Inhibitors of malt1 and methods of their use
A compound of Formula (I) inhibits MALT1 to treat B-cell malignancies by targeting specific mutations, addressing patient selection needs and improving treatment efficacy for DLBCL.
Patent Information
- Application Number
- PCT/EP2025/061322
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2024-07-02
- Filing Date
- 2025-04-25
- Publication Date
- 2025-10-30
AI Technical Summary
There is a need for a method of patient selection for patients who would benefit from MALT1 therapy, as constitutive activation of NF-KB signaling is a hallmark of ABC-DLBCL, and existing treatments like BTK inhibitors may not be effective for all patients, leading to relapse and resistance.
The use of a compound of Formula (I) or its pharmaceutically acceptable salts, hydrates, or solvates to inhibit MALT1, combined with biomarker detection of B-cell pathway activating mutations such as BTK V416L, BTK T474I, BTK C481S, and BTK L528W, to predict patient responsiveness and treat B-cell malignancies like DLBCL.
The compound effectively inhibits MALT1, increasing the likelihood of response in patients with B-cell malignancies by targeting specific mutations, providing a therapeutic option for relapsed/refractory cases.
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Figure EP2025061322_30102025_PF_FP_ABST
Abstract
Description
INHIBITORS OF MALT1 AND METHODS OF THEIR USEBACKGROUND
[0001] MALT1 (mucosa-associated lymphoid tissue lymphoma translocation) is a key mediator of the classical NFKB signaling pathway. MALT1 is the only human paracaspase and transduces signals from the B cell receptor (B-CELL RECEPTOR) and T cell receptor (TCR). MALT1 is the active subunit of the CBM complex which is formed upon receptor activation.The CBM complex consists of multiple subunits of three proteins: CARD 11 (caspase recruitment domain family member 11), BCL10 (B-cell CLL / Lymphoma 10) and MALTE MALT1 affects NFKB signaling by two mechanisms: firstly, MALT1 functions as a scaffolding protein and recruits NF-KB signaling proteins such as TRAF6, TAB-TAK1 or NEMO-IKKa / 0; and secondly, MALT1, as a cysteine protease, cleaves and thereby deactivates negative regulators of NF-KB signaling, such as RelB, A20 or CYLD.
[0002] Constitutive activation of NF-KB signaling is the hallmark of ABC-DLBCL (Diffuse Large B Cell Lymphoma of the Activated B Cell-like subtype), the more aggressive form of DLBCL. DLBCL is the most common form of non-Hodgkin’s lymphoma (NHL), accounting for approximately 30-40% of lymphoma cases while ABC-DLBCL comprises approximately 40% of DLBCL. NF-KB pathway activation is driven by mutations of signaling components, such as CD79a / b, CARD 11, MYD88 or A20, in ABC-DLBCL patients.
[0003] The use of BTK inhibitors, for example Ibrutinib, provides clinical proof-of-concept that inhibiting NF-KB signaling in ABC-DLBCL is efficacious. Patients whose cancers are no longer responsive or insufficiently responsive to Ibrutinib or other BTK inhibitors may benefit from a treatment option that focuses on a different segment of the NF-KB signal transduction pathway. Thus, there remains a need for a method of patient selection for patients who would benefit from MALT1 therapy.
[0004] DLBCL is the most prevalent type of aggressive non-Hodgkin's lymphoma (NHL) in the United States. While majority of the patients with DLBCL show response to the initial treatment, some patients do not respond as hoped. In addition, for patients who do have an initial response, approximately one-third experience relapse after the standard therapies. Thus, there remains a need for both predicting whether a patient will respond to a prescribed chemotherapy, as well as new treatment options for patients who have stopped responding to initial treatment.DETAILED DESCRIPTION
[0005] Tumor specific characteristics, such as the expression of one or more specific genes and / or encoded proteins may be useful as a prognostic biomarker for identifying potential patients likely to respond or fail treatment with a new chemotherapeutic agent.DEFINITIONS
[0006] The term “about” as used herein when immediately preceding a numerical value means a range of plus or minus 10% of that value, for example, “about 50” means 45 to 55, “about 25,000” means 22,500 to 27,500, etc., unless the context of the disclosure indicates otherwise, or is inconsistent with such an interpretation.
[0007] The term “B-cell receptor (BCR) pathway activating mutation” as used herein refers to a genetic alteration that enhances BCR signaling. Examples of genes that can become mutated with the effect of enhancing B-cell receptor signaling include Bruton tyrosine kinase (BTK), CARD1 1, CD79a, CD79b, and BCL10. B-cell receptor pathway activating mutations can play a role in B-cell malignancies.
[0008] As used herein, the term “BTK gene” refers to Bruton tyrosine kinase gene.
[0009] As used herein, the term “BTK protein” refers to Bruton tyrosine kinase protein.
[0010] As used herein, the term “BTK inhibitor” refers to a compound that binds to the BTK protein with the effect of abrogating the kinase activity of BTK and disrupting the B-cell receptor signaling pathway. Some BTK inhibitors are used to treat B-cell malignancies. Nonlimiting examples of BTK inhibitors include: ibrutinib, acalabrutinib, zanubrutinib, and pirtobrutinib. Other examples of BTK inhibitors include Roche BTKi RN486, CT-1530, DTRMWXHS-12, spebrutinib besylate, vecabrutinib, evobrutinib, tirabrutinib, fenebrutinib, poseltinib, BMS-986142, ARQ- 531, LOU-064, PRN-1008, ABBV-599, AC-058, BIIB-068, BMS-986195, HWH-486, PRN-2246, TAK-020, GDC-0834, BMX-IN-1, RN486, SNS-062, LFM-A13, and. Another example of a BTK inhibitor is 7V-((17?,25)-2-acrylamidocyclopentyl)-5-CS')-(6-isobutyl-4-methylpyridin-3-yl)-4-oxo-4,5-dihydro-3 / / - l -thia-3, 5, 8-tri azaacenaphthylene- 2-carboxamide (Form P-II):Formula P-(ll)
[0011] The term “mutation” as used herein refers to a change in the DNA sequence of a gene and can refer to DNA base(s) substitution, deletion or insertion that as a consequence, leads to a change to the amino acid sequence of a protein or alters its expression level (loss or overexpression). Mutations can also lead to translocations in which a chromosome breaks and is wrongly repaired and fused to another region in the same or different chromosome, on occasion leading to a fusion protein. Some mutations can be oncogenic.
[0012] The term “C-terminal truncating mutation” as used herein refers to a genetic mutation or change in the DNA that results in the creation of an early stop codon, which encodes for the end of the protein. The introduction of a premature stop codon leads to the production of a shortened or truncated protein, wherein the truncation occurs at the C-terminus of the protein.
[0013] The term “Pharmaceutically acceptable” means approved or approvable by a regulatory agency of the Federal or a state government or the corresponding agency in countries other than the United States, or that is listed in the U.S. Pharmacopoeia or other generally recognized pharmacopoeia for use in animals, and more particularly, in humans.
[0014] The term “Pharmaceutically acceptable salt” refers to a salt of a compound of the disclosure that is pharmaceutically acceptable and that possesses the desired pharmacological activity of the parent compound. In particular, such salts are non-toxic may be inorganic or organic acid addition salts and base addition salts. Specifically, such salts include: (1) acidaddition salts, formed with inorganic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like; or formed with organic acids such as acetic acid, propionic acid, hexanoic acid, cyclopentanepropionic acid, glycolic acid, pyruvic acid, lactic acid, malonic acid, succinic acid, malic acid, maleic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, 1,2-ethane-disulfonic acid, 2-hydroxy ethanesulfonic acid, benzenesulfonic acid, 4-chlorobenzenesulfonic acid, 2-naphthalenesulfonic acid, 4- toluenesulfonic acid, camphorsulfonic acid, 4-methylbicyclo[2.2.2]-oct-2-ene-l-carboxylic acid, glucoheptonic acid, 3 -phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, lauryl sulfuric acid, gluconic acid, glutamic acid, hydroxynaphthoic acid, salicylic acid, stearic acid, muconic acid, and the like; or (2) salts formed when an acidic proton present in the parent compound either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base such as ethanolamine, diethanolamine, triethanolamine, N-methylglucamine and the like. Salts further include, by way of example only, sodium, potassium, calcium, magnesium, ammonium, tetraalkylammonium, and the like; and when the compound contains a basic functionality, salts of non-toxic organic or inorganic acids, such as hydrochloride, hydrobromide, tartrate, mesylate, acetate, maleate, oxalate and the like.
[0015] The term “Pharmaceutically acceptable vehicle” refers to a diluent, adjuvant, excipient or carrier with which a compound of the disclosure is administered. A "pharmaceutically acceptable excipient" refers to a substance that is non-toxic, biologically tolerable, and otherwise biologically suitable for administration to a subject, such as an inert substance, added to a pharmacological composition or otherwise used as a vehicle, carrier, or diluent to facilitate administration of an agent and that is compatible therewith. Examples of excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils, and polyethylene glycols.
[0016] The term “subject” includes humans. The terms “human,” “patient,” and “subject” are used interchangeably herein.
[0017] The term “Treating” or “treatment” of any disease or disorder refers, in one aspect, to ameliorating the disease or disorder (i.e., arresting or reducing the development of the disease or at least one of the clinical symptoms thereof). In another aspect “treating” or “treatment” refers to ameliorating at least one physical parameter, which may not be discernible by the subject. In yet another aspect, “treating” or “treatment” refers to modulating the disease or disorder, either physically, (e.g., stabilization of a discernible symptom), physiologically, (e.g., stabilization of a physical parameter), or both. In yet another aspect, “treating” or “treatment” refers to delaying the onset of the disease or disorder.
