U.S. patent application number 17/044884 was filed with the patent office on 2021-04-08 for ret inhibitor for use in treating cancer having a ret alteration.
The applicant listed for this patent is BLUEPRINT MEDICINES CORPORATION. Invention is credited to Erica Evans Raab, Beni B. Wolf.
Application Number | 20210100795 17/044884 |
Document ID | / |
Family ID | 1000005307147 |
Filed Date | 2021-04-08 |
View All Diagrams
United States Patent
Application |
20210100795 |
Kind Code |
A1 |
Evans Raab; Erica ; et
al. |
April 8, 2021 |
RET INHIBITOR FOR USE IN TREATING CANCER HAVING A RET
ALTERATION
Abstract
Disclosed herein is the treatment of a subject afflicted with a
cancer having an activating RET alteration by administering an
effective amount of a selective RET inhibitor, e.g., Compound 1 or
pharmaceutically acceptable salts thereof, including, e.g.,
administering an amount of 300 mg to 400 mg of the selective RET
inhibitor once daily.
Inventors: |
Evans Raab; Erica;
(Cambridge, MA) ; Wolf; Beni B.; (Cambridge,
MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
BLUEPRINT MEDICINES CORPORATION |
Cambridge |
MA |
US |
|
|
Family ID: |
1000005307147 |
Appl. No.: |
17/044884 |
Filed: |
April 3, 2019 |
PCT Filed: |
April 3, 2019 |
PCT NO: |
PCT/US2019/025655 |
371 Date: |
October 2, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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62741683 |
Oct 5, 2018 |
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62657605 |
Apr 13, 2018 |
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62656297 |
Apr 11, 2018 |
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62652284 |
Apr 3, 2018 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
A61P 35/04 20180101;
A61K 31/506 20130101; A61P 35/00 20180101 |
International
Class: |
A61K 31/506 20060101
A61K031/506; A61P 35/00 20060101 A61P035/00; A61P 35/04 20060101
A61P035/04 |
Claims
1. A method of treating a subject afflicted with a cancer having an
activating rearranged during transfection (RET) alteration, the
method comprising administering to the subject a therapeutically
effective amount of 300 to 400 mg of Compound 1 or a
pharmaceutically acceptable salt thereof once daily.
2. The method of claim 1, wherein the amount administered is 300
mg.
3. The method of claim 1 or 2, wherein the amount administered is
400 mg.
4. The method of any one of claims 1-3, wherein the cancer is
chosen from papillary thyroid carcinoma (PTC), medullary thyroid
cancer (MTC), pheochromocytoma (PCC), pancreatic ductal
adenocarcinoma, multiple endocrine neoplasia (MEN2A and MEN2B),
metastatic breast cancer, testicular cancer, small cell lung
cancer, non-small cell lung cancer (NSCLC), chronic myelomonocytic
leukemia (CMML), colorectal cancer, ovarian cancer, inflammatory
myofibroblastic tumor, and cancer of the salivary gland.
5. The method of any one of claims 1-3, wherein the cancer is
chosen from esophageal cancer, skin cancer (non-melanoma),
endometrial cancer, head and neck cancer, bladder cancer, prostate
cancer, hematological cancer, leukemia, soft tissue sarcoma, renal
cell carcinoma (RCC), non-Hodgkin lymphoma, hepatobiliary cancer,
adrenocortical carcinoma, myelodysplasia (MDS), uterine sarcoma,
germ cell tumor, cervical cancer, central nervous system cancer,
bone cancer, ampullary carcinoma, gastrointestinal stromal tumor,
small bowel cancer, mesothelioma, rectal cancer, paraganglioma, and
intrahepatic bile duct cancer.
6. The method of any one of claims 1-3, wherein the cancer is
chosen from adenocarcinoma, spitzoid neoplasm, lung adenocarcinoma,
adenosquamous carcinoma, colon cancer, metastatic colon cancer,
metastatic papillary thyroid cancer, diffuse sclerosing variant of
papillary thyroid cancer, primary myelofibrosis with secondary
acute myeloid leukemia, diffuse gastric cancer, thyroid gland
carcinoma, and bronchioles lung cell carcinoma.
7. The method of any one of claims 1-3, wherein the cancer is
chosen from hepatobiliary cancer, ampullary carcinoma, small bowel
cancer, intrahepatic bile duct cancer, metastatic colon cancer,
brain cancer associated with lung cancer, brain metastasis
associated with lung cancer, and retropentoneal paraganglioma.
8. The method of any one of claims 1-3, wherein the cancer is
chosen from medullary thyroid cancer (MTC) and non-small cell lung
cancer (NSCLC).
9. The method of claim 8, wherein the cancer is chosen from
sporadic MTC, metastatic RET-altered NSCLC, tyrosine kinase
inhibitor (TKI)-refractory KIF5B-RET NSCLC, and KIF5B-RET
NSCLC.
10. The method of any one of claims 1-3, wherein the cancer is
chosen from a brain cancer associated with a lung cancer.
11. The method of claim 10, wherein the brain cancer is brain
metastasis.
12. The method of any one of claims 1-11, wherein the activating
RET alteration comprises a RET mutation or a RET gene rearrangement
(fusion).
13. The method of any one of claims 1-11, wherein the activating
RET alteration is a RET mutation.
14. The method of claim 12 or 13, wherein the RET mutation is a
point mutation.
15. The method of any one of claims 12-14, wherein the RET mutation
is a resistance mutation.
16. The method of any one of claims 12-15, wherein the RET
alteration is a RET mutation chosen from Table 1.
17. The method of any one of claims 12-16, wherein the RET mutation
is V804M, M918T, C634R, or C634W.
18. The method of any one of claims 1-4, 8, 9, and 12-16, wherein
the cancer is RET-altered medullary thyroid cancer (MTC).
