WO2020046966A1 - Treatment of adenocarcinomas with mapk pathway inhibitors - Google Patents

Treatment of adenocarcinomas with mapk pathway inhibitors Download PDF

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Publication number
WO2020046966A1
WO2020046966A1 PCT/US2019/048379 US2019048379W WO2020046966A1 WO 2020046966 A1 WO2020046966 A1 WO 2020046966A1 US 2019048379 W US2019048379 W US 2019048379W WO 2020046966 A1 WO2020046966 A1 WO 2020046966A1
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Prior art keywords
iohetaryl
ioheterocyclyl
ioalkyl
oaryl
ioheterocydyl
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PCT/US2019/048379
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French (fr)
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Francis Burrows
Yi Liu
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Kura Oncology, Inc.
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Publication of WO2020046966A1 publication Critical patent/WO2020046966A1/en
Priority to US17/582,227 priority Critical patent/US20220146758A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57423—Specifically defined cancers of lung
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/5748—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving oncogenic proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease

Definitions

  • the MAPK pathway also known as the RAS/RAF/MEK/ERK pathway, plays a central role in regulating cellular processes by relaying extracellular signals from ligand-bound cell surface receptor tyrosine kinases (RTKs) such as ErbB (e.g. EGFR, Her-2, etc), VEGF, PDGF, and FGF receptor tyrosine kinases.
  • RTKs ligand-bound cell surface receptor tyrosine kinases
  • ErbB e.g. EGFR, Her-2, etc
  • VEGF vascular endothelial growth factor
  • PDGF vascular endothelial growth factor
  • FGF receptor tyrosine kinases Activation of an RTK triggers a series of phosphorylation events, beginning with the activation of RAS, followed by recruitment and activation of RAF.
  • Activated RAF then phosphorylates MAP kinase kinase (MEK) 1/2, which then
  • ERK phosphorylation by MEK occurs on Y204 and T202 for ERK1 and Y185 and T183 for ERK2 (Ahn et ah, Methods in Emymology 2001, 332, 417-431).
  • Phosphorylated ERK dimerizes and translocates to and accumulates in the nucleus (Khokhlatchev et ah, Cell 1998, 93, 605-615).
  • ERK is involved in several important cellular functions, including but not limited to nuclear transport, signal transduction, DNA repair, nucleosome assembly and translocation, and mRNA processing and translation (Ahn et ah, Molecular Cell 2000, 6, 1343-1354).
  • ERK2 phosphorylates a multitude of regulatory proteins, including the protein kinases RSK90 and MAPKAP2 ((Bjorbaek et ah, 1995, J. Biol. Chem. 270, 18848; Rouse et ah, 1994, Cell 78, 1027), and transcription factors such as ATF2, ELK-l, c-FOS, and c-MYC (Raingeaud et ah, 1996, o/ . Cell Biol. 16, 1247; Chen et ah, 1993, Proc. Natl. Acad. Sci. U.S. A. 90, 10952; Oliver et ah, 1995, Proc. Soc. Exp. Biol. Med. 210, 162).
  • RSK90 and MAPKAP2 (Bjorbaek et ah, 1995, J. Biol. Chem. 270, 18848; Rouse et ah, 1994, Cell 78, 10
  • bRAF mutations have been identified in more than malignant melanomas (60%), thyroid cancers (greater than 40%) and colorectal cancers. These mutations in bRAF result in a constitutively active MAPK pathway cascade. Studies of primary tumor samples and cell lines have also shown constitutive or overactivation of the MAPK pathway in cancers of the pancreas, colon, lung, ovary and kidney (Hoshino, R. et ah, Oncogene 1999, 18, 813-822). Further, ERK2 has been shown to play a role in the negative growth control of breast cancer cells (Frey and Mulder, 1997, Cancer Res.
  • ERK2 ERK2 Activated ERK2 has also been implicated in the proliferation of endothelin-stimulated airway smooth muscle cells, suggesting a role for this kinase in asthma (Whelchel et ak, 1997, Am. J. Respir. Cell Mol. Biol. 16, 589).
  • upstream e.g. RAS, RAF
  • downstream e.g. ATF2, c-FOS, c- MYC
  • ADC Adenocarcinoma
  • compositions and methods herein may be useful for treating diseases dependent on the activity of the MAPK pathway, such as cancer.
  • the cancer is an adenocarcinoma, such as an adenocarcinoma of the lung.
  • the present disclosure provides a method of treating a cancer in a subject in need thereof, wherein said cancer exhibits a KRAS mutation and wherein said cancer overexpresses CCNDl, comprising administering to the subject an effective dose of a mitogen- activated protein kinase (MAPK) pathway inhibitor.
  • the method comprises (a) assessing the cancer for overexpression of CCNDl; (b) evaluating the cancer for the presence of a KRAS mutation; and (c) administering the MAPK pathway inhibitor to the subject if both the CCND1 overexpression and the KRAS mutation are determined to be present.
  • the present disclosure provides a method of treating a subject having cancer, wherein said cancer exhibits a KRAS mutation, comprising: (a) assessing the cancer for overexpression of CCND1; and (b) administering an effective dose of a MAPK pathway inhibitor to the subject if the overexpression of CCND1 is found to be present.
  • the overexpression may be assessed by: (a) detecting a level of mRNA; (b) detecting a level of cDNA produced from reverse transcription of mRNA; (c) detecting a level of polypeptide; (d) detecting a level of cell-free DNA; or (e) a nucleic acid amplification assay, a hybridization assay, sequencing, or a combination thereof.
  • the overexpression may be characterized by an expression level of CCND1 in the cancer that is higher than a reference expression level of CCND1.
  • the KRAS mutation may be determined by sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography (DHPLC), or restriction fragment length polymorphism (RFLP) assay.
  • PCR polymerase chain reaction
  • MS mass spectrometry
  • SNP single nucleotide polymorphism
  • DPLC denaturing high-performance liquid chromatography
  • RFLP restriction fragment length polymorphism
  • the KRAS mutation is determined by sequencing or PCR.
  • the present disclosure provides a method of assessing a likelihood of a subject having cancer exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, the method comprising: (a) assessing an expression profile of CCND1 in a biological sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell; (b) evaluating the biological sample for the presence of a KRAS mutation; and (c) calculating, using a computer system, a weighted probability of MAPK pathway inhibitor responsiveness based on the expression profile and KRAS mutation status.
  • the method further comprises designating the subject as having a high probability of exhibiting a clinically beneficial response to treatment with the MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability of (c).
  • the method may further comprise transmitting information concerning the likelihood to a receiver.
  • the method further comprises providing a recommendation based on the weighted probability.
  • recommendation may comprise treating the subject with a MAPK pathway inhibitor.
  • a method described herein further comprises selecting a treatment based on the weighted probability.
  • the method further comprises administering the MAPK pathway inhibitor to the subject if the subject is designated as having a high probability of exhibiting a clinically beneficial response.
  • the present disclosure provides a method of categorizing a cancer status of a subject, comprising: (a) obtaining a biological sample from the subject, the sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell of the subject; (b) assessing (1) a total expression level of CCND1 in the sample, and (2) the presence or absence of a KRAS mutation in the sample; (c) generating an expression profile based on a comparison between the total expression level and a reference level, wherein the reference level is derivable from a reference sample from a different subject having a known cancer status; (d) categorizing the cancer status of the subject of (a) based on the expression profile and the presence or absence of the KRAS mutation.
  • the cancer may be categorized as likely sensitive to treatment with a MAPK pathway inhibitor if the total expression level is greater than the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
  • the known cancer status of the different subject is categorized as resistant to a MAPK pathway inhibitor or sensitive to a MAPK pathway inhibitor.
  • the categorizing step includes calculating, using a computer system, a likelihood of response of the subject to treatment with a MAPK pathway inhibitor based on the expression profile, wherein the likelihood is adjusted upward for each fold increase in the total expression level relative to the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
  • the method further comprises preparing a report comprising a prediction of the likelihood of response of the subject to treatment with the MAPK pathway inhibitor.
  • the reference level may represent an average total expression level of CCND1 in a plurality of cancer samples.
  • a biological sample described herein may be a tissue biopsy or a tumor biopsy.
  • the assessing may be performed using a nucleic acid or protein from the subject.
  • the evaluating is performed using a nucleic acid or protein from the subject.
  • the cancer is an adenocarcinoma, such as a lung adenocarcinoma.
  • the cancer is non-small cell lung cancer.
  • the present disclosure provides a method of downregulating MAPK signaling output in a plurality of lung adenocarcinoma cells with a MAPK pathway inhibitor, wherein at least one cell of the plurality exhibits a KRAS mutation, the method comprising: (a) assessing, in a biological sample comprising nucleic acid from the subject, a total expression level of CCND1; and (b) administering an effective dose of the MAPK pathway inhibitor to the plurality of cells if the total expression level is greater than a reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
  • the MAPK pathway inhibitor may be a MEK inhibitor.
  • the MEK inhibitor is selected from cobimetinib, trametinib, binimetinib, selumetinib, HL-085, antroquinonol, E-6201, refametinib, pimasertib hydrochloride, CKI-27, WX-554, CIP- 137401, SHR-7390, sorafenib, SRX-2626, PD-0325901, ATR-002, ATR- 004, ATR-005, ATR-006, CS-3006, FCN-159, EDV-2209, GDC-0623, TAK-733, E-6201, RG- 7167, AZD-8330, PD-184352, GSK-2091976A, AS-703988, BI-847325, JTP-70902, CZ-775, RO- 5068760, RDEA-436, MEK-300, AD-GL0001, SL-327, ATR-001,
  • the MEK inhibitor is selected from:
  • the MAPK pathway inhibitor may be a pan-RAF inhibitor.
  • the pan-RAF inhibitor is selected from LY3009120, LXH254, CCT3833 and AZ628.
  • the pan-RAF inhibitor is selected from LY3009120 and LXH254.
  • the MAPK pathway inhibitor may be an ERK inhibitor.
  • the ERK inhibitor is selected from ulixertinib, RG7842, GDC- 0994, CC-90003, ASN-007, AMO-01, KO-947, AEZS-134, AEZS-131, AEZS-140, AEZS-136, AEZS-132, D-87503, KIN-2118, RB-l, RB-3, SCH-772984, MK-8353, SCH-900353, FR-180204, IDN-5491, hyperforin trimethoxybenzoate, ERK1-2067, ERK1-23211, ERK1-624, LY3214996, AZ6197, ASTX029, and LTT462.
  • the ERK inhibitor is selected from ulixertinib, GDC-0994, SCH-772984, and MK-8353.
  • the ERK inhibitor is a compound of Formula I:
  • X 4 is N or CR 4 ;
  • X 5 is N or C;
  • X 6 is N or C;
  • X 7 is O, N, NR 72 or CR 7i ;
  • X 8 is O, N, NR 82 or CR 8l ;
  • X 9 is O, N, NR 22 or CR 23 ;
  • X l0 is O, N, NR 3 ⁇ 4 or CR 91 ;
  • Ri is-Ci-ioalkyl, -C 2-i oalkenyl, -C 2-i oalkynyl, -Ci-ioheteroalkyl, -C 3.l0 aryl, -Ci-iohetaryl, - C 3-i ocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C 3-i oaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci-ioalkyl-C 3- iocydoalkyl, -Ci-ioalkyl-Ci-ioheterocydyl, -C 2-i oalkenyl-C 3-i0 aryl, -C 2-i0 alkenyl-Ci.iohetaryl, -C 2- l0 alkenyl-C 3-l ocydoalkyl
  • oaryl -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci-ioheteroalkyl-C 3-i ocydoalkyl, -Ci-ioheteroalkyl-Ci.
  • Ri’ is hydrogen, -Ci-ioalkyl, -C 2-i oalkenyl, -C 2-i oalkynyl, -Ci-ioheteroalkyl, -C 3.l0 aryl, -Ci. ! ohetaryl, -C 3-i ocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C 3-i oaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.
  • iohetaryl -L-C 2-i oalkynyl-C 3-i0 cycloalkyl, -L-C 2-i oalkynyl-Ci.ioheterocyclyl, -L-Ci-ioheteroalkyl- C 3.l0 aryl, -L -Ci-ioheteroalkyl-Ci-iohetaryl, -L -Ci-ioheteroalkyl-C 3-i ocycloalkyl, -L -Ci.
  • i oheteroal kyl -C M oheterocyd yl , -L-Ci-ioalkoxy-C 3-i oaryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci.
  • ioheterocydyl -L-Ci.ioalkoxy-C 3-i0 aryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci.i 0 alkoxy-C 3- iocydoalkyl, -L-Ci-ioalkoxy-Ci-ioheterocydyl, -L-C 3-i0 aryl-Ci.ioalkyl, -L-C 3-i oaryl-C 2-i0 alkenyl, -L-C 3 -ioaryl-C 2 -ioalkynyl, -L-C -1 oaryl -C 1.1 ohetaryl , -L-C 3 .ioaryl-C 3 .iocycloalkyl, -L-C 3 .ioaryl-Ci.
  • ioheteroalkyl-Ci-iohetaryl -Ci.ioheteroalkyl-C 3 .iocycloalkyl, -Ci-ioheteroalkyl-Ci-ioheterocyclyl, - Ci-ioalkoxy-C 3 -ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci.ioalkoxy-C 3 .iocycloalkyl, -Ci-ioalkoxy-Ci. !
  • each of R5, R71, Rxi and R91 is independently hydrogen, halogen, -C M O alkyl, -C 2 .10 alkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C 3 -i 0 aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -
  • R 6 is hydrogen, -Ci.i 0 alkyl, -C 2-i0 alkenyl, -C 2-i0 alkynyl, -Ci-ioheteroalkyl, -C 3.l0 aryl, -Ci. !
  • ohetaryl -C3-iocycloalkyl, -Ci-ioheterocyclyl,— C 1.1 oal kyl -Cs- 1 oaryl , -Ci-ioalkyl-Ci-iohetaryl, -Ci- i 0 alkyl-C 3 -i 0 cycloalkyl, -Ci-i 0 alkyl-Ci-i 0 heterocyclyl, -C 2 -i 0 alkenyl-C 3 -ioaryl, -C 2-i0 alkenyl-Ci.
  • each of Rio and R M is independently -C MO alkyl, -C 2-i0 alkenyl, -C 2-i0 alkynyl, -Ci.
  • loheteroalkyl -C 3 .i 0 aryl, -Ci-iohetaryl, -C 3 .i 0 cycloalkyl, -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
  • each of R , R , R and R J t is independently hydrogen, halogen, -Cmo alkyl, -C 2- l0 alkenyl, -C 2. l0 alkynyl, -Ci-ioheteroalkyl, -C 3-i oaryl, -Ci-iohetaryl, -C3.i 0 cycloalkyl, -Ci- ioheterocyclyl, or wherein R 31 together with R 32 form a heterocyclic ring;
  • the ERK inhibitor is a compound of Formula I-A:
  • Ri is 3- to 6-membered heterocyclyl, -Ci.i 0 alkyl-(3- to 6-membered heterocyclyl), -(3- to 6- membered heterocyclyl)-Ci.i 0 alkyl, -(3- to 6-membered heterocyclyl)-C3-ioaryl, or -(3- to 6- membered heterocyclyl)-Ci.i 0 hetaryl, each of which is unsubstituted or substituted by one or more independent Ri 0 or Rn substituents;
  • R 2I is -L-C3.i 0 aryl or -L-Ci-iohetaryl, each of which is unsubstituted or substituted by one or more independent R i2 substituents;
  • L is a bond or -N(R 31 )-;
  • R 72 is hydrogen
  • each of Rio is independently-C3.i 0 aryl, -Ci-iohetaryl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
  • each of Rn and Ri 2 is independently halogen,—Cmo alkyl, -OH, -CF 3 or -OR 31 ; and each of R 3 1 is independently hydrogen or -Cmo alkyl.
  • the ERK inhibitor is selected from the group consisting of:
  • the MAPK pathway inhibitor may be selected from cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, and MK-8353.
  • a method of the present disclosure further comprising administering a second therapeutic agent to the subject.
  • the present disclosure provides a method of treating an adenocarcinoma in a subject in need thereof, comprising administering to said subject a MAPK pathway inhibitor and a second therapeutic agent.
  • the second therapeutic agent is a CDK4/6 inhibitor.
  • the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF-06873600, voruciclib, FLX-925, ON-123300, BPI-16350, VS2-370, FCN-437c, BPI-l 178, IIIM-290, TQB-3616, BEBT-209, SRX-3177, GZ-38-1, IIIM-985, birociclib, CGP-82996, PD-171851, R-547, PAN-1215, NSC-625987, staurosporine, G1T28-1, G1T30-1, gossypin, AT-7519, P-276-00, AG-024322, PD-0183812 and INOC-005.
  • the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF-06873600, voruciclib and FLX-925. In some embodiments, the second therapeutic agent is selected from palbociclib, ribociclib and abemaciclib. INCORPORATION BY REFERENCE
  • FIG. 1 depicts tumor volumes of four sets of KRAS-mutant non-small cell lung
  • NSCLC-ADC adenocarcinoma
  • Each of the models depicted exhibits overexpression of CCND1.
  • the specific KRAS mutations are provided in the figure for each set.
  • FIG. 2 presents a receiver operator characteristic (ROC) analysis of KRAS-mutant NSCLC- ADC models that display tumor growth inhibition of greater than 100% following treatment with a MAPK pathway inhibitor, using fragments per kilobase million (FKPM) of CCND1 as the criterion.
  • ROC receiver operator characteristic
  • FIG. 3 presents an ROC analysis of KRAS-mutant NSCLC-ADC models that display tumor growth inhibition of greater than or equal to 80% following treatment with a MAPK pathway inhibitor, using FKPM of CCND1 as the criterion.
  • FIG. 4 illustrates percent tumor growth for KRAS-mutant NSCLC-ADC models treated with a MAPK pathway inhibitor.
  • FIG. 5 illustrates percent tumor growth for KRAS-mutant NSCLC-ADC models treated with a MAPK pathway inhibitor, with the models stratified into two sets based on CCND1 expression levels.
  • FIG. 6 presents a comparison of ROC analyses of CCND1, CDK6, EGFR, KRAS and TOPO-2.
  • FIG. 7 summarizes the IHC scores (% CCND1 positive) of a series of KRAS-mutant NSCLC-ADC samples.
  • FIG. 8 depicts tumor volumes of KRAS-mutant NSCLC-ADC models treated with either vehicle (black squares), a MAPK pathway inhibitor (black circles), a CDK4/6 inhibitor (open triangles) or the MAPK pathway inhibitor and the CDK4/6 inhibitor (open diamonds).
  • FIG. 9 depicts body weights of KRAS-mutant NSCLC-ADC murine models treated with either vehicle (black squares), a MAPK pathway inhibitor (black circles), a CDK4/6 inhibitor (open triangles) or the MAPK pathway inhibitor and the CDK4/6 inhibitor (open diamonds) over the study duration.
  • FIG. 10 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, and trametinib in a murine xenograft model produced using patient-derived 1 lql3-amplified ES0136 esophageal squamous-cell carcinoma cells.
  • FIG. 11 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, and trametinib in a murine xenograft model produced using patient-derived 1 lql3-amplified HN2195 head and neck squamous-cell carcinoma cells.
  • FIG. 12 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, and trametinib in a murine xenograft model produced using patient-derived 1 lql3-amplified LU6429 lung squamous-cell carcinoma cells.
  • FIG. 13 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, BVD-523 (ulixertinib), and trametinib in a murine xenograft model produced using patient-derived KRAS-mutated CCND1 -overexpressed LU11786 lung squamous-cell carcinoma cells.
  • FIG. 14 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, BVD-523 (ulixertinib), and trametinib in a murine xenograft model produced using patient-derived KRAS-mutated CCND1 -overexpressed LU11692 lung squamous-cell carcinoma cells.
  • polynucleotide refers to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof.
  • Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown.
  • loci locus
  • a polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer.
  • the sequence of nucleotides may be interrupted by non- nucleotide components.
  • a polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.
  • A“nucleotide probe” or“probe” refers to a polynucleotide used for detecting or identifying its corresponding target polynucleotide in a hybridization reaction.
  • Hybridization refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues.
  • the hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi -stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR, or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • “expression” refers to the process by which a polynucleotide is transcribed into mRNA and/or the process by which the transcribed mRNA (also referred to as a“transcript”) is subsequently translated into peptides, polypeptides, or proteins.
  • the transcripts and the encoded polypeptides are collectedly referred to as“gene product.” If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell.
  • the level of expression (or alternatively, the“expression level”) of a CCND1 gene can be determined, for example, by determining the level of CCND1 polynucleotides, polypeptides, and/or gene products.
  • “Differentially expressed” or“differential expression” as applied to a nucleotide sequence (e.g ., a gene) or polypeptide sequence in a subject refers to the differential production of the mRNA transcribed and/or translated from the nucleotide sequence or the protein product encoded by the nucleotide sequence.
  • a differentially expressed sequence may be overexpressed or underexpressed as compared to the expression level of a reference sample (i.e., a reference level).
  • overexpression is an increase in expression and generally is at least 1.25 fold, or alternatively, at least 1.5 fold, or alternatively, at least 2 fold, or alternatively, at least 3 fold, or alternatively, at least 4 fold, or alternatively, at least 10 fold expression over that detected in a reference sample.
  • underexpression is a reduction in expression and generally is at least 1.25 fold, or alternatively, at least 1.5 fold, or alternatively, at least 2 fold, or alternatively, at least 3 fold, or alternatively, at least 4 fold, or alternatively, at least 10 fold expression under that detected in a reference sample. Underexpression also encompasses absence of expression of a particular sequence as evidenced by the absence of detectable expression in a test subject when compared to a reference sample.
  • “Signal transduction” is a process during which stimulatory or inhibitory signals are transmitted into and within a cell to elicit an intracellular response.
  • a molecule can mediate its signaling effect via direct or indirect interaction with downstream molecules of the same pathway or related pathway(s).
  • MAPK signaling can involve a host of downstream molecules including but not limited to one or more of the following proteins: RAS, RAF, MEK, EGFR,
  • polypeptide “peptide” and“protein” are used interchangeably herein to refer to polymers of amino acids of any length.
  • the polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids.
  • the terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component.
  • amino acid refers to either natural and/or unnatural or synthetic amino acids, including glycine and both the D or L optical isomers, and amino acid analogs and peptidomimetics.
  • biomarker and“marker” are used interchangeably herein to refer to a molecule which is differentially present in a sample taken from a subject of one phenotypic status (e.g ., having an adenocarcinoma that is sensitive to a MAPK pathway inhibitor) as compared with another phenotypic status (e.g., having an adenocarcinoma that has low sensitivity to a MAPK pathway inhibitor).
  • a biomarker is differentially present between different phenotypic statuses if the mean or median expression level of the biomarker in the different groups is calculated to be statistically significant.
  • Biomarkers alone or in combination, can provide measures of relative risk that a subject belongs to one phenotypic status or another. Therefore, they are useful as markers for disease (diagnostics), therapeutic effectiveness of a drug (theranostics) and drug toxicity.
  • the polynucleotides and polypeptides described herein can be used as biomarkers for certain cancers described herein.
  • A“reference sample” is an alternative sample or subject used in an experiment for comparison purpose.
  • a reference level refers to a control level used to evaluate a test level.
  • a reference level may be a control.
  • a biomarker may be considered to be underexpressed when the expression level of that biomarker is lower than a reference level.
  • the reference level can be determined by a plurality of methods, provided that the resulting reference level accurately provides a level of a biomarker above which exists a first group of subjects having a different probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor than that of a second group of patients having levels of the biomarker below the reference level.
  • the reference level may be determined, for example, by measuring the level of expression of a biomarker in tumorous or non-tumorous cancer cells from the same tissue as the tissue of the cancer cells to be tested.
  • the reference level may be a level of a biomarker determined in vitro.
  • a reference level may be determined by comparison of the level of a biomarker in populations of subjects having the same cancer. Two or more separate groups of subjects may be determined by identification of subsets of populations of the cohort that have the same or similar levels of a biomarker. Determination of a reference level can then be made based on a level that distinguishes these separate groups.
  • a reference level may be a single number, equally applicable to every subject, or a reference level can vary according to specific
  • the reference level may be some level determined for each subject individually.
  • the reference level may be a ratio of a biomarker level in a cancer cell of a subject relative to the biomarker level in a normal cell within the same subject.
  • a reference level is a numerical range of gene expression that is obtained from a statistical sampling from a population of individuals having cancer. The sensitivity of the individuals having cancer to treatment with a MAPK pathway inhibitor may be known.
  • the reference level is derived by comparing gene expression to a control gene that is expressed in the same cellular environment at relatively stable levels (e.g . a housekeeping gene such as an actin). Comparison to a reference level may be a qualitative assessment or a quantitative determination.
  • determining means determining if an analyte is present or not (e.g., detection). These terms can include both quantitative and/or qualitative determinations. Assessing may be relative or absolute. A relative amount could be, for example, high, medium or low. An absolute amount could reflect the measured strength of a signal or the translation of this signal strength into another quantitative format, such as micrograms/mL.“Detecting the presence of’ can include determining the amount of something present, as well as determining whether it is present or absent.
  • “agent” or“biologically active agent” refers to a biological, pharmaceutical, or chemical compound or other moiety.
  • Non-limiting examples include a simple or complex organic or inorganic molecule, a peptide, a protein, an oligonucleotide, an antibody, an antibody derivative, antibody fragment, a vitamin derivative, a carbohydrate, a toxin, or a chemotherapeutic compound.
  • Various compounds can be synthesized, for example, small molecules and oligomers (e.g, oligopeptides and oligonucleotides), and synthetic organic compounds based on various core structures.
  • various natural sources can provide compounds for screening, such as plant or animal extracts, and the like. A skilled artisan can readily recognize that there is no limit as to the structural nature of the agents of the present disclosure.
  • the terms“antagonist” and“inhibitor” are used interchangeably, and they refer to a compound having the ability to inhibit a biological function of a target protein or pathway (e.g., MAPK), whether by inhibiting the activity or expression of the target protein. Accordingly, the terms“antagonist” and“inhibitors” are defined in the context of the biological role of the target protein. While preferred antagonists herein specifically interact with (e.g., bind to) the target, compounds that inhibit a biological activity of the target protein by interacting with other members of the signal transduction pathway of which the target protein is a member are also specifically included within this definition.
  • a preferred biological activity inhibited by an antagonist is associated with the development, growth, or spread of an adenocarcinoma, such as non-small cell lung cancer.
  • cell proliferation refers to a phenomenon by which the cell number has changed as a result of division. This term also encompasses cell growth by which the cell morphology has changed (e.g, increased in size) consistent with a proliferative signal.
  • Co-administration encompass administration of two or more agents to a subject so that both agents and/or their metabolites are present in the subject at the same time.
  • Co-administration includes
  • the term“effective amount” or“therapeutically effective amount” refers to that amount of a compound described herein that is sufficient to effect the intended application including but not limited to disease treatment, as defined below.
  • the therapeutically effective amount may vary depending upon the intended application (in vitro or in vivo), or the subject and disease condition being treated, e.g, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
  • the term also applies to a dose that will induce a particular response in target cells, e.g, reduction of platelet adhesion and/or cell migration.
  • the specific dose will vary depending on the particular compounds chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.
  • the terms“treatment”,“treating”,“palliating” and“ameliorating” are used interchangeably. These terms refer to an approach for obtaining beneficial or desired results including, but are not limited to, therapeutic benefit and/or a prophylactic benefit.
  • therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated (e.g., adenocarcinoma).
  • a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the patient, notwithstanding that the patient can still be afflicted with the underlying disorder.
  • the pharmaceutical compositions may be administered to a patient at risk of developing a particular disease, or to a patient reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
  • A“therapeutic effect,” as used herein, encompasses a therapeutic benefit and/or a prophylactic benefit as described above.
  • a prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.
  • the term“selective inhibition” or“selectively inhibit” as applied to a biologically active agent refers to the agent’s ability to selectively reduce the target signaling activity as compared to off-target signaling activity, via direct or indirect interaction with the target.
  • the term“subject” includes, but is not limited to, humans of any age group, e.g., a pediatric subject (e.g, infant, child or adolescent) or adult subject (e.g, young adult, middle-aged adult or senior adult)) and/or other primates (e.g, cynomolgus monkeys or rhesus monkeys); mammals, including commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs; and/or birds, including commercially relevant birds such as chickens, ducks, geese, quail, and/or turkeys.
  • the methods described herein can be useful in both human therapeutics and veterinary applications.
  • the patient is a mammal, and in some embodiments, the patient is human.
  • “Radiation therapy” or“radiation treatment” means exposing a patient, using routine methods and compositions known to the practitioner, to radiation emitters such as alpha-particle emitting radionucleotides (e.g, actinium and thorium radionuclides), low linear energy transfer (LET) radiation emitters (e.g, beta emitters), conversion electron emitters (e.g, strontium-89 and samarium- 153 -ED TMP), or high-energy radiation, including without limitation x-rays, gamma rays, and neutrons.
  • radionucleotides e.g, actinium and thorium radionuclides
  • LET low linear energy transfer
  • beta emitters e.g, beta emitters
  • conversion electron emitters e.g, strontium-89 and samarium- 153 -ED TMP
  • high-energy radiation including without limitation x-rays, gamma rays, and neutrons.
  • in vivo refers to an event that takes place in a subject’s body.
  • in vitro refers to an event that takes place outside of a subject’s body.
  • an in vitro assay encompasses any assay run outside of a subject’s body.
  • in vitro assays encompass cell-based assays in which cells alive or dead are employed.
  • In vitro assays also encompass a cell-free assay in which no intact cells are employed.
  • “MAPK pathway activity” as applied to a biologically active agent refers to the agent’s ability to modulate signal transduction mediated by Ras, Raf, MEK, and/or ERK.
  • modulation of MAPK pathway activity is evidenced by alteration in signaling output from the MAPK pathway.
  • inhibitory MAPK pathway activity refers to slowing, reducing, altering, as well as completely eliminating and/or preventing MAPK pathway activity.
  • the present inventors have discovered certain genes that are differentially expressed in adenocarcinoma cells that are sensitive to therapy with a MAPK pathway inhibitor, such as a compound described herein. More specifically, the disclosure relates to the use of an inhibitor of the mitogen-activated protein kinase (MAPK) pathway to treat adenocarcinoma, such as adenocarcinoma of the lung.
  • MAPK mitogen-activated protein kinase
  • overexpression of one or more of the genes may be indicative of sensitivity to therapy with a MAPK pathway inhibitor.
  • the presence of certain mutations may further be indicative of sensitivity to therapy with a MAPK pathway inhibitor.
  • ETse of certain DNA- and RNA-based biomarkers to identify adenocarcinomas more likely to display a robust therapeutic response to MAPK pathway inhibition are described.
  • the present disclosure provides a method of treating a cancer in a subject in need thereof, wherein said cancer exhibits a KRAS mutation and wherein said cancer overexpresses CCND1.
  • the method comprises administering to the subject an effective dose of a mitogen-activated protein kinase (MAPK) pathway inhibitor.
  • the method comprises (a) assessing the cancer for overexpression of CCND1; (b) evaluating the cancer for the presence of a KRAS mutation; and (c) administering the MAPK pathway inhibitor to the subject if both the CCNDl overexpression and the KRAS mutation are determined to be present. Steps (a) and (b) may be performed in either order.
  • the present disclosure provides a method of treating a subject having cancer, wherein said cancer exhibits a KRAS mutation, comprising (a) assessing the cancer for overexpression of CCNDl; and (b) administering an effective dose of a MAPK pathway inhibitor to the subject if the overexpression of CCNDl is found to be present.
  • An alternative therapy such as chemotherapy, immunotherapy, radiotherapy or surgery, may be applied to the subject if the overexpression of CCND1 is found to be absent.
  • the present disclosure provides a method of downregulating MAPK signaling output in a plurality of lung adenocarcinoma cells with a MAPK pathway inhibitor, wherein at least one cell of the plurality exhibits a KRAS mutation.
  • the method comprises (a) assessing, in a biological sample comprising a nucleic acid from the subject, a total expression level of CCND1; and (b) administering an effective dose of the MAPK pathway inhibitor to the plurality of cells if the total expression level is greater than a reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
  • the present disclosure provides a method of categorizing a cancer status of a subject.
  • the method comprises (a) obtaining a biological sample from the subject, the sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell of the subject; (b) assessing (1) a total expression level of CCND1 in the sample, and (2) the presence or absence of a KRAS mutation in the sample; (c) generating an expression profile based on a comparison between the total expression level and a reference level, wherein the reference level is derivable from a reference sample from a different subject having a known cancer status; and (d) categorizing the cancer status of the subject of (a) based on the expression profile and the presence or absence of the KRAS mutation.
  • the cancer may be categorized as likely sensitive to treatment with a MAPK pathway inhibitor if the total expression level is greater than the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
  • the known cancer status of the different subject is categorized as resistant to a MAPK pathway inhibitor or sensitive to a MAPK pathway inhibitor.
  • the categorizing step includes calculating, using a computer system, a likelihood of response of the subject to treatment with a MAPK pathway inhibitor based on the expression profile, wherein the likelihood is adjusted upward for each fold increase in the total expression level relative to the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
  • the method further comprises preparing a report comprising a prediction of the likelihood of response of the subject to treatment with the MAPK pathway inhibitor.
  • the present disclosure provides a method of assessing a likelihood of a subject having cancer exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, the method comprising: (a) assessing an expression profile of CCND1 in a biological sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell; (b) evaluating the biological sample for the presence of a KRAS mutation; and (c) calculating, using a computer system, a weighted probability of MAPK pathway inhibitor responsiveness based on the expression profile and KRAS mutation status.
  • the method further comprises designating the subject as having a high probability of exhibiting a clinically beneficial response to treatment with the MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability of (c).
  • the method further comprises transmitting information concerning the likelihood to a receiver.
  • the method further comprises providing a recommendation based on the weighted probability. The recommendation may comprise treating the subject with the MAPK pathway inhibitor, or, alternatively, discontinuing therapy, or administering one or more of chemotherapy, immunotherapy, radiotherapy or surgery.
  • the method further comprises selecting a treatment based on the weighted probability. In some embodiments, the method further comprises administering the MAPK pathway inhibitor to the subject based on the weighted probability. In some embodiments, the method further comprises administering the MAPK pathway inhibitor to the subject if the subject is designated as having a high probability of exhibiting a clinically beneficial response.
  • the expression level is assessed by (a) detecting a level of mRNA
  • the presence or absence of a KRAS mutation is determined by sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography (DHPLC), or restriction fragment length polymorphism (RFLP) assay.
  • PCR polymerase chain reaction
  • MS mass spectrometry
  • SNP single nucleotide polymorphism
  • DPLC denaturing high-performance liquid chromatography
  • RFLP restriction fragment length polymorphism
  • the presence or absence of a KRAS mutation is determined by sequencing or PCR.
  • a cancer such as an adenocarcinoma, having a total expression level of CCND1 that is greater than a reference level of CCND1 may be more likely to respond to treatment with a MAPK pathway inhibitor than a cancer having a total expression level of CCND1 that is less than a reference level of CCND1.
  • the reference level of CCND1 may be obtained by assessing a total expression level of CCND1 in a biological sample from one or more subjects having a cancer exhibiting low sensitivity to treatment with the MAPK pathway inhibitor.
  • the reference level is the average total expression level of CCND1 in a plurality of cancer samples.
  • the plurality may comprise at least 5, 10, 20, 30, 40 or at least 50 samples.
  • Overexpression of CCND1 may be characterized by an expression level of CCND1 in the cancer that is higher than a reference expression level of CCND1.
  • the total expression level of CCND1 may be compared to the reference level of CCND1 to calculate a weighted probability of MAPK pathway inhibitor responsiveness.
  • calculation of a weighted probability of MAPK pathway inhibitor responsiveness comprises assessment of both the total expression level of CCND1 and the KRAS mutation status.
  • the calculation is performed by a computer system.
  • Any method of the present disclosure may further comprise designating a subject having cancer as having a high probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, or at least 20, such as at least 2 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability.
  • the methods described herein for qualifying or quantifying the expression of polypeptides and/or polynucleotides provide information which can be correlated with pathological conditions, predisposition to disease, therapeutic monitoring, risk stratification, among others.
  • a method of the disclosure is particularly useful for diagnosing conditions, evaluating whether a MAPK pathway inhibitor will have a desired effect, i.e., predicting responsiveness to a MAPK pathway inhibitor, and determining prognoses.
  • the present methods may be used for the optimization of treatment protocols.
  • evaluation of the expression profile of the biomarkers disclosed herein can be used to gain information on the treatment potential of a tissue sample with a MAPK pathway inhibitor.
  • the disclosure provides methods for assessing a likelihood that a subject having cancer, especially adenocarcinoma, will exhibit a clinically beneficial response to treatment with a MAPK pathway inhibitor based on an expression profile of a gene or gene product.
  • An“expression profile” refers to a pattern of expression of at least one biomarker, such as CCND1, that recurs in multiple samples and reflects a property shared by those samples, such as tissue type, response to treatment with a MAPK pathway inhibitor, or activation of a particular biological process or pathway in the cells.
  • an expression profile differentiates between samples that share that common property and those that do not with better accuracy than would likely be achieved by assigning the samples to the two groups at random.
  • An expression profile may be used to predict whether samples of unknown status share that common property or not. Some variation between the levels of the biomarker and the typical profile is to be expected, but the overall similarity of the expression levels to the typical profile is such that it is statistically unlikely that the similarity would be observed by chance in samples not sharing the common property that the expression profile reflects.
  • An expression profile may be generated based on a comparison between a total expression level of a biomarker, such as CCND1, in a sample from a test subject and a corresponding reference level.
  • the expression profile is used in a method of the disclosure to assess a likelihood of response to treatment with a MAPK pathway inhibitor.
  • the likelihood of response may be adjusted upward when CCND1 is overexpressed. In some embodiments, the likelihood of response may be adjusted downward when CCND1 is underexpressed. The magnitude of under- or over-expression may be used to weight the amount of adjustment to the likelihood of response. Similarly, the likelihood of response may be adjusted upward when a KRAS mutation is present in the cancer, or the likelihood of response may be adjusted downward when a KRAS mutation is absent in the cancer.
  • a method of the disclosure provides a reference level above which a biomarker, such as CCND1, must be expressed to be considered in assessing the likelihood of response to treatment with a MAPK pathway inhibitor.
  • the biomarker may be differentially expressed at least 1.1 fold, at least 1.2 fold, at least 1.3 fold, at least 1.4 fold, at least 1.5 fold, at least 2.0 fold, at least 2.25 fold, at least 2.5 fold, at least 2.75 fold, at least 3.0 fold, at least 3.5 fold, at least 4.0 fold, at least 5.0, or even at least 10 fold higher or lower relative to a reference level to be considered in adjusting the likelihood of response.
  • the reference level is a numerical range of biomarker expression that is obtained from a statistical sampling from a population of individuals having cancer that has low sensitivity to treatment with a MAPK pathway inhibitor. In some embodiments, the reference level is a numerical range of biomarker expression that is obtained from a statistical sampling from a population of individuals having cancer that is resistant to treatment with a MAPK pathway inhibitor. The reference level may be a numerical range of biomarker expression that is obtained from a statistical sampling from a population of individuals having cancer, e.g ., the same cancer as the test subject. In some embodiments, the reference level is derived by comparison of sensitive and resistant populations.
  • the MAPK pathway inhibitor may be administered to the subject if a cancer of the subject exhibits both overexpression of CCND1 and a KRAS mutation.
  • a non-human subject for example a non-human primate such as a macaque, chimpanzee, gorilla, vervet, orangutan, baboon or other non-human primate, including such non-human subjects that can be known to the art as preclinical models.
  • the subject or biological source can be a non-human primate
  • transgenic animal is a non-human animal in which one or more of the cells of the animal includes a nucleic acid that is non-endogenous (i.e., heterologous) and is present as an extrachromosomal element in a portion of its cell or stably integrated into its germ line DNA (i.e., in the genomic sequence of most or all of its cells).
  • any cancer may be analyzed and/or treated according to the methods of the disclosure.
  • the methods described herein are particularly effective in analyzing and/or treating adenocarcinoma.
  • Exemplary adenocarcinomas include adenocarcinomas of the esophagus, pancreas, prostate, cervix, stomach, breast, colon and lung.
  • the cancer is a lung adenocarcinoma, such as non-small cell lung cancer.
  • the cancer is non-small cell lung
  • the cancer is an adenocarcinoma selected from lung, esophageal and pancreatic adenocarcinomas. In some embodiments, the cancer is selected from lung, esophageal, cervical, head and neck, bladder, gastric and pancreatic cancer. In some embodiments, the cancer is selected from breast cancer, pancreatic cancer, lung cancer, thyroid cancer, seminomas, melanoma, bladder cancer, liver cancer, kidney cancer, myelodysplastic syndrome, acute myelogenous leukemia and colorectal cancer. Preferably, the cancer is lung adenocarcinoma. In some embodiments, the lung adenocarcinoma is selected from lepidic adenocarcinoma, acinar adenocarcinoma, papillary adenocarcinoma, micropapillary
  • adenocarcinoma solid adenocarcinoma, invasive mucinous adenocarcinoma, mixed invasive mucinous and nonmucinous adenocarcinoma, colloid adenocarcinoma, fetal adenocarcinoma, enteric adenocarcinoma, minimally invasive adenocarcinoma, preinvasive lesions, atypical adenomatous hyperplasia and adenocarcinoma in situ.
  • the adenocarcinoma is a non-small cell lung cancer.
  • a sample of a subject comprises cancerous or pre- cancerous cells.
  • the biological sample may be a tissue sample.
  • the sample may be a solid biological sample, for example, a tissue biopsy or a tumor biopsy.
  • a biopsy may be fixed, paraffin- embedded, fresh, or frozen.
  • Samples may be obtained by any suitable means, including but not limited to needle aspiration, fine needle aspiration, core needle biopsy, vacuum assisted biopsy, large core biopsy, incisional biopsy, excisional biopsy, punch biopsy, shave biopsy, skin biopsy, and venipuncture.
  • a sample may be derived from fine needle, core, or other types of biopsy, or may comprise circulating tumor cells.
  • a sample comprises cell-free DNA
  • a biological sample may be a whole blood or plasma sample.
  • a sample may be analyzed directly for its contents, or may be processed to purify one or more of its contents for analysis.
  • one or more components are purified from the sample for the detection of a biomarker for MAPK pathway inhibitor response.
  • the purified component of the sample is protein (e.g . total protein, cytoplasmic protein, or membrane protein).
  • the purified component of the sample is a nucleic acid, such as DNA (e.g. genomic DNA, cDNA, ctDNA, or cfDNA) or RNA (e.g. total RNA or mRNA).
  • the nucleic acid is from a cancer cell, such as an adenocarcinoma cell.
  • nucleic acids can be purified by organic extraction with phenol,
  • phenol/chloroform/isoamyl alcohol or similar formulations, including TRIzol and TriReagent.
  • extraction techniques include: organic extraction followed by ethanol precipitation, e.g. , using a phenol/chloroform organic reagent (Ausubel el al. , 1993), with or without the use of an automated nucleic acid extractor, e.g. , the Model 341 DNA Extractor available from Applied Biosystems (Foster City, Calif); stationary phase adsorption methods (U.S. Pat. No. 5,234,809; Walsh et al. , 1991); and salt-induced nucleic acid precipitation methods (Miller et al ., (1988), such precipitation methods being typically referred to as“salting-out” methods.
  • nucleic acid isolation and/or purification includes the use of magnetic particles to which nucleic acids can specifically or non-specifically bind, followed by isolation of the beads using a magnet, and washing and eluting the nucleic acids from the beads (see e.g. U.S. Pat. No. 5,705,628).
  • the above isolation methods may be preceded by an enzyme digestion step to help eliminate unwanted protein from the sample, e.g. , digestion with proteinase K, or other like proteases. See, e.g. , U.S. Pat. No. 7,001,724.
  • RNase inhibitors may be added to the lysis buffer.
  • RNA denaturati on/digestion step For certain cell or sample types, it may be desirable to add a protein denaturati on/digestion step to the protocol.
  • Purification methods may be directed to isolate DNA, RNA, or both. When both DNA and RNA are isolated together during or subsequent to an extraction procedure, further steps may be employed to purify one or both separately from the other. Sub-fractions of extracted nucleic acids can also be generated, for example, purification by size, sequence, or other physical or chemical characteristics. In addition to an initial nucleic acid isolation step, purification of nucleic acids can be performed after any step in the methods of the disclosure, such as to remove excess or unwanted reagents, reactants, or products.
  • sample polynucleotides are fragmented into a population of fragmented DNA molecules of one or more specific size range(s).
  • fragments are generated from about or at least about 1, 10, 100, 1000, 10000, 100000, 300000, 500000, or more genome-equivalents of starting DNA. Fragmentation may be accomplished by methods known in the art, including chemical, enzymatic, and mechanical fragmentation.
  • the fragments have an average length from about 10 to about 10,000 nucleotides. In some embodiments, the fragments have an average length from about 50 to about 2,000
  • the fragments have an average or median length from about 10- 2,500, 10-1,000, 10-800, 10-500, 50-500, 50-250, 50-150, or 100-2,500 nucleotides. In some embodiments, the fragmentation is accomplished mechanically by subjecting sample
  • the fragmentation comprises treating the sample polynucleotides with one or more enzymes under conditions suitable for the one or more enzymes to generate double-stranded nucleic acid breaks.
  • enzymes useful in the generation of polynucleotide fragments include sequence specific and non-sequence specific nucleases.
  • nucleases include DNase I, Fragmentase, restriction endonucleases, variants thereof, and combinations thereof. For example, digestion with DNase I can induce random double-stranded breaks in DNA in the absence of Mg ++ and in the presence of Mn ++ .
  • fragmentation comprises treating the sample polynucleotides with one or more restriction endonucleases. Fragmentation can produce fragments having 5’ overhangs, 3’ overhangs, blunt ends, or a combination thereof. In some embodiments, such as when fragmentation comprises the use of one or more restriction endonucleases, cleavage of sample polynucleotides leaves overhangs having a predictable sequence. In some embodiments, the method includes the step of size selecting the fragments via standard methods such as column purification or isolation from an agarose gel.
  • one or more polynucleotides from a sample of a subject are amplified.
  • amplification comprises generating one or more copies of all or a portion of polynucleotides in a template-dependent manner.
  • Amplification may be primer-dependent, or primer-independent.
  • primer-dependent amplification may be directed to one or more specific polynucleotides in a sample or portions thereof, such as one or more regions ( e.g .
  • Amplification may be linear or non-linear (e.g. exponential). Amplification may comprise directed changes in temperature, or may be isothermal. Methods for primer-directed amplification of target polynucleotides are known in the art, and include without limitation, methods based on the polymerase chain reaction (PCR).
  • Conditions favorable to the amplification of target sequences by PCR can be optimized at a variety of steps in the process, and depend on characteristics of elements in the reaction, such as target type, target concentration, sequence length to be amplified, sequence of the target and/or one or more primers, primer length, primer concentration, polymerase used, reaction volume, ratio of one or more elements to one or more other elements, some or all of which can be altered.
  • PCR involves the steps of denaturation of the target to be amplified (if double stranded), hybridization of one or more primers to the target, and extension of the primers by a DNA polymerase, with the steps repeated (or “cycled”) in order to amplify the target sequence.
  • Steps in this process can be optimized for various outcomes, such as to enhance yield, decrease the formation of spurious products, and/or increase or decrease specificity of primer annealing.
  • Methods of optimization are well known in the art and include adjustments to the type or amount of elements in the amplification reaction and/or to the conditions of a given step in the process, such as temperature at a particular step, duration of a particular step, and/or number of cycles.
  • an amplification reaction comprises at least 5, 10, 15, 20, 25, 30, 35, 50, or more cycles.
  • an amplification reaction comprises no more than 5, 10, 15, 20, 25, 35, 50, or more cycles. Cycles can contain any number of steps, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more steps.
  • Steps can comprise any temperature or gradient of temperatures, suitable for achieving the purpose of the given step, including but not limited to, primer annealing, primer extension, and strand denaturation. Steps can be of any duration, including but not limited to about, less than about, or more than about 1, 5, 10,
  • Cycles of any number comprising different steps can be combined in any order. In some embodiments, different cycles comprising different steps are combined such that the total number of cycles in the combination is about, less that about, or more than about 5, 10, 15, 20, 25, 30, 35, 50, or more cycles.
  • a total expression level of a biomarker may be assessed by any appropriate method.
  • the expression level of a biomarker may be assessed by detecting a level of mRNA transcribed from the biomarker, by detecting a level of cDNA produced from reverse transcription of mRNA transcribed from the biomarker, by detecting a level of polypeptide encoded by the biomarker, or by a nucleic acid amplification assay, a hybridization assay, sequencing, or a combination thereof.
  • Regulation of a target gene or gene transcript can also be determined indirectly, such as by measuring the effect on a phenotypic indicator of the gene or gene transcript activity, such as by cellular assay.
  • Methods of detecting gene expression products are known in the art, examples of which are described herein. These methods can be performed on a sample by sample basis or modified for high throughput analysis, for example, using AffymetrixTM U133 microarray chips.
  • assessment of a total expression level of a gene comprises forming a plurality of complexes, each complex comprising an association between an expression product of the gene and a nucleic acid probe that hybridizes to the expression product of the gene.
  • the nucleic acid probe may comprise a first nucleic acid complex, wherein the complex comprises (i) a first target-specific sequence capable of binding to a target nucleic acid, (ii) a first label attachment region, which is non-overlapping with the first target-specific sequence, comprising a first DNA sequence hybridized to a first nucleic acid molecule that is attached to one or more detectable labels that emit light which constitutes a first signal, (iii) a second label attachment region, which is non-overlapping with the first target-specific sequence and the first label attachment region, comprising a second DNA sequence hybridized to a second nucleic acid molecule that is attached to one or more detectable labels that emit light which constitutes a second signal, and (iv) a first moiety that is capable of selectively binding to the substrate.
  • the complex comprises (i) a first target-specific sequence capable of binding to a target nucleic acid, (ii) a first label attachment region, which is non-overlapping with the first target-specific sequence, comprising
  • the nucleic acid probe further comprises a second nucleic acid complex, the second complex comprising (i) a second target-specific sequence capable of binding to the target nucleic acid, wherein the first target-specific sequence and the second target-specific sequence bind to different regions of the target nucleic acid, and (ii) a second moiety that is capable of selectively binding to the substrate.
  • the first nucleic acid molecule comprises at least one additional attachment region which is non-overlapping with other label attachment regions.
  • the at least one additional label attachment region may comprise a DNA sequence hybridized to a nucleic acid molecule that is attached to at least one detectable label that emits light.
  • the at least one additional label attachment region may comprise a DNA sequence hybridized to a nucleic acid molecule that is not attached to a detectable label that emits light.
  • the first and second nucleic acid molecules each comprise four or more aminoallyl-modified UTP nucleotides, wherein one or more fluorophore labels is attached to each aminoallyl-modified UTP nucleotide.
  • the first moiety and/or the second moiety may each be independently selected from biotin, digoxigenin, FITC, avidin, streptavidin, antidigoxigenin and anti-FITC.
  • the nCounter® Analysis system is used to detect gene expression.
  • the basis of the nCounter® Analysis system is the unique code assigned to each nucleic acid target to be assayed (see, e.g., W02008/0124847, U.S. Pat. No. 8,415,102 and Geiss et al. Nature Biotechnology 2008 26(3): 317-325, the contents of which are each incorporated herein by reference in their entireties).
  • the code is composed of an ordered series of colored fluorescent spots which create a unique barcode for each target to be assayed.
  • a pair of nucleic acid probes is designed for each DNA or RNA target described herein, a capture probe and a reporter probe carrying the fluorescent barcode.
  • This system is also referred to herein as the nanoreporter code system. See also WO2016/085841, WO2016/081740, WO2016/022559, and U.S. Pub. Nos.
  • Detection of nucleic acids may involve the use of a hybridization reaction, such as between a target nucleic acid and an oligonucleotide probe or primer (e.g ., a nucleic acid hybridization assay).
  • the oligonucleotide probe is immobilized on a substrate.
  • Substrates include, but are not limited to, arrays, microarrays, wells of a multi-well plate, and beads (e.g. non magnetic, magnetic, paramagnetic, hydrophobic, and hydrophilic beads). Examples of materials useful as substrates include but are not limited to nitrocellulose, glass, silicon, and a variety of gene arrays.
  • a preferred hybridization assay is conducted on high-density gene chips as described in U.S. Pat. No. 5,445,934.
  • the expression level of a gene may be determined through exposure of a nucleic acid sample to the probe-modified chip. Extracted nucleic acid is labeled, for example, with a
  • Hybridization of the labeled sample is performed at an appropriate stringency level.
  • the degree of probe-nucleic acid hybridization may be quantitatively measured using a detection device. See U.S. Pat. Nos. 5,578,832 and 5,631,734.
  • any one of gene copy number, transcription, or translation can be determined using known techniques.
  • an amplification method such as PCR may be useful.
  • PCR conditions used for each application reaction are empirically determined. A number of parameters influence the success of a reaction. Among them are annealing temperature and time, extension time, Mg 2+ and/or ATP concentration, pH, and the relative concentration of primers, templates, and deoxyribonucleotides. After amplification, the resulting DNA fragments can be detected by agarose gel electrophoresis followed by visualization with ethidium bromide staining and ultraviolet illumination.
  • the hybridized nucleic acids may be detected by detecting one or more labels attached to the sample nucleic acids.
  • the labels can be incorporated by any of a number of means well known to those of skill in the art. However, in one embodiment, the label is simultaneously incorporated during the amplification step in the preparation of the sample nucleic acid.
  • PCR polymerase chain reaction
  • labeled primers or labeled nucleotides will provide a labeled amplification product.
  • transcription amplification as described above, using a labeled nucleotide (e.g. fluorescein-labeled UTP and/or CTP) incorporates a label in to the transcribed nucleic acids.
  • a labeled nucleotide e.g. fluorescein-labeled UTP and/or CTP
  • a label may be added directly to the original nucleic acid sample (e.g, mRNA, polyA, cDNA, etc.) or to the amplification product after the amplification is completed.
  • Means of attaching labels to nucleic acids are well known to those of skill in the art and include, for example nick translation or end-labeling (e.g. with a labeled RNA) by kinasing of the nucleic acid and subsequent attachment (ligation) of a nucleic acid linker joining the sample nucleic acid to a label (e.g, a fluorophore).
  • Suitable detectable labels may include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means.
  • Useful labels include, for example, biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g, DynabeadsTM), fluorescent dyes (e.g, fluorescein, Texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g, 3H, 1251, 35S, 14C, or 32P) enzymes (e.g, horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and calorimetric labels such as colloidal gold or colored glass or plastic (e.g, polystyrene, polypropylene, latex, etc.) beads.
  • Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241.
  • Radiolabels may be detected using photographic film or scintillation counters.
  • Fluorescent markers may be detected using a photodetector to detect emitted light.
  • Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate.
  • Calorimetric labels may be detected by simply visualizing the colored label.
  • a biomarker e.g, CCND1
  • CCND1 may be detected in a biological sample using a microarray. Differential gene expression can also be identified, or confirmed using the microarray technique. Thus, the expression profile can be measured in either fresh or fixed tissue, using microarray technology.
  • polynucleotide sequences of interest including cDNAs and
  • oligonucleotides are plated, or arrayed, on a microchip substrate.
  • the arrayed sequences are then hybridized with specific DNA probes from cells or tissues of interest.
  • the source of mRNA typically is total RNA isolated from a biological sample, and corresponding normal tissues or cell lines may be used to determine differential expression.
  • PCR amplified inserts of cDNA clones are applied to a substrate in a dense array.
  • Preferably at least 10,000 nucleotide sequences are applied to the substrate.
  • the microarrayed genes, immobilized on the microchip at 10,000 elements each, are suitable for hybridization under stringent conditions.
  • Fluorescently labeled cDNA probes may be generated through incorporation of fluorescent nucleotides by reverse transcription of RNA extracted from tissues of interest. Labeled cDNA probes applied to the chip hybridize with specificity to each spot of DNA on the array.
  • the microarray chip is scanned by a device, such as confocal laser microscopy, or by another detection method, such as a CCD camera. Quantitation of hybridization of each arrayed element allows for assessment of corresponding mRNA abundance. With dual color fluorescence, separately labeled cDNA probes generated from two sources of RNA are hybridized pair-wise to the array. The relative abundance of the transcripts from the two sources corresponding to each specified gene is thus determined simultaneously. Microarray analysis can be performed by commercially available equipment, following manufacturer’s protocols.
  • the biomarker may be detected in a biological sample using qRT-PCR, which can be used to compare mRNA levels in different sample populations, in normal and tumor tissues, with or without drug treatment, to characterize patterns of gene expression, to discriminate between closely related mRNAs, and to analyze RNA structure.
  • the first step in gene expression profiling by RT- PCR is extracting RNA from a biological sample followed by the reverse transcription of the RNA template into cDNA and amplification by a PCR reaction.
  • the reverse transcription reaction step is generally primed using specific primers, random hexamers, or oligo-dT primers, depending on the goal of expression profiling.
  • the two commonly used reverse transcriptases are avilo
  • AMV-RT myeloblastosis virus reverse transcriptase
  • MMV-RT Moloney murine leukemia virus reverse transcriptase
  • Taq DNA polymerase typically employs the Taq DNA polymerase, which has a 5’-3’ nuclease activity but lacks a 3’-5’ proofreading endonuclease activity.
  • TaqManTM PCR typically utilizes the 5’- nuclease activity of Taq or Tth polymerase to hydrolyze a hybridization probe bound to its target amplicon, but any enzyme with equivalent 5’ nuclease activity can be used.
  • Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction.
  • a third oligonucleotide, or probe is designed to detect the nucleotide sequence located between the two PCR primers.
  • the probe is non-extendible by Taq DNA polymerase enzyme, and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe.
  • the Taq DNA polymerase enzyme cleaves the probe in a template- dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore.
  • One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.
  • Differential expression of a biomarker can also be determined by examining protein expression or the protein product of the biomarker, for example, using a suitable protein assay. Determining the protein level involves measuring the amount of any immunospecific binding that occurs between an antibody that selectively recognizes and binds to the polypeptide of the biomarker in a test sample and comparing this to the amount of immunospecific binding of at least one biomarker in a reference sample. The amount of protein expression of the biomarker may be increased or reduced when compared with a reference expression level.
  • a variety of techniques are available in the art for protein analysis. They include but are not limited to radioimmunoassays, ELISA (enzyme linked immunosorbent assays),“sandwich” immunoassays, immunoradiometric assays, in situ immunoassays (using e.g., colloidal gold, enzyme or radioisotope labels), western blot analysis, immunoprecipitation assays,
  • the present disclosure provides methods for detecting biomarkers, such as CCND1, in a biological sample.
  • Useful analyte capture agents that can be used with the present disclosure include but are not limited to antibodies, such as crude serum containing antibodies, purified antibodies, monoclonal antibodies, polyclonal antibodies, synthetic antibodies, antibody fragments (for example, Fab fragments); antibody interacting agents, such as protein A, carbohydrate binding proteins, and other interactants; protein interactants (for example avidin and its derivatives);
  • Antibodies may be modified or chemically treated to optimize binding to targets or solid surfaces (e.g. biochips and columns).
  • the biomarker can be detected in a biological sample using an immunoassay.
  • Immunoassays are assays that use an antibody that specifically binds to or recognizes an antigen (e.g. site on a protein or peptide, biomarker target).
  • the method includes the steps of contacting the biological sample with the antibody and allowing the antibody to form a complex with the antigen in the sample, washing the sample and detecting the antibody-antigen complex with a detection reagent.
  • antibodies that recognize the biomarkers may be commercially available.
  • an antibody that recognizes the biomarkers may be generated by known methods of antibody production.
  • the biomarker in the sample can be detected using an indirect assay, wherein, for example, a second, labeled antibody is used to detect bound biomarker-specific antibody.
  • exemplary detectable labels include magnetic beads (e.g ., DYNABEADSTM), fluorescent dyes, radiolabels, enzymes (e.g., horse radish peroxide, alkaline phosphatase and others commonly used), and calorimetric labels such as colloidal gold or colored glass or plastic beads.
  • the biomarker in the sample can be detected using and/or in a competition or inhibition assay wherein, for example, a monoclonal antibody which binds to a distinct epitope of the marker is incubated simultaneously with the mixture.
  • the conditions to detect an antigen using an immunoassay will be dependent on the particular antibody used. Also, the incubation time will depend upon the assay format, biomarker, volume of solution, concentrations and the like. In general, the immunoassays will be carried out at room temperature, although they can be conducted over a range of temperatures, such as 10 to 40 °C, depending on the antibody used.
