1
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Ketcham JM, Harwood SJ, Aranda R, Aloiau AN, Bobek BM, Briere DM, Burns AC, Caddell Haatveit K, Calinisan A, Clarine J, Elliott A, Engstrom LD, Gunn RJ, Ivetac A, Jones B, Kuehler J, Lawson JD, Nguyen N, Parker C, Pearson KE, Rahbaek L, Saechao B, Wang X, Waters A, Waters L, Watkins AH, Olson P, Smith CR, Christensen JG, Marx MA. Discovery of Pyridopyrimidinones that Selectively Inhibit the H1047R PI3Kα Mutant Protein. J Med Chem 2024; 67:4936-4949. [PMID: 38477582 PMCID: PMC10983000 DOI: 10.1021/acs.jmedchem.4c00078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024]
Abstract
The H1047R mutation of PIK3CA is highly prevalent in breast cancers and other solid tumors. Selectively targeting PI3KαH1047R over PI3KαWT is crucial due to the role that PI3KαWT plays in normal cellular processes, including glucose homeostasis. Currently, only one PI3KαH1047R-selective inhibitor has progressed into clinical trials, while three pan mutant (H1047R, H1047L, H1047Y, E542K, and E545K) selective PI3Kα inhibitors have also reached the clinical stage. Herein, we report the design and discovery of a series of pyridopyrimidinones that inhibit PI3KαH1047R with high selectivity over PI3KαWT, resulting in the discovery of compound 17. When dosed in the HCC1954 tumor model in mice, 17 provided tumor regressions and a clear pharmacodynamic response. X-ray cocrystal structures from several PI3Kα inhibitors were obtained, revealing three distinct binding modes within PI3KαH1047R including a previously reported cryptic pocket in the C-terminus of the kinase domain wherein we observe a ligand-induced interaction with Arg1047.
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Affiliation(s)
| | | | - Ruth Aranda
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Athenea N. Aloiau
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Briana M. Bobek
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - David M. Briere
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Aaron C. Burns
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | | | - Andrew Calinisan
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Jeffery Clarine
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Adam Elliott
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Lars D. Engstrom
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Robin J. Gunn
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Anthony Ivetac
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Benjamin Jones
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Jon Kuehler
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - J. David Lawson
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Natalie Nguyen
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Cody Parker
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Kelly E. Pearson
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Lisa Rahbaek
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Barbara Saechao
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Xiaolun Wang
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Anna Waters
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Laura Waters
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Ashlee H. Watkins
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Peter Olson
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Christopher R. Smith
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - James G. Christensen
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Matthew A. Marx
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
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2
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Smith CR, Chen D, Christensen JG, Coulombe R, Féthière J, Gunn RJ, Hollander J, Jones B, Ketcham JM, Khare S, Kuehler J, Lawson JD, Marx MA, Olson P, Pearson KE, Ren C, Tsagris D, Ulaganathan T, Van’t Veer I, Wang X, Ivetac A. Discovery of Five SOS2 Fragment Hits with Binding Modes Determined by SOS2 X-Ray Cocrystallography. J Med Chem 2024; 67:774-781. [PMID: 38156904 PMCID: PMC10788894 DOI: 10.1021/acs.jmedchem.3c02140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
SOS1 and SOS2 are guanine nucleotide exchange factors that mediate RTK-stimulated RAS activation. Selective SOS1:KRAS PPI inhibitors are currently under clinical investigation, whereas there are no reports to date of SOS2:KRAS PPI inhibitors. SOS2 activity is implicated in MAPK rebound when divergent SOS1 mutant cell lines are treated with the SOS1 inhibitor BI-3406; therefore, SOS2:KRAS inhibitors are of therapeutic interest. In this report, we detail a fragment-based screening strategy to identify X-ray cocrystal structures of five diverse fragment hits bound to SOS2.