[0018] All embodiments and aspects described herein “for use in a method of treating”, are also applicable “for use in treating” or “for use in the treatment of’.
[0019] All embodiments and aspects described herein for “a method of treating”, are also applicable “for use in treating” or “for use in the treatment of’.
[0020] The present disclosure is directed to the use of a compound of Formula (I)
[0021] or pharmaceutically acceptable salts, hydrates, polymorphs or solvates thereof. The compound of Formula (I) is also known as (lS,3R)-3-(4-((R)-2-chloro-8-methyl-8- (trifluoromethyl)-7,8-dihydro-6H-pyrazolo[l,5-a]pyrrolo[2,3-e]pyrimidin-6-yl)phenyl)-2,2- difluoro- 1 -methyl -N-((trans)-3 -(methylsulfonyl)cyclobutyl)cyclopropane- 1 -carboxamide.
[0022] Unless otherwise indicated or clear from the context, all references to the structure of Formula (I) or (lS,3R)-3-(4-((R)-2-chloro-8-methyl-8-(trifluoromethyl)-7,8-dihydro-6H- pyrazolo[l,5-a]pyrrolo[2,3-e]pyrimidin-6-yl)phenyl)-2,2-difluoro-l-methyl-N-((trans)-3- (methylsulfonyl)cyclobutyl)cyclopropane-l -carboxamide in the context of this invention, might also refer to the pharmaceutically acceptable salts and solvates thereof, including hydrates, and including any subgroup thereof or any combination of pharmaceutically acceptable salts and solvates thereof.
[0023] Where stereochemistry is specified by bonds which are shown as solid wedged or hashed wedged bonds, hashed or bold bonds, then that stereoisomer is so specified and defined.
[0024] It will be clear for a skilled person that a hashed bond and a bold bond on a 1,3 -di substituted cyclobutyl moiety as shown below:, whereby X1and X2represent substituents, indicate that the substituents on the cyclobutyl moiety have trans-configuration.
[0025] The stereodescriptor label “R” or “( ?)” at a stereocenter designates that the stereocenter is purely of the ^-configuration as defined in the art; likewise, the stereodescriptor label “S” or “6S ” means that the stereocenter is purely of the ^'-configuration.
[0026] The disclosure also relates to methods of using the compounds described herein to treat subjects diagnosed with or suffering from a disease, disorder, or condition mediated by Bruton’s tyrosine kinase. These methods are accomplished by administering to the subject a compound of the disclosure in an amount sufficient to inhibit Bruton’s tyrosine kinase. In a further aspect, provided herein are methods for inhibiting Bruton's tyrosine kinase in a subject in need of treatment by administering to the subject a composition containing a therapeutically effective amount of the compound of Formula (I).
[0027] Some aspects of the disclosure are directed to methods of treating a subject suffering from a B-cell malignancy by administering to the subject a composition containing a therapeutically effective amount of the compound of Formula (I).
[0028] In some aspects, the B-cell malignancy is follicular lymphoma (FL), mantle cell lymphoma (MCL), marginal zone lymphoma (MZL), or Waldenstrom macroglobulinemia (WM).
[0029] In some aspects, the B-cell malignancy is MALT lymphoma, B-cell non-Hodgkin lymphoma (B-cell NHL), follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma. A skilled person will understand that non-limiting examples of B-cell non-Hodgkin lymphomas are MALT lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, and diffuse large B-cell lymphoma.
[0030] In some aspects, the B-cell malignancy is diffuse large B-cell lymphoma (DLBCL). It will be clear for a skilled person that DLBCL is a type of NHL, in particular a type of B-cell NHL.
[0031] In some aspects, the B-cell malignancy is B-cell non-Hodgkin lymphoma.
[0032] In some aspects, the B-cell malignancy is relapsed / refractory B-cell non-Hodgkin lymphoma.
[0033] In some aspects, the B-cell malignancy is MALT lymphoma.
[0034] In some aspects, the B-cell malignancy is germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) or nongerminal center B-cell diffuse large B-cell lymphoma (non- GCB-DLBCL).
[0035] In some aspects, the B-cell malignancy is ABC-DLBCL.
[0036] In some aspects the non-GCB DLBCL is unclassified DLBCL. In some aspects, the malignancy is MCD DLBCL or C5 (cluster 5) DLBCL. In some instances the malignancy is BN2 or Cl (cluster 1) DLBCL.
[0037] In some aspects, the B-cell malignancy is relapsed / refractory. In some aspects, any of the exemplified B-cell malignancies herein are relapsed / refractory. In some aspects, the B-cell malignancy is relapsed / refractory DLBCL. In some aspects, the B-cell malignancy isrelapsed / refractory GCB-DLBCL. In some aspects, the B-cell malignancy is relapsed / refractory non-GCB-DLBCL. In some aspects, the B-cell malignancy is relapsed / refractory ABC-DLBCL.Mutant Detection
[0038] B-cell pathway activating mutations are detectable by methods known in the art. Such methods include, but are not limited to, DNA or RNA sequencing and mutant calling.In some aspects the B-cell pathway activating mutations are in CD79a, CD79b, CARD11, BCL10, BTK, PLCG2, LYN, SYK, KLHL6, MALT1 genes as well as mutations in BTK (for example but not limiting to BTK V416L, BTK T474I, BTK T474M, BTK C481S, or BTK L528W) or any combination thereof. In particular the mutation in BTK is V416L. In particular the mutation in BTK is T474I. In particular the mutation in BTK is C481S. In particular the mutation in BTK is L528W.
[0039] In some aspects the mutation is in a gene selected from the group consisting of BTK, CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6, BCL10 and MALT1. In some aspects the mutation is in a gene selected from the group consisting of CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6, BCL10 and MALT1. In some aspects the mutation is in a gene selected from the group consisting of CARD11, CD79a, CD79b and BCL10. In some aspects the mutation is in a gene selected from the group consisting of CARD11, CD79a and CD79b. In some aspects the mutation is in CARD11. In some aspects the mutation is in CD79a. In some aspects the mutation is in CD79b. In some aspects the mutation is in BCL10.
[0040] In some aspects the B-cell pathway activating mutation is in a gene selected from the group consisting of BTK, CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6, BCL10 and MALT1. In some aspects the B-cell pathway activating mutation is in a gene selected from the group consisting of CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6, BCL10 and MALT1. In some aspects the B-cell pathway activating mutation is in a gene selected from the group consisting of CARD11, CD79a, CD79b and BCL10. In some aspects the B-cell pathway activating mutation is in a gene selected from the group consisting of CARD11, CD79a andCD79b. In some aspects the B-cell pathway activating mutation is in CARD11. In some aspects the B-cell pathway activating mutation is in CD79a. In some aspects the B-cell pathway activating mutation is in CD79b. In some aspects the B-cell pathway activating mutation is in BCL10.
[0041] PROTEIN expression profiling
[0042] Protein products from the patient may be assayed by immunohistochemistry of tumor samples, solid phase immunoassay with microtitre plates, Western blotting, 2-dimensional SDS- polyacrylamide gel electrophoresis, ELISA, flow cytometry and other methods known in the art for detection of specific proteins. Detection methods would include the use of site-specific antibodies. The skilled person will recognize that all such well-known techniques for detection of upregulation of wild type or mutant proteins, in particular mutant BTK proteins such as for example and without limitation: BTK V416L, BTK T474I, BTK T474M, BTK C481S, and BTK L528W or any combination thereof, could be applicable in the present case. Mutant protein activation or expression could be detected in a tissue sample, for example, a tumor tissue.
[0043] Therefore, all of these techniques could also be used to identify tumors particularly suitable for treatment with the compounds of the invention.
[0044] The methods provided herein relate to the use of mutated gene or protein expression as a predictive biomarker for identifying responder populations, especially those patients that are likely to be sensitive to treatment with a compound of Formula (I). In some aspects, presence of mutations BTK V416L, BTK T474I, BTK C481 S, and BTK L528W or any combination thereof can be detected by sequencing of DNA and RNA in tumor tissue or plasma or may be detected by Enzyme-Linked Immunosorbent Assay (ELISA) or other rapid protein detection methods.
[0045] In some aspects, the methods provided herein relate to the detection of mutated CARD11 gene as a predictive biomarker for identifying responder populations, especially those patients that are likely to be sensitive to treatment with a compound of Formula (I).
[0046] In some aspects, the methods provided herein relate to the detection of mutated CD79a gene as a predictive biomarker for identifying responder populations, especially those patients that are likely to be sensitive to treatment with a compound of Formula (I).
[0047] In some aspects, the methods provided herein relate to the detection of mutated CD79b gene as a predictive biomarker for identifying responder populations, especially those patients that are likely to be sensitive to treatment with a compound of Formula (I).
[0048] In some aspects, the methods provided herein relate to the detection of mutated BCL10 gene as a predictive biomarker for identifying responder populations, especially those patients that are likely to be sensitive to treatment with a compound of Formula (I).
[0049] In some aspects, the methods provided herein relate to the detection of mutated BTK gene as a predictive biomarker for identifying responder populations, especially those patients that are likely to be sensitive to treatment with a compound of Formula (I).