19. The method of claim 18, wherein the cancer is familial MTC.
20. The method of claim 18, wherein the cancer is sporadic MTC.
21. The method of any one of claims 1-3 and 12-19, wherein the
cancer is MTC having a M918T mutation.
22. The method of any one of claims 1-3 and 12-19, wherein the
cancer is MTC having a C634R mutation.
23. The method of any one of claims 1-3 and 12-19, wherein the
cancer is MTC having a V804M mutation.
24. The method of any one of claims 1-3, 6, and 12-16, wherein the
cancer is paraganglioma.
25. The method of claim 24, wherein the cancer is retropentoneal
paraganglioma.
26. The method of any one of claims 1-3, 6, 12-16, 24, and 25,
wherein the paraganglioma has a R77H mutation.
27. The method of any one of claims 1-11, wherein the activating
RET alteration is a gene-rearrangement (fusion).
28. The method of claim 27, wherein the activating RET alteration
is a fusion with a RET fusion partner chosen from Table 2.
29. The method of claim 27 or 28, wherein the fusion is KIF5B-RET,
CCDC6-RET, KIAA1468-RET, or NCOA4-RET.
30. The method of any one of claims 1-4 and 27-29, wherein the
cancer is RET-altered NSCLC.
31. The method of claim 30, wherein the cancer is NSCLC having a
KIF5B-RET fusion.
32. The method of claim 30, wherein the cancer is NSCLC having a
CCDC6-RET fusion.
33. The method of claim 30, wherein the cancer is NSCLC having a
KIAA1468-RET fusion.
34. The method of claim 30, wherein the cancer is NSCLC having a
RET fusion identified as FISH positive.
35. The method of claim 29 or 30, wherein the RET alteration is
KIF5B-RET V804L (cabozantinib resistant).
36. The method of claim 29 or 30, wherein the RET alteration is
CCDC6-RET V804M (ponatinib resistant).
37. The method of any one of claims 1-4 and 27-29, wherein the
cancer is RET-altered PTC.
38. The method of claim 37, wherein the cancer is PTC having a
CCDC6-RET fusion.
39. The method of claim 37, wherein the cancer is PTC having a
NCOA4-RET fusion.
40. The method of any one of claims 1-3 and 27-29, wherein the
cancer is RET-altered intrahepatic bile duct carcinoma.
41. The method of claim 40, wherein the cancer is intrahepatic bile
duct carcinoma having a NCOA4-RET fusion.
42. The method of any one of claims 1-41, wherein the subject has
not received prior treatment with a multikinase RET inhibitor.
43. The method of any one of claims 1-41 wherein the subject has
received one or more prior treatments with a multikinase RET
inhibitor.
44. The method of claim 43, wherein the multikinase RET inhibitor
is chosen from lenvatinib, vandetanib, cabozantinib, and
RXDX-105.
45. The method of any one of claims 1-41, wherein the subject has
not received prior treatment with platinum.
46. The method of any one of claims 1-41, wherein the subject has
received prior treatment with platinum.
47. The method of any one of claims 1-41, wherein the subject has
received prior treatment with a selective RET inhibitor.
48. The method of any one of claims 1-47, wherein the subject has
not received prior chemotherapy.
49. The method of any one of claims 1-47, wherein the subject has
received prior chemotherapy.
50. The method of claim 49, wherein the prior chemotherapy is
chosen from carboplatin, pemetrexed, abraxane, cisplatin,
bevacizumab, and combinations thereof.
51. The method of any one of claims 1-42, wherein the subject has
not received prior immunotherapy.
52. The method of any one of claims 1-42, wherein the subject has
received prior immunotherapy.
53. The method of claim 52, wherein the prior immunotherapy is
chosen from ipilimumab, pembrolizumab, nivolumab, MPDL3280A,
MEDI4736, and combinations thereof.
54. A method of treating a subject afflicted with a brain cancer
associated with a RET-altered lung cancer, the method comprising
administering to the subject a therapeutically effective amount of
Compound 1 or a pharmaceutically acceptable salt thereof.
55. The method of claim 54, wherein the brain cancer is brain
metastasis.
56. A method of treating a subject afflicted with a cancer having
an activating RET mutation, the comprising administering to the
subject a physiologically effective amount of a RET inhibitor,
wherein administration of the RET inhibitor is associated with a
sustained down-regulation of at least one effect marker in the
subject.
57. The method of claim 56, wherein the RET inhibitor is orally
administered.
58. The method of claim 56 or 57, wherein the RET inhibitor is
Compound 1 or a pharmaceutically acceptable salt thereof.
59. The method of any one of claims 56-58, wherein the effect
marker is chosen from DUSP6 mRNA expression, SPRY4 mRNA expression,
carcinoembryonic antigen level, and calcitonin level.
60. The method of any one of claims 56-58, wherein the effect
marker is KIF5B ctDNA level or TP53 ctDNA level.
61. The method of any one of claims 56-59, wherein the amount
administered to the subject produces a greater than 95%
down-regulation of at least one effect marker.
62. The method of any one of claims 56-59, wherein the amount
administered to the subject produces a greater than 94%, greater
than 93%, greater than 92%, greater than 91%, greater than 90%,
greater than 89%, greater than 88%, greater than 87%, greater than
86% greater than 85%, greater than 80%, greater than 75%, greater
than 70%, greater than 65%, greater than 60%, greater than 55%, or
greater than 50% down-regulation in at least one effect marker.
63. The method of claim 61, wherein the amount administered to the
subject produces a greater than 89%, greater than 88%, greater than
87%, greater than 86%, greater than 85%, greater than 80%, greater
than 75%, or greater than 70% down-regulation in at least one
effect marker.
64. The method of any one of claims 56-59, wherein at least two
effect markers are down-regulated.