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Affiliation(s)
| | - Dan Chen
- ZoBio
BV, J.H. Oortweg 19, Leiden 2333 CH, Netherlands
| | | | - René Coulombe
- Inixium, 3000-275 Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - James Féthière
- Inixium, 3000-275 Armand Frappier, Laval, Quebec H7V 4A7, Canada
| | - Robin J. Gunn
- Mirati
Therapeutics, San Diego, California 92130, United States
| | | | - Benjamin Jones
- Mirati
Therapeutics, San Diego, California 92130, United States
| | - John M. Ketcham
- Mirati
Therapeutics, San Diego, California 92130, United States
| | - Shilpi Khare
- Mirati
Therapeutics, San Diego, California 92130, United States
| | - Jon Kuehler
- Mirati
Therapeutics, San Diego, California 92130, United States
| | - J. David Lawson
- Mirati
Therapeutics, San Diego, California 92130, United States
| | - Matthew A. Marx
- Mirati
Therapeutics, San Diego, California 92130, United States
| | - Peter Olson
- Mirati
Therapeutics, San Diego, California 92130, United States
| | | | - Cynthia Ren
- Mirati
Therapeutics, San Diego, California 92130, United States
| | | | | | | | - Xiaolun Wang
- Mirati
Therapeutics, San Diego, California 92130, United States
| | - Anthony Ivetac
- Mirati
Therapeutics, San Diego, California 92130, United States
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3
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Smith CR, Kulyk S, Ahmad MUD, Arkhipova V, Christensen JG, Gunn RJ, Ivetac A, Ketcham JM, Kuehler J, Lawson JD, Thomas NC, Wang X, Marx MA. Fragment optimization and elaboration strategies - the discovery of two lead series of PRMT5/MTA inhibitors from five fragment hits. RSC Med Chem 2022; 13:1549-1564. [PMID: 36545438 PMCID: PMC9749961 DOI: 10.1039/d2md00163b] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/27/2022] [Indexed: 12/24/2022] Open
Abstract
Here we describe the early stages of a fragment-based lead discovery (FBLD) project for a recently elucidated synthetic lethal target, the PRMT5/MTA complex, for the treatment of MTAP-deleted cancers. Starting with five fragment/PRMT5/MTA X-ray co-crystal structures, we employed a two-phase fragment elaboration process encompassing optimization of fragment hits and subsequent fragment growth to increase potency, assess synthetic tractability, and enable structure-based drug design. Two lead series were identified, one of which led to the discovery of the clinical candidate MRTX1719.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jon Kuehler
- Mirati TherapeuticsSan DiegoCalifornia92121USA
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4
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Smith CR, Aranda R, Christensen JG, Engstrom LD, Gunn RJ, Ivetac A, Ketcham JM, Kuehler J, David Lawson J, Marx MA, Olson P, Thomas NC, Wang X, Waters LM, Kulyk S. Design and evaluation of achiral, non-atropisomeric 4-(aminomethyl)phthalazin-1(2H)-one derivatives as novel PRMT5/MTA inhibitors. Bioorg Med Chem 2022; 71:116947. [PMID: 35926325 DOI: 10.1016/j.bmc.2022.116947] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023]
Abstract
MRTX1719 is an inhibitor of the PRMT5/MTA complex and recently entered clinical trials for the treatment of MTAP-deleted cancers. MRTX1719 is a class 3 atropisomeric compound that requires a chiral synthesis or a chiral separation step in its preparation. Here, we report the SAR and medicinal chemistry design strategy, supported by structural insights from X-ray crystallography, to discover a class 1 atropisomeric compound from the same series that does not require a chiral synthesis or a chiral separation step in its preparation.
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Affiliation(s)
| | - Ruth Aranda
- Mirati Therapeutics, San Diego, CA 92121, United States
| | | | | | - Robin J Gunn
- Mirati Therapeutics, San Diego, CA 92121, United States
| | | | | | - Jon Kuehler
- Mirati Therapeutics, San Diego, CA 92121, United States
| | | | | | - Peter Olson
- Mirati Therapeutics, San Diego, CA 92121, United States
| | | | - Xiaolun Wang
- Mirati Therapeutics, San Diego, CA 92121, United States
| | | | - Svitlana Kulyk
- Mirati Therapeutics, San Diego, CA 92121, United States.