  • ETseful assays can include, for example, an enzyme immune assay (EIA) such as enzyme-linked immunosorbent assay (ELISA).
  • EIA enzyme immune assay
  • ELISA enzyme-linked immunosorbent assay
  • an antibody can be bound to a solid surface and the antigen added.
  • a second antibody that recognizes a distinct epitope on the antigen can then be added and detected. This is frequently called a‘sandwich assay’ and can frequently be used to avoid problems of high background or non-specific reactions.
  • Proximity ligation assay is another type of immunoassay known in the art useful for the detection of the biomarkers of the present disclosure.
  • the term“proximity ligation assay” or “PLA” as used herein refers to an immunoassay utilizing so-called PLA probes - affinity reagents such as antibodies modified with DNA oligonucleotides - for detecting and reporting the presence of proteins either in solution or in situ. When two PLA probes bind the same or two interacting target molecules, the attached oligonucleotides are brought in close proximity.
  • a proximity ligation assay may be tailored to detect the biomarkers disclosed herein.
  • Immunoassays can be used to determine presence or absence of a biomarker in a sample as well as the quantity of a biomarker in a sample.
  • Methods for measuring the amount of, or presence of, an antibody-biomarker complex include but are not limited to, fluorescence, luminescence, chemiluminescence, absorbance, reflectance, transmittance, birefringence or refractive index (e.g, surface plasmon resonance, ellipsometry, a resonant mirror method, a grating coupler waveguide method or interferometry). In general these regents are used with optical detection methods, such as various forms of microscopy, imaging methods and non-imaging methods. Electrochemical methods include voltametry and amperometry methods. Radio frequency methods include multipolar resonance spectroscopy.
  • Biochips can be designed with immobilized nucleic acid molecules, full-length proteins, antibodies, affibodies (small molecules engineered to mimic monoclonal antibodies), aptamers (nucleic acid-based ligands) or chemical compounds.
  • a chip could be designed to detect multiple macromolecule types on one chip.
  • a chip could be designed to detect nucleic acid molecules, proteins and metabolites on one chip.
  • the biochip is used to and designed to
  • biochip allows for the multiple analyses to be performed reducing the overall processing time and the amount of sample required.
  • Protein microarrays are a particular type of biochip which can be used with the present disclosure.
  • the chip consists of a support surface such as a glass slide, nitrocellulose membrane, bead, or microtitre plate, to which an array of capture proteins are bound in an arrayed format onto a solid surface.
  • Protein array detection methods must give a high signal and a low background. Detection probe molecules, typically labeled with a fluorescent dye, are added to the array. Any reaction between the probe and the immobilized protein emits a fluorescent signal that is read by a laser scanner.
  • Such protein microarrays are rapid, automated, and offer high sensitivity of protein biomarker read-outs for diagnostic tests. However, it would be immediately appreciated to those skilled in the art that there are a variety of detection methods that can be used with this technology.
  • Mass spectrometry is an analytical technique that measures the mass-to-charge ratio of charged particles. It is primarily used for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and other chemical compounds. MS works by ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratios.
  • MS instruments typically consist of three modules (1) an ion source, which can convert gas phase sample molecules into ions (or, in the case of electrospray ionization, move ions that exist in solution into the gas phase) (2) a mass analyzer, which sorts the ions by their masses by applying electromagnetic fields and (3) a detector, which measures the value of an indicator quantity and thus provides data for calculating the abundances of each ion present.
  • an ion source which can convert gas phase sample molecules into ions (or, in the case of electrospray ionization, move ions that exist in solution into the gas phase)
  • a mass analyzer which sorts the ions by their masses by applying electromagnetic fields
  • a detector which measures the value of an indicator quantity and thus provides data for calculating the abundances of each ion present.
  • Suitable mass spectrometry methods to be used with the present disclosure include but are not limited to, one or more of electrospray ionization mass spectrometry (ESI-MS), ESI-MS/MS, ESI-MS/(MS) n , matrix-assisted laser desorption ionization time-of-flight mass spectrometry
  • ESI-MS electrospray ionization mass spectrometry
  • MS/(MS) n matrix-assisted laser desorption ionization time-of-flight mass spectrometry
  • MALDI-TOF-MS surface-enhanced laser desorption/ionization time-of-flight mass spectrometry
  • SELDI-TOF-MS surface-enhanced laser desorption/ionization time-of-flight mass spectrometry
  • LC -MS/MS tandem liquid chromatography-mass spectrometry
  • DIOS desorption/ionization on silicon
  • SIMS secondary ion mass spectrometry
  • Q-TOF quadrupole time-of-flight
  • APCI-MS atmospheric pressure chemical ionization mass spectrometry
  • APCI-MS atmospheric pressure chemical ionization mass spectrometry
  • APCI-MS atmospheric pressure chemical ionization mass spectrometry
  • APCI-MS atmospheric pressure chemical ionization mass spectrometry
  • APPI-MS atmospheric pressure photoionization mass spectrometry
  • APPI-MS APPI-MS/MS
  • APPI-(MS) n quadrupole mass
  • LC-MS is commonly used to resolve the components of a complex mixture.
  • LC-MS methods generally involves protease digestion and denaturation (usually involving a protease, such as trypsin, a denaturant (e.g ., urea) to denature tertiary structure, and iodoacetamide to cap cysteine residues) followed by LC-MS with peptide mass fingerprinting or LC-MS/MS (tandem MS) to derive sequence of individual peptides.
  • LC-MS/MS is most commonly used for proteomic analysis of complex samples where peptide masses may overlap even with a high-resolution mass spectrometer. Samples of complex biological fluids like human serum may be first separated on an SDS-PAGE gel or HPLC-SCX and then run in LC-MS/MS allowing for the identification of over 1000 proteins.
  • HPLC and UHPLC can be coupled to a mass spectrometer.
  • a number of other peptide and protein separation techniques can be performed prior to mass spectrometric analysis.
  • Some exemplary separation techniques which can be used for separation of the desired analyte (e.g., peptide or protein) from the matrix background include but are not limited to Reverse Phase Liquid Chromatography (RP-LC) of proteins or peptides, offline Liquid Chromatography (LC), 1 -dimensional gel separation, 2-dimensional gel separation, Strong Cation Exchange (SCX) chromatography, Strong Anion Exchange (SAX) chromatography, Weak Cation Exchange (WCX), and Weak Anion Exchange (WAX).
  • RP-LC Reverse Phase Liquid Chromatography
  • SCX Strong Cation Exchange
  • SAX Strong Anion Exchange
  • WCX Weak Cation Exchange
  • WAX Weak Anion Exchange
  • the methods of the present disclosure are based, in part, on the discovery that the mutation status of Ras is associated with clinical benefits of MAPK pathway inhibition.
  • the KRAS mutation status of a cancer in a subject can be used to predict the responsiveness of the subject to treatment with a MAPK pathway inhibitor.
  • provided herein are methods for assessing a likelihood of a subject having cancer exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, methods of treating cancer in a subject with a MAPK pathway inhibitor, methods of categorizing the sensitivity of a cancer to treatment with a MAPK pathway inhibitor, and methods of downregulating MAPK signaling output in cancer cells with an effective dose of a MAPK pathway inhibitor, based on the mutation status of Ras in the cancer.
  • a method of treating a cancer in a subject based on the mutation status of KRAS provides a method of treating a cancer in a subject in need thereof, wherein said cancer exhibits a KRAS mutation and wherein said cancer overexpresses CCND1.
  • the method comprises administering to the subject an effective dose of a mitogen-activated protein kinase (MAPK) pathway inhibitor.
  • MAPK mitogen-activated protein kinase
  • the method comprises (a) assessing the cancer for overexpression of CCND1; (b) evaluating the cancer for the presence of a KRAS mutation; wherein steps (a) and (b) may be performed in either order; and (c) administering the MAPK pathway inhibitor to the subject if both the CCND1 overexpression and the KRAS mutation are determined to be present.
  • the sample is determined to have a KRAS other than wild type KRAS.
  • the KRAS mutation may include a mutation at a codon selected from G12, G13, and Q61.
  • the KRAS mutation includes a mutation selected from G12C, G12D, G12A, G12V, G12S, G12F, G12R, G12N, G13C, G13D, G13R, G13S, G13N, Q61K, Q61H, Q61L,
  • the sample is determined to have at least one amino acid substitution at G12, G13, and Q61 of KRAS. In some embodiments, the sample is determined not to have wild type KRAS.
  • a method described herein comprises determining the presence or absence of a KRAS mutation in a sample from the subject prior to beginning treatment. Tumors or cancers that exhibit a KRAS mutation are more likely to be responsive to treatment with a MAPK pathway inhibitor.
  • patients are selected for MAPK pathway inhibitor treatment based on the presence of a KRAS mutation.
  • patients are further selected based on the overexpression of CCND1 by the cancer or tumor.
  • the mutation status of KRAS can be detected at the nucleic acid or protein level.
  • the KRAS mutation status is determined by analyzing nucleic acids obtained from the sample.
  • the KRAS mutation status is determined by analyzing protein obtained from the sample.
  • Techniques useful in the methods provided herein include in situ hybridization (Stoler, Clin. Lab. Med. 12:215-36 (1990)), using radioisotope or fluorophore-labeled probes; polymerase chain reaction (PCR); and quantitative Southern blotting, dot blotting and other techniques for
  • probes or primers selected for gene amplification evaluation are highly specific to avoid detecting closely related homologous genes.
  • antibodies can be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn can be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon formation of the duplex on the surface, the presence of antibody bound to the duplex can be detected.
  • the KRAS mutation status is determined by analyzing nucleic acids obtained from the sample.
  • the nucleic acids may be mRNA or genomic DNA molecules from the subject.
  • Methods for determining KRAS mutation status by analyzing nucleic acids include sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography (DHPLC), and restriction fragment length polymorphism (RFLP) assay.
  • the KRAS mutation status is determined using standard sequencing methods, including, for example, Sanger sequencing or next generation sequencing (NGS).
  • the KRAS mutation status is determined using MS.
  • a method of the present disclosure includes determining the presence or absence of a KRAS mutation by amplifying KRAS nucleic acid from a sample by PCR.
  • PCR technology and primer pairs that can be used are known to the person skilled in the art (e.g., Chang et al., Clinical Biochemistry, 43 (2010), 296-301; WO2015144184).
  • a multiplex PCR can be used to amplify codons 12 and 13 of exon 2 and codon 61 of exon 3 of a KRAS gene with two pairs of universal primers for exons 2 and 3.
  • the products can be purified to remove the primers and unincorporated deoxynucleotide triphosphates using PCR-MTM Clean Up System
  • Various concentrations of probe for either codon 12, 13, or 61 can be employed (e.g. 0.03- 0.6 mM) in reactions containing 1.5 pL of purified PCR products and 4 pL of ABI PRISM
  • ddNTPs dideoxynucleotide triphosphates
  • RMG-labeled dideoxyadenosine triphosphate dideoxyadenosine triphosphate
  • TAMRA-labeled dideoxycytidine triphosphate dideoxycytidine triphosphate
  • ROX-labeled dideoxythymidine triphosphate dideoxythymidine triphosphate
  • Rl lO-labeled dideoxyguanosine triphosphate dideoxyguanosine triphosphate.
  • Each 10 pL mixture can then be subjected to 25 single-base extension cycles consisting of a denaturing step at 96 °C for 10 s and primer annealing and extension at 55 °C for 35 s.
  • unincorporated fluorescent ddNTPs can then be incubated with 1 pL of shrimp alkaline phosphatase (United States Biochemical Co., Cleveland, USA) at 37 °C for 1 h, followed by enzyme deactivation at 75 °C for 15 min.
  • the primer extension reaction products can then be resolved by automated capillary electrophoresis on a capillary electrophoresis platform (e.g. 14 pL of Hi-DiTMFormamide (Applied Biosystems) and 0.28 pL of GeneScanTM-l20LIZ® Size Standard (Applied Biosystems) can be added to 6 pL of primer extension products). All samples may then be analyzed, for example, on an ABI Prism 310 DNA Genetic Analyzer (Applied Biosystems) according to manufacturer's instructions using GeneScanTM 3.1 (Applied Biosystems).
  • KRAS nucleic acid can be amplified using primers as described above and sequenced. For example,
  • KRAS nucleic acid can be amplified by PCR as described above and subsequently subcloned using, for example, the TOPO TA Cloning Kit for sequencing (Invitrogen).
  • KRAS nucleic acid may be obtained from a tumor sample by any method known to a person skilled in the art.
  • a commercial kit may be used to isolate the genomic DNA or mRNA from a tumor sample, such as the Qlamp DNA mini kit, or RNeasy mini kit (Qiagen, Hilden, Germany).
  • a nucleic acid isolated from a biological sample may be selected from genomic DNA, total RNA, mRNA or poly(A)+mRNA.
  • the mRNA may be used for cDNA synthesis according to technologies known in the art, such as those provided in commercial cDNA synthesis kits (e.g. Superscript® III First Strand Synthesis Kit).
  • the cDNA can then be further amplified by suitable means, such as PCR, and subsequently subjected to sequencing, such as Sanger sequencing or pyro-sequencing, to determine the nucleotide sequence, preferably of codons 12 and/or 13 of the KRAS gene.
  • suitable means such as PCR
  • sequencing such as Sanger sequencing or pyro-sequencing
  • the PCR product can be subcloned into a TA TOPO cloning vector for sequencing.
  • the presence or absence of a KRAS mutation may also be determined by other methods, including single nucleotide primer extension (SNPE) (PLoS One, 2013, 8(8):e72239); DNA microarray, mass spectrometry (MS) (e.g.
  • SNPE single nucleotide primer extension
  • MS mass spectrometry
  • MALDI-TOF matrix-assisted laser desorption/ionization time-of- flight
  • SNP single nucleotide polymorphism
  • DPLC denaturing high-performance liquid chromatography
  • RFLP restriction fragment length polymorphism
  • single nucleotide polymorphism (SNP) assay is used to determine the KRAS mutation status in a sample.
  • SNP assay can be performed on an HT7900 from Applied Biosystems, following the allelic discrimination assay protocol provided by the SNP assay.
  • the KRAS mutation status can also be determined by DHPLC or RFLP. [0128] In some embodiments, the KRAS mutation status is determined by analyzing protein obtained from a biological sample.
  • the mutated KRAS protein can be detected by a variety of immunohistochemistry (IHC) approaches or other immunoassay methods known in the art. IHC staining of tissue sections has been shown to be a reliable method of assessing or detecting presence of proteins in a sample. Immunohistochemistry techniques utilize an antibody to probe and visualize cellular antigens in situ, generally by chromogenic or fluorescent methods. Thus, antibodies or antisera, preferably polyclonal antisera, and most preferably monoclonal antibodies that specifically target mutant KRAS, can be used to detect expression.
  • the antibodies can be detected by direct labeling of the antibodies themselves, for example, with radioactive labels, fluorescent labels, hapten labels such as, biotin, or an enzyme such as horse radish peroxidase or alkaline phosphatase.
  • unlabeled primary antibody may be used in conjunction with a labeled secondary antibody, comprising antisera, polyclonal antisera or a monoclonal antibody specific for the primary antibody.
  • a labeled secondary antibody comprising antisera, polyclonal antisera or a monoclonal antibody specific for the primary antibody.
  • Commercially available immunohistochemistry kits may be utilized.
  • Automated systems for slide preparation and IHC processing may be commercially available (e.g., The Ventana® BenchMark XT system).
  • Assays to detect KRAS mutations include noncompetitive assays, such as sandwich assays, and competitive assays.
  • an assay such as an ELISA assay can be used.
  • ELISA assays may be used to assay a wide variety of tissues and samples, including blood, plasma, serum or bone marrow.
  • a second antibody specific to the antigen labeled with a reporter molecule capable of producing a detectable signal, is then added and incubated, allowing time sufficient for the formation of another complex of antibody-antigen-labeled antibody. Any unreacted material is washed away, and the presence of the antigen is determined by observation of a signal produced by the reporter molecule. The results may either be qualitative, by simple observation of the visible signal, or may be quantitated by comparing with a control sample.
  • Variations on the forward assay include a simultaneous assay, in which both sample and labeled antibody are added simultaneously to the bound antibody.
  • a first antibody having specificity for the mutant KRAS protein is either covalently or passively bound to a solid surface.
  • the solid surface may be glass or a polymer, the most commonly used polymers being cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride, or polypropylene.
  • the solid supports may be in the form of tubes, beads, discs of microplates, or any other surface suitable for conducting an immunoassay.
  • An aliquot of a sample to be tested may be added to the solid phase complex and incubated for a sufficient time and under suitable conditions to allow binding of a subunit present in the antibody. Following the incubation period, the antibody subunit solid phase is washed, dried and incubated with a second antibody specific for a portion of the mutant KRAS protein. The second antibody is linked to a reporter molecule which is used to indicate the binding of the second antibody to the mutant KRAS protein.
  • flow cytometry can be used to detect a mutant KRAS using antibodies to target the mutant KRAS.
  • the flow cytometer detects and reports the intensity of the fluorochrome-tagged antibody, which indicates the presence of the mutant KRAS.
  • Non-fluorescent cytoplasmic proteins can also be observed by staining permeabilized cells.
  • the stain can either be a fluorescent compound able to bind to certain molecules, or a fluorochrome-tagged antibody to bind the molecule of choice.
  • a mutant KRAS in a biological sample may be immobilized and exposed to a mutant specific antibody which may or may not be labeled with a reporter molecule.
  • a bound mutant KRAS can be detectable by direct labeling with the antibody.
  • a second labeled antibody, specific to the first antibody is exposed to the KRAS-first antibody complex to form a KRAS-first antibody-second antibody tertiary complex. The complex is detected by the signal emitted by a labeled reporter molecule.
  • an enzyme is conjugated to the second antibody, generally by means of glutaraldehyde or periodate.
  • glutaraldehyde or periodate As will be readily recognized, however, a wide variety of different conjugation techniques exist, which are readily available to the skilled artisan. Commonly used enzymes include horseradish peroxidase, glucose oxidase, beta-galactosidase, and alkaline phosphatase, and other are discussed herein.
  • the substrates to be used with the specific enzymes are generally chosen for the production, upon hydrolysis by the corresponding enzyme, of a detectable color change. Examples of suitable enzymes include alkaline phosphatase and peroxidase.
  • fluorogenic substrates which yield a fluorescent product rather than the chromogenic substrates noted above.
  • the enzyme-labeled antibody is added to the first antibody-molecular marker complex, allowed to bind, and then the excess reagent is washed away. A solution containing the appropriate substrate is then added to the complex of antibody-antigen-antibody. The substrate will react with the enzyme linked to the second antibody, giving a qualitative visual signal, which may be further quantitated, usually spectrophotometrically, to give an indication of the amount of mutant KRAS protein present in the sample.
  • fluorescent compounds such as fluorescein and rhodamine, can be chemically coupled to antibodies without altering their binding capacity.
  • the fluorochrom e-lab el ed antibody When activated by illumination with light of a particular wavelength, the fluorochrom e-lab el ed antibody adsorbs the light energy, inducing a state to excitability in the molecule, followed by emission of the light at a characteristic color visually detectable with a light microscope. As in the EIA, the fluorescently labeled antibody is allowed to bind to the first antibody-molecular marker complex. After washing off the unbound reagent, the remaining tertiary complex is then exposed to the light of the appropriate wavelength, wherein the fluorescence observed indicates the presence of the molecular marker of interest.
  • one or more steps in the assessment and/or reporting of a likelihood of response to treatment with a MAPK pathway inhibitor is performed with the aid of a processor, such as with a computer system executing instructions contained in computer-readable media.
  • the disclosure provides a system for of assessing a likelihood of a subject having cancer, such as adenocarcinoma, exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor.
  • the system comprises (a) a memory unit configured to store information concerning: (i) a total expression level of CCND1 and (ii) the KRAS mutation status in a biological sample comprising genomic, transcriptomic and/or proteomic material from an adenocarcinoma cell.
  • the system further comprises (b) one or more processors alone or in combination programmed to: (1) determine a weighted probability of MAPK pathway inhibitor responsiveness based on the total expression level and the KRAS mutation status; and (2) designate the subject as having a high probability of exhibiting a clinically beneficial response to treatment with the MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability of (b)(1).
  • the methods provided herein can further include determining a reference expression level of each individual biomarker, such as CCND1.
  • the reference expression level of a biomarker is the expression level of the biomarker in a sample from a healthy individual, or the average or median expression level of the biomarker in multiple samples from one or multiple healthy individuals.
  • the reference expression level of a biomarker is the average expression level of the biomarker in samples from 2, 3, 5, 10, 15, 20, 30, 40, 50 or more healthy individuals.
  • the reference expression level of a biomarker is the median expression level of the biomarker in samples from 2, 3, 5, 10, 15, 20, 30, 40, 50 or more healthy individuals.
  • the reference expression level of CCND1 is the expression level of CCND1 in a sample from a healthy individual, or the average or median expression level of CCND1 in multiple samples from one or multiple healthy individuals.
  • the reference expression level of a biomarker can be determined based on statistical analysis of data from previous clinical trials, including outcome of a group of patients, namely, the patients' responsiveness to treatment with a MAPK pathway inhibitor, as well as the expression levels of the biomarker of the group of patients.
  • a number of statistical methods are well known in the art to determine the reference level (also referred to as the “cut-off value”) of one or more biomarkers when used to predict the responsiveness of a patient to a particular treatment, or to stratify patients for a particular treatment.
  • One method includes analyzing gene expression profiles for biomarkers identified herein that distinguish responder from non-responder to determine the reference expression level for one or more biomarkers. Comparisons between responders and non-responders can be performed using the Mann-Whitney U-test, Chi-square test, or Fisher's Exact test. Analysis of descriptive statistics and comparisons can be performed using SigmaStat Software (Systat Software, Inc., San Jose, Calif., USA).
  • a classification and regression tree (CART) analysis can be adopted to determine the reference level.
  • CART analysis is based on a binary recursive partitioning algorithm and allows for the discovery of complex predictor variable interactions that may not be apparent with more traditional methods, such as multiple linear regression.
  • Binary recursive partitioning refers to the analysis that is: 1) binary, meaning there were two possible outcome variables, namely“responder” and“non-responder”, with the effect of splitting patients into 2 groups; 2) recursive, meaning the analysis can be performed multiple times; and 3) partitioned, meaning the entire data set can be split into sections.
  • This analysis also has the ability to eliminate predictor variables with poor performance.
  • the classification tree can be built using Salford Predictive Modeler v6.6 (Salford Systems, San Diego, Calif., USA).
  • Representations of gene expression profiles useful for predicting the responsiveness of a cancer patient to treatment with a MAPK pathway inhibitor may be reduced to a medium that can be automatically read, such as computer readable media (magnetic, optical, and the like).
  • the representations may further comprise instructions for assessing the gene expression profiles in such media.
  • Gene expression profiles may be digitally recorded so that they can be compared with gene expression data from other patient samples. Clustering algorithms such as those incorporated in “OMNIVIZ” and“TREE VIEW” computer programs can assist in the visualization of such data.
  • Receiver Operator Characteristic (ROC) analysis can be utilized to determine the reference expression level or test the overall predictive value of individual genes.
  • ROC Receiver Operator Characteristic
  • the reference level can be determined from the ROC curve of the training set to ensure both high sensitivity and high specificity.
  • the leave-one-out cross validation (LOOCV) test can be used to confirm that sufficient biomarkers are included in the predictor.
  • the response scores for the T eft- out’ samples based on different numbers of genes are recorded.
  • the performances of the predictors with different numbers of genes can be assessed based on misclassification error rate, sensitivity, specificity, and p values measuring the separation of Kaplan-Meier curves of the two predicted groups.
  • the Top Scoring Pair (TSP) algorithm first introduced by Geman et al. (2004) can be used. In essence, the algorithm ranks all the gene pairs (genes i and j) based on the absolute difference (Dij) in the frequency of event where gene i has higher expression value than gene j in samples among class Cl to C2. In cases where there are multiple top scoring pairs (all sharing the same Dij), the top pair by a secondary rank score that measures the magnitude to which inversions of gene expression levels occur from one class to the other within a pair of genes is selected. The top pair with highest frequency of absolute Dij>2 fold in all samples will be selected as a candidate pair. The candidate pair can then be assessed in an independent testing data set.
  • TSP Top Scoring Pair
  • Leave-one-out cross validation can be carried out in the training data set to evaluate how the algorithm performs.
  • the performances of the predictors can be assessed based on maximum misclassification error rate. All the statistical analyses can be done using R (R Development Core Team, 2006).
  • Clinically reportable range is the range of analyte values that a method can measure, allowing for specimen dilution, concentration, or other pretreatment used to extend the direct analytical measurement range.
  • the experiment to be performed is often called a“linearity experiment”, though there technically is no requirement that a method provide a linear response unless two-point calibration is being used.
  • This range can also be referred as the“linear range”,“analytical range” or“working range” for a method.
  • the reportable range is assessed by inspection of the linearity graph.
  • That inspection can involve manually drawing the best straight line through the linear portion of the points, drawing a point-to-point line through all the points then comparing with the best straight line, or fitting a regression line through the points in the linear range.
  • CLSI Clinical Laboratory Standards Institute
  • EP-6 protocol for evaluating the linearity of analytical methods.
  • CLSI Clinical Laboratory Standards Institute
  • the Clinical Laboratory Standards Institute (CLSI) recommends a minimum of at least 4, preferably 5, different levels of concentrations. More than 5 can be used, particularly if the upper limit of reportable range needs to be maximized, but 5 levels are convenient and typically sufficient.
  • a reference interval is typically established by assaying specimens that are obtained from individuals that meet carefully defined criteria (reference sample group). Protocols such as those of the International Federation of Clinical Chemistry (IFCC) Expert Panel on Theory of Reference Values and the CLSI delineate comprehensive systematic processes that use carefully selected reference sample groups to establish reference intervals. These protocols typically use a minimum of 120 reference individuals for each group (or subgroup) that needs to be characterized.
  • IFCC International Federation of Clinical Chemistry
  • CLSI delineate comprehensive systematic processes that use carefully selected reference sample groups to establish reference intervals.
  • the CLSI Approved Guideline C28-A2 describes different ways for a laboratory to validate the transfer of established reference intervals to an individual laboratory, including (1) divine judgment, wherein the laboratory simply reviews the information submitted and subjectively verifies that the reference intervals are applicable to the adopting laboratory's patient population and test methods; (2) verification with 20 samples, wherein experimental validation is performed by collecting and analyzing specimens from 20 individuals who represent the reference sample population; (3) estimation with 60 samples, wherein an experimental validation is performed by collecting and analyzing specimens from 60 individuals who represent the reference sample population, and the actual reference interval is estimated and compared to the claimed or reported interval using a statistical formula comparing the means and standard deviations of the two populations; and (4) calculation from a comparative method, wherein one can adjust or correct the claimed or reported reference intervals on the basis of the observed methodological bias and the mathematical relationship demonstrated between the analytical methods being used.
  • the present disclosure provides a method of (a) determining a reference expression level of CCND1, and (b) administering a therapeutically effective amount of a MAPK pathway inhibitor to a subject having cancer, wherein said cancer exhibits a KRAS mutation and wherein the expression level of CCND1 in the cancer is higher than the reference expression level.
  • the present disclosure provides a method of (a) determining a reference mRNA level of CCND1, and (b) administering a therapeutically effective amount of a MAPK pathway inhibitor to a subject having cancer, wherein said cancer exhibits a KRAS mutation and wherein the mRNA level of CCND1 in the cancer is higher than the reference mRNA level.
  • the present disclosure provides a method of (a) determining a reference protein level of CCND1, and (b) administering a therapeutically effective amount of a MAPK pathway inhibitor to a subject having cancer, wherein said cancer exhibits a KRAS mutation and wherein the protein level of CCND1 in the cancer is higher than the reference protein level.
  • a processor or computational algorithm may aid in the assessment of a likelihood of a subject having cancer, such as adenocarcinoma, exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor.
  • a processor or computational algorithm may aid in the assessment of a likelihood of a subject having cancer, such as adenocarcinoma, exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor.
  • one or more steps of methods or systems described herein may be implemented in hardware.
  • one or more steps may be implemented in software stored in, for example, one or more memories or other computer readable medium and implemented on one or more processors.
  • the processors may be associated with one or more controllers, calculation units, and/or other units of a computer system, or implanted in firmware as desired.
  • routines may be stored in any computer readable memory such as in RAM, ROM, flash memory, a magnetic disk, a laser disk, a remote server (e.g . the cloud), or other storage medium, as is also known.
  • this software may be delivered to a computing device via any known delivery method including, for example, over a communication channel such as a telephone line, the internet, a wireless connection, etc., or via a transportable medium, such as a computer readable disk, flash drive, etc.
  • the various steps may be implemented as various blocks, operations, tools, modules and techniques which, in turn, may be implemented in hardware, firmware, software, or any combination of hardware, firmware, and/or software.
  • IC integrated circuit
  • ASIC application specific integrated circuit
  • FPGA field programmable logic array
  • PPA programmable logic array
  • a computer system may be involved in one or more of sample collection, sample processing, data analysis, expression profile assessment, calculation of weighted probabilities, calculation of baseline probabilities, comparison of a weighted probability to a reference level and/or control sample, determination of a subject’s absolute or increased probability, generating a report, and reporting results to a receiver.
  • a client-server, relational database architecture can be used in embodiments of the disclosure.
  • a client-server architecture is a network architecture in which each computer or process on the network is either a client or a server.
  • Server computers are typically powerful computers dedicated to managing disk drives (file servers), printers (print servers), or network traffic (network servers).
  • Client computers include PCs (personal computers), workstations, or mobile computing devices (e.g ., a tablets or smart phones) on which users run applications, as well as example output devices as disclosed herein.
  • Client computers may rely on server computers for resources, such as files, devices, and even processing power.
  • the server computer handles all of the database functionality.
  • the client computer can have software that handles all the front-end data management and can also receive data input from users.
  • the computer system is connected to an analysis system by a network connection.
  • the computer system may be understood as a logical apparatus that can read instructions from media and/or a network port, which can optionally be connected to server having fixed media.
  • the system can include a CPU, disk drives, optional input devices such as keyboard and/or mouse, and optional monitor.
  • Data communication can be achieved through the indicated communication medium to a server at a local or a remote location.
  • the communication medium can include any means of transmitting and/or receiving data.
  • the communication medium can be a network connection, a wireless connection, or an internet connection. Such a connection can provide for communication over the World Wide Web.
  • a physical report is generated and delivered to a receiver.
  • a computer readable medium encoded with computer executable software that includes instructions for a computer to execute functions associated with the identified biomarkers.
  • Such computer system may include any combination of such codes or computer executable software, depending upon the types of evaluations desired to be completed.
  • the system can have code for calculating a weighted probability of MAPK pathway inhibitor responsiveness, and optionally for calculating an aggregated probability based on a plurality of weighted probabilities.
  • the weighted probability of MAPK pathway inhibitor responsiveness is increased if an adenocarcinoma cell (1) overexpresses CCND1 or (2) exhibits a KRAS mutation.
  • the weighted probability of MAPK pathway inhibitor responsiveness may be decreased if an adenocarcinoma cell (1) underexpresses CCND1 or (2) does not exhibit a KRAS mutation.
  • the system can also have code for one or more of the following: conducting, analyzing, organizing, or reporting the results, as described herein.
  • the system can also have code for generating a report.
  • the test subject may be designated as having a high probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to at least about 0.55, at least about 0.6, at least about 0.65, at least about 0.7, at least about 0.75, at least about 0.8, at least about 0.85, at least about 0.9, at least about 0.95, or at least about 0.99.
  • the test subject may be designated as having a low probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to less than about 0.45, less than about 0.4, less than about 0.35, less than about 0.3, less than about 0.25, less than about 0.2, less than about 0.15, less than about 0.1, less than about 0.05, less than about 0.01.
  • the system may further comprise code for comparing a weighted probability to a baseline probability, a threshold value, and/or a reference level, and assigning a fold-baseline probability based on whether or not the baseline probability, threshold value, or reference level is exceeded. Assessing a weighted probability, threshold value, or reference level can be linked to at least one recommendation. Exceeding a weighted probability, threshold value, or reference level may be linked to a recommendation of treatment with a MAPK pathway inhibitor.
  • the baseline probability represents the average probability of a subject having cancer, such as adenocarcinoma, exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, either in general or for a specific population.
  • the baseline probability represents a pre-test likelihood that a particular subject will exhibit a clinically beneficial response to treatment with a MAPK pathway inhibitor before applying a method of the disclosure to determine a post-test risk.
  • a weighted probability above a baseline probability may correspond to a specified fold-baseline probability, whatever the pre-test baseline for the subject may be.
  • the test subject may be designated as having a high probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to about or at least about 1.1 -times, 1.2-times, 1.3-times, 1.4- times, 1.5-times, 1.8-times, 2-times, 2.5-times, 3-times, 4-times, 5-times, 6-times, 7-times, 8-times, 9-times, 10-times, 25-times, 50-times, or lOO-times the baseline probability.
  • the test subject may be designated as having a low probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to about or at less than about 0.9-times, 0.8-times, 0.7-times, 0.6-times, 0.5-times, 0.4-times, 0.3- times, 0.2-times, O. l-times, 0.05-times, 0.01 -times the baseline probability.
  • a processor can provide the output, such as from a calculation, back to, for example, the input device or storage unit, to another storage unit of the same or different computer system, or to an output device.
  • Output from the processor can be displayed by data display.
  • a data display can be a display screen (for example, a monitor or a screen on a digital device), a print-out, a data signal (for example, a packet), an alarm (for example, a flashing light or a sound), a graphical user interface (for example, a webpage), or a combination of any of the above.
  • an output is transmitted over a network (for example, a wireless network) to an output device.
  • the output device can be used by a user to receive the output from the data-processing computer system. After an output has been received by a user, the user can determine a course of action, or can carry out a course of action, such as a medical treatment when the user is medical personnel.
  • an output device is the same device as the input device.
  • Example output devices include, but are not limited to, a telephone, a wireless telephone, a mobile phone, a PDA, a tablet, a flash memory drive, a light source, a sound generator, a fax machine, a computer, a computer monitor, a printer, an iPod, and a webpage.
  • the user station may be in communication with a printer or a display monitor to output the information processed by the server.
  • a computer-readable medium includes a medium suitable for transmission of a result of an analysis of a biological sample, such as analysis of one or more biomarkers.
  • the medium can include a result regarding one or more biomarker expression level or amplification status of an individual, probability (such as fold-baseline probability) of having a cancer that is sensitive to treatment with a MAPK pathway inhibitor, and/or a treatment plan for the individual, wherein such a result is derived using the methods described herein.
  • the subject or a third party e.g. a heath care provider, health care manager, other health professional, or other caretaker
  • a third party e.g. a heath care provider, health care manager, other health professional, or other caretaker
  • the analysis generated can be reviewed and further analyzed by a medical professional such as a managing doctor or licensed physician, or other third party.
  • the medical professional or other third party can meet with the subject to discuss the results, analysis, and report.
  • Information provided can include recommendations, such as treatment (e.g, with a MAPK pathway inhibitor or an alternative therapy).
  • the method further comprises providing a recommendation for treatment based on an assessment of the likelihood that a subject having adenocarcinoma will exhibit a clinically beneficial response to treatment with a MAPK pathway inhibitor, such as designation as having high probability.
  • a recommendation may form part of a report generated based on biomarker expression and KRAS mutation status, or may be made by a receiver on the basis of such report.
  • a recommendation may be for further action on the part of the subject and/or for a third party, such as a heath care provider, health care manager, other health professional, or other caretaker.
  • Recommendations may include, but are not limited to, treatment with a MAPK pathway inhibitor; continued monitoring of the subject; screening exams or laboratory tests that may further characterize the cancer; prescription and/or administration of one or more therapeutic agents that are not MAPK pathway inhibitors; discontinued therapy; and treatment with an alternative therapy, e.g. chemotherapy, immunotherapy, radiotherapy, or surgery.
  • an alternative therapy e.g. chemotherapy, immunotherapy, radiotherapy, or surgery.
  • the disclosure provides a method of categorizing an adenocarcinoma status of a subject.
  • the status of the subject may be categorized based on an expression profile of a biological sample from the subject.
  • a cancer status may be categorized as likely sensitive to treatment with a MAPK pathway inhibitor or likely resistant to treatment with a MAPK pathway inhibitor.
  • the likely sensitive categorization may be assigned to an adenocarcinoma having (1) overexpression CCND1 and (2) a KRAS mutation.
  • A“likely resistant” categorization may be assigned to an adenocarcinoma (1) having underexpression of CCND1 and/or (2) lacking a KRAS mutation.
  • a method of the disclosure provides a reference level above which CCND1 must be expressed to be considered in assessing the likelihood of response to treatment with a MAPK pathway inhibitor.
  • CCND1 may be differentially expressed at least 1.1 fold, at least 1.2 fold, at least 1.3 fold, at least 1.4 fold, at least 1.5 fold, at least 2.0 fold, at least 2.25 fold, at least 2.5 fold, at least 2.75 fold, at least 3.0 fold, at least 3.5 fold, at least 4.0 fold, at least 5.0, or even at least 10 fold higher relative to a reference level to be considered in adjusting the likelihood of response.
  • the reference level is a numerical range of CCND1 expression that is obtained from a statistical sampling from a population of individuals having adenocarcinoma that has low sensitivity, such as resistance, to treatment with a MAPK pathway inhibitor. In some embodiments, the reference level is a numerical range of CCND1 expression that is obtained from a statistical sampling from a population of individuals having cancer that is sensitive to treatment with a MAPK pathway inhibitor. The reference level may be a numerical range of CCND1 expression that is obtained from a statistical sampling from a population of individuals having cancer, e.g. , the same cancer as the test subject. In some embodiments, the reference level is derived by comparison of sensitive and resistant populations.
  • low sensitivity to a MAPK pathway inhibitor refers to a disease condition that progresses after treatment with a MAPK pathway inhibitor.
  • low sensitivity to a MAPK pathway inhibitor is characterized by tumor growth inhibition of less than 60%, optionally less than 80% following treatment with a MAPK pathway inhibitor.
  • a disease condition that responds to treatment with a MAPK pathway inhibitor is one that exhibits a therapeutically beneficial response, such as regression or stabilization of a tumor, in response to treatment with a MAPK pathway inhibitor.
  • tumor growth inhibition of greater than 80% is indicative of a response to treatment with a MAPK pathway inhibitor.
  • RECIST Response Evaluation Criteria in Solid Tumors
  • a complete response is evidenced by disappearance of all target lesions
  • a partial response is evidenced by at least a 30% decrease in the sum of the longest diameter (LD) of target lesions, taking as reference the baseline sum LD
  • a stable disease is evidenced by neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD, taking as reference the smallest sum LD since the treatment started
  • progressive disease is evidenced by at least a 20% increase in the sum of the LD of target lesions, taking as reference the smallest sum LD recorded since the treatment started or the appearance of one or more new lesions.
  • a disease condition is classified as responsive to treatment with a MAPK pathway inhibitor if categorized in accordance with the RECIST criteria as a CR, PR or SD in response to treatment with a MAPK pathway inhibitor.
  • a disease condition that is resistant to treatment may be classified as a PD by the RECIST criteria.
  • the present disclosure provides a method of treating a cancer condition, such as adenocarcinoma, comprising administering an effective dose of a MAPK pathway inhibitor.
  • the MAPK pathway inhibitor may be effective in one or more of inhibiting proliferation of cancer cells, inhibiting invasion or metastasis of cancer cells, killing cancer cells, increasing the sensitivity of cancer cells to treatment with a second antitumor agent and reducing severity or incidence of symptoms associated with the presence of cancer cells.
  • said method comprises administering to the cancer cells a therapeutically effective amount of a MAPK pathway inhibitor.
  • the administration takes place in vitro. In other embodiments, the administration takes place in vivo.
  • a MAPK pathway inhibitor suitable for use in the subject methods can be selected from a variety of types of molecules.
  • the MAPK pathway inhibitor can be a biological or chemical compound, such as a simple or complex organic or inorganic molecule, peptide, peptido mimetic, protein (e.g., antibody), liposome, or a polynucleotide (e.g., small interfering RNA, microRNA, antisense, aptamer, ribozyme, or triple helix).
  • a biological or chemical compound such as a simple or complex organic or inorganic molecule, peptide, peptido mimetic, protein (e.g., antibody), liposome, or a polynucleotide (e.g., small interfering RNA, microRNA, antisense, aptamer, ribozyme, or triple helix).
  • a MAPK pathway inhibitor for use in the present disclosure can be any MAPK pathway inhibitor that is known in the art, and can include any chemical entity that, upon administration to a subject, results in inhibition of any portion of the MAPK pathway in the subject.
  • a MAPK pathway inhibitor for use in the treatment of adenocarcinoma is a small molecule.
  • the term “small molecule” refers to a low molecular weight organic compound, such as a compound having a molecular weight of less than 800 g/mol.
  • a MAPK pathway inhibitor may inhibit any component of the MAPK pathway.
  • the MAPK pathway inhibitor may be selected from a Ras inhibitor, a Raf inhibitor, a MEK inhibitor, and an ERK inhibitor.
  • the MAPK pathway inhibitor is a Ras inhibitor.
  • the MAPK pathway inhibitor is a Raf inhibitor.
  • the MAPK pathway inhibitor is a MEK inhibitor.
  • the MAPK pathway inhibitor is an ERK inhibitor.
  • the MAPK pathway inhibitor is selected from a MEK inhibitor and an ERK inhibitor.
  • Ras inhibitor refers to compounds capable of fully or partially reducing or inhibiting Ras signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the Ras signaling pathway, such as H-Ras, K-Ras and/or N-Ras mRNA. In some examples, said Ras inhibitor inhibits one or more of H-Ras, K-Ras or N-Ras GTPase activity. Inhibition of Ras can be achieved by a variety of mechanisms, including, but not limited to, binding directly to H-Ras, K- Ras or N-Ras, or inhibiting expression of a Ras gene.
  • Any component of the Ras pathway is a potential therapeutic target for inhibition in accordance with the present disclosure.
  • the mechanism of inhibition may be at the genetic level (e.g., interference with transcription or translation) or at the protein level (e.g., binding, competition).
  • Exemplary Ras inhibitors include, but are not limited to lonafamib, MRTX-849 and AMG510.
  • Exemplary Ras inhibitors and their syntheses have been described in WO 97/23478, WO 98/57959, and WO 97/40006, the disclosures of which are incorporated by reference herein.
  • Raf inhibitor refers to compounds capable of fully or partially reducing or inhibiting Raf signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the Raf signaling pathway, such as A-Raf, B-Raf and/or C-Raf mRNA. In some examples, said Raf inhibitor inhibits one or more of A-Raf, B-Raf or C-Raf kinase activity. Inhibition of Raf can be achieved by a variety of mechanisms, including, but not limited to, binding directly to A-Raf, B- Raf or C-Raf, or inhibiting expression of a Raf gene.
  • a Raf inhibitor is a pan-RAF in inhibitor, such as LY3009120, LXH254, CCT3833 or AZ628.
  • the pan-RAF inhibitor is selected from LY3009120 and LXH254. Exemplary pan-RAF inhibitors and their syntheses have been described in WO 2013/134243, WO 2014/151616, WO 2009/077766, and WO 2006/024834, the disclosures of which are incorporated by reference herein.
  • MEK inhibitor refers to compounds capable of fully or partially reducing or inhibiting MEK signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the MEK signaling pathway, such as MEK1, MEK2, ERK1 and/or ERK2 mRNA. In some examples, said MEK inhibitor inhibits one or more of MEK1, MEK2, ERK1 or ERK2 kinase activity.
  • Inhibition of MEK can be achieved by a variety of mechanisms, including, but not limited to, binding directly to MEK1 or MEK2, or inhibiting expression of the MEK gene.
  • any component of the MEK pathway is a potential therapeutic target for inhibition in accordance with the present disclosure.
  • the mechanism of inhibition may be at the genetic level (e.g., interference with transcription or translation) or at the protein level (e.g., binding, competition). Because of their converging function, specific inhibition of MEK1/2 or ERK1/2 is expected to effectively intercept a wide variety of upstream mitogenic signals.
  • the MEK inhibitor is a specific inhibitor that either acts on MEK1/2 at the genetic level or protein level. Either or both approaches may be used in accordance with the present disclosure.
  • an inhibitor may be utilized that interferes with expression of MEK1 and/or MEK2, or which sequesters MEK1 and/or MEK2 in the cytoplasm of the cell, preventing nuclear translocation.
  • Exemplary MEK inhibitors include, but are not limited to cobimetinib, trametinib, binimetinib, selumetinib, HL-085, antroquinonol, E-6201, refametinib, pimasertib hydrochloride, CKI-27, WX-554, CIP- 137401, SHR-7390, sorafenib, SRX-2626, PD-0325901, ATR-002, ATR- 004, ATR-005, ATR-006, CS-3006, FCN-159, EDV-2209, GDC-0623, TAK-733, E-6201, RG- 7167, AZD-8330, PD-184352, GSK-2091976A, AS-703988, BI-847325, JTP-70902, CZ-775, RO- 5068760, RDEA-436, MEK-300, AD-GL0001, SL-327,
  • the MEK inhibitor is selected from cobimetinib, trametinib, binimetinib, and selumetinib.
  • the MEK inhibitor is trametinib.
  • Exemplary MEK inhibitors and their syntheses have been described in WO 2007/044515 (cobimetinib), WO 2005/121142 (trametinib), and WO 2003/077914 (binimetinib and selumetinib), the disclosures of which are incorporated by reference herein.
  • the MEK inhibitor is a compound selected from
  • MEK inhibitors examples include, but are not limited to, MEK1/2 inhibitors, such as PD98059, PD184352, EG0126 (Dudley D. T. et al., Proc. Natl. Acad. Sci. USA, 1995, 92:7686-7689; Sepolt-Leopold J. S. et al., Nat. Med., 1999, 5:810-816; and Favata M. F. et al., J. Biol. Chem., 273: 18623-18632, respectively).
  • MEK1/2 inhibitors such as PD98059, PD184352, EG0126 (Dudley D. T. et al., Proc. Natl. Acad. Sci. USA, 1995, 92:7686-7689; Sepolt-Leopold J. S. et al., Nat. Med., 1999, 5:810-816; and Favata M. F. et al., J
  • Imidazolium trans-imidazoledimethyl sulfoxide- tetrachlororuthenate is a ruthenium-containing inhibitor of the phosphorylation of MEK (Pintus G. et al., Eur. J. Biochem., 2002, 269:5861-5870).
  • the MEK inhibitor is selected from the group consisting of trametinib, BVD-523 (ulixertinib), FR 180204, MK-8353 (SCH900353), pluripotin, SCH772984, VX-l le (ERK-l le; TCS ERK l le), SL327, hypericin, purvalanol, PD173074, GW5074, BAY 43-9006, AG99, CAY10561, ISIS 5132, apigenin, SP600125, SU4984, SB203580, PD169316, K0947, GDC0994, and AG1478.
  • inhibitors include, but are not limited to, chromone and flavone type inhibitors; PD 98059 (Runden E et al, J Neurosci 1998, 18(18) 7296-305); PD0325901 (Pfizer); Selumetinib, a selective MEK inhibitor (AstraZeneca/ Array BioPharma, also known as AZD6244); ARRY-438162 (Array BioPharma); PD198306 (Pfizer); PD0325901 (Pfizer); AZD8330 (AstraZeneca/ Array Biopharma, also called ARRY-424704); PD 184352 (Pfizer, also called Cl- 1040); PD 184161 (Pfizer); a-[Amino[(4- aminophenyl)thio]methylene]-2-(trifluoromethyl)benzeneacetonitrile (SL327); l,4-Diamino-2,3- dicyano-l,4-bis
  • CAY10561 (CAS 933786-58-4; Cayman Chemical); GSK 1120212; RDEA119 (Ardea).
  • MAPK pathway inhibitors include, but are not limited to, Raf-l inhibitors, such as GW5074, BAY 43-9006, and ISIS 5132 (Lackey, K. et al., Bioorg. Med. Chem. Lett., 2000, 10:223-226; Lyons, J. F. et al., Endocrine-related Cancer, 2001, 8:219-225; and Monia, B. P. et al., Nat. Med., 1996, 2(6):668-675, respectively); and MEK1/2 inhibitors, such as PD98059, PD184352, U0126 (Dudley D. T. et al., Proc. Natl.
  • Raf-l inhibitors such as GW5074, BAY 43-9006, and ISIS 5132 (Lackey, K. et al., Bioorg. Med. Chem. Lett., 2000, 10:223-226; Lyons, J. F. et al., Endocrine-related Cancer, 2001
  • Imidazolium trans-imidazoledimethyl sulfoxide- tetrachlororuthenate is a ruthenium-containing inhibitor of the phosphorylation of MEK, the upstream activator of ERK (Pintus G. et al., Eur. J. Biochem., 2002, 269:5861-5870).
  • the ERK inhibitor is selected from the group consisting of BVD-523, FR 180204, MK-8353 (SCH900353), pluripotin, SCH772984, VX-l le (ERK-l le; TCS ERK l le), SL327, hypericin, purvalanol, PD173074, GW5074, BAY 43-9006, AG99, CAY10561, ISIS 5132, apigenin, SP600125, SU4984, SB203580, PD169316, K0947, GDC0994, and AG1478.
  • inhibitors include, but are not limited to, chromone and flavone type inhibitors; PD 98059 (Runden E et al, J Neurosci 1998, 18(18) 7296-305); PD0325901 (Pfizer); Selumetinib, a selective MEK inhibitor (AstraZeneca/ Array BioPharma, also known as AZD6244); ARRY-438162 (Array BioPharma); PD198306 (Pfizer); PD0325901 (Pfizer); AZD8330 (AstraZeneca/ Array Biopharma, also called ARRY-424704); PD 184352 (Pfizer, also called Cl- 1040); PD 184161 (Pfizer); a- [Amino[(4-aminophenyl)thio]methylene]-2-(trifluoromethyl)benzeneacetonitrile (SL327); 1,4- Diamino-2,3-dicyano-l,4-
  • ERK inhibitor refers to compounds capable of fully or partially reducing or inhibiting ERK signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the ERK signaling pathway, such as MEK1, MEK2, ERK1 and/or ERK2 mRNA. In some examples, said ERK inhibitor inhibits one or more of MEK1, MEK2, ERK1 or ERK2 kinase activity.
  • Inhibition of ERK can be achieved by a variety of mechanisms, including, but not limited to, binding directly to ERK1 or ERK2, binding directly to MEK1 or MEK2, or inhibiting expression of the ERK or MEK genes.
  • Any component of the ERK pathway is a potential therapeutic target for inhibition in accordance with the present disclosure.
  • the mechanism of inhibition may be at the genetic level (e.g., interference with transcription or translation) or at the protein level (e.g., binding,
  • the ERK inhibitor is a specific inhibitor that either acts on ERK1/2 at the genetic level or protein level.
  • an inhibitor may be utilized that interferes with expression of ERK1 and/or ERK2, or which sequesters ERK1 and/or ERK2 in the cytoplasm of the cell, preventing nuclear translocation.
  • Exemplary ERK inhibitors include, but are not limited to ulixertinib, RG7842, GDC-0994, CC-90003, ASN-007, AMO-01, KO-947, AEZS-134, AEZS-131, AEZS-140, AEZS-136, AEZS- 132, D-87503, KIN-2118, RB-l, RB-3, SCH-772984, MK-8353, SCH-900353, FR-180204, IDN- 5491, hyperforin trimethoxybenzoate, ERK1-2067, ERK1-23211, ERK1-624, LY3214996,
  • the ERK inhibitor is selected from ulixertinib, GDC-0994, SCH-772984, and MK-8353. In some embodiments, the ERK inhibitor is selected from ulixertinib, GDC-0994, SCH-772984, MK-8353, and KO-947. In some embodiments, the ERK inhibitor is selected from SCH772984, GDC-0994, CC-90003, BVD-523 (ulixertinib) and KO-947. Preferably, the ERK inhibitor is KO-947.
  • ERK inhibitors and their syntheses have been described in WO 2005/113541 (ulixertinib), WO 2013/130976 (GDC- 0994), WO 2007/070398 (SCH-772984), WO 2009/105500 (MK-8353), and WO 2015/051341 (KO-947), the disclosures of which are incorporated by reference herein.
  • the ERK inhibitor is a compound selected from
  • MAPK pathway inhibitors and their syntheses have been described in ETS 5,525,625, US 2003/0060469, US 2004/0048861, US 2004/0082631, WO 98/43960, WO 99/01426, WO 00/41505, WO 00/42002, WO 00/42003, WO 00/41994, WO 00/42022, WO 00/42029, WO 00/68201, WO 01/68619, WO 02/06213, WO 03/077855 and WO 2005/23251.
  • the MAPK pathway inhibitor is selected from the group consisting of selumetinib, U0126, PD98059, PD0325901, AZD8330 (ARKY-42704), CI-1040 (PD 184352), and PD318088.
  • the MAPK pathway inhibitor is an ERK inhibitor described in WO/2015051341, the disclosure of which is incorporated by reference herein.
  • the present disclosure provides an ERK inhibitor which is a compound of Formula I:
  • Y is CR 5 ;
  • W is N or C;
  • Ri is-Ci-ioalkyl, -C 2-i oalkenyl, -C 2-i oalkynyl, -Ci-ioheteroalkyl, -C 3.l0 aryl, -Ci-iohetaryl, - C 3-i ocycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C 3-i0 aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.i 0 alkyl-C 3- iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C 2-i oalkenyl-C 3-i0 aryl, -C 2-i oalkenyl-C 3-i0 aryl, -C 2-i oalkenyl-C 3-i0 aryl, -C 2-i oal
  • loheterocyclyl -Ci-ioalkoxy-C 3-i oaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci-ioalkoxy-C 3-i ocycloalkyl, -Ci.
  • Ri’ is hydrogen, -Ci.i 0 alkyl, -C 2-i0 alkenyl, -C 2-i0 alkynyl, -Ci-ioheteroalkyl, -C 3-i0 aryl, -Ci.
  • l oheteroalkyl-C 3-l0 aryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci.ioheteroalkyl-C 3 .iocycloalkyl, -Ci. ioheteroalkyl-Ci-ioheterocyclyl, -Ci.ioalkoxy-C 3 .ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci.ioalkoxy-C 3 .
  • iocydoalkyl -Ci-ioalkoxy-Ci-ioheterocydyl, -C 3 .ioaryl-Ci.ioalkyl, -C 3 -ioaryl-C 2 -ioalkenyl, -C 3 - ioaryl-C -ioalkynyl, -C 3 .ioaryl-C 3 .iohetaryl, -C 3 .ioaryl-C 3 .iocydoalkyl, -C 3 .ioaryl-Ci.ioheterocydyl, -Ci.iohetaryl-Ci.ioalkyl, -Ci_iohetaryl-C 2 -i oal kenyl, -Ci.iohetaryl-C 2 -ioalkynyl, -C 3 .iohetaryl
  • iohetaryl -L-C 2 .ioalkynyl-C 3 .iocycloalkyl, -L-C 2.1 oal kynyl -C M oheterocyd yl , -L-Ci-ioheteroalkyl- C 3.l0 aryl, -L -Ci-ioheteroalkyl-Ci-iohetaryl, -L -Ci.ioheteroalkyl-C 3 .iocycloalkyl, -L -Ci.
  • ioheterocyclyl -L-C 2-i oalkynyl-C 3-i0 aryl, -L-C 2-i0 alkynyl-Ci.iohetaryl, -L-C 2-i0 alkynyl-C 3- iocycloalkyl, -L-C 2-i0 alkynyl-Ci.ioheterocyclyl, -L-Ci.ioheteroalkyl-C 3-i0 aryl, -L -Ci.
  • i oheteroal kyl -C M ohetaryl , -L -Ci-ioheteroalkyl-C 3-i ocycloalkyl, -L -Ci-ioheteroalkyl-Ci.
  • ioheterocyclyl -Ci.ioalkyl-C 3-i0 aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.ioalkyl-C 3-i0 cycloalkyl, -Ci.
  • ioalkyl-Ci-ioheterocyclyl -C 2-i oalkenyl-C 3-i0 aryl, -C 2-i0 alkenyl-Ci.iohetaryl, -C 2-i0 alkenyl-C 3- iocycloalkyl, -C 2-i oalkenyl-Ci.ioheterocyclyl, -C 2-i oalkynyl-C 3-i0 aryl, -C 2-i0 alkynyl-Ci.iohetaryl, - C 2-i0 alkynyl-C 3-i ocycloalkyl, -C 2-i0 alkynyl-Ci.ioheterocyclyl, -Ci.ioheteroalkyl-C 3-i oaryl, -Ci.
  • ioheterocydyl -C 3 .ioaryl-Ci.ioalkyl, -C 3 .ioaryl-C 2 -ioalkenyl, -C 3 .ioaryl-C 2 -ioalkynyl, -C 3 .ioaryl-C 3 . iohetaryl, -C 3 .ioaryl-C 3 .iocycloalkyl, -C 3 .ioaryl-Ci.ioheterocydyl, -Ci-iohetaryl-Ci-ioalkyl, -Ci.
  • iocydoalkyl -Ci-iohetaryl-Ci-ioheterocydyl, -C 3 .iocydoalkyl-Ci.ioalkyl, -C 3 .iocycloalkyl-C 2 - l0 alkenyl, -C 3 .iocydoalkyl-C 2-i oalkynyl, -C 3 .iocydoalkyl-C 3 .ioaryl, -C 3 .iocycloalkyl-Ci.iohetaryl, - C 3 .iocydoalkyl-Ci.iohetaryl, - C 3 .iocydoalkyl-Ci.ioheterocydyl, -Ci-ioheterocydyl-Ci-ioalkyl, -Ci.iohete
  • each of R 5 , R 7l , R 8I and R 9i is independently hydrogen, halogen, -C l-l0 alkyl, -C 2.l0 alkenyl, -C 2-10 alkynyl, -Ci-ioheteroalkyl, -C 3 -i 0 aryl, -Ci-iohetaryl, -C 3 -iocycloalkyl, -Ci-ioheterocyclyl, -
  • R 6 is hydrogen, -Ci.i 0 alkyl, -C 2-i oalkenyl, -C 2-i oalkynyl, -Ci-ioheteroalkyl, -C 3-i oaryl, -Ci. iohetaryl, -C 3 .i 0 cycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C 3 .ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.
  • l oheteroalkyl-C 3-l oaryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci-ioheteroalkyl ⁇ .iocycloalkyl, -Ci.
  • each of Rio and R i is independently -C MO alkyl, -C 2-i oalkenyl, -C 2-i o alkynyl, -Ci.
  • each of Rn, R 12, R 13 and R 15 is independently hydrogen, halogen, -C MO alkyl, -C 2-i oalkenyl, -C 2-10 alkynyl, -Ci-ioheteroalkyl, -C 3-i oaryl, -Ci-iohetaryl, -C 3 .i 0 cycloalkyl, -Ci-ioheterocyclyl, -
  • each of R , R , R and R is independently hydrogen, halogen, -CMO alkyl, -C 2 -ioalkenyl, -C 2-10 alkynyl, -Ci-ioheteroalkyl, -C 3-i oaryl, -Ci-iohetaryl, -C 3 .i 0 cycloalkyl, -Ci-ioheterocyclyl, or wherein R 31 together with R 32 form a heterocyclic ring;
  • ring A comprises one or more heteroatoms selected from N, O, or S;
  • ring A comprises at least two heteroatoms selected from N, O, or S;
  • X 2 is NRi or CRiRi’
  • X 3 is CR 3 R 3 ⁇ W is C
  • Y is CR 5
  • X 4 is N or CIO
  • X 5 is N or C
  • X 6 is C
  • X 7 is NR 72 or CR 7i
  • X 8 is N
  • X 9 is NR 22 or CR 21 .
  • X 2 is NRi
  • X 3 is CR 3 R 3 ⁇ W is C
  • Y is CR 5
  • X 4 is CIO
  • X 5 is C
  • X 6 is C
  • X 7 is NR 72
  • X 8 is N
  • X 9 is CR 2i .
  • X 2 is NRi or CRiRk
  • W is C
  • Y is CR 5
  • X is N or CR
  • X 5 is N or C
  • X 6 is C
  • X 7 is N or NR 72 or CR 7i
  • X 8 is N or CR 8i
  • X 9 is NR 22 or CR 2i
  • X 10 is N or CR 9i
  • Ri is -Ci-ioalkyl, -C 3 -i 0 aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl- C 3 -i 0 aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.ioal
  • Ri’ is hydrogen, -Ci.i 0 alkyl, -C 3-i oaryl, -Ci-iohetaryl, -C3.i 0 cycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3.ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.ioalkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci.