Description
[0001] This application claims priority to U.S. Provisional
Application No. 62/652,284, filed Apr. 3, 2018, U.S. Provisional
Application No. 62/656,297, filed Apr. 11, 2018, U.S. Provisional
Application No. 62/657,605, filed Apr. 13, 2018, and U.S.
Provisional Application No. 62/741,683, filed Oct. 5, 2018, the
contents of which are incorporated by reference herein in its
entirety.
[0002] This disclosure relates to methods for treating a subject
afflicted with a cancer having an activating RET alteration by
administering an effective amount of a selective RET inhibitor,
i.e., a compound which is specifically designed to selectively
target one or more RET or RET-altered kinases. As used herein, the
term "afflicted with a cancer" means having a cancer. Said another
way, a subject afflicted with a cancer has a cancer. More
specifically, the methods described herein relate to treating a
subject having a cancer characterized by an activating RET
alteration. In some embodiments, the selective RET inhibitor is
Compound 1 or pharmaceutically acceptable salts thereof. In some
embodiments, the selective RET inhibitor is administered once
daily. In some embodiments, the effective amount is 60 mg to 400
mg, 100 mg to 400 mg, 300 mg, or 400 mg. In some embodiments, the
effective amount is 60 mg to 400 mg, 100 mg to 400 mg, 300 mg, or
400 mg administered once daily. In some embodiments, the cancer is
a RET-altered solid tumor, a RET-altered non-small cell lung
cancer, or a RET-altered thyroid cancer. In some embodiments, the
cancer is a brain cancer, wherein the brain cancer is associated
with non-small cell lung cancer. This disclosure also relates to
methods of treating RET-altered cancers by administering a
physiological effective dose of a selective RET inhibitor that
produces a sustained down-regulation of at least one effect
marker.
[0003] The receptor tyrosine kinase (RTK) RET, along with glial
cell line-derived neurotrophic factors (GDNF) and GDNF family
receptors-.alpha. (GFR.alpha.), is required for the development,
maturation, and maintenance of several neural, neuroendocrine, and
genitourinary tissue types. However, increasing evidence implicates
aberrant activation of RET as a critical driver of tumor growth and
proliferation across a broad number of solid tumors (Mulligan L M.,
Nat. Rev. Cancer. 14:173-186 (2014)). Oncogenic RET activation
occurs via gain of function mutation or RET gene rearrangement
resulting in the production of a RET fusion protein with
constitutively active RET signaling that promotes
ligand-independent tumor growth. Oncogenic RET activation was
initially described in hereditary and sporadic thyroid cancers and
subsequently in non-small cell lung cancer (NSCLC).
[0004] Oncogenic RET rearrangements have been identified in 1-2% of
NSCLC (Lipson, D. et al., Nat. Med. 18:382-384 (2012); Takeuchi, K.
et al., Nat. Med. 18:378-381 (2012); Stransky, N. et al., Nat.
Commun. 5:4846 (2014)). This generates a constitutively active
kinase that promotes tumorigenesis. As with anaplastic lymphoma
kinase (ALK) and c-ros oncogene (ROS) 1-rearranged NSCLC,
RET-rearranged NSCLC typically has adenocarcinoma histology (though
occasionally squamous) and occurs in young, non-smoking patients.
Because diagnostic testing for RET is not standard of care,
RET-rearranged patients with advanced NSCLC are treated per NCCN
guidelines for epidermal growth factor receptor (EGFR-) and
ALK-negative adenocarcinoma. This usually includes chemotherapy
with a platinum doublet or more recently with a checkpoint
inhibitor however, clinical response and overall survival
specifically in RET-rearranged NSCLC with these agents is not well
understood. Subsequent therapy beyond chemotherapy and checkpoint
inhibitors for refractory patients per NCCN guidelines is best
supportive care or clinical trial.
[0005] Initial case reports and single-arm studies with the
multikinase RET inhibitors (MKIs) cabozantinib, vandetanib,
sorafenib, and alectinib in patients with known RET-rearranged
NSCLC have demonstrated clinical activity, suggesting that RET may
be a valid target in NSCLC. Although encouraging response rates
(.about.12%-60%) (Horiike A et al., Lung Cancer 93:43-6 (March
2016); Lin J J et al., J Thorac Oncol. 11(11):2027-32 (November
2016); Gautshi O et al., J Clin Oncol. 34 (suppl; abstr 9014)
(2016)) have been observed in these early studies, duration of
response is typically less than a year. MKI treatment was
associated with significant toxicity, requiring dose interruption
and/or dose modification, which likely limit exposures required to
effectively inhibit RET.
[0006] Oncogenic RET activation is also associated with thyroid
cancer. Thyroid cancer consists primarily of differentiated thyroid
cancer (DTC; .about.90% of cases), medullary thyroid cancer (MTC;
.about.5% of cases), and anaplastic thyroid cancer (<5% of
cases). DTC arises sporadically from thyroid follicular cells and
consists of papillary thyroid cancer (PTC) (.about.80% of all
thyroid cancer cases) and follicular thyroid cancer. In contrast,
MTC arises from parafollicular C cells and occurs in both
hereditary and sporadic forms. Oncogenic RET activation has been
implicated as a driver in both MTC and PTC.
[0007] Recurrent gene rearrangements involving RET and a
dimerization domain-encoding gene have been identified in
approximately 5%-20% of sporadic papillary tumors in adults.
Kinase-activating RET mutations occur in nearly all cases of
hereditary MTC (87%-97%) (Machens A et al., N Engl J Med
349:1517-25 (2003); Mulligan L M et al., Nature 363(6428):458-60
(1993 Jun. 3); Mulligan L M et al., J Int Med. 238(4):343-346
(1995)) and approximately 43%-65% of sporadic MTC (Elisei R. et
al., J Clin Endocrinol Metab. 93:682-687 (2008); Moura M M et al.,
British Journal of Cancer 100:1777-1783 (2009)). These RET
mutations occur in the extracellular domain (primarily at the C634
position) which promote ligand-independent dimerization and
activation of RET, and kinase domains mutations (primarily M918T,
A883F or V804L/M) which promote RET auto-activation and consequent
oncogenic signaling (Romei C et al., Nat Rev Endocrinol.