[0050] In some aspects, methods are provided for treating DLBCL comprising selection of patients who express one or more of the following mutated proteins: BTK V416L, BTK T474I, BTK C481 S, and BTK L528W, followed by treatment with a therapeutically effective amount of the compound of Formula (I), thereby increasing the likelihood of a response, in the patient, to the compound of Formula (I).Biomarkers based on gene modifications
[0051] In some aspects, the methods disclosed herein are based on detecting the presence or absence of a gene modification, wherein a gene modification is a base substitution, an insertion, a deletion, a DNA rearrangement, a translocation, a copy number alteration, or a combination thereof.
[0052] In some aspects, a method of treating DLBCL in a subject comprises: (a) determining the presence or absence of a modification in one or more biomarker genes in a subject, the biomarker genes selected from BTK, CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6,and BCL10; and (b) administering to the subject a therapeutically effective amount of compound of Formula (I) if there is a presence of a modification in the one or more biomarker genes. In some embodiments, the DLBCL subtype is activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL), germinal center B-cell diffuse large B-cell lymphoma (GCB-DLBCL) or non- germinal center B-cell diffuse large B-cell lymphoma (non-GCB-DLBCL).
[0053] The term “therapeutically effective amount” refers to an amount of an active compound or pharmaceutical agent, including a compound of the present invention, which elicits the biological or medicinal response in a tissue system, animal or human that is being sought by a researcher, veterinarian, medical doctor or other clinician, including reduction or inhibition of an enzyme or a protein activity, or ameliorating symptioms, alleviating conditions, slowing or delaying disease progression, or preventing a disease.
[0054] In one embodiment, the term “therapeutically effective amount” refers to the amount of a compound of the present invention that, when administered to a subject, is effective to (1) at least partially alleviate, inhibit, prevent, and / or ameliorate a condition, or a disorder or a disease (i) mediated by MALT1; or (ii) associated with MALT1 activity; or (iii) characterized by activity (normal or abnormal) of MALT 1; or (2) reduce or inhibit the activity of MALT 1; or (3) reduce or inhibit the expression of MALT1; or (4) modify the protein levels of MALT1. The term “MALT 1 -mediated” refers to any disease, syndrome, condition, or disorder that might occur in the absence of MALT 1 but can occur in the presence of MALT 1.
[0055] The term “composition” refers to a product that includes the specified ingredients in therapeutically effective amounts, as well as any product that results, directly, or indirectly, from combinations of the specified ingredients in the specified amounts.
[0056] Even though the compounds of embodiments of the present invention (including their pharmaceutically acceptable salts and pharmaceutically acceptable solvates) can be administered alone, they will generally be administered in admixture with a pharmaceutically acceptable carrier, a pharmaceutically acceptable excipient and / or a pharmaceutically acceptable diluent selected with regard to the intended route of administration and standard pharmaceutical or veterinary practice. Thus, particular embodiments of the present invention are directed to pharmaceutical and veterinary compositions comprising compounds of Formula (I) and at least one pharmaceutically acceptable carrier, pharmaceutically acceptable excipient, and / or pharmaceutically acceptable diluent.By way of example, in the pharmaceutical compositions of embodiments of the present invention, the compounds of Formula (I) may be admixed with any suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), solubilizing agent(s), and combinations thereof.
[0057] Solid oral dosage forms such as, tablets or capsules, containing the compounds of the present invention may be administered in at least one dosage form at a time, as appropriate. It is also possible to administer the compounds in sustained release formulations.
[0058] A therapeutically effective amount of a compound of Formula (I) or a pharmaceutical composition thereof includes a dose range from about 0.1 mg to about 3000 mg, or any particular amount or range therein; although, it is apparent to one skilled in the art that the therapeutically effective amount for a compound of Formula (I) will vary as will the diseases, syndromes, conditions, and disorders being treated.
[0059] In another embodiment of the present invention, the compounds of the present invention may be employed in combination with one or more other medicinal agents, more particularly with other anti-cancer agents, e.g. chemotherapeutic, anti-proliferative or immunomodulating agents, or with adjuvants in cancer therapy, e.g. immunosuppressive or anti-inflammatory agents.
[0060] Possible combinations of the compounds of the present invention may include, but are not limited to, BTK (Bruton’s tyrosine kinase) inhibitors such as ibrutinib, SYK inhibitors, PKC inhibitors, PI3K pathway inhibitors, BCL family inhibitors, JAK inhibitors, PIM kinase inhibitors, rituximab or other B cell antigen-binding antibodies, as well as immune cell redirection agents (e.g. blinatumomab or CAR T-cells) and immunomodulatory agents such as daratumumab, anti- PD1 antibodies, and anti-PD-Ll antibodies.
[0061] Compounds of the disclosure can be prepared using the knowledge of one skilled in the art in combination with the present disclosure.Materials and Methods
[0062] Several methods for preparing the intermediates and Compounds of this invention are illustrated in the following examples. Unless otherwise noted, all starting materials were obtained from commercial suppliers and used without further purification, or alternatively can be synthesized by a skilled person by using well-known methods.
[0063] A skilled person will realize that, even where not mentioned explicitly in the experimental protocols below, typically after a column chromatography purification, the desired fractions were collected, and the solvent was evaporated.
[0064] In case no stereochemistry is indicated, this means it is a mixture of stereoisomers, unless otherwise is indicated or is clear from the context.Preparation of intermediates
[0065] Procedures for intermediates used in the next reaction step as crude or as partially purifiedmay not mention mol amounts for such intermediate in the next reaction step or alternatively may mention estimated mol amounts or theoretical mol amounts for such intermediate in the next reaction step.Intermediate 1
[0066] Into a 10 L 3-necked flask was placed ethyl 2-(benzylamino)acetate (550 g, 2.85 mol, 1.00 equiv), CHC13 (5.5 L), TEA (576 g, 5.70 mmol, 2.00 equiv). Propanoyl chloride (290 g, 3.13 mol, 1.10 equiv) in CHC13 (300 mL) was added dropwise at 0 °C. The mixture was stirred for 1 h at 25 °C. The mixture was poured into H2O (6 L). The resulting solution was extracted with DCM (2x 2 L). The organic layers were combined, dried over anhydrous MgSO4, and concentrated under vacuum. The resulting residue was purified by flash column chromatography over silica gel (eluent: EtOAc / PE 1 :2) to give Intermediate 1 (561 g, 79% yield) as a light-yellow oil.Intermediate 2Intermediate 1 (561 g, 2.25 mol, 1.00 equiv) in THF (2 L) was added dropwise at 75 °C to a mixture of NaH (108 g, 2.70 mol, 1.20 equiv, 60%) and THF (10 L). After 12 h at 75 °C, the reaction was cooled to 20 °C, water (100 mL) was added, and the mixture was concentrated under vacuum. The resulting residue was purified by flash column chromatography over silica gel (eluent: MeOH / DCM 1 :30) to give Intermediate 2 (231 g, 50% yield) as an off-white solid.Intermediate 3
[0067] NaH (45.5 g, 1.14 mol, 1.00 equiv, 60%) was added portionwise at 0 °C to Intermediate 2 (231 g, 1.14 mol, 1.00 equiv) in DMF (4.6 L). The mixture was stirred for 0.5 h at 25 °C. 5- (trifluoromethyl)dibenzothiophenium trifluoromethanesulfonate (457 g, 1.14 mol, 1.00 equiv) was added to the mixture at -55 °C. The mixture was gradually warmed up to 25 °C and stirred for 1 h. The mixture was poured into a mixture of ice / water (10 L) and extracted with EtOAc (2x 5 L). The organic layers were combined, dried over anhydrous Na2SO4, filtered, and concentrated under vacuum. The resulting residue was purified by flash column chromatography over silica gel (eluent: EtOAc / PE 1 :4) to give Intermediate 3 (275 g, 89% yield) as a light-yellow oil.Intermediate 4
[0068] LAH (154 g, 4.10 mol, 4.00 equiv) was added at 0 °C to a mixture of Intermediate 3 (275 g, 1.01 mol, 1.00 equiv) in THF (5.5 L). The mixture was warmed up to 80 °C and stirred at this temperature for 15 h. The mixture was cooled to 0 °C, and were added 154 g of water, 154 g of aqueous of NaOH solution (10%), and 154 g of H2O. The mixture was stirred for 30 min at 25 °C and the precipitate was filtered off. The filtrate was concentrated under vacuum. The resulting residue was purified by flash column chromatography over silica gel (eluent: MeOH / DCM 1 :50) to give Intermediate 4 (204 g, 78% yield) as a colorless oil.Intermediate 5 salt