  • ioheteroalkyl -L-C 3-i oaryl, -L-Cmohetaryl, -L-C3.i 0 cycloalkyl, or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent R I2 substituents;
  • R 6 is -Cmoalkyl, -C 3-i oaryl, -Cmohetaryl, -C3.i 0 cycloalkyl, -Ci-ioheterocyclyl, -Ci.i 0 alkyl- C 3-i oaryl, -Ci-ioalkyl-Cmohetaryl, -Ci.ioalkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C 3- l ocycloalkyl-Ci-ioalkyl, -C3.iocycloalkyl-C3.ioaryl, -C3.iocycloalkyl-Ci.iohetaryl, -C3.i 0 cycloalkyl- Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl
  • each of Rio and R 34 is independently -Ci 40 alkyl, -C 2-i0 alkenyl, -C 2-i0 alkynyl, - Ci.
  • each of R 31 , R 32 and R 34 is independently hydrogen,— C l-lo alkyl,— C 3-lo aryl, or— C 3- ! ocycloalkyl, or wherein R 3 1 together with R 32 form a heterocyclic ring;
  • ring A comprises one or more heteroatoms selected from N, O, or S.
  • Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C 3-i0 aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci. l0 alkyl-C 3-l0 cycloalkyl, -Ci-ioalkyl-Ci-ioheterocydyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
  • Ri’ is hydrogen -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C 3-i oaryl, -Ci-ioalkyl-Ci.
  • lohetaryl -Ci.ioalkyl-C 3-i ocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C 3-i oaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
  • R 6 is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C 3-i oaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci- l oalkyl-C 3-l ocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
  • loheterocyclyl-C 3-l0 aryl each of which is unsubstituted or substituted by one or more independent R14 or R15 substituents;
  • each of Rio and R l4 independently -C O alkyl, -C 3-l0 aryl, -Ci-iohetaryl, -C 3-i0 cycloalkyl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
  • ring A comprises one or more heteroatoms selected from N, O, or S.
  • Ri is -Ci.ioalkyl, -Ci-ioheterocyclyl, -C M0 alkyl-C 3-i oaryl, -Ci-ioheterocyclyl-C M oalkyl, or -Ci-ioheterocyclyl-C 3-i oaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
  • R 6 is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Cmoalkyl ⁇ -ioaryl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C3.ioaryl, each of which is unsubstituted or substituted by one or more independent R I4 or R I5 substituents;
  • each of Rn, R i2 and R I5 is independently hydrogen, halogen, -C MO alkyl, -OH, -CF 3 , -OR 3 , -NR 31 R 32 , -N0 2 , -CN, or -S(0)O -2 R 3 1 ;
  • each of R 31 , R 32 and R 34 is independently hydrogen or -CMO alkyl, or wherein R 31 together with R 32 form a heterocyclic ring;
  • ring A comprises one or more heteroatoms selected from N, O, or S.
  • Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -C M0 alkyl-C3.ioaryl, -Ci-ioheterocyclyl-C M oalkyl, or -Ci.ioheterocyclyl-C3.ioaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
  • R 2i is halogen, -CN, , -L-Cmoalkyl, -L-C3-ioaryl, -L-Cmohetaryl, -L-C3-iocycloalkyl, or - L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent R I2 substituents;
  • each of R 3 R 3 ’ and R is independently hydrogen, halogen, -OH, -CF 3 , or -Cmoalkyl; or R 3 ’ is -OR 6 or -NR 6 R 34 , wherein R 6 together with R 34 can optionally form a heterocyclic ring;
  • R5 is hydrogen
  • R 6 is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Cmoalkyl ⁇ -ioaryl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C3.ioaryl, each of which is unsubstituted or substituted by one or more independent R I4 or R ⁇ substituents;
  • each of Rn, Rn and Rn is independently hydrogen, halogen, -C MO alkyl, -OH or -CF 3 ; each of R 31 and R 34 is independently hydrogen or -C MO alkyl; and
  • ring A comprises one or more heteroatoms selected from N, O, or S.
  • the present disclosure provides an ERK inhibitor which is a compound of Formula I-A:
  • Ri is-Ci-ioalkyl, -C 3 -i 0 aryl, -Ci-iohetaryl, -C 3- iocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Cmoalkyl ⁇ .
  • iocycloalkyl -Ci-ioalkyl-Ci-ioheterocyclyl, -C3.iocycloalkyl-Ci.ioalkyl, -C3.iocycloalkyl-C3.ioaryl, - C3.iocycloalkyl-Ci.iohetaryl, -C3 -i ocycloalkyl-Ci -i oheterocydyl, -Ci-ioheterocyclyl -Ci.i 0 alkyl, -Ci.
  • Ri is -Ci.i 0 alkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3.ioaryl, -Ci-ioalkyl-Ci-iohetaryl, - Ci.ioalkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocydyl-Ci-ioalkyl, or -Ci. ioheterocyclyl-C3-ioaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents.
  • Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Cmoalkyl ⁇ . l oaryl, -Cmoheterocyclyl-Cmoalkyl, or -Ci.ioheterocyclyl-C3.i 0 aryl, each of which is unsubstituted or substituted by one or more independent Ri 0 or Rn substituents.
  • Ri is -Ci. ioheterocyclyl-Ci-ioalkyl, unsubstituted or substituted by one or more independent Rio or Rn substituents.
  • i oheteroal kyl -L-C3-ioaryl, -L-Cmohetaryl, -L- C3-iocycloalkyl, or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent R I2 substituents.
  • R 2i is halogen, -CN, , -L-Cm 0 alkyl, -L-C3.i 0 aryl, -L-Cmohetaryl, -L-C 3 .
  • locycloalkyl or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent R i2 substituents.
  • R 2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent Rn substituents; wherein the Cmohetaryl of R 2 1 comprises one or more nitrogen atoms; each R I2 substituent, when present, is independently selected from the group consisting of -Cmo alkyl, -Cmoalkenyl, -C 2-i o alkynyl, -Cmoheteroalkyl, -C 3 -ioaryl, -Cmohetaryl, -C3-iocycloalkyl, -Cmoheterocyclyl, -OH, -CF 3 , -OCF 3 , -OR 31 ; wherein each R 3l is independently hydrogen or -Cmo alkyl; L is a bond; and Ri is -Cmoalkyl-Csuoaryl, -Cmoalky
  • R 2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent Rn substituents; wherein the Cmohetaryl of R 2 1 comprises one or more nitrogen atoms; each R I2 substituent, when present, is independently selected from the group consisting of -Cmo alkyl, -Cmoalkenyl, -C 2-i o alkynyl, -Cmoheteroalkyl, -C 3 -ioaryl, -Cmohetaryl, -C3-iocycloalkyl, -Cmoheterocyclyl, -OH, -CF 3 , -OCF 3 , -OR 31 ; wherein each R 3l is independently hydrogen or -Cmo alkyl; L is a bond; and Ri is , unsubstituted or substituted by one or more independent R l0 or Rn
  • R 2I is -L-Ci-iohetaryl unsubstituted or substituted by one or more independent R i2 substituents; wherein the Ci-iohetaryl of R 2l comprises one or more nitrogen atoms; each R I2 substituent, when present, is independently selected from the group consisting of -C l - l0 alkyl, -C 2-i0 alkenyl, -C 2- l0 alkynyl, -Ci-ioheteroalkyl, -C 3-l0 aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, -CF 3 , -OCF 3 , -OR 31 ; wherein each R 3l is independently
  • R 1 0 unsubstituted or substituted by one or more independent R l0 or Rn substituents.
  • R 2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent R i2 substituents; wherein the Cmohetaryl of R 2l comprises one or more nitrogen atoms; each R I2 substituent, when present, is independently selected from the group consisting of -C mo alkyl, -C 2-i0 alkenyl, -C 2- l0 alkynyl, -Cmoheteroalkyl, -C 3.l0 aryl, -Cmohetaryl, -C3-iocycloalkyl, -Cmoheterocyclyl, -OH, -CF 3 , -OCF 3 , -OR 31 ; wherein each R3 1 is independently hydrogen or -C o alkyl; L is a bond; and Ri is unsubstituted or substituted by one or more independent R l0 or Rn substitu
  • R 2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent R i2 substituents;
  • the Cmohetaryl of R 2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl;
  • each R I2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -zz-Pr, OH, - OMe, -OEt, -OPr;
  • L is a bond;
  • Ri is -Cmoalkyl-Cs-ioaryl, -Ci-ioalkyl-Cmohetaryl, -Cn !
  • R 2I is -L-Cmohetaryl unsubstituted or substituted by one or more independent R i2 substituents; the Cmohetaryl of R 2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl; each R i2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -zz-Pr, OH, -
  • OMe, -OEt, -OPr OMe, -OEt, -OPr
  • L is a bond
  • Ri is , unsubstituted or substituted by one or more independent R l0 or Rn substituents.
  • R 2I is -L-Ci-iohetaryl unsubstituted or substituted by one or more independent Rn substituents;
  • the Ci-iohetaryl of R 2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl;
  • each R I2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -//-Pr, OH, -
  • OMe, -OEt, -OPr OMe, -OEt, -OPr
  • L is a bond
  • Ri is R 10 , unsubstituted or substituted by one or more independent R l0 or Rn substituents.
  • R 2l is -L-Ci-iohetaryl unsubstituted or substituted by one or more independent Rn substituents; the Cmohetaryl of R 2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl; each R I2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -zz-Pr, OH, -
  • OMe, -OEt, -OPr OMe, -OEt, -OPr
  • L is a bond
  • Ri is unsubstituted or substituted by one or more independent R l0 or Rn substituents.
  • R 72 is independently hydrogen, -C MO alkyl, -C 3-i0 aryl, -C 3- !
  • R 72 is independently hydrogen or -Ci-ioalkyl. In some embodiments, R 72 is independently hydrogen.
  • each of Rio independently is -C MO alkyl, -C 2- l0 alkenyl, -C 2-i0 alkynyl, -Ci-ioheteroalkyl, -C 3-i0 aryl, -Ci-iohetaryl, -C 3-i0 cycloalkyl, -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents.
  • each of Rio is independently -CMO alkyl, -C 3-i oaryl, -Ci-iohetaryl, -C 3-i ocycloalkyl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents.
  • each of Rio is independently -CMO alkyl, -C 3-i0 aryl, -Ci-iohetaryl, or -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents.
  • each of Rn, R12 , and R i3 is independently hydrogen, halogen, -C MO alkyl, -OH, -CF 3 , -OR 3 , - NR 31 R 32 , -N0 2 , -CN, or -S(O) 0- 2R 31 ⁇
  • each of Rn, R12, and R i3 is independently hydrogen, halogen, -C MO alkyl, -OH, -CF 3 , -OR 3 , - NR 31 R 32 , -N0 2 , -CN, or -S(O) 0- 2R 31 ⁇
  • each of Rn, R12, and R i3 is
  • each of R , R , and R is independently hydrogen, halogen, -C MO alkyl, -C 2-i0 alkenyl, -C 2-i0 alkynyl, -Ci-ioheteroalkyl, -C 3-i0 aryl, -Cmohetaryl, -C 3- l ocycloalkyl, -Ci-ioheterocyclyl, or wherein R 31 together with R 32 form a heterocyclic ring.
  • each of R , R , and R is independently hydrogen, -CMO alkyl, -C 3-i oaryl, or -C 3- l ocycloalkyl, or wherein R 31 together with R 32 form a heterocyclic ring.
  • each of R 31 , R 32 , and R 33 is independently hydrogen or -Cmoalkyl, or wherein R 31 together with R 32
  • each of R , R , and R is independently hydrogen or -Ci-ioalkyl.
  • Ri is-Cmoalkyl, -C 3-i0 aryl, -Cmohetaryl, -C 3-i0 cycloalkyl, -Cmoheterocyclyl, -Cmoalkyl- C 3-i0 aryl, -Cmoalkyl-C M ohetaryl, -Cmoalkyl-Cmocycloalkyl, -Cmoalkyl-C M oheterocyclyl, -C 3 .
  • each of Rio is independently -C O alkyl, -C 2-i0 alkenyl, -C 2-i0 alkynyl, -Ci-ioheteroalkyl, - C 3-i0 aryl, -Ci-iohetaryl, -C 3-i0 cycloalkyl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
  • each of R 31 and R 32 is independently hydrogen, -Cmoalkyl, -C 3-i oaryl, or -C 3-i ocycloalkyl, or wherein R 31 together with R 32 form a heterocyclic ring.
  • Ri is -Cmoalkyl, -Ci-ioheterocyclyl, -Cmoalkyl-Cmoaryl, -Cmoalkyl-Cmohetaryl, -Ci. ioalkyl-C 3-i ocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
  • RI O is -Cmoalkyl, -C 3-i0 aryl, -Cmohetaryl, -C 3-i0 cycloalkyl, or -Cmoheterocyclyl, optionally substituted by one or more independent Rn substituents;
  • Ri is Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C 3-i oaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci- ioalkyl-C 3-i ocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
  • R 72 is hydrogen or -Ci.i 0 alkyl
  • each of Rio is independently -Ci.i 0 alkyl, -C 3-i0 aryl, -Ci-iohetaryl, -C 3-i0 cycloalkyl, or -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
  • each of R 31 and R 32 is independently hydrogen or -Cmoalkyl.
  • Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C 3-i oaryl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C 3-i oaryl, each of which is unsubstituted or substituted by one or more independent Ri 0 or Rn substituents;
  • R 2i is halogen, -CN, -L-Cmoalkyl, -L-C 3-i oaryl, -L-Cmohetaryl, -L-C 3-i ocycloalkyl, or - L-Cnioheterocyclyl, each of which is unsubstituted or substituted by one or more independent R i2 substituents;
  • R 72 is hydrogen
  • each of Rio is independently -Cno alkyl, -C 3-i oaryl, -Cmohetaryl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
  • each of Rn and R i2 is independently hydrogen, halogen, -Cno alkyl, -OH, -CF 3 -OR 31 or - CN;
  • each of R 31 is independently hydrogen or -Cno alkyl.
  • Ri is -Ci-ioalkyl, -Cmoalkyl-Cmoaryl, or -Ci-ioheterocyclyl-Ci-ioalkyl, each of which is unsubstituted or substituted by one or more independent R l0 or Rn substituents;
  • R 2I is -L-C 3-i oaryl or -L-Ci-iohetaryl, each of which is unsubstituted or substituted by one or more independent R i2 substituents;
  • L is a bond or -N(R 31 )-;
  • R 72 is hydrogen
  • each of Rio is independently-C 3-i0 aryl, -Ci-iohetaryl, or -C l-l0 heterocyclyl, optionally substituted by one or more independent Rn substituents;
  • each of Rn and Ri 2 is independently halogen,— C l-l0 alkyl, -OH, -CF 3 or -OR 31 ; and each of R 31 is independently hydrogen or -C l-l0 alkyl.
  • Ri is -Ci-ioheterocyclyl-Ci-ioalkyl, unsubstituted or substituted by one or more independent Rn substituents;
  • R 2I is pyridyl selected from the group consisting of 2-pyridyl, 3-pyridyl and 4-pyridyl, which is unsubstituted or substituted by one or more independent R 32 substituents;
  • L is a bond
  • R 72 is hydrogen
  • each of Rn and R i2 is independently halogen, -Cmo alkyl, -CF 3 or -OR 31 ;
  • each of R 31 is independently hydrogen or -C l-l0 alkyl.
  • Ri is -Cmoheterocyclyl-Ci. l0 alkyl, which is unsubstituted. In some embodiments, Ri is -Ci-ioheterocyclyl-Ci-ioalkyl, substituted by one or more independent Ri 0 substituents. In some embodiments, Ri is -Ci.
  • Ri is -C l-l0 heterocyclyl-C l-l0 alkyl, substituted by one or more independent Rio or Rn substituents.
  • Rio and Rn are selected from aryl, such as phenyl.
  • Ri is -Cmoalkyl, -Cn l oheterocyclyl, -Ci.ioalkyl-C 3-i oheterocyclyl, -Ci.ioalkyl-C 3-i oaryl, -Cmoalkyl -Cmohetaryl, -Cn l oheterocyclyl-Cmoalkyl, or -Ci-ioheterocyclyl-C 3-i oaryl, unsubstituted or substituted by one or more independent Rio or Rn substituents.
  • Ri is -Cmoalkyl, -Cn
  • Ri is -Cmoalkyl-Cmoaryl, - Cmoalkyl-Cmohetaryl, -Cmoheterocyclyl-Cmoalkyl, or -Cmoheterocyclyl-Cmoaryl, unsubstituted or substituted by one or more independent R l0 or Rn substituents.
  • Ri is - C M0 alkyl-C 3 -i 0 aryl or -C M0 heterocyclyl-C 3 -i 0 aryl, unsubstituted or substituted by one or more independent R l0 or Rn substituents.
  • Ri is ,
  • Rl is Ri is -Cnioheterocyclyl, -C M oheterocycl yl -C M oal kyl , or -Ci-ioheterocyclyl- C 3-l0 aryl, unsubstituted or substituted by one or more independent R l0 or Rn substituents.
  • Ri is
  • each of Ri or Rf is independently selected from:
  • an ERK inhibitor which is a compound selected from the group consisting of:
  • the present disclosure provides an ERK inhibitor which is a compound selected from the group consisting of:
  • the present disclosure provides a subject ERK inhibitor (including but not limited to Compound A) selected from the group consisting of:
  • Compounds of the present disclosure also include crystalline and amorphous forms of those compounds, pharmaceutically acceptable salts, and active metabolites of these compounds having the same type of activity, including, for example, polymorphs, pseudopolymorphs, solvates, hydrates, unsolvated polymorphs (including anhydrates), conformational polymorphs, and amorphous forms of the compounds, as well as mixtures thereof.
  • the compounds described herein may exhibit their natural isotopic abundance, or one or more of the atoms may be artificially enriched in a particular isotope having the same atomic number, but an atomic mass or mass number different from the atomic mass or mass number predominantly found in nature. All isotopic variations of the compounds of the present disclosure, whether radioactive or not, are encompassed within the scope of the present disclosure.
  • hydrogen has three naturally occurring isotopes, denoted 1H (protium), 2 H (deuterium), and 3 H (tritium). Protium is the most abundant isotope of hydrogen in nature.
  • Enriching for deuterium may afford certain therapeutic advantages, such as increased in vivo half-life and/or exposure, or may provide a compound useful for investigating in vivo routes of drug elimination and metabolism.
  • Isotopically-enriched compounds may be prepared by conventional techniques well known to those skilled in the art.
  • “Isomers” are different compounds that have the same molecular formula.
  • “Stereoisomers” are isomers that differ only in the way the atoms are arranged in space.
  • “Enantiomers” are a pair of stereoisomers that are non superimposable mirror images of each other. A 1 :1 mixture of a pair of enantiomers is a“racemic: mixture.
  • the term“( ⁇ )” is used to designate a racemic mixture where appropriate.
  • “Diastereoisomers” or“diastereomers” are stereoisomers that have at least two asymmetric atoms but are not mirror images of each other. The absolute stereochemistry is specified according to the Cahn-Ingold-Prelog R-S system.
  • stereochemistry at each chiral carbon can be specified by either R or S.
  • Resolved compounds whose absolute configuration is unknown can be designated (+) or (-) depending on the direction (dextro- or levorotatory) in which they rotate plane polarized light at the wavelength of the sodium D line.
  • Certain compounds described herein contain one or more asymmetric centers and can thus give rise to enantiomers, diastereomers, and other stereoisomeric forms, the asymmetric centers of which can be defined, in terms of absolute stereochemistry, as (R)- or (S)-.
  • Optically active (R)- and (S)-isomers can be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques.
  • the optical activity of a compound can be analyzed via any suitable method, including but not limited to chiral chromatography and polarimetry, and the degree of predominance of one stereoisomer over the other isomer can be determined.
  • Chemical entities having carbon-carbon double bonds or carbon-nitrogen double bonds may exist in Z- or E- form (or cis- or trans- form). Furthermore, some chemical entities may exist in various tautomeric forms. Unless otherwise specified, chemical entities described herein are intended to include all Z-, E- and tautomeric forms as well.
  • salts or“pharmaceutically acceptable salt” refers to salts derived from a variety of organic and inorganic counter ions well known in the art.
  • Pharmaceutically acceptable acid addition salts can be formed with inorganic acids and organic acids.
  • Inorganic acids from which salts can be derived include, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like.
  • Organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like.
  • Pharmaceutically acceptable base addition salts can be formed with inorganic and organic bases.
  • Inorganic bases from which salts can be derived include, for example, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum, and the like.
  • Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, basic ion exchange resins, and the like, specifically such as isopropylamine, trimethylamine,
  • the pharmaceutically acceptable base addition salt is chosen from ammonium, potassium, sodium, calcium, and magnesium salts.
  • “Optional” or“optionally” means that the subsequently described event of circumstances may or may not occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not.
  • “optionally substituted aryl” means that the aryl group may or may not be substituted and that the description includes both substituted aryl groups and aryl groups having no substitution.
  • “Pharmaceutically acceptable carrier, diluent or excipient” includes without limitation any adjuvant, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye, colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, or emulsifier which has been approved by the United States Food and Drug Administration as being acceptable for use in humans or domestic animals.
  • the present disclosure provides a method of inhibiting the activity of a member of the MAPK pathway in a cell, comprising contacting the cell with an effective amount of one or more compounds disclosed herein.
  • Inhibition of kinase activity can be assessed and demonstrated by a wide variety of ways known in the art. Non-limiting examples include (a) immunoblotting and immunoprecipitation with antibodies such as anti-phosphotyrosine, anti-phosphoserine or anti- phosphothreonine antibodies that recognize phosphorylated proteins; (b) using antibodies that specifically recognize a particular phosphorylated form of a kinase substrate (e.g.
  • cell proliferation assays such as but not limited to tritiated thymidine uptake assays, BrdU (5’-bromo-2’-deoxyuridine) uptake (kit marketed by Calibochem), MTS uptake (kit marketed by Promega), MTT uptake (kit marketed by Cayman Chemical), CyQUANT® dye uptake
  • Selective inhibition of a particular target may also be determined by expression levels of the target gene, its downstream signaling genes (for example by RT-PCR), or expression levels of the target protein (for example by immunocytochemistry, immunohistochemistry, Western blots) as compared to other related enzymes.
  • the practice of a subject method involves a contacting step taking place in vitro. In other embodiments, the contacting step takes place in vivo.
  • any of the compounds shown above may show a biological activity in an inhibition assay, such as a MEK or ERK inhibition assay, of between about 1 pM and 25 mM (IC50).
  • an inhibition assay such as a MEK or ERK inhibition assay
  • one or more compounds of the disclosure may bind specifically to an ERK (MAPK) kinase or a protein kinase selected from the group consisting of Ras, Raf, JNK, ErbB-l (EGFR), Her2 (ErbB-2), Her 3 (ErbB-3), Her 4 (ErbB-4), MAP2K1 (MEK1), MAP2K2 (MEK2), MAP2K3 (MEK3), MAP2K4 (MEK4), MAP2K5 (MEK5), MAP2K6 (MEK6), MAP2K7 (MEK7), CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK11 and any other protein kinases listed in the appended tables and figures, as well as any functional mutants thereof.
  • MAPK ERK
  • the IC50 of a compound of the disclosure for the target member of the MAPK pathway is less than about 1 mM, less than about 100 nM, less than about 50 nM, less than about 10 nM, less than 1 nM or even less than about 0.5 nM. In some embodiments, the IC50 of a compound of the disclosure for the target member of the MAPK pathway is less than about 1 pM, less than about 100 nM, less than about 50 nM, less than about 10 nM, less than 1 nM or even less than about 0.5 nM.
  • one or more compounds of the disclosure exhibit dual binding specificity and are capable of inhibiting an ERK kinase (e.g., ERK-l kinase, ERK-2 kinase, etc.) as well as a protein kinase (e.g., Ras, Raf, Her-2, MEK1, etc.) with an IC50 value less than about 1 pM, less than about 100 nM, less than about 50 nM, less than about 10 nM, less than 1 nM or even less than about 0.5 nM.
  • an ERK kinase e.g., ERK-l kinase, ERK-2 kinase, etc.
  • a protein kinase e.g., Ras, Raf, Her-2, MEK1, etc.
  • one or more compounds of the disclosure may be capable of inhibiting kinases involved in the Ras-Raf-MEK-ERK pathway (MAPK pathway) including, for example, Ras, Raf, INK, ErbB-l (EGFR), Her2 (ErbB-2), Her3 (ErbB-3), Her4 (ErbB-4), MAP2K1 (MEK1), MAP2K2 (MEK2), MAP2K3 (MEK3), MAP2K4 (MEK4), MAP2K5 (MEK5), MAP2K6 (MEK6), MAP2K7 (MEK7), CDK1, CDK2, CDK3,
  • the kinase is Ras, Raf, INK, ErbB-l (EGFR), Her2 (ErbB-2), MAP2K1 (MEK1), CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, or any other kinases listed in the tables and figures herein.
  • the compounds of the disclosure selectively inhibit ERK
  • the IC50 value of the compound of the disclosure can be 1/2, l/3 rd , l/4 th , 1 /5 th , 1 /7 th , l/l0 th , 1120 th , 1125 th , 1/50 th , 1/100* 11 , 11200 th , 1/300 th , 11400 th , l/500 th , 1/1000* 11 , 112000 th or less as compared to that of a reference protein kinase.
  • the compounds of the disclosure lack substantial cross-reactivity with at least about 100, 200, 300, or more protein kinases other than ERK, MEK, Ras or Raf.
  • the lack of substantial cross-reactivity with other non-MAPK pathway proteins can be evidenced by, e.g., at least 50%, 60%, 70%, 80%, 90% or higher kinase activity retained when the compound of the disclosure is applied to the protein kinase at a concentration of 1 mM, 5 mM, 10 mM or higher.
  • one or more compounds of the disclosure selectively inhibits ERK, MEK, Ras or Raf activity with an IC50 value of about 100 nM, 50 nM, 10 nM, 5 nM, 100 pM, 10 pM or even 1 pM, or less as ascertained in an in vitro kinase assay.
  • one or more compounds of the disclosure is capable of inhibiting and/or otherwise modulating cellular signal transduction via one or more protein kinases or lipid kinases disclosed herein.
  • one or more compounds of the disclosure is capable of inhibiting or modulating the output of a signal transduction pathway. Output of signaling transduction of a given pathway can be measured by the level of phosphorylation,
  • the output of the pathway may be a cellular or phenotypic output (e.g. modulating/inhibition of cellular proliferation, cell death, apoptosis, autophagy, phagocytocis, cell cycle progression, metastases, cell invasion, angiogenesis, vascularization, ubiquitination, translation, transcription, protein trafficking, mitochondrial function, golgi function, endoplasmic reticular function, etc).
  • a cellular or phenotypic output e.g. modulating/inhibition of cellular proliferation, cell death, apoptosis, autophagy, phagocytocis, cell cycle progression, metastases, cell invasion, angiogenesis, vascularization, ubiquitination, translation, transcription, protein trafficking, mitochondrial function, golgi function, endoplasmic reticular function, etc).
  • one or more compounds of the disclosure is capable of, by way of example, causing apoptosis, causing cell cycle arrest, inhibiting cellular proliferation, inhibiting tumor growth, inhibiting angiogenesis, inhibiting vascularization, inhibiting metastases, and/or inhibiting cell invasion.
  • one or more compounds of the disclosure causes apoptosis of said cell or cell cycle arrest.
  • Cell cycle can be arrested at the G0/G1 phase, S phase, and/or G2/M phase by the subject compounds.
  • one or more compounds of the disclosure including but not limited to the compounds listed above are capable of inhibiting cellular proliferation.
  • one or more compounds of the disclosure may inhibit proliferation of tumor cells or tumor cell lines with a wide range of genetic makeup.
  • the compounds of the disclosure may inhibit NSCLC cell proliferation in vitro or in an in vivo model such as a xenograft mouse model.
  • in vitro cultured NSCLC cell proliferation may be inhibited with an IC50 of less than 100 nM, 75 nM, 50 nM, 25 nM, 15 nM, 10 nM, 5 nM, 3 nM, 2 nM, 1 nM, 0.5 nM, 0.1 nM or less by one or more compounds of the disclosure.
  • proliferation of primary tumors derived from subjects can be inhibited by a compound of the disclosure as shown by in vitro assays, or in vivo models (e.g. using the subjects’ tumor cells for generating a xenograft mode).
  • primary tumor cell line proliferation may be inhibited with an IC50 of less than 100 nM, 75 nM, 50 nM, 25 nM, 15 nM, 10 nM, 5 nM, 3 nM, 2 nM, 1 nM, 0.5 nM, 0.1 nM or even less by one or more compounds of the disclosure.
  • the average IC50 of a compound of the disclosure for inhibiting a panel 10, 20, 30, 40, 50, 100 or more primary tumor cells may be about 200 nM, 100 nM, 75 nM, 50 nM, 25 nM, 15 nM, 10 nM, 5 nM, 3 nM, 2 nM, 1 nM, 0.5 nM, 0.1 nM or even less.
  • the tumor cells that can be inhibited by the compounds of the present disclosure include but are not limited to adenocarcinomas, such as adenocarcinomas of the lung.
  • the compounds of the disclosure are effective in blocking cell proliferation signals in cells.
  • cell proliferation signaling may be inhibited by one or more compounds of the disclosure as evidenced by Western blot analysis of phosphorylation of proteins such as FOXOl (phosphorylation at T24/3a T32), GSK3P(phosphorylation at S9),
  • the compounds of the disclosure can inhibit phosphorylation of signaling proteins and suppress proliferation of cells containing these signaling proteins but are resistant to existing chemotherapeutic agents including but not limited to rapamycin, Gleevec, dasatinib, alkylating agents, antimetabolites, anthracyclines, plant alkaloids, topoisomerase inhibitors and other antitumor agents disclosed herein.
  • one or more compounds of the disclosure may cause cell cycle arrest.
  • cells treated with one or more compounds of the disclosure may arrest or take longer to proceed through one or more cell cycle stages such as G0/G1, S, or G2/M.
  • cells treated with one or more compounds of the disclosure may arrest or take longer to proceed through the G0/G1 cell cycle stage.
  • about 35%, 40%, 50%, 55%, 60%, 65%, 70% or more of cells treated with one or more compounds of the disclosure may be in the G0/G1 cell cycle stage.
  • cells exhibiting cell cycle arrest in the G0/G1 cell cycle stage in response to treatment with the compounds of the disclosure are tumor cells or rapidly dividing cells.
  • the compounds of the disclosure affect a comparable or a greater degree of G0/G1 arrest as compared to doxorubicin.
  • the disclosure further provides methods of modulating MAPK pathway activity by contacting a member of the MAPK pathway with an effective amount of a compound of the disclosure. Modulation can be inhibiting or activating kinase activity. In some embodiments, the disclosure provides methods of inhibiting kinase activity by contacting the kinase with an effective amount of a compound of the disclosure in solution. In some embodiments, the disclosure provides methods of inhibiting the kinase activity by contacting a cell, tissue, organ that expresses the kinase of interest.
  • the disclosure provides methods of inhibiting kinase activity in subject including but not limited to rodents and mammal (e.g., human) by administering into the subject an effective amount of a compound of the disclosure.
  • the percentage of inhibiting exceeds 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%.
  • the kinase is selected from the group consisting of ERK, including different isoforms such as ERK1 and ERK2; Ras; Raf; INK; ErbB-l (EGFR); Her2 (ErbB-2); Her 3 (ErbB-3); Her 4 (ErbB-4); MAP2K1 (MEK1); MAP2K2 (MEK2); MAP2K3 (MEK3); MAP2K4 (MEK4); MAP2K5 (MEK5); MAP2K6 (MEK6); MAP2K7 (MEK7); CDK1; CDK2; CDK3;
  • the disclosure further provides methods of modulating MAPK pathway activity by contacting a member of the MAPK pathway with an amount of a compound of the disclosure sufficient to modulate MAPK pathway activity. Modulate can be inhibiting or activating MAPK pathway activity. In some embodiments, the disclosure provides methods of inhibiting a member of the MAPK pathway by contacting the member with an amount of a compound of the disclosure sufficient to inhibit the activity of the member. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a solution by contacting said solution with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said solution.
  • the disclosure provides methods of inhibiting MAPK pathway activity in a cell by contacting said cell with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said cell. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a tissue by contacting said tissue with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said tissue. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in an animal by contacting said animal with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said animal.
  • the disclosure provides methods of inhibiting MAPK pathway activity in a mammal by contacting said mammal with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said mammal. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a human by contacting said human with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said human. The present disclosure provides methods of treating a disease mediated by MAPK pathway activity in a subject in need of such treatment.
  • a method of the disclosure provides an effective dose of a MAPK pathway inhibitor.
  • An effective dose refers to an amount sufficient to effect the intended application, including but not limited to, disease treatment, as defined herein. Also contemplated in the subject methods is the use of a sub-therapeutic amount of a MAPK pathway inhibitor for treating an intended disease condition.
  • the amount of the MAPK pathway inhibitor administered may vary depending upon the intended application (in vitro or in vivo), or the subject and disease condition being treated, e.g., the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
  • a subject being treated with a MAPK pathway inhibitor may be monitored to determine the effectiveness of treatment, and the treatment regimen may be adjusted based on the subject’s physiological response to treatment. For example, if inhibition of a biological effect of MAPK pathway inhibition is above or below a threshold, the dosing amount or frequency may be decreased or increased, respectively.
  • the methods can further comprise continuing the therapy if the therapy is determined to be efficacious.
  • the methods can comprise maintaining, tapering, reducing, or stopping the administered amount of a compound in the therapy if the therapy is determined to be efficacious.
  • the methods can comprise increasing the administered amount of a compound in the therapy if it is determined not to be efficacious. Alternatively, the methods can comprise stopping therapy if it is determined not to be efficacious.
  • treatment with a MAPK pathway inhibitor is discontinued if inhibition of the biological effect is above or below a threshold, such as in a lack of response or an adverse reaction.
  • the biological effect may be a change in any of a variety of physiological indicators.
  • therapeutic efficacy of the methods of the disclosure is measured based on an effect of treating a cancer.
  • therapeutic efficacy of the methods of the disclosure may be measured by the degree to which the methods and compositions promote inhibition of tumor cell proliferation, the inhibition of tumor vascularization, the eradication of tumor cells, the reduction in the rate of growth of a tumor, and/or a reduction in the size of at least one tumor.
  • the progress of the inventive method in treating cancer can be ascertained using any suitable method, such as those methods currently used in the clinic to track tumor size and cancer progress.
  • the primary efficacy parameter used to evaluate the treatment of cancer by the disclosed methods and compositions preferably is a reduction in the size of a tumor.
  • Tumor size can be figured using any suitable technique, such as measurement of dimensions, or estimation of tumor volume using available computer software, such as FreeFlight software developed at Wake Forest University that enables accurate estimation of tumor volume.
  • Tumor size can be determined by tumor visualization using, for example, CT, ultrasound, SPECT, spiral CT, MRI, photographs, and the like.
  • the presence of tumor tissue and tumor size can be determined by gross analysis of the tissue to be resected, and/or by pathological analysis of the resected tissue.
  • a tumor is stabilized (i.e., one or more tumors do not increase more than 1%, 5%, 10%, 15%, or 20% in size, and/or do not metastasize) as a result of the subject methods and compositions.
  • a tumor is stabilized for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more weeks. In some embodiments, a tumor is stabilized for at least about 1, 2, 3, 4,
  • a tumor is stabilized for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more years.
  • the inventive method reduces the size of a tumor at least about 5% (e.g., at least about 10%, 15%, 20%, or 25%). More preferably, tumor size is reduced at least about 30% (e.g., at least about 35%, 40%, 45%, 50%, 55%, 60%, or 65%). Even more preferably, tumor size is reduced at least about 70% (e.g., at least about 75%, 80%,
  • a subject remains tumor free (e.g. in remission) for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more weeks following treatment. In some embodiments, a subject remains tumor free for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more months following treatment. In some embodiments, a subject remains tumor free for at least about 1, 2, 3,
  • the efficacy of the disclosed methods in reducing tumor size can be determined by measuring the percentage of necrotic (i.e., dead) tissue of a surgically resected tumor following completion of the therapeutic period.
  • a treatment is therapeutically effective if the necrosis percentage of the resected tissue is greater than about 20% (e.g., at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%), more preferably about 90% or greater (e.g., about 90%, 95%, or 100%). Most preferably, the necrosis percentage of the resected tissue is 100%, that is, no tumor tissue is present or detectable.
  • the efficacy of the disclosed methods can be determined by a number of secondary parameters.
  • secondary parameters include, but are not limited to, detection of new tumors, detection of tumor antigens or markers, biopsy, surgical downstaging (i.e., conversion of the surgical stage of a tumor from unresectable to resectable), PET scans, survival, disease progression-free survival, time to disease progression, quality of life assessments such as the Clinical Benefit Response Assessment, and the like, all of which can point to the overall progression (or regression) of cancer in a human.
  • Biopsy is particularly useful in detecting the eradication of cancerous cells within a tissue.
  • Radioimmunodetection is used to locate and stage tumors using serum levels of markers (antigens) produced by and/or associated with tumors (“tumor markers” or“tumor-associated antigens”), and can be useful as a pre-treatment diagnostic predicate, a post-treatment diagnostic indicator of recurrence, and a post-treatment indicator of therapeutic efficacy.
  • tumor markers or tumor-associated antigens that can be evaluated as indicators of therapeutic efficacy include, but are not limited to, carcinembryonic antigen (CEA), prostate-specific antigen (PSA), erythropoietin (EPO), CA-125, CA19-9, ganglioside molecules (e.g., GM2, GD2, and GD3), MART-l, heat shock proteins (e.g., gp96), sialyl Tn (STn), tyrosinase, MUC-l, HER-2/neu, c-erb-B2, KSA, PSMA, p53, RAS, EGF-R, VEGF, MAGE, and gplOO.
  • CCA carcinembryonic antigen
  • PSA prostate-specific antigen
  • EPO erythropoietin
  • CA-125 CA19-9
  • CA19-9 ganglioside molecules
  • MART-l heat shock proteins
  • STn sialyl Tn
  • the treatment of cancer in a human patient in accordance with the disclosed methods is evidenced by one or more of the following results: (a) the complete disappearance of a tumor (i.e., a complete response), (b) about a 25% to about a 50% reduction in the size of a tumor for at least four weeks after completion of the therapeutic period as compared to the size of the tumor before treatment, (c) at least about a 50% reduction in the size of a tumor for at least four weeks after completion of the therapeutic period as compared to the size of the tumor before the therapeutic period, and (d) at least a 2% decrease (e.g., about a 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% decrease) in a specific tumor-associated antigen level at about 4-12 weeks after completion of the therapeutic period as compared to the tumor-associated antigen level before the therapeutic period. While at least a 2% decrease in a tumor-associated antigen level is preferred, any decrease in the tumor-associated antigen level
  • the therapeutic benefit of the treatment in accordance with the disclosure can be evidenced in terms of pain intensity, analgesic consumption, and/or the Karnofsky Performance Scale score.
  • the treatment of cancer in a human patient is evidenced by (a) at least a 50% decrease (e.g., at least a 60%, 70%, 80%, 90%, or 100% decrease) in pain intensity reported by a patient, such as for any consecutive four week period in the 12 weeks after completion of treatment, as compared to the pain intensity reported by the patient before treatment, (b) at least a 50% decrease (e.g., at least a 60%, 70%, 80%, 90%, or 100% decrease) in analgesic consumption reported by a patient, such as for any consecutive four week period in the 12 weeks after completion of treatment as compared to the analgesic consumption reported by the patient before treatment, and/or (c) at least a 20 point increase (e.g., at least a 30
  • tumor size is reduced as a result of the inventive method preferably without significant adverse events in the subject.
  • Adverse events are categorized or“graded” by the Cancer Therapy Evaluation Program (CTEP) of the National Cancer Institute (NCI), with Grade 0 representing minimal adverse side effects and Grade 4 representing the most severe adverse events.
  • CEP Cancer Therapy Evaluation Program
  • Grade 0 representing minimal adverse side effects
  • Grade 4 representing the most severe adverse events.
  • the disclosed methods are associated with minimal adverse events, e.g. Grade 0, Grade 1, or Grade 2 adverse events, as graded by the CTEP/NCI.
  • reduction of tumor size although preferred, is not required in that the actual size of tumor may not shrink despite the eradication of tumor cells. Eradication of cancerous cells is sufficient to realize a therapeutic effect. Likewise, any reduction in tumor size is sufficient to realize a therapeutic effect.
  • Detection, monitoring and rating of various cancers in a human are further described in Cancer Facts and Figures 2001, American Cancer Society, New York, N.Y., and International Patent Application WO 01/24684. Accordingly, a clinician can use standard tests to determine the efficacy of the various embodiments of the inventive method in treating cancer. However, in addition to tumor size and spread, the clinician also may consider quality of life and survival of the patient in evaluating efficacy of treatment.
  • the disclosure provides a pharmaceutical composition comprising an amount of a MAPK pathway inhibitor formulated for administration to a subject in need thereof.
  • the pharmaceutical composition comprises between about 0.0001-500 g, 0.001-250 g, 0.01-100 g, 0.1-50 g, or 1 - 10 g of the MAPK pathway inhibitor.
  • the pharmaceutical composition comprises about or more than about 0.0001 g, 0.001 g, O.Olg, 0.1, 0.5 g, 1 g, 2 g, 3 g, 4 g, 5 g, 6 g, 7 g, 8 g, 9 g, 10 g, 15 g, 20 g, 25 g, 50g, 100 g, 200 g, 250 g, 300 g, 350 g, 400 g, 450 g, 500 g, or more of the MAPK pathway inhibitor.
  • the pharmaceutical composition comprises between 0.001 - 2 g of an MAPK pathway inhibitor in a single dose.
  • the therapeutic amount can be an amount between about 0.001-0.1 g of an MAPK pathway inhibitor. In some embodiments, the therapeutic amount can be an amount between about 0.01-30 g of a MAPK pathway inhibitor. In some embodiments, the therapeutic amount can be an amount between about 0.45 mg/kg/week to 230.4 mg/kg/week of a MAPK pathway inhibitor. In some embodiments, the MAPK pathway inhibitor is given as an intravenous infusion once per week. Preferably, the MAPK pathway inhibitor is given as an intravenous infusion once per week at a dose of about 0.45 mg/kg/week to about 1000 mg/kg/week, such as about 10 mg/kg/week to about 50 mg/kg/week.
  • the MAPK pathway inhibitor is given as an intravenous infusion once per week at a dose of about 5 mg/kg/week, about 10 mg/kg/week, about 20 mg/kg/week, about 30 mg/kg/week, about 40 mg/kg/week, or about 50 mg/kg/week, such as about 20 mg/kg/week.
  • the MAPK pathway inhibitor can be administered as part of a therapeutic regimen that comprises administering one or more second agents (e.g. 1, 2, 3, 4, 5, or more second agents), either simultaneously or sequentially with the MAPK pathway inhibitor.
  • the MAPK pathway inhibitor may be administered before or after the one or more second agents.
  • the MAPK pathway inhibitor and the one or more second agents may be administered by the same route (e.g. injections to the same location; tablets taken orally at the same time), by a different route (e.g. a tablet taken orally while receiving an intravenous infusion), or as part of the same combination (e.g. a solution comprising a MAPK pathway inhibitor and one or more second agents).
  • the MAPK pathway inhibitor is administered in combination with anti-EGFR therapy.
  • a method described herein further comprises administering a second therapeutic agent to a subject.
  • the present disclosure provides methods for combination therapies in which an agent known to modulate other pathways, or other components of the same pathway, or even overlapping sets of target enzymes, are used in combination with a compound of the present disclosure, or a pharmaceutically acceptable salt, ester, prodrug, solvate, hydrate or derivative thereof.
  • such therapy includes, but is not limited to, the combination of one or more compounds of the disclosure with chemotherapeutic agents, therapeutic antibodies, and/or radiation treatment to provide a synergistic or additive therapeutic effect.
  • the present disclosure provides a method of treating adenocarcinoma in a subject in need thereof, comprising administering to said subject a MAPK pathway inhibitor and a second therapeutic agent.
  • the second therapeutic agent is a CDK4/6 inhibitor, such as palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF- 06873600, voruciclib, FLX-925, ON-123300, BPI-16350, VS2-370, FCN-437c, BPI-1178, IIIM- 290, TQB-3616, BEBT-209, SRX-3177, GZ-38-1, IIIM-985, birociclib, CGP-82996, PD-171851, R-547, PAN-1215, NSC-625987, staurosporine, G1T28-1, G1T30-1, gossypin, AT-7519,
  • the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR- 6390, PF-06873600, voruciclib and FLX-925.
  • the second therapeutic agent is selected from palbociclib, ribociclib and abemaciclib.
  • Exemplary CDK4/6 inhibitors and their syntheses have been described in WO 2003/062236 (palbociclib), WO 2010/020675 (ribociclib), and US 2010/0160340 (abemaciclib), the disclosures of which are incorporated by reference herein.
  • the present disclosure provides methods and pharmaceutical compositions for inhibiting abnormal cell growth in a subject, comprising an amount of a compound of the disclosure, or a pharmaceutically acceptable salt, ester, prodrug, solvate, hydrate or derivative thereof, in combination with an amount of a second therapeutic agent, such as an anti cancer agent.
  • a second therapeutic agent such as an anti cancer agent.
  • Many chemotherapeutics are presently known in the art and can be used in
  • the chemotherapeutic is selected from the group consisting of mitotic inhibitors, alkylating agents, anti-metabolites, intercalating antibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes, topoisomerase inhibitors, biological response modifiers, anti-hormones, angiogenesis inhibitors, and anti androgens.
  • Non-limiting examples are chemotherapeutic agents, cytotoxic agents, and non-peptide small molecules such as Gleevec® (Imatinib Mesylate), Velcade® (bortezomib), Casodex
  • chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide (CYTOXANTM); alkyl sulfonates such as busulfan, improsulfan and
  • piposulfan such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethylenethiophosphaoramide and trimethylolomelamine; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, ranimustine; antibiotics such as aclacinomysins, actinomycin, authramycin, azaserine, bleomycins,
  • trimetrexate purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine;
  • pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine,
  • dromostanolone propionate epitiostanol, mepitiostane, testolactone
  • anti-adrenals such as aminoglutethimide, mitotane, trilostane
  • folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfomithine; elliptinium acetate; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidamine; mitoguazone; mitoxantrone; mopidamol; nitracrine;
  • pentostatin phenamet; pirarubicin; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK.RTM; razoxane; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2 , ,2''-trichlorotriethylamine; urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxanes, e.g.
  • paclitaxel TAXOLTM, Bristol- Myers Squibb Oncology, Princeton, N.J.
  • docetaxel TAXOTERETM, Rhone-Poulenc Rorer, Antony, France
  • retinoic acid esperamicins
  • capecitabine ecitabine
  • pharmaceutically acceptable salts, acids or derivatives of any of the above TAXOLTM, Bristol- Myers Squibb Oncology, Princeton, N.J.
  • anti-hormonal agents that act to regulate or inhibit hormone action on tumors
  • anti-estrogens including for example tamoxifen, (NolvadexTM), raloxifene, aromatase inhibiting 4(5)-imidazoles, 4-hydroxytamoxifen, trioxifene, keoxifene, LY 117018, onapristone, and toremifene (Fareston); and anti -androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; platinum; etoposide (VP- 16); ifosfamide; mitomycin C; mitoxantrone; vincristine; vinorelbine; navel
  • anti-estrogens including for example
  • the compounds or pharmaceutical composition of the present disclosure can be used in combination with commonly prescribed anti -cancer drugs such as Herceptin®, Avastin®, Erbitux®, Rituxan®, Taxol®, Arimidex®, Taxotere®, ABVD, AVICINE, Abagovomab, Acridine carboxamide, Adecatumumab, l7-N-Allylamino-l7-demethoxygeldanamycin, Alpharadin, Alvocidib, 3-Aminopyridine-2- carboxaldehyde thiosemicarbazone, Amonafide, Anthracenedione, Anti-CD22 immunotoxins, Antineoplastic, Antitumori genic herbs, Apaziqu
  • chemotherapy regimen IT-101, Imexon, Imiquimod, Indolocarbazole, Irofulven, Laniquidar, Larotaxel, Lenalidomide, Lucanthone, Lurtotecan, Mafosfamide, Mitozolomide, Nafoxidine, Nedaplatin, Olaparib, Ortataxel, PAC-l, palbociclib, Pawpaw, Pixantrone, Proteasome inhibitor, Rebeccamycin, Resiquimod, Rubitecan, SN-38, Salinosporamide A, Sapacitabine, Stanford V, Swainsonine, Talaporfm, Tariquidar, Tegafur-uracil, Temodar, Tesetaxel, Triplatin tetranitrate, Tris(2-chloroethyl)amine, Troxacitabine, Uramustine, Vadimezan, Vinflunine, ZD6126, and Zosuquidar.
  • the present disclosure provides a method of treating an
  • the second therapeutic agent may be selected from gemcitabine, cisplatin, an EGFR inhibitor and a CDK inhibitor.
  • the second therapeutic agent is selected from gemcitabine, cisplatin, cetuximab, erlotinib and palbociclib.
  • the second therapeutic agent is selected from gemcitabine, cisplatin, cetuximab.
  • the second therapeutic agent is an EGFR inhibitor, such as cetuximab or erlotinib.
  • the second therapeutic agent is a CDK inhibitor, preferably a CDK4/6 inhibitor, such as palbociclib.
  • the second therapeutic agent is selected from gemcitabine, cisplatin, cetuximab, wherein the adenocarcinoma is an adenocarcinoma of the lung.
  • the second therapeutic agent is cetuximab, wherein the adenocarcinoma is an adenocarcinoma of the lung.
  • the second therapeutic agent is adenocarcinoma is an adenocarcinoma of the lung.
  • the second therapeutic agent may be selected from osimertinib, olmutinib, icotinib hydrochloride, afatinib, necitumumab, lapatinib, pertuzumab, vandetanib, BV-NSCLC-001, nimotuzumab, panitumumab, erlotinib, gefitinib, cetuximab, brigatinib, naquotinib mesylate, anti-EGFR antibody , depatuxizumab mafodotin, tesevatinib , dacomitinib, neratinib, anti-EGFR CART cell therapy, PF-06747775, AP-32788, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-37
  • the second therapeutic agent is selected from osimertinib, olmutinib, icotinib hydrochloride, afatinib, necitumumab, lapatinib, pertuzumab, vandetanib, BV-NSCLC- 001, nimotuzumab, panitumumab, erlotinib, gefitinib, cetuximab, brigatinib, naquotinib mesylate, anti-EGFR antibody , depatuxizumab mafodotin, tesevatinib , dacomitinib, neratinib, anti-EGFR CART cell therapy, PF-06747775, AP-32788, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-3759, AZD-37
  • the second therapeutic agent is selected from palbociclib, abemaciclib, ribociclib, G1T-28, AT- 7519, alvocidib, FLX-925, G1T-38, GZ-38-1, ON-123300 and voruciclib. In some embodiments, the second therapeutic agent is selected from palbociclib, abemaciclib, ribociclib, G1T-28, AT- 7519 and alvocidib. In some embodiments, the second therapeutic agent is selected from
  • palbociclib osimertinib, olmutinib, icotinib hydrochloride, afatinib, necitumumab, lapatinib, pertuzumab, vandetanib, BV-NSCLC-001, nimotuzumab, panitumumab, erlotinib, gefitinib and cetuximab.
  • This disclosure further relates to a method for using the compounds or pharmaceutical compositions provided herein in combination with radiation therapy for inhibiting abnormal cell growth or treating the hyperproliferative disorder in the mammal.
  • Techniques for administering radiation therapy are known in the art, and these techniques can be used in the combination therapy described herein.
  • the administration of the compound of the disclosure in this combination therapy can be determined as described herein.
  • Radiation therapy can be administered through one of several methods, or a combination of methods, including without limitation external-beam therapy, internal radiation therapy, implant radiation, stereotactic radiosurgery, systemic radiation therapy, radiotherapy and permanent or temporary interstitial brachytherapy.
  • brachytherapy refers to radiation therapy delivered by a spatially confined radioactive material inserted into the body at or near a tumor or other proliferative tissue disease site.
  • the term is intended without limitation to include exposure to radioactive isotopes (e.g. At-2l l, 1-131, 1-125, Y-90, Re-l86, Re-l88, Sm-l53, B ⁇ -212, P-32, and radioactive isotopes of Lu).
  • Suitable radiation sources for use as a cell conditioner of the present disclosure include both solids and liquids.
  • the radiation source can be a radionuclide, such as 1-125, 1-131, Yb-l69, Ir-l92 as a solid source, 1-125 as a solid source, or other radionuclides that emit photons, beta particles, gamma radiation, or other therapeutic rays.
  • the radioactive material can also be a fluid made from any solution of
  • radionuclide(s) e.g., a solution of 1-125 or 1-131, or a radioactive fluid can be produced using a slurry of a suitable fluid containing small particles of solid radionuclides, such as Au-l98, Y-90.
  • the radionuclide(s) can be embodied in a gel or radioactive micro spheres.
  • the compounds of the present disclosure can render abnormal cells more sensitive to treatment with radiation for purposes of killing and/or inhibiting the growth of such cells. Accordingly, this disclosure further relates to a method for sensitizing abnormal cells in a mammal to treatment with radiation which comprises administering to the mammal an amount of a compound of the present disclosure or pharmaceutically acceptable salt, ester, prodrug, solvate, hydrate or derivative thereof, which amount is effective is sensitizing abnormal cells to treatment with radiation.
  • the amount of the compound, salt, or solvate in this method can be determined according to the means for ascertaining effective amounts of such compounds described herein.
  • anti -angiogenesis agents selected from anti -angiogenesis agents, signal transduction inhibitors, antiproliferative agents, glycolysis inhibitors, or autophagy inhibitors.
  • Anti-angiogenesis agents such as MMP-2 (matrix-metalloproteinase 2) inhibitors, MMP-9 (matrix-metalloprotienase 9) inhibitors, and COX-l 1 (cyclooxygenase 11) inhibitors, can be used in conjunction with a compound of the disclosure and pharmaceutical compositions described herein.
  • Anti -angiogenesis agents include, for example, rapamycin, temsirolimus (CCI-779), everolimus (RAD001), sorafenib, sunitinib, and bevacizumab.
  • Examples of useful COX- II inhibitors include CELEBREXTM (alecoxib), valdecoxib, and rofecoxib.
  • Examples of useful matrix metalloproteinase inhibitors are described in WO 96/33172 (published Oct. 24, 1996), WO
  • MMP-2 and MMP-9 inhibitors are those that have little or no activity inhibiting MMP-l.
  • MMP-2 and/or AMP-9 are those that selectively inhibit MMP-2 and/or AMP-9 relative to the other matrix-metalloproteinases (i. e., MAP-l, MMP- 3, MMP-4, MMP-5, MMP-6, MMP-7, MMP-8, MMP-10, MMP-l 1, MMP-12, and MMP-13).
  • MMP-2 and/or AMP-9 relative to the other matrix-metalloproteinases (i. e., MAP-l, MMP- 3, MMP-4, MMP-5, MMP-6, MMP-7, MMP-8, MMP-10, MMP-l 1, MMP-12, and MMP-13).
  • MMP inhibitors useful in the disclosure are AG-3340, RO 32-3555, and RS 13-0830.
  • Autophagy inhibitors include, but are not limited to chloroquine, 3-methyladenine, hydroxychloroquine (PlaquenilTM), bafilomycin Al, 5-amino-4-imidazole carboxamide riboside (AICAR), okadaic acid, autophagy-suppressive algal toxins which inhibit protein phosphatases of type 2A or type 1, analogues of cAMP, and drugs which elevate cAMP levels such as adenosine, LY204002, N6-mercaptopurine riboside, and vinblastine.
  • antisense or siRNA that inhibits expression of proteins including but not limited to ATG5 (which are implicated in autophagy), may also be used.
  • Administration of the compounds of the present disclosure can be effected by any method that enables delivery of the compounds to the site of action.
  • An effective amount of a compound of the disclosure may be administered in either single or multiple doses by any of the accepted modes of administration of agents having similar utilities, including rectal, buccal, intranasal and transdermal routes, by intra-arterial injection, intravenously, intraperitoneally, parenterally, intramuscularly, subcutaneously, orally, topically, as an inhalant, or via an impregnated or coated device such as a stent, for example, or an artery-inserted cylindrical polymer.
  • the MAPK pathway inhibitor is administered intravenously or orally.
  • the amount of the compound administered will be dependent on the mammal being treated, the severity of the disorder or condition, the rate of administration, the disposition of the compound and the discretion of the prescribing physician.
  • an effective dosage is in the range of about 0.001 to about 100 mg per kg body weight per day, preferably about 1 to about 35 mg/kg/day, in single or divided doses. For a 70 kg human, this would amount to about 0.05 to 7 g/day, preferably about 0.05 to about 2.5 g/day.
  • dosage levels below the lower limit of the aforesaid range may be more than adequate, while in other cases still larger doses may be employed without causing any harmful side effect, e.g. by dividing such larger doses into several small doses for administration throughout the day.
  • the MAPK pathway inhibitor When used in combination with a second therapeutic agent, can be administered at a dosage that is the same as the effective amount for that agent when administered as a monotherapy. In some embodiments, the MAPK pathway inhibitor is
  • a sub-therapeutic amount of an agent is an amount less than the effective amount of the agent.
  • the MAPK pathway inhibitor when administered in combination with a second therapeutic agent, can be administered in an amount less than 90% of the effective amount, such as less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, or less than 10% of the effective amount.
  • a sub -therapeutic amount of the second therapeutic agent is administered in combination with a MAPK pathway inhibitor.
  • sub-therapeutic amounts of both a MAPK pathway inhibitor and a second therapeutic agent are administered.
  • a MAPK pathway inhibitor described herein, such as a compound provided in Table 3, is expected to produce a synergistic effect when used in
  • the synergistic effect is more pronounced when a sub-therapeutic amount of the MAPK pathway inhibitor is administered.
  • the individual components of the combination though one or more is present in a sub-therapeutic amount, synergistically yield an efficacious effect and/or reduced a side effect in an intended application.
  • a compound of the disclosure is administered in a single dose.
  • Such administration will be by injection, e.g., intravenous injection, in order to introduce the agent quickly.
  • injection e.g., intravenous injection
  • other routes may be used as appropriate.
  • a single dose of a compound of the disclosure may also be used for treatment of an acute condition.
  • a compound of the disclosure is administered in multiple doses. Dosing may be about once, twice, three times, four times, five times, six times, or more than six times per day. Dosing may be about once a month, once every two weeks, once a week, or once every other day. In another embodiment a compound of the disclosure and another agent are administered together about once per day to about 6 times per day. In another embodiment the administration of a compound of the disclosure and an agent continues for less than about 7 days.
  • the administration continues for more than about 6, 10, 14, 28 days, two months, six months, or one year. In some cases, continuous dosing is achieved and maintained as long as necessary.
  • Administration of the agents of the disclosure may continue as long as necessary.
  • an agent of the disclosure is administered for more than 1, 2, 3, 4, 5, 6, 7, 14, or 28 days.
  • an agent of the disclosure is administered for less than 28, 14, 7, 6, 5, 4, 3, 2, or 1 day.
  • an agent of the disclosure is administered chronically on an ongoing basis, e.g., for the treatment of chronic effects.
  • the compounds described herein can be used in combination with other agents disclosed herein or other suitable agents, depending on the condition being treated. Hence, in some embodiments, the one or more compounds of the disclosure will be co-administered with other agents as described above. In some embodiments, the other agent is an anti -cancer agent.
  • the compounds described herein may be administered with the second agent simultaneously, or separately.
  • the administration in combination can include simultaneous administration of the two agents in the same dosage form, simultaneous administration in separate dosage forms, or separate administration. That is, a compound described herein and any of the agents described above can be formulated together in the same dosage form and administered simultaneously. Alternatively, a compound of the disclosure and any of the agents described above can be simultaneously administered, wherein both the agents are present in separate formulations.
  • a compound of the present disclosure can be administered just followed by and any of the agents described above, or vice versa.
  • a compound of the disclosure and any of the agents described above may be administered a few minutes apart, or a few hours apart, or a few days apart.
  • Example 1 Efficacy studies in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma. Tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 200 mm 3 . Animals were treated with vehicle or Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3) at the doses indicated in Fig. 1.