12(4):192-202 (2016 April)).
[0008] Both PTC and MTC are treated with surgery when localized
(Fagin J A & Wells S A Jr., N Engl J Med. 375(11):1054-67 (2016
Sep. 15)). Ablative therapy with radioactive iodine (RAI) is
effective in PTC patients with recurrence; however, patients
eventually become refractory to RAI. As MTC arises from follicular
C-cells, RAI is not effective. Once advanced, RAI-refractory PTC
and MTC are poorly responsive to chemotherapy and systemic
treatment with a small molecule MKI is the standard of care for
both. Sorafenib and lenvatinib are approved MKIs for progressive
and/or symptomatic RAI-refractory PTC. Cabozantinib and vandetanib
are approved MKIs for advanced MTC and are used regardless of RET
mutational status. MKIs used to treat thyroid cancer have broad
activity against many kinases (e.g., RAF, MET, EGFR, VEGFR1-3,
PDGFR, RET and others), and are associated with significant
dermatologic, cardiovascular, and gastrointestinal side effects.
Therefore, National Clinical Practice Guidelines in Oncology from
the National Comprehensive Cancer Network (available at
https://www.nccn.org/professionals/physician_gls/f_guidelines.asp)
recommends careful monitoring and dose interruption and/or dose
modification for drug-related side effects with these agents. For
patients with disease progression on MKI therapy or MKI
intolerance, there are no effective therapies and NCCN guidelines
recommend clinical trial participation.
[0009] Given the strong genetic and preclinical evidence that
activated RET is an oncogenic disease driver, the lack of selective
RET inhibitors available, and the poor prognosis of many patients
with RET-altered tumors, a need remains for identifying dosing
amounts and schedules with the appropriate safety, exposures, and
tolerability for selective RET inhibitors for the treatment of
RET-altered cancers.
[0010] Small molecule compounds that selectively inhibit RET are a
desirable means for treating cancers having an activating RET
alteration. One small molecule is
(S,4R)-N-((S)-1-(6-(4-fluoro-1H-pyrazol-1-yl)pyridin-3-yl)ethyl)-1-methox-
y-4-(4-methyl-6-((5-methyl-1H-pyrazol-3-yl)amino)pyrimidin-2-yl)cyclohexan-
ecarboxamide (Compound 1). Compound 1 has the chemical
structure:
##STR00001##
[0011] In March 2017, Compound 1 (also known as BLU-667) entered
Phase I clinical trials in the United States for the treatment of
patients with thyroid cancer, non-small cell lung cancer, and other
advanced solid tumors (NCT03037385). WO 2017/079140, incorporated
herein by reference, describes the synthesis of Compound 1 (Example
Compound 130) and also discloses the therapeutic activity of this
molecule to inhibit, regulate, and/or modulate RET kinase (Assays,
Example 10 on pp. 72-74).
BRIEF DESCRIPTION OF THE FIGURES
[0012] FIGS. 1A, 1B, and 1C are a series of bar graphs which show
the impact of Compound 1 on expression of DUSP6 and SPRY4 in LC2/ad
(FIG. 1A), MZ-CRC-1 (FIG. 1B), and TT (FIG. 1C) cells.
[0013] FIG. 2 is a bar graph which shows the sustained decrease in
expression of the MAPK target genes DUSP6 and SPRY4 in a KIF5B-RET
NSCLC PDX model.
[0014] FIG. 3 is a graph which shows in vivo anti-tumor activity of
Compound 1 in a cabozantinib-resistant tumor model generated from
an engineered KIF5B-RET V804L cell line.
[0015] FIG. 4A is a graph which shows tumor size and levels of
calcitonin and CEA (carcinoembryonic antigen) decrease over the
course of treatment with Compound 1. The RET-mutant MTC patient
(RET L629P, D631_R635DELINSG, V637R MTC) was treated with 60 mg
once daily and then received successive dose escalation up to 300
mg once daily. FIG. 4B is a CT scan of the same RET-mutant MTC
patient of FIG. 4A at baseline (top) and after 8 weeks of Compound
1 treatment (bottom) demonstrating rapid reduction in tumor
growth.
[0016] FIG. 4C is a graph which shows tumor size and the levels of
calcitonin and CEA decrease in a patient with RET M918T-mutant MTC
over the course of treatment with Compound 1 with 300 mg once
daily. FIG. 4D is a CT scan of the RET M918T-mutant patient of FIG.
4C's tumor at baseline (top) and after 24 weeks of Compound 1
treatment (bottom). FIG. 4E is a graph which shows ctDNA analysis
of RET M918T levels in plasma from an MTC patient during treatment.
Pre- and post-treatment tumor biopsy revealed a 93% decrease in
DUSP6 and 86% decrease in SPRY4 mRNA expression after 28 days of
treatment with Compound 1.
[0017] FIG. 5A is a graph which shows lung tumor and KIF5B-RET and
TP53 ctDNA reduction over the course of treatment with 200 mg once
daily Compound 1; FIG. 5B is a CT scan which illustrates tumor at
baseline (top) and after 32 weeks of Compound 1 treatment
(bottom).
[0018] FIG. 6A is a graph which shows the mean plasma concentration
(ng/mL) vs. time (h); FIG. 6B is a bar graph which shows the
percent change from baseline in mean gene expression levels of
DUSP6 and SPRY4.
[0019] FIG. 7A is a bar graph which shows dose-dependent reduction
in CEA in patients measured on cycle 2, day 1. FIG. 7B is a bar
graph which shows dose-dependent reduction in calcitonin in
patients measured on cycle 2 day 1.