[0069] HCI (787 mL, 1 M) and Pd / C (8.37 g, 78.7 mmol, 0.10 equiv) were added to a solution of Intermediate 4 (204 g, 787 mmol, 1.00 equiv) in EtOH (2 L). The mixture was degassed and flushed with hydrogen. The mixture was stirred for 18 h at 25 °C under an atmosphere of hydrogen (balloon). Then was added HCI (787 mL, 1 M) and the mixture was stirred for 30 min at 25 °C. The solid was filtered out and the filtrate was concentrated under vacuum to give Intermediate 5 (106 g, 66% yield; as a HCI salt, number of equivalents not determined) as a yellow solid which was used without further purifications.Intermediate 6
[0070] Di-tert-butyl dicarbonate (169 g, 773 mmol, 1.50 equiv) was added to a mixture of Intermediate 5 (106 g, 515 mmol, 1.00 equiv), THF (2 L), and TEA (2089 g, 2.06 mol, 4.00 equiv). The flask was stirred for 2 h at 25 °C. The mixture was concentrated under vacuum. The resulting residue was purified by flash column chromatography over silica gel (eluent: EtOAc / PE 1 :4) to give Intermediate 6 (134 g, 96% yield) as a white solid.Intermediate 7
[0071] A mixture of Intermediate 6 (134 g, 0.496 mol, 1.00 equiv), DCM (2.6 L), PCC (534 g, 2.48 mol, 5.00 equiv) and silica gel (268 g, 4.46 mol, 9.00 equiv) was stirred for 12 h at 40 °C. The mixture was concentrated under vacuum and the resulting residue was purified by flashcolumn chromatography over silica gel (eluent: EtOAc / PE 1 : 10) to give Intermediate 7 (79 g, 60% yield) as a white solid.Intermediate 8
[0072] Intermediate 7 (79 g, 296 mmol, 1.00 equiv) and DMF-DMA (790 mL) were stirred for 1 h at 35 °C. The mixture was concentrated to give Intermediate 8 (100 g, crude) as a light-yellow oil which was used without any further purification.Intermediate 9
[0073] A mixture of Intermediate 8 (100 g, 310 mmol, 1.00 equiv), 5-chloro-2H-pyrazol-3- amine [CAS: 916211-79-5] (36.5 g, 310 mmol, 1.00 equiv), toluene (1 L) and AcOH (100 mL) was stirred for 15 h at 95 °C. The reaction was cooled to 25 °C and concentrated under vacuum.NaHC03 (1000 mL) was added to the mixture, and the resulting solution was extracted with EtOAc (2x 1 L). The organic layers were combined, dried over anhydrous MgSO4, and concentrated under vacuum. The resulting residue was purified by flash column chromatography over silica gel (eluent: EtOAc / PE 15:85) to give Intermediate 9 (39.7 g, 34% yield) as a yellow oil.Intermediate 10
[0074] A mixture of Intermediate 9 (39.7 g, 105 mmol, 1.00 equiv), DCM (400 mL) and TFA (80 mL) was stirred for 1 h at 25 °C. The mixture was concentrated under vacuum and NaHCO3 (500 mL) was added. The resulting mixture was extracted with DCM (3x300 mL). The organic layers were combined, dried over anhydrous MgSO4, and concentrated under vacuum. The resulting residue was purified by flash column chromatography over silica gel (eluent: EtOAc:PE (1 : 1). This resulted in 2-chloro-8-methyl-8-(trifluoromethyl)-7,8-dihydro-6H-pyrazolo[l,5- a]pyrrolo[2,3-e]pyrimidine (Intermediate 10, [CAS: 2661482-67-1], 15.2 g, 51% yield) as a yellow solid.Intermediates 11 and 12Intermediate 11 Intermediate 12
[0075] Intermediate 10 (5.0 g) was separated in enantiomers via chiral SFC, using as stationary phase: Chiralcel Diacel IH 20 x 250 mm, Mobile phase: CO2, EtOH + 0.4 iPrNH2 to provide two fractions as follows: Fraction 1 : Intermediate 11 (2.35 g, 47% yield) Fraction 2: Intermediate 12 (2.35 g, 47% yield)Intermediate 13
[0076] To a cooled (0 °C) suspension of NaH (60% in mineral oil, 2.59 g, 64.85 mmol) in THF (100 mL) was added triethylphosphonopropionate (13.9 mL, 64.85 mmol) dropwise. Thereaction was stirred for 30 minutes, then a solution of 4-bromobenzaldehyde [1122-91-4] (10.0 g, 54.0 mmol) in THF (20 mL) was added dropwise, keeping the internal temperature between 0 °C and 5 °C. The mixture was allowed to warm to RT and stirred for 16 h. The reaction was quenched with a saturated aqueous solution of NH4C1 (60 mL), and the aqueous layer was extracted with EtOAc (3 x 100 mL). The combined organic layers were dried over anhydrous MgSO4, filtered, and concentrated under reduced pressure. The crude product was purified by flash column chromatography over silica gel (eluent: heptane / EtOAc up to 90 / 10). The fractions containing compound were combined and concentrated in vacuo to give Intermediate 13 (12.3 g, 84% yield) as a colorless oil.Intermediate 14
[0077] To a cooled (0 °C) solution of Intermediate 13 (12.3 g, 45.7 mmol) in dry THF (230 mL) under nitrogen, was added DIBAL-H (IM in THF, 115 mL, 115 mmol) dropwise. The mixture was then allowed to slowly warm up to RT and stirred for 1 h. The reaction was cooled down to 0 °C, diluted with EtOAc (100 mL) and quenched with a saturated aqueous solution of Rochelle's salt (250 mL). After stirring for 1 h, the reaction was allowed to warm up to RT, the organic layer was separated, and the aqueous layer was extracted with EtOAc (200 mL). The combined organic layers were dried over anhydrous MgSO4, filtered, and concentrated under reduced pressure to give Intermediate 14 (9.8 g, 94% yield) as a white solid.Intermediate 15
[0078] To a solution of Intermediate 14 (8.70 g, 38.3 mmol) and imidazole (3.13 g, 46.0 mmol) in DCM (100 mL) pre-cooled to 0 °C, was added triisopropyl silyl chloride (9.0 mL, 42.1 mmol) dropwise. The mixture was allowed to warm up to RT and stirred for 16 h. The mixture was diluted with water (100 mL) and DCM (100 mL). The organic layer was separated, and the aqueous layer was extracted with DCM (100 mL). The combined organic layers were washedwith brine (100 mL), dried over anhydrous MgSO4, filtered, and concentrated in vacuo. The crude was purified by flash column chromatography over silica gel (eluent: heptane / DCM up to 90 / 10) to obtain Intermediate 15 (14 g, 95% yield) as a colorless oil.Intermediate 16
[0079] In a 20 mL pressure tube charged with Intermediate 15 (1.15 g, 3.0 mmol) and tetrabutylammonium bromide (48.3 mg, 0.15 mmol), were added toluene (6 mL) and (bromodifluoromethyl)trimethylsilane (1.4 mL, 9 mmol). The reaction was stirred at 110 °C for 6 h. Six identical reactions were run in parallel and combined before work-up and purification. The reactions were cooled down to RT, each diluted with water (10-15 mL), EtOAc (20-25 mL), and combined. The organic layer was separated, and the aqueous layer was extracted with EtOAc (50 mL). The combined organic layers were dried over anhydrous MgSO4, filtered, and concentrated under reduced pressure. The residue was dissolved in anhydrous THF (50 mL), cooled to 0 °C and TBAF (IM in THF, 27 mL, 27 mmol) was added. The reaction was allowed to warm up to RT and stirred for 1 h. Volatiles were removed under reduced pressure and the residue was diluted with water (50 mL) and EtOAc (100 mL). The aqueous layer was separated, and the organic layer was washed with brine (50 mL), dried over anhydrous MgSO4, filtered, and concentrated under reduced pressure. The crude product was purified by flash column chromatography over silica gel (eluent: heptane / EtOAc 70 / 30) to obtain Intermediate 16 (4.6 g, 92% yield) as a yellowish oil.Intermediate 17
[0080] To a solution of Intermediate 16 (3.81 g, 13.75 mmol) in water / CHiCN (87 mL / 87 mL), were added TEMPO (1.07 g, 6.87 mmol), (di acetoxy iodo)benzene (13.29 g, 41.25 mmol) andNaHCCh (2.89 g, 34.37 mmol). The mixture was stirred for 6 h at RT, the mixture was diluted with water, and aq HC1 (I M) was added until the pH reached approximately 2. EtOAc was added and the organic layer was separated. The aqueous layer was extracted with EtOAc, and the combined organic layers were dried over anhydrous MgSO4, filtered, and evaporated. The product was stirred in diisopropyl ether and filtered. The filtrate was evaporated and stirred in heptane to obtain a precipitate that was filtered and dried over anhydrous MgSO4 to give Intermediate 17 (3.46 g, 86% yield) as white solid.Intermediate 18
[0081] To a mixture of Intermediate 17 (200.0 mg, 0.687 mmol) and N-[(dimethylamino)-lH- l,2,3-triazolo-[4,5-b]pyridin-l-ylmethylene]-N-methylmethanaminium hexafluorophosphate N- oxide (522.5 mg, 1.37 mmol) and N,N-diethylethanamine (0.38 mL, 2.75 mmol) in CH3CN (5.2 mL) was added 3-(methylsulfonyl)cyclobutan-l-amine hydrochloride [2639792-63-3] (205.0 mg, 1.37 mmol). The reaction was stirred at RT for 1 h. The reaction was diluted with EtOAc and water. The water layer was separated, and the aqueous phase was extracted with EtOAc. The combined organic layers were then dried over anhydrous Na2SO4, filtered, and concentrated under reduced pressure. The crude product was purified by flash column chromatography over silica gel (eluent: MeOH / DCM 0 to 7%) to give Intermediate 18 (264 mg, 91% yield) as a white solid.Intermediate 19
[0082] Intermediate 19 was prepared by an analogous reaction protocol as Intermediate 18, starting from trans-3-methylsulfonylcyclobutylamine hydrochloride [1408075-97-7] (1.25 g,6.73 mmol) instead of 3-(methylsulfonyl)cyclobutan-l-amine hydrochloride [2639792-63-3] to give Intermediate 19 (1.16 g, 73% yield) as a light-yellow solid.Compound 1
[0083] A pressure tube was charged with Intermediate 19 (175 mg, 0.41 mmol), Intermediate 11 (126.11 mg, 0.46 mmol), BrettPhos Pd G3 (37.57 mg, 0.041 mmol), BrettPhos (22.24 mg, 0.041 mmol), Cs2CO3 (202.53 mg, 0.62 mmol), and 1,4-dioxane (4.05 mL). The mixture was degassed, then stirred at 60 °C for 8 h. The reaction was cooled down to RT and filtered through celite. The filtrate was concentrated under reduced pressure and the crude was purified by Prep HPLC (Stationary phase: RP XBridge Prep C18 OBD-lOpm, 30x150mm, Mobile phase: 0.25% NH4HCO3 solution in water, CH3CN) to obtain Compound 1 as a yellow solid (147 mg, 58% yield).