  • Compound A a MAPK pathway inhibitor of Formula I-A and provided in Table 3
  • Fig. 4 A waterfall plot illustrating percent tumor growth each for KRAS- mutant NSCLC- ADC models treated with the MAPK pathway inhibitor is presented in Fig. 4. Four examples of models that responded to treatment with the MAPK pathway inhibitor are shown in Fig. 1
  • Example 2 Analysis of gene expression in KRAS-mutant NSCLC adenocarcinomas.
  • Example 1 Results of the analyses are presented in Fig. 6, which shows that only overexpression of CCND1 was predictive of response to treatment with the MAPK pathway inhibitor (both for tumor growth inhibition (TGI) > 100% and > 80%).
  • Fig. 2 presents a receiver operator characteristic (ROC) analysis of the models that display tumor growth inhibition of > 100% following treatment with Compound A, using fragments per kilobase million (FKPM) of CCND1 as the criterion.
  • FKPM fragments per kilobase million
  • Fig. 3 presents the same ROC analysis, but for models that display tumor growth inhibition of > 80% following treatment with Compound A. With the 150 FKPM cutoff applied, 13 out of 24 samples were predicted to be sensitive to treatment with a MAPK pathway inhibitor.
  • Fig. 5 illustrates percent tumor growth for each model treated with Compound A, with the models stratified into two sets based on a CCND1 150 FKPM cutoff.
  • 21 out of 31 models predicted to be sensitive to treatment with a MAPK pathway inhibitor displayed at least 80% tumor growth inhibition following treatment with a MAPK pathway inhibitor (i.e., a disease control rate of 68%).
  • only 4 out of 30 models predicted to be resistant to treatment with a MAPK pathway inhibitor displayed at least 80% tumor growth inhibition following treatment with Compound A (i.e., a disease control rate of 13%).
  • the unselected population displayed a disease control rate of only 40%. Accordingly, the selection of subjects having a KRAS-mutant adenocarcinoma that overexpresses CCND1 for treatment with a MAPK pathway inhibitor represents a promising approach for more effectively treating this subpopulation.
  • Fig. 7 summarizes the IHC scores (% CCND1 positive) of a series of KRAS-mutant NSCLC-ADC samples and illustrates that there exists a dynamic range in the expression of CCND1 in KRAS-mutant NSCLC adenocarcinoma clinical biopsy specimens to use this criterion for patient selection.
  • Example 3 Efficacy studies in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in Example 1 is followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm 3 . Animals are treated with vehicle, cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, MK-8353, or
  • Example 4 Efficacy studies in cell-based models of CCNDl-high KRAS-mutant NSCLC adenocarcinoma.
  • Human CCNDl-high, KRAS-mutant NSCLC adenocarcinoma cell lines are grown to confluency, washed with Tumor Cell Media (DMEM + 10% FBS or IMDM + 20% FBS), and plated in 90 pL Tumor Cell Media at 5,000-10,000 cells/well.
  • Tumor Cell Media DMEM + 10% FBS or IMDM + 20% FBS
  • Example 5 Efficacy studies of combination treatments in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in Example 1 is followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm 3 . Animals are treated with vehicle, Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3), or Compound A in combination with a CDK4/6 inhibitor, such as palbociclib.
  • Compound A a MAPK pathway inhibitor of Formula I-A and provided in Table 3
  • Compound A in combination with a CDK4/6 inhibitor such as palbociclib.
  • Additional arms of the experiment test reduced dosage levels of Compound A (e.g., 50% of the maximum tolerated dose).
  • the combination of Compound A and palbociclib is expected to produce a synergistic effect in treating the KRAS-mutant NSCLC adenocarcinoma models.
  • Example 6 Efficacy studies of combination treatments in patient-derived xenograft models of CCNDl-high KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in
  • Example 1 tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm 3 . Animals are treated with vehicle; or cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, MK-8353, alone or in combination with a CDK4/6 inhibitor, such as palbociclib or ademaciclib.
  • a CDK4/6 inhibitor such as palbociclib or ademaciclib.
  • the combination of a MAPK pathway inhibitor with a CDK4/6 inhibitor is expected to produce a synergistic effect in treating the CCNDl-high KRAS-mutant NSCLC adenocarcinoma models.
  • Example 7 Efficacy studies of combination treatments in cell-based models of CCNDl- high KRAS-mutant NSCLC adenocarcinoma. Human CCNDl-high, KRAS-mutant NSCLC adenocarcinoma cell lines are grown to confluency, washed with Tumor Cell Media (DMEM +
  • the plates are allowed to stand at room temperature for 20 minutes before measuring the luminescent signal of each well.
  • IC 50 values of each compound are calculated for each cell line.
  • the combination of a MAPK pathway inhibitor and a CDK4/6 inhibitor is expected to produce a synergistic effect in treating the CCNDl-high KRAS-mutant NSCLC adenocarcinoma cell-based models.
  • Example 8 Efficacy studies in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma having differential expression of CDKN2A.
  • the general procedure outlined in Example 1 is followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm 3 . Animals are treated with vehicle or Compound A (a MAPK pathway inhibitor of Formula I- A and provided in Table 3), alone or in combination with palbociclib.
  • vehicle or Compound A a MAPK pathway inhibitor of Formula I- A and provided in Table 3
  • CDKN2A expression is expected to be a predictor of sensitivity to treatment with a MAPK pathway inhibitor.
  • Example 9 Inhibition Assays ofERK.
  • the inhibition of ERK activity by the compounds disclosed herein was determined using the Z’-LYTE kinase assay kit (Life Technologies) with a Ser/Thr 3 peptide substrate (Life Technologies) according to manufacturer’s instructions.
  • the assay was run with an ERK2 enzyme (Life Technologies) concentration of 0.47 ng/pL at 100 mM ATP (approximately the ATP K m for ERK2).
  • the IC50 values for the compounds were determined with 3-fold serial dilutions in duplicate.
  • the compounds were first diluted in 1 :3 dilutions in 100% DMSO at 100X the desired concentration, and then further diluted (1 :25) in 20 mM HEPES buffer (Invitrogen) to make 4X solutions prior to adding to the enzyme solution.
  • the final DMSO concentration in the assay was 1%.
  • Final reaction volume was 20 pL/well in 384-well plates.
  • Table 3 In vitro Erk2 IC50 data for select compounds (+++ represents 50 nM to 250 nM, and ++++ represents less than 50 nM).
  • Example 10 Tumor cell line proliferation assay.
  • the ability of one or more compounds of the disclosure to inhibit tumor cell line proliferation was determined according to standard procedures known in the art. For instance, an in vitro cellular proliferation assay was performed to measure the metabolic activity of live cells.
  • A375 cells ATCC
  • A375 cells ATCC were grown to near 80% confluence, trypsinized and seeded at 1500 cells/well at volume of 100 pL per well in full growth medium (10% FBS in DMEM or l0%FBS in RPMI) in a 96 well plate. The cells were incubated at 37 °C under 5% C0 2 for two hours to allow for attachment to the plates.
  • DMSO in l0%FBS DMEM or in l0%FBS RPMI DMSO in l0%FBS DMEM or in l0%FBS RPMI. Each concentration of the compounds was tested in duplicate. After 96 hours of compound treatment, CellTiter Glo reagent (Promega) was added at a 1 :5 dilution to each well of the cell plate and the cell plate was placed at room temperature for 30 minutes. The luminescence of the wells was determined using a Tecan plate reader. Each compound presented in Table 3 exhibited an IC50 of 250 nM or less in A375 cells (ATCC) when tested in this assay.
  • ATCC A375 cells
  • Example 11 Efficacy studies of combination treatments in patient-derived xenograft models of CCNDl-high KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in Example 1 was followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 200 mm 3 . Animals were treated with vehicle, Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3), palbociclib, or Compound A in combination with palbociclib. Compound A was administered at a dose of 125 mg/kg QW.
  • Compound A a MAPK pathway inhibitor of Formula I-A and provided in Table 3
  • a total of three NSCLC patient-derived xenograft models were treated in the same manner with either vehicle, Compound A, palbociclib, or Compound A in combination with palbociclib as presented in Fig. 8. The body weights of the treated animals over the study duration are depicted in Fig. 9.
  • the MAPK pathway inhibitor e.g., Compound A of Formula I-A
  • when administered in a sub-therapeutic dose in combination with a CDK4/6 inhibitor produced a pronounced synergistic effect in treating all three models.
  • Example 12 Comparative efficacy studies of single agents in patient-derived xenograft models of 1 lql3-amplified esophageal squamous-cell carcinoma.
  • Tumor fragments (2-3 mm in diameter) from stock mice inoculated with primary human ESCC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 250-300 mm 3 . Animals were treated with vehicle, Compound A (a MAPK inhibitor of Formula I-A and provided in Table 3), GDC-0994, or trametinib.
  • Compounds A was administered at a dose of 175 mg/kg QW or at a dose of 350 mg/kg QW.
  • GDC-0994 was administered at a dose of 100 mg/kg QD.
  • Trametinib was administered at a dose of 1 mg/kg QD.
  • the tumor volumes of the treated animals over the study duration are depicted in Fig. 10.
  • Compounds A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.
  • Example 13 Comparative efficacy studies of single agents in patient-derived xenograft models of 1 lql3-amplified head and neck squamous-cell carcinoma. The general procedure outlined in Example 12 was followed. Briefly, tumor fragments (2-3 mm in diameter) from stock mice inoculated with primary human HNSCC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 250- 300 mm 3 . Animals were treated with vehicle, Compound A (a MAPK inhibitor of Formula I-A and provided in Table 3), GDC-0994, or trametinib.
  • Compound A a MAPK inhibitor of Formula I-A and provided in Table 3
  • GDC-0994 a MAPK inhibitor of Formula I-A and provided in Table 3
  • trametinib trametinib.
  • Compound A was administered at a dose of 175 mg/kg QW or at a dose of 350 mg/kg QW.
  • GDC-0994 was administered at a dose of 100 mg/kg QD.
  • Trametinib was administered at a dose of 1 mg/kg QD.
  • the tumor volumes of the treated animals over the study duration are depicted in Fig. 11.
  • Compound A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.
  • Example 14 Comparative efficacy studies of single agents in patient-derived xenograft models of 1 lql3-amplified lung squamous-cell carcinoma. The general procedure outlined in
  • Example 12 was followed. Briefly, tumor fragments (2-3 mm in diameter) from stock mice inoculated with primary human LSCC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 250-300 mm 3 . Animals were treated with vehicle, Compound A (a MAPK inhibitor of Formula I-A and provided in Table 3), GDC-0994, or trametinib. Compound A was administered at a dose of 175 mg/kg QW or at a dose of 350 mg/kg QW. GDC-0994 was administered at a dose of 100 mg/kg QD. Trametinib was administered at a dose of 1 mg/kg QD.
  • Compound A was administered at a dose of 175 mg/kg QW or at a dose of 350 mg/kg QW.
  • GDC-0994 was administered at a dose of 100 mg/kg QD.
  • Trametinib was administered at a dose of 1 mg/kg QD.
  • the tumor volumes of the treated animals over the study duration are depicted in Fig. 12.
  • Compound A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.
  • Example 15 Comparative efficacy studies of single agents in patient-derived xenograft models of KRAS-mutated CCND 1 -over expressed non-small cell lung cancer .
  • Two comparative efficacy studies were carried out using KRAS-mutated CCND 1 -overexpressed non-small cell lung cancer cell lines, one utilizing LU11786 cells and the other utilizing LU11692 cells. Both studies were carried out according to the same procedure, which is as follows. Cryo-preserved tumor cells were thawed and inoculated subcutaneously into shaved NOD-SCID mice. The mice were stratified into groups when the average tumor size reached about 250-350 mm 3 .
  • Compound A a MAPK inhibitor of Formula I-A and provided in Table 3
  • GDC-0994 a MAPK inhibitor of Formula I-A and provided in Table 3
  • BVD-523 a trametinib
  • Compound A was administered at a dose of 300 mg/kg QW.
  • GDC-0994 was administered at a dose of 100 mg/kg QD.
  • BVD-523 (ulixertinib) was administered at a dose of 50 mg/kg BID.
  • Trametinib was administered at a dose of 1 mg/kg QD.
  • V 0.5(a x b) 2 , where a and b are the long and short diameters of the tumor, respectively.
  • Fig. 13 For the study using LU11786 tumor cells, the tumor volumes of the treated animals over the study duration are depicted in Fig. 13.
  • LU11692 tumor cells the tumor volumes of the treated animals over the study duration are depicted in Fig. 14.
  • Compound A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.

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Abstract

The present disclosure provides methods and systems for identifying and/or treating subjects having cancer, such as adenocarcinoma, who are more likely to respond to treatment with a MAPK pathway inhibitor.

Description

TREATMENT OF ADENOCARCINOMAS WITH MAPK PATHWAY INHIBITORS
CROSS-REFERENCE
[0001] This application claims the benefit of U.S. Provisional Application No. 62/723,368, filed August 27, 2018, and U.S. Provisional Application No. 62/780,707, filed December 17, 2018, each of which are incorporated herein by reference in their entirety.
BACKGROUND OF THE INVENTION
[0002] The MAPK pathway, also known as the RAS/RAF/MEK/ERK pathway, plays a central role in regulating cellular processes by relaying extracellular signals from ligand-bound cell surface receptor tyrosine kinases (RTKs) such as ErbB (e.g. EGFR, Her-2, etc), VEGF, PDGF, and FGF receptor tyrosine kinases. Activation of an RTK triggers a series of phosphorylation events, beginning with the activation of RAS, followed by recruitment and activation of RAF. Activated RAF then phosphorylates MAP kinase kinase (MEK) 1/2, which then phosphorylates ERK 1/2. ERK phosphorylation by MEK occurs on Y204 and T202 for ERK1 and Y185 and T183 for ERK2 (Ahn et ah, Methods in Emymology 2001, 332, 417-431). Phosphorylated ERK dimerizes and translocates to and accumulates in the nucleus (Khokhlatchev et ah, Cell 1998, 93, 605-615). In the nucleus, ERK is involved in several important cellular functions, including but not limited to nuclear transport, signal transduction, DNA repair, nucleosome assembly and translocation, and mRNA processing and translation (Ahn et ah, Molecular Cell 2000, 6, 1343-1354). ERK2 phosphorylates a multitude of regulatory proteins, including the protein kinases RSK90 and MAPKAP2 ((Bjorbaek et ah, 1995, J. Biol. Chem. 270, 18848; Rouse et ah, 1994, Cell 78, 1027), and transcription factors such as ATF2, ELK-l, c-FOS, and c-MYC (Raingeaud et ah, 1996, o/ . Cell Biol. 16, 1247; Chen et ah, 1993, Proc. Natl. Acad. Sci. U.S. A. 90, 10952; Oliver et ah, 1995, Proc. Soc. Exp. Biol. Med. 210, 162).
[0003] A wealth of studies have shown that genetic mutations and/or overexpression of protein kinases in the MAPK pathway lead to uncontrolled cell proliferation and tumor formation in proliferative diseases such as cancer. For example, some cancers contain mutations which result in the continuous activation of this pathway due to continuous production of growth factors. Other mutations can lead to defects in the deactivation of the activated GTP -bound RAS complex, again resulting in activation of the MAPK pathway. Mutated, oncogenic forms of RAS are found in 50% of colon and >90% pancreatic cancers as well as many others types of cancers (Kohl et ah, Science 1993, 260, 1834-1837). Recently, bRAF mutations have been identified in more than malignant melanomas (60%), thyroid cancers (greater than 40%) and colorectal cancers. These mutations in bRAF result in a constitutively active MAPK pathway cascade. Studies of primary tumor samples and cell lines have also shown constitutive or overactivation of the MAPK pathway in cancers of the pancreas, colon, lung, ovary and kidney (Hoshino, R. et ah, Oncogene 1999, 18, 813-822). Further, ERK2 has been shown to play a role in the negative growth control of breast cancer cells (Frey and Mulder, 1997, Cancer Res. 57, 628) and hyperexpression of ERK2 in human breast cancer has been reported (Sivaraman et ak, 1997, J Clin. Invest. 99, 1478). Activated ERK2 has also been implicated in the proliferation of endothelin-stimulated airway smooth muscle cells, suggesting a role for this kinase in asthma (Whelchel et ak, 1997, Am. J. Respir. Cell Mol. Biol. 16, 589). In view of the multitude of upstream (e.g. RAS, RAF) and downstream (e.g. ATF2, c-FOS, c- MYC) signaling proteins in the MAPK pathway that have been implicated in a wide range of disorders, including but not limited to cancer, the MAPK pathway has emerged as a prime target for drug development.
[0004] Cancer is the second leading cause of human death. Worldwide, millions of people die from cancer every year. In the ETnited States alone, cancer causes the death of well over a half-million people annually, with some 1.7 million new cases diagnosed per year (excluding basal cell and squamous cell skin cancers). Adenocarcinoma (ADC) is a histologically distinct form of cancer formed from glandular structures in epithelial tissue. Certain therapies are known to be more effective in some patient populations than others. Understanding these drug-responsive subtypes is of significant interest to patients and health care professionals so as to avoid a trial and error approach of treatment.
SUMMARY OF THE INVENTION
[0005] As such, there is a pressing need for a method of stratifying patients into populations based on the predicted sensitivity or resistance of a patient population to a particular treatment, including treatment with a MAPK pathway inhibitor. The present disclosure addresses this need in the art through the assessment of biomarkers that are indicative of patient populations that would be responsive to treatment with a MAPK pathway inhibitor. This allows for more timely and aggressive treatment as opposed to a trial and error approach. The compositions and methods herein may be useful for treating diseases dependent on the activity of the MAPK pathway, such as cancer. Preferably, the cancer is an adenocarcinoma, such as an adenocarcinoma of the lung.
[0006] In certain aspects, the present disclosure provides a method of treating a cancer in a subject in need thereof, wherein said cancer exhibits a KRAS mutation and wherein said cancer overexpresses CCNDl, comprising administering to the subject an effective dose of a mitogen- activated protein kinase (MAPK) pathway inhibitor. In some embodiments, the method comprises (a) assessing the cancer for overexpression of CCNDl; (b) evaluating the cancer for the presence of a KRAS mutation; and (c) administering the MAPK pathway inhibitor to the subject if both the CCND1 overexpression and the KRAS mutation are determined to be present.
[0007] In certain aspects, the present disclosure provides a method of treating a subject having cancer, wherein said cancer exhibits a KRAS mutation, comprising: (a) assessing the cancer for overexpression of CCND1; and (b) administering an effective dose of a MAPK pathway inhibitor to the subject if the overexpression of CCND1 is found to be present.
[0008] In practicing any of the subject methods, the overexpression may be assessed by: (a) detecting a level of mRNA; (b) detecting a level of cDNA produced from reverse transcription of mRNA; (c) detecting a level of polypeptide; (d) detecting a level of cell-free DNA; or (e) a nucleic acid amplification assay, a hybridization assay, sequencing, or a combination thereof. The overexpression may be characterized by an expression level of CCND1 in the cancer that is higher than a reference expression level of CCND1.
[0009] In practicing any of the subject methods, the KRAS mutation may be determined by sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography (DHPLC), or restriction fragment length polymorphism (RFLP) assay. In some embodiments, the KRAS mutation is determined by sequencing or PCR.
[0010] In certain aspects, the present disclosure provides a method of assessing a likelihood of a subject having cancer exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, the method comprising: (a) assessing an expression profile of CCND1 in a biological sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell; (b) evaluating the biological sample for the presence of a KRAS mutation; and (c) calculating, using a computer system, a weighted probability of MAPK pathway inhibitor responsiveness based on the expression profile and KRAS mutation status. In some embodiments, the method further comprises designating the subject as having a high probability of exhibiting a clinically beneficial response to treatment with the MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability of (c). The method may further comprise transmitting information concerning the likelihood to a receiver. In some embodiments, the method further comprises providing a recommendation based on the weighted probability. The
recommendation may comprise treating the subject with a MAPK pathway inhibitor. In some embodiments, a method described herein further comprises selecting a treatment based on the weighted probability. In some embodiments, the method further comprises administering the MAPK pathway inhibitor to the subject if the subject is designated as having a high probability of exhibiting a clinically beneficial response.
[0011] In certain aspects, the present disclosure provides a method of categorizing a cancer status of a subject, comprising: (a) obtaining a biological sample from the subject, the sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell of the subject; (b) assessing (1) a total expression level of CCND1 in the sample, and (2) the presence or absence of a KRAS mutation in the sample; (c) generating an expression profile based on a comparison between the total expression level and a reference level, wherein the reference level is derivable from a reference sample from a different subject having a known cancer status; (d) categorizing the cancer status of the subject of (a) based on the expression profile and the presence or absence of the KRAS mutation. The cancer may be categorized as likely sensitive to treatment with a MAPK pathway inhibitor if the total expression level is greater than the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor. In some embodiments, the known cancer status of the different subject is categorized as resistant to a MAPK pathway inhibitor or sensitive to a MAPK pathway inhibitor. In some embodiments, the categorizing step includes calculating, using a computer system, a likelihood of response of the subject to treatment with a MAPK pathway inhibitor based on the expression profile, wherein the likelihood is adjusted upward for each fold increase in the total expression level relative to the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor. In some embodiments, the method further comprises preparing a report comprising a prediction of the likelihood of response of the subject to treatment with the MAPK pathway inhibitor.
[0012] In practicing any of the subject methods, the reference level may represent an average total expression level of CCND1 in a plurality of cancer samples. A biological sample described herein may be a tissue biopsy or a tumor biopsy.
[0013] In practicing any of the subject methods, the assessing may be performed using a nucleic acid or protein from the subject. In some embodiments, the evaluating is performed using a nucleic acid or protein from the subject. In some embodiments, the cancer is an adenocarcinoma, such as a lung adenocarcinoma. In some embodiments, the cancer is non-small cell lung cancer.
[0014] In certain aspects, the present disclosure provides a method of downregulating MAPK signaling output in a plurality of lung adenocarcinoma cells with a MAPK pathway inhibitor, wherein at least one cell of the plurality exhibits a KRAS mutation, the method comprising: (a) assessing, in a biological sample comprising nucleic acid from the subject, a total expression level of CCND1; and (b) administering an effective dose of the MAPK pathway inhibitor to the plurality of cells if the total expression level is greater than a reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor. [0015] In practicing any of the subject methods, the MAPK pathway inhibitor may be a MEK inhibitor. In some embodiments, the MEK inhibitor is selected from cobimetinib, trametinib, binimetinib, selumetinib, HL-085, antroquinonol, E-6201, refametinib, pimasertib hydrochloride, CKI-27, WX-554, CIP- 137401, SHR-7390, sorafenib, SRX-2626, PD-0325901, ATR-002, ATR- 004, ATR-005, ATR-006, CS-3006, FCN-159, EDV-2209, GDC-0623, TAK-733, E-6201, RG- 7167, AZD-8330, PD-184352, GSK-2091976A, AS-703988, BI-847325, JTP-70902, CZ-775, RO- 5068760, RDEA-436, MEK-300, AD-GL0001, SL-327, ATR-001, PD-98059, RO-4987655, RO- 4927350, and AS-703026. In some embodiments, the MEK inhibitor is selected from cobimetinib, trametinib, binimetinib, and selumetinib. In some embodiments, the MEK inhibitor is trametinib. In
some embodiments, the MEK inhibitor is selected from
Figure imgf000007_0001
Figure imgf000007_0002
[0016] In practicing any of the subject methods, the MAPK pathway inhibitor may be a pan-RAF inhibitor. In some embodiments, the pan-RAF inhibitor is selected from LY3009120, LXH254, CCT3833 and AZ628. In some embodiments, the pan-RAF inhibitor is selected from LY3009120 and LXH254.
[0017] In practicing any of the subject methods, the MAPK pathway inhibitor may be an ERK inhibitor. In some embodiments, the ERK inhibitor is selected from ulixertinib, RG7842, GDC- 0994, CC-90003, ASN-007, AMO-01, KO-947, AEZS-134, AEZS-131, AEZS-140, AEZS-136, AEZS-132, D-87503, KIN-2118, RB-l, RB-3, SCH-772984, MK-8353, SCH-900353, FR-180204, IDN-5491, hyperforin trimethoxybenzoate, ERK1-2067, ERK1-23211, ERK1-624, LY3214996, AZ6197, ASTX029, and LTT462. In some embodiments, the ERK inhibitor is selected from ulixertinib, GDC-0994, SCH-772984, and MK-8353. In some embodiments, the ERK inhibitor is
selected from the group consisting of:
Figure imgf000008_0001
Figure imgf000008_0002
[0018] Optionally, the ERK inhibitor is a compound of Formula I:
Figure imgf000008_0003
(Formula I), wherein:
Figure imgf000008_0004
X2 is NRi or CRiRk and X3 is null, CR3R3’ or C=0; or X2-X is RIC=CR3 or RiC=N or N=CR3 or NR12-CRH=CR3;
X4 is N or CR4; X5 is N or C; X6 is N or C; X7 is O, N, NR72 or CR7i; X8 is O, N, NR82 or CR8l; X9 is O, N, NR22 or CR23; Xl0 is O, N, NR¾ or CR91;
Ri is-Ci-ioalkyl, -C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3.l0aryl, -Ci-iohetaryl, - C3-iocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci-ioalkyl-C3- iocydoalkyl, -Ci-ioalkyl-Ci-ioheterocydyl, -C2-ioalkenyl-C3-i0aryl, -C2-i0alkenyl-Ci.iohetaryl, -C2- l0alkenyl-C3-locydoalkyl, -C2-ioalkenyl-Ci.ioheterocyclyl, -C2-ioalkynyl-C3-i0aryl, -C2-i0alkynyl- C i-iohetaryl, -C2-ioalkynyl-C3-iocydoalkyl, -C2-ioalkynyl-Ci.ioheterocyclyl, -Ci-ioheteroalkyl-C3- !oaryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci-ioheteroalkyl-C3-iocydoalkyl, -Ci-ioheteroalkyl-Ci.
!oheterocydyl, -Ci-ioalkoxy-C3-ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci-ioalkoxy-C3-iocydoalkyl, -Ci. ioalkoxy-Ci-ioheterocydyl, -C3-i0aryl-Ci.ioalkyl, -C3-ioaryl-C2-i0alkenyl, -C3-ioaryl-C2-i0alkynyl, - C3-ioaryl-C3-iohetaryl, -C3-ioaryl-C3-iocydoalkyl, -C3-ioaryl-Ci-ioheterocydyl, -Ci-iohetaryl-Ci. !oalkyl, -Ci-iohetaryl-C2-ioalkenyl, -Ci-iohetaryl-C2-ioalkynyl, -C3-iohetaryl-C3-ioaryl, -Ci-iohetaryl- C3-l0cydoalkyl, -Ci-iohetaryl-Ci-ioheterocydyl, -C3-i0cydoalkyl-Ci.ioalkyl, -C3-i0cydoalkyl-C2- l0alkenyl, -C3-iocydoalkyl-C2-i0alkynyl, -C3-iocydoalkyl-C3-i0aryl, -C3-i0cydoalkyl-Ci.iohetaryl, - C3-iocydoalkyl-Ci-ioheterocydyl, -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci-ioheterocydyl-C2-ioalkenyl, - Ci-ioheterocydyl-C2-ioalkynyl, -Ci-ioheterocydyl-C3-ioaryl, -Ci-ioheterocydyl-Ci-iohetaryl, or -Ci. l0heterocydyl-C3-locydoalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
Ri’ is hydrogen, -Ci-ioalkyl, -C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3.l0aryl, -Ci. !ohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci. loalkyl-C3-locydoalkyl, -Ci-ioalkyl-Ci-ioheterocydyl, -C2-ioalkenyl-C3-i0aryl, -C2-i0alkenyl-Ci. iohetaryl, -C2-ioalkenyl-C3-i0cycloalkyl, -C2-ioalkenyl-Ci.ioheterocyclyl, -C2-ioalkynyl-C3-i0aryl, - C2-ioalkynyl-Ci-iohetaryl, -C2-ioalkynyl-C3-iocycloalkyl, -C2-ioalkynyl-Ci.ioheterocyclyl, -Ci.
loheteroalkyl-C3-loaryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci.ioheteroalkyl-C3-iocycloalkyl, -Ci.
ioheteroalkyl-Ci-ioheterocydyl, -Ci.ioalkoxy-C3-i0aryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci.i0alkoxy-C3- iocycloalkyl, -Ci-ioalkoxy-Ci-ioheterocydyl, -C3-i0aryl-Ci.ioalkyl, -C3-ioaryl-C2-i0alkenyl, -C3- loaryl-C2-loalkynyl, -C3-ioaryl-C3-iohetaryl, -C3-ioaryl-C3-iocycloalkyl, -C3-ioaryl-Ci.ioheterocyclyl, -Ci-iohetaryl-Ci-ioalkyl, -Ci-iohetaryl-C2-ioalkenyl, -Ci-iohetaryl-C2-ioalkynyl, -C3-iohetaryl-C3- l0aryl, -Ci.iohetaryl-C3-iocycloalkyl, -Ci-iohetaryl-Ci-ioheterocydyl, -C3-iocycloalkyl-Ci.ioalkyl, - C3-iocycloalkyl-C2-ioalkenyl, -C3-iocycloalkyl-C2-ioalkynyl, -C3-iocycloalkyl-C3-ioaryl, -C3- iocydoalkyl-Ci-iohetaryl, -C3-iocydoalkyl-Ci.ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci. loheterocyclyl-C2-loalkenyl, -Ci.ioheterocyclyl-C2-ioalkynyl, -Ci.ioheterocyclyl-C3-ioaryl, -Ci. loheterocyclyl-Ci-iohetaryl, or -Ci.ioheterocyclyl-C3-iocycloalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
R21 is hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, - C(=0)NR31, -N02, -CN, -S(0)O-2R31, -S02NR31R32, -NR31C(=0)R32, -NR31C(=0)0R32, - NR31C(=0)NR32R33, -NR31S(0)O-2R32, -C(=S)OR31, -C(=0)SR31, -NR31C(=NR32)NR32R33, - NR31C(=NR32)OR33, -NR31C(=NR32)SR33, -0C(=0)0R33, -0C(=0)NR31R32, -0C(=0)SR31, - SC(=0)SR31, -P(0)0R3 I0R32, -SC(=0)NR31R32, -L-Cl.ioalkyl, -L-C2-i0alkenyl, -L-C2-i0alkynyl, -L-Ci.ioheteroalkyl, -L-C3-i0aryl, -L-Ci.i0hetaryl, -L-C3-i0cycloalkyl, -L-Ci-ioheterocydyl, -L- Cl-loalkyl-C3-loaryl, -L-Ci-ioalkyl-Ci-iohetaryl, -L-Ci-ioalkyl-C3-iocycloalkyl, -L-Ci-ioalkyl-Ci. !oheterocyclyl, -L-C2-ioalkenyl-C3-ioaryl, -L-C2-ioalkenyl-Ci-iohetaryl, -L-C2-ioalkenyl-C3- iocycloalkyl, -L-C2-ioalkenyl-Ci.ioheterocyclyl, -L-C2-ioalkynyl-C3-i0aryl, -L-C2-i0alkynyl-Ci. iohetaryl, -L-C2-ioalkynyl-C3-i0cycloalkyl, -L-C2-ioalkynyl-Ci.ioheterocyclyl, -L-Ci-ioheteroalkyl- C3.l0aryl, -L -Ci-ioheteroalkyl-Ci-iohetaryl, -L -Ci-ioheteroalkyl-C3-iocycloalkyl, -L -Ci.
i oheteroal kyl -CM oheterocyd yl , -L-Ci-ioalkoxy-C3-ioaryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci. loalkoxy-C3-locycloalkyl, -L-Ci-ioalkoxy-Ci-ioheterocydyl, -L-C3-ioaryl-Ci-ioalkyl, -L-C3-ioaryl- C2-l0alkenyl, -L-C3-ioaryl-C2-i0alkynyl, -L-C3-i0aryl-Ci.iohetaryl, -L-C3-ioaryl-C3-i0cycloalkyl, - L-C3-ioaryl-Ci.ioheterocyclyl, -L-Ci-iohetaryl-Ci-ioalkyl, -L-Ci-iohetaryl-C2-ioalkenyl, -L-Ci. lohetaryl-C2-loalkynyl, -L-Ci-iohetaryl-C3-ioaryl, -L-Ci-iohetaryl-C3-iocycloalkyl, -L-Ci-iohetaryl- Cl-loheterocyclyl,-L-C3-locydoalkyl-Cl-loalkyl, -L-C3-iocydoalkyl-C2-i0alkenyl, -L-C3.
locycloalkyl-C2-loalkynyl, -L-C3-iocycloalkyl-C3-i0aryl, -L-C3-iocycloalkyl-Ci.iohetaryl, -L-C3. i ocycl oal kyl -C i . mheterocycl yl , -L-Ci-ioheterocyclyl-Ci-ioalkyl, -L-Ci-ioheterocyclyl-C2-ioalkenyl, -L-Ci-ioheterocyclyl-C2-ioalkynyl, -L-Ci-ioheterocyclyl-C3-ioaryl, -L-Ci-ioheterocydyl-Ci.
iohetaryl, or -L-Ci.ioheterocyclyl-C3-iocycloalkyl, each of which is unsubstituted or substituted by one or more independent R32 substituents;
R22 is hydrogen, -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, -S(O)0-2R31, -C(=S)OR31, - C(=0)SR31,-L-Ci-ioalkyl, -L-C2-ioalkenyl, -L-C2-ioalkynyl, -L-Ci-ioheteroalkyl, -L-C3-ioaryl, - L-Ci.iohetaryl, -L-C3-i0cycloalkyl, -L-Ci-ioheterocydyl, -L-Ci.ioalkyl-C3-i0aryl, -L-Ci.i0alkyl- Cl-l0hetaryl, -L-Ci.ioalkyl-C3-iocycloalkyl, -L-Ci-ioalkyl-Ci-ioheterocydyl, -L-C2-i0alkenyl-C3- !oaryl, -L-C2-ioalkenyl-Ci-iohetaryl, -L-C2-ioalkenyl-C3-iocycloalkyl, -L-C2-ioalkenyl-Ci.
!oheterocyclyl, -L-C2-ioalkynyl-C3-ioaryl, -L-C2-ioalkynyl-Ci-iohetaryl, -L-C2-ioalkynyl-C3- iocycloalkyl, -L-C2-ioalkynyl-Ci.ioheterocyclyl, -L-Ci.ioheteroalkyl-C3-ioaryl, -L -Ci.
ioheteroalkyl-Ci-iohetaryl, -L -Ci.ioheteroalkyl-C3-iocycloalkyl, -L -Ci-ioheteroalkyl-Ci.
ioheterocydyl, -L-Ci.ioalkoxy-C3-i0aryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci.i0alkoxy-C3- iocydoalkyl, -L-Ci-ioalkoxy-Ci-ioheterocydyl, -L-C3-i0aryl-Ci.ioalkyl, -L-C3-ioaryl-C2-i0alkenyl, -L-C3-ioaryl-C2-ioalkynyl, -L-C -1 oaryl -C 1.1 ohetaryl , -L-C3.ioaryl-C3.iocycloalkyl, -L-C3.ioaryl-Ci. !oheterocyclyl, -L-Ci-iohetaryl-Ci-ioalkyl, -L-C 1.1 ohetaryl -C2- 1 oal kenyl , -L-C M ohetaryl -C2.
l0alkynyl, -L-Ci-iohetaryl-C3-ioaryl,-L-Ci-iohetaryl-C3-iocycloalkyl, -L-Ci-iohetaryl-Ci.
ioheterocyclyl, -L-C3.iocycloalkyl-Ci.ioalkyl, -L-C3.iocydoalkyl-C2-ioalkenyl, -L-C3.i0cydoalkyl- C2-loalkynyl, -L-C3.iocydoalkyl-C3.ioaryl, -L-C3.iocydoalkyl-Ci.iohetaryl, -L-C3.iocydoalkyl-Ci. !oheterocydyl, -L-Ci-ioheterocydyl-Ci-ioalkyl, -L-Ci-ioheterocydyl-C2-ioalkenyl, -L-Ci.
1 oheterocyd yl -C2.10al kynyl , -L-Ci.ioheterocydyl-C3.ioaryl, -L-Ci-ioheterocydyl-Ci-iohetaryl, or - L-Ci.ioheterocydyl-C3.iocydoalkyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2- -C(=0)-, -C(=0)0- -0C(=0)-, -C(=0)N(R31)-, -
Figure imgf000011_0001
each of R3, R,’ and R4 is independently hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, - R31C(=0)R32,
Figure imgf000011_0002
i-ioalkyl, - C2-i0alkenyl, -C2-i0alkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci.
ioheterocyclyl, -Ci.ioalkyl-C3.ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.ioalkyl-C3.iocycloalkyl, -Ci.
1 oal kyl -C M oheterocyd yl , -C2-ioalkenyl-C3-ioaryl, -C2-ioalkenyl-Ci-iohetaryl, -C2-ioalkenyl-C3- iocycloalkyl, -C2-ioalkenyl-Ci.ioheterocyclyl, -C2-ioalkynyl-C3-ioaryl, -C2-ioalkynyl-Ci-iohetaryl, - C2-ioalkynyl-C3.iocycloalkyl, -C2-ioalkynyl-Ci.ioheterocyclyl, -Ci-ioheteroalkyl^.ioaryl, -Ci. ioheteroalkyl-Ci-iohetaryl, -Ci.ioheteroalkyl-C3.iocycloalkyl, -Ci-ioheteroalkyl-Ci-ioheterocyclyl, - Ci-ioalkoxy-C3-ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci.ioalkoxy-C3.iocycloalkyl, -Ci-ioalkoxy-Ci. !oheterocyclyl, -C3.ioaryl-Ci.ioalkyl, -C3-ioaryl-C2-ioalkenyl, -C3-ioaryl-C2-ioalkynyl, -C3.ioaryl-C3. iohetaryl, -C3.ioaryl-C3.iocycloalkyl, -C3.ioaryl-Ci.ioheterocyclyl, -Ci-iohetaryl-Ci-ioalkyl, -Ci.
1 ohetaryl -C2_i 0al kenyl, -Ci.iohetaryl-C2-ioalkynyl, -C3.iohetaryl-C3.ioaryl, -Ci.iohetaryl-C3.
iocycloalkyl, -Ci-iohetaryl-Ci-ioheterocyclyl, -C3.iocycloalkyl-Ci.ioalkyl, -C3.iocycloalkyl-C2- ioalkenyl, -C3.iocycloalkyl-C2-ioalkynyl, -C3-iocycloalkyl-C3-ioaryl, -C3.iocycloalkyl-Ci.iohetaryl, - C3-iocycloalkyl-Ci-ioheterocydyl, -Ci-ioheterocydyl-Ci-ioalkyl, -Ci.ioheterocyclyl-C2-ioalkenyl, - Ci.ioheterocyclyl-C2-ioalkynyl, -Ci.ioheterocyclyl-C3.ioaryl, -Ci-ioheterocydyl-Ci-iohetaryl, or -Ci. loheterocyclyl-C3-locydoalkyl, each of which is unsubstituted or substituted by one or more independent R13 substituents; or R3’ is -OR6, -NR6R34, -S(O)0-2R6, -C(=0)R6, -C(=0)0R6, - 0C(=0)R6, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring; or R3’ is -OR6, -NR6R34, -S(O)0-2R6, -C(=0)R6, -C(=0)0R6, - 0C(=0)R6, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring;
each of R5, R71, Rxi and R91 is independently hydrogen, halogen, -C M O alkyl, -C2.10 alkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -
Figure imgf000012_0001
R6 is hydrogen, -Ci.i0alkyl, -C2-i0alkenyl, -C2-i0alkynyl, -Ci-ioheteroalkyl, -C3.l0aryl, -Ci. !ohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl,— C 1.1 oal kyl -Cs- 1 oaryl , -Ci-ioalkyl-Ci-iohetaryl, -Ci- i0alkyl-C3-i0cycloalkyl, -Ci-i0alkyl-Ci-i0heterocyclyl, -C2-i0alkenyl-C3-ioaryl, -C2-i0alkenyl-Ci. lohetaryl, -C2.i0alkenyl-C3.i0cycloalkyl, -C2.i0alkenyl -Ci-ioheterocyclyl, -C2.ioalkynyl-C3.ioaryl, - C2.i0alkynyl-Ci-iohetaryl, -C2.i0alkynyl-C3.i0cycloalkyl, -C2.i0alkynyl-Ci.i0heterocyclyl, -Ci.
i0heteroalkyl-C3-i0aryl, -Ci-i0heteroalkyl-Ci-i0hetaryl, -C M oheteroal kyl -C 3- iocycl oal kyl , -Ci- ioheteroalkyl-Ci-ioheterocyclyl, -C M oal koxy-Ci- 1 oaryl , -Ci-i0alkoxy-Ci-iohetaryl, -C i-ioalkoxy-Cs- locycloalkyl, -Ci.i0alkoxy-Ci.ioheterocyclyl, -C3.ioaryl-Ci.i0alkyl, -C3.ioaryl-C2.i0alkenyl, -C3. i0aryl-C2.i0alkynyl, -C3.ioaryl-C3.iohetaryl, -C3.ioaryl-C3.i0cycloalkyl, -C3.i0aryl -Ci-ioheterocyclyl, -Ci-iohetaryl-Ci-ioalkyl, -CM0hetaryl-C2-i0alkenyl, -CM0hetaryl-C2-i0alkynyl, -C3-iohetaryl-C3- loaryl, -Ci-iohetaryl-C3-iocycloalkyl, -Ci-iohetaryl-Ci-ioheterocyclyl, -C3-iocycloalkyl-Ci-i0alkyl, - C3-iocycloalkyl-C2.i0alkenyl, -C3.i0cycloalkyl-C2.i0alkynyl, -C3.iocycloalkyl-C3.ioaryl, -C3.
locycloalkyl -Ci-iohetaryl, -C3.1 ocycl oal kyl -C M oheterocyd yl , -Ci.ioheterocyclyl-Ci.i0alkyl, -Ci. i0heterocyclyl-C2-i0alkenyl, -CM0heterocyclyl-C2-i0alkynyl, -C M oheterocyd yl -C3- 1 oaryl , -Ci- ioheterocyclyl-Ci-iohetaryl, or -Ci-ioheterocyclyl-C3-iocycloalkyl, each of which is unsubstituted or substituted by one or more independent R14 or R15 substituents;
each of R72, R82 and R92 is independently hydrogen, -CMO alkyl, -C2-i0alkenyl, -C2-i0 alkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, - CF3, -C(0)R31, -C02R31, -C(=0)NR31, -S(0)O-2R31, -C(=S)OR31, -C(=0)SR31;
each of Rio and RM is independently -CMO alkyl, -C2-i0alkenyl, -C2-i0 alkynyl, -Ci.
loheteroalkyl, -C3.i0aryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, RI2 R13 and R15 is independently hydrogen, halogen, -CMO alkyl, -C2-i0alkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, - OH, -CF3 -OCF3, -OR31, -NR3 1R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(0)O-2R31, - S02NR3 1R32, -NR31C(=0)R32, -NR3 1C(=0)0R32, -NR3 1C(=0)NR32R33, -NR31 S(0)O-2R32, - C(=S)OR31, -C(=0)SR31, -NR3 1C(=NR32)NR32R33, -NR3 1C(=NR32)OR33, -NR3 1C(=NR32)SR33, - 0C(=0)0R33, -0C(=0)NR3 1R32, -0C(=0)SR31, -SC(=0)SR31, -P(0)0R310R32, or - SC(=0)NR3 1NR32;
31 32 33 34
each of R , R , R and RJ t is independently hydrogen, halogen, -Cmo alkyl, -C2- l0alkenyl, -C2. l0 alkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci- ioheterocyclyl, or wherein R31 together with R32 form a heterocyclic ring;
wherein ring A comprises one or more heteroatoms selected from N, O, or S; and wherein if X7 is O or X2-X3 is RIC=CR3, ring A comprises at least two heteroatoms selected from N, O, or S; and
wherein if X2-X3 is RiC=N, at least one of X7 or X9 is not N.
[0019] In some embodiments, the ERK inhibitor is a compound of Formula I-A:
Figure imgf000013_0001
(Formula I-A),
or a pharmaceutically acceptable salt thereof.
[0020] In some embodiments, for a compound of Formula (I) or (I-A):
Ri is 3- to 6-membered heterocyclyl, -Ci.i0alkyl-(3- to 6-membered heterocyclyl), -(3- to 6- membered heterocyclyl)-Ci.i0alkyl, -(3- to 6-membered heterocyclyl)-C3-ioaryl, or -(3- to 6- membered heterocyclyl)-Ci.i0hetaryl, each of which is unsubstituted or substituted by one or more independent Ri0 or Rn substituents;
R2I is -L-C3.i0aryl or -L-Ci-iohetaryl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
L is a bond or -N(R31)-;
R72 is hydrogen;
each of Rio is independently-C3.i0aryl, -Ci-iohetaryl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn and Ri2 is independently halogen,—Cmo alkyl, -OH, -CF3 or -OR31; and each of R3 1 is independently hydrogen or -Cmo alkyl.
[0021] In some embodiments, the ERK inhibitor is selected from the group consisting of:
Figure imgf000014_0001
[0022] In practicing any of the subject methods, the MAPK pathway inhibitor may be selected from cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, and MK-8353.
[0023] In some embodiments, a method of the present disclosure further comprising administering a second therapeutic agent to the subject. In certain aspects, the present disclosure provides a method of treating an adenocarcinoma in a subject in need thereof, comprising administering to said subject a MAPK pathway inhibitor and a second therapeutic agent. In some embodiments, the second therapeutic agent is a CDK4/6 inhibitor. In some embodiments, the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF-06873600, voruciclib, FLX-925, ON-123300, BPI-16350, VS2-370, FCN-437c, BPI-l 178, IIIM-290, TQB-3616, BEBT-209, SRX-3177, GZ-38-1, IIIM-985, birociclib, CGP-82996, PD-171851, R-547, PAN-1215, NSC-625987, staurosporine, G1T28-1, G1T30-1, gossypin, AT-7519, P-276-00, AG-024322, PD-0183812 and INOC-005. In some embodiments, the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF-06873600, voruciclib and FLX-925. In some embodiments, the second therapeutic agent is selected from palbociclib, ribociclib and abemaciclib. INCORPORATION BY REFERENCE
[0024] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
BRIEF DESCRIPTION OF THE DRAWINGS
[0025] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:
[0026] FIG. 1 depicts tumor volumes of four sets of KRAS-mutant non-small cell lung
adenocarcinoma (NSCLC-ADC) models following treatment with a MAPK pathway inhibitor.
Each of the models depicted exhibits overexpression of CCND1. The specific KRAS mutations are provided in the figure for each set.
[0027] FIG. 2 presents a receiver operator characteristic (ROC) analysis of KRAS-mutant NSCLC- ADC models that display tumor growth inhibition of greater than 100% following treatment with a MAPK pathway inhibitor, using fragments per kilobase million (FKPM) of CCND1 as the criterion.
[0028] FIG. 3 presents an ROC analysis of KRAS-mutant NSCLC-ADC models that display tumor growth inhibition of greater than or equal to 80% following treatment with a MAPK pathway inhibitor, using FKPM of CCND1 as the criterion.
[0029] FIG. 4 illustrates percent tumor growth for KRAS-mutant NSCLC-ADC models treated with a MAPK pathway inhibitor.
[0030] FIG. 5 illustrates percent tumor growth for KRAS-mutant NSCLC-ADC models treated with a MAPK pathway inhibitor, with the models stratified into two sets based on CCND1 expression levels.
[0031] FIG. 6 presents a comparison of ROC analyses of CCND1, CDK6, EGFR, KRAS and TOPO-2.
[0032] FIG. 7 summarizes the IHC scores (% CCND1 positive) of a series of KRAS-mutant NSCLC-ADC samples.
[0033] FIG. 8 depicts tumor volumes of KRAS-mutant NSCLC-ADC models treated with either vehicle (black squares), a MAPK pathway inhibitor (black circles), a CDK4/6 inhibitor (open triangles) or the MAPK pathway inhibitor and the CDK4/6 inhibitor (open diamonds).
[0034] FIG. 9 depicts body weights of KRAS-mutant NSCLC-ADC murine models treated with either vehicle (black squares), a MAPK pathway inhibitor (black circles), a CDK4/6 inhibitor (open triangles) or the MAPK pathway inhibitor and the CDK4/6 inhibitor (open diamonds) over the study duration.
[0035] FIG. 10 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, and trametinib in a murine xenograft model produced using patient-derived 1 lql3-amplified ES0136 esophageal squamous-cell carcinoma cells.
[0036] FIG. 11 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, and trametinib in a murine xenograft model produced using patient-derived 1 lql3-amplified HN2195 head and neck squamous-cell carcinoma cells.
[0037] FIG. 12 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, and trametinib in a murine xenograft model produced using patient-derived 1 lql3-amplified LU6429 lung squamous-cell carcinoma cells.
[0038] FIG. 13 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, BVD-523 (ulixertinib), and trametinib in a murine xenograft model produced using patient-derived KRAS-mutated CCND1 -overexpressed LU11786 lung squamous-cell carcinoma cells.
[0039] FIG. 14 depicts comparative efficacy data for a MAPK pathway inhibitor, GDC-0994, BVD-523 (ulixertinib), and trametinib in a murine xenograft model produced using patient-derived KRAS-mutated CCND1 -overexpressed LU11692 lung squamous-cell carcinoma cells.
DETAILED DESCRIPTION OF THE INVENTION
[0040] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs.
[0041]“About” as used herein when referring to a measurable value such as an amount, a duration, and the like, is meant to encompass variations of ± 10% of a stated number or value.
[0042] The terms“polynucleotide”,“nucleotide”,“nucleotide sequence”,“nucleic acid” and “oligonucleotide” are used interchangeably. They refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA
(mRNA), transfer RNA, ribosomal RNA, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, primers, cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non- nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.
[0043] A“nucleotide probe” or“probe” refers to a polynucleotide used for detecting or identifying its corresponding target polynucleotide in a hybridization reaction.
[0044]“Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi -stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR, or the enzymatic cleavage of a polynucleotide by a ribozyme.
[0045] As used herein,“expression” refers to the process by which a polynucleotide is transcribed into mRNA and/or the process by which the transcribed mRNA (also referred to as a“transcript”) is subsequently translated into peptides, polypeptides, or proteins. The transcripts and the encoded polypeptides are collectedly referred to as“gene product.” If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell. The level of expression (or alternatively, the“expression level”) of a CCND1 gene can be determined, for example, by determining the level of CCND1 polynucleotides, polypeptides, and/or gene products.
[0046]“Differentially expressed” or“differential expression” as applied to a nucleotide sequence ( e.g ., a gene) or polypeptide sequence in a subject, refers to the differential production of the mRNA transcribed and/or translated from the nucleotide sequence or the protein product encoded by the nucleotide sequence. A differentially expressed sequence may be overexpressed or underexpressed as compared to the expression level of a reference sample (i.e., a reference level). As used herein, overexpression is an increase in expression and generally is at least 1.25 fold, or alternatively, at least 1.5 fold, or alternatively, at least 2 fold, or alternatively, at least 3 fold, or alternatively, at least 4 fold, or alternatively, at least 10 fold expression over that detected in a reference sample. As used herein, underexpression is a reduction in expression and generally is at least 1.25 fold, or alternatively, at least 1.5 fold, or alternatively, at least 2 fold, or alternatively, at least 3 fold, or alternatively, at least 4 fold, or alternatively, at least 10 fold expression under that detected in a reference sample. Underexpression also encompasses absence of expression of a particular sequence as evidenced by the absence of detectable expression in a test subject when compared to a reference sample.
[0047]“Signal transduction” is a process during which stimulatory or inhibitory signals are transmitted into and within a cell to elicit an intracellular response. A molecule can mediate its signaling effect via direct or indirect interaction with downstream molecules of the same pathway or related pathway(s). For instance, MAPK signaling can involve a host of downstream molecules including but not limited to one or more of the following proteins: RAS, RAF, MEK, EGFR,
ERK1, CCND1, KRAS, ERK2 and HRAS.
[0048] The terms“polypeptide”,“peptide” and“protein” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. As used herein the term“amino acid” refers to either natural and/or unnatural or synthetic amino acids, including glycine and both the D or L optical isomers, and amino acid analogs and peptidomimetics.
[0049] The terms“biomarker” and“marker” are used interchangeably herein to refer to a molecule which is differentially present in a sample taken from a subject of one phenotypic status ( e.g ., having an adenocarcinoma that is sensitive to a MAPK pathway inhibitor) as compared with another phenotypic status (e.g., having an adenocarcinoma that has low sensitivity to a MAPK pathway inhibitor). A biomarker is differentially present between different phenotypic statuses if the mean or median expression level of the biomarker in the different groups is calculated to be statistically significant. Common tests for statistical significance include, for example, t-test, ANOVA, Kruskal-Wallis, Wilcoxon, Mann-Whitney and odds ratio. Biomarkers, alone or in combination, can provide measures of relative risk that a subject belongs to one phenotypic status or another. Therefore, they are useful as markers for disease (diagnostics), therapeutic effectiveness of a drug (theranostics) and drug toxicity. The polynucleotides and polypeptides described herein can be used as biomarkers for certain cancers described herein.
[0050] A“reference sample” is an alternative sample or subject used in an experiment for comparison purpose.
[0051] The term“reference level” refers to a control level used to evaluate a test level. In some examples, a reference level may be a control. For example, a biomarker may be considered to be underexpressed when the expression level of that biomarker is lower than a reference level. The reference level can be determined by a plurality of methods, provided that the resulting reference level accurately provides a level of a biomarker above which exists a first group of subjects having a different probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor than that of a second group of patients having levels of the biomarker below the reference level. The reference level may be determined, for example, by measuring the level of expression of a biomarker in tumorous or non-tumorous cancer cells from the same tissue as the tissue of the cancer cells to be tested. In some examples, the reference level may be a level of a biomarker determined in vitro. A reference level may be determined by comparison of the level of a biomarker in populations of subjects having the same cancer. Two or more separate groups of subjects may be determined by identification of subsets of populations of the cohort that have the same or similar levels of a biomarker. Determination of a reference level can then be made based on a level that distinguishes these separate groups. A reference level may be a single number, equally applicable to every subject, or a reference level can vary according to specific
subpopulations of subjects. For example, older men may have a different reference level than younger men for the same cancer, and women may have a different reference level than men for the same cancer. Furthermore, the reference level may be some level determined for each subject individually. For example, the reference level may be a ratio of a biomarker level in a cancer cell of a subject relative to the biomarker level in a normal cell within the same subject. In some embodiments, a reference level is a numerical range of gene expression that is obtained from a statistical sampling from a population of individuals having cancer. The sensitivity of the individuals having cancer to treatment with a MAPK pathway inhibitor may be known. In certain embodiments, the reference level is derived by comparing gene expression to a control gene that is expressed in the same cellular environment at relatively stable levels ( e.g . a housekeeping gene such as an actin). Comparison to a reference level may be a qualitative assessment or a quantitative determination.
[0052] The terms“determining,”“measuring,”“evaluating,”“assessing,”“assaying,”“testing,” and“analyzing” are used interchangeably herein to refer to any form of measurement, and include determining if an analyte is present or not (e.g., detection). These terms can include both quantitative and/or qualitative determinations. Assessing may be relative or absolute. A relative amount could be, for example, high, medium or low. An absolute amount could reflect the measured strength of a signal or the translation of this signal strength into another quantitative format, such as micrograms/mL.“Detecting the presence of’ can include determining the amount of something present, as well as determining whether it is present or absent.
[0053] As used herein,“agent” or“biologically active agent” refers to a biological, pharmaceutical, or chemical compound or other moiety. Non-limiting examples include a simple or complex organic or inorganic molecule, a peptide, a protein, an oligonucleotide, an antibody, an antibody derivative, antibody fragment, a vitamin derivative, a carbohydrate, a toxin, or a chemotherapeutic compound. Various compounds can be synthesized, for example, small molecules and oligomers (e.g, oligopeptides and oligonucleotides), and synthetic organic compounds based on various core structures. In addition, various natural sources can provide compounds for screening, such as plant or animal extracts, and the like. A skilled artisan can readily recognize that there is no limit as to the structural nature of the agents of the present disclosure.
[0054] The terms“antagonist” and“inhibitor” are used interchangeably, and they refer to a compound having the ability to inhibit a biological function of a target protein or pathway (e.g., MAPK), whether by inhibiting the activity or expression of the target protein. Accordingly, the terms“antagonist” and“inhibitors” are defined in the context of the biological role of the target protein. While preferred antagonists herein specifically interact with (e.g., bind to) the target, compounds that inhibit a biological activity of the target protein by interacting with other members of the signal transduction pathway of which the target protein is a member are also specifically included within this definition. A preferred biological activity inhibited by an antagonist is associated with the development, growth, or spread of an adenocarcinoma, such as non-small cell lung cancer.
[0055] The term“cell proliferation” refers to a phenomenon by which the cell number has changed as a result of division. This term also encompasses cell growth by which the cell morphology has changed (e.g, increased in size) consistent with a proliferative signal.
[0056] The terms“co-administration,”“administered in combination with,” and their grammatical equivalents, encompass administration of two or more agents to a subject so that both agents and/or their metabolites are present in the subject at the same time. Co-administration includes
simultaneous administration in separate compositions, administration at different times in separate compositions, or administration in a composition in which both agents are present.
[0057] The term“effective amount” or“therapeutically effective amount” refers to that amount of a compound described herein that is sufficient to effect the intended application including but not limited to disease treatment, as defined below. The therapeutically effective amount may vary depending upon the intended application (in vitro or in vivo), or the subject and disease condition being treated, e.g, the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art. The term also applies to a dose that will induce a particular response in target cells, e.g, reduction of platelet adhesion and/or cell migration. The specific dose will vary depending on the particular compounds chosen, the dosing regimen to be followed, whether it is administered in combination with other compounds, timing of administration, the tissue to which it is administered, and the physical delivery system in which it is carried.
[0058] As used herein, the terms“treatment”,“treating”,“palliating” and“ameliorating” are used interchangeably. These terms refer to an approach for obtaining beneficial or desired results including, but are not limited to, therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant eradication or amelioration of the underlying disorder being treated (e.g., adenocarcinoma). Also, a therapeutic benefit is achieved with the eradication or amelioration of one or more of the physiological symptoms associated with the underlying disorder such that an improvement is observed in the patient, notwithstanding that the patient can still be afflicted with the underlying disorder. For prophylactic benefit, the pharmaceutical compositions may be administered to a patient at risk of developing a particular disease, or to a patient reporting one or more of the physiological symptoms of a disease, even though a diagnosis of this disease may not have been made.
[0059] A“therapeutic effect,” as used herein, encompasses a therapeutic benefit and/or a prophylactic benefit as described above. A prophylactic effect includes delaying or eliminating the appearance of a disease or condition, delaying or eliminating the onset of symptoms of a disease or condition, slowing, halting, or reversing the progression of a disease or condition, or any combination thereof.
[0060] The term“selective inhibition” or“selectively inhibit” as applied to a biologically active agent refers to the agent’s ability to selectively reduce the target signaling activity as compared to off-target signaling activity, via direct or indirect interaction with the target.
[0061] The term“subject” includes, but is not limited to, humans of any age group, e.g., a pediatric subject (e.g, infant, child or adolescent) or adult subject (e.g, young adult, middle-aged adult or senior adult)) and/or other primates (e.g, cynomolgus monkeys or rhesus monkeys); mammals, including commercially relevant mammals such as cattle, pigs, horses, sheep, goats, cats, and/or dogs; and/or birds, including commercially relevant birds such as chickens, ducks, geese, quail, and/or turkeys. The methods described herein can be useful in both human therapeutics and veterinary applications. In some embodiments, the patient is a mammal, and in some embodiments, the patient is human.
[0062]“Radiation therapy” or“radiation treatment” means exposing a patient, using routine methods and compositions known to the practitioner, to radiation emitters such as alpha-particle emitting radionucleotides (e.g, actinium and thorium radionuclides), low linear energy transfer (LET) radiation emitters (e.g, beta emitters), conversion electron emitters (e.g, strontium-89 and samarium- 153 -ED TMP), or high-energy radiation, including without limitation x-rays, gamma rays, and neutrons.
[0063] The term“in vivo” refers to an event that takes place in a subject’s body.
[0064] The term“in vitro’’ refers to an event that takes place outside of a subject’s body. For example, an in vitro assay encompasses any assay run outside of a subject’s body. In vitro assays encompass cell-based assays in which cells alive or dead are employed. In vitro assays also encompass a cell-free assay in which no intact cells are employed.
[0065]“MAPK pathway activity” as applied to a biologically active agent refers to the agent’s ability to modulate signal transduction mediated by Ras, Raf, MEK, and/or ERK. For example, modulation of MAPK pathway activity is evidenced by alteration in signaling output from the MAPK pathway.