[0020] FIG. 8 is a waterfall plot which shows maximum tumor
reduction-sum of diameter change from baseline percent--from
patients in the phase I clinical study. Data cut-off: Apr. 6,
2018.
[0021] FIG. 9A is a brain CT scan at baseline prior to treatment
with Compound 1. FIG. 9B is a brain CT scan after 8 weeks of
treatment with Compound 1 treatment.
[0022] FIG. 10 is a chart which shows patient response rate in
RET-altered NSCLC. Data cut-off: Apr. 6, 2018.
[0023] FIG. 11A is a CT scan at baseline prior to treatment with
Compound 1. FIG. 11B is a CT scan after 8 weeks of treatment with
Compound 1. FIG. 11C is a CT scan at baseline prior to treatment
with Compound 1. FIG. 11D is a CT scan after 8 weeks of treatment
with Compound 1.
[0024] FIG. 12 is a graph which shows that the response rate in
medullary thyroid cancer patients increases with dose and duration
of therapy. Specifically, the graph shows the response rate for
dosing Compound 1 at 60 to 200 mg once daily and 300/400 mg once
daily over a period of 8 to 24+ weeks.
[0025] FIG. 13 is a CT scan at baseline (BSL) and after 5 months of
treatment with Compound 1 at 400 mg once daily.
ABBREVIATIONS AND DEFINITIONS
[0026] The following abbreviations and terms have the indicated
means throughout:
[0027] "Compound 1" is
(1S,4R)-N-((S)-1-(6-(4-fluoro-1H-pyrazol-1-yl)pyridine-3-yl)ethyl)-1-meth-
oxy-4-(4-methyl-6-((5-methyl-1H-pyrazol-3-yl)amino)pyrimidin-2-yl)cyclohex-
anecarboxamide:
##STR00002##
[0028] As used herein, "DOR" means duration of response.
[0029] As used herein, "PD" means progressive disease.
[0030] As used herein, "SD" means stable disease.
[0031] As used herein, "CR" means complete response.
[0032] As used herein, "ORR" means overall all response rate.
[0033] As used herein, "CBR" means clinical benefit rate.
[0034] As used herein, "PFS" means progression free survival.
[0035] As used herein, a "fusion" is a protein that results from a
chromosomal translocation in which two genes are joined with an
in-frame coding sequence and results in a chimeric protein. In some
embodiments, a fusion is a chromosomal translocation where the
kinase domain of one protein fuses to a dimerization domain of
another gene.
[0036] As used herein, a "RET-altered cancer" is a cancer having an
activating rearranged during transfection (RET) alteration, which
drives tumorigenesis. Non-limiting examples of activating RET
alterations include mutations, fusions, and copy number
variations.
[0037] As used herein, a "RET fusion" is a gene rearrangement. RET
rearrangements create a fusion protein juxtaposing the RET kinase
domain and a dimerization domain of another protein, creating a
constitutively activated dimer, which drives tumorigenesis.
[0038] As used herein, a "RET fusion protein" is the result of a
gene rearrangement.
[0039] As used herein, a "RET activating mutation" means a mutation
in RET kinase which promotes ligand-independent, constitutive RET
kinase activation, which drives tumorigenesis. For example, RET
mutations can occur in the extracellular cysteine residues (e.g.,
C620R or C634R/W), which trigger aberrant receptor dimerization, or
RET mutations can occur in the intracellular kinase domain.
[0040] As used herein, a "RET inhibitor" is a compound which
inhibits the activity of RET kinase. RET kinase is wild-type RET
kinase and/or one or more RET-altered kinases (e.g., RET fusion,
RET mutation, or RET copy number variation).
[0041] Examples of RET inhibitors include, but are not limited to,
Compound 1, LOXO-292 (selpercatinib), cabozantinib, vandetanib,
alectinib, sorafenib, levatinib, ponatinib, dovitinib, sunitinib,
foretinib, sitravatinib, DS-5010 (BOS172738), and RXDX-105.
[0042] In some embodiments, a RET inhibitor may also inhibit other
kinases. As used herein, a "multi-kinase RET inhibitor" is a
compound which inhibits wild type RET kinase and inhibits at least
one other kinase equally or more potently than wild type RET
kinase. Examples of multikinase RET inhibitors include:
cabozantinib; vandetanib; alectinib; sorafenib; levatinib,
ponatinib; dovitinib; sunitinib; foretinib; sitravatinib; DS-5010;
and RXDX-105.
[0043] As used herein, the term "selective RET inhibitor" means a
compound which selectively inhibits RET kinase. RET kinase can
include RET wild type kinase and/or one or more RET-altered kinases
(e.g., RET fusion, RET mutation, or RET copy number variation). A
selective RET inhibitor's inhibitory activity against RET kinase is
more potent in terms of IC.sub.50 value (i.e., the IC.sub.50 value
is subnanomolar) when compared with its inhibitory activity against
many other kinases (e.g., KDR, VEGFR-2, ABL, EGFR, FGFR2, HER2,
IGFIR, JAKI, KIT, MET, AKTI, MEKI). Potency can be measured using
known biochemical assays. Examples of selective RET inhibitors
include Compound 1 and selpercatinib.
[0044] As used herein, the term "subject" or "patient" refers to
organisms to be treated by the methods of the present disclosure.
Such organisms include, but are not limited to, mammals (e.g.,
murines, simians, equines, bovines, porcines, canines, felines, and
the like), and in some embodiments, humans.