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5
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Hallin J, Bowcut V, Calinisan A, Briere DM, Hargis L, Engstrom LD, Laguer J, Medwid J, Vanderpool D, Lifset E, Trinh D, Hoffman N, Wang X, David Lawson J, Gunn RJ, Smith CR, Thomas NC, Martinson M, Bergstrom A, Sullivan F, Bouhana K, Winski S, He L, Fernandez-Banet J, Pavlicek A, Haling JR, Rahbaek L, Marx MA, Olson P, Christensen JG. Anti-tumor efficacy of a potent and selective non-covalent KRAS G12D inhibitor. Nat Med 2022; 28:2171-2182. [PMID: 36216931 DOI: 10.1038/s41591-022-02007-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 08/09/2022] [Indexed: 12/12/2022]
Abstract
Recent progress in targeting KRASG12C has provided both insight and inspiration for targeting alternative KRAS mutants. In this study, we evaluated the mechanism of action and anti-tumor efficacy of MRTX1133, a potent, selective and non-covalent KRASG12D inhibitor. MRTX1133 demonstrated a high-affinity interaction with GDP-loaded KRASG12D with KD and IC50 values of ~0.2 pM and <2 nM, respectively, and ~700-fold selectivity for binding to KRASG12D as compared to KRASWT. MRTX1133 also demonstrated potent inhibition of activated KRASG12D based on biochemical and co-crystal structural analyses. MRTX1133 inhibited ERK1/2 phosphorylation and cell viability in KRASG12D-mutant cell lines, with median IC50 values of ~5 nM, and demonstrated >1,000-fold selectivity compared to KRASWT cell lines. MRTX1133 exhibited dose-dependent inhibition of KRAS-mediated signal transduction and marked tumor regression (≥30%) in a subset of KRASG12D-mutant cell-line-derived and patient-derived xenograft models, including eight of 11 (73%) pancreatic ductal adenocarcinoma (PDAC) models. Pharmacological and CRISPR-based screens demonstrated that co-targeting KRASG12D with putative feedback or bypass pathways, including EGFR or PI3Kα, led to enhanced anti-tumor activity. Together, these data indicate the feasibility of selectively targeting KRAS mutants with non-covalent, high-affinity small molecules and illustrate the therapeutic susceptibility and broad dependence of KRASG12D mutation-positive tumors on mutant KRAS for tumor cell growth and survival.
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Affiliation(s)
- Jill Hallin
- Mirati Therapeutics, Inc., San Diego, CA, USA
| | | | | | | | | | | | - Jade Laguer
- Mirati Therapeutics, Inc., San Diego, CA, USA
| | | | | | - Ella Lifset
- Mirati Therapeutics, Inc., San Diego, CA, USA
| | - David Trinh
- Mirati Therapeutics, Inc., San Diego, CA, USA
| | | | | | | | | | | | | | | | - Alex Bergstrom
- Array BioPharma, Inc. (acquired by Pfizer), Boulder, CO, USA
| | | | - Karyn Bouhana
- Array BioPharma, Inc. (acquired by Pfizer), Boulder, CO, USA
| | - Shannon Winski
- Array BioPharma, Inc. (acquired by Pfizer), Boulder, CO, USA
| | - Leo He
- Monoceros Biosystems, LLC, San Diego, CA, USA
| | | | | | | | | | | | - Peter Olson
- Mirati Therapeutics, Inc., San Diego, CA, USA
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6
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Ketcham JM, Haling J, Khare S, Bowcut V, Briere DM, Burns AC, Gunn RJ, Ivetac A, Kuehler J, Kulyk S, Laguer J, Lawson JD, Moya K, Nguyen N, Rahbaek L, Saechao B, Smith CR, Sudhakar N, Thomas NC, Vegar L, Vanderpool D, Wang X, Yan L, Olson P, Christensen JG, Marx MA. Design and Discovery of MRTX0902, a Potent, Selective, Brain-Penetrant, and Orally Bioavailable Inhibitor of the SOS1:KRAS Protein-Protein Interaction. J Med Chem 2022; 65:9678-9690. [PMID: 35833726 PMCID: PMC9340770 DOI: 10.1021/acs.jmedchem.2c00741] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
SOS1 is one of the major guanine nucleotide exchange
factors that
regulates the ability of KRAS to cycle through its “on”
and “off” states. Disrupting the SOS1:KRASG12C protein–protein interaction (PPI) can increase the proportion
of GDP-loaded KRASG12C, providing a strong mechanistic
rationale for combining inhibitors of the SOS1:KRAS complex with inhibitors
like MRTX849 that target GDP-loaded KRASG12C. In this report,
we detail the design and discovery of MRTX0902—a potent, selective,
brain-penetrant, and orally bioavailable SOS1 binder that disrupts
the SOS1:KRASG12C PPI. Oral administration of MRTX0902
in combination with MRTX849 results in a significant increase in antitumor
activity relative to that of either single agent, including tumor
regressions in a subset of animals in the MIA PaCa-2 tumor mouse xenograft
model.