[0066] The term“inhibiting MAPK pathway activity”, as used herein, refers to slowing, reducing, altering, as well as completely eliminating and/or preventing MAPK pathway activity.
[0067] The present inventors have discovered certain genes that are differentially expressed in adenocarcinoma cells that are sensitive to therapy with a MAPK pathway inhibitor, such as a compound described herein. More specifically, the disclosure relates to the use of an inhibitor of the mitogen-activated protein kinase (MAPK) pathway to treat adenocarcinoma, such as adenocarcinoma of the lung. Methods of using information about the expression status of the genes and/or the gene expression products to identify adenocarcinoma cells that will likely respond to therapy with a MAPK pathway inhibitor as well as methods of identifying subjects having adenocarcinoma that are predicted to exhibit a clinically beneficial response to treatment with a MAPK pathway inhibitor are described herein. In particular, overexpression of one or more of the genes may be indicative of sensitivity to therapy with a MAPK pathway inhibitor. The presence of certain mutations may further be indicative of sensitivity to therapy with a MAPK pathway inhibitor. ETse of certain DNA- and RNA-based biomarkers to identify adenocarcinomas more likely to display a robust therapeutic response to MAPK pathway inhibition are described.
[0068] In certain aspects, the present disclosure provides a method of treating a cancer in a subject in need thereof, wherein said cancer exhibits a KRAS mutation and wherein said cancer overexpresses CCND1. In some embodiments, the method comprises administering to the subject an effective dose of a mitogen-activated protein kinase (MAPK) pathway inhibitor. In some embodiments, the method comprises (a) assessing the cancer for overexpression of CCND1; (b) evaluating the cancer for the presence of a KRAS mutation; and (c) administering the MAPK pathway inhibitor to the subject if both the CCNDl overexpression and the KRAS mutation are determined to be present. Steps (a) and (b) may be performed in either order.
[0069] In certain aspects, the present disclosure provides a method of treating a subject having cancer, wherein said cancer exhibits a KRAS mutation, comprising (a) assessing the cancer for overexpression of CCNDl; and (b) administering an effective dose of a MAPK pathway inhibitor to the subject if the overexpression of CCNDl is found to be present. An alternative therapy, such as chemotherapy, immunotherapy, radiotherapy or surgery, may be applied to the subject if the overexpression of CCND1 is found to be absent.
[0070] In certain aspects, the present disclosure provides a method of downregulating MAPK signaling output in a plurality of lung adenocarcinoma cells with a MAPK pathway inhibitor, wherein at least one cell of the plurality exhibits a KRAS mutation. In some embodiments, the method comprises (a) assessing, in a biological sample comprising a nucleic acid from the subject, a total expression level of CCND1; and (b) administering an effective dose of the MAPK pathway inhibitor to the plurality of cells if the total expression level is greater than a reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
[0071] In certain aspects, the present disclosure provides a method of categorizing a cancer status of a subject. In some embodiments, the method comprises (a) obtaining a biological sample from the subject, the sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell of the subject; (b) assessing (1) a total expression level of CCND1 in the sample, and (2) the presence or absence of a KRAS mutation in the sample; (c) generating an expression profile based on a comparison between the total expression level and a reference level, wherein the reference level is derivable from a reference sample from a different subject having a known cancer status; and (d) categorizing the cancer status of the subject of (a) based on the expression profile and the presence or absence of the KRAS mutation. The cancer may be categorized as likely sensitive to treatment with a MAPK pathway inhibitor if the total expression level is greater than the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor. In some embodiments, the known cancer status of the different subject is categorized as resistant to a MAPK pathway inhibitor or sensitive to a MAPK pathway inhibitor. In some embodiments, the categorizing step includes calculating, using a computer system, a likelihood of response of the subject to treatment with a MAPK pathway inhibitor based on the expression profile, wherein the likelihood is adjusted upward for each fold increase in the total expression level relative to the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor. Optionally, the method further comprises preparing a report comprising a prediction of the likelihood of response of the subject to treatment with the MAPK pathway inhibitor.
[0072] In certain aspects, the present disclosure provides a method of assessing a likelihood of a subject having cancer exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, the method comprising: (a) assessing an expression profile of CCND1 in a biological sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell; (b) evaluating the biological sample for the presence of a KRAS mutation; and (c) calculating, using a computer system, a weighted probability of MAPK pathway inhibitor responsiveness based on the expression profile and KRAS mutation status. In some embodiments, the method further comprises designating the subject as having a high probability of exhibiting a clinically beneficial response to treatment with the MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability of (c). In some embodiments, the method further comprises transmitting information concerning the likelihood to a receiver. In some embodiments, the method further comprises providing a recommendation based on the weighted probability. The recommendation may comprise treating the subject with the MAPK pathway inhibitor, or, alternatively, discontinuing therapy, or administering one or more of chemotherapy, immunotherapy, radiotherapy or surgery. In some embodiments, the method further comprises selecting a treatment based on the weighted probability. In some embodiments, the method further comprises administering the MAPK pathway inhibitor to the subject based on the weighted probability. In some embodiments, the method further comprises administering the MAPK pathway inhibitor to the subject if the subject is designated as having a high probability of exhibiting a clinically beneficial response.
[0073] In some embodiments, the expression level is assessed by (a) detecting a level of mRNA;
(b) detecting a level of cDNA produced from reverse transcription of mRNA; (c) detecting a level of polypeptide; (d) detecting a level of cell-free DNA; and/or (e) a nucleic acid amplification assay, a hybridization assay, sequencing, or a combination thereof. In some embodiments, the presence or absence of a KRAS mutation is determined by sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography (DHPLC), or restriction fragment length polymorphism (RFLP) assay. Preferably, the presence or absence of a KRAS mutation is determined by sequencing or PCR.
[0074] A cancer, such as an adenocarcinoma, having a total expression level of CCND1 that is greater than a reference level of CCND1 may be more likely to respond to treatment with a MAPK pathway inhibitor than a cancer having a total expression level of CCND1 that is less than a reference level of CCND1. The reference level of CCND1 may be obtained by assessing a total expression level of CCND1 in a biological sample from one or more subjects having a cancer exhibiting low sensitivity to treatment with the MAPK pathway inhibitor. In some examples, the reference level is the average total expression level of CCND1 in a plurality of cancer samples. The plurality may comprise at least 5, 10, 20, 30, 40 or at least 50 samples. Overexpression of CCND1 may be characterized by an expression level of CCND1 in the cancer that is higher than a reference expression level of CCND1.
[0075] The total expression level of CCND1 may be compared to the reference level of CCND1 to calculate a weighted probability of MAPK pathway inhibitor responsiveness. Optionally, calculation of a weighted probability of MAPK pathway inhibitor responsiveness comprises assessment of both the total expression level of CCND1 and the KRAS mutation status. Optionally, the calculation is performed by a computer system. Any method of the present disclosure may further comprise designating a subject having cancer as having a high probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 15, or at least 20, such as at least 2 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability.
[0076] The methods described herein for qualifying or quantifying the expression of polypeptides and/or polynucleotides provide information which can be correlated with pathological conditions, predisposition to disease, therapeutic monitoring, risk stratification, among others. In some embodiments, a method of the disclosure is particularly useful for diagnosing conditions, evaluating whether a MAPK pathway inhibitor will have a desired effect, i.e., predicting responsiveness to a MAPK pathway inhibitor, and determining prognoses. The present methods may be used for the optimization of treatment protocols. In this context, evaluation of the expression profile of the biomarkers disclosed herein can be used to gain information on the treatment potential of a tissue sample with a MAPK pathway inhibitor.
[0077] In some embodiments, the disclosure provides methods for assessing a likelihood that a subject having cancer, especially adenocarcinoma, will exhibit a clinically beneficial response to treatment with a MAPK pathway inhibitor based on an expression profile of a gene or gene product. An“expression profile” refers to a pattern of expression of at least one biomarker, such as CCND1, that recurs in multiple samples and reflects a property shared by those samples, such as tissue type, response to treatment with a MAPK pathway inhibitor, or activation of a particular biological process or pathway in the cells. Furthermore, an expression profile differentiates between samples that share that common property and those that do not with better accuracy than would likely be achieved by assigning the samples to the two groups at random. An expression profile may be used to predict whether samples of unknown status share that common property or not. Some variation between the levels of the biomarker and the typical profile is to be expected, but the overall similarity of the expression levels to the typical profile is such that it is statistically unlikely that the similarity would be observed by chance in samples not sharing the common property that the expression profile reflects. An expression profile may be generated based on a comparison between a total expression level of a biomarker, such as CCND1, in a sample from a test subject and a corresponding reference level.
[0078] In some embodiments, the expression profile is used in a method of the disclosure to assess a likelihood of response to treatment with a MAPK pathway inhibitor. The likelihood of response may be adjusted upward when CCND1 is overexpressed. In some embodiments, the likelihood of response may be adjusted downward when CCND1 is underexpressed. The magnitude of under- or over-expression may be used to weight the amount of adjustment to the likelihood of response. Similarly, the likelihood of response may be adjusted upward when a KRAS mutation is present in the cancer, or the likelihood of response may be adjusted downward when a KRAS mutation is absent in the cancer.
[0079] In some embodiments, a method of the disclosure provides a reference level above which a biomarker, such as CCND1, must be expressed to be considered in assessing the likelihood of response to treatment with a MAPK pathway inhibitor. The biomarker may be differentially expressed at least 1.1 fold, at least 1.2 fold, at least 1.3 fold, at least 1.4 fold, at least 1.5 fold, at least 2.0 fold, at least 2.25 fold, at least 2.5 fold, at least 2.75 fold, at least 3.0 fold, at least 3.5 fold, at least 4.0 fold, at least 5.0, or even at least 10 fold higher or lower relative to a reference level to be considered in adjusting the likelihood of response. In some embodiments, the reference level is a numerical range of biomarker expression that is obtained from a statistical sampling from a population of individuals having cancer that has low sensitivity to treatment with a MAPK pathway inhibitor. In some embodiments, the reference level is a numerical range of biomarker expression that is obtained from a statistical sampling from a population of individuals having cancer that is resistant to treatment with a MAPK pathway inhibitor. The reference level may be a numerical range of biomarker expression that is obtained from a statistical sampling from a population of individuals having cancer, e.g ., the same cancer as the test subject. In some embodiments, the reference level is derived by comparison of sensitive and resistant populations.
[0080] In practicing any of the subject methods, the MAPK pathway inhibitor may be administered to the subject if a cancer of the subject exhibits both overexpression of CCND1 and a KRAS mutation.
[0081] Certain embodiments contemplate a human subject such as a subject that has been diagnosed as having or being at risk for developing or acquiring cancer, such as adenocarcinoma. Certain other embodiments contemplate a non-human subject, for example a non-human primate such as a macaque, chimpanzee, gorilla, vervet, orangutan, baboon or other non-human primate, including such non-human subjects that can be known to the art as preclinical models. Certain other embodiments contemplate a non-human subject that is a mammal, for example, a mouse, rat, rabbit, pig, sheep, horse, bovine, goat, gerbil, hamster, guinea pig or other mammal. There are also contemplated other embodiments in which the subject or biological source can be a non
mammalian vertebrate, for example, another higher vertebrate, or an avian, amphibian or reptilian species, or another subject or biological source. In certain embodiments of the present disclosure, a transgenic animal is utilized. A transgenic animal is a non-human animal in which one or more of the cells of the animal includes a nucleic acid that is non-endogenous (i.e., heterologous) and is present as an extrachromosomal element in a portion of its cell or stably integrated into its germ line DNA (i.e., in the genomic sequence of most or all of its cells).
[0082] Any cancer may be analyzed and/or treated according to the methods of the disclosure. The methods described herein are particularly effective in analyzing and/or treating adenocarcinoma. Exemplary adenocarcinomas include adenocarcinomas of the esophagus, pancreas, prostate, cervix, stomach, breast, colon and lung. In some embodiments, the cancer is a lung adenocarcinoma, such as non-small cell lung cancer. In some embodiments, the cancer is non-small cell lung
adenocarcinoma. In some embodiments, the cancer is an adenocarcinoma selected from lung, esophageal and pancreatic adenocarcinomas. In some embodiments, the cancer is selected from lung, esophageal, cervical, head and neck, bladder, gastric and pancreatic cancer. In some embodiments, the cancer is selected from breast cancer, pancreatic cancer, lung cancer, thyroid cancer, seminomas, melanoma, bladder cancer, liver cancer, kidney cancer, myelodysplastic syndrome, acute myelogenous leukemia and colorectal cancer. Preferably, the cancer is lung adenocarcinoma. In some embodiments, the lung adenocarcinoma is selected from lepidic adenocarcinoma, acinar adenocarcinoma, papillary adenocarcinoma, micropapillary
adenocarcinoma, solid adenocarcinoma, invasive mucinous adenocarcinoma, mixed invasive mucinous and nonmucinous adenocarcinoma, colloid adenocarcinoma, fetal adenocarcinoma, enteric adenocarcinoma, minimally invasive adenocarcinoma, preinvasive lesions, atypical adenomatous hyperplasia and adenocarcinoma in situ. In some embodiments, the adenocarcinoma is a non-small cell lung cancer.
[0083] Typically, a sample of a subject (e.g. a biological sample) comprises cancerous or pre- cancerous cells. The biological sample may be a tissue sample. The sample may be a solid biological sample, for example, a tissue biopsy or a tumor biopsy. A biopsy may be fixed, paraffin- embedded, fresh, or frozen. Samples may be obtained by any suitable means, including but not limited to needle aspiration, fine needle aspiration, core needle biopsy, vacuum assisted biopsy, large core biopsy, incisional biopsy, excisional biopsy, punch biopsy, shave biopsy, skin biopsy, and venipuncture. A sample may be derived from fine needle, core, or other types of biopsy, or may comprise circulating tumor cells. In some examples, a sample comprises cell-free DNA
(cfDNA). A biological sample may be a whole blood or plasma sample. A sample may be analyzed directly for its contents, or may be processed to purify one or more of its contents for analysis.
Methods of direct analysis of samples are known in the art and include, without limitation, mass spectrometry and histological staining procedures. In some embodiments, one or more components are purified from the sample for the detection of a biomarker for MAPK pathway inhibitor response. In some embodiments, the purified component of the sample is protein ( e.g . total protein, cytoplasmic protein, or membrane protein). In some embodiments, the purified component of the sample is a nucleic acid, such as DNA (e.g. genomic DNA, cDNA, ctDNA, or cfDNA) or RNA (e.g. total RNA or mRNA). In some embodiments, the nucleic acid is from a cancer cell, such as an adenocarcinoma cell.
[0084] Methods for the extraction, purification, and amplification of nucleic acids are known in the art. For example, nucleic acids can be purified by organic extraction with phenol,
phenol/chloroform/isoamyl alcohol, or similar formulations, including TRIzol and TriReagent.
Other non-limiting examples of extraction techniques include: organic extraction followed by ethanol precipitation, e.g. , using a phenol/chloroform organic reagent (Ausubel el al. , 1993), with or without the use of an automated nucleic acid extractor, e.g. , the Model 341 DNA Extractor available from Applied Biosystems (Foster City, Calif); stationary phase adsorption methods (U.S. Pat. No. 5,234,809; Walsh et al. , 1991); and salt-induced nucleic acid precipitation methods (Miller et al ., (1988), such precipitation methods being typically referred to as“salting-out” methods.
Another example of nucleic acid isolation and/or purification includes the use of magnetic particles to which nucleic acids can specifically or non-specifically bind, followed by isolation of the beads using a magnet, and washing and eluting the nucleic acids from the beads (see e.g. U.S. Pat. No. 5,705,628). In some embodiments, the above isolation methods may be preceded by an enzyme digestion step to help eliminate unwanted protein from the sample, e.g. , digestion with proteinase K, or other like proteases. See, e.g. , U.S. Pat. No. 7,001,724. If desired, RNase inhibitors may be added to the lysis buffer. For certain cell or sample types, it may be desirable to add a protein denaturati on/digestion step to the protocol. Purification methods may be directed to isolate DNA, RNA, or both. When both DNA and RNA are isolated together during or subsequent to an extraction procedure, further steps may be employed to purify one or both separately from the other. Sub-fractions of extracted nucleic acids can also be generated, for example, purification by size, sequence, or other physical or chemical characteristics. In addition to an initial nucleic acid isolation step, purification of nucleic acids can be performed after any step in the methods of the disclosure, such as to remove excess or unwanted reagents, reactants, or products.
[0085] In some embodiments, sample polynucleotides are fragmented into a population of fragmented DNA molecules of one or more specific size range(s). In some embodiments, fragments are generated from about or at least about 1, 10, 100, 1000, 10000, 100000, 300000, 500000, or more genome-equivalents of starting DNA. Fragmentation may be accomplished by methods known in the art, including chemical, enzymatic, and mechanical fragmentation. In some embodiments, the fragments have an average length from about 10 to about 10,000 nucleotides. In some embodiments, the fragments have an average length from about 50 to about 2,000
nucleotides. In some embodiments, the fragments have an average or median length from about 10- 2,500, 10-1,000, 10-800, 10-500, 50-500, 50-250, 50-150, or 100-2,500 nucleotides. In some embodiments, the fragmentation is accomplished mechanically by subjecting sample
polynucleotides to acoustic sonication. In some embodiments, the fragmentation comprises treating the sample polynucleotides with one or more enzymes under conditions suitable for the one or more enzymes to generate double-stranded nucleic acid breaks. Examples of enzymes useful in the generation of polynucleotide fragments include sequence specific and non-sequence specific nucleases. Non-limiting examples of nucleases include DNase I, Fragmentase, restriction endonucleases, variants thereof, and combinations thereof. For example, digestion with DNase I can induce random double-stranded breaks in DNA in the absence of Mg++ and in the presence of Mn++. In some embodiments, fragmentation comprises treating the sample polynucleotides with one or more restriction endonucleases. Fragmentation can produce fragments having 5’ overhangs, 3’ overhangs, blunt ends, or a combination thereof. In some embodiments, such as when fragmentation comprises the use of one or more restriction endonucleases, cleavage of sample polynucleotides leaves overhangs having a predictable sequence. In some embodiments, the method includes the step of size selecting the fragments via standard methods such as column purification or isolation from an agarose gel.
[0086] In some embodiments, one or more polynucleotides from a sample of a subject are amplified. In general, amplification comprises generating one or more copies of all or a portion of polynucleotides in a template-dependent manner. Amplification may be primer-dependent, or primer-independent. When primer-dependent, amplification may be directed to one or more specific polynucleotides in a sample or portions thereof, such as one or more regions ( e.g . about or more than about 1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 200, 500, or more regions), each region comprising one or more sequences of interest, and having a length of about, less than about, or more than about 1, 5, 10, 25, 50, 100, 150, 200, 250, 350, 500, 1000, 2000, or more nucleotides. Amplification may be linear or non-linear (e.g. exponential). Amplification may comprise directed changes in temperature, or may be isothermal. Methods for primer-directed amplification of target polynucleotides are known in the art, and include without limitation, methods based on the polymerase chain reaction (PCR). Conditions favorable to the amplification of target sequences by PCR are known in the art, can be optimized at a variety of steps in the process, and depend on characteristics of elements in the reaction, such as target type, target concentration, sequence length to be amplified, sequence of the target and/or one or more primers, primer length, primer concentration, polymerase used, reaction volume, ratio of one or more elements to one or more other elements, some or all of which can be altered. In general, PCR involves the steps of denaturation of the target to be amplified (if double stranded), hybridization of one or more primers to the target, and extension of the primers by a DNA polymerase, with the steps repeated (or “cycled”) in order to amplify the target sequence. Steps in this process can be optimized for various outcomes, such as to enhance yield, decrease the formation of spurious products, and/or increase or decrease specificity of primer annealing. Methods of optimization are well known in the art and include adjustments to the type or amount of elements in the amplification reaction and/or to the conditions of a given step in the process, such as temperature at a particular step, duration of a particular step, and/or number of cycles. In some embodiments, an amplification reaction comprises at least 5, 10, 15, 20, 25, 30, 35, 50, or more cycles. In some embodiments, an amplification reaction comprises no more than 5, 10, 15, 20, 25, 35, 50, or more cycles. Cycles can contain any number of steps, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more steps. Steps can comprise any temperature or gradient of temperatures, suitable for achieving the purpose of the given step, including but not limited to, primer annealing, primer extension, and strand denaturation. Steps can be of any duration, including but not limited to about, less than about, or more than about 1, 5, 10,
15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 120, 180, 240, 300, 360, 420, 480, 540, 600, or more seconds, including indefinitely until manually interrupted. Cycles of any number comprising different steps can be combined in any order. In some embodiments, different cycles comprising different steps are combined such that the total number of cycles in the combination is about, less that about, or more than about 5, 10, 15, 20, 25, 30, 35, 50, or more cycles.
[0087] A total expression level of a biomarker, such as CCND1, may be assessed by any appropriate method. The expression level of a biomarker may be assessed by detecting a level of mRNA transcribed from the biomarker, by detecting a level of cDNA produced from reverse transcription of mRNA transcribed from the biomarker, by detecting a level of polypeptide encoded by the biomarker, or by a nucleic acid amplification assay, a hybridization assay, sequencing, or a combination thereof. Regulation of a target gene or gene transcript can also be determined indirectly, such as by measuring the effect on a phenotypic indicator of the gene or gene transcript activity, such as by cellular assay. Methods of detecting gene expression products are known in the art, examples of which are described herein. These methods can be performed on a sample by sample basis or modified for high throughput analysis, for example, using Affymetrix™ U133 microarray chips.
[0088] Optionally, assessment of a total expression level of a gene, such as CCND1, comprises forming a plurality of complexes, each complex comprising an association between an expression product of the gene and a nucleic acid probe that hybridizes to the expression product of the gene. The nucleic acid probe may comprise a first nucleic acid complex, wherein the complex comprises (i) a first target-specific sequence capable of binding to a target nucleic acid, (ii) a first label attachment region, which is non-overlapping with the first target-specific sequence, comprising a first DNA sequence hybridized to a first nucleic acid molecule that is attached to one or more detectable labels that emit light which constitutes a first signal, (iii) a second label attachment region, which is non-overlapping with the first target-specific sequence and the first label attachment region, comprising a second DNA sequence hybridized to a second nucleic acid molecule that is attached to one or more detectable labels that emit light which constitutes a second signal, and (iv) a first moiety that is capable of selectively binding to the substrate. Optionally, the nucleic acid probe further comprises a second nucleic acid complex, the second complex comprising (i) a second target-specific sequence capable of binding to the target nucleic acid, wherein the first target-specific sequence and the second target-specific sequence bind to different regions of the target nucleic acid, and (ii) a second moiety that is capable of selectively binding to the substrate. In some embodiments, the first nucleic acid molecule comprises at least one additional attachment region which is non-overlapping with other label attachment regions. The at least one additional label attachment region may comprise a DNA sequence hybridized to a nucleic acid molecule that is attached to at least one detectable label that emits light. The at least one additional label attachment region may comprise a DNA sequence hybridized to a nucleic acid molecule that is not attached to a detectable label that emits light. In some embodiments, the first and second nucleic acid molecules each comprise four or more aminoallyl-modified UTP nucleotides, wherein one or more fluorophore labels is attached to each aminoallyl-modified UTP nucleotide. The first moiety and/or the second moiety may each be independently selected from biotin, digoxigenin, FITC, avidin, streptavidin, antidigoxigenin and anti-FITC.
[0089] In a preferred embodiment, the nCounter® Analysis system is used to detect gene expression. The basis of the nCounter® Analysis system is the unique code assigned to each nucleic acid target to be assayed (see, e.g., W02008/0124847, U.S. Pat. No. 8,415,102 and Geiss et al. Nature Biotechnology 2008 26(3): 317-325, the contents of which are each incorporated herein by reference in their entireties). The code is composed of an ordered series of colored fluorescent spots which create a unique barcode for each target to be assayed. A pair of nucleic acid probes is designed for each DNA or RNA target described herein, a capture probe and a reporter probe carrying the fluorescent barcode. This system is also referred to herein as the nanoreporter code system. See also WO2016/085841, WO2016/081740, WO2016/022559, and U.S. Pub. Nos.
2013/0017971, 2013/0230851 and 2014/0154681, each incorporated herein by reference.
[0090] Detection of nucleic acids may involve the use of a hybridization reaction, such as between a target nucleic acid and an oligonucleotide probe or primer ( e.g ., a nucleic acid hybridization assay). In some embodiments, the oligonucleotide probe is immobilized on a substrate. Substrates include, but are not limited to, arrays, microarrays, wells of a multi-well plate, and beads (e.g. non magnetic, magnetic, paramagnetic, hydrophobic, and hydrophilic beads). Examples of materials useful as substrates include but are not limited to nitrocellulose, glass, silicon, and a variety of gene arrays. A preferred hybridization assay is conducted on high-density gene chips as described in U.S. Pat. No. 5,445,934.
[0091] The expression level of a gene may be determined through exposure of a nucleic acid sample to the probe-modified chip. Extracted nucleic acid is labeled, for example, with a
fluorescent tag, preferably during an amplification step. Hybridization of the labeled sample is performed at an appropriate stringency level. The degree of probe-nucleic acid hybridization may be quantitatively measured using a detection device. See U.S. Pat. Nos. 5,578,832 and 5,631,734.
[0092] Alternatively any one of gene copy number, transcription, or translation can be determined using known techniques. For example, an amplification method such as PCR may be useful.
General procedures for PCR are taught in MacPherson et al ., PCR: A Practical Approach, (IRL Press at Oxford University Press (1991)). PCR conditions used for each application reaction are empirically determined. A number of parameters influence the success of a reaction. Among them are annealing temperature and time, extension time, Mg2+ and/or ATP concentration, pH, and the relative concentration of primers, templates, and deoxyribonucleotides. After amplification, the resulting DNA fragments can be detected by agarose gel electrophoresis followed by visualization with ethidium bromide staining and ultraviolet illumination.
[0093] The hybridized nucleic acids may be detected by detecting one or more labels attached to the sample nucleic acids. The labels can be incorporated by any of a number of means well known to those of skill in the art. However, in one embodiment, the label is simultaneously incorporated during the amplification step in the preparation of the sample nucleic acid. Thus, for example, polymerase chain reaction (PCR) with labeled primers or labeled nucleotides will provide a labeled amplification product. In a separate embodiment, transcription amplification, as described above, using a labeled nucleotide (e.g. fluorescein-labeled UTP and/or CTP) incorporates a label in to the transcribed nucleic acids.
[0094] Alternatively, a label may be added directly to the original nucleic acid sample (e.g, mRNA, polyA, cDNA, etc.) or to the amplification product after the amplification is completed. Means of attaching labels to nucleic acids are well known to those of skill in the art and include, for example nick translation or end-labeling (e.g. with a labeled RNA) by kinasing of the nucleic acid and subsequent attachment (ligation) of a nucleic acid linker joining the sample nucleic acid to a label (e.g, a fluorophore).
[0095] Suitable detectable labels may include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels include, for example, biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g, Dynabeads™), fluorescent dyes (e.g, fluorescein, Texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g, 3H, 1251, 35S, 14C, or 32P) enzymes (e.g, horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and calorimetric labels such as colloidal gold or colored glass or plastic (e.g, polystyrene, polypropylene, latex, etc.) beads.
Patents teaching the use of such labels include U.S. Pat. Nos. 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149; and 4,366,241.
[0096] Detection of labels is well known to those of skill in the art. Thus, for example, radiolabels may be detected using photographic film or scintillation counters. Fluorescent markers may be detected using a photodetector to detect emitted light. Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate. Calorimetric labels may be detected by simply visualizing the colored label.
[0097] A biomarker (e.g, CCND1) may be detected in a biological sample using a microarray. Differential gene expression can also be identified, or confirmed using the microarray technique. Thus, the expression profile can be measured in either fresh or fixed tissue, using microarray technology. In this method, polynucleotide sequences of interest (including cDNAs and
oligonucleotides) are plated, or arrayed, on a microchip substrate. The arrayed sequences are then hybridized with specific DNA probes from cells or tissues of interest. The source of mRNA typically is total RNA isolated from a biological sample, and corresponding normal tissues or cell lines may be used to determine differential expression.
[0098] In a specific embodiment of the microarray technique, PCR amplified inserts of cDNA clones are applied to a substrate in a dense array. Preferably at least 10,000 nucleotide sequences are applied to the substrate. The microarrayed genes, immobilized on the microchip at 10,000 elements each, are suitable for hybridization under stringent conditions. Fluorescently labeled cDNA probes may be generated through incorporation of fluorescent nucleotides by reverse transcription of RNA extracted from tissues of interest. Labeled cDNA probes applied to the chip hybridize with specificity to each spot of DNA on the array. After stringent washing to remove non-specifically bound probes, the microarray chip is scanned by a device, such as confocal laser microscopy, or by another detection method, such as a CCD camera. Quantitation of hybridization of each arrayed element allows for assessment of corresponding mRNA abundance. With dual color fluorescence, separately labeled cDNA probes generated from two sources of RNA are hybridized pair-wise to the array. The relative abundance of the transcripts from the two sources corresponding to each specified gene is thus determined simultaneously. Microarray analysis can be performed by commercially available equipment, following manufacturer’s protocols.
[0099] The biomarker may be detected in a biological sample using qRT-PCR, which can be used to compare mRNA levels in different sample populations, in normal and tumor tissues, with or without drug treatment, to characterize patterns of gene expression, to discriminate between closely related mRNAs, and to analyze RNA structure. The first step in gene expression profiling by RT- PCR is extracting RNA from a biological sample followed by the reverse transcription of the RNA template into cDNA and amplification by a PCR reaction. The reverse transcription reaction step is generally primed using specific primers, random hexamers, or oligo-dT primers, depending on the goal of expression profiling. The two commonly used reverse transcriptases are avilo
myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MLV-RT).
[0100] Although the PCR step can use a variety of thermostable DNA-dependent DNA
polymerases, it typically employs the Taq DNA polymerase, which has a 5’-3’ nuclease activity but lacks a 3’-5’ proofreading endonuclease activity. Thus, TaqMan™ PCR typically utilizes the 5’- nuclease activity of Taq or Tth polymerase to hydrolyze a hybridization probe bound to its target amplicon, but any enzyme with equivalent 5’ nuclease activity can be used. Two oligonucleotide primers are used to generate an amplicon typical of a PCR reaction. A third oligonucleotide, or probe, is designed to detect the nucleotide sequence located between the two PCR primers. The probe is non-extendible by Taq DNA polymerase enzyme, and is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe. During the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template- dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.
[0101] Differential expression of a biomarker ( e.g ., CCND1) can also be determined by examining protein expression or the protein product of the biomarker, for example, using a suitable protein assay. Determining the protein level involves measuring the amount of any immunospecific binding that occurs between an antibody that selectively recognizes and binds to the polypeptide of the biomarker in a test sample and comparing this to the amount of immunospecific binding of at least one biomarker in a reference sample. The amount of protein expression of the biomarker may be increased or reduced when compared with a reference expression level.
[0102] A variety of techniques are available in the art for protein analysis. They include but are not limited to radioimmunoassays, ELISA (enzyme linked immunosorbent assays),“sandwich” immunoassays, immunoradiometric assays, in situ immunoassays (using e.g., colloidal gold, enzyme or radioisotope labels), western blot analysis, immunoprecipitation assays,
immunofluorescent assays, flow cyto etry, immunohistochemistry, confocal microscopy, enzymatic assays, surface plasmon resonance and PAGE-SDS.
[0103] The present disclosure provides methods for detecting biomarkers, such as CCND1, in a biological sample. Useful analyte capture agents that can be used with the present disclosure include but are not limited to antibodies, such as crude serum containing antibodies, purified antibodies, monoclonal antibodies, polyclonal antibodies, synthetic antibodies, antibody fragments (for example, Fab fragments); antibody interacting agents, such as protein A, carbohydrate binding proteins, and other interactants; protein interactants (for example avidin and its derivatives);
peptides; and small chemical entities, such as enzyme substrates, cofactors, metal ions/chelates, and haptens. Antibodies may be modified or chemically treated to optimize binding to targets or solid surfaces (e.g. biochips and columns).
[0104] In some embodiments, the biomarker can be detected in a biological sample using an immunoassay. Immunoassays are assays that use an antibody that specifically binds to or recognizes an antigen (e.g. site on a protein or peptide, biomarker target). The method includes the steps of contacting the biological sample with the antibody and allowing the antibody to form a complex with the antigen in the sample, washing the sample and detecting the antibody-antigen complex with a detection reagent. In one embodiment, antibodies that recognize the biomarkers may be commercially available. In another embodiment, an antibody that recognizes the biomarkers may be generated by known methods of antibody production.
[0105] Alternatively, the biomarker in the sample can be detected using an indirect assay, wherein, for example, a second, labeled antibody is used to detect bound biomarker-specific antibody. Exemplary detectable labels include magnetic beads ( e.g ., DYNABEADS™), fluorescent dyes, radiolabels, enzymes (e.g., horse radish peroxide, alkaline phosphatase and others commonly used), and calorimetric labels such as colloidal gold or colored glass or plastic beads. The biomarker in the sample can be detected using and/or in a competition or inhibition assay wherein, for example, a monoclonal antibody which binds to a distinct epitope of the marker is incubated simultaneously with the mixture.
[0106] The conditions to detect an antigen using an immunoassay will be dependent on the particular antibody used. Also, the incubation time will depend upon the assay format, biomarker, volume of solution, concentrations and the like. In general, the immunoassays will be carried out at room temperature, although they can be conducted over a range of temperatures, such as 10 to 40 °C, depending on the antibody used.
[0107] There are various types of immunoassays known in the art that as a starting basis can be used to tailor the assay for the detection of the biomarkers (e.g, CCNDl) of the present disclosure. ETseful assays can include, for example, an enzyme immune assay (EIA) such as enzyme-linked immunosorbent assay (ELISA). There are many variants of these approaches, but those are based on a similar idea. For example, if an antigen can be bound to a solid support or surface, it can be detected by reacting it with a specific antibody, and the antibody can be quantitated by reacting it with either a secondary antibody or by incorporating a label directly into the primary antibody. Alternatively, an antibody can be bound to a solid surface and the antigen added. A second antibody that recognizes a distinct epitope on the antigen can then be added and detected. This is frequently called a‘sandwich assay’ and can frequently be used to avoid problems of high background or non-specific reactions. These types of assays are sensitive and reproducible enough to measure low concentrations of antigens in a biological sample.
[0108] Proximity ligation assay (PLA) is another type of immunoassay known in the art useful for the detection of the biomarkers of the present disclosure. The term“proximity ligation assay” or “PLA” as used herein refers to an immunoassay utilizing so-called PLA probes - affinity reagents such as antibodies modified with DNA oligonucleotides - for detecting and reporting the presence of proteins either in solution or in situ. When two PLA probes bind the same or two interacting target molecules, the attached oligonucleotides are brought in close proximity. A proximity ligation assay may be tailored to detect the biomarkers disclosed herein.
[0109] Immunoassays can be used to determine presence or absence of a biomarker in a sample as well as the quantity of a biomarker in a sample. Methods for measuring the amount of, or presence of, an antibody-biomarker complex include but are not limited to, fluorescence, luminescence, chemiluminescence, absorbance, reflectance, transmittance, birefringence or refractive index (e.g, surface plasmon resonance, ellipsometry, a resonant mirror method, a grating coupler waveguide method or interferometry). In general these regents are used with optical detection methods, such as various forms of microscopy, imaging methods and non-imaging methods. Electrochemical methods include voltametry and amperometry methods. Radio frequency methods include multipolar resonance spectroscopy.
[0110] Biochips can be designed with immobilized nucleic acid molecules, full-length proteins, antibodies, affibodies (small molecules engineered to mimic monoclonal antibodies), aptamers (nucleic acid-based ligands) or chemical compounds. A chip could be designed to detect multiple macromolecule types on one chip. For example, a chip could be designed to detect nucleic acid molecules, proteins and metabolites on one chip. The biochip is used to and designed to
simultaneously analyze a panel biomarker in a single sample, producing a subject’s profile for these biomarkers. The use of the biochip allows for the multiple analyses to be performed reducing the overall processing time and the amount of sample required.
[0111] Protein microarrays are a particular type of biochip which can be used with the present disclosure. The chip consists of a support surface such as a glass slide, nitrocellulose membrane, bead, or microtitre plate, to which an array of capture proteins are bound in an arrayed format onto a solid surface. Protein array detection methods must give a high signal and a low background. Detection probe molecules, typically labeled with a fluorescent dye, are added to the array. Any reaction between the probe and the immobilized protein emits a fluorescent signal that is read by a laser scanner. Such protein microarrays are rapid, automated, and offer high sensitivity of protein biomarker read-outs for diagnostic tests. However, it would be immediately appreciated to those skilled in the art that there are a variety of detection methods that can be used with this technology.
[0112] The present disclosure provides for the detection of biomarkers using mass spectrometry. Mass spectrometry (MS) is an analytical technique that measures the mass-to-charge ratio of charged particles. It is primarily used for determining the elemental composition of a sample or molecule, and for elucidating the chemical structures of molecules, such as peptides and other chemical compounds. MS works by ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratios. MS instruments typically consist of three modules (1) an ion source, which can convert gas phase sample molecules into ions (or, in the case of electrospray ionization, move ions that exist in solution into the gas phase) (2) a mass analyzer, which sorts the ions by their masses by applying electromagnetic fields and (3) a detector, which measures the value of an indicator quantity and thus provides data for calculating the abundances of each ion present.
[0113] Suitable mass spectrometry methods to be used with the present disclosure include but are not limited to, one or more of electrospray ionization mass spectrometry (ESI-MS), ESI-MS/MS, ESI-MS/(MS)n, matrix-assisted laser desorption ionization time-of-flight mass spectrometry
(MALDI-TOF-MS), surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS), tandem liquid chromatography-mass spectrometry (LC -MS/MS) mass spectrometry, desorption/ionization on silicon (DIOS), secondary ion mass spectrometry (SIMS), quadrupole time-of-flight (Q-TOF), atmospheric pressure chemical ionization mass spectrometry (APCI-MS), APCI-MS/MS, APCI-(MS), atmospheric pressure photoionization mass spectrometry (APPI-MS), APPI-MS/MS, and APPI-(MS)n, quadrupole mass spectrometry, Fourier transform mass spectrometry (FTMS), and ion trap mass spectrometry, where n is an integer greater than zero.
[0114] To gain insight into the underlying proteomics of a sample, LC-MS is commonly used to resolve the components of a complex mixture. LC-MS methods generally involves protease digestion and denaturation (usually involving a protease, such as trypsin, a denaturant ( e.g ., urea) to denature tertiary structure, and iodoacetamide to cap cysteine residues) followed by LC-MS with peptide mass fingerprinting or LC-MS/MS (tandem MS) to derive sequence of individual peptides. LC-MS/MS is most commonly used for proteomic analysis of complex samples where peptide masses may overlap even with a high-resolution mass spectrometer. Samples of complex biological fluids like human serum may be first separated on an SDS-PAGE gel or HPLC-SCX and then run in LC-MS/MS allowing for the identification of over 1000 proteins.
[0115] In some applications, HPLC and UHPLC can be coupled to a mass spectrometer. A number of other peptide and protein separation techniques can be performed prior to mass spectrometric analysis. Some exemplary separation techniques which can be used for separation of the desired analyte (e.g., peptide or protein) from the matrix background include but are not limited to Reverse Phase Liquid Chromatography (RP-LC) of proteins or peptides, offline Liquid Chromatography (LC), 1 -dimensional gel separation, 2-dimensional gel separation, Strong Cation Exchange (SCX) chromatography, Strong Anion Exchange (SAX) chromatography, Weak Cation Exchange (WCX), and Weak Anion Exchange (WAX). One or more of the above techniques can be used prior to mass spectrometric analysis.
[0116] The methods of the present disclosure are based, in part, on the discovery that the mutation status of Ras is associated with clinical benefits of MAPK pathway inhibition. Specifically, the KRAS mutation status of a cancer in a subject can be used to predict the responsiveness of the subject to treatment with a MAPK pathway inhibitor. Accordingly, provided herein are methods for assessing a likelihood of a subject having cancer exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, methods of treating cancer in a subject with a MAPK pathway inhibitor, methods of categorizing the sensitivity of a cancer to treatment with a MAPK pathway inhibitor, and methods of downregulating MAPK signaling output in cancer cells with an effective dose of a MAPK pathway inhibitor, based on the mutation status of Ras in the cancer.
[0117] In certain aspects, provided herein is a method of treating a cancer in a subject based on the mutation status of KRAS. In some embodiments, the present disclosure provides a method of treating a cancer in a subject in need thereof, wherein said cancer exhibits a KRAS mutation and wherein said cancer overexpresses CCND1. In some embodiments, the method comprises administering to the subject an effective dose of a mitogen-activated protein kinase (MAPK) pathway inhibitor. In some embodiments, the method comprises (a) assessing the cancer for overexpression of CCND1; (b) evaluating the cancer for the presence of a KRAS mutation; wherein steps (a) and (b) may be performed in either order; and (c) administering the MAPK pathway inhibitor to the subject if both the CCND1 overexpression and the KRAS mutation are determined to be present. In some embodiments, the sample is determined to have a KRAS other than wild type KRAS.
[0118] The KRAS mutation may include a mutation at a codon selected from G12, G13, and Q61. In some embodiments, the KRAS mutation includes a mutation selected from G12C, G12D, G12A, G12V, G12S, G12F, G12R, G12N, G13C, G13D, G13R, G13S, G13N, Q61K, Q61H, Q61L,
Q61P, Q61R and A146V. In some embodiments, the sample is determined to have at least one amino acid substitution at G12, G13, and Q61 of KRAS. In some embodiments, the sample is determined not to have wild type KRAS.
[0119] In some embodiments, a method described herein comprises determining the presence or absence of a KRAS mutation in a sample from the subject prior to beginning treatment. Tumors or cancers that exhibit a KRAS mutation are more likely to be responsive to treatment with a MAPK pathway inhibitor. In some embodiments, patients are selected for MAPK pathway inhibitor treatment based on the presence of a KRAS mutation. In some embodiments, patients are further selected based on the overexpression of CCND1 by the cancer or tumor. The mutation status of KRAS can be detected at the nucleic acid or protein level. In some embodiments, the KRAS mutation status is determined by analyzing nucleic acids obtained from the sample. In some embodiments, the KRAS mutation status is determined by analyzing protein obtained from the sample.
[0120] Techniques useful in the methods provided herein include in situ hybridization (Stoler, Clin. Lab. Med. 12:215-36 (1990)), using radioisotope or fluorophore-labeled probes; polymerase chain reaction (PCR); and quantitative Southern blotting, dot blotting and other techniques for
quantitating individual genes. In some embodiments, probes or primers selected for gene amplification evaluation are highly specific to avoid detecting closely related homologous genes. Alternatively, antibodies can be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turn can be labeled and the assay may be carried out where the duplex is bound to a surface, so that upon formation of the duplex on the surface, the presence of antibody bound to the duplex can be detected.
[0121] In some embodiments, the KRAS mutation status is determined by analyzing nucleic acids obtained from the sample. The nucleic acids may be mRNA or genomic DNA molecules from the subject. Methods for determining KRAS mutation status by analyzing nucleic acids include sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography (DHPLC), and restriction fragment length polymorphism (RFLP) assay. In some embodiments, the KRAS mutation status is determined using standard sequencing methods, including, for example, Sanger sequencing or next generation sequencing (NGS). In some embodiments, the KRAS mutation status is determined using MS.
[0122] In some embodiments, a method of the present disclosure includes determining the presence or absence of a KRAS mutation by amplifying KRAS nucleic acid from a sample by PCR. For example, PCR technology and primer pairs that can be used are known to the person skilled in the art (e.g., Chang et al., Clinical Biochemistry, 43 (2010), 296-301; WO2015144184). For example, a multiplex PCR can be used to amplify codons 12 and 13 of exon 2 and codon 61 of exon 3 of a KRAS gene with two pairs of universal primers for exons 2 and 3.
[0123] Following multiplex PCR amplification, the products can be purified to remove the primers and unincorporated deoxynucleotide triphosphates using PCR-M™ Clean Up System
(Viogenebiotek Co., Sunnyvale, Calif., USA). Purified DNA can then be semiquantified on a 1% agarose gel in 0.5x TBE and visualized by staining with ethidium bromide. The products can then be subjected to primer extension analysis using primers as disclosed in Chang et al., Clinical Biochemistry 43 (2010), 296-301.
[0124] Various concentrations of probe for either codon 12, 13, or 61 can be employed (e.g. 0.03- 0.6 mM) in reactions containing 1.5 pL of purified PCR products and 4 pL of ABI PRISM
SNaPshot Multiplex Kit (Applied Biosystems, Foster City, Calif.) containing AmpliTaq® DNA polymerase and fluorescently labeled dideoxynucleotide triphosphates (ddNTPs) (RGG-labeled dideoxyadenosine triphosphate, TAMRA-labeled dideoxycytidine triphosphate, ROX-labeled dideoxythymidine triphosphate, and Rl lO-labeled dideoxyguanosine triphosphate). Each 10 pL mixture can then be subjected to 25 single-base extension cycles consisting of a denaturing step at 96 °C for 10 s and primer annealing and extension at 55 °C for 35 s. After cycle extension, unincorporated fluorescent ddNTPs can then be incubated with 1 pL of shrimp alkaline phosphatase (United States Biochemical Co., Cleveland, USA) at 37 °C for 1 h, followed by enzyme deactivation at 75 °C for 15 min. The primer extension reaction products can then be resolved by automated capillary electrophoresis on a capillary electrophoresis platform (e.g. 14 pL of Hi-Di™Formamide (Applied Biosystems) and 0.28 pL of GeneScan™-l20LIZ® Size Standard (Applied Biosystems) can be added to 6 pL of primer extension products). All samples may then be analyzed, for example, on an ABI Prism 310 DNA Genetic Analyzer (Applied Biosystems) according to manufacturer's instructions using GeneScan™ 3.1 (Applied Biosystems).
[0125] The presence or absence of a KRAS mutation may be assessed by amplifying KRAS nucleic acid from a tumor sample and sequencing the amplified nucleic acid. Accordingly, KRAS nucleic acid can be amplified using primers as described above and sequenced. For example,
KRAS nucleic acid can be amplified by PCR as described above and subsequently subcloned using, for example, the TOPO TA Cloning Kit for sequencing (Invitrogen).
[0126] In practicing any of the subject methods, KRAS nucleic acid may be obtained from a tumor sample by any method known to a person skilled in the art. For example, a commercial kit may be used to isolate the genomic DNA or mRNA from a tumor sample, such as the Qlamp DNA mini kit, or RNeasy mini kit (Qiagen, Hilden, Germany). A nucleic acid isolated from a biological sample may be selected from genomic DNA, total RNA, mRNA or poly(A)+mRNA. For example, if mRNA has been isolated from a biological sample, the mRNA may be used for cDNA synthesis according to technologies known in the art, such as those provided in commercial cDNA synthesis kits (e.g. Superscript® III First Strand Synthesis Kit). The cDNA can then be further amplified by suitable means, such as PCR, and subsequently subjected to sequencing, such as Sanger sequencing or pyro-sequencing, to determine the nucleotide sequence, preferably of codons 12 and/or 13 of the KRAS gene. Alternatively, the PCR product can be subcloned into a TA TOPO cloning vector for sequencing. The presence or absence of a KRAS mutation may also be determined by other methods, including single nucleotide primer extension (SNPE) (PLoS One, 2013, 8(8):e72239); DNA microarray, mass spectrometry (MS) (e.g. matrix-assisted laser desorption/ionization time-of- flight (MALDI-TOF) mass spectrometry), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography (DHPLC), or restriction fragment length polymorphism (RFLP) assay.
[0127] In some embodiments, single nucleotide polymorphism (SNP) assay is used to determine the KRAS mutation status in a sample. The SNP assay can be performed on an HT7900 from Applied Biosystems, following the allelic discrimination assay protocol provided by the
manufacturer. The KRAS mutation status can also be determined by DHPLC or RFLP. [0128] In some embodiments, the KRAS mutation status is determined by analyzing protein obtained from a biological sample. The mutated KRAS protein can be detected by a variety of immunohistochemistry (IHC) approaches or other immunoassay methods known in the art. IHC staining of tissue sections has been shown to be a reliable method of assessing or detecting presence of proteins in a sample. Immunohistochemistry techniques utilize an antibody to probe and visualize cellular antigens in situ, generally by chromogenic or fluorescent methods. Thus, antibodies or antisera, preferably polyclonal antisera, and most preferably monoclonal antibodies that specifically target mutant KRAS, can be used to detect expression. The antibodies can be detected by direct labeling of the antibodies themselves, for example, with radioactive labels, fluorescent labels, hapten labels such as, biotin, or an enzyme such as horse radish peroxidase or alkaline phosphatase. Alternatively, unlabeled primary antibody may be used in conjunction with a labeled secondary antibody, comprising antisera, polyclonal antisera or a monoclonal antibody specific for the primary antibody. Commercially available immunohistochemistry kits may be utilized. Automated systems for slide preparation and IHC processing may be commercially available (e.g., The Ventana® BenchMark XT system).
[0129] Assays to detect KRAS mutations include noncompetitive assays, such as sandwich assays, and competitive assays. Typically, an assay such as an ELISA assay can be used. ELISA assays may be used to assay a wide variety of tissues and samples, including blood, plasma, serum or bone marrow.
[0130] Many immunoassay techniques are available, such as those described in U.S. Pat. Nos. 4,016,043; 4,424,279; and 4,018,653, each of which is incorporated by reference in its entirety. Such techniques include both single-site and two-site or“sandwich” assays of the non-competitive types, as well as in the traditional competitive binding assays. These assays also include direct binding of a labeled antibody to a target mutant KRAS protein. A number of variations of the sandwich assay technique exist. For example, in a typical forward assay, an unlabeled antibody is immobilized on a solid substrate, and the sample to be tested brought into contact with the bound molecule. After a suitable period of incubation for a period of time sufficient to allow formation of an antibody-antigen complex, a second antibody specific to the antigen, labeled with a reporter molecule capable of producing a detectable signal, is then added and incubated, allowing time sufficient for the formation of another complex of antibody-antigen-labeled antibody. Any unreacted material is washed away, and the presence of the antigen is determined by observation of a signal produced by the reporter molecule. The results may either be qualitative, by simple observation of the visible signal, or may be quantitated by comparing with a control sample.
[0131] Variations on the forward assay include a simultaneous assay, in which both sample and labeled antibody are added simultaneously to the bound antibody. In a typical forward sandwich assay, a first antibody having specificity for the mutant KRAS protein is either covalently or passively bound to a solid surface. The solid surface may be glass or a polymer, the most commonly used polymers being cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride, or polypropylene. The solid supports may be in the form of tubes, beads, discs of microplates, or any other surface suitable for conducting an immunoassay. An aliquot of a sample to be tested may be added to the solid phase complex and incubated for a sufficient time and under suitable conditions to allow binding of a subunit present in the antibody. Following the incubation period, the antibody subunit solid phase is washed, dried and incubated with a second antibody specific for a portion of the mutant KRAS protein. The second antibody is linked to a reporter molecule which is used to indicate the binding of the second antibody to the mutant KRAS protein.
[0132] In some embodiments, flow cytometry (FACS) can be used to detect a mutant KRAS using antibodies to target the mutant KRAS. The flow cytometer detects and reports the intensity of the fluorochrome-tagged antibody, which indicates the presence of the mutant KRAS. Non-fluorescent cytoplasmic proteins can also be observed by staining permeabilized cells. The stain can either be a fluorescent compound able to bind to certain molecules, or a fluorochrome-tagged antibody to bind the molecule of choice.
[0133] Alternatively, a mutant KRAS in a biological sample may be immobilized and exposed to a mutant specific antibody which may or may not be labeled with a reporter molecule. Depending on the amount of the mutant KRAS and the strength of the reporter molecule signal, a bound mutant KRAS can be detectable by direct labeling with the antibody. Alternatively, a second labeled antibody, specific to the first antibody, is exposed to the KRAS-first antibody complex to form a KRAS-first antibody-second antibody tertiary complex. The complex is detected by the signal emitted by a labeled reporter molecule.
[0134] In the case of an enzyme immunoassay, an enzyme is conjugated to the second antibody, generally by means of glutaraldehyde or periodate. As will be readily recognized, however, a wide variety of different conjugation techniques exist, which are readily available to the skilled artisan. Commonly used enzymes include horseradish peroxidase, glucose oxidase, beta-galactosidase, and alkaline phosphatase, and other are discussed herein. The substrates to be used with the specific enzymes are generally chosen for the production, upon hydrolysis by the corresponding enzyme, of a detectable color change. Examples of suitable enzymes include alkaline phosphatase and peroxidase. It is also possible to employ fluorogenic substrates, which yield a fluorescent product rather than the chromogenic substrates noted above. In all cases, the enzyme-labeled antibody is added to the first antibody-molecular marker complex, allowed to bind, and then the excess reagent is washed away. A solution containing the appropriate substrate is then added to the complex of antibody-antigen-antibody. The substrate will react with the enzyme linked to the second antibody, giving a qualitative visual signal, which may be further quantitated, usually spectrophotometrically, to give an indication of the amount of mutant KRAS protein present in the sample. Alternately, fluorescent compounds, such as fluorescein and rhodamine, can be chemically coupled to antibodies without altering their binding capacity. When activated by illumination with light of a particular wavelength, the fluorochrom e-lab el ed antibody adsorbs the light energy, inducing a state to excitability in the molecule, followed by emission of the light at a characteristic color visually detectable with a light microscope. As in the EIA, the fluorescently labeled antibody is allowed to bind to the first antibody-molecular marker complex. After washing off the unbound reagent, the remaining tertiary complex is then exposed to the light of the appropriate wavelength, wherein the fluorescence observed indicates the presence of the molecular marker of interest.
[0135] In some embodiments, one or more steps in the assessment and/or reporting of a likelihood of response to treatment with a MAPK pathway inhibitor is performed with the aid of a processor, such as with a computer system executing instructions contained in computer-readable media. In one aspect, the disclosure provides a system for of assessing a likelihood of a subject having cancer, such as adenocarcinoma, exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor. In one embodiment, the system comprises (a) a memory unit configured to store information concerning: (i) a total expression level of CCND1 and (ii) the KRAS mutation status in a biological sample comprising genomic, transcriptomic and/or proteomic material from an adenocarcinoma cell. In some embodiments, the system further comprises (b) one or more processors alone or in combination programmed to: (1) determine a weighted probability of MAPK pathway inhibitor responsiveness based on the total expression level and the KRAS mutation status; and (2) designate the subject as having a high probability of exhibiting a clinically beneficial response to treatment with the MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability of (b)(1).
[0136] The methods provided herein can further include determining a reference expression level of each individual biomarker, such as CCND1. In some embodiments, the reference expression level of a biomarker is the expression level of the biomarker in a sample from a healthy individual, or the average or median expression level of the biomarker in multiple samples from one or multiple healthy individuals. In some embodiments, the reference expression level of a biomarker is the average expression level of the biomarker in samples from 2, 3, 5, 10, 15, 20, 30, 40, 50 or more healthy individuals. In some embodiments, the reference expression level of a biomarker is the median expression level of the biomarker in samples from 2, 3, 5, 10, 15, 20, 30, 40, 50 or more healthy individuals. In some embodiments, the reference expression level of CCND1 is the expression level of CCND1 in a sample from a healthy individual, or the average or median expression level of CCND1 in multiple samples from one or multiple healthy individuals.
[0137] In some embodiments, the reference expression level of a biomarker, such as CCND1, can be determined based on statistical analysis of data from previous clinical trials, including outcome of a group of patients, namely, the patients' responsiveness to treatment with a MAPK pathway inhibitor, as well as the expression levels of the biomarker of the group of patients. A number of statistical methods are well known in the art to determine the reference level (also referred to as the “cut-off value”) of one or more biomarkers when used to predict the responsiveness of a patient to a particular treatment, or to stratify patients for a particular treatment.
[0138] One method includes analyzing gene expression profiles for biomarkers identified herein that distinguish responder from non-responder to determine the reference expression level for one or more biomarkers. Comparisons between responders and non-responders can be performed using the Mann-Whitney U-test, Chi-square test, or Fisher's Exact test. Analysis of descriptive statistics and comparisons can be performed using SigmaStat Software (Systat Software, Inc., San Jose, Calif., USA).
[0139] In some embodiments, a classification and regression tree (CART) analysis can be adopted to determine the reference level. CART analysis is based on a binary recursive partitioning algorithm and allows for the discovery of complex predictor variable interactions that may not be apparent with more traditional methods, such as multiple linear regression. Binary recursive partitioning refers to the analysis that is: 1) binary, meaning there were two possible outcome variables, namely“responder” and“non-responder”, with the effect of splitting patients into 2 groups; 2) recursive, meaning the analysis can be performed multiple times; and 3) partitioned, meaning the entire data set can be split into sections. This analysis also has the ability to eliminate predictor variables with poor performance. The classification tree can be built using Salford Predictive Modeler v6.6 (Salford Systems, San Diego, Calif., USA).
[0140] Representations of gene expression profiles useful for predicting the responsiveness of a cancer patient to treatment with a MAPK pathway inhibitor may be reduced to a medium that can be automatically read, such as computer readable media (magnetic, optical, and the like). The representations may further comprise instructions for assessing the gene expression profiles in such media. Gene expression profiles may be digitally recorded so that they can be compared with gene expression data from other patient samples. Clustering algorithms such as those incorporated in “OMNIVIZ” and“TREE VIEW” computer programs can assist in the visualization of such data.
[0141] Receiver Operator Characteristic (ROC) analysis can be utilized to determine the reference expression level or test the overall predictive value of individual genes. A review of the ROC analysis can be found in Soreide, K., Journal of Clinical Pathology 2009, (52, 1-5, incorporated by reference in its entirety.
[0142] The reference level can be determined from the ROC curve of the training set to ensure both high sensitivity and high specificity. The leave-one-out cross validation (LOOCV) test can be used to confirm that sufficient biomarkers are included in the predictor. The response scores for the T eft- out’ samples based on different numbers of genes are recorded. The performances of the predictors with different numbers of genes can be assessed based on misclassification error rate, sensitivity, specificity, and p values measuring the separation of Kaplan-Meier curves of the two predicted groups.
[0143] The Top Scoring Pair (TSP) algorithm first introduced by Geman et al. (2004) can be used. In essence, the algorithm ranks all the gene pairs (genes i and j) based on the absolute difference (Dij) in the frequency of event where gene i has higher expression value than gene j in samples among class Cl to C2. In cases where there are multiple top scoring pairs (all sharing the same Dij), the top pair by a secondary rank score that measures the magnitude to which inversions of gene expression levels occur from one class to the other within a pair of genes is selected. The top pair with highest frequency of absolute Dij>2 fold in all samples will be selected as a candidate pair. The candidate pair can then be assessed in an independent testing data set. Leave-one-out cross validation (LOOCV) can be carried out in the training data set to evaluate how the algorithm performs. The performances of the predictors can be assessed based on maximum misclassification error rate. All the statistical analyses can be done using R (R Development Core Team, 2006).
[0144] A review of the methods and statistic tools useful for determining a reference level can be found in James Westgard, Ph.D., Basic Methods Validation, 3rd edition (2008), which is hereby incorporated by reference in its entirety.
[0145] Clinically reportable range (CRR) is the range of analyte values that a method can measure, allowing for specimen dilution, concentration, or other pretreatment used to extend the direct analytical measurement range. As provided in the Basic Methods Validation by Dr. Westgard, the experiment to be performed is often called a“linearity experiment”, though there technically is no requirement that a method provide a linear response unless two-point calibration is being used. This range can also be referred as the“linear range”,“analytical range” or“working range” for a method. [0146] The reportable range is assessed by inspection of the linearity graph. That inspection can involve manually drawing the best straight line through the linear portion of the points, drawing a point-to-point line through all the points then comparing with the best straight line, or fitting a regression line through the points in the linear range. There are more complicated statistical calculations that are recommended in some guidelines, such as Clinical Laboratory Standards Institute’s (CLSI) EP-6 protocol for evaluating the linearity of analytical methods. It is commonly accepted that the reportable range can be adequately determined from a“visual” assessment, i.e., by manually drawing the best straight line that fits the lowest points in the series. The Clinical Laboratory Standards Institute (CLSI) recommends a minimum of at least 4, preferably 5, different levels of concentrations. More than 5 can be used, particularly if the upper limit of reportable range needs to be maximized, but 5 levels are convenient and typically sufficient.
