Unique pharmacodynamic properties conferred by differential binding to BTK, pirtobrutinib vs covalent inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2780.
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Affiliation(s)
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- 1Loxo@Lilly, Stamford, CT
| | | | - Leticia Cano
- 2Centro de Investigación Lilly S.A., Alcobendas, Spain
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Dyck B, Branstetter B, Gharbaoui T, Hudson AR, Breitenbucher JG, Gomez L, Botrous I, Marrone T, Barido R, Allerston CK, Cedervall EP, Xu R, Sridhar V, Barker R, Aertgeerts K, Schmelzer K, Neul D, Lee D, Massari ME, Andersen CB, Sebring K, Zhou X, Petroski R, Limberis J, Augustin M, Chun LE, Edwards TE, Peters M, Tabatabaei A. Discovery of Selective Phosphodiesterase 1 Inhibitors with Memory Enhancing Properties. J Med Chem 2017; 60:3472-3483. [DOI: 10.1021/acs.jmedchem.7b00302] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Brian Dyck
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Bryan Branstetter
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Tawfik Gharbaoui
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Andrew R. Hudson
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - J. Guy Breitenbucher
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Laurent Gomez
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Iriny Botrous
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Tami Marrone
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Richard Barido
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Charles K. Allerston
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - E. Peder Cedervall
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Rui Xu
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Vandana Sridhar
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Ryan Barker
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Kathleen Aertgeerts
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Kara Schmelzer
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - David Neul
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Dong Lee
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Mark Eben Massari
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Carsten B. Andersen
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Kristen Sebring
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Xianbo Zhou
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Robert Petroski
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - James Limberis
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Martin Augustin
- Proteros Biostructures GmbH, Bunsenstraße 7a, D-82152 Martinsried, Germany
| | - Lawrence E. Chun
- Berylllium, 7869 NE Day Road West, Bainbridge
Island, Washington 98110, United States
| | - Thomas E. Edwards
- Berylllium, 7869 NE Day Road West, Bainbridge
Island, Washington 98110, United States
| | - Marco Peters
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
| | - Ali Tabatabaei
- Dart Neuroscience LLC, 12278 Scripps Summit Drive, San Diego, California 92131, United States
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