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Affiliation(s)
- John M Ketcham
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Jacob Haling
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Shilpi Khare
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Vickie Bowcut
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - David M Briere
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Aaron C Burns
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Robin J Gunn
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Anthony Ivetac
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Jon Kuehler
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Svitlana Kulyk
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Jade Laguer
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Krystal Moya
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Natalie Nguyen
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Lisa Rahbaek
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Barbara Saechao
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Christopher R Smith
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Niranjan Sudhakar
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Nicole C Thomas
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Laura Vegar
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Darin Vanderpool
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Xiaolun Wang
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Larry Yan
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Peter Olson
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - James G Christensen
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
| | - Matthew A Marx
- Mirati Therapeutics, 3545 Cray Court, San Diego, California 92121, United States
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7
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Ketcham JM, Briere DM, Burns AC, Christensen JG, Gunn RJ, Haling J, Ivetac A, Khare S, Kuehler J, Kulyk S, Laguer J, Lawson JD, Moya K, Nguyen N, Olson P, Rahbaek L, Smith CR, Sudhakar N, Thomas NC, Vanderpool D, Wang X, Marx MA. Abstract LB505: Design and discovery of MRTX0902, a potent, selective, and orally bioavailable SOS1 inhibitor. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb505] [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: 11/16/2022]
Abstract
Abstract
KRAS mutations are the most common activating mutations in human cancer that ultimately lead to hyperactivation of the MAPK pathway and uncontrolled growth. KRAS functions as a small GTPase that cycles through its GTP-loaded “on” state and its GDP-loaded “off” state, a highly regulated process that is crucial for normal cell proliferation and survival. The guanine nucleotide exchange factor (GEF) SOS1 plays a critical role in this process by regulating the “on/off” state of KRAS. The protein-protein interaction between SOS1 and KRAS facilitates turnover of KRAS from the GDP-loaded inactive state to its activated and GTP-loaded state, a critical step to enable productive KRAS effector binding and activation of downstream signaling. The KRASG12C inhibitor, adagrasib (MRTX849), irreversibly binds to the GDP-loaded inactive conformation of KRASG12C and has recently shown encouraging clinical activity across several cancer types. As adagrasib binds preferentially to the inactive state of KRAS, blockade of SOS1 is anticipated to shift KRASG12C into the adagrasib-susceptible GDP-loaded state. Furthermore, this combination strategy could be used to target other mutant-driven cancers within the MAPK pathway using the appropriate KRASmut inhibitors and/or inhibitors of other targets within the MAPK pathway including MEK or EGFR. MRTX0902 was identified using iterative structure-based design as a selective inhibitor of SOS1 that demonstrates an IC50 value of 2 nM in a SOS1 HTRF binding assay and 30 nM in an MKN1 cellular assay. In pharmacokinetic evaluation across species, MRTX0902 demonstrated low extraction ratios and moderate to high bioavailability in mice, rats, and dogs. In preclinical models, MRTX0902 augmented the antitumor activity of adagrasib and other selected therapies. The design, discovery, and preclinical characterization of the potential best-in-class candidate MRTX0902 will be described.