[0147] A reference interval is typically established by assaying specimens that are obtained from individuals that meet carefully defined criteria (reference sample group). Protocols such as those of the International Federation of Clinical Chemistry (IFCC) Expert Panel on Theory of Reference Values and the CLSI delineate comprehensive systematic processes that use carefully selected reference sample groups to establish reference intervals. These protocols typically use a minimum of 120 reference individuals for each group (or subgroup) that needs to be characterized.
[0148] The CLSI Approved Guideline C28-A2 describes different ways for a laboratory to validate the transfer of established reference intervals to an individual laboratory, including (1) divine judgment, wherein the laboratory simply reviews the information submitted and subjectively verifies that the reference intervals are applicable to the adopting laboratory's patient population and test methods; (2) verification with 20 samples, wherein experimental validation is performed by collecting and analyzing specimens from 20 individuals who represent the reference sample population; (3) estimation with 60 samples, wherein an experimental validation is performed by collecting and analyzing specimens from 60 individuals who represent the reference sample population, and the actual reference interval is estimated and compared to the claimed or reported interval using a statistical formula comparing the means and standard deviations of the two populations; and (4) calculation from a comparative method, wherein one can adjust or correct the claimed or reported reference intervals on the basis of the observed methodological bias and the mathematical relationship demonstrated between the analytical methods being used.
[0149] In certain aspects, the present disclosure provides a method of (a) determining a reference expression level of CCND1, and (b) administering a therapeutically effective amount of a MAPK pathway inhibitor to a subject having cancer, wherein said cancer exhibits a KRAS mutation and wherein the expression level of CCND1 in the cancer is higher than the reference expression level. In some embodiments, the present disclosure provides a method of (a) determining a reference mRNA level of CCND1, and (b) administering a therapeutically effective amount of a MAPK pathway inhibitor to a subject having cancer, wherein said cancer exhibits a KRAS mutation and wherein the mRNA level of CCND1 in the cancer is higher than the reference mRNA level. In some embodiments, the present disclosure provides a method of (a) determining a reference protein level of CCND1, and (b) administering a therapeutically effective amount of a MAPK pathway inhibitor to a subject having cancer, wherein said cancer exhibits a KRAS mutation and wherein the protein level of CCND1 in the cancer is higher than the reference protein level.
[0150] In some embodiments, a processor or computational algorithm may aid in the assessment of a likelihood of a subject having cancer, such as adenocarcinoma, exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor. For example, one or more steps of methods or systems described herein may be implemented in hardware. Alternatively, one or more steps may be implemented in software stored in, for example, one or more memories or other computer readable medium and implemented on one or more processors. As is known, the processors may be associated with one or more controllers, calculation units, and/or other units of a computer system, or implanted in firmware as desired. If implemented in software, the routines may be stored in any computer readable memory such as in RAM, ROM, flash memory, a magnetic disk, a laser disk, a remote server ( e.g . the cloud), or other storage medium, as is also known. Likewise, this software may be delivered to a computing device via any known delivery method including, for example, over a communication channel such as a telephone line, the internet, a wireless connection, etc., or via a transportable medium, such as a computer readable disk, flash drive, etc. The various steps may be implemented as various blocks, operations, tools, modules and techniques which, in turn, may be implemented in hardware, firmware, software, or any combination of hardware, firmware, and/or software. When implemented in hardware, some or all of the blocks, operations, techniques, etc. may be implemented in, for example, a custom integrated circuit (IC), an application specific integrated circuit (ASIC), a field programmable logic array (FPGA), a programmable logic array (PLA), etc. A computer system may be involved in one or more of sample collection, sample processing, data analysis, expression profile assessment, calculation of weighted probabilities, calculation of baseline probabilities, comparison of a weighted probability to a reference level and/or control sample, determination of a subject’s absolute or increased probability, generating a report, and reporting results to a receiver.
[0151] A client-server, relational database architecture can be used in embodiments of the disclosure. A client-server architecture is a network architecture in which each computer or process on the network is either a client or a server. Server computers are typically powerful computers dedicated to managing disk drives (file servers), printers (print servers), or network traffic (network servers). Client computers include PCs (personal computers), workstations, or mobile computing devices ( e.g ., a tablets or smart phones) on which users run applications, as well as example output devices as disclosed herein. Client computers may rely on server computers for resources, such as files, devices, and even processing power. In some embodiments of the disclosure, the server computer handles all of the database functionality. The client computer can have software that handles all the front-end data management and can also receive data input from users.
[0152] In some embodiments, the computer system is connected to an analysis system by a network connection. The computer system may be understood as a logical apparatus that can read instructions from media and/or a network port, which can optionally be connected to server having fixed media. The system can include a CPU, disk drives, optional input devices such as keyboard and/or mouse, and optional monitor. Data communication can be achieved through the indicated communication medium to a server at a local or a remote location. The communication medium can include any means of transmitting and/or receiving data. For example, the communication medium can be a network connection, a wireless connection, or an internet connection. Such a connection can provide for communication over the World Wide Web. In some embodiments, a physical report is generated and delivered to a receiver.
[0153] In some embodiments, there is provided a computer readable medium encoded with computer executable software that includes instructions for a computer to execute functions associated with the identified biomarkers. Such computer system may include any combination of such codes or computer executable software, depending upon the types of evaluations desired to be completed. The system can have code for calculating a weighted probability of MAPK pathway inhibitor responsiveness, and optionally for calculating an aggregated probability based on a plurality of weighted probabilities. In some embodiments, the weighted probability of MAPK pathway inhibitor responsiveness is increased if an adenocarcinoma cell (1) overexpresses CCND1 or (2) exhibits a KRAS mutation. The weighted probability of MAPK pathway inhibitor responsiveness may be decreased if an adenocarcinoma cell (1) underexpresses CCND1 or (2) does not exhibit a KRAS mutation. The system can also have code for one or more of the following: conducting, analyzing, organizing, or reporting the results, as described herein. The system can also have code for generating a report. In some embodiments, the test subject may be designated as having a high probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to at least about 0.55, at least about 0.6, at least about 0.65, at least about 0.7, at least about 0.75, at least about 0.8, at least about 0.85, at least about 0.9, at least about 0.95, or at least about 0.99. In some embodiments, the test subject may be designated as having a low probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to less than about 0.45, less than about 0.4, less than about 0.35, less than about 0.3, less than about 0.25, less than about 0.2, less than about 0.15, less than about 0.1, less than about 0.05, less than about 0.01.
[0154] The system may further comprise code for comparing a weighted probability to a baseline probability, a threshold value, and/or a reference level, and assigning a fold-baseline probability based on whether or not the baseline probability, threshold value, or reference level is exceeded. Assessing a weighted probability, threshold value, or reference level can be linked to at least one recommendation. Exceeding a weighted probability, threshold value, or reference level may be linked to a recommendation of treatment with a MAPK pathway inhibitor. In some embodiments, the baseline probability represents the average probability of a subject having cancer, such as adenocarcinoma, exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, either in general or for a specific population. In some embodiments, the baseline probability represents a pre-test likelihood that a particular subject will exhibit a clinically beneficial response to treatment with a MAPK pathway inhibitor before applying a method of the disclosure to determine a post-test risk. A weighted probability above a baseline probability may correspond to a specified fold-baseline probability, whatever the pre-test baseline for the subject may be. In some embodiments, the test subject may be designated as having a high probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to about or at least about 1.1 -times, 1.2-times, 1.3-times, 1.4- times, 1.5-times, 1.8-times, 2-times, 2.5-times, 3-times, 4-times, 5-times, 6-times, 7-times, 8-times, 9-times, 10-times, 25-times, 50-times, or lOO-times the baseline probability. In some embodiments, the test subject may be designated as having a low probability of exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor if the weighted probability corresponds to about or at less than about 0.9-times, 0.8-times, 0.7-times, 0.6-times, 0.5-times, 0.4-times, 0.3- times, 0.2-times, O. l-times, 0.05-times, 0.01 -times the baseline probability.
[0155] After performing a calculation, a processor can provide the output, such as from a calculation, back to, for example, the input device or storage unit, to another storage unit of the same or different computer system, or to an output device. Output from the processor can be displayed by data display. A data display can be a display screen (for example, a monitor or a screen on a digital device), a print-out, a data signal (for example, a packet), an alarm (for example, a flashing light or a sound), a graphical user interface (for example, a webpage), or a combination of any of the above. In an embodiment, an output is transmitted over a network (for example, a wireless network) to an output device. The output device can be used by a user to receive the output from the data-processing computer system. After an output has been received by a user, the user can determine a course of action, or can carry out a course of action, such as a medical treatment when the user is medical personnel. In some embodiments, an output device is the same device as the input device. Example output devices include, but are not limited to, a telephone, a wireless telephone, a mobile phone, a PDA, a tablet, a flash memory drive, a light source, a sound generator, a fax machine, a computer, a computer monitor, a printer, an iPod, and a webpage. The user station may be in communication with a printer or a display monitor to output the information processed by the server.
[0156] It is envisioned that data relating to the present disclosure can be transmitted over a network or connections for reception and/or review by a receiver. The receiver can be but is not limited to an individual; the subject to whom the report pertains; a health care provider, manager, other healthcare professional, or other caretaker; an oncologist; a genetic counselor; a person or entity that performed and/or ordered the biomarker expression analysis; or a local or remote system for storing such reports ( e.g . servers or other systems of a“cloud computing” architecture). In one embodiment, a computer-readable medium includes a medium suitable for transmission of a result of an analysis of a biological sample, such as analysis of one or more biomarkers. The medium can include a result regarding one or more biomarker expression level or amplification status of an individual, probability (such as fold-baseline probability) of having a cancer that is sensitive to treatment with a MAPK pathway inhibitor, and/or a treatment plan for the individual, wherein such a result is derived using the methods described herein.
[0157] In some embodiments, the subject or a third party (e.g. a heath care provider, health care manager, other health professional, or other caretaker) is alerted if a subject is designated as having a“high probability” of having a beneficial response to treatment with a MAPK pathway inhibitor. The analysis generated can be reviewed and further analyzed by a medical professional such as a managing doctor or licensed physician, or other third party. The medical professional or other third party can meet with the subject to discuss the results, analysis, and report. Information provided can include recommendations, such as treatment (e.g, with a MAPK pathway inhibitor or an alternative therapy).
[0158] In some embodiments, the method further comprises providing a recommendation for treatment based on an assessment of the likelihood that a subject having adenocarcinoma will exhibit a clinically beneficial response to treatment with a MAPK pathway inhibitor, such as designation as having high probability. A recommendation may form part of a report generated based on biomarker expression and KRAS mutation status, or may be made by a receiver on the basis of such report. A recommendation may be for further action on the part of the subject and/or for a third party, such as a heath care provider, health care manager, other health professional, or other caretaker. Recommendations may include, but are not limited to, treatment with a MAPK pathway inhibitor; continued monitoring of the subject; screening exams or laboratory tests that may further characterize the cancer; prescription and/or administration of one or more therapeutic agents that are not MAPK pathway inhibitors; discontinued therapy; and treatment with an alternative therapy, e.g. chemotherapy, immunotherapy, radiotherapy, or surgery.
[0159] In some embodiments, the disclosure provides a method of categorizing an adenocarcinoma status of a subject. The status of the subject may be categorized based on an expression profile of a biological sample from the subject. A cancer status may be categorized as likely sensitive to treatment with a MAPK pathway inhibitor or likely resistant to treatment with a MAPK pathway inhibitor. The likely sensitive categorization may be assigned to an adenocarcinoma having (1) overexpression CCND1 and (2) a KRAS mutation. A“likely resistant” categorization may be assigned to an adenocarcinoma (1) having underexpression of CCND1 and/or (2) lacking a KRAS mutation.
[0160] In some embodiments, a method of the disclosure provides a reference level above which CCND1 must be expressed to be considered in assessing the likelihood of response to treatment with a MAPK pathway inhibitor. CCND1 may be differentially expressed at least 1.1 fold, at least 1.2 fold, at least 1.3 fold, at least 1.4 fold, at least 1.5 fold, at least 2.0 fold, at least 2.25 fold, at least 2.5 fold, at least 2.75 fold, at least 3.0 fold, at least 3.5 fold, at least 4.0 fold, at least 5.0, or even at least 10 fold higher relative to a reference level to be considered in adjusting the likelihood of response. In some embodiments, the reference level is a numerical range of CCND1 expression that is obtained from a statistical sampling from a population of individuals having adenocarcinoma that has low sensitivity, such as resistance, to treatment with a MAPK pathway inhibitor. In some embodiments, the reference level is a numerical range of CCND1 expression that is obtained from a statistical sampling from a population of individuals having cancer that is sensitive to treatment with a MAPK pathway inhibitor. The reference level may be a numerical range of CCND1 expression that is obtained from a statistical sampling from a population of individuals having cancer, e.g. , the same cancer as the test subject. In some embodiments, the reference level is derived by comparison of sensitive and resistant populations. As used herein, low sensitivity to a MAPK pathway inhibitor refers to a disease condition that progresses after treatment with a MAPK pathway inhibitor. In some examples, low sensitivity to a MAPK pathway inhibitor is characterized by tumor growth inhibition of less than 60%, optionally less than 80% following treatment with a MAPK pathway inhibitor. A disease condition that responds to treatment with a MAPK pathway inhibitor is one that exhibits a therapeutically beneficial response, such as regression or stabilization of a tumor, in response to treatment with a MAPK pathway inhibitor. In some examples, tumor growth inhibition of greater than 80% is indicative of a response to treatment with a MAPK pathway inhibitor.
[0161] Published criteria for evaluating treatment with a MAPK pathway inhibitor, such as the Response Evaluation Criteria in Solid Tumors (RECIST) criteria, may be used to evaluate a solid tumor. According to the RECIST criteria, a complete response (CR) is evidenced by disappearance of all target lesions; a partial response (PR) is evidenced by at least a 30% decrease in the sum of the longest diameter (LD) of target lesions, taking as reference the baseline sum LD; a stable disease (SD) is evidenced by neither sufficient shrinkage to qualify for PR nor sufficient increase to qualify for PD, taking as reference the smallest sum LD since the treatment started; and progressive disease (PD) is evidenced by at least a 20% increase in the sum of the LD of target lesions, taking as reference the smallest sum LD recorded since the treatment started or the appearance of one or more new lesions. In some examples, a disease condition is classified as responsive to treatment with a MAPK pathway inhibitor if categorized in accordance with the RECIST criteria as a CR, PR or SD in response to treatment with a MAPK pathway inhibitor. A disease condition that is resistant to treatment may be classified as a PD by the RECIST criteria.
[0162] In a further embodiment, the present disclosure provides a method of treating a cancer condition, such as adenocarcinoma, comprising administering an effective dose of a MAPK pathway inhibitor. The MAPK pathway inhibitor may be effective in one or more of inhibiting proliferation of cancer cells, inhibiting invasion or metastasis of cancer cells, killing cancer cells, increasing the sensitivity of cancer cells to treatment with a second antitumor agent and reducing severity or incidence of symptoms associated with the presence of cancer cells. In some embodiments, said method comprises administering to the cancer cells a therapeutically effective amount of a MAPK pathway inhibitor. In some embodiments, the administration takes place in vitro. In other embodiments, the administration takes place in vivo.
[0163] A MAPK pathway inhibitor suitable for use in the subject methods can be selected from a variety of types of molecules. For example, the MAPK pathway inhibitor can be a biological or chemical compound, such as a simple or complex organic or inorganic molecule, peptide, peptido mimetic, protein (e.g., antibody), liposome, or a polynucleotide (e.g., small interfering RNA, microRNA, antisense, aptamer, ribozyme, or triple helix). Some exemplary classes of chemical compounds suitable for use in the subject methods are detailed in the sections below. A MAPK pathway inhibitor for use in the present disclosure can be any MAPK pathway inhibitor that is known in the art, and can include any chemical entity that, upon administration to a subject, results in inhibition of any portion of the MAPK pathway in the subject. Optionally, a MAPK pathway inhibitor for use in the treatment of adenocarcinoma is a small molecule. As used herein, the term “small molecule” refers to a low molecular weight organic compound, such as a compound having a molecular weight of less than 800 g/mol.
[0164] A MAPK pathway inhibitor may inhibit any component of the MAPK pathway. For example, the MAPK pathway inhibitor may be selected from a Ras inhibitor, a Raf inhibitor, a MEK inhibitor, and an ERK inhibitor. In some embodiments, the MAPK pathway inhibitor is a Ras inhibitor. In some embodiments, the MAPK pathway inhibitor is a Raf inhibitor. In some embodiments, the MAPK pathway inhibitor is a MEK inhibitor. In some embodiments, the MAPK pathway inhibitor is an ERK inhibitor. In some embodiments, the MAPK pathway inhibitor is selected from a MEK inhibitor and an ERK inhibitor.
[0165] The term“Ras inhibitor” as used herein refers to compounds capable of fully or partially reducing or inhibiting Ras signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the Ras signaling pathway, such as H-Ras, K-Ras and/or N-Ras mRNA. In some examples, said Ras inhibitor inhibits one or more of H-Ras, K-Ras or N-Ras GTPase activity. Inhibition of Ras can be achieved by a variety of mechanisms, including, but not limited to, binding directly to H-Ras, K- Ras or N-Ras, or inhibiting expression of a Ras gene. Any component of the Ras pathway is a potential therapeutic target for inhibition in accordance with the present disclosure. The mechanism of inhibition may be at the genetic level (e.g., interference with transcription or translation) or at the protein level (e.g., binding, competition). Exemplary Ras inhibitors include, but are not limited to lonafamib, MRTX-849 and AMG510. Exemplary Ras inhibitors and their syntheses have been described in WO 97/23478, WO 98/57959, and WO 97/40006, the disclosures of which are incorporated by reference herein.
[0166] The term“Raf inhibitor” as used herein refers to compounds capable of fully or partially reducing or inhibiting Raf signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the Raf signaling pathway, such as A-Raf, B-Raf and/or C-Raf mRNA. In some examples, said Raf inhibitor inhibits one or more of A-Raf, B-Raf or C-Raf kinase activity. Inhibition of Raf can be achieved by a variety of mechanisms, including, but not limited to, binding directly to A-Raf, B- Raf or C-Raf, or inhibiting expression of a Raf gene. Any component of the Raf pathway is a potential therapeutic target for inhibition in accordance with the present disclosure. The mechanism of inhibition may be at the genetic level (e.g., interference with transcription or translation) or at the protein level (e.g., binding, competition). Preferably, a Raf inhibitor is a pan-RAF in inhibitor, such as LY3009120, LXH254, CCT3833 or AZ628. In some embodiments, the pan-RAF inhibitor is selected from LY3009120 and LXH254. Exemplary pan-RAF inhibitors and their syntheses have been described in WO 2013/134243, WO 2014/151616, WO 2009/077766, and WO 2006/024834, the disclosures of which are incorporated by reference herein.
[0167] The term“MEK inhibitor” as used herein refers to compounds capable of fully or partially reducing or inhibiting MEK signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the MEK signaling pathway, such as MEK1, MEK2, ERK1 and/or ERK2 mRNA. In some examples, said MEK inhibitor inhibits one or more of MEK1, MEK2, ERK1 or ERK2 kinase activity.
Inhibition of MEK can be achieved by a variety of mechanisms, including, but not limited to, binding directly to MEK1 or MEK2, or inhibiting expression of the MEK gene.
[0168] Any component of the MEK pathway is a potential therapeutic target for inhibition in accordance with the present disclosure. The mechanism of inhibition may be at the genetic level (e.g., interference with transcription or translation) or at the protein level (e.g., binding, competition). Because of their converging function, specific inhibition of MEK1/2 or ERK1/2 is expected to effectively intercept a wide variety of upstream mitogenic signals. Preferably, the MEK inhibitor is a specific inhibitor that either acts on MEK1/2 at the genetic level or protein level. Either or both approaches may be used in accordance with the present disclosure. For example, an inhibitor may be utilized that interferes with expression of MEK1 and/or MEK2, or which sequesters MEK1 and/or MEK2 in the cytoplasm of the cell, preventing nuclear translocation.
[0169] Exemplary MEK inhibitors include, but are not limited to cobimetinib, trametinib, binimetinib, selumetinib, HL-085, antroquinonol, E-6201, refametinib, pimasertib hydrochloride, CKI-27, WX-554, CIP- 137401, SHR-7390, sorafenib, SRX-2626, PD-0325901, ATR-002, ATR- 004, ATR-005, ATR-006, CS-3006, FCN-159, EDV-2209, GDC-0623, TAK-733, E-6201, RG- 7167, AZD-8330, PD-184352, GSK-2091976A, AS-703988, BI-847325, JTP-70902, CZ-775, RO- 5068760, RDEA-436, MEK-300, AD-GL0001, SL-327, ATR-001, PD-98059, RO-4987655, RO- 4927350, and AS-703026. Preferably, the MEK inhibitor is selected from cobimetinib, trametinib, binimetinib, and selumetinib. In some embodiments, the MEK inhibitor is trametinib. Exemplary MEK inhibitors and their syntheses have been described in WO 2007/044515 (cobimetinib), WO 2005/121142 (trametinib), and WO 2003/077914 (binimetinib and selumetinib), the disclosures of which are incorporated by reference herein.
[0170] In some embodiments, the MEK inhibitor is a compound selected from
Figure imgf000056_0001
[0171] Examples of MEK inhibitors that may be used in accordance with the disclosure include, but are not limited to, MEK1/2 inhibitors, such as PD98059, PD184352, EG0126 (Dudley D. T. et al., Proc. Natl. Acad. Sci. USA, 1995, 92:7686-7689; Sepolt-Leopold J. S. et al., Nat. Med., 1999, 5:810-816; and Favata M. F. et al., J. Biol. Chem., 273: 18623-18632, respectively). A series of 3- cyano-4-(phenoxyanilo)quinolines with MEK inhibitory activity has also been developed by Wyeth-Ayerst (Zhang N. et al., Bioorg. Med. Chem. Lett., 2000, 10:2825-2828). Several resorcylic acid lactones having inhibitor activity toward MEK have been isolated from microbial extracts. For example, RO 09-2210, isolated from fungal broth FC2506, and L-783,277, purified from organic extracts of Phoma sp. (ATCC 74403), are competitive with ATP, and the MEK1 inhibition is reversible (Williams D. H. et al., Biochemistry, 1998, 37:9579-9585; and Zhao A. et al., J.
Antibiot., 1999, 52: 1086-1094). Imidazolium trans-imidazoledimethyl sulfoxide- tetrachlororuthenate (NAMI- A) is a ruthenium-containing inhibitor of the phosphorylation of MEK (Pintus G. et al., Eur. J. Biochem., 2002, 269:5861-5870). In some examples, the MEK inhibitor is selected from the group consisting of trametinib, BVD-523 (ulixertinib), FR 180204, MK-8353 (SCH900353), pluripotin, SCH772984, VX-l le (ERK-l le; TCS ERK l le), SL327, hypericin, purvalanol, PD173074, GW5074, BAY 43-9006, AG99, CAY10561, ISIS 5132, apigenin, SP600125, SU4984, SB203580, PD169316, K0947, GDC0994, and AG1478. Other inhibitors include, but are not limited to, chromone and flavone type inhibitors; PD 98059 (Runden E et al, J Neurosci 1998, 18(18) 7296-305); PD0325901 (Pfizer); Selumetinib, a selective MEK inhibitor (AstraZeneca/ Array BioPharma, also known as AZD6244); ARRY-438162 (Array BioPharma); PD198306 (Pfizer); PD0325901 (Pfizer); AZD8330 (AstraZeneca/ Array Biopharma, also called ARRY-424704); PD 184352 (Pfizer, also called Cl- 1040); PD 184161 (Pfizer); a-[Amino[(4- aminophenyl)thio]methylene]-2-(trifluoromethyl)benzeneacetonitrile (SL327); l,4-Diamino-2,3- dicyano-l,4-bis(2-aminophenylthio)butadiene; U0126 (Kohno & Pouyssegur (2003) Prog. Cell. Cyc. Res. 5: 219-224); GW 5074 (Santa Cruz Biotechnology); BAY 43-9006 (Bayer, Sorafenib); RO 09-2210 (Roche, Williams et al, Biochemistry. 1998 Jun 30;37(26):9579-85); FR 180204 (Ohori,
M. et al. (2005) Biochem. Biophys. Res. Comm. 336: 357-363); 3-(2-aminoethyl)-5-))4- ethoxyphenyl)methylene)-2,4-thiazolidinedione (PKI-ERK-005) (Chen, F. et al. (2006) Bioorg.
Med. Chem. 16:6281- 6288. 171. Hancock, CN. et al. (2005) J. Med. Chem. 48: 4586- 4595);
CAY10561 (CAS 933786-58-4; Cayman Chemical); GSK 1120212; RDEA119 (Ardea
Biosciences); XL518; and ARRY-704 (AstraZeneca).
[0172] Further examples of MAPK pathway inhibitors that may be used in accordance with the disclosure include, but are not limited to, Raf-l inhibitors, such as GW5074, BAY 43-9006, and ISIS 5132 (Lackey, K. et al., Bioorg. Med. Chem. Lett., 2000, 10:223-226; Lyons, J. F. et al., Endocrine-related Cancer, 2001, 8:219-225; and Monia, B. P. et al., Nat. Med., 1996, 2(6):668-675, respectively); and MEK1/2 inhibitors, such as PD98059, PD184352, U0126 (Dudley D. T. et al., Proc. Natl. Acad. Sci. USA, 1995, 92:7686-7689; Sepolt-Leopold J. S. et al., Nat. Med., 1999, 5:810-816; and Favata M. F. et al., J. Biol. Chem., 273: 18623-18632, respectively). A series of 3- cyano-4-(phenoxyanilo)quinolines with MEK inhibitory activity has also been developed by
Wyeth-Ayerst (Zhang N. et al., Bioorg. Med. Chem. Lett., 2000, 10:2825-2828). Several resorcylic acid lactones having inhibitor activity toward MEK have been isolated from microbial extracts. For example, RO 09-2210, isolated from fungal broth FC2506, and L-783,277, purified from organic extracts of Phoma sp. (ATCC 74403), are competitive with ATP, and the MEK1 inhibition is reversible (Williams D. H. et al., Biochemistry, 1998, 37:9579-9585; and Zhao A. et al., J.
Antibiot., 1999, 52: 1086-1094). Imidazolium trans-imidazoledimethyl sulfoxide- tetrachlororuthenate (NAMI-A) is a ruthenium-containing inhibitor of the phosphorylation of MEK, the upstream activator of ERK (Pintus G. et al., Eur. J. Biochem., 2002, 269:5861-5870). In some examples, the ERK inhibitor is selected from the group consisting of BVD-523, FR 180204, MK-8353 (SCH900353), pluripotin, SCH772984, VX-l le (ERK-l le; TCS ERK l le), SL327, hypericin, purvalanol, PD173074, GW5074, BAY 43-9006, AG99, CAY10561, ISIS 5132, apigenin, SP600125, SU4984, SB203580, PD169316, K0947, GDC0994, and AG1478. Other inhibitors include, but are not limited to, chromone and flavone type inhibitors; PD 98059 (Runden E et al, J Neurosci 1998, 18(18) 7296-305); PD0325901 (Pfizer); Selumetinib, a selective MEK inhibitor (AstraZeneca/ Array BioPharma, also known as AZD6244); ARRY-438162 (Array BioPharma); PD198306 (Pfizer); PD0325901 (Pfizer); AZD8330 (AstraZeneca/ Array Biopharma, also called ARRY-424704); PD 184352 (Pfizer, also called Cl- 1040); PD 184161 (Pfizer); a- [Amino[(4-aminophenyl)thio]methylene]-2-(trifluoromethyl)benzeneacetonitrile (SL327); 1,4- Diamino-2,3-dicyano-l,4-bis(2-aminophenylthio)butadiene; U0126 (Kohno & Pouyssegur (2003) Prog. Cell. Cyc. Res. 5: 219-224); GW 5074 (Santa Cruz Biotechnology); BAY 43-9006 (Bayer, Sorafenib); RO 09-2210 (Roche, Williams et al, Biochemistry. 1998 Jun 30;37(26):9579-85); FR 1 80204 (Ohori, M. et al. (2005) Biochem. Biophys. Res. Comm. 336: 357-363) ; 3-(2-aminoethyl)- 5-))4- ethoxyphenyl)methylene)-2,4-thiazolidinedione (PKI-ERK-005) (Chen, F. et al. (2006) Bioorg. Med. Chem. 16:6281- 6288. 171. Hancock, CN. et al. (2005) J. Med. Chem. 48: 4586- 4595); CAY10561 (CAS 933786-58-4; Cayman Chemical); GSK 120212; RDEA1 19 (Ardea Biosciences); XL518; and ARRY-704 (AstraZeneca).
[0173] The term“ERK inhibitor” as used herein refers to compounds capable of fully or partially reducing or inhibiting ERK signaling activity. Inhibition may be effective at the transcriptional level, for example by preventing or reducing or inhibiting mRNA synthesis of key members of the ERK signaling pathway, such as MEK1, MEK2, ERK1 and/or ERK2 mRNA. In some examples, said ERK inhibitor inhibits one or more of MEK1, MEK2, ERK1 or ERK2 kinase activity.
Inhibition of ERK can be achieved by a variety of mechanisms, including, but not limited to, binding directly to ERK1 or ERK2, binding directly to MEK1 or MEK2, or inhibiting expression of the ERK or MEK genes.
[0174] Any component of the ERK pathway is a potential therapeutic target for inhibition in accordance with the present disclosure. The mechanism of inhibition may be at the genetic level (e.g., interference with transcription or translation) or at the protein level (e.g., binding,
competition). Because of their converging function, specific inhibition of MEK1/2 or ERK1/2 is expected to effectively intercept a wide variety of upstream mitogenic signals. Preferably, the ERK inhibitor is a specific inhibitor that either acts on ERK1/2 at the genetic level or protein level.
Either or both approaches may be used in accordance with the present disclosure. For example, an inhibitor may be utilized that interferes with expression of ERK1 and/or ERK2, or which sequesters ERK1 and/or ERK2 in the cytoplasm of the cell, preventing nuclear translocation.
[0175] Exemplary ERK inhibitors include, but are not limited to ulixertinib, RG7842, GDC-0994, CC-90003, ASN-007, AMO-01, KO-947, AEZS-134, AEZS-131, AEZS-140, AEZS-136, AEZS- 132, D-87503, KIN-2118, RB-l, RB-3, SCH-772984, MK-8353, SCH-900353, FR-180204, IDN- 5491, hyperforin trimethoxybenzoate, ERK1-2067, ERK1-23211, ERK1-624, LY3214996,
AZ6197, ASTX029, and LTT462. In some embodiments, the ERK inhibitor is selected from ulixertinib, GDC-0994, SCH-772984, and MK-8353. In some embodiments, the ERK inhibitor is selected from ulixertinib, GDC-0994, SCH-772984, MK-8353, and KO-947. In some embodiments, the ERK inhibitor is selected from SCH772984, GDC-0994, CC-90003, BVD-523 (ulixertinib) and KO-947. Preferably, the ERK inhibitor is KO-947. Exemplary ERK inhibitors and their syntheses have been described in WO 2005/113541 (ulixertinib), WO 2013/130976 (GDC- 0994), WO 2007/070398 (SCH-772984), WO 2009/105500 (MK-8353), and WO 2015/051341 (KO-947), the disclosures of which are incorporated by reference herein.
[0176] In some examples, the ERK inhibitor is a compound selected from
Figure imgf000059_0001
[0177] Other MAPK pathway inhibitors and their syntheses have been described in ETS 5,525,625, US 2003/0060469, US 2004/0048861, US 2004/0082631, WO 98/43960, WO 99/01426, WO 00/41505, WO 00/42002, WO 00/42003, WO 00/41994, WO 00/42022, WO 00/42029, WO 00/68201, WO 01/68619, WO 02/06213, WO 03/077855 and WO 2005/23251. Optionally, the MAPK pathway inhibitor is selected from the group consisting of selumetinib, U0126, PD98059, PD0325901, AZD8330 (ARKY-42704), CI-1040 (PD 184352), and PD318088. Preferably, the MAPK pathway inhibitor is an ERK inhibitor described in WO/2015051341, the disclosure of which is incorporated by reference herein. [0178] In certain embodiments, the present disclosure provides an ERK inhibitor which is a compound of Formula I:
Figure imgf000060_0001
wherein:
Figure imgf000060_0002
Xi is C=0, C=S, SO, S02, or P02 ; Y is CR5; W is N or C;
X2 is NRi or CRiRf and X3 is null, CR3R3’ or C=0; or X2-X3 is RIC=CR3 or RiC=N or N=CR3 or NR12-CR1 1=CR3;
X4 is N or CR4; X5 is N or C; X6 is N or C; X7 is O, N, NR72 or CR7i; X8 is O, N, NR82 or CR8l; X9 is O, N, NR22 or CR23; Xl0 is O, N, NR92 or CR91;
Ri is-Ci-ioalkyl, -C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3.l0aryl, -Ci-iohetaryl, - C3-iocycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3-i0aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.i0alkyl-C3- iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C2-ioalkenyl-C3-i0aryl, -C2-ioalkenyl-Ci.iohetaryl, -C2- loalkenyl-C3-locycloalkyl, -C2-ioalkenyl -Ci-ioheterocyclyl, -C2-ioalkynyl-C3-i0aryl, -C2-i0alkynyl- Ci-iohetaryl, -C2-i0alkynyl-C3-iocycloalkyl, -C2-ioalkynyl-Ci.ioheterocyclyl, -Ci.i0heteroalkyl-C3- i0aryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci.ioheteroalkyl-C3-iocycloalkyl, -Ci-ioheteroalkyl-Ci.
loheterocyclyl, -Ci-ioalkoxy-C3-ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci-ioalkoxy-C3-iocycloalkyl, -Ci. loalkoxy-Ci-ioheterocyclyl, -C3-ioaryl-Ci.ioalkyl, -C3-ioaryl-C2-i0alkenyl, -C3-ioaryl-C2-i0alkynyl, - C3-i0aryl-C3-i0hetaryl, -C3-i0aryl-C3-i0cycloalkyl, -C3-ioaryl-Ci.ioheterocyclyl, -Ci-iohetaryl-Ci. i0alkyl, -Ci.iohetaryl-C2-ioalkenyl, -Ci.iohetaryl-C2-ioalkynyl, -C3-iohetaryl-C3-i0aryl, -Ci-iohetaryl- C3-i0cycloalkyl, -Ci-iohetaryl-Ci-ioheterocyclyl, -C3-i0cycloalkyl-Ci.ioalkyl, -C3-i0cycloalkyl-C2- loalkenyl, -C3-iocycloalkyl-C2-i0alkynyl, -C3-i0cycloalkyl-C3-i0aryl, -C3-iocycloalkyl-Ci.iohetaryl, - C3-i0cycloalkyl -Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci-ioheterocyclyl-C2-ioalkenyl, - Ci.ioheterocyclyl-C2-ioalkynyl, -Ci.ioheterocyclyl-C3-ioaryl, -Ci-ioheterocyclyl-Ci-iohetaryl, or -Ci. ioheterocyclyl-C3-i0cycloalkyl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
Ri’ is hydrogen, -Ci.i0alkyl, -C2-i0alkenyl, -C2-i0alkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Ci. lohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci- ioalkyl-C3-iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C2-ioalkenyl-C3-ioaryl, -C2-ioalkenyl-Ci. lohetaryl, -C2.ioalkenyl-C3.iocydoalkyl, -C2- 1 oal kenyl -C M oheterocyd yl , -C2-ioalkynyl-C3-i0aryl, - C2-ioalkynyl-Ci-iohetaryl, -C2.ioalkynyl-C3.iocycloalkyl, -C2- 1 oal kynyl -C M oheterocyd yl , -Ci. loheteroalkyl-C3-l0aryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci.ioheteroalkyl-C3.iocycloalkyl, -Ci. ioheteroalkyl-Ci-ioheterocyclyl, -Ci.ioalkoxy-C3.ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci.ioalkoxy-C3. iocydoalkyl, -Ci-ioalkoxy-Ci-ioheterocydyl, -C3.ioaryl-Ci.ioalkyl, -C3-ioaryl-C2-ioalkenyl, -C3- ioaryl-C -ioalkynyl, -C3.ioaryl-C3.iohetaryl, -C3.ioaryl-C3.iocydoalkyl, -C3.ioaryl-Ci.ioheterocydyl, -Ci.iohetaryl-Ci.ioalkyl, -Ci_iohetaryl-C2-i oal kenyl, -Ci.iohetaryl-C2-ioalkynyl, -C3.iohetaryl-C3. l0aryl, -Ci.iohetaryl-C3.iocycloalkyl, -Ci-iohetaryl-Ci-ioheterocydyl, -C3.iocydoalkyl-Ci.ioalkyl, - C3-iocydoalkyl-C2-ioalkenyl, -C3-iocydoalkyl-C2-ioalkynyl, -C3-iocydoalkyl-C3-ioaryl, -C3- iocydoalkyl-CMohetaryl, -C3.iocydoalkyl-Ci.ioheterocydyl, -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci.
1 oheterocyd yl -C2.1 oal kenyl , -C M oheterocyd yl -C2.1 oal kynyl , -Ci.ioheterocyclyl-C3.ioaryl, -Ci. ioheterocydyl-Ci-iohetaryl, or -Cl-loheterocyclyl-C3-locydoalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
R21 is hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, - C(=0)NR31, -NO2, -CN, -S(0)O-2R31, -S02NR31R32, -NR31C(=0)R32, -NR31C(=0)0R32, - NR31C(=0)NR32R33, -NR31S(0)O-2R32, -C(=S)OR31, -C(=0)SR31, -NR31C(=NR32)NR32R33, - NR31C(=NR32)OR33, -NR31C(=NR32)SR33, -0C(=0)0R33, -0C(=0)NR31R32, -0C(=0)SR31, - SC(=0)SR31, -P(0)0R3 l0R32, -SC(=0)NR31R32, -L-Ci-ioalkyl, -L-C2-ioalkenyl, -L-C2-ioalkynyl, -L-Ci.ioheteroalkyl, -L-C3-ioaryl, -L-Ci.i0hetaryl, -L-C3.i0cycloalkyl, -L-Ci-ioheterocydyl, -L- Cl-loalkyl-C3-loaryl, -L-Ci-ioalkyl-Ci-iohetaryl, -L-Ci.ioalkyl-C3.iocycloalkyl, -L-Ci-ioalkyl-Ci. !oheterocyclyl, -L-C2.ioalkenyl-C3.ioaryl, -L-C7-1 oal kenyl -CM ohetaryl, -L-C2-ioalkenyl-C3- iocycloalkyl, -L-C2- 1 oal kenyl -C M oheterocyd yl , -L-C2-ioalkynyl-C3-i0aryl, -L-C -ioalkynyl-Ci. iohetaryl, -L-C2.ioalkynyl-C3.iocycloalkyl, -L-C 2.1 oal kynyl -C M oheterocyd yl , -L-Ci-ioheteroalkyl- C3.l0aryl, -L -Ci-ioheteroalkyl-Ci-iohetaryl, -L -Ci.ioheteroalkyl-C3.iocycloalkyl, -L -Ci.
1 oheteroal kyl -C M oheterocyd yl , -L-Ci.ioalkoxy-C3.ioaryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci. loalkoxy-C3-locydoalkyl, -L-Ci-ioalkoxy-Ci-ioheterocyclyl, -L-C3-ioaryl-Ci-ioalkyl, -L-C3-ioaryl- C2-ioalkenyl, -L-C3.ioaryl-C2.ioalkynyl, -L-C3.ioaryl-Ci.iohetaryl, -L-C3.ioaryl-C3.iocycloalkyl, - L-C3.ioaryl-Ci.ioheterocyclyl, -L-Ci-iohetaryl-Ci-ioalkyl, -L-C 1.1 ohetaryl -C 2.1 oal kenyl , -L-Ci.
1 ohetaryl -C2- 1 oal kynyl , -L-Ci.iohetaryl-C3.ioaryl, -L-Ci-iohetaryl-C3-iocycloalkyl, -L-Ci-iohetaryl- Cl-loheterocyclyl,-L-C3-iocydoalkyl-Cl-loalkyl, -L-C3-iocycloalkyl-C2-ioalkenyl, -L-C3- 1 ocycl oal kyl -C 2.1 oal kynyl , -L-C3.l0cycloalkyl-C3.l0aryl, -L-C3.iocycloalkyl-Ci.iohetaryl, -L-C3. iocycloalkyl-Ci-ioheterocydyl, -L-Ci-ioheterocydyl-Ci-ioalkyl, -L-C 1.1 oheterocyd yl -C 2.1 oal kenyl , -L-C 1.1 oheterocydyl -C2.1 oal kynyl , -L-Ci-ioheterocydyl -C3.l0aryl, -L-Ci-ioheterocyclyl-Ci.
iohetaryl, or -L-Ci-ioheterocyclyl-C3-iocydoalkyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
R22 is hydrogen, -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, -S(O)0-2R31, -C(=S)OR31, - C(=0)SR31,-L-Ci.ioalkyl, -L-C2-i0alkenyl, -L-C2-i0alkynyl, -L-Ci.i0heteroalkyl, -L-C3-i0aryl, - L-Ci.iohetaryl, -L-C3-i0cycloalkyl, -L-Ci-ioheterocyclyl, -L-Ci.ioalkyl-C3-i0aryl, -L-Ci.i0alkyl- C i-iohetaryl, -L-Ci-ioalkyl-C3-iocycloalkyl, -L-Ci-ioalkyl-Ci-ioheterocyclyl, -L-C2-ioalkenyl-C3- !oaryl, -L-C2-ioalkenyl-Ci-iohetaryl, -L-C2-ioalkenyl-C3-iocycloalkyl, -L-C2-ioalkenyl-Ci.
ioheterocyclyl, -L-C2-ioalkynyl-C3-i0aryl, -L-C2-i0alkynyl-Ci.iohetaryl, -L-C2-i0alkynyl-C3- iocycloalkyl, -L-C2-i0alkynyl-Ci.ioheterocyclyl, -L-Ci.ioheteroalkyl-C3-i0aryl, -L -Ci.
i oheteroal kyl -CM ohetaryl , -L -Ci-ioheteroalkyl-C3-iocycloalkyl, -L -Ci-ioheteroalkyl-Ci.
!oheterocyclyl, -L-Ci-ioalkoxy-C3-ioaryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci-ioalkoxy-C3- iocycloalkyl, -L-Ci-ioalkoxy-Ci-ioheterocyclyl, -L-C3-i0aryl-Ci.ioalkyl, -L-C3-ioaryl-C2-i0alkenyl, -L-C3-ioaryl-C2-i0alkynyl, -L-C3-i0aryl-Ci.iohetaryl, -L-C3-i0aryl-C3-iocycloalkyl, -L-C3-i0aryl-Ci. !oheterocyclyl, -L-Ci-iohetaryl-Ci-ioalkyl, -L-Ci-iohetaryl-C2-ioalkenyl, -L-Ci-iohetaryl-C2- !oalkynyl, -L-Ci.iohetaryl-C3-ioaryl,-L-Ci.iohetaryl-C3-iocycloalkyl, -L-Ci-iohetaryl-Ci.
ioheterocyclyl, -L-C3-i0cycloalkyl-Ci.ioalkyl, -L-C3-iocycloalkyl-C2-i0alkenyl, -L-C3-i0cycloalkyl- C2-l0alkynyl, -L-C3-iocycloalkyl-C3-i0aryl, -L-C3-i0cycloalkyl-Ci.iohetaryl, -L-C3-i0cycloalkyl-Ci. !oheterocyclyl, -L-Ci-ioheterocyclyl-Ci-ioalkyl, -L-Ci-ioheterocyclyl-C2-ioalkenyl, -L-Ci.
loheterocyclyl-C2-loalkynyl, -L-Ci-ioheterocyclyl-C3-ioaryl, -L-Ci-ioheterocyclyl-Ci-iohetaryl, or - L-Ci.ioheterocyclyl-C3-iocycloalkyl, each of which is unsubstituted or substituted by one or more independent R32 substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2-, -C(=0)-, -C(=0)0-, -0C(=0)-, -C(=0)N(R31)-, -
Figure imgf000062_0001
each of R3, R3’ and R4 is independently hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, - R31C(=0)R32,
Figure imgf000062_0002
i-ioalkyl, - C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci.
ioheterocyclyl, -Ci.ioalkyl-C3-i0aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.ioalkyl-C3-i0cycloalkyl, -Ci. ioalkyl-Ci-ioheterocyclyl, -C2-ioalkenyl-C3-i0aryl, -C2-i0alkenyl-Ci.iohetaryl, -C2-i0alkenyl-C3- iocycloalkyl, -C2-ioalkenyl-Ci.ioheterocyclyl, -C2-ioalkynyl-C3-i0aryl, -C2-i0alkynyl-Ci.iohetaryl, - C2-i0alkynyl-C3-iocycloalkyl, -C2-i0alkynyl-Ci.ioheterocyclyl, -Ci.ioheteroalkyl-C3-ioaryl, -Ci. loheteroalkyl-Ci-iohetaryl, -Ci-ioheteroalkyl-Cs-iocycloalkyl, -Ci-ioheteroalkyl-Ci-ioheterocyclyl, - Ci-ioalkoxy-C3-ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci-ioalkoxy-C3-iocydoalkyl, -Ci-ioalkoxy-Ci. ioheterocydyl, -C3.ioaryl-Ci.ioalkyl, -C3.ioaryl-C2-ioalkenyl, -C3.ioaryl-C2-ioalkynyl, -C3.ioaryl-C3. iohetaryl, -C3.ioaryl-C3.iocycloalkyl, -C3.ioaryl-Ci.ioheterocydyl, -Ci-iohetaryl-Ci-ioalkyl, -Ci. lohetaryl-C2-ioalkenyl, -Ci-iohetaryl-C2-ioalkynyl, -C3.iohetaryl-C3.ioaryl, -Ci-iohetaryl-C3.
iocydoalkyl, -Ci-iohetaryl-Ci-ioheterocydyl, -C3.iocydoalkyl-Ci.ioalkyl, -C3.iocycloalkyl-C2- l0alkenyl, -C3.iocydoalkyl-C2-ioalkynyl, -C3.iocydoalkyl-C3.ioaryl, -C3.iocycloalkyl-Ci.iohetaryl, - C3.iocydoalkyl-Ci.ioheterocydyl, -Ci-ioheterocydyl-Ci-ioalkyl, -Ci.ioheterocydyl-C2-ioalkenyl, - Ci.ioheterocydyl-C2.ioalkynyl, -Ci-ioheterocyclyl^-ioaryl, -Ci-ioheterocydyl-Ci-iohetaryl, or -Ci. loheterocydyl-C3-iocydoalkyl, each of which is unsubstituted or substituted by one or more independent R13 substituents; or R3’ is -OR6, -NR6R34, -S(O)0-2R6, -C(=0)R6, -C(=0)0R6, - 0C(=0)R6, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring; or R3’ is -OR6, -NR6R34, -S(O)0-2R6, -C(=0)R6, -C(=0)0R6, - 0C(=0)R6, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring;
each of R5, R7l, R8I and R9i is independently hydrogen, halogen, -Cl-l0 alkyl, -C2.l0 alkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -
Figure imgf000063_0001
R6 is hydrogen, -Ci.i0alkyl, -C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci. iohetaryl, -C3.i0cycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3.ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci. loalkyl-C3-iocydoalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C2-ioalkenyl-C3.ioaryl, -C2-ioalkenyl-Ci. !ohetaryl, -C2-ioalkenyl-C3-iocycloalkyl, -C2.ioalkenyl-Ci.ioheterocyclyl, -C2.ioalkynyl-C3.ioaryl, - C2-ioalkynyl-Ci.iohetaryl, -C2.ioalkynyl-C3.iocycloalkyl, -C2.ioalkynyl-Ci.ioheterocyclyl, -Ci. loheteroalkyl-C3-loaryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci-ioheteroalkyl^.iocycloalkyl, -Ci.
1 oheteroal kyl -CM oheterocyd yl , -Ci.ioalkoxy-C3.ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci-ioalkoxy-C3- iocycloalkyl, -Ci-ioalkoxy-Ci-ioheterocyclyl, -C3.ioaryl-Ci.ioalkyl, -C3-ioaryl-C2-ioalkenyl, -C3- loaryl-C2-ioalkynyl, -C3.ioaryl-C3.iohetaryl, -C3.ioaryl-C3.iocycloalkyl, -C3.ioaryl-Ci.ioheterocyclyl, -Ci-iohetaryl-Ci-ioalkyl, -Ci.iohetaryl-C2.ioalkenyl, -Ci.iohetaryl-C2-ioalkynyl, -C3.iohetaryl-C3. l0aryl, -Ci.iohetaryl-C3.iocycloalkyl, -Ci-iohetaryl-Ci-ioheterocydyl, -C3.iocycloalkyl-Ci.ioalkyl, - C3.iocydoalkyl-C2.ioalkenyl, -C3.iocydoalkyl-C2.ioalkynyl, -C3.iocycloalkyl-C3.ioaryl, -C3. locycloalkyl-Ci-iohetaryl, -CC,. i ocycl oal kyl -CM oheterocyd yl , -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci. i oheterocycl yl -C2- 1 oal kenyl , -C M oheterocyd yl -C2- 1 oal kynyl , -C M oheterocyd yl -CC,. i oaryl , -Ci.
ioheterocyclyl-CMohetaryl, or -C Moheterocyclyl-Ci.iocycloalkyl, each of which is unsubstituted or substituted by one or more independent RI4 or RI5 substituents;
each of R72, FO2 and R92 is independently hydrogen, -CMO alkyl, -C2-ioalkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, - CF3, -C(0)R31, -CO2R31, -C(=0)NR31, -S(0)O-2R31, -C(=S)OR31, -C(=0)SR31;
each of Rio and Ri is independently -CMO alkyl, -C2-ioalkenyl, -C2-io alkynyl, -Ci.
!oheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, R12, R13 and R15 is independently hydrogen, halogen, -CMO alkyl, -C2-ioalkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci-ioheterocyclyl, -
Figure imgf000064_0001
each of R , R , R and R is independently hydrogen, halogen, -CMO alkyl, -C2-ioalkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci-ioheterocyclyl, or wherein R31 together with R32 form a heterocyclic ring;
wherein ring A comprises one or more heteroatoms selected from N, O, or S; and
wherein if X7 is O or X2-X3 is RiC=CR3, ring A comprises at least two heteroatoms selected from N, O, or S; and
wherein if X2-X3 is RiC=N, at least one of X7 or X9 is not N.
[0179] In some embodiments of Formula I, Xi is C=0, X2 is NRi or CRiRf , and X3 is CR3R3’· In some embodiments, Xi is C=0, X2 is NRi, and X3 is C=0. In some embodiments, W is C, Y is CR5, X is CR , X5 is C and X6 is C. In some embodiments, X7 is NH, X8 is N and X9 is CR2i. In some embodiments, X7 is CR7i, X8 is N and X9 is NR22. In some embodiments, Xi is C=0, X2 is NRi or CRiRi’, X3 is CR3R3\ W is C, Y is CR5, X4 is N or CIO, X5 is N or C, X6 is C, X7 is NR72 or CR7i, X8 is N, and X9 is NR22 or CR21. In some embodiments, Xi is C=0, X2 is NRi, X3 is CR3R3\ W is C, Y is CR5, X4 is CIO, X5 is C, X6 is C, X7 is NR72, X8 is N, and X9 is CR2i.
[0180] In some embodiments of Formula I, Xi is C=0, X2 is NRi or CRiRk, X3 is CR3R3’ or C=0, W is C, Y is CR5, X is N or CR , X5 is N or C, X6 is C, X7 is N or NR72 or CR7i, X8 is N or CR8i, X9 is NR22 or CR2i, and X10 is N or CR9i; Ri is -Ci-ioalkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl- C3-i0aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.ioalkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C3- iocydoalkyl-Ci-ioalkyl, -C3.iocydoalkyl-C3.ioaryl, -C3.iocydoalkyl-Ci.iohetaryl, -C3.i0cydoalkyl- Ci-ioheterocydyl, -Ci-ioheterocydyl-Ci-ioalkyl, -Ci.ioheterocydyl-C3.ioaryl, -Ci-ioheterocydyl-Ci. !ohetaryl, or -Ci.ioheterocydyl-C3.iocydoalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
Ri’ is hydrogen, -Ci.i0alkyl, -C3-ioaryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3.ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.ioalkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci.
!oheterocyclyl, -C3.iocycloalkyl-Ci.ioalkyl, -C3-iocycloalkyl-C3-ioaryl, -C3-iocycloalkyl-Ci-iohetaryl, -C3-iocycloalkyl-Ci-ioheterocydyl, -Ci-ioheterocydyl-Ci-ioalkyl, -Ci-ioheterocyclyl-C3-ioaryl, -Ci- ioheterocydyl-Ci-iohetaryl, or -Cl-loheterocyclyl-C3-locydoalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
R2i is halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(0)O-2R3 1, -NR31C(=0)R32, -L-Ci.ioalkyl, -L-C2-i0alkenyl, -L-C2-i0alkynyl, - L-Ci.
ioheteroalkyl, -L-C3-ioaryl, -L-Cmohetaryl, -L-C3.i0cycloalkyl, or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent RI2 substituents;
R22 is -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, -S(O)0-2R31, -L-Ci.ioalkyl, -L-C2- ioalkenyl, -L-C2-ioalkynyl, - L-Ci-ioheteroalkyl, -L-C3-ioaryl, -L-Ci-iohetaryl, -L-C3-iocycloalkyl, or -L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent Rn substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2-, -C(=0)-, -C(=0)0-, -0C(=0)-, -C(=0)N(R31)-, - N(R31)C(=0)-, -NR31C(=0)0-, -NR31C(=0)NR32-, -NR31S(0)O-2-, or -S(O)0-2N(R31)-;
each of R3 R3’ and R4 is independently hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, - NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(0)O-2R31, -C1-10alkyl, -C2-10alkenyl, -C2- ioalkynyl, - L-Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, or -Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent Ri3 substituents; or R3’ is -OR6, -NR6R34, -S(0)O-2R6, -C(=0)R6, -C(=0)0R6, -0C(=0)R6, -C(=0)N(R34)R6, or - N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring;
each of R5, R71, and R8I is independently hydrogen, halogen, -C MO alkyl, -C3-ioaryl, -Ci. lohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, - C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R31or -NR31C(=O)R32;
R6 is -Cmoalkyl, -C3-ioaryl, -Cmohetaryl, -C3.i0cycloalkyl, -Ci-ioheterocyclyl, -Ci.i0alkyl- C3-ioaryl, -Ci-ioalkyl-Cmohetaryl, -Ci.ioalkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C3- locycloalkyl-Ci-ioalkyl, -C3.iocycloalkyl-C3.ioaryl, -C3.iocycloalkyl-Ci.iohetaryl, -C3.i0cycloalkyl- Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci-ioheterocyclyl-C3-ioaryl, -Ci-ioheterocydyl-Ci. !ohetaryl, or -Ci.ioheterocydyl-C3-iocydoalkyl, each of which is unsubstituted or substituted by one or more independent RI4 or Rn substituents;
R72 is hydrogen, -Cl - l0 alkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-i0cycloalkyl, -Ci-ioheterocyclyl, -OH, -CF3, -C(0)R31, -CO2R31, -C(=0)NR31, or -S(O)0-2R31;
each of Rio and R34 is independently -Ci40 alkyl, -C2-i0alkenyl, -C2-i0 alkynyl, - Ci.
l0heteroalkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-i0cycloalkyl, or -Cl-l0heterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, RI2 RI3 and R15 is independently hydrogen, halogen, -Cl - l0 alkyl, -C3-i0aryl, - Cs.iocydoalkyl, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R31or -NR3 1C(=0)R32;
each of R 31 , R 32 and R 34 is independently hydrogen,— Cl-lo alkyl,— C3-loaryl, or— C3- !ocycloalkyl, or wherein R3 1 together with R32 form a heterocyclic ring; and
wherein ring A comprises one or more heteroatoms selected from N, O, or S.
[0181] In some embodiments of Formula I, Xi is C=0, X2 is NRi or CRiRk, X3 is CR3R3’, W is C, Y is CR5, X4 is N or CRi, X5 is N or C, X6 is C, X7 is NR72 or CR7I, X8 is N, X9 is NR2i or CR2I and X10 is N or CR91;
Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3-i0aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci. l0alkyl-C3-l0cycloalkyl, -Ci-ioalkyl-Ci-ioheterocydyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
l0heterocydyl-C3-l0aryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
Ri’ is hydrogen -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci.
lohetaryl, -Ci.ioalkyl-C3-iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C3-ioaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
R2I is halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, - S(0)O-2R3 1, -NR31C(=0)R32, -L-Ci.ioalkyl, -L-C3-i0aryl, -L-Ci.i0hetaryl, -L-C3- locycloalkyl, or -L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
R22 is -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, -S(O)0-2R31, -L-Ci.ioalkyl, -L-C3- i0aryl, -L-Ci.i0hetaryl, -L-C3-i0cycloalkyl, or -L-Ci-ioheterocyclyl, , each of which is
unsubstituted or substituted by one or more independent Rn substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2-, -C(=0)-, -C(=0)0-, -0C(=0)-, -C(=0)N(R31)-, or -N(R31)C(=0)-; each of R3 R3’ and R4 is independently hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, - NR3 1R32, -C(0)R31, -C02R31, -C(=0)NR31, -NO2, -CN, -S(0)O-2R31, -Ci.ioalkyl, -C2.10alkenyl, or - C2-l0alkynyl, each of which is unsubstituted or substituted by one or more independent R33 substituents; or R3’ is -OR6, -NR6R34, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring;
each of R5 and R71 is independently hydrogen, halogen, -C MO alkyl, -C3.l0aryl, -C3- locycloalkyl, -OH, -CF3, -OR31, -NR3 1R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(O)0. 2R31or -NR3 1C(=0)R32;
R6 is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci- loalkyl-C3-locycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
loheterocyclyl-C3-l0aryl, each of which is unsubstituted or substituted by one or more independent R14 or R15 substituents;
R72 is hydrogen, -CMO alkyl, -C3-l0aryl, -C3-i0cycloalkyl, -OH, -CF3, -C(0)R31, -C02R31, - C(=0)NR31, or -S(O)0-2R31;
each of Rio and Rl4 independently -C O alkyl, -C3-l0aryl, -Ci-iohetaryl, -C3-i0cycloalkyl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, RI2 RI3 and R15 is independently hydrogen, halogen, -CMO alkyl, -OH, -CF3, - OR31, -NR3 1R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R3 1or -NR3 1C(=0)R32; each of R 31 , R 32 and R 34 is independently hydrogen or -CMO alkyl, or wherein R 31 together with R32 form a heterocyclic ring; and
wherein ring A comprises one or more heteroatoms selected from N, O, or S.
[0182] In some embodiments of Formula I, Xi is C=0, X2 is NRi, X3 is CR3R3’, W is C, Y is CR5, X4 is CRi, X5 is C, X6 is C, X7 is NR72, X8 is N, X9 is CR2I and X10 is N or CR91;
Ri is -Ci.ioalkyl, -Ci-ioheterocyclyl, -CM0alkyl-C3-ioaryl, -Ci-ioheterocyclyl-CMoalkyl, or -Ci-ioheterocyclyl-C3-ioaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
R2I is halogen, -OH, -CF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, , -L-Cmoalkyl, -L-C3-i0aryl, -L-Ci.i0hetaryl, -L-C3-i0cycloalkyl, or -L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
L is a bond, -N(R31)-, -C(=0)N(R31)-, or -N(R3 1)C(=0)-;
each of R3 R3’ and R4 is independently hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, - NR3 1R32, - -N02, -CN, -S(0)O-2R3 1, -Ci.ioalkyl, -C2-i0alkenyl, or -C2-i0alkynyl; or R3’ is -OR6, - NR6R34, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring; R5 is hydrogen, halogen, or -C MO alkyl;
R6 is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Cmoalkyl^-ioaryl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C3.ioaryl, each of which is unsubstituted or substituted by one or more independent RI4 or RI5 substituents;
RV2 is hydrogen, -CMO alkyl, -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, or -S(O)0-2R31; each of Rio and RI4 is independently -CMO alkyl, -C3-ioaryl, -Ci-iohetaryl, or -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, Ri2 and RI5 is independently hydrogen, halogen, -CMO alkyl, -OH, -CF3, -OR3, -NR31R32, -N02, -CN, or -S(0)O-2R3 1;
each of R 31 , R 32 and R 34 is independently hydrogen or -CMO alkyl, or wherein R 31 together with R32 form a heterocyclic ring; and
wherein ring A comprises one or more heteroatoms selected from N, O, or S.