[0045] Many cancers have been linked to aberrant RET expression
(Kato et al., Clin. Cancer Res. 23(8):1988-97 (2017)). Non-limiting
examples of "cancer" as used herein include lung cancer, head and
neck cancer, gastrointestinal cancer, breast cancer, skin cancer,
genitourinary tract cancer, gynecological cancer, hematological
cancer, central nervous system (CNS) cancer, peripheral nervous
system cancer, endometrial cancer, colorectal cancer, bone cancer,
sarcoma, spitzoid neoplasm, adenosquamous carcinoma,
pheochromocytoma (PCC), hepatocellular carcinoma, multiple
endocrine neoplasia (MEN2A and MEN2B), and inflammatory
myofibroblastic tumor. For other examples, see Nature Reviews
Cancer 14:173-86(2014).
[0046] Additional non-limiting examples of cancer include
hemangiopericytoma, differentiated thyroid carcinoma, anaplastic
thyroid carcinoma, lung carcinosarcoma, ureter urothelial
carcinoma, uterine carcinosarcoma, basal cell carcinoma, Merkel
cell carcinoma, atypical lung carcinoma, fallopian tube
adenocarcinoma, ovarian epithelial carcinoma, salivary gland
adenocarcinoma, meningioma, duodenal adenocarcinoma, cervical
adenocarcinoma, adrenal carcinoma, gastroesophageal junction
carcinoma, cutaneous squamous cell carcinoma, pancreatic ductal
adenocarcinoma, prostate adenocarcinoma, esophageal adenocarcinoma,
endometrial adenocarcinoma, ovarian serous carcinoma, carcinoma
unknown primary, bladder urothelial (transition cell) carcinoma,
lung squamous cell carcinoma, colorectal adenocarcinoma, head and
neck squamous cell carcinoma, and gastric adenocarcinoma.
[0047] In some embodiments, the cancer is liver cholangiocarcinoma.
In some embodiments, the cancer is duodenum adenocarcinoma. In some
embodiments, the cancer is uterus endometrial adenocarcinoma
endometrioid.
[0048] In some embodiments, MEN2A is associated with
pheochromocytoma and parathyroidhyperplasia.
[0049] In some embodiments, MEN2B is associated with mucosal
neuromas, pheochromocytomas, intestinal ganglioneuromas and
marfanoid habitus.
[0050] In some embodiments, the lung cancer is chosen from small
cell lung cancer (SCLC), lung adenocarcinoma, non-small cell lung
cancer (NSCLC), bronchioles lung cell carcinoma, and mesothelioma.
In some embodiments, the lung cancer is SCLC. In some embodiments,
the lung cancer is NSCLC.
[0051] In some embodiments, the head and neck cancer is chosen from
thyroid cancer and cancer of the salivary gland. In some
embodiments, the thyroid cancer is chosen from papillary thyroid
carcinoma (PTC), metastatic papillary thyroid cancer, medullary
thyroid cancer (MTC), diffuse sclerosing variant of papillary
thyroid cancer, and thyroid gland carcinoma. In some embodiments,
the cancer is familial medullary thyroid cancer. In some
embodiments, the thyroid cancer is PTC. In some embodiments, the
thyroid cancer is MTC.
[0052] In some embodiments, the gastrointestinal cancer is chosen
from esophageal cancer, esophagogastric cancer, gastrointestinal
stromal tumor (e.g., imatinib-resistant gastrointestinal stromal
tumor), small bowel cancer, diffuse gastric cancer, and ampullary
carcinoma.
[0053] In some embodiments, the breast cancer is metastatic breast
cancer. In some embodiments, skin cancer is melanoma or
non-melanoma.
[0054] In some embodiments, the genitourinary tract cancer is
chosen from colon cancer, metastatic colon cancer, bladder cancer,
renal cell carcinoma (RCC), prostate cancer, hepatobiliary cancer,
intrahepatic bile duct cancer, adrenocortical carcinoma, pancreatic
cancer, and pancreatic ductal adenocarcinoma.
[0055] In some embodiments, the gynecological cancer is chosen from
uterine sarcoma, germ cell tumor, cervical cancer, rectal cancer,
testicular cancer, and ovarian cancer. In some embodiments, the
hematological cancer is chosen from leukemia, primary myelofibrosis
with secondary acute myeloid leukemia, myelodysplasia (MDS),
non-Hodgkin lymphoma, chronic myeloid leukemia, Philadelphia
chromosome-positive acute lymphoblastic leukemia, and chronic
myelomonocytic leukemia (CMML).
[0056] In some embodiments, the peripheral nervous system cancer is
paraganglioma. In some embodiments, the endometrial cancer
isendometrial adenocarcinoma. In some embodiments, the sarcoma is a
soft tissue sarcoma.
[0057] In some embodiments, the central nervous system (CNS) cancer
is chosen from brain cancer associated with lung cancer and
glioma.
[0058] Lung cancer is known to spread to the brain in about 40
percent of cases in which a metastasis has occurred. With lung
cancer, this is considered stage 4 of the disease, and the average
survival time with brain metastases is usually less than a year.
Lung cancers with metastases to the brain have a relatively poor
prognosis, e.g., chemotherapy drugs. Brain metastases are difficult
to treat for many reasons. Often, by the time the patient first
exhibits symptoms, they already have multiple lesions. Brain
metastases tend to be very aggressive. The brain has many defenses
to reduce the penetration of harmful substances. Specifically, the
blood-brain-barrier prevents many medications, e.g., compounds from
entering the brain. Treatment options may damage surrounding normal
tissue and have a significant impact on the quality of life. In
particular, there is a need to provide compounds that can be
administered at a safe dose, with good tolerability, and which
penetrate the brain for treatment of brain metastases.
[0059] In some embodiments, the cancer is brain metastasis
associated with lung cancer.
[0060] In some embodiments, the cancer is a "RET-altered cancer,"
which, as used herein, means the cancer has an activating RET
alteration. In some embodiments, the RET-altered cancer has a RET
mutation or a RET gene rearrangement. In some embodiments, the
RET-altered cancer is a RET-altered solid tumor.