Citation Format: John M. Ketcham, David M. Briere, Aaron C. Burns, James G. Christensen, Robin J. Gunn, Jacob Haling, Anthony Ivetac, Shilpi Khare, Jon Kuehler, Svitlana Kulyk, Jade Laguer, John D. Lawson, Krystal Moya, Natalie Nguyen, Peter Olson, Lisa Rahbaek, Christopher R. Smith, Niranjan Sudhakar, Nicole C. Thomas, Darin Vanderpool, Xiaolun Wang, Matthew A. Marx. Design and discovery of MRTX0902, a potent, selective, and orally bioavailable SOS1 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB505.
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8
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Ketcham JM, Khare S, Sudhakar N, Briere DM, Yan L, Laguer J, Vegar L, Vanderpool D, Hallin J, Hargis L, Bowcut V, Lawson D, Gunn RJ, Ivetac A, Thomas NC, Saechao B, Nguyen N, Clarine J, Rahbaek L, Smith CR, Burns AC, Marx MA, Christensen JG, Olson P, Haling JR. Abstract ND02: MRTX0902: A SOS1 inhibitor for therapeutic intervention of KRAS-driven cancers. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-nd02] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
KRAS is the most frequently mutated oncogene in cancer and drives uncontrolled growth through hyperactivation of the MAPK pathway. Significant progress has been made in the past several years to directly target KRASG12C with the FDA approval of sotorasib and the reported clinical activity of adagrasib (MRTX849). Despite these remarkable breakthroughs, additional therapies that enhance the depth and duration of response to KRASG12C inhibitors provide the opportunity to build upon the initial progress. SOS proteins are guanine nucleotide exchange factors (GEFs) that transduce receptor tyrosine kinase (RTK) signaling from the cell surface and facilitate the activation of RAS family proteins. In addition, SOS1 is a target of negative feedback signaling following RAS-mediated activation of the RAF-MEK-ERK cascade. Thus, SOS proteins represent a significant therapeutic node that maintains RAS pathway equilibrium as well as oncogenic signaling dynamics. Here we highlight the discovery and preclinical evaluation of MRTX0902, a potent, selective, and orally bioavailable inhibitor of SOS1 presently in IND-enabling studies. A structure-based approach was used to identify a novel chemical series that disrupts the protein-protein interaction between SOS1 and KRAS, thereby preventing SOS1-mediated GTP-exchange on GDP-bound KRAS. Considering MRTX849 preferentially binds to inactive GDP-bound KRASG12C, targeting SOS1 in this genetic context increases the ability of MRTX849 to bind and inhibit KRASG12C. The combination of MRTX0902 with MRTX849 enhances the depth and durability of an anti-tumor response when compared to MRTX849 alone in pre-clinical KRASG12C tumor models. MRTX0902 augments additional targeted therapies across a variety of RAS-addicted tumors, indicating that SOS1 inhibition is effective against a broad spectrum of mutations within the MAPK pathway. Furthermore, drug-anchored CRISPR experiments with MRTX0902 and MRTX849 uncovered a previously underappreciated functional role of the SOS1 paralog, SOS2, in KRAS-addicted tumors. In addition to aiding in the understanding of SOS and RAS family signaling dynamics, these studies implicate SOS2 as a potential cancer drug target in the context of SOS1/KRASG12C inhibition. In summary, we have used a structure-based approach to discover a SOS1 inhibitor that augments the anti-tumor activity of MRTX849 and additional targeted MAPK pathway inhibitors. We anticipate our findings to translate into the clinic and make an impact in patients with RAS-addicted tumors.
Citation Format: John M. Ketcham, Shilpi Khare, Niranjan Sudhakar, David M. Briere, Larry Yan, Jade Laguer, Laura Vegar, Darin Vanderpool, Jill Hallin, Lauren Hargis, Vickie Bowcut, David Lawson, Robin J. Gunn, Anthony Ivetac, Nicole C. Thomas, Barbara Saechao, Natalie Nguyen, Jeffrey Clarine, Lisa Rahbaek, Christopher R. Smith, Aaron C. Burns, Matthew A. Marx, James G. Christensen, Peter Olson, Jacob R. Haling. MRTX0902: A SOS1 inhibitor for therapeutic intervention of KRAS-driven cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr ND02.