[0084] 1H NMR (CHLOROFORM-d, 400 MHz) 5 ppm: 8.29 - 8.25 (m, IH), 7.26 - 7.23 (m, IH), 7.18 - 7.06 (m, 2H), 6.70 (s, IH), 6.08 (d, J=6.2 Hz, IH), 4.55 (sxt, J=7.6 Hz, IH), 4.25 (d, J=12.3 Hz, IH), 4.06 (d, J=11.7 Hz, IH), 3.80 (tt, J=4.6, 9.5 Hz, IH), 3.62 (d, J=15.6 Hz, IH), 3.04 - 2.90 (m, 2H), 2.87 (s, 3H), 2.70 - 2.60 (m, 2H), 2.00 (s, 3H), 1.25 (s, 3H).Compound 2 and Compound 3Compound 2 Compound 3
[0085] Compound 1 (147 mg) was separated via chiral SFC (Stationary phase: Chiralcel DiacelIH 20 x 250 mm, Mobile phase: CO2, EtOH + 0.4 iPrNH2). The fractions containing compoundwere combined and the solvent was concentrated in vacuo to provide two fractions as follows:Fraction 1 : Compound 2 (61 mg, 24% yield starting from intermediate 19)
[0086] 1H NMR (CHLOROFORM-d, 400 MHz) 5 ppm: 8.26 (d, J=1.3 Hz, 1H), 7.26 - 7.22 (m, 1H), 7.15 (d, J=11.9 Hz, 1H), 7.08 (d, J=8.3 Hz, 1H), 6.71 (s, 1H), 6.08 (br d, J=6.4 Hz, 1H), 4.55 (sxt, J=7.6 Hz, 1H), 4.26 (d, J=10.5 Hz, 1H), 4.06 (d, J=11.4 Hz, 1H), 3.79 (tt, J=4.7, 9.5 Hz, 1H), 3.64 - 3.59 (m, 1H), 3.00 - 2.92 (m, 2H), 2.87 (s, 3H), 2.70 - 2.61 (m, 2H), 2.00 (s, 3H), 1.25 (s, 3H). Fraction 2: Compound 3 (63 mg, 25% yield starting from intermediate 19)
[0087] 1H NMR (CHLOROFORM-d, 400 MHz) 5 ppm: 8.26 (d, J=1.3 Hz, 1H), 7.25 - 7.05 (m, 3H), 6.70 (s, 1H), 6.06 (d, J=6.2Hz, 1H), 4.59 - 4.50 (m, 1H), 4.24 (d, J=10.5 Hz, 1H), 4.06 (d, J=11.5 Hz, 1H), 3.83 - 3.75 (m, 1H), 3.61 (d, J=16.0 Hz, 1H), 2.99 - 2.92 (m, 2H), 2.86 (s, 3H), 2.69 - 2.60 (m, 2H), 1.99 (s, 3H), 1.24 (s, 3H).
[0088] 1H NMR spectra were recorded on Bruker Avance III 400MHz and Avance NEO 400MHz spectrometers. CHLOROFORM-d was used as solvent, unless otherwise mentioned. The chemical shifts are expressed in ppm relative to tetramethylsilane.
[0089] Table 1 : LCMS results. Rt means retention time, in minutes (min.); [M+H]+ means the protonated mass of the compound; method refers to the method used for LCMS analysis of compounds; No. means number. Rt means retention time (in minutes).Table 1Analytical Analysis
[0090] The High Performance Liquid Chromatography (HPLC) measurement was performed using a LC pump, a diode-array (DAD) or a UV detector and a column as specified in the respective methods. If necessary, additional detectors were included (see table of methods below).
[0091] Flow from the column was brought to the Mass Spectrometer (MS) which was configured with an atmospheric pressure ion source. It is within the knowledge of the skilled person to set the tune parameters (e.g., scanning range, dwell time. . .) to obtain ions allowing the identification of the compound’s nominal monoisotopic molecular weight (MW). Data acquisition was performed with appropriate software.
[0092] Compounds are described by their experimental retention times (Rt) and ions. If not specified differently in the table of data, the reported molecular ion corresponds to the [M+H]+ (protonated molecule) and / or [M-H]- (deprotonated molecule). In case the compound was not directly ionizable the type of adduct is specified (i.e. [M+NH4]+, [M+HCOO]-, etc. . .). For molecules with multiple isotopic patterns (Br, Cl), the reported value is the one obtained for the lowest isotope mass. All results were obtained with experimental uncertainties that are commonly associated with the method used.
[0093] Hereinafter, “SQD” means Single Quadrupole Detector, “MSD” Mass Selective Detector, “RT” room temperature, “BEH” bridged ethylsiloxane / silica hybrid, “DAD” Diode Array Detector, ”HSS” High Strength silica.Table 2: LCMS Method Codes (Flow expressed in mL / min, column temperature (T) in °C, Run time in minutes, ‘ ACN' means acetonitrile)LC-MS methods:Biological Assays
[0094] In vitro assays include assays that determine cell morphology, gene sequence, protein expression, and / or the cytotoxicity, enzyme inhibitory activity, and / or the subsequent functional consequences of treatment of cells with compounds of the invention. Alternate or additional in vitro assays may be used to quantitate the ability of the inhibitor to bind to protein or nucleic acid molecules within the cell.
[0095] Such assays are exemplary and not intended to limit the scope of the invention. The skilled practitioner can appreciate that modifications can be made to conventional assays to develop equivalent or other assays that can be employed to comparably assess activity or otherwise characterize compounds and / or compositions as described herein.In Vitro AssaysBiological Assay 1MALT1 Biochemical Protease Assay
[0096] MALT1 protease activity was assessed in an in vitro assay using a tetrapeptide as substrate and full-length MALT1 protein (Strep-MALTl(l-824)-His) purified from baculovirus- infected insect cells. The tetrapeptide LRSR is coupled to AMC (7-amino-4-methylcoumarin) and provides a quenched, fluorescent substrate for the MALT1 protease (SM Biochemicals). Cleavage of AMC from the Arginine residue results in an increase in coumarin fluorescencemeasured at 460 nm (excitation 355 nm). The final assay buffer consisted of 10 nM FL MALT1 protein, 200 pM Ac-LRSR-AMC, 50 mM Tris pH 7.5, 0.6 M Citrate, 1 mM dithiothreitol (DTT), 1 mM ethylenediaminetetraacetic acid (EDTA), 0.05% bovine serum albumin (BSA) and 1.5% dimethyl sulfoxide (DMSO). Test compounds were spotted at 50 nL in 100% DMSO per well of a black 384-Proxiplate (Perkin Elmer). Test compound concentrations ranged from 30 pM to 0.5 nM using 11 dilution steps (1 :3). Background signal was measured from control wells containing assay buffer without enzyme which functions as low control (LC). High control (HC) values were generated using the reaction with enzyme but no compound treatment. Compounds were pre-incubated with MALT1 enzyme for 50 minutes at RT. Substrate was added subsequently, and fluorescence was measured in Labsystems fluoroskan at excitation 355 nm and emission 460 nm to determine time 0. The reaction was subsequently incubated for 4 h at RT and fluorescence was measured. For IC50 calculations, timepoint 0 was subtracted from the 4 h timepoint to correct for any potential autofluorescence of the compounds. The enzyme reaction was linear during the 4 h incubation period. Characterization of the substrate Ac-LRSR-AMC determined the Michaelis constant KM at 200 pM.IC50 values were calculated using the following formula (Z prime should be >0.5):LC = Median of the low control values= Low control: Reaction without enzyme HC = Median of the High control values = High Control: Reaction with enzyme%Effect = 100-[((sample-LC) / (HC-LC)) x 100] %Control = (sample / HC) x 100 %Controlmin = ((sample-LC) / (HC-LC)) x 100
[0097] A best-fit curve was fitted by a minimum sum of squares method to the plot of %Controlmin vs. compound concentration. From this an IC50 value (inhibitory concentration causing 50 % inhibition) can be obtained. An estimate of the slope of the plot in terms of the Hill coefficient was also obtained. 1IC50 Calculation: yt = LB + UB -LB y I jQ(h*(pCONCi-pIC50))With y = estimated responseUB = upper boundLB = lower bound h = Hill slope of curve CONC = concentration
[0098] Used in “Lexis Dose Response Curve Fitting” Version 1.0. Resultant data are shown in Table 3 (‘Cpd No.’ means Compound Number, ‘n.d.’ means not determined, ‘Int’ means intermediate).Table 3Biological Assay 2GloSensor reporter MALT 1 -mediated cleavage In Jurkat Cells
[0099] MALT1 GloSensor™ is a split luciferase reporter, which utilizes a genetically modified form of firefly luciferase (CP UltraGio) split into 2 distinct domains by insertion of a RelB MALT1 cleavage site sequence PRLVSRGA. MALT 1 -induced cleavage allows for a conformational change that reestablishes a functional luciferase protein resulting in luminescence, and hence luciferase activity would be a surrogate of endogenous MALT1protease activity. Jurkat MALT1 GloSensor™ were generated by electroporation and selected and maintained in the presence of 0.5 mg / mL Geneticin. MALT1 protease is basally inactive in Jurkat cells and can be activated by treatment with PMA / Ionomycin. Small molecule MALT1 inhibitors added prior to PMA / Ionomycin addition prevent MALT1 protease activation and, therefore, the cleavage of the MALT1 GloSensor split luciferase reporter in a dose-dependent manner.