[0061] As used herein, the term "effective amount" refers to the
amount of a selective RET inhibitor (e.g., Compound 1 or a
pharmaceutically acceptable salt thereof) sufficient to effect
beneficial or desired results. Beneficial or desired results may be
a therapeutic benefit or result or a physiological benefit or
result. An effective amount can be administered in one or more
administrations, applications, or dosages and is not intended to be
limited to a specific formulation or administration route.
[0062] As used herein, the term "therapeutically effective amount"
refers to the amount of a selective inhibitor (e.g., Compound 1 or
a pharmaceutically acceptable salt thereof) sufficient to effect
beneficial or desired therapeutic results in a subject. A
therapeutically effective amount can be administered to a subject
in need thereof in one or more administrations, applications, or
dosages and is not intended to be limited to a specific formulation
or administration route. In some embodiments, a therapeutically
effective amount provides the desired safety, exposure, and
tolerability. Selecting the therapeutically effective amount, i.e.,
the right dose for administering a compound, is a required step in
the development of a pharmaceutical drug for clinical use. Without
adequate information on dosage, it is not possible for doctors to
prescribe a particular drug to patients. Therefore, determining the
correct drug dosage is a key question that can only be answered in
clinical studies. If the dose and frequency of administration that
allows safe and predictable administration cannot be identified,
then the compound cannot be a medically useful or commercially
viable pharmaceutical product.
[0063] As used herein, the term "physiologically effective amount"
refers to the amount of a selective inhibitor (e.g., Compound 1 or
a pharmaceutically acceptable salt thereof) sufficient to effect
beneficial or desired physiological result in a subject. A
physiological result may be a sustained down-regulation of at least
one effect marker in the subject.
[0064] As used herein, the term "treating" includes any effect,
e.g., lessening, reducing, modulating, ameliorating, or
eliminating, that results in the improvement of the condition,
disease, disorder, and the like, or ameliorating a symptom
thereof.
[0065] As used herein, an "effect marker" means DUSP6 mRNA
expression, SPRY4 mRNA expression, CEA, calcitonin, KIF5B ctDNA or
TP53 ctDNA.
[0066] Some example embodiments of the disclosure include the
following:
1. A method of treating a subject afflicted with a cancer having an
activating rearranged during transfection (RET) alteration, the
method comprising administering to the subject a therapeutically
effective amount of 300 to 400 mg of Compound 1 or a
pharmaceutically acceptable salt thereof once daily. 2. The method
of embodiment 1, wherein the amount administered is 300 mg. 3. The
method of embodiment 1 or 2, wherein the amount administered is 400
mg. 4. The method of any one of embodiments 1-3, wherein the cancer
is chosen from papillary thyroid carcinoma (PTC), medullary thyroid
cancer (MTC), pheochromocytoma (PCC), pancreatic ductal
adenocarcinoma, multiple endocrine neoplasia (MEN2A and MEN2B),
metastatic breast cancer, testicular cancer, small cell lung
cancer, non-small cell lung cancer (NSCLC), chronic myelomonocytic
leukemia (CMML), colorectal cancer, ovarian cancer, inflammatory
myofibroblastic tumor, and cancer of the salivary gland. 5. The
method of any one of embodiments 1-3, wherein the cancer is chosen
from esophageal cancer, skin cancer (non-melanoma), endometrial
cancer, head and neck cancer, bladder cancer, prostate cancer,
hematological cancer, leukemia, soft tissue sarcoma, renal cell
carcinoma (RCC), non-Hodgkin lymphoma, hepatobiliary cancer,
adrenocortical carcinoma, myelodysplasia (MDS), uterine sarcoma,
germ cell tumor, cervical cancer, central nervous system cancer,
bone cancer, ampullary carcinoma, gastrointestinal stromal tumor,
small bowel cancer, mesothelioma, rectal cancer, paraganglioma, and
intrahepatic bile duct cancer. 6. The method of any one of
embodiments 1-3, wherein the cancer is chosen from adenocarcinoma,
spitzoid neoplasm, lung adenocarcinoma, adenosquamous carcinoma,
colon cancer, metastatic colon cancer, metastatic papillary thyroid
cancer, diffuse sclerosing variant of papillary thyroid cancer,
primary myelofibrosis with secondary acute myeloid leukemia,
diffuse gastric cancer, thyroid gland carcinoma, and bronchioles
lung cell carcinoma. 7. The method of any one of embodiments 1-3,
wherein the cancer is chosen from hepatobiliary cancer, ampullary
carcinoma, small bowel cancer, intrahepatic bile duct cancer,
metastatic colon cancer, brain cancer associated with lung cancer,
brain metastasis associated with lung cancer, and retropentoneal
paraganglioma. 8. The method of any one of embodiments 1-3, wherein
the cancer is chosen from medullary thyroid cancer (MTC) and
non-small cell lung cancer (NSCLC). 9. The method of embodiment 8,
wherein the cancer is chosen from sporadic MTC, metastatic
RET-altered NSCLC, tyrosine kinase inhibitor (TKI)-refractory
KIF5B-RET NSCLC, and KIF5B-RET NSCLC. 10. The method of any one of
embodiments 1-3, wherein the cancer is chosen from a brain cancer
associated with a lung cancer. 11. The method of embodiment 10,
wherein the brain cancer is brain metastasis. 12. The method of any
one of embodiments 1-11, wherein the activating RET alteration
comprises a RET mutation or a RET gene rearrangement (fusion). 13.