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Affiliation(s)
| | | | | | | | - Larry Yan
- 1Mirati Therapeutics, Inc, San Diego, CA
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9
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Smith CR, Aranda R, Bobinski TP, Briere DM, Burns AC, Christensen JG, Clarine J, Engstrom LD, Gunn RJ, Ivetac A, Jean-Baptiste R, Ketcham JM, Kobayashi M, Kuehler J, Kulyk S, Lawson JD, Moya K, Olson P, Rahbaek L, Thomas NC, Wang X, Waters LM, Marx MA. Fragment-Based Discovery of MRTX1719, a Synthetic Lethal Inhibitor of the PRMT5•MTA Complex for the Treatment of MTAP-Deleted Cancers. J Med Chem 2022; 65:1749-1766. [PMID: 35041419 DOI: 10.1021/acs.jmedchem.1c01900] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The PRMT5•MTA complex has recently emerged as a new synthetically lethal drug target for the treatment of MTAP-deleted cancers. Here, we report the discovery of development candidate MRTX1719. MRTX1719 is a potent and selective binder to the PRMT5•MTA complex and selectively inhibits PRMT5 activity in MTAP-deleted cells compared to MTAP-wild-type cells. Daily oral administration of MRTX1719 to tumor xenograft-bearing mice demonstrated dose-dependent inhibition of PRMT5-dependent symmetric dimethylarginine protein modification in MTAP-deleted tumors that correlated with antitumor activity. A 4-(aminomethyl)phthalazin-1(2H)-one hit was identified through a fragment-based screen, followed by X-ray crystallography, to confirm binding to the PRMT5•MTA complex. Fragment growth supported by structural insights from X-ray crystallography coupled with optimization of pharmacokinetic properties aided the discovery of development candidate MRTX1719.
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Affiliation(s)
| | - Ruth Aranda
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - David M Briere
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Aaron C Burns
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Jeffery Clarine
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Lars D Engstrom
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Robin J Gunn
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Anthony Ivetac
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - John M Ketcham
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Jon Kuehler
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Svitlana Kulyk
- Mirati Therapeutics, San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Krystal Moya
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Peter Olson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Lisa Rahbaek
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Nicole C Thomas
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Xiaolun Wang
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Laura M Waters
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Matthew A Marx
- Mirati Therapeutics, San Diego, California 92121, United States
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10
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Wang X, Allen S, Blake JF, Bowcut V, Briere DM, Calinisan A, Dahlke JR, Fell JB, Fischer JP, Gunn RJ, Hallin J, Laguer J, Lawson JD, Medwid J, Newhouse B, Nguyen P, O'Leary JM, Olson P, Pajk S, Rahbaek L, Rodriguez M, Smith CR, Tang TP, Thomas NC, Vanderpool D, Vigers GP, Christensen JG, Marx MA. Identification of MRTX1133, a Noncovalent, Potent, and Selective KRAS G12D Inhibitor. J Med Chem 2021; 65:3123-3133. [PMID: 34889605 DOI: 10.1021/acs.jmedchem.1c01688] [Citation(s) in RCA: 213] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
KRASG12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of solid tumors. However, when compared to KRASG12C, selective inhibition of KRASG12D presents a significant challenge due to the requirement of inhibitors to bind KRASG12D with high enough affinity to obviate the need for covalent interactions with the mutant KRAS protein. Here, we report the discovery and characterization of the first noncovalent, potent, and selective KRASG12D inhibitor, MRTX1133, which was discovered through an extensive structure-based activity improvement and shown to be efficacious in a KRASG12D mutant xenograft mouse tumor model.