[0100] Jurkat MALT1 GloSensor™ cells were maintained in complete RPMI 1640 media containing 10% fetal bovine serum, lOmM 4-(2-hy droxy ethyl)- 1 -piperazineethanesulfonic acid (HEPES), 100 units / mL of penicillin, 100 pg / mL of streptomycin and 0.5 mg / mL Geneticin. Prior to the assay, compounds were made 2.5-fold serial dilutions in DMSO. 100 nL of of test compounds were spotted per well of 384-well plates (Perkin Elmer, catalogue number 6007688). Jurkat cells were harvested by centrifuge at 1200 RPM for 5 min and suspended in fresh complete RPMI 1640 media with 2% GloSensor™ cAMP Reagent and preincubated for 45-60 minutes at 37 °C in a 5% CO2 incubator. A volume of 50 uL of preincubated Jurkat MALT1 GloSensor™ cells (1 x 105 cells) were seeded in each well of 384-well plate. Next, a volume 2 pL of diluted PMA / lonomycin (2.5 mg / mL / 25 pM respectively, Sigma, catalogue number P1585 and 407953) in DMSO were added to each well. After incubation at 37 °C in 5% CO2 incubator for 4 h, luminescence was measured on the Envision (Perkin Elmer) at 37 °C.IC50 values were calculated using SmartFit in GeneData Screener®:. SmartFit uses the 4p curve fit equation seen below:Where: x = concentration y = activitySo = activity at bottom plateau of curveSinf = activity at top plateau of curveSso = inflection point, halfway between So and Sinfh = Hill slope of curve
[0101] Resultant data are shown in Table 4 (‘Cpd No.’ means Compound Number, ‘Int’ means intermediate).Table 4Biological Assay 3Human IL-6 / IL-10 Mesoscale Assay
[0102] OCI-Ly3 cells were propagated in RPMI-1640 (Sigma Aldrich) supplemented with 10% fetal bovine serum (HyClone), 2 mM L-glutamine (Sigma Aldrich) and 1% PenStrep (Sigma Aldrich). Cell passage number should not exceed 30. Cells should be kept between 0.5 - 1.5 million cells per mL during culturing.
[0103] For the Mesoscale assay, 100,000 OCI-Ly3 cells were seeded per well into black-colored 96-well plates with clear bottom (Coming® #3904) and test compounds were added in 9 dilution steps (1 :2) ranging from 15 pM to 58.6 nM (final DMSO concentration 0.3%). DMSO control wells were used to determine the maximum signal (High Control (HC)). Treatment with reference compounds at an appropriate dose served as positive control for MALT1 inhibition and was used to determine the maximum inhibition (Low Control (LC)). Compounds and cells were incubated for 24 h at 37 °C and 5% CO2 (assay volume is 150 pL). After 24 h of incubation 50 pL of the supernatant was transferred to an MSD plate (V-Plex Proinflammation Panel 1 (human) kit, Mesoscale (MSD)) and incubated for 2 h with vigorous shaking (600 rpm) at room temperature. Following incubation, plates were washed 3x with phosphate-buffered saline (PBS) + 0.05% Tween-20 and 25 pL detection antibody solution (IL-6 & IL- 10 antibodies in diluent 3 (MSD)) was added per well followed by 2 h of incubation with vigorous shaking (600 rpm) atroom temperature. After 3x washes with PBS + 0.05% Tween-20, plates were incubated with 150 pL 2x Read Buffer T and read on SECTOR imager. Resultant data are shown in Table 5 (‘Cpd No.’ means Compound Number, ‘Int’ means intermediate, ‘n.d.’ means not determined).Table 5Biological Assay 4Proliferation Assays
[0104] OCI-Ly3 cells were propagated in RPMI-1640 with Glutamax (ThermoFisher) supplemented with 10% heat inactivated fetal bovine serum (ThermoFisher). Cells should be kept between 0.2 - 1.5 million cells per mL and passed every 3-4 days during culturing. OCI- Ly7 cells were propagated in IMDM (ThermoFisher) supplemented with 10% fetal bovine serum (HyClone), 2 mM L-glutamine (Sigma Aldrich) and 50 pg / mL Gentamycin. Cells should be kept between 0.15 - 3 million cells per mL and passed every 3-4 days during culturing. Cell passage numbers should not exceed 20.
[0105] To assess anti-proliferative effects, 450 nL of test compounds were spotted per well of U- bottom 96-well plates (Corning®, #3975). 500 OCI-Ly3 or OCI-Ly7 cells were seeded in 150 pL media per well and incubated for 8 days at 37 °C and 5% CO2. Cell plating numbers were chosen based on growth curves to ensure linear cell growth. After 8 days of incubation, 100 pL of the plated cells were resuspended up and down by pipette and transferred to a flat bottom black plate (Corning®, #3904). 50 pL CellTiterGLO reagent (Promega) were added to each well and luminescence was measured on Envision (Perkin Elmer) after 10 minutes shaking at 300 rpm followed by 10 minutes of incubation at room temperature in the dark.ICso values were calculated using SmartFit in GeneData ScreenerO:SmartFit uses the 4p curve fit equation seen below:Where: x = concentration y = activitySo = activity at bottom plateau of curveSinf = activity at top plateau of curveSso = inflection point, halfway between So and Sinf h = Hill slope of curve
[0106] Resultant data are shown in Table 6 (‘Cpd No.’ means Compound Number, ‘n.d.’ means not determined, ‘Inf means intermediate)Specific ExamplesThe following examples further illustrate the present invention.EXAMPLESPROLIFERATION OF B-NHL CELL LINESEXAMPLE 1
[0107] To determine the antiproliferative activity of the compound of Formula (I), a panel of 9 DLBCL cell lines (OCI-Ly3 [CARD11 mutant], TMD8, HBL-1, OCLLylO [CD79a / b mutant], U2932, HLY-1, OCI-Ly7, OCI-Lyl, and SU-DHL-4 [CARD 11 and CD79a / b wild-type]) were treated with different concentrations of the compound of Formula (I) for 8 days.
[0108] Cells were harvested by centrifugation at 200 g for 5 minutes at RT, then counted after dilution with Trypan Blue using a Countess II Cell Counter. Cells were diluted to the appropriate concentration for each cell line in complete culture medium. Then, 150 pL / well was aliquoted into 96-well round-bottom ultra-low attachment plates and exposed to a concentration range of the compound of Formula (I) (10-point, 2-fold serial dilution range of 4 pM to 7.81 nM). Duplicate wells were prepared and the DMSO content was normalized to 0.2% in all wells. Compounds were spotted using a Tecan D300e (Tecan). Cell seeding numbers were chosen based on growth curves to ensure linear growth throughout the experiment: OCI-Ly3 (500 cells / well), TMD8 (800 cells / well), HBL-1 (500 cells / well), OCLLylO (1,500 cells / well), U2932 (800 cells / well), HLY-1 (300 cells / well), OCLLy7 (500 cells / well), OCI-Lyl (1,200 cells / well), and SU-DHL-4 (700 cells / well). Cells were incubated for 8 days at 37°C, 5% CO2. Viability at the end of the experiment was determined by adding 50 pL of CellTiter-Glo to 100 pL of cells in a new 96-well flat-bottom black plate. Plates were incubated at RT for 10 minutes in the dark and centrifuged at 200*g for 2 minutes to remove bubbles. Luminescence was read on an Envision 7 (Perkin Elmer). The experiment was performed at least 3 times for each cell line.
[0109] The activity of a test compound was defined as percent change in cell growth inhibition, calculated as %Effect = 100 - ([sample - LC] / [HC - LC]) xl00, where ‘LC’ is the median value of the low control values (ie, reaction without cells, only medium) and ‘HC’ is the median value of the high control values (reaction with cells without drug, containing DMSO). Data were fitted using nonlinear regression variable slope (4 parameters) to the observed data and 50% inhibitory concentration (IC50) growth inhibition values were determined using Genedata Screener (Version 20.0.3). The data were plotted using GraphPad Prism (Version 9).Table 6. Antiproliferative Activity of the Compound of Formula (I) Against DLBCL cell lines.Cell B-CELL RECEPTOR pathway activating IC50 (pM) line mutationCARD11 CD79a CD79bOCL L244P wt wt 0.042Ly3TMD wt wt Y196H 0.0528 HBL- wt wt Y196F 0.0501OCL wt A4275- wt 0.038LylO 4316U293 wt wt wt >4a2 HLY- wt wt wt >4a1 SU-D wt wt wt >4aHL-4 OCL wt wt wt >4aLy7OCL wt wt wt >4aLylB-CELL RECEPTOR, B-cell receptor; B-NHL, B-cell non-Hodgkin lymphoma; CARD11, caspase recruitment domain-containing protein 11; CD, cluster of differentiation; DLBCL, diffuse large B-cell lymphoma; IC50, 50% inhibitory concentration.Cells were incubated with serial dilutions of the compound of Formula (I) for 8 days. IC50, unbound is geometric mean of n=3-8. a Highest dose tested in the assay, 50% inhibition not reached.