[0183] In some embodiments of Formula I, Xi is C=0, X2 is NRi, X3 is CR3R3’, W is C, Y is CR5, X4 is CRi, X5 is C, X6 is C, X7 is NR72, X8 is N, Xg is CR2I and X10 is N;
Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -CM0alkyl-C3.ioaryl, -Ci-ioheterocyclyl-CMoalkyl, or -Ci.ioheterocyclyl-C3.ioaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
R2i is halogen, -CN, , -L-Cmoalkyl, -L-C3-ioaryl, -L-Cmohetaryl, -L-C3-iocycloalkyl, or - L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent RI2 substituents;
L is a bond, -N(R31)-, or -C(=0)N(R31)-; or R3’ is -OR6 or -NR6R34, wherein R6 together with R34 can optionally form a heterocyclic ring;
each of R3 R3’ and R is independently hydrogen, halogen, -OH, -CF3, or -Cmoalkyl; or R3’ is -OR6 or -NR6R34, wherein R6 together with R34 can optionally form a heterocyclic ring;
R5 is hydrogen;
R6 is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Cmoalkyl^-ioaryl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C3.ioaryl, each of which is unsubstituted or substituted by one or more independent RI4 or R^ substituents;
R72 is hydrogen, -CMO alkyl, -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, or -S(O)0-2R31; each of Rio and RI4 is independently -CMO alkyl, -C3-ioaryl, -Cmohetaryl, or -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, Rn and Rn is independently hydrogen, halogen, -CMO alkyl, -OH or -CF3; each of R31 and R34 is independently hydrogen or -CMO alkyl; and
wherein ring A comprises one or more heteroatoms selected from N, O, or S. [0184] In certain embodiments, the present disclosure provides an ERK inhibitor which is a compound of Formula I-A:
Figure imgf000069_0001
or a pharmaceutically acceptable salt or prodrug thereof, and wherein the substituents are as defined above.
[0185] In some embodiments of Formula I-A, Ri is-Ci-ioalkyl, -C3-i0aryl, -Ci-iohetaryl, -C3- iocycloalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Cmoalkyl^. iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C3.iocycloalkyl-Ci.ioalkyl, -C3.iocycloalkyl-C3.ioaryl, - C3.iocycloalkyl-Ci.iohetaryl, -C3-iocycloalkyl-Ci-ioheterocydyl, -Ci-ioheterocyclyl -Ci.i0alkyl, -Ci. ioheterocyclyl-C3.ioaryl, -Ci-ioheterocyclyl-Ci-iohetaryl, or -Ci-i0heterocydyl-C3-iocycloalkyl, each of which is unsubstituted or substituted by one or more independent Ri0 or Rn substituents. In some embodiments, Ri is -Ci.i0alkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3.ioaryl, -Ci-ioalkyl-Ci-iohetaryl, - Ci.ioalkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocydyl-Ci-ioalkyl, or -Ci. ioheterocyclyl-C3-ioaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents. In some embodiments, Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Cmoalkyl^. loaryl, -Cmoheterocyclyl-Cmoalkyl, or -Ci.ioheterocyclyl-C3.i0aryl, each of which is unsubstituted or substituted by one or more independent Ri0 or Rn substituents. In some embodiments, Ri is -Ci. ioheterocyclyl-Ci-ioalkyl, unsubstituted or substituted by one or more independent Rio or Rn substituents.
[0186] In some embodiments of Formula I-A, R2I is hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(0)O-2R31, -NR31C(=0)R32, -L-CI. loalkyl, -L-C2-ioalkenyl, -L-C2-ioalkynyl, -L-C i . i oheteroal kyl , -L-C3-ioaryl, -L-Cmohetaryl, -L- C3-iocycloalkyl, or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent RI2 substituents. In some embodiments, R2i is halogen, -OH, -CF3, -OCF3, - OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R31, -NR31C(=0)R32, -L- Cmoalkyl, -L-C3-ioaryl, -L-Cmohetaryl, -L-C3-iocycloalkyl, or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents. In some embodiments, R2 I is halogen, -OH, -CF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -L-Cmoalkyl, -L-C3.i0aryl, -L-Cmohetaryl, -L-C3.i0cycloalkyl, or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent RI2 substituents. In some embodiments, R2i is halogen, -CN, , -L-Cm0alkyl, -L-C3.i0aryl, -L-Cmohetaryl, -L-C3.
locycloalkyl, or -L-Cmoheterocyclyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents.
[0187] In some embodiments of Formula I- A, R2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent Rn substituents; wherein the Cmohetaryl of R21 comprises one or more nitrogen atoms; each RI2 substituent, when present, is independently selected from the group consisting of -Cmo alkyl, -Cmoalkenyl, -C2-io alkynyl, -Cmoheteroalkyl, -C3-ioaryl, -Cmohetaryl, -C3-iocycloalkyl, -Cmoheterocyclyl, -OH, -CF3, -OCF3, -OR31; wherein each R3l is independently hydrogen or -Cmo alkyl; L is a bond; and Ri is -Cmoalkyl-Csuoaryl, -Cmoalkyl-Cmohetaryl, -Cn ioheterocyclyl-Cmoalkyl, or -C M oheterocycl yl -C3.10aryl , unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0188] In some embodiments of Formula I- A, R2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent Rn substituents; wherein the Cmohetaryl of R21 comprises one or more nitrogen atoms; each RI2 substituent, when present, is independently selected from the group consisting of -Cmo alkyl, -Cmoalkenyl, -C2-io alkynyl, -Cmoheteroalkyl, -C3-ioaryl, -Cmohetaryl, -C3-iocycloalkyl, -Cmoheterocyclyl, -OH, -CF3, -OCF3, -OR31; wherein each R3l is independently hydrogen or -Cmo alkyl; L is a bond; and Ri is
Figure imgf000070_0001
, unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0189] In some embodiments of Formula I- A, R2I is -L-Ci-iohetaryl unsubstituted or substituted by one or more independent Ri2 substituents; wherein the Ci-iohetaryl of R2l comprises one or more nitrogen atoms; each RI2 substituent, when present, is independently selected from the group consisting of -C l - l0 alkyl, -C2-i0alkenyl, -C2- l0 alkynyl, -Ci-ioheteroalkyl, -C3-l0aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, -CF3, -OCF3, -OR31; wherein each R3l is independently
Figure imgf000070_0002
hydrogen or -Cl - l0 alkyl; L is a bond; and Ri is R1 0 , unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0190] In some embodiments of Formula I- A, R2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent Ri2 substituents; wherein the Cmohetaryl of R2l comprises one or more nitrogen atoms; each RI2 substituent, when present, is independently selected from the group consisting of -C mo alkyl, -C2-i0alkenyl, -C2- l0 alkynyl, -Cmoheteroalkyl, -C3.l0aryl, -Cmohetaryl, -C3-iocycloalkyl, -Cmoheterocyclyl, -OH, -CF3, -OCF3, -OR31; wherein each R3 1 is independently hydrogen or -C o alkyl; L is a bond; and Ri is
Figure imgf000070_0003
unsubstituted or substituted by one or more independent Rl0 or Rn substituents. [0191] In some embodiments of Formula I-A, R2l is -L-Cmohetaryl unsubstituted or substituted by one or more independent Ri2 substituents; the Cmohetaryl of R2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl; each RI2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -zz-Pr, OH, - OMe, -OEt, -OPr; L is a bond; and Ri is -Cmoalkyl-Cs-ioaryl, -Ci-ioalkyl-Cmohetaryl, -Cn !oheterocyclyl-Cmoalkyl, or -C M oheterocycl yl -Cm oaryl , unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0192] In some embodiments of Formula I-A, R2I is -L-Cmohetaryl unsubstituted or substituted by one or more independent Ri2 substituents; the Cmohetaryl of R2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl; each Ri2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -zz-Pr, OH, -
OMe, -OEt, -OPr; L is a bond; and Ri is
Figure imgf000071_0001
, unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0193] In some embodiments of Formula I- A, R2I is -L-Ci-iohetaryl unsubstituted or substituted by one or more independent Rn substituents; the Ci-iohetaryl of R2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl; each RI2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -//-Pr, OH, -
Figure imgf000071_0002
OMe, -OEt, -OPr; L is a bond; and Ri is R10 , unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0194] In some embodiments of Formula I- A, R2l is -L-Ci-iohetaryl unsubstituted or substituted by one or more independent Rn substituents; the Cmohetaryl of R2l is selected from the group consisting of pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, and pyridazinyl; each RI2 substituent, when present, is independently selected from the group consisting -Me, -Et, -z-Pr, -zz-Pr, OH, -
OMe, -OEt, -OPr; L is a bond; and Ri is
Figure imgf000071_0003
unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0195] In some embodiments of Formula I-A, L is a bond, -0-, -N(R31)-, -S(O)0-2-, -C(=0)-, - C(=0)0-, -OC(=0)-, -C(=0)N(R31)-, -N(R31)C(=0)-, -NR31C(=0)0-, -NR31C(=0)NR32-, - NR31S(0)O-2-, or -S(0)O-2N(R31)-. In some embodiments, L is a bond, -0-, -N(R31)-, -S(0)0.2-, - C(=0)-, -C(=0)0-, -0C(=0)-, -C(=0)N(R31)-, or -N(R31)C(=0)-. In some embodiments, L is a bond, -N(R31)-, -C(=0)N(R31)-, or -N(R31)C(=0)-. In some embodiments, L is a bond, -N(R31)-, or -C(=0)N(R31)-.
[0196] In some embodiments of Formula I-A, R72 is hydrogen,— Ci-io alkyl,— C3-loaryl,— Ci- iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, or - S(0)O-2R3 1. In some embodiments, R72 is independently hydrogen, -C MO alkyl, -C3-i0aryl, -C3- !ocycloalkyl, -C(0)R31, -C02R31, -C(=0)NR31, or -S(0)o-2R31. In some embodiments, R72 is independently hydrogen or -Ci-ioalkyl. In some embodiments, R72 is independently hydrogen.
[0197] In some embodiments of Formula I-A, each of Rio independently is -CMO alkyl, -C2- l0alkenyl, -C2-i0 alkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-i0cycloalkyl, -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents. In some embodiments, each of Rio is independently -CMO alkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents. In some embodiments, each of Rio is independently -CMO alkyl, -C3-i0aryl, -Ci-iohetaryl, or -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents.
[0198] In some embodiments of Formula I-A, each of Rn, R12, and Rn is independently hydrogen, halogen, -CMO alkyl, -C3-i0aryl, -C3-i0cycloalkyl, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, - C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R31or -NR31C(=O)R32. In some embodiments, each of Rn, R12, and R is independently hydrogen, halogen, -CMO alkyl, -OH, -CF3, -OR31, -NR31R32, - C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R31or -NR31C(=O)R32. In some embodiments, each of Rn, R12, and Ri3 is independently hydrogen, halogen, -CMO alkyl, -OH, -CF3, -OR3, - NR31R32, -N02, -CN, or -S(O)0-2R31· In some embodiments, each of Rn, R12, and Ri3 is
independently hydrogen, halogen, -CMO alkyl, -OH or -CF3.
[0199] In some embodiments of Formula I-A, each of R , R , and R is independently hydrogen, halogen, -CMO alkyl, -C2-i0alkenyl, -C2-i0 alkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Cmohetaryl, -C3- locycloalkyl, -Ci-ioheterocyclyl, or wherein R31 together with R32 form a heterocyclic ring. In some embodiments, each of R , R , and R is independently hydrogen, -CMO alkyl, -C3-ioaryl, or -C3- locycloalkyl, or wherein R31 together with R32 form a heterocyclic ring. In some embodiments, each of R 31 , R 32 , and R 33 is independently hydrogen or -Cmoalkyl, or wherein R 31 together with R 32
31 32 33
form a heterocyclic ring. In some embodiments, each of R , R , and R is independently hydrogen or -Ci-ioalkyl.
[0200] In some embodiments of Formula I-A,
Ri is-Cmoalkyl, -C3-i0aryl, -Cmohetaryl, -C3-i0cycloalkyl, -Cmoheterocyclyl, -Cmoalkyl- C3-i0aryl, -Cmoalkyl-CMohetaryl, -Cmoalkyl-Cmocycloalkyl, -Cmoalkyl-CMoheterocyclyl, -C3. locycloalkyl -Cmoalkyl, -C3-iocycloalkyl-C3-i0aryl, -C3-i0cycloalkyl -Cmohetaryl, -C3-i0cycloalkyl- Cmoheterocyclyl, -Cmoheterocyclyl-CMoalkyl, -Cmoheterocyclyl-Cmoaryl, -Cmoheterocyclyl-Ci. lohetaryl, or -C M oheterocycl yl -Cm ocycl oal kyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
R21 is hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, - C(=0)NR31, -N02, -CN, -S(0)O-2R31, -NR31C(=0)R32, -L-Ci.i0alkyl, -L-C2-i0alkenyl, -L-C2- !oalkynyl, -L-C3-ioaryl, -L-Ci-iohetaryl, -L-C3-iocycloalkyl, or -L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2-, -C(=0)-, -C(=0)0-, -0C(=0)-, -C(=0)N(R31)-, - N(R31)C(=0)-, -NR31C(=0)0-, -NR31C(=0)NR32-, -NR31S(0)O-2-, or -S(O)0-2N(R31)-;
R72 is hydrogen, -CMO alkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, or -S(O)0-2R31;
each of Rio is independently -C O alkyl, -C2-i0alkenyl, -C2-i0 alkynyl, -Ci-ioheteroalkyl, - C3-i0aryl, -Ci-iohetaryl, -C3-i0cycloalkyl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, Rn, and R is independently hydrogen, halogen, -Cmoalkyl, -C3-ioaryl, -C3- locycloalkyl, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, - S(O)0-2R31or -NR31C(=0)R32; and
each of R31and R32 is independently hydrogen, -Cmoalkyl, -C3-ioaryl, or -C3-iocycloalkyl, or wherein R31 together with R32 form a heterocyclic ring.
[0201] In some embodiments of Formula I- A,
Ri is -Cmoalkyl, -Ci-ioheterocyclyl, -Cmoalkyl-Cmoaryl, -Cmoalkyl-Cmohetaryl, -Ci. ioalkyl-C3-iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
ioheterocyclyl-C3-ioaryl, each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
R2I is halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(0)O-2R31, -NR31C(=0)R32, -L-Cmoalkyl, -L-C3-i0aryl, -L-Cmohetaryl, -L-C3- locycloalkyl, or -L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent RI2 substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2-, -C(=0)-, -C(=0)0-, -0C(=0)-, -C(=0)N(R31)-, or -N(R31)C(=0)-;
R72 is hydrogen, -Cmoalkyl, -C3-ioaryl, -C3-iocycloalkyl, -C(0)R31, -C02R31, -C(=0)NR31, -S(0)O-2R31;
RIO is -Cmoalkyl, -C3-i0aryl, -Cmohetaryl, -C3-i0cycloalkyl, or -Cmoheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, Rn, and Ri3 is independently hydrogen, halogen, -Cmoalkyl, -OH, -CF3, -OR31, -NR3 IR32, -C(0)R31, -CO2R31, -C(=0)NR31, -NO2, -CN, -S(O)0-2R31or -NR31C(=O)R32; and each of R 31 and R 32 is independently hydrogen or -Cmoalkyl, or wherein R 31 together with R32 form a heterocyclic ring.
[0202] In some embodiments of Formula I- A,
Ri is Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci- ioalkyl-C3-iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.
i oheterocycl yl -C3 - 10aryl , each of which is unsubstituted or substituted by one or more independent Rio or Rn substituents;
R21 is halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(0)O-2R31, -NR31C(=0)R32, -L-Ci.ioalkyl, -L-C3-ioaryl, -L-Ci-iohetaryl, -L-C3- iocycloalkyl, or -L-Ci-ioheterocyclyl, each of which is unsubstituted or substituted by one or more independent R32 substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2-, -C(=0)-, -C(=0)0-, -0C(=0)-, -C(=0)N(R31)-, or -N(R31)C(=0)-;
R72 is hydrogen or -Ci.i0alkyl;
each of Rio is independently -Ci.i0alkyl, -C3-i0aryl, -Ci-iohetaryl, -C3-i0cycloalkyl, or -Ci- ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn and Ri2 is independently hydrogen, halogen, -Ci- alkyl, -OH, -CF3, -OR31, - NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R31or -NR31C(=O)R32; and
each of R31 and R32 is independently hydrogen or -Cmoalkyl.
[0203] In some embodiments of Formula I- A,
Ri is -Ci-ioalkyl, -Ci-ioheterocyclyl, -Ci-ioalkyl-C3-ioaryl, -Ci-ioheterocyclyl-Ci-ioalkyl, or -Ci.ioheterocyclyl-C3-ioaryl, each of which is unsubstituted or substituted by one or more independent Ri0 or Rn substituents;
R2i is halogen, -CN, -L-Cmoalkyl, -L-C3-ioaryl, -L-Cmohetaryl, -L-C3-iocycloalkyl, or - L-Cnioheterocyclyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
L is a bond, -N(R31)-, or -C(=0)N(R31)-;
R72 is hydrogen;
each of Rio is independently -Cno alkyl, -C3-ioaryl, -Cmohetaryl, or -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn and Ri2 is independently hydrogen, halogen, -Cno alkyl, -OH, -CF3 -OR31 or - CN; and
each of R31 is independently hydrogen or -Cno alkyl. [0204] In some embodiments of Formula I- A,
Ri is -Ci-ioalkyl, -Cmoalkyl-Cmoaryl, or -Ci-ioheterocyclyl-Ci-ioalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
R2I is -L-C3-ioaryl or -L-Ci-iohetaryl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
L is a bond or -N(R31)-;
R72 is hydrogen;
each of Rio is independently-C3-i0aryl, -Ci-iohetaryl, or -Cl-l0heterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn and Ri2 is independently halogen,— Cl-l0 alkyl, -OH, -CF3 or -OR31; and each of R31 is independently hydrogen or -Cl-l0 alkyl.
[0205] In some embodiments of Formula I- A,
Ri is -Ci-ioheterocyclyl-Ci-ioalkyl, unsubstituted or substituted by one or more independent Rn substituents;
R2I is pyridyl selected from the group consisting of 2-pyridyl, 3-pyridyl and 4-pyridyl, which is unsubstituted or substituted by one or more independent R32 substituents;
L is a bond;
R72 is hydrogen;
each of Rn and Ri2 is independently halogen, -Cmo alkyl, -CF3 or -OR31; and
each of R31 is independently hydrogen or -Cl-l0 alkyl.
[0206] In certain embodiments, for a compound of Formula I or I-A, Ri is -Cmoheterocyclyl-Ci. l0alkyl, which is unsubstituted. In some embodiments, Ri is -Ci-ioheterocyclyl-Ci-ioalkyl, substituted by one or more independent Ri0 substituents. In some embodiments, Ri is -Ci.
l0heterocyclyl-Cl-l0alkyl, substituted by one or more independent Rn substituents. In some embodiments, Ri is -Cl-l0heterocyclyl-Cl-l0alkyl, substituted by one or more independent Rio or Rn substituents. In some embodiments, Rio and Rn are selected from aryl, such as phenyl.
[0207] In certain embodiments, for a compound of Formula I or I-A, Ri is -Cmoalkyl, -Cn loheterocyclyl, -Ci.ioalkyl-C3-ioheterocyclyl, -Ci.ioalkyl-C3-ioaryl, -Cmoalkyl -Cmohetaryl, -Cn loheterocyclyl-Cmoalkyl, or -Ci-ioheterocyclyl-C3-ioaryl, unsubstituted or substituted by one or more independent Rio or Rn substituents. In other embodiments, Ri is -Cmoalkyl, -Cn
loheterocyclyl, -Cmoalkyl-C3-ioheterocyclyl, -Cmoalkyl-Cmoaryl, -Cmoalkyl -Cmohetaryl, -Cn loheterocyclyl-Cmoalkyl, or -Cmoheterocyclyl-Cmoaryl, unsubstituted or substituted by one or more independent Ri0 or Rn substituents. In yet other embodiments, Ri is -Cmoalkyl-Cmoaryl, - Cmoalkyl-Cmohetaryl, -Cmoheterocyclyl-Cmoalkyl, or -Cmoheterocyclyl-Cmoaryl, unsubstituted or substituted by one or more independent Rl0 or Rn substituents. In yet other embodiments, Ri is - CM0alkyl-C3-i0aryl or -CM0heterocyclyl-C3-i0aryl, unsubstituted or substituted by one or more independent Rl0 or Rn substituents. In further embodiments, wherein Ri is
Figure imgf000076_0001
,
unsubstituted or substituted by one or more independent Rl0 or Rn substituents. In some embodiments, Rl is Ri is -Cnioheterocyclyl, -C M oheterocycl yl -CM oal kyl , or -Ci-ioheterocyclyl- C3-l0aryl, unsubstituted or substituted by one or more independent Rl0 or Rn substituents. In some embodiments, Ri is
Figure imgf000076_0002
unsubstituted or substituted by one or more independent Rl0 or Rn substituents.
[0208] In certain embodiments, for a compound of Formula I or I-A, each of Ri or Rf is independently selected from:
Figure imgf000076_0003
Figure imgf000077_0001
[0209] In certain embodiments, the present disclosure provides an ERK inhibitor which is a compound selected from the group consisting of:
Figure imgf000077_0002
Figure imgf000078_0001
Figure imgf000079_0001
Figure imgf000080_0001
Figure imgf000081_0001
Figure imgf000083_0001
Figure imgf000084_0001
Figure imgf000085_0001
Figure imgf000086_0001
Figure imgf000087_0001
Figure imgf000088_0001
Figure imgf000089_0001
87
Figure imgf000090_0001
Figure imgf000091_0001
 [0210] In certain embodiments, the present disclosure provides an ERK inhibitor which is a compound selected from the group consisting of:
Figure imgf000092_0001
[0211] In certain embodiments, the present disclosure provides a subject ERK inhibitor (including but not limited to Compound A) selected from the group consisting of:
Figure imgf000092_0002
Figure imgf000093_0001
[0212] Compounds of the present disclosure also include crystalline and amorphous forms of those compounds, pharmaceutically acceptable salts, and active metabolites of these compounds having the same type of activity, including, for example, polymorphs, pseudopolymorphs, solvates, hydrates, unsolvated polymorphs (including anhydrates), conformational polymorphs, and amorphous forms of the compounds, as well as mixtures thereof.
[0213] The compounds described herein may exhibit their natural isotopic abundance, or one or more of the atoms may be artificially enriched in a particular isotope having the same atomic number, but an atomic mass or mass number different from the atomic mass or mass number predominantly found in nature. All isotopic variations of the compounds of the present disclosure, whether radioactive or not, are encompassed within the scope of the present disclosure. For example, hydrogen has three naturally occurring isotopes, denoted 1H (protium), 2H (deuterium), and 3H (tritium). Protium is the most abundant isotope of hydrogen in nature. Enriching for deuterium may afford certain therapeutic advantages, such as increased in vivo half-life and/or exposure, or may provide a compound useful for investigating in vivo routes of drug elimination and metabolism. Isotopically-enriched compounds may be prepared by conventional techniques well known to those skilled in the art.
[0214]“ Isomers” are different compounds that have the same molecular formula.“Stereoisomers” are isomers that differ only in the way the atoms are arranged in space.“Enantiomers” are a pair of stereoisomers that are non superimposable mirror images of each other. A 1 :1 mixture of a pair of enantiomers is a“racemic: mixture. The term“(±)” is used to designate a racemic mixture where appropriate.“Diastereoisomers” or“diastereomers” are stereoisomers that have at least two asymmetric atoms but are not mirror images of each other. The absolute stereochemistry is specified according to the Cahn-Ingold-Prelog R-S system. When a compound is a pure enantiomer, the stereochemistry at each chiral carbon can be specified by either R or S. Resolved compounds whose absolute configuration is unknown can be designated (+) or (-) depending on the direction (dextro- or levorotatory) in which they rotate plane polarized light at the wavelength of the sodium D line. Certain compounds described herein contain one or more asymmetric centers and can thus give rise to enantiomers, diastereomers, and other stereoisomeric forms, the asymmetric centers of which can be defined, in terms of absolute stereochemistry, as (R)- or (S)-. The present chemical entities, pharmaceutical compositions and methods are meant to include all such possible stereoisomers, including racemic mixtures, optically pure forms, mixtures of diastereomers and intermediate mixtures. Optically active (R)- and (S)-isomers can be prepared using chiral synthons or chiral reagents, or resolved using conventional techniques. The optical activity of a compound can be analyzed via any suitable method, including but not limited to chiral chromatography and polarimetry, and the degree of predominance of one stereoisomer over the other isomer can be determined.
[0215] Chemical entities having carbon-carbon double bonds or carbon-nitrogen double bonds may exist in Z- or E- form (or cis- or trans- form). Furthermore, some chemical entities may exist in various tautomeric forms. Unless otherwise specified, chemical entities described herein are intended to include all Z-, E- and tautomeric forms as well.
[0216] The term“salt” or“pharmaceutically acceptable salt” refers to salts derived from a variety of organic and inorganic counter ions well known in the art. Pharmaceutically acceptable acid addition salts can be formed with inorganic acids and organic acids. Inorganic acids from which salts can be derived include, for example, hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, and the like. Organic acids from which salts can be derived include, for example, acetic acid, propionic acid, glycolic acid, pyruvic acid, oxalic acid, maleic acid, malonic acid, succinic acid, fumaric acid, tartaric acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid, salicylic acid, and the like. Pharmaceutically acceptable base addition salts can be formed with inorganic and organic bases. Inorganic bases from which salts can be derived include, for example, sodium, potassium, lithium, ammonium, calcium, magnesium, iron, zinc, copper, manganese, aluminum, and the like. Organic bases from which salts can be derived include, for example, primary, secondary, and tertiary amines, substituted amines including naturally occurring substituted amines, cyclic amines, basic ion exchange resins, and the like, specifically such as isopropylamine, trimethylamine,
diethylamine, triethylamine, tripropylamine, and ethanolamine. In some embodiments, the pharmaceutically acceptable base addition salt is chosen from ammonium, potassium, sodium, calcium, and magnesium salts.
[0217]“Optional” or“optionally” means that the subsequently described event of circumstances may or may not occur, and that the description includes instances where the event or circumstance occurs and instances in which it does not. For example,“optionally substituted aryl” means that the aryl group may or may not be substituted and that the description includes both substituted aryl groups and aryl groups having no substitution.
[0218]“Pharmaceutically acceptable carrier, diluent or excipient” includes without limitation any adjuvant, carrier, excipient, glidant, sweetening agent, diluent, preservative, dye, colorant, flavor enhancer, surfactant, wetting agent, dispersing agent, suspending agent, stabilizer, isotonic agent, solvent, or emulsifier which has been approved by the United States Food and Drug Administration as being acceptable for use in humans or domestic animals.
[0219] Any combination of the groups described above for the various variables is contemplated herein. Throughout the specification, groups and substituents thereof can be chosen to provide stable moieties and compounds.
[0220] The chemical entities described herein can be synthesized according to one or more illustrative schemes herein and/or techniques known in the art, for example, as described in PCT/US2014/059197, the disclosure of which is incorporated by reference herein. Materials used herein are either commercially available or prepared by synthetic methods generally known in the art.
[0221] The present disclosure provides a method of inhibiting the activity of a member of the MAPK pathway in a cell, comprising contacting the cell with an effective amount of one or more compounds disclosed herein. Inhibition of kinase activity can be assessed and demonstrated by a wide variety of ways known in the art. Non-limiting examples include (a) immunoblotting and immunoprecipitation with antibodies such as anti-phosphotyrosine, anti-phosphoserine or anti- phosphothreonine antibodies that recognize phosphorylated proteins; (b) using antibodies that specifically recognize a particular phosphorylated form of a kinase substrate (e.g. anti-phospho ERK); (c) cell proliferation assays, such as but not limited to tritiated thymidine uptake assays, BrdU (5’-bromo-2’-deoxyuridine) uptake (kit marketed by Calibochem), MTS uptake (kit marketed by Promega), MTT uptake (kit marketed by Cayman Chemical), CyQUANT® dye uptake
(marketed by Invitrogen).
[0222] Selective inhibition of a particular target may also be determined by expression levels of the target gene, its downstream signaling genes (for example by RT-PCR), or expression levels of the target protein (for example by immunocytochemistry, immunohistochemistry, Western blots) as compared to other related enzymes.
[0223] In some embodiments, the practice of a subject method involves a contacting step taking place in vitro. In other embodiments, the contacting step takes place in vivo.
[0224] Any of the compounds shown above may show a biological activity in an inhibition assay, such as a MEK or ERK inhibition assay, of between about 1 pM and 25 mM (IC50).
[0225] In some embodiments, one or more compounds of the disclosure may bind specifically to an ERK (MAPK) kinase or a protein kinase selected from the group consisting of Ras, Raf, JNK, ErbB-l (EGFR), Her2 (ErbB-2), Her 3 (ErbB-3), Her 4 (ErbB-4), MAP2K1 (MEK1), MAP2K2 (MEK2), MAP2K3 (MEK3), MAP2K4 (MEK4), MAP2K5 (MEK5), MAP2K6 (MEK6), MAP2K7 (MEK7), CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK11 and any other protein kinases listed in the appended tables and figures, as well as any functional mutants thereof.
[0226] In some embodiments, the IC50 of a compound of the disclosure for the target member of the MAPK pathway is less than about 1 mM, less than about 100 nM, less than about 50 nM, less than about 10 nM, less than 1 nM or even less than about 0.5 nM. In some embodiments, the IC50 of a compound of the disclosure for the target member of the MAPK pathway is less than about 1 pM, less than about 100 nM, less than about 50 nM, less than about 10 nM, less than 1 nM or even less than about 0.5 nM. In some embodiments, one or more compounds of the disclosure exhibit dual binding specificity and are capable of inhibiting an ERK kinase (e.g., ERK-l kinase, ERK-2 kinase, etc.) as well as a protein kinase (e.g., Ras, Raf, Her-2, MEK1, etc.) with an IC50 value less than about 1 pM, less than about 100 nM, less than about 50 nM, less than about 10 nM, less than 1 nM or even less than about 0.5 nM. In some embodiments, one or more compounds of the disclosure may be capable of inhibiting kinases involved in the Ras-Raf-MEK-ERK pathway (MAPK pathway) including, for example, Ras, Raf, INK, ErbB-l (EGFR), Her2 (ErbB-2), Her3 (ErbB-3), Her4 (ErbB-4), MAP2K1 (MEK1), MAP2K2 (MEK2), MAP2K3 (MEK3), MAP2K4 (MEK4), MAP2K5 (MEK5), MAP2K6 (MEK6), MAP2K7 (MEK7), CDK1, CDK2, CDK3,
CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK11, and functional mutants thereof. In some embodiments, the kinase is Ras, Raf, INK, ErbB-l (EGFR), Her2 (ErbB-2), MAP2K1 (MEK1), CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, or any other kinases listed in the tables and figures herein.
[0227] In still another embodiment, the compounds of the disclosure selectively inhibit ERK,
MEK, Ras or Raf activity relative to one or more protein kinases including but not limited to serine/threonine kinase such as DNA-PK and mTor. Such selective inhibition can be evidenced by, e.g., the IC50 value of the compound of the disclosure that can be 1/2, l/3rd, l/4th, 1 /5th, 1 /7th, l/l0th, 1120th, 1125th , 1/50th, 1/100*11, 11200th, 1/300th, 11400th, l/500th, 1/1000*11, 112000th or less as compared to that of a reference protein kinase. In some instances, the compounds of the disclosure lack substantial cross-reactivity with at least about 100, 200, 300, or more protein kinases other than ERK, MEK, Ras or Raf. The lack of substantial cross-reactivity with other non-MAPK pathway proteins can be evidenced by, e.g., at least 50%, 60%, 70%, 80%, 90% or higher kinase activity retained when the compound of the disclosure is applied to the protein kinase at a concentration of 1 mM, 5 mM, 10 mM or higher.
[0228] In some embodiments, one or more compounds of the disclosure selectively inhibits ERK, MEK, Ras or Raf activity with an IC50 value of about 100 nM, 50 nM, 10 nM, 5 nM, 100 pM, 10 pM or even 1 pM, or less as ascertained in an in vitro kinase assay.
[0229] In some embodiments, one or more compounds of the disclosure is capable of inhibiting and/or otherwise modulating cellular signal transduction via one or more protein kinases or lipid kinases disclosed herein. For example, one or more compounds of the disclosure is capable of inhibiting or modulating the output of a signal transduction pathway. Output of signaling transduction of a given pathway can be measured by the level of phosphorylation,
dephosphorylation, fragmentation, reduction, oxidation of a signaling molecule in the pathway of interest. In another specific embodiment, the output of the pathway may be a cellular or phenotypic output (e.g. modulating/inhibition of cellular proliferation, cell death, apoptosis, autophagy, phagocytocis, cell cycle progression, metastases, cell invasion, angiogenesis, vascularization, ubiquitination, translation, transcription, protein trafficking, mitochondrial function, golgi function, endoplasmic reticular function, etc). In some embodiments, one or more compounds of the disclosure is capable of, by way of example, causing apoptosis, causing cell cycle arrest, inhibiting cellular proliferation, inhibiting tumor growth, inhibiting angiogenesis, inhibiting vascularization, inhibiting metastases, and/or inhibiting cell invasion.
[0230] In some embodiments, one or more compounds of the disclosure causes apoptosis of said cell or cell cycle arrest. Cell cycle can be arrested at the G0/G1 phase, S phase, and/or G2/M phase by the subject compounds.
[0231] In some embodiments, one or more compounds of the disclosure including but not limited to the compounds listed above are capable of inhibiting cellular proliferation. For example, in some cases, one or more compounds of the disclosure may inhibit proliferation of tumor cells or tumor cell lines with a wide range of genetic makeup. In some cases, the compounds of the disclosure may inhibit NSCLC cell proliferation in vitro or in an in vivo model such as a xenograft mouse model. In some cases, in vitro cultured NSCLC cell proliferation may be inhibited with an IC50 of less than 100 nM, 75 nM, 50 nM, 25 nM, 15 nM, 10 nM, 5 nM, 3 nM, 2 nM, 1 nM, 0.5 nM, 0.1 nM or less by one or more compounds of the disclosure.
[0232] In some embodiments, proliferation of primary tumors derived from subjects (e.g. cancer patients) can be inhibited by a compound of the disclosure as shown by in vitro assays, or in vivo models (e.g. using the subjects’ tumor cells for generating a xenograft mode). In some cases primary tumor cell line proliferation may be inhibited with an IC50 of less than 100 nM, 75 nM, 50 nM, 25 nM, 15 nM, 10 nM, 5 nM, 3 nM, 2 nM, 1 nM, 0.5 nM, 0.1 nM or even less by one or more compounds of the disclosure. In some cases, the average IC50 of a compound of the disclosure for inhibiting a panel 10, 20, 30, 40, 50, 100 or more primary tumor cells may be about 200 nM, 100 nM, 75 nM, 50 nM, 25 nM, 15 nM, 10 nM, 5 nM, 3 nM, 2 nM, 1 nM, 0.5 nM, 0.1 nM or even less. The tumor cells that can be inhibited by the compounds of the present disclosure include but are not limited to adenocarcinomas, such as adenocarcinomas of the lung.
[0233] In some embodiments, the compounds of the disclosure are effective in blocking cell proliferation signals in cells. In some cases, cell proliferation signaling may be inhibited by one or more compounds of the disclosure as evidenced by Western blot analysis of phosphorylation of proteins such as FOXOl (phosphorylation at T24/3a T32), GSK3P(phosphorylation at S9),
PRAS40 (phosphorylation at T246), or MAPK phosphorylation. In some cases, the compounds of the disclosure can inhibit phosphorylation of signaling proteins and suppress proliferation of cells containing these signaling proteins but are resistant to existing chemotherapeutic agents including but not limited to rapamycin, Gleevec, dasatinib, alkylating agents, antimetabolites, anthracyclines, plant alkaloids, topoisomerase inhibitors and other antitumor agents disclosed herein.
[0234] In some embodiments, one or more compounds of the disclosure may cause cell cycle arrest. In some cases, cells treated with one or more compounds of the disclosure may arrest or take longer to proceed through one or more cell cycle stages such as G0/G1, S, or G2/M. For example, cells treated with one or more compounds of the disclosure may arrest or take longer to proceed through the G0/G1 cell cycle stage. In some cases, about 35%, 40%, 50%, 55%, 60%, 65%, 70% or more of cells treated with one or more compounds of the disclosure may be in the G0/G1 cell cycle stage. In some cases, cells exhibiting cell cycle arrest in the G0/G1 cell cycle stage in response to treatment with the compounds of the disclosure are tumor cells or rapidly dividing cells. In some cases, the compounds of the disclosure affect a comparable or a greater degree of G0/G1 arrest as compared to doxorubicin.
[0235] The disclosure further provides methods of modulating MAPK pathway activity by contacting a member of the MAPK pathway with an effective amount of a compound of the disclosure. Modulation can be inhibiting or activating kinase activity. In some embodiments, the disclosure provides methods of inhibiting kinase activity by contacting the kinase with an effective amount of a compound of the disclosure in solution. In some embodiments, the disclosure provides methods of inhibiting the kinase activity by contacting a cell, tissue, organ that expresses the kinase of interest. In some embodiments, the disclosure provides methods of inhibiting kinase activity in subject including but not limited to rodents and mammal (e.g., human) by administering into the subject an effective amount of a compound of the disclosure. In some embodiments, the percentage of inhibiting exceeds 25%, 30%, 40%, 50%, 60%, 70%, 80%, or 90%. [0236] In some embodiments, the kinase is selected from the group consisting of ERK, including different isoforms such as ERK1 and ERK2; Ras; Raf; INK; ErbB-l (EGFR); Her2 (ErbB-2); Her 3 (ErbB-3); Her 4 (ErbB-4); MAP2K1 (MEK1); MAP2K2 (MEK2); MAP2K3 (MEK3); MAP2K4 (MEK4); MAP2K5 (MEK5); MAP2K6 (MEK6); MAP2K7 (MEK7); CDK1; CDK2; CDK3;
CDK4; CDK5; CDK6; CDK7; CDK8; CDK9; CDK11.
[0237] The disclosure further provides methods of modulating MAPK pathway activity by contacting a member of the MAPK pathway with an amount of a compound of the disclosure sufficient to modulate MAPK pathway activity. Modulate can be inhibiting or activating MAPK pathway activity. In some embodiments, the disclosure provides methods of inhibiting a member of the MAPK pathway by contacting the member with an amount of a compound of the disclosure sufficient to inhibit the activity of the member. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a solution by contacting said solution with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said solution. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a cell by contacting said cell with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said cell. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a tissue by contacting said tissue with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said tissue. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in an animal by contacting said animal with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said animal. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a mammal by contacting said mammal with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said mammal. In some embodiments, the disclosure provides methods of inhibiting MAPK pathway activity in a human by contacting said human with an amount of a compound of the disclosure sufficient to inhibit the activity of the MAPK pathway in said human. The present disclosure provides methods of treating a disease mediated by MAPK pathway activity in a subject in need of such treatment.
[0238] In some embodiments, a method of the disclosure provides an effective dose of a MAPK pathway inhibitor. An effective dose refers to an amount sufficient to effect the intended application, including but not limited to, disease treatment, as defined herein. Also contemplated in the subject methods is the use of a sub-therapeutic amount of a MAPK pathway inhibitor for treating an intended disease condition.
[0239] The amount of the MAPK pathway inhibitor administered may vary depending upon the intended application (in vitro or in vivo), or the subject and disease condition being treated, e.g., the weight and age of the subject, the severity of the disease condition, the manner of administration and the like, which can readily be determined by one of ordinary skill in the art.
[0240] A subject being treated with a MAPK pathway inhibitor may be monitored to determine the effectiveness of treatment, and the treatment regimen may be adjusted based on the subject’s physiological response to treatment. For example, if inhibition of a biological effect of MAPK pathway inhibition is above or below a threshold, the dosing amount or frequency may be decreased or increased, respectively. The methods can further comprise continuing the therapy if the therapy is determined to be efficacious. The methods can comprise maintaining, tapering, reducing, or stopping the administered amount of a compound in the therapy if the therapy is determined to be efficacious. The methods can comprise increasing the administered amount of a compound in the therapy if it is determined not to be efficacious. Alternatively, the methods can comprise stopping therapy if it is determined not to be efficacious. In some embodiments, treatment with a MAPK pathway inhibitor is discontinued if inhibition of the biological effect is above or below a threshold, such as in a lack of response or an adverse reaction. The biological effect may be a change in any of a variety of physiological indicators.
[0241] The effectiveness of treatment (or, alternatively,“therapeutic efficacy” or“clinically beneficial response”) is measured based on an effect of treating a cancer. In general, therapeutic efficacy of the methods of the disclosure, with regard to the treatment of a cancer (whether benign or malignant), may be measured by the degree to which the methods and compositions promote inhibition of tumor cell proliferation, the inhibition of tumor vascularization, the eradication of tumor cells, the reduction in the rate of growth of a tumor, and/or a reduction in the size of at least one tumor. Several parameters to be considered in the determination of therapeutic efficacy are discussed herein. The proper combination of parameters for a particular situation can be established by the clinician. The progress of the inventive method in treating cancer (e.g., reducing tumor size or eradicating cancerous cells) can be ascertained using any suitable method, such as those methods currently used in the clinic to track tumor size and cancer progress. The primary efficacy parameter used to evaluate the treatment of cancer by the disclosed methods and compositions preferably is a reduction in the size of a tumor. Tumor size can be figured using any suitable technique, such as measurement of dimensions, or estimation of tumor volume using available computer software, such as FreeFlight software developed at Wake Forest University that enables accurate estimation of tumor volume. Tumor size can be determined by tumor visualization using, for example, CT, ultrasound, SPECT, spiral CT, MRI, photographs, and the like. In embodiments where a tumor is surgically resected after completion of the therapeutic period, the presence of tumor tissue and tumor size can be determined by gross analysis of the tissue to be resected, and/or by pathological analysis of the resected tissue.
[0242] Several parameters as described herein may be considered by the clinician in determining if a subject having cancer exhibits a clinically beneficial response. In some desirable embodiments, the growth of a tumor is stabilized (i.e., one or more tumors do not increase more than 1%, 5%, 10%, 15%, or 20% in size, and/or do not metastasize) as a result of the subject methods and compositions. In some embodiments, a tumor is stabilized for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more weeks. In some embodiments, a tumor is stabilized for at least about 1, 2, 3, 4,
5, 6, 7, 8, 9, 10, 11, 12, or more months. In some embodiments, a tumor is stabilized for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more years. Preferably, the inventive method reduces the size of a tumor at least about 5% (e.g., at least about 10%, 15%, 20%, or 25%). More preferably, tumor size is reduced at least about 30% (e.g., at least about 35%, 40%, 45%, 50%, 55%, 60%, or 65%). Even more preferably, tumor size is reduced at least about 70% (e.g., at least about 75%, 80%,
85%, 90%, or 95%). Most preferably, the tumor is completely eliminated, or reduced below a level of detection. In some embodiments, a subject remains tumor free (e.g. in remission) for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more weeks following treatment. In some embodiments, a subject remains tumor free for at least about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or more months following treatment. In some embodiments, a subject remains tumor free for at least about 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, or more years after treatment.
[0243] In some embodiments, the efficacy of the disclosed methods in reducing tumor size can be determined by measuring the percentage of necrotic (i.e., dead) tissue of a surgically resected tumor following completion of the therapeutic period. In some further embodiments, a treatment is therapeutically effective if the necrosis percentage of the resected tissue is greater than about 20% (e.g., at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%), more preferably about 90% or greater (e.g., about 90%, 95%, or 100%). Most preferably, the necrosis percentage of the resected tissue is 100%, that is, no tumor tissue is present or detectable.
[0244] The efficacy of the disclosed methods can be determined by a number of secondary parameters. Examples of secondary parameters include, but are not limited to, detection of new tumors, detection of tumor antigens or markers, biopsy, surgical downstaging (i.e., conversion of the surgical stage of a tumor from unresectable to resectable), PET scans, survival, disease progression-free survival, time to disease progression, quality of life assessments such as the Clinical Benefit Response Assessment, and the like, all of which can point to the overall progression (or regression) of cancer in a human. Biopsy is particularly useful in detecting the eradication of cancerous cells within a tissue. Radioimmunodetection (RAID) is used to locate and stage tumors using serum levels of markers (antigens) produced by and/or associated with tumors (“tumor markers” or“tumor-associated antigens”), and can be useful as a pre-treatment diagnostic predicate, a post-treatment diagnostic indicator of recurrence, and a post-treatment indicator of therapeutic efficacy. Examples of tumor markers or tumor-associated antigens that can be evaluated as indicators of therapeutic efficacy include, but are not limited to, carcinembryonic antigen (CEA), prostate-specific antigen (PSA), erythropoietin (EPO), CA-125, CA19-9, ganglioside molecules (e.g., GM2, GD2, and GD3), MART-l, heat shock proteins (e.g., gp96), sialyl Tn (STn), tyrosinase, MUC-l, HER-2/neu, c-erb-B2, KSA, PSMA, p53, RAS, EGF-R, VEGF, MAGE, and gplOO. Other tumor-associated antigens are known in the art. RAID technology in combination with endoscopic detection systems also can efficiently distinguish small tumors from surrounding tissue (see, for example, ET.S. Pat. No. 4,932,412).
[0245] In additional desirable embodiments, the treatment of cancer in a human patient in accordance with the disclosed methods is evidenced by one or more of the following results: (a) the complete disappearance of a tumor (i.e., a complete response), (b) about a 25% to about a 50% reduction in the size of a tumor for at least four weeks after completion of the therapeutic period as compared to the size of the tumor before treatment, (c) at least about a 50% reduction in the size of a tumor for at least four weeks after completion of the therapeutic period as compared to the size of the tumor before the therapeutic period, and (d) at least a 2% decrease (e.g., about a 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% decrease) in a specific tumor-associated antigen level at about 4-12 weeks after completion of the therapeutic period as compared to the tumor-associated antigen level before the therapeutic period. While at least a 2% decrease in a tumor-associated antigen level is preferred, any decrease in the tumor-associated antigen level is evidence of treatment of a cancer in a patient by the inventive method.
[0246] With respect to quality of life assessments, such as the Clinical Benefit Response Criteria, the therapeutic benefit of the treatment in accordance with the disclosure can be evidenced in terms of pain intensity, analgesic consumption, and/or the Karnofsky Performance Scale score. The treatment of cancer in a human patient alternatively, or in addition, is evidenced by (a) at least a 50% decrease (e.g., at least a 60%, 70%, 80%, 90%, or 100% decrease) in pain intensity reported by a patient, such as for any consecutive four week period in the 12 weeks after completion of treatment, as compared to the pain intensity reported by the patient before treatment, (b) at least a 50% decrease (e.g., at least a 60%, 70%, 80%, 90%, or 100% decrease) in analgesic consumption reported by a patient, such as for any consecutive four week period in the 12 weeks after completion of treatment as compared to the analgesic consumption reported by the patient before treatment, and/or (c) at least a 20 point increase (e.g., at least a 30 point, 50 point, 70 point, or 90 point increase) in the Karnofsky Performance Scale score reported by a patient, such as for any consecutive four week period in the 12 weeks after completion of the therapeutic period as compared to the Karnofsky Performance Scale score reported by the patient before the therapeutic period.
[0247] In some embodiments, tumor size is reduced as a result of the inventive method preferably without significant adverse events in the subject. Adverse events are categorized or“graded” by the Cancer Therapy Evaluation Program (CTEP) of the National Cancer Institute (NCI), with Grade 0 representing minimal adverse side effects and Grade 4 representing the most severe adverse events. Desirably, the disclosed methods are associated with minimal adverse events, e.g. Grade 0, Grade 1, or Grade 2 adverse events, as graded by the CTEP/NCI. However, as discussed herein, reduction of tumor size, although preferred, is not required in that the actual size of tumor may not shrink despite the eradication of tumor cells. Eradication of cancerous cells is sufficient to realize a therapeutic effect. Likewise, any reduction in tumor size is sufficient to realize a therapeutic effect.
[0248] Detection, monitoring and rating of various cancers in a human are further described in Cancer Facts and Figures 2001, American Cancer Society, New York, N.Y., and International Patent Application WO 01/24684. Accordingly, a clinician can use standard tests to determine the efficacy of the various embodiments of the inventive method in treating cancer. However, in addition to tumor size and spread, the clinician also may consider quality of life and survival of the patient in evaluating efficacy of treatment.
[0249] In some embodiments, the disclosure provides a pharmaceutical composition comprising an amount of a MAPK pathway inhibitor formulated for administration to a subject in need thereof. In some embodiments, the pharmaceutical composition comprises between about 0.0001-500 g, 0.001-250 g, 0.01-100 g, 0.1-50 g, or 1 - 10 g of the MAPK pathway inhibitor. In some
embodiments, the pharmaceutical composition comprises about or more than about 0.0001 g, 0.001 g, O.Olg, 0.1, 0.5 g, 1 g, 2 g, 3 g, 4 g, 5 g, 6 g, 7 g, 8 g, 9 g, 10 g, 15 g, 20 g, 25 g, 50g, 100 g, 200 g, 250 g, 300 g, 350 g, 400 g, 450 g, 500 g, or more of the MAPK pathway inhibitor. In some embodiments, the pharmaceutical composition comprises between 0.001 - 2 g of an MAPK pathway inhibitor in a single dose. In some embodiments, the therapeutic amount can be an amount between about 0.001-0.1 g of an MAPK pathway inhibitor. In some embodiments, the therapeutic amount can be an amount between about 0.01-30 g of a MAPK pathway inhibitor. In some embodiments, the therapeutic amount can be an amount between about 0.45 mg/kg/week to 230.4 mg/kg/week of a MAPK pathway inhibitor. In some embodiments, the MAPK pathway inhibitor is given as an intravenous infusion once per week. Preferably, the MAPK pathway inhibitor is given as an intravenous infusion once per week at a dose of about 0.45 mg/kg/week to about 1000 mg/kg/week, such as about 10 mg/kg/week to about 50 mg/kg/week. In some embodiments, the MAPK pathway inhibitor is given as an intravenous infusion once per week at a dose of about 5 mg/kg/week, about 10 mg/kg/week, about 20 mg/kg/week, about 30 mg/kg/week, about 40 mg/kg/week, or about 50 mg/kg/week, such as about 20 mg/kg/week.
[0250] In some embodiments, the MAPK pathway inhibitor can be administered as part of a therapeutic regimen that comprises administering one or more second agents (e.g. 1, 2, 3, 4, 5, or more second agents), either simultaneously or sequentially with the MAPK pathway inhibitor. When administered sequentially, the MAPK pathway inhibitor may be administered before or after the one or more second agents. When administered simultaneously, the MAPK pathway inhibitor and the one or more second agents may be administered by the same route (e.g. injections to the same location; tablets taken orally at the same time), by a different route (e.g. a tablet taken orally while receiving an intravenous infusion), or as part of the same combination (e.g. a solution comprising a MAPK pathway inhibitor and one or more second agents). In some embodiments, the MAPK pathway inhibitor is administered in combination with anti-EGFR therapy.
[0251] In certain aspects, a method described herein further comprises administering a second therapeutic agent to a subject. The present disclosure provides methods for combination therapies in which an agent known to modulate other pathways, or other components of the same pathway, or even overlapping sets of target enzymes, are used in combination with a compound of the present disclosure, or a pharmaceutically acceptable salt, ester, prodrug, solvate, hydrate or derivative thereof. In some embodiments, such therapy includes, but is not limited to, the combination of one or more compounds of the disclosure with chemotherapeutic agents, therapeutic antibodies, and/or radiation treatment to provide a synergistic or additive therapeutic effect.
[0252] In certain aspects, the present disclosure provides a method of treating adenocarcinoma in a subject in need thereof, comprising administering to said subject a MAPK pathway inhibitor and a second therapeutic agent. Preferably, the second therapeutic agent is a CDK4/6 inhibitor, such as palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF- 06873600, voruciclib, FLX-925, ON-123300, BPI-16350, VS2-370, FCN-437c, BPI-1178, IIIM- 290, TQB-3616, BEBT-209, SRX-3177, GZ-38-1, IIIM-985, birociclib, CGP-82996, PD-171851, R-547, PAN-1215, NSC-625987, staurosporine, G1T28-1, G1T30-1, gossypin, AT-7519, P-276- 00, AG-024322, PD-0183812 or INOC-005. In some embodiments, the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR- 6390, PF-06873600, voruciclib and FLX-925. In some embodiments, the second therapeutic agent is selected from palbociclib, ribociclib and abemaciclib. Exemplary CDK4/6 inhibitors and their syntheses have been described in WO 2003/062236 (palbociclib), WO 2010/020675 (ribociclib), and US 2010/0160340 (abemaciclib), the disclosures of which are incorporated by reference herein.
[0253] In some embodiments, the present disclosure provides methods and pharmaceutical compositions for inhibiting abnormal cell growth in a subject, comprising an amount of a compound of the disclosure, or a pharmaceutically acceptable salt, ester, prodrug, solvate, hydrate or derivative thereof, in combination with an amount of a second therapeutic agent, such as an anti cancer agent. Many chemotherapeutics are presently known in the art and can be used in
combination with the compounds of the disclosure. In some embodiments, the chemotherapeutic is selected from the group consisting of mitotic inhibitors, alkylating agents, anti-metabolites, intercalating antibiotics, growth factor inhibitors, cell cycle inhibitors, enzymes, topoisomerase inhibitors, biological response modifiers, anti-hormones, angiogenesis inhibitors, and anti androgens.
[0254] Non-limiting examples are chemotherapeutic agents, cytotoxic agents, and non-peptide small molecules such as Gleevec® (Imatinib Mesylate), Velcade® (bortezomib), Casodex
(bicalutamide), Iressa® (gefitinib), and Adriamycin as well as a host of chemotherapeutic agents. Non-limiting examples of chemotherapeutic agents include alkylating agents such as thiotepa and cyclosphosphamide (CYTOXAN™); alkyl sulfonates such as busulfan, improsulfan and
piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethylenethiophosphaoramide and trimethylolomelamine; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, ranimustine; antibiotics such as aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, calicheamicin, carabicin, carminomycin, carzinophilin, Casodex™, chromomycins, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, doxorubicin, epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5- fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin,
trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine;
pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine,
dideoxyuridine, doxifluridine, enocitabine, floxuridine, androgens such as calusterone,
dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfomithine; elliptinium acetate; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidamine; mitoguazone; mitoxantrone; mopidamol; nitracrine;
pentostatin; phenamet; pirarubicin; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK.R™; razoxane; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2,,2''-trichlorotriethylamine; urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside (“Ara-C”); cyclophosphamide; thiotepa; taxanes, e.g. paclitaxel (TAXOL™, Bristol- Myers Squibb Oncology, Princeton, N.J.) and docetaxel (TAXOTERE™, Rhone-Poulenc Rorer, Antony, France); retinoic acid; esperamicins; capecitabine; and pharmaceutically acceptable salts, acids or derivatives of any of the above. Also included as suitable chemotherapeutic cell conditioners are anti-hormonal agents that act to regulate or inhibit hormone action on tumors such as anti-estrogens including for example tamoxifen, (Nolvadex™), raloxifene, aromatase inhibiting 4(5)-imidazoles, 4-hydroxytamoxifen, trioxifene, keoxifene, LY 117018, onapristone, and toremifene (Fareston); and anti -androgens such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; platinum; etoposide (VP- 16); ifosfamide; mitomycin C; mitoxantrone; vincristine; vinorelbine; navelbine; novantrone; teniposide;
daunomycin; aminopterin; xeloda; ibandronate; camptothecin-l 1 (CPT-l l); topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO). Where desired, the compounds or pharmaceutical composition of the present disclosure can be used in combination with commonly prescribed anti -cancer drugs such as Herceptin®, Avastin®, Erbitux®, Rituxan®, Taxol®, Arimidex®, Taxotere®, ABVD, AVICINE, Abagovomab, Acridine carboxamide, Adecatumumab, l7-N-Allylamino-l7-demethoxygeldanamycin, Alpharadin, Alvocidib, 3-Aminopyridine-2- carboxaldehyde thiosemicarbazone, Amonafide, Anthracenedione, Anti-CD22 immunotoxins, Antineoplastic, Antitumori genic herbs, Apaziquone, Atiprimod, Azathioprine, Belotecan,
Bendamustine, BIBW 2992, Biricodar, Brostallicin, Bryostatin, Buthionine sulfoximine, CBV (chemotherapy), Calyculin, cell-cycle nonspecific antineoplastic agents, cetuximab, cisplatin,
Diehl oroacetic acid, Discodermolide, Elsamitrucin, Enocitabine, Epothilone, Eribulin, erlotinib, Everolimus, Exatecan, Exisulind, Ferruginol, Forodesine, Fosfestrol, gemcitabine, ICE
chemotherapy regimen, IT-101, Imexon, Imiquimod, Indolocarbazole, Irofulven, Laniquidar, Larotaxel, Lenalidomide, Lucanthone, Lurtotecan, Mafosfamide, Mitozolomide, Nafoxidine, Nedaplatin, Olaparib, Ortataxel, PAC-l, palbociclib, Pawpaw, Pixantrone, Proteasome inhibitor, Rebeccamycin, Resiquimod, Rubitecan, SN-38, Salinosporamide A, Sapacitabine, Stanford V, Swainsonine, Talaporfm, Tariquidar, Tegafur-uracil, Temodar, Tesetaxel, Triplatin tetranitrate, Tris(2-chloroethyl)amine, Troxacitabine, Uramustine, Vadimezan, Vinflunine, ZD6126, and Zosuquidar.
[0255] In certain embodiments, the present disclosure provides a method of treating an
adenocarcinoma in a subject in need thereof, comprising administering to said subject a MAPK pathway inhibitor and a second therapeutic agent. In practicing any of the subject methods, the second therapeutic agent may be selected from gemcitabine, cisplatin, an EGFR inhibitor and a CDK inhibitor. In some embodiments, the second therapeutic agent is selected from gemcitabine, cisplatin, cetuximab, erlotinib and palbociclib. In some embodiments, the second therapeutic agent is selected from gemcitabine, cisplatin, cetuximab. In some embodiments, the second therapeutic agent is an EGFR inhibitor, such as cetuximab or erlotinib. In some embodiments, the second therapeutic agent is a CDK inhibitor, preferably a CDK4/6 inhibitor, such as palbociclib. In some embodiments, the second therapeutic agent is selected from gemcitabine, cisplatin, cetuximab, wherein the adenocarcinoma is an adenocarcinoma of the lung. In some embodiments, the second therapeutic agent is cetuximab, wherein the adenocarcinoma is an adenocarcinoma of the lung. In some embodiments, the second therapeutic agent is adenocarcinoma is an adenocarcinoma of the lung.