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Affiliation(s)
- Xiaolun Wang
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Shelley Allen
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - James F Blake
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Vickie Bowcut
- Mirati Therapeutics, San Diego, California 92121, United States
| | - David M Briere
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Joshua R Dahlke
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Jay B Fell
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - John P Fischer
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Robin J Gunn
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Jill Hallin
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Jade Laguer
- Mirati Therapeutics, San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - James Medwid
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Brad Newhouse
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Phong Nguyen
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Jacob M O'Leary
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Peter Olson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Spencer Pajk
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Lisa Rahbaek
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Mareli Rodriguez
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | | | - Tony P Tang
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Nicole C Thomas
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Guy P Vigers
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | | | - Matthew A Marx
- Mirati Therapeutics, San Diego, California 92121, United States
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11
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Das N, Dewan V, Grace PM, Gunn RJ, Tamura R, Tzarum N, Watkins LR, Wilson IA, Yin H. HMGB1 Activates Proinflammatory Signaling via TLR5 Leading to Allodynia. Cell Rep 2017; 17:1128-1140. [PMID: 27760316 DOI: 10.1016/j.celrep.2016.09.076] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 08/19/2016] [Accepted: 09/22/2016] [Indexed: 12/11/2022] Open
Abstract
Infectious and sterile inflammatory diseases are correlated with increased levels of high mobility group box 1 (HMGB1) in tissues and serum. Extracellular HMGB1 is known to activate Toll-like receptors (TLRs) 2 and 4 and RAGE (receptor for advanced glycation endproducts) in inflammatory conditions. Here, we find that TLR5 is also an HMGB1 receptor that was previously overlooked due to lack of functional expression in the cell lines usually used for studying TLR signaling. HMGB1 binding to TLR5 initiates the activation of NF-κB signaling pathway in a MyD88-dependent manner, resulting in proinflammatory cytokine production and pain enhancement in vivo. Biophysical and in vitro results highlight an essential role for the C-terminal tail region of HMGB1 in facilitating interactions with TLR5. These results suggest that HMGB1-modulated TLR5 signaling is responsible for pain hypersensitivity.
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Affiliation(s)
- Nabanita Das
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Varun Dewan
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Peter M Grace
- Department of Psychology and Neuroscience and the Center for Neuroscience, University of Colorado, Boulder, CO 80309, USA
| | - Robin J Gunn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ryo Tamura
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Netanel Tzarum
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Linda R Watkins
- Department of Psychology and Neuroscience and the Center for Neuroscience, University of Colorado, Boulder, CO 80309, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hang Yin
- Department of Chemistry and Biochemistry and the BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA.
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12
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Collins BC, Gunn RJ, McKitrick TR, Cummings RD, Cooper MD, Herrin BR, Wilson IA. Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates. Structure 2017; 25:1667-1678.e4. [PMID: 28988747 DOI: 10.1016/j.str.2017.09.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 07/10/2017] [Revised: 08/16/2017] [Accepted: 09/01/2017] [Indexed: 12/28/2022]
Abstract
High-quality reagents to study and detect glycans with high specificity for research and clinical applications are severely lacking. Here, we structurally and functionally characterize several variable lymphocyte receptor (VLR)-based antibodies from lampreys immunized with O erythrocytes that specifically recognize the blood group H-trisaccharide type II antigen. Glycan microarray analysis and biophysical data reveal that these VLRs exhibit greater specificity for H-trisaccharide compared with the plant lectin UEA-1, which is widely used in blood typing. Among these antibodies, O13 exhibits superior specificity for H-trisaccharide, the basis for which is revealed by comparative analysis of high-resolution VLR:glycan crystal structures. Using a structure-guided approach, we designed an O13 mutant with further enhanced specificity for H-trisaccharide. These insights into glycan recognition by VLRs suggest that lampreys can produce highly specific glycan antibodies, and are a valuable resource for the production of next-generation glycan reagents for biological and biomedical research and as diagnostics and therapeutics.
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Affiliation(s)
- Bernard C Collins
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robin J Gunn
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tanya R McKitrick
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Richard D Cummings
- National Center for Functional Glycomics, Beth Israel Deaconess Medical Center Department of Surgery, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA
| | - Max D Cooper
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Brantley R Herrin
- Emory Vaccine Center and Department of Pathology and Laboratory Medicine, Emory University, 1462 Clifton Road North-East, Atlanta, GA 30322, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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