[0110] Proliferation of TMD8 BTK and CARD11 Mutant Isogenic Cell LinesEXAMPLE 2
[0111] The antiproliferative activity of the compound of Formula (I) in TMD8 cells overexpressing BTK C481S or CARD 11 L244P mutant proteins was measured and compared to that of parental TMD8 cells. In a separate set of experiments, the antiproliferative activity of the compound of Formula (I) in TMD8 cells overexpressing BTK-v5 V416L, BTK-v5 T474I, BTK- v5 C481S, or BTK-v5 L528W mutant proteins was measured and compared to that of parental TMD8 cells.
[0112] Cells were harvested by centrifugation at 200*g for 5 minutes at RT, then counted after dilution with Trypan Blue using a Countess II Cell Counter. Cells were diluted to the appropriate concentration for each cell line in complete culture medium. Then, 150 pL / well was aliquoted into 96-well round bottom ultra-low attachment plates and exposed to a concentration range of the compound of Formula (I) (9-point, 3-fold serial dilution range of 6 pM to 1 nM in duplicate). The DMSO content was normalized to 0.2%. Compounds were spotted using a Tecan D300e instrument. Cell seeding numbers were chosen based on growth curves to ensure linear growth throughout the experiment: TMD8 (800 cells / well), TMD8 BTK C481S (2,000 cells / well), TMD8 CARD11 L244P (700 cells / well) or TMD8 (800 cells / well), TMD8 BTK-v5 C481S (800 cells / well), TMD8 BTK-v5 V416L (800 cells / well), TMD8 BTK-v5 T474I (800 cells / well), TMD8 BTK-v5 L528W (800 cells / well). Cells were incubated for 8 days at 37°C, 5% CO2. Viability at the end of the experiment was determined by adding 50 pL of CellTiter-Glo to 100 pL of cells in a new 96-well flat-bottom black plate. Plates were incubated at RT for 10 minutes in the dark and centrifuged at 200 g for 2 minutes. Luminescence was read on an Envision 7. The experiment was performed 2 times for each cell line.Table 7: Antiproliferative Activity of the Compound of Formula (I) AgainstTMD8 Parental and Engineered Cell Lines That Overexpress mutant CARD11.Cell line IC50(uM>TMD8 parental 0.054TMD8 - CARPI 1 L244P _ 0,044 _CARD11, caspase recruitment domain 11; IC50, 50% inhibitory concentration. Proliferation assays were conducted for 8 days in duplicate. Results are average of 2 independent experiments.Table 8: Antiproliferative Activity of the Compound of Formula (I) AgainstTMD8 Parental and Engineered Cell Lines Resistant to Covalent and Non-covalent BTKi.Cell line IC50 ( M)TMD8 parental 0.037TMD8 - BTK-v5 V416L 0.077TMD8 - BTK-v5 T474I 0.046TMD8 - BTK-v5 C481S 0.046TMD8 - BTK-v5 L528W 0.038BTK, Bruton’s tyrosine kinase; BTKi, Bruton’s tyrosine kinase inhibitor; IC50, 50% inhibitory concentration.Proliferation assays were conducted for 8 days once or in duplicate. Results are average of 2 independent experiments.
[0113] Proliferation of U2932 KLHL6 Knockout Cell LinesEXAMPLE 3
[0114] The antiproliferative activity of the compound of Formula (I) in U2932 cells knockout for KLHL6 (KLHL6 KO) was measured and compared to that of parental U2932 cells.
[0115] Cells were harvested by centrifugation at 200 / g for 5 minutes at RT, then counted after dilution with Trypan Blue using a Countess II Cell Counter. Cells were diluted to the appropriate concentration for each cell line in complete culture medium. Then, 150 pL / well was aliquoted into 96-well round bottom ultra-low attachment plates and exposed to a concentration range of the compound of Formula (I) (9-point, 3-fold serial dilution range of 10 pM to 1 nM in duplicate). The DMSO content was normalized to 0.2%. Compounds were spotted using a Tecan D300e instrument. Cell seeding numbers were chosen based on growth curves to ensure linear growth throughout the experiment: U2932 (1,000 cells / well), U2932 KLHL6 KO (1,500 cells / well). Cells were incubated for 8 days at 37°C, 5% CO2. Viability at the end of the experiment was determined by adding 75 pL of CellTiter-Glo to 150 pL of cells and 200 pL transferred to a new 96-well flatbottom black plate. Plates were incubated at RT for 10 minutes in the dark and centrifuged at 200 xg for 2 minutes. Luminescence was read on an Envision 7. The experiment was performed 2 times for each cell line.Table 9: Antiproliferative Activity of the Compound of Formula (I) AgainstU2932 Parental and KLHL6 Knockout Engineered Cell Lines.Cell line IC50 (u )U2932 parental 1.14U2932 KLHL6 KO 0.29KLHL6, kelch like family member 6; IC50, 50% inhibitory concentration.Proliferation assays were conducted for 8 days in triplicate. Results are average of 2 independent experiments and 4 independent KLHL6 KO clones.Patients suffering from DLBCL expressing such a biomarker can be selected for treatment with a compound of Formula (I). In addition, the biomarker can be employed for assessing the response to treatment with a compound of Formula (I).ASPECTS:1. An aspect of the invention is a method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)2. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)3. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCLIO;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)4. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)5. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene, wherein the gene is CARD11;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)6. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene, wherein the gene is CD79a;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)7. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene, wherein the gene is CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)8. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene, wherein the gene is BCL10;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)9. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, andCD79b; wherein the mutation is L244P in CARD11, A4275-4316 in CD79a, Y196H in CD79b, or Y196F in CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)10. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is L244P in CARD11;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)11. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is A4275-4316 in CD79a;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)12. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is Y196H in CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)13. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is Y196F in CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)14. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a in a gene, wherein the gene is BCL10, wherein the mutation is L174X;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)15. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a C-terminal truncating mutation in a gene selected from the group consisting of BCL10, CD79a, and CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)16. An aspect of the invention is a method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)17. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)18. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation a gene, wherein the gene is BTK, wherein the mutation is selected from A428D, M437R, C481F, G409R, L528S, G480R, D539H, V416L, T474I, T474M, C481S, or L528W;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)19. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK, wherein the mutation is selected from V416L, T474I, C481S, or L528W;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)20. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK, wherein the mutation is V416L;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)21. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK, wherein the mutation is T474I;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)22. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK, wherein the mutation is C481S;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)23. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK, wherein the mutation is L528W;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)24. An aspect of the invention is a method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in the subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)25. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in the subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)26. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCLIO;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)27. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)28. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from CARD11;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)29. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from CD79a;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)30. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)31. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from BCL10;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)32. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is selected from L244P in CARD11, A4275-4316 in CD79a, Y196H in CD79b, or Y196F in CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)33. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is L244P in CARD11;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)34. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is A4275-4316 in CD79a;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)35. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is Y196H in CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)36. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b; wherein the mutation is Y196F in CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)37. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation in a gene selected from BCL10, wherein the mutation is L174X;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)38. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence of a C-terminal truncating mutation in a gene selected from the group consisting of CARD11, CD79a, and CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)39. An aspect of the invention is a method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)40. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in the BTK gene;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)41. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in the BTK gene, wherein the mutation is selected from A428D, M437R, C481F, G409R, L528S, G480R, D539H, V416L, T474I, T474M, C481S, or L528W;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)42. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in the BTK gene, wherein the mutation is selected from V416L, T474I, C481S, or L528W;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)43. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in the BTK gene, wherein the mutation is V416L;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)44. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in the BTK gene, wherein the mutation is T474I;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)45. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in the BTK gene, wherein the mutation is C481S;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)46. An aspect of the invention is a method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B-cell lymphoma, in a subject, wherein the subject has been previously treated with a BTK inhibitor comprising:(a) determining in a subject the presence or absence a mutation in the BTK gene, wherein the mutation is L528W;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)47. An aspect of the invention is a method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, or Waldenstrom macroglobulinemia, in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)48. An aspect of the invention is a method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, or Waldenstrom macroglobulinemia, in a subject comprising:(a) determining in a subject the presence or absence of a C-terminal truncating mutation in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCL10;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)49. An aspect of the invention is a method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, or Waldenstrom macroglobulinemia, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)50. An aspect of the invention is a therapeutically effective amount of the compound of Formula (I)for use in a method of treating a B-cell malignancy, such as for example MALT lymphoma, B- cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, in a subject comprising(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).51. An aspect of the invention is a compound of Formula (I)for use in the treatment of a B-cell malignancy, wherein the B-cell malignancy is diffuse large B- cell lymphoma, comprising(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).52. An aspect of the invention is a compound of Formula (I)for use in the treatment of a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, comprising(a) determining in a subject the presence or absence of a mutation in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCL10;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).53. An aspect of the invention is a compound of Formula (I)for use in the treatment of a B-cell malignancy, wherein the B-cell malignancy is diffuse large B- cell lymphoma, comprising(a) determining in a subject the presence or absence of a mutation in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCL10;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).54. An aspect of the invention is a compound of Formula (I)for use in the treatment of a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, comprising(a) determining in a subject the presence or absence of a C-terminal truncating mutation in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCL10;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).55. An aspect of the invention is a compound of Formula (I)for use the treatment of a B-cell malignancy, wherein the B-cell malignancy is diffuse large B- cell lymphoma, comprising(a) determining in a subject the presence or absence of a C-terminal truncating mutation in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCL10;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).56. An aspect of the invention is a compound of Formula (I)for use in the treatment of a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, comprising(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).57. An aspect of the invention is a therapeutically effective amount of the compound of Formulafor use in the treatment of a B-cell malignancy, wherein the B-cell malignancy is diffuse large B- cell lymphoma, comprising(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).More aspects:Al. A method of treating a B-cell malignancy in a subject comprising:(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of theA2. The method of aspect Al, wherein the B-cell malignancy is MALT lymphoma, B-cell nonHodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma.A3. The method of aspect A2, wherein the B-cell malignancy is B-cell non-Hodgkin lymphoma, in particular diffuse large B-cell lymphoma.A4. The method of aspect A3, wherein the mutation is in a gene selected from the group consisting of BTK, CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6, BCL10 and MALT1.A5. The method of aspect A4, wherein the mutation is in a gene selected from the group consisting ofCARD11, CD79a, CD79b, and BCL10.A6. The method of aspect A5, wherein the mutation is in a gene selected from the group consisting ofCARD11, CD79a, and CD79b.A7. The method of aspect A5, wherein the gene is CARD 11.A8. The method of aspect A5, wherein the gene is CD79a.A9. The method of aspect A5, wherein the gene is CD79b.A10. The method of aspect A5, wherein the gene is BCL10.Al 1. The method of aspect A6, wherein the mutation is L244P in CARD11, A4275-4316 in CD79a, Y196H in CD79b, or Y196F in CD79b.A12. The method of aspect All, wherein the mutation is L244P in CARD11.A13. The method of aspect All, wherein the mutation is A4275-4316 in CD79a.A14. The method of aspect All, wherein the mutation is Y196H in CD79b.A15. The method of aspect All, wherein the mutation is Y196F in CD79b.A16. The method of aspect A10, wherein the mutation is L174X.Al 7. A method of treating a B-cell malignancy, wherein the B-cell malignancy is diffuse large B- cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence of a C-terminal truncating mutation in a gene selected from the group consisting of B CL 10, CD79a, and CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)Al 8. A method of treating a B-cell malignancy, such as for example MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma, in a subject comprising:(a) determining in a subject the presence or absence a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I)A19. The method of aspect A18, wherein the B-cell malignancy is B-cell non-Hodgkin lymphoma, in particular diffuse large B-cell lymphoma.A20. The method of aspect A19, wherein the mutation is selected from A428D, M437R, C481F, G409R, L528S, G480R, D539H, V416L, T474I, T474M, C481S, or L528W.A21. The method of aspect A20, wherein the mutation is selected from V416L, T474I, C481S, or L528W.A22. The method of aspect A21, wherein the mutation is V416L.A23. The method of aspect A21, wherein the mutation is T474I.A24. The method of aspect A21, wherein the mutation is C481S.A25. The method of aspect A21, wherein the mutation is L528W.A26. The method of any of aspects A1-A25, wherein the subject has been previously treated with a BTK inhibitor.More aspects:Bl. A compound of Formula (I)for use in the treatment of a B-cell malignancy having a B-cell receptor pathway activating mutation.B2. The compound for use according to aspect Bl, wherein the B-cell malignancy is MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma.B3. The compound for use according to aspect B2, wherein the B-cell malignancy is B-cell nonHodgkin lymphoma, in particular diffuse large B-cell lymphoma.B4. The compound for use according to aspect B3, wherein the mutation is in a gene selected from the group consisting of BTK, CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6, BCLIO and MALT1.B5. The compound for use according to aspect B4, wherein the mutation is in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCL10.B6. The compound for use according to aspect B5, wherein the mutation is in a gene selected from the group consisting of CARD11, CD79a, and CD79b.B7. The compound for use according to aspect B5, wherein the gene is CARD11.B8. The compound for use according to aspect B5, wherein the gene is CD79a.B9. The compound for use according to aspect B5, wherein the gene is CD79b.BIO. The compound for use according to aspect B5, wherein the gene is BCL10.B 11. The compound for use according to aspect B6, wherein the mutation is L244P in CARD 11 , A4275-4316 in CD79a, Y196H in CD79b, or Y196F in CD79b.B12. The compound for use according to aspect Bll, wherein the mutation is L244P in CARD11.B13. The compound for use according to aspect Bll, wherein the mutation is A4275-4316 in CD79a.B14. The compound for use according to aspect Bll, wherein the mutation is Y196H in CD79b.B15. The compound for use according to aspect Bll, wherein the mutation is Y196F in CD79b.B16. The compound for use according to aspect BIO, wherein the mutation is L174X.Bl 7. A compound of Formula (I)for use in the treatment of diffuse large B-cell lymphoma having a C-terminal truncating mutation in a gene selected from the group consisting of BCL10, CD79a, and CD79b.Bl 8. A compound of Formula (I)for use in the treatment of a B-cell malignancy having a mutation in the BTK gene.Bl 9. The compound for use according to aspect Bl 8, wherein the B-cell malignancy is MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma.B20. The compound for use according to aspact B19, wherein the B-cell malignancy is B-cell non-Hodgkin lymphoma, in particular diffuse large B-cell lymphoma.B21. The compound for use according to aspect B20, wherein the mutation is selected from A428D, M437R, C481F, G409R, L528S, G480R, D539H, V416L, T474I, T474M, C481S, or L528W.B22. The compound for use according to aspect B21, wherein the mutation is selected from V416L, T474I, C481S, or L528W.B23. The compound for use according to any one of aspects B1-B22, wherein the malignancy of lymphoma has been previously treated with a BTK inhibitor.B24. Any of aspects Bl to B23 reworded as a method of treating said malignancy or lymphoma comprising administering to a subject in need thereof a therapeutically effective amount of the compound of Formula (I).
[0116] While the foregoing specification teaches the principles of the present invention, with examples provided for the purpose of illustration, it will be understood that the practice of the invention encompasses all of the usual variations, adaptations and / or modifications as come within the scope of the following claims and their equivalents.
Claims
We claim:
1. A compound of Formula (I)for use in the treatment of a B-cell malignancy comprising(a) determining in a subject the presence or absence of a B-cell receptor pathway activating mutation;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).
2. A compound of Formula (I)for use in the treatment of a B-cell malignancy having a B-cell receptor pathway activating mutation.
3. The compound for use according to claim 1 or 2, wherein the B-cell malignancy is MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma.
4. The compound for use according to claim 3, wherein the B-cell malignancy is B-cell nonHodgkin lymphoma, in particular diffuse large B-cell lymphoma.
5. The compound for use according to claim 4, wherein the mutation is in a gene selected from the group consisting of BTK, CARD11, CD79a, CD79b, PLCG2, LYN, SYK, KLHL6, BCL10 and MALT 1.
6. The compound for use according to claim 5, wherein the mutation is in a gene selected from the group consisting of CARD11, CD79a, CD79b, and BCL10.
7. The compound for use according to claim 6, wherein the mutation is in a gene selected from the group consisting of CARD11, CD79a, and CD79b.
8. The compound for use according to claim 7, wherein the mutation is L244P in CARD11, A4275-4316 in CD79a, Y196H in CD79b, or Y196F in CD79b.
9. The compound for use according to claim 8, wherein the mutation is L244P in CARD11.
10. The compound for use according to claim 8, wherein the mutation is A4275-4316 in CD79a.
11. The compound for use according to claim 8, wherein the mutation is Y196H in CD79b.
12. The compound for use according to claim 8, wherein the mutation is Y196F in CD79b.
13. The compound for use according to claim 6, wherein the mutation is L174X in BCL10.for use in the treatment of diffuse large B-cell lymphoma, comprising:(a) determining in a subject the presence or absence of a C-terminal truncating mutation in a gene selected from the group consisting of BCL10, CD79a, and CD79b;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).
15. A compound of Formula (I)for use in the treatment of a B-cell malignancy comprising:(a) determining in a subject the presence or absence of a mutation in a gene, wherein the gene is BTK;(b) administering to the subject having the mutation a therapeutically effective amount of the compound of Formula (I).
16. The compound for use according to claim 15, wherein the B-cell malignancy is MALT lymphoma, B-cell non-Hodgkin lymphoma, follicular lymphoma, mantle cell lymphoma, marginal zone lymphoma, Waldenstrom macroglobulinemia, or diffuse large B-cell lymphoma.
17. The compound for use according to claim 16, wherein the B-cell malignancy is B-cell nonHodgkin lymphoma, in particular diffuse large B-cell lymphoma.
18. The compound for use according to claim 17, wherein the mutation is selected from A428D, M437R, C481F, G409R, L528S, G480R, D539H, V416L, T474I, T474M, C481S, or L528W.
19. The compound for use according to claim 18, wherein the mutation is selected from V416L, T474I, C481S, or L528W.
20. The compound for use according to any one of claims 1-19, wherein the subject has been previously treated with a BTK inhibitor.
Citation Information
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