[0256] In practicing any of the subject methods, the second therapeutic agent may be selected from osimertinib, olmutinib, icotinib hydrochloride, afatinib, necitumumab, lapatinib, pertuzumab, vandetanib, BV-NSCLC-001, nimotuzumab, panitumumab, erlotinib, gefitinib, cetuximab, brigatinib, naquotinib mesylate, anti-EGFR antibody , depatuxizumab mafodotin, tesevatinib , dacomitinib, neratinib, anti-EGFR CART cell therapy, PF-06747775, AP-32788, AZD-3759, nazartinib, entinostat + erlotinib , allitinib tosylate, tarloxotinib bromide, S-222611, pyrroltinib maleate , poziotinib, second generation cetuximab , RXDX-105, futuximab, seribantumab, varlitinib, icotinib hydrochloride , SYN-004 (Synermore Biologies), anti-EGFR CAR-T therapy, durvalumab + osimertinib, LY-3164530, tremelimumab + gefitinib, durvalumab + gefitinib , GC- 1118, JNJ-61186372, Pirotinib, SKLB-1028, PB-357, BGB-283, SCT-200, QLNC-120, TAS-121, Hemay-020, Hemay-022, theliatinib, NRC-2694-A, epitinib succinate, MM-151, simotinib hydrochloride, depatuxizumab, AFM-24, HTI-1511, EGFR/Axl dual inhibitors, RC-68, EGFRvIII CAR T cell therapy, ETBP-1215, LL-067, Probody T cell-engaging bispecific targeting CD3 and EGFR, YH-25448, SKLB-287, AFM-22 (Affimed), AK-568, panitumumab biosimilar, RJS-013, RJS-012, recombinant EGF/CRM-197 vaccine, recombinant fully human anti-EGFR mAb, nimotuzumab biosimilar, EGFR-targeted siRNA therapeutics, anti-EGFR recombinant Fc engineered IgA2m antibody, sirotinib malate, anti-EGFR targeting mAbs, anti-EGFR/anti-CD3 bispecific antibody, alpha-c-Met/EGFR-0286 bispecific antibody drug conjugate, small molecule therapeutic, HLX-07, JHL-1189, KN-023, panitumumab biosimilar, anti-EGFR monoclonal antibody, FV-225, EGFR T790M inhibitors (Beta Pharma), cetuximab biosimilar, MP-0274, EGFR T790M inhibitor (Genentech/Argenta), STI-A020X, KL-ON113, neratinib, l8F-afatinib, PMIP, DBPR-l 12, SKI-O-751, PTZ-09, bi-specific anti-Her3 Zybodies (Zyngenia), SHR-1258, G5-7, bispecific centyrins (Janssen), AG-321, kahalalide F, E-10C, JRP-980, JRP-890, MED-1007, LA22-MMC, NT-004, NT-113, Sym-0l3, anti-Her-2/anti-Ang2 mAb ( Zyngenia), MT-062, trastuzumab biosimilar, AFM-21, NT-219, ANG-MAB (AngioChem), ISU- 101, and VRCTC-310. In some embodiments, the second therapeutic agent is selected from osimertinib, olmutinib, icotinib hydrochloride, afatinib, necitumumab, lapatinib, pertuzumab, vandetanib, BV-NSCLC- 001, nimotuzumab, panitumumab, erlotinib, gefitinib, cetuximab, brigatinib, naquotinib mesylate, anti-EGFR antibody , depatuxizumab mafodotin, tesevatinib , dacomitinib, neratinib, anti-EGFR CART cell therapy, PF-06747775, AP-32788, AZD-3759, nazartinib, entinostat + erlotinib , allitinib tosylate, tarloxotinib bromide, S-222611, pyrroltinib maleate , poziotinib, second generation cetuximab , RXDX-105, futuximab, seribantumab, and varlitinib. In some embodiments, the second therapeutic agent is selected from palbociclib, abemaciclib, ribociclib, G1T-28, AT- 7519, alvocidib, FLX-925, G1T-38, GZ-38-1, ON-123300 and voruciclib. In some embodiments, the second therapeutic agent is selected from palbociclib, abemaciclib, ribociclib, G1T-28, AT- 7519 and alvocidib. In some embodiments, the second therapeutic agent is selected from
palbociclib, osimertinib, olmutinib, icotinib hydrochloride, afatinib, necitumumab, lapatinib, pertuzumab, vandetanib, BV-NSCLC-001, nimotuzumab, panitumumab, erlotinib, gefitinib and cetuximab.
[0257] This disclosure further relates to a method for using the compounds or pharmaceutical compositions provided herein in combination with radiation therapy for inhibiting abnormal cell growth or treating the hyperproliferative disorder in the mammal. Techniques for administering radiation therapy are known in the art, and these techniques can be used in the combination therapy described herein. The administration of the compound of the disclosure in this combination therapy can be determined as described herein.
[0258] Radiation therapy can be administered through one of several methods, or a combination of methods, including without limitation external-beam therapy, internal radiation therapy, implant radiation, stereotactic radiosurgery, systemic radiation therapy, radiotherapy and permanent or temporary interstitial brachytherapy. The term“brachytherapy,” as used herein, refers to radiation therapy delivered by a spatially confined radioactive material inserted into the body at or near a tumor or other proliferative tissue disease site. The term is intended without limitation to include exposure to radioactive isotopes (e.g. At-2l l, 1-131, 1-125, Y-90, Re-l86, Re-l88, Sm-l53, Bί-212, P-32, and radioactive isotopes of Lu). Suitable radiation sources for use as a cell conditioner of the present disclosure include both solids and liquids. By way of non-limiting example, the radiation source can be a radionuclide, such as 1-125, 1-131, Yb-l69, Ir-l92 as a solid source, 1-125 as a solid source, or other radionuclides that emit photons, beta particles, gamma radiation, or other therapeutic rays. The radioactive material can also be a fluid made from any solution of
radionuclide(s), e.g., a solution of 1-125 or 1-131, or a radioactive fluid can be produced using a slurry of a suitable fluid containing small particles of solid radionuclides, such as Au-l98, Y-90. Moreover, the radionuclide(s) can be embodied in a gel or radioactive micro spheres.
[0259] Without being limited by any theory, the compounds of the present disclosure can render abnormal cells more sensitive to treatment with radiation for purposes of killing and/or inhibiting the growth of such cells. Accordingly, this disclosure further relates to a method for sensitizing abnormal cells in a mammal to treatment with radiation which comprises administering to the mammal an amount of a compound of the present disclosure or pharmaceutically acceptable salt, ester, prodrug, solvate, hydrate or derivative thereof, which amount is effective is sensitizing abnormal cells to treatment with radiation. The amount of the compound, salt, or solvate in this method can be determined according to the means for ascertaining effective amounts of such compounds described herein.
[0260] The compounds or pharmaceutical compositions of the disclosure can be used in
combination with an amount of one or more substances selected from anti -angiogenesis agents, signal transduction inhibitors, antiproliferative agents, glycolysis inhibitors, or autophagy inhibitors.
[0261] Anti-angiogenesis agents, such as MMP-2 (matrix-metalloproteinase 2) inhibitors, MMP-9 (matrix-metalloprotienase 9) inhibitors, and COX-l 1 (cyclooxygenase 11) inhibitors, can be used in conjunction with a compound of the disclosure and pharmaceutical compositions described herein. Anti -angiogenesis agents include, for example, rapamycin, temsirolimus (CCI-779), everolimus (RAD001), sorafenib, sunitinib, and bevacizumab. Examples of useful COX- II inhibitors include CELEBREX™ (alecoxib), valdecoxib, and rofecoxib. Examples of useful matrix metalloproteinase inhibitors are described in WO 96/33172 (published Oct. 24, 1996), WO
96/27583 (published Mar. 7, 1996), European Patent Application No. 97304971.1 (filed Jul. 8, 1997), European Patent Application No. 99308617.2 (filed Oct. 29, 1999), WO 98/07697
(published Feb. 26, 1998), WO 98/03516 (published Jan. 29, 1998), WO 98/34918 (published Aug. 13, 1998), WO 98/34915 (published Aug. 13, 1998), WO 98/33768 (published Aug. 6, 1998), WO 98/30566 (published Jul. 16, 1998), European Patent Publication 606,046 (published Jul. 13, 1994), European Patent Publication 931, 788 (published Jul. 28, 1999), WO 90/05719 (published May 31, 1990), WO 99/52910 (published Oct. 21, 1999), WO 99/52889 (published Oct. 21, 1999), WO 99/29667 (published Jun. 17, 1999), PCT International Application No. PCT/IB98/01113 (filed Jul. 21, 1998), European Patent Application No. 99302232.1 (filed Mar. 25, 1999), Great Britain Patent Application No. 9912961.1 (filed Jun. 3, 1999), U.S. Provisional Application No. 60/148,464 (filed Aug. 12, 1999), U.S. Pat. No. 5,863,949 (issued Jan. 26, 1999), U.S. Pat. No. 5,861,510 (issued Jan. 19, 1999), and European Patent Publication 780,386 (published Jun. 25, 1997), all of which are incorporated herein in their entireties by reference. Preferred MMP-2 and MMP-9 inhibitors are those that have little or no activity inhibiting MMP-l. More preferred, are those that selectively inhibit MMP-2 and/or AMP-9 relative to the other matrix-metalloproteinases (i. e., MAP-l, MMP- 3, MMP-4, MMP-5, MMP-6, MMP-7, MMP-8, MMP-10, MMP-l 1, MMP-12, and MMP-13).
Some specific examples of MMP inhibitors useful in the disclosure are AG-3340, RO 32-3555, and RS 13-0830.
[0262] Autophagy inhibitors include, but are not limited to chloroquine, 3-methyladenine, hydroxychloroquine (Plaquenil™), bafilomycin Al, 5-amino-4-imidazole carboxamide riboside (AICAR), okadaic acid, autophagy-suppressive algal toxins which inhibit protein phosphatases of type 2A or type 1, analogues of cAMP, and drugs which elevate cAMP levels such as adenosine, LY204002, N6-mercaptopurine riboside, and vinblastine. In addition, antisense or siRNA that inhibits expression of proteins including but not limited to ATG5 (which are implicated in autophagy), may also be used.
[0263] Administration of the compounds of the present disclosure can be effected by any method that enables delivery of the compounds to the site of action. An effective amount of a compound of the disclosure may be administered in either single or multiple doses by any of the accepted modes of administration of agents having similar utilities, including rectal, buccal, intranasal and transdermal routes, by intra-arterial injection, intravenously, intraperitoneally, parenterally, intramuscularly, subcutaneously, orally, topically, as an inhalant, or via an impregnated or coated device such as a stent, for example, or an artery-inserted cylindrical polymer. Preferably, the MAPK pathway inhibitor is administered intravenously or orally.
[0264] The amount of the compound administered will be dependent on the mammal being treated, the severity of the disorder or condition, the rate of administration, the disposition of the compound and the discretion of the prescribing physician. However, an effective dosage is in the range of about 0.001 to about 100 mg per kg body weight per day, preferably about 1 to about 35 mg/kg/day, in single or divided doses. For a 70 kg human, this would amount to about 0.05 to 7 g/day, preferably about 0.05 to about 2.5 g/day. In some instances, dosage levels below the lower limit of the aforesaid range may be more than adequate, while in other cases still larger doses may be employed without causing any harmful side effect, e.g. by dividing such larger doses into several small doses for administration throughout the day.
[0265] When used in combination with a second therapeutic agent, the MAPK pathway inhibitor can be administered at a dosage that is the same as the effective amount for that agent when administered as a monotherapy. In some embodiments, the MAPK pathway inhibitor is
administered in a sub-therapeutic amount in combination with a second therapeutic agent, such as a CDK inhibitor. A sub-therapeutic amount of an agent is an amount less than the effective amount of the agent. For example, the MAPK pathway inhibitor, when administered in combination with a second therapeutic agent, can be administered in an amount less than 90% of the effective amount, such as less than 80%, less than 70%, less than 60%, less than 50%, less than 40%, less than 30%, less than 20%, or less than 10% of the effective amount. In some embodiments, a sub -therapeutic amount of the second therapeutic agent is administered in combination with a MAPK pathway inhibitor. In some embodiments, sub-therapeutic amounts of both a MAPK pathway inhibitor and a second therapeutic agent are administered. A MAPK pathway inhibitor described herein, such as a compound provided in Table 3, is expected to produce a synergistic effect when used in
combination with a second therapeutic agent, such as a CDK inhibitor. In some embodiments, the synergistic effect is more pronounced when a sub-therapeutic amount of the MAPK pathway inhibitor is administered. The individual components of the combination, though one or more is present in a sub-therapeutic amount, synergistically yield an efficacious effect and/or reduced a side effect in an intended application.
[0266] In some embodiments, a compound of the disclosure is administered in a single dose.
Typically, such administration will be by injection, e.g., intravenous injection, in order to introduce the agent quickly. However, other routes may be used as appropriate. A single dose of a compound of the disclosure may also be used for treatment of an acute condition.
[0267] In some embodiments, a compound of the disclosure is administered in multiple doses. Dosing may be about once, twice, three times, four times, five times, six times, or more than six times per day. Dosing may be about once a month, once every two weeks, once a week, or once every other day. In another embodiment a compound of the disclosure and another agent are administered together about once per day to about 6 times per day. In another embodiment the administration of a compound of the disclosure and an agent continues for less than about 7 days.
In yet another embodiment the administration continues for more than about 6, 10, 14, 28 days, two months, six months, or one year. In some cases, continuous dosing is achieved and maintained as long as necessary.
[0268] Administration of the agents of the disclosure may continue as long as necessary. In some embodiments, an agent of the disclosure is administered for more than 1, 2, 3, 4, 5, 6, 7, 14, or 28 days. In some embodiments, an agent of the disclosure is administered for less than 28, 14, 7, 6, 5, 4, 3, 2, or 1 day. In some embodiments, an agent of the disclosure is administered chronically on an ongoing basis, e.g., for the treatment of chronic effects.
[0269] When a compound of the disclosure is administered in a composition that comprises one or more agents, and the agent has a shorter half-life than the compound of the disclosure, unit dose forms of the agent and the compound of the disclosure may be adjusted accordingly.
[0270] The compounds described herein can be used in combination with other agents disclosed herein or other suitable agents, depending on the condition being treated. Hence, in some embodiments, the one or more compounds of the disclosure will be co-administered with other agents as described above. In some embodiments, the other agent is an anti -cancer agent. When used in combination therapy, the compounds described herein may be administered with the second agent simultaneously, or separately. The administration in combination can include simultaneous administration of the two agents in the same dosage form, simultaneous administration in separate dosage forms, or separate administration. That is, a compound described herein and any of the agents described above can be formulated together in the same dosage form and administered simultaneously. Alternatively, a compound of the disclosure and any of the agents described above can be simultaneously administered, wherein both the agents are present in separate formulations.
In another alternative, a compound of the present disclosure can be administered just followed by and any of the agents described above, or vice versa. In the separate administration protocol, a compound of the disclosure and any of the agents described above may be administered a few minutes apart, or a few hours apart, or a few days apart.
[0271] The following examples are given for the purpose of illustrating various embodiments of the disclosure and are not meant to limit the present disclosure in any fashion. The present examples, along with the methods and compositions described herein, are presently representative of preferred embodiments, are exemplary, and are not intended as limitations on the scope of the disclosure. Changes therein and other uses which are encompassed within the spirit of the disclosure as defined by the scope of the claims will occur to those skilled in the art.
EXAMPLES
[0272] Example 1: Efficacy studies in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma. Tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 200 mm3. Animals were treated with vehicle or Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3) at the doses indicated in Fig. 1. Tumor volumes were measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. A total of 61 animals bearing NSCLC patient-derived xenograft (PDX) tumors were treated in the same manner with either vehicle or Compound A. A waterfall plot illustrating percent tumor growth each for KRAS- mutant NSCLC- ADC models treated with the MAPK pathway inhibitor is presented in Fig. 4. Four examples of models that responded to treatment with the MAPK pathway inhibitor are shown in Fig. 1
[0273] Example 2: Analysis of gene expression in KRAS-mutant NSCLC adenocarcinomas.
Several gene signatures were evaluated across the panel of adenocarcinoma models tested in
Example 1. Results of the analyses are presented in Fig. 6, which shows that only overexpression of CCND1 was predictive of response to treatment with the MAPK pathway inhibitor (both for tumor growth inhibition (TGI) > 100% and > 80%).
[0274] Fig. 2 presents a receiver operator characteristic (ROC) analysis of the models that display tumor growth inhibition of > 100% following treatment with Compound A, using fragments per kilobase million (FKPM) of CCND1 as the criterion. When a statistically significant cutoff of 150 FKPM is applied, 8 out of 24 samples were predicted to be sensitive to treatment with a MAPK pathway inhibitor.
[0275] Fig. 3 presents the same ROC analysis, but for models that display tumor growth inhibition of > 80% following treatment with Compound A. With the 150 FKPM cutoff applied, 13 out of 24 samples were predicted to be sensitive to treatment with a MAPK pathway inhibitor.
[0276] Fig. 5 illustrates percent tumor growth for each model treated with Compound A, with the models stratified into two sets based on a CCND1 150 FKPM cutoff. As illustrated in the left panel, 21 out of 31 models predicted to be sensitive to treatment with a MAPK pathway inhibitor displayed at least 80% tumor growth inhibition following treatment with a MAPK pathway inhibitor (i.e., a disease control rate of 68%). In contrast, only 4 out of 30 models predicted to be resistant to treatment with a MAPK pathway inhibitor displayed at least 80% tumor growth inhibition following treatment with Compound A (i.e., a disease control rate of 13%). As shown in Fig. 4, the unselected population displayed a disease control rate of only 40%. Accordingly, the selection of subjects having a KRAS-mutant adenocarcinoma that overexpresses CCND1 for treatment with a MAPK pathway inhibitor represents a promising approach for more effectively treating this subpopulation.
[0277] Fig. 7 summarizes the IHC scores (% CCND1 positive) of a series of KRAS-mutant NSCLC-ADC samples and illustrates that there exists a dynamic range in the expression of CCND1 in KRAS-mutant NSCLC adenocarcinoma clinical biopsy specimens to use this criterion for patient selection.
[0278] Example 3: Efficacy studies in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in Example 1 is followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm3. Animals are treated with vehicle, cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, MK-8353, or
Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3). Tumor volumes are measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. Models that overexpress CCND1, such as those models having 150 FKPM CCND1, are expected to display sensitivity to treatment with each MAPK pathway inhibitor.
[0279] Example 4: Efficacy studies in cell-based models of CCNDl-high KRAS-mutant NSCLC adenocarcinoma. Human CCNDl-high, KRAS-mutant NSCLC adenocarcinoma cell lines are grown to confluency, washed with Tumor Cell Media (DMEM + 10% FBS or IMDM + 20% FBS), and plated in 90 pL Tumor Cell Media at 5,000-10,000 cells/well. Either cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, MK-8353, Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3), or vehicle is added to each well. Plates are incubated for 72 hours at 37 °C and 5% C02. A volume of 100 pL of CellTiter-Glo® reagent is added to each well and plates are mixed for 2 minutes on an orbital shaker. The plates are allowed to stand at room temperature for 20 minutes before measuring the luminescent signal of each well. IC50 values of each compound are calculated for each cell line. Each of the tested MAPK pathway inhibitors is expected to potently inhibit proliferation of the CCNDl-high KRAS-mutant NSCLC adenocarcinoma cell lines.
[0280] Example 5: Efficacy studies of combination treatments in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in Example 1 is followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm3. Animals are treated with vehicle, Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3), or Compound A in combination with a CDK4/6 inhibitor, such as palbociclib. Additional arms of the experiment test reduced dosage levels of Compound A (e.g., 50% of the maximum tolerated dose). Tumor volumes are measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. The combination of Compound A and palbociclib is expected to produce a synergistic effect in treating the KRAS-mutant NSCLC adenocarcinoma models.
[0281] Example 6: Efficacy studies of combination treatments in patient-derived xenograft models of CCNDl-high KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in
Example 1 is followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm3. Animals are treated with vehicle; or cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, MK-8353, alone or in combination with a CDK4/6 inhibitor, such as palbociclib or ademaciclib. Tumor volumes are measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. The combination of a MAPK pathway inhibitor with a CDK4/6 inhibitor is expected to produce a synergistic effect in treating the CCNDl-high KRAS-mutant NSCLC adenocarcinoma models.
[0282] Example 7: Efficacy studies of combination treatments in cell-based models of CCNDl- high KRAS-mutant NSCLC adenocarcinoma. Human CCNDl-high, KRAS-mutant NSCLC adenocarcinoma cell lines are grown to confluency, washed with Tumor Cell Media (DMEM +
10% FBS or IMDM + 20% FBS), and plated in 90 pL Tumor Cell Media at 5,000-10,000 cells/well. Either cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH- 772984, MK-8353, alone or in combination with a CDK4/6 inhibitor, such as palbociclib or ademaciclib, or vehicle is added to each well. Plates are incubated for 72 hours at 37 °C and 5% C02. A volume of 100 pL of CellTiter-Glo® reagent is added to each well and plates are mixed for 2 minutes on an orbital shaker. The plates are allowed to stand at room temperature for 20 minutes before measuring the luminescent signal of each well. IC50 values of each compound are calculated for each cell line. The combination of a MAPK pathway inhibitor and a CDK4/6 inhibitor is expected to produce a synergistic effect in treating the CCNDl-high KRAS-mutant NSCLC adenocarcinoma cell-based models.
[0283] Example 8: Efficacy studies in patient-derived xenograft models of KRAS-mutant NSCLC adenocarcinoma having differential expression of CDKN2A. The general procedure outlined in Example 1 is followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues are inoculated subcutaneously into BALB/C nude mice. The mice are stratified into groups when the average tumor size reaches about 200 mm3. Animals are treated with vehicle or Compound A (a MAPK pathway inhibitor of Formula I- A and provided in Table 3), alone or in combination with palbociclib. Tumor volumes are measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively.
CDKN2A expression is expected to be a predictor of sensitivity to treatment with a MAPK pathway inhibitor.
[0284] Example 9: Inhibition Assays ofERK. The inhibition of ERK activity by the compounds disclosed herein was determined using the Z’-LYTE kinase assay kit (Life Technologies) with a Ser/Thr 3 peptide substrate (Life Technologies) according to manufacturer’s instructions. The assay was run with an ERK2 enzyme (Life Technologies) concentration of 0.47 ng/pL at 100 mM ATP (approximately the ATP Km for ERK2). The IC50 values for the compounds were determined with 3-fold serial dilutions in duplicate. The compounds were first diluted in 1 :3 dilutions in 100% DMSO at 100X the desired concentration, and then further diluted (1 :25) in 20 mM HEPES buffer (Invitrogen) to make 4X solutions prior to adding to the enzyme solution. The final DMSO concentration in the assay was 1%. Final reaction volume was 20 pL/well in 384-well plates.
Kinase reactions were conducted for 1 hour followed by the assay development reaction (1 hour) in a 384 well plate format (20 pL/well). One or more compounds disclosed herein exhibited an IC50 less than 10 nM when tested in this assay. Results for select compounds are presented in Table 3.
Table 3: In vitro Erk2 IC50 data for select compounds (+++ represents 50 nM to 250 nM, and ++++ represents less than 50 nM).
Figure imgf000116_0001
Figure imgf000117_0001
Figure imgf000118_0001
Figure imgf000119_0001
Figure imgf000120_0001
Figure imgf000121_0001
[0285] Example 10: Tumor cell line proliferation assay. The ability of one or more compounds of the disclosure to inhibit tumor cell line proliferation was determined according to standard procedures known in the art. For instance, an in vitro cellular proliferation assay was performed to measure the metabolic activity of live cells. A375 cells (ATCC) were grown to near 80% confluence, trypsinized and seeded at 1500 cells/well at volume of 100 pL per well in full growth medium (10% FBS in DMEM or l0%FBS in RPMI) in a 96 well plate. The cells were incubated at 37 °C under 5% C02 for two hours to allow for attachment to the plates. Compounds were first diluted in 1 :3 dilutions in 100% DMSO at 250X the desired concentration, and then further diluted (1 :50) in 10% DMEM growth medium. The diluted compounds were added to the cell plate (25 pL for a 5X dilution) and the cells incubated with compounds (0.4%DMSO in l0%FBS DMEM) for 96 hours at 37 °C under 5% C02. The cell control wells were added with vehicle only (0.4%
DMSO in l0%FBS DMEM or in l0%FBS RPMI). Each concentration of the compounds was tested in duplicate. After 96 hours of compound treatment, CellTiter Glo reagent (Promega) was added at a 1 :5 dilution to each well of the cell plate and the cell plate was placed at room temperature for 30 minutes. The luminescence of the wells was determined using a Tecan plate reader. Each compound presented in Table 3 exhibited an IC50 of 250 nM or less in A375 cells (ATCC) when tested in this assay.
[0286] Example 11: Efficacy studies of combination treatments in patient-derived xenograft models of CCNDl-high KRAS-mutant NSCLC adenocarcinoma. The general procedure outlined in Example 1 was followed. Briefly, tumor fragments (2-4 mm in diameter) from stock mice inoculated with primary human NSCLC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 200 mm3. Animals were treated with vehicle, Compound A (a MAPK pathway inhibitor of Formula I-A and provided in Table 3), palbociclib, or Compound A in combination with palbociclib. Compound A was administered at a dose of 125 mg/kg QW. Palbociclib was administered at a dose of 70 mg/kg QD on a 5 on, 2 off schedule. Tumor volumes were measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. A total of three NSCLC patient-derived xenograft models were treated in the same manner with either vehicle, Compound A, palbociclib, or Compound A in combination with palbociclib as presented in Fig. 8. The body weights of the treated animals over the study duration are depicted in Fig. 9. The MAPK pathway inhibitor (e.g., Compound A of Formula I-A), when administered in a sub-therapeutic dose in combination with a CDK4/6 inhibitor, produced a pronounced synergistic effect in treating all three models.
[0287] Example 12: Comparative efficacy studies of single agents in patient-derived xenograft models of 1 lql3-amplified esophageal squamous-cell carcinoma. Tumor fragments (2-3 mm in diameter) from stock mice inoculated with primary human ESCC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 250-300 mm3. Animals were treated with vehicle, Compound A (a MAPK inhibitor of Formula I-A and provided in Table 3), GDC-0994, or trametinib. Compounds A was administered at a dose of 175 mg/kg QW or at a dose of 350 mg/kg QW. GDC-0994 was administered at a dose of 100 mg/kg QD. Trametinib was administered at a dose of 1 mg/kg QD. Tumor volumes were measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. The tumor volumes of the treated animals over the study duration are depicted in Fig. 10. Compounds A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.
[0288] Example 13: Comparative efficacy studies of single agents in patient-derived xenograft models of 1 lql3-amplified head and neck squamous-cell carcinoma. The general procedure outlined in Example 12 was followed. Briefly, tumor fragments (2-3 mm in diameter) from stock mice inoculated with primary human HNSCC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 250- 300 mm3. Animals were treated with vehicle, Compound A (a MAPK inhibitor of Formula I-A and provided in Table 3), GDC-0994, or trametinib. Compound A was administered at a dose of 175 mg/kg QW or at a dose of 350 mg/kg QW. GDC-0994 was administered at a dose of 100 mg/kg QD. Trametinib was administered at a dose of 1 mg/kg QD. Tumor volumes were measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. The tumor volumes of the treated animals over the study duration are depicted in Fig. 11. Compound A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.
[0289] Example 14: Comparative efficacy studies of single agents in patient-derived xenograft models of 1 lql3-amplified lung squamous-cell carcinoma. The general procedure outlined in
Example 12 was followed. Briefly, tumor fragments (2-3 mm in diameter) from stock mice inoculated with primary human LSCC tissues were inoculated subcutaneously into BALB/C nude mice. The mice were stratified into groups when the average tumor size reached about 250-300 mm3. Animals were treated with vehicle, Compound A (a MAPK inhibitor of Formula I-A and provided in Table 3), GDC-0994, or trametinib. Compound A was administered at a dose of 175 mg/kg QW or at a dose of 350 mg/kg QW. GDC-0994 was administered at a dose of 100 mg/kg QD. Trametinib was administered at a dose of 1 mg/kg QD. Tumor volumes were measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. The tumor volumes of the treated animals over the study duration are depicted in Fig. 12. Compound A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.
[0290] Example 15: Comparative efficacy studies of single agents in patient-derived xenograft models of KRAS-mutated CCND 1 -over expressed non-small cell lung cancer . Two comparative efficacy studies were carried out using KRAS-mutated CCND 1 -overexpressed non-small cell lung cancer cell lines, one utilizing LU11786 cells and the other utilizing LU11692 cells. Both studies were carried out according to the same procedure, which is as follows. Cryo-preserved tumor cells were thawed and inoculated subcutaneously into shaved NOD-SCID mice. The mice were stratified into groups when the average tumor size reached about 250-350 mm3. Animals were treated with vehicle, Compound A (a MAPK inhibitor of Formula I-A and provided in Table 3), GDC-0994, BVD-523, or trametinib. Compound A was administered at a dose of 300 mg/kg QW. GDC-0994 was administered at a dose of 100 mg/kg QD. BVD-523 (ulixertinib) was administered at a dose of 50 mg/kg BID. Trametinib was administered at a dose of 1 mg/kg QD. Tumor volumes were measured twice weekly in two dimensions using a caliper, with volume expressed in mm3 (mean +/- SEM) using the formula V = 0.5(a x b)2, where a and b are the long and short diameters of the tumor, respectively. For the study using LU11786 tumor cells, the tumor volumes of the treated animals over the study duration are depicted in Fig. 13. For the study using LU11692 tumor cells, the tumor volumes of the treated animals over the study duration are depicted in Fig. 14.
Compound A displayed pronounced single agent efficacy in reducing tumor volume compared to vehicle.
[0291] While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

CLAIMS What is claimed is:
1. A method of treating a cancer in a subject in need thereof, wherein said cancer exhibits a KRAS mutation and wherein said cancer overexpresses CCND1, comprising administering to the subject an effective dose of a mitogen-activated protein kinase (MAPK) pathway inhibitor.
2. The method of claim 1, comprising:
(a) assessing the cancer for overexpression of CCND 1 ;
(b) evaluating the cancer for the presence of a KRAS mutation; and
(c) administering the MAPK pathway inhibitor to the subject if both the CCND1 overexpression and the KRAS mutation are determined to be present.
3. A method of treating a subject having cancer, wherein said cancer exhibits a KRAS mutation, comprising:
(a) assessing the cancer for overexpression of CCND1; and
(b) administering an effective dose of a MAPK pathway inhibitor to the subject if the overexpression of CCND1 is found to be present.
4. The method of any one of claims 1 to 3, wherein the overexpression is assessed by:
(a) detecting a level of mRNA;
(b) detecting a level of cDNA produced from reverse transcription of mRNA;
(c) detecting a level of polypeptide;
(d) detecting a level of cell-free DNA; or
(e) a nucleic acid amplification assay, a hybridization assay, sequencing, or a combination thereof.
5. The method of any one of claims 1 to 4, wherein the overexpression is characterized by an expression level of CCND1 in the cancer that is higher than a reference expression level of CCND1.
6. The method of any one of claims 1 to 5, wherein the KRAS mutation is determined by sequencing, polymerase chain reaction (PCR), DNA microarray, mass spectrometry (MS), single nucleotide polymorphism (SNP) assay, denaturing high-performance liquid chromatography
(DHPLC), or restriction fragment length polymorphism (RFLP) assay.
7. The method of claim 6, wherein the KRAS mutation is determined by sequencing or PCR.
8. A method of assessing a likelihood of a subject having cancer exhibiting a clinically beneficial response to treatment with a MAPK pathway inhibitor, the method comprising:
(a) assessing an expression profile of CCND1 in a biological sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell; (b) evaluating the biological sample for the presence of a KRAS mutation; and
(b) calculating, using a computer system, a weighted probability of MAPK pathway inhibitor responsiveness based on the expression profile and KRAS mutation status.
9. The method of claim 8, further comprising designating the subject as having a high probability of exhibiting a clinically beneficial response to treatment with the MAPK pathway inhibitor if the weighted probability corresponds to at least 1.5 times a baseline probability, wherein the baseline probability represents a likelihood that the subject will exhibit a clinically beneficial response to treatment with the MAPK pathway inhibitor before obtaining the weighted probability of (c).
10. The method of claim 9, further comprising transmitting information concerning the likelihood to a receiver.
11. The method of any one of claims 8 to 10, further comprising providing a recommendation based on the weighted probability.
12. The method of claim 11, wherein the recommendation comprising treating the subject with a MAPK pathway inhibitor.
13. The method of any one of claims 8 to 12, further comprising selecting a treatment based on the weighted probability.
14. The method of any one of claims 8 to 13, further comprising administering the MAPK pathway inhibitor to the subject if the subject is designated as having a high probability of exhibiting a clinically beneficial response.
15. A method of categorizing a cancer status of a subject, comprising:
(a) obtaining a biological sample from the subject, the sample comprising genomic, transcriptomic and/or proteomic material from a cancer cell of the subject;
(b) assessing (1) a total expression level of CCND1 in the sample, and (2) the presence or absence of a KRAS mutation in the sample;
(c) generating an expression profile based on a comparison between the total expression level and a reference level, wherein the reference level is derivable from a reference sample from a different subject having a known cancer status;
(d) categorizing the cancer status of the subject of (a) based on the expression profile and the presence or absence of the KRAS mutation.
16. The method of claim 15, wherein the cancer is categorized as likely sensitive to treatment with a MAPK pathway inhibitor if the total expression level is greater than the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
17. The method of claim 15 or 16, wherein the known cancer status of the different subject is categorized as resistant to a MAPK pathway inhibitor or sensitive to a MAPK pathway inhibitor.
18. The method of any one of claims 15 to 17, wherein the categorizing step includes calculating, using a computer system, a likelihood of response of the subject to treatment with a MAPK pathway inhibitor based on the expression profile, wherein the likelihood is adjusted upward for each fold increase in the total expression level relative to the reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
19. The method of claim 18, further comprising preparing a report comprising a prediction of the likelihood of response of the subject to treatment with the MAPK pathway inhibitor.
20. The method of any one of claims 5 or 15 to 19, wherein the reference level represents an average total expression level of CCND1 in a plurality of cancer samples.
21. The method of any one of claims 8 to 19, wherein the biological sample is a tissue biopsy.
22. The method of any one of claims 8 to 19, wherein the biological sample is a tumor biopsy.
23. The method of any one of claims 2 to 22, wherein the assessing is performed using a nucleic acid or protein from the subject.
24. The method of any one of claims 2 to 23, wherein the evaluating is performed using a nucleic acid or protein from the subject.
25. The method of any one of the preceding claims, wherein the cancer is an adenocarcinoma.
26. The method of claim 25, wherein the cancer is a lung adenocarcinoma.
27. The method of claim 25, wherein the cancer is non-small cell lung cancer.
28. A method of downregulating MAPK signaling output in a plurality of lung adenocarcinoma cells with a MAPK pathway inhibitor, wherein at least one cell of the plurality exhibits a KRAS mutation, the method comprising:
(a) assessing, in a biological sample comprising nucleic acid from the subject, a total expression level of CCND1; and
(b) administering an effective dose of the MAPK pathway inhibitor to the plurality of cells if the total expression level is greater than a reference level, wherein the reference level is indicative of low sensitivity to the MAPK pathway inhibitor.
29. The method of any one of claims 1 to 28, wherein the MAPK pathway inhibitor is a MEK inhibitor.
30. The method of claim 29, wherein the MEK inhibitor is selected from cobimetinib, trametinib, binimetinib, selumetinib, HL-085, antroquinonol, E-6201, refametinib, pimasertib hydrochloride, CKI-27, WX-554, CIP- 137401, SHR-7390, sorafenib, SRX-2626, PD-0325901, ATR-002, ATR-004, ATR-005, ATR-006, CS-3006, FCN-159, EDV-2209, GDC-0623, TAK-733, E-6201, RG-7167, AZD-8330, PD-184352, GSK-2091976A, AS-703988, BI-847325, JTP-70902, CZ-775, RO-5068760, RDEA-436, MEK-300, AD-GL0001, SL-327, ATR-001, PD-98059, RO- 4987655, RO-4927350, and AS-703026.
31. The method of claim 30, wherein the MEK inhibitor is selected from cobimetinib, trametinib, binimetinib, and selumetinib.
32. The method of claim 31, wherein the MEK inhibitor is trametinib.
33. The method of claim 29, wherein the MEK inhibitor is selected from:
Figure imgf000128_0001
34. The method of any one of claims 1 to 28, wherein the MAPK pathway inhibitor is a pan- RAF inhibitor.
35. The method of claim 34, wherein the pan-RAF inhibitor is selected from LY3009120, LXH254, CCT3833 and AZ628.
36. The method of claim 35, wherein the pan-RAF inhibitor is selected from LY3009120 and LXH254.
37. The method of any one of claims 1 to 28, wherein the MAPK pathway inhibitor is an ERK inhibitor.
38. The method of claim 37, wherein the ERK inhibitor is selected from ulixertinib, RG7842, GDC-0994, CC-90003, ASN-007, AMO-Ol, KO-947, AEZS-134, AEZS-131, AEZS-140, AEZS- 136, AEZS-132, D-87503, KIN-2118, RB-l, RB-3, SCH-772984, MK-8353, SCH-900353, FR- 180204, IDN-5491, hyperforin trimethoxybenzoate, ERK1-2067, ERK1-23211, ERK1-624, LY3214996, AZ6197, ASTX029, and LTT462.
39. The method of claim 38, wherein the ERK inhibitor is selected from ulixertinib, GDC-0994, SCH-772984, and MK-8353.
40. The method of claim 37, wherein the ERK inhibitor is selected from the group consisting of:
Figure imgf000129_0001
41. The method of claim 37, wherein the ERK inhibitor is a compound of Formula I:
Figure imgf000129_0002
(Formula I), wherein:
Figure imgf000129_0003
X2 is NRi or CRiRi’ and X3 is null, CR3R3’ or C=0; or X2-X3 is RIC=CR3 or R3C=N or N=CR3 or NR12-CR11=CR3;
X4 is N or CR4; X5 is N or C; X6 is N or C; X7 is O, N, NR72 or CR73; X8 is O, N, NR82 or CR8I; X9 is O, N, NR22 or CR2I; Xl0 is O, N, NR¾ or CR91;
Ri is-Ci-ioalkyl, -C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Ci-iohetaryl, - C3-iocycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3-i0aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci.i0alkyl-C3- iocydoalkyl, -Ci-ioalkyl-Ci-ioheterocydyl, -C2-ioalkenyl-C3-i0aryl, -C2-i0alkenyl-Ci.iohetaryl, -C2- loalkenyl-C3-locydoalkyl, -C2-ioalkenyl-Ci.ioheterocyclyl, -C2-ioalkynyl-C3-ioaryl, -C2-ioalkynyl- C i-iohetaryl, -C2-ioalkynyl-C3-iocydoalkyl, -C2-ioalkynyl-Ci.ioheterocyclyl, -Ci-ioheteroalkyl-C3- l0aryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci.ioheteroalkyl-C3-iocydoalkyl, -Ci-ioheteroalkyl-Ci.
!oheterocydyl, -Ci-ioalkoxy-C3-ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci-ioalkoxy-C3-iocydoalkyl, -Ci.
1 oal koxy-C 1.1 oheterocyd yl , -C3-ioaryl-Ci-ioalkyl, -C3-ioaryl-C2-ioalkenyl, -C3-ioaryl-C2-ioalkynyl, - C3-ioaryl-C3-iohetaryl, -C3-ioaryl-C3-iocydoalkyl, -C3-ioaryl-Ci-ioheterocydyl, -Ci-iohetaryl-Ci. l0alkyl, -Ci.iohetaryl-C2-i0alkenyl, -Ci.iohetaryl-C2-i0alkynyl, -C3-iohetaryl-C3-i0aryl, -Ci-iohetaryl- C3-l0cydoalkyl, -Ci-iohetaryl-Ci-ioheterocydyl, -C3-i0cydoalkyl-Ci.ioalkyl, -C3-i0cydoalkyl-C2- !oalkenyl, -C3-iocydoalkyl-C2-ioalkynyl, -C3-iocydoalkyl-C3-ioaryl, -C3-iocycloalkyl-Ci.iohetaryl, - C3-iocydoalkyl-Ci-ioheterocydyl, -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci-ioheterocydyl-C2-ioalkenyl, - Ci.ioheterocydyl-C2-ioalkynyl, -Ci.ioheterocydyl-C3-i0aryl, -Ci-ioheterocydyl-Ci-iohetaryl, or -Ci. l0heterocydyl-C3-locydoalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
Ri’ is hydrogen, -Ci-ioalkyl, -C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3.l0aryl, -Ci. iohetaryl, -C3-i0cycloalkyl, -Ci-ioheterocyclyl, -Ci.ioalkyl-C3-i0aryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci. loalkyl-C3-locydoalkyl, -Ci-ioalkyl-Ci-ioheterocydyl, -C2-ioalkenyl-C3-i0aryl, -C2-i0alkenyl-Ci. !ohetaryl, -C2-ioalkenyl-C3-iocycloalkyl, -C2-ioalkenyl-Ci.ioheterocyclyl, -C2-ioalkynyl-C3-ioaryl, - C2-ioalkynyl-Ci-iohetaryl, -C2-ioalkynyl-C3-iocycloalkyl, -C2-ioalkynyl-Ci.ioheterocyclyl, -Ci.
loheteroalkyl-C3-loaryl, -Ci-ioheteroalkyl-Ci-iohetaryl, -Ci.ioheteroalkyl-C3-iocycloalkyl, -Ci.
ioheteroalkyl-Ci-ioheterocydyl, -Ci.ioalkoxy-C3-i0aryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci.i0alkoxy-C3- !ocycloalkyl, -Ci-ioalkoxy-Ci-ioheterocyclyl, -C3-ioaryl-Ci-ioalkyl, -C3-ioaryl-C2-ioalkenyl, -C3- loaryl-C2-loalkynyl, -C3-ioaryl-C3-iohetaryl, -C3-ioaryl-C3-iocycloalkyl, -C3-ioaryl-Ci.ioheterocyclyl, -Ci.iohetaryl-Ci.ioalkyl, -Ci.iohetaryl-C2-ioalkenyl, -Ci.iohetaryl-C2-ioalkynyl, -C3-i0hetaryl-C3- l0aryl, -Ci.iohetaryl-C3-iocycloalkyl, -Ci-iohetaryl-Ci-ioheterocydyl, -C3-iocycloalkyl-Ci.ioalkyl, - C3-iocydoalkyl-C2-ioalkenyl, -C3-iocycloalkyl-C2-ioalkynyl, -C3-iocycloalkyl-C3-ioaryl, -C3- 1 ocyd oal kyl -C 1. mhetaryl , -C3-iocydoalkyl-Ci.ioheterocyclyl, -Ci-ioheterocyclyl-Ci-ioalkyl, -Ci. loheterocyclyl-C2-loalkenyl, -Ci.ioheterocyclyl-C2-ioalkynyl, -Ci.ioheterocyclyl-C3-ioaryl, -Ci. ioheterocydyl-Ci-iohetaryl, or -Cl-loheterocyclyl-C3-locydoalkyl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
R21 is hydrogen, halogen, -OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -
Figure imgf000131_0001
-L-Ci-ioheteroalkyl, -L-C3-ioaryl, -L-Ci-iohetaryl, -L-C3-iocydoalkyl, -L-Ci-ioheterocyclyl, -L- C i -loalkyl-Cs-ioaryl, -L-Ci-ioalkyl-Ci-iohetaryl, -L-C i . i oal kyl -C3- 1 ocyd oal kyl , -L-Ci-ioalkyl-Ci. ioheterocydyl, -L-C2-ioalkenyl-C3-ioaryl, -L-C2-ioalkenyl-Ci.iohetaryl, -L-C2-i0alkenyl-C3- iocydoalkyl, -L-C2-i0alkenyl-Ci.ioheterocydyl, -L-C2-ioalkynyl-C3-i0aryl, -L-C2-i0alkynyl-Ci. !ohetaryl, -L-C2-ioalkynyl-C3-iocydoalkyl, -L-C2-ioalkynyl-Ci-ioheterocydyl, -L-Ci-ioheteroalkyl- C3-loaryl, -L -Ci-ioheteroalkyl-Ci-iohetaryl, -L -Ci-ioheteroalkyl-C3-iocydoalkyl, -L -Ci.
ioheteroalkyl-Ci-ioheterocydyl, -L-Ci.ioalkoxy-C3-ioaryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci. loalkoxy-C3-locydoalkyl, -L-Ci-ioalkoxy-Ci-ioheterocydyl, -L-C3-ioaryl-Ci-ioalkyl, -L-C3-ioaryl- C2-loalkenyl, -L-C3-ioaryl-C2-ioalkynyl, -L-C3-ioaryl-Ci-iohetaryl, -L-C3-ioaryl-C3-iocydoalkyl, - L-C3-ioaryl-Ci-ioheterocydyl, -L-Ci-iohetaryl-Ci-ioalkyl, -L-Ci-iohetaryl-C2-ioalkenyl, -L-Ci. lohetaryl-C2-l0alkynyl, -L-Ci.iohetaryl-C3-ioaryl, -L-Ci.iohetaryl-C3-iocydoalkyl, -L-Ci-iohetaryl- Cl-loheterocydyl,-L-C3-locydoalkyl-Cl-loalkyl, -L-C3-iocydoalkyl-C2-i0alkenyl, -L-C3- locydoalkyl-C2-loalkynyl, -L-C3-iocydoalkyl-C3-ioaryl, -L-C3-iocydoalkyl-Ci.iohetaryl, -L-C3- i ocyd oal kyl -C i . loheterocyd yl , -L-Ci-ioheterocydyl-Ci-ioalkyl, -L-Ci-ioheterocydyl-C2-ioalkenyl, -L-Ci.ioheterocydyl-C2-i0alkynyl, -L-Ci.ioheterocyclyl-C3-ioaryl, -L-Ci-ioheterocydyl-Ci.
iohetaryl, or -L-Ci.ioheterocydyl-C3-i0cydoalkyl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
R22 is hydrogen, -OH, -CF3, -C(0)R31, -C02R31, -C(=0)NR31, -S(O)0-2R31, -C(=S)OR31, - C(=O)SR31,-L-Ci.i0alkyl, -L-C2-i0alkenyl, -L-C2-i0alkynyl, -L-Ci-ioheteroalkyl, -L-C3-i0aryl, - L-Ci.iohetaryl, -L-C3-i0cycloalkyl, -L-Ci-ioheterocydyl, -L-Ci.ioalkyl-C3-i0aryl, -L-Ci.i0alkyl- C i-iohetaryl, -L-Ci-ioalkyl-C3-iocycloalkyl, -L-Ci-ioalkyl-Ci-ioheterocyclyl, -L-C2-ioalkenyl-C3- !oaryl, -L-C2-ioalkenyl-Ci-iohetaryl, -L-C2-ioalkenyl-C3-iocycloalkyl, -L-C2-ioalkenyl-Ci.
ioheterocyclyl, -L-C2-ioalkynyl-C3-i0aryl, -L-C2-ioalkynyl-Ci.iohetaryl, -L-C2-i0alkynyl-C3- iocycloalkyl, -L-C2-ioalkynyl-Ci.ioheterocyclyl, -L-Ci.ioheteroalkyl-C3-ioaryl, -L -Ci.
i oheteroal kyl -C M ohetaryl , -L -Ci-ioheteroalkyl-C3-iocycloalkyl, -L -Ci-ioheteroalkyl-Ci.
!oheterocyclyl, -L-Ci-ioalkoxy-C3-ioaryl, -L-Ci-ioalkoxy-Ci-iohetaryl, -L-Ci-ioalkoxy-C3- iocydoalkyl, -L-Ci-ioalkoxy-Ci-ioheterocydyl, -L-C3-i0aryl-Ci.ioalkyl, -L-C3-ioaryl-C2-i0alkenyl, -L-C3-ioaryl-C2-i0alkynyl, -L-C3-ioaryl-Ci.iohetaryl, -L-C3-ioaryl-C3-i0cycloalkyl, -L-C3-i0aryl-Ci. ioheterocydyl, -L-Ci-iohetaryl-Ci-ioalkyl, -L-Ci.iohetaryl-C2-ioalkenyl, -L-Ci.iohetaryl-C2- l0alkynyl, -L-Ci-iohetaryl-C3-ioaryl,-L-Ci-iohetaryl-C3-iocydoalkyl, -L-Ci-iohetaryl-Ci. loheterocyclyl, -L-Cs-iocycloalkyl-Ci-ioalkyl, -L-C3-iocycloalkyl-C2-ioalkenyl, -L-C3-iocycloalkyl- C2-ioalkynyl, -L-C3.iocydoalkyl-C3.ioaryl, -L-C3.iocydoalkyl-Ci.iohetaryl, -L-C3.iocydoalkyl-Ci. ioheterocydyl, -L-Ci-ioheterocydyl-Ci-ioalkyl, -L-Ci.ioheterocydyl-C2.ioalkenyl, -L-Ci.
loheterocydyl-C2-loalkynyl, -L-Ci.ioheterocydyl-C3.ioaryl, -L-Ci-ioheterocydyl-Ci-iohetaryl, or - L-Ci-ioheterocydyl-C3-iocydoalkyl, each of which is unsubstituted or substituted by one or more independent RI2 substituents;
L is a bond, -0-, -N(R31)-, -S(O)0-2- -C(=0)-, -C(=0)0- -0C(=0)-, -C(=0)N(R31)-, -
Figure imgf000132_0001
C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci. !oheterocyclyl, -Ci.ioalkyl-C3.ioaryl, -Ci-ioalkyl-Ci-iohetaryl, -Ci-ioalkyl-C3-iocycloalkyl, -Ci. i oal kyl -CM oheterocyd yl , -C2.ioalkenyl-C3.ioaryl, -C2-ioalkenyl-Ci-iohetaryl, -C2-ioalkenyl-C3- iocycloalkyl, -C2.ioalkenyl-Ci.ioheterocyclyl, -C2-ioalkynyl-C3.ioaryl, -C2-ioalkynyl-Ci.iohetaryl, - C2.ioalkynyl-C3.iocycloalkyl, -C2.ioalkynyl-Ci.ioheterocyclyl, -Ci.ioheteroalkyl-C3.ioaryl, -Ci. i oheteroal kyl -C M ohetaryl , -Ci-ioheteroalkyl-C3-iocycloalkyl, -Ci-ioheteroalkyl-Ci-ioheterocyclyl, - Ci-ioalkoxy-C3-ioaryl, -Ci-ioalkoxy-Ci-iohetaryl, -Ci.ioalkoxy-C3.iocycloalkyl, -Ci-ioalkoxy-Ci. ioheterocyclyl, -C3.ioaryl-Ci.ioalkyl, -C3.ioaryl-C2-ioalkenyl, -C3.ioaryl-C2-ioalkynyl, -C3.ioaryl-C3. iohetaryl, -C3.ioaryl-C3.iocycloalkyl, -C3.ioaryl-Ci.ioheterocyclyl, -Ci-iohetaryl-Ci-ioalkyl, -Ci. lohetaryl-C2-ioalkenyl, -Ci-iohetaryl-C2-ioalkynyl, -C3-iohetaryl-C3-ioaryl, -Ci-iohetaryl-C3- iocycloalkyl, -Ci-iohetaryl-Ci-ioheterocyclyl, -C3.iocycloalkyl-Ci.ioalkyl, -C3.iocycloalkyl-C2. l0alkenyl, -C3.iocycloalkyl-C2.ioalkynyl, -C3.iocycloalkyl-C3.ioaryl, -C3.iocycloalkyl-Ci.iohetaryl, - C3-iocycloalkyl-Ci-ioheterocydyl, -Ci-ioheterocydyl-Ci-ioalkyl, -Ci.ioheterocyclyl-C2.ioalkenyl, - Ci.ioheterocydyl-C2.ioalkynyl, -Ci.ioheterocydyl-C3.ioaryl, -Ci-ioheterocyclyl-Ci-iohetaryl, or -Ci. loheterocyclyl-C3-iocycloalkyl, each of which is unsubstituted or substituted by one or more independent R13 substituents; or R3’ is -OR6, -NR6R34, -S(O)0-2R6, -C(=0)R6, -C(=0)0R6, - 0C(=0)R6, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring; or R3’ is -OR6, -NR6R34, -S(O)0-2R6, -C(=0)R6, -C(=0)0R6, - 0C(=0)R6, -C(=0)N(R34)R6, or -N(R34)C(=0)R6, wherein R6 together with R34 can optionally form a heterocyclic ring;
each of R5, R71, Rxi and R91 is independently hydrogen, halogen, -C MO alkyl, -C2.10 alkenyl, -C2-10 alkynyl, -Ci-ioheteroalkyl, -C3.l0aryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -
Figure imgf000133_0001
R6 is hydrogen, -Ci-ioalkyl, -C2-ioalkenyl, -C2-ioalkynyl, -Ci-ioheteroalkyl, -C3-i0aryl, -Ci- !ohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl,— C 1.1 oal kyl -Cs- 1 oaryl , -Ci-ioalkyl-Ci-iohetaryl, -Ci- i0alkyl-C3.iocycloalkyl, -Ci-ioalkyl-Ci-ioheterocyclyl, -C2-i0alkenyl-C3.ioaryl, -C2-i0alkenyl-Ci. lohetaryl, -C2-i0alkenyl-C3.iocycloalkyl, -C2-ioalkenyl-Ci.ioheterocyclyl, -C2-i0alkynyl-C3.ioaryl, - C2-ioalkynyl-Ci.iohetaryl, -C2-i0alkynyl-C3.iocycloalkyl, -C2-ioalkynyl-Ci.ioheterocyclyl, -Ci- i0heteroalkyl-C3-i0aryl, -Ci-i0heteroalkyl-Ci-i0hetaryl, -C M oheteroal kyl -C3- iocycl oal kyl , -Ci- loheteroalkyl-Ci-ioheterocyclyl, -C M 0al koxy-Ci.1 oaryl , -Ci.i0alkoxy-Ci.i0hetaryl, -C Moalkoxy-Ci. locycloalkyl, -Ci.i0alkoxy-Ci.i0heterocyclyl, -C3.i0aryl-Ci.i0alkyl, -C3.i0aryl-C2.i0alkenyl, -C3. i0aryl-C2-i0alkynyl, -C3-ioaryl-C3-iohetaryl, -C3-ioaryl-C3-iocycloalkyl, -C3-i0aryl -Ci-ioheterocyclyl, -Ci-iohetaryl-Ci-ioalkyl, -Ci-i0hetaryl-C2-i0alkenyl, -Ci-i0hetaryl-C2-i0alkynyl, -C3-iohetaryl-C3- i0aryl, -Ci-iohetaryl-C3.iocycloalkyl, -Ci.i0hetaryl-Ci.i0heterocyclyl, -C3.iocycloalkyl-Ci.i0alkyl, - C3-iocycloalkyl-C2.i0alkenyl, -C3.i0cycloalkyl-C2.i0alkynyl, -C3.iocycloalkyl-C3.ioaryl, -C3.
iocycloalkyl-Ci-iohetaryl, -Cm ocycl oal kyl -CM oheterocycl yl , -Ci-ioheterocyclyl-Ci-i0alkyl, -Ci- i0heterocyclyl-C2-i0alkenyl, -CM0heterocyclyl-C2-i0alkynyl, -C M oheterocycl yl -C3- 1 oaryl , -Ci- loheterocyclyl-Ci-iohetaryl, or -Ci.ioheterocyclyl-C3.iocycloalkyl, each of which is unsubstituted or substituted by one or more independent R14 or R15 substituents;
each of R72, RX? and R¾ is independently hydrogen, -CMO alkyl, -C2-ioalkenyl, -C2-io alkynyl, -Ci-ioheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, -OH, - CF3, -C(0)R31, -C02R31, -C(=0)NR31, -S(0)O-2R31, -C(=S)OR31, -C(=0)SR31;
each of Rio and Ri is independently -CMO alkyl, -C2-i0alkenyl, -C2-i0 alkynyl, -Ci.
loheteroalkyl, -C3-ioaryl, -Ci-iohetaryl, -C3-iocycloalkyl, -Ci-ioheterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn, RI2 R13 and R15 is independently hydrogen, halogen, -CMO alkyl, -C2-i0alkenyl, -C2-io alkynyl, -Ci-ioheteroalkyl, -C3.i0aryl, -Ci-iohetaryl, -C3.i0cycloalkyl, -Ci-ioheterocyclyl, - OH, -CF3, -OCF3, -OR31, -NR31R32, -C(0)R31, -C02R31, -C(=0)NR31, -N02, -CN, -S(O)0-2R31, - S02NR31R32, -NR31C(=0)R32, -NR31C(=0)0R32, -NR31C(=0)NR32R33, -NR31S(0)O-2R32, - C(=S)OR31, -C(=0)SR31, -NR31C(=NR32)NR32R33, -NR31C(=NR32)OR33, -NR31C(=NR32)SR33, - 0C(=0)0R33, -0C(=0)NR31R32, -0C(=0)SR31, -SC(=0)SR31, -P(0)0R310R32, or - SC(=0)NR31NR32;
31 32 33 34
each of R , R , R and R t is independently hydrogen, halogen, -Cmo alkyl, -C2- l0alkenyl, -C2-i0 alkynyl, -Cmoheteroalkyl, -C3-ioaryl, -Cmohetaryl, -C3-iocycloalkyl, -Ci.
!oheterocyclyl, or wherein R31 together with R32 form a heterocyclic ring;
wherein ring A comprises one or more heteroatoms selected from N, O, or S; and
wherein if X7 is O or X2-X3 is RIC=CR3, ring A comprises at least two heteroatoms selected from N, O, or S; and
wherein if X2-X3 is RiC=N, at least one of X7 or X9 is not N.
42. The method of claim 41, wherein the ERK inhibitor is a compound of Formula I-A:
Figure imgf000134_0001
(Formula I- A)
or a pharmaceutically acceptable salt thereof.
43. The method of claim 41 or 42, wherein:
Ri is 3- to 6-membered heterocyclyl, -Ci-ioalkyl-(3- to 6-membered heterocyclyl), -(3- to 6- membered heterocyclyl)-Ci-ioalkyl, -(3- to 6-membered heterocyclyl)-C3-ioaryl, or -(3- to 6- membered heterocyclyl)-Ci.i0hetaryl, each of which is unsubstituted or substituted by one or more independent Rl0 or Rn substituents;
R21 is -L-C3-ioaryl or -L-Ci-iohetaryl, each of which is unsubstituted or substituted by one or more independent Ri2 substituents;
L is a bond or -N(R31)-;
R72 is hydrogen;
each of Rio is independently-C3-ioaryl, -Ci-iohetaryl, or -Cl-l0heterocyclyl, optionally substituted by one or more independent Rn substituents;
each of Rn and Ri2 is independently halogen, -Cmo alkyl, -OH, -CF3 or -OR31; and each of R31 is independently hydrogen or -Cl-l0 alkyl.
44. The method of claim 41, wherein the ERK inhibitor is selected from the group consisting of:
Figure imgf000134_0002
Figure imgf000135_0001
45. The method of any one of claims 1 to 28, wherein the MAPK pathway inhibitor is selected from cobimetinib, trametinib, binimetinib, selumetinib, ulixertinib, GDC-0994, SCH-772984, and MK-8353.
46. The method of any one of claims 1 to 7 or 14 to 45, further comprising administering a second therapeutic agent to the subject.
47. A method of treating an adenocarcinoma in a subject in need thereof, comprising administering to said subject a MAPK pathway inhibitor and a second therapeutic agent.
48. The method of claim 46 or 47, wherein the second therapeutic agent is a CDK4/6 inhibitor.
49. The method of claim 48, wherein the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF-06873600, voruciclib, FLX-925, ON-123300, BPI-16350, VS2-370, FCN-437c, BPI-1178, IIIM-290, TQB- 3616, BEBT-209, SRX-3177, GZ-38-1, IIIM-985, birociclib, CGP-82996, PD-171851, R-547, PAN-1215, NSC-625987, staurosporine, G1T28-1, G1T30-1, gossypin, AT-7519, P-276-00, AG- 024322, PD-0183812 and INOC-005.
50. The method of claim 49, wherein the second therapeutic agent is selected from palbociclib, ribociclib, abemaciclib, milciclib, alvocidib, lerociclib, trilaciclib, SHR-6390, PF-06873600, voruciclib and FLX-925.
51. The method of claim 49, wherein the second therapeutic agent is selected from palbociclib, ribociclib and abemaciclib.
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Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021229439A1 (en) * 2020-05-12 2021-11-18 Novartis Ag Therapeutic combinations comprising a craf inhibitor
WO2022221547A1 (en) * 2021-04-16 2022-10-20 Erasca, Inc. Uses of heterocyclic inhibitors of erk1/2
WO2022271939A1 (en) * 2021-06-24 2022-12-29 Erasca, Inc. Erk1/2 and cdk4/6 inhibitors combination therapy
US11925629B2 (en) 2015-06-15 2024-03-12 Asana Biosciences, Llc Heterocyclic inhibitors of ERK1 and ERK2 and their use in the treatment of cancer
US12011449B2 (en) 2016-09-19 2024-06-18 Novartis Ag Therapeutic combinations comprising a c-RAF inhibitor

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017180581A1 (en) * 2016-04-15 2017-10-19 Genentech, Inc. Diagnostic and therapeutic methods for cancer
WO2018170485A1 (en) * 2017-03-16 2018-09-20 The Board Of Trustees Of The Leland Stanford Junior University Diagnostic and therapeutic methods for kras positive cancers

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017180581A1 (en) * 2016-04-15 2017-10-19 Genentech, Inc. Diagnostic and therapeutic methods for cancer
WO2018170485A1 (en) * 2017-03-16 2018-09-20 The Board Of Trustees Of The Leland Stanford Junior University Diagnostic and therapeutic methods for kras positive cancers

Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11925629B2 (en) 2015-06-15 2024-03-12 Asana Biosciences, Llc Heterocyclic inhibitors of ERK1 and ERK2 and their use in the treatment of cancer
US12011449B2 (en) 2016-09-19 2024-06-18 Novartis Ag Therapeutic combinations comprising a c-RAF inhibitor
WO2021229439A1 (en) * 2020-05-12 2021-11-18 Novartis Ag Therapeutic combinations comprising a craf inhibitor
WO2022221547A1 (en) * 2021-04-16 2022-10-20 Erasca, Inc. Uses of heterocyclic inhibitors of erk1/2
WO2022271939A1 (en) * 2021-06-24 2022-12-29 Erasca, Inc. Erk1/2 and cdk4/6 inhibitors combination therapy

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