The method of any one of embodiments 1-11, wherein the activating
RET alteration is a RET mutation. 14. The method of embodiment 12
or 13, wherein the RET mutation is a point mutation. 15. The method
of any one of embodiments 12-14, wherein the RET mutation is a
resistance mutation. 16. The method of any one of embodiments
12-15, wherein the RET alteration is a RET mutation chosen from
Table 1. 17. The method of any one of embodiments 12-16, wherein
the RET mutation is V804M, M918T, C634R, or C634W. 18. The method
of any one of embodiments 1-4, 8, 9, and 12-16, wherein the cancer
is RET-altered medullary thyroid cancer (MTC). 19. The method of
embodiment 18, wherein the cancer is familial MTC. 20. The method
of embodiment 18, wherein the cancer is sporadic MTC. 21. The
method of any one of embodiments 1-3 and 12-19, wherein the cancer
is MTC having a M918T mutation. 22. The method of any one of
embodiments 1-3 and 12-19, wherein the cancer is MTC having a C634R
mutation. 23. The method of any one of embodiments 1-3 and 12-19,
wherein the cancer is MTC having a V804M mutation. 24. The method
of any one of embodiments 1-3, 6, and 12-16, wherein the cancer is
paraganglioma. 25. The method of embodiment 24, wherein the cancer
is retropentoneal paraganglioma. 26. The method of any one of
embodiments 1-3, 6, 12-16, 24, and 25, wherein the paraganglioma
has a R77H mutation. 27. The method of any one of embodiments 1-11,
wherein the activating RET alteration is a gene-rearrangement
(fusion). 28. The method of embodiment 27, wherein the activating
RET alteration is a fusion with a RET fusion partner chosen from
Table 2. 29. The method of embodiment 27 or 28, wherein the fusion
is KIF5B-RET, CCDC6-RET, KIAA1468-RET, or NCOA4-RET. 30. The method
of any one of embodiments 1-4 and 27-29, wherein the cancer is
RET-altered NSCLC. 31. The method of embodiment 30, wherein the
cancer is NSCLC having a KIF5B-RET fusion. 32. The method of
embodiment 30, wherein the cancer is NSCLC having a CCDC6-RET
fusion. 33. The method of embodiment 30, wherein the cancer is
NSCLC having a KIAA1468-RET fusion. 34. The method of embodiment
30, wherein the cancer is NSCLC having a RET fusion identified as
FISH positive. 35. The method of embodiment 29 or 30, wherein the
RET alteration is KIF5B-RET V804L (cabozantinib resistant). 36. The
method of embodiment 29 or 30, wherein the RET alteration is
CCDC6-RET V804M (ponatinib resistant). 37. The method of any one of
embodiments 1-4 and 27-29, wherein the cancer is RET-altered PTC.
38. The method of embodiment 37, wherein the cancer is PTC having a
CCDC6-RET fusion. 39. The method of embodiment 37, wherein the
cancer is PTC having a NCOA4-RET fusion. 40. The method of any one
of embodiments 1-3 and 27-29, wherein the cancer is RET-altered
intrahepatic bile duct carcinoma. 41. The method of embodiment 40,
wherein the cancer is intrahepatic bile duct carcinoma having a
NCOA4-RET fusion. 42. The method of any one of embodiments 1-41,
wherein the subject has not received prior treatment with a
multikinase RET inhibitor. 43. The method of any one of embodiments
1-41 wherein the subject has received one or more prior treatments
with a multikinase RET inhibitor. 44. The method of embodiment 43,
wherein the multikinase RET inhibitor is chosen from lenvatinib,
vandetanib, cabozantinib, and RXDX-105. 45. The method of any one
of embodiments 1-41, wherein the subject has not received prior
treatment with platinum. 46. The method of any one of embodiments
1-41, wherein the subject has received prior treatment with
platinum. 47. The method of any one of embodiments 1-41, wherein
the subject has received prior treatment with a selective RET
inhibitor. 48. The method of any one of embodiments 1-47, wherein
the subject has not received prior chemotherapy. 49. The method of
any one of embodiments 1-47, wherein the subject has received prior
chemotherapy. 50. The method of embodiment 49, wherein the prior
chemotherapy is chosen from carboplatin, pemetrexed, abraxane,
cisplatin, bevacizumab, and combinations thereof. 51. The method of
any one of embodiments 1-42, wherein the subject has not received
prior immunotherapy. 52. The method of any one of embodiments 1-42,
wherein the subject has received prior immunotherapy. 53. The
method of embodiment 52, wherein the prior immunotherapy is chosen
from ipilimumab, pembrolizumab, nivolumab, MPDL3280A, MEDI4736, and
combinations thereof. 54. A method of treating a subject afflicted
with a brain cancer associated with a RET-altered lung cancer, the
method comprising administering to the subject a therapeutically
effective amount of Compound 1 or a pharmaceutically acceptable
salt thereof. 55. The method of embodiment 54, wherein the brain
cancer is brain metastasis. 56. A method of treating a subject
afflicted with a cancer having an activating RET mutation, the
comprising administering to the subject a physiologically effective
amount of a RET inhibitor, wherein administration of the RET
inhibitor is associated with a sustained down-regulation of at
least one effect marker in the subject. 57. The method of
embodiment 56, wherein the RET inhibitor is orally administered.
58. The method of embodiment 56 or 57, wherein the RET inhibitor is
Compound 1 or a pharmaceutically acceptable salt thereof. 59. The
method of any one of embodiments 56-58, wherein the effect marker
is chosen from DUSP6 mRNA expression, SPRY4 mRNA expression,
carcinoembryonic antigen level, and calcitonin level. 60. The
method of any one of embodiments 56-58, wherein the effect marker
is KIF5B ctDNA level or TP53 ctDNA level. 61. The method of any one
of embodiments 56-59, wherein the amount administered to the
subject produces a greater than 95% down-regulation of at least one
effect marker. 62. The method of any one of embodiments 56-59,
wherein the amount administered to the subject produces a greater
than 94%, greater than 93%, greater than 92%, greater than 91%,
greater than 90%, greater than 89%, greater than 88%, greater than
87%, greater than 86% greater than 85%, greater than 80%, greater
than 75%, greater than 70%, greater than 65%, greater than 60%,
greater than 55%, or greater than 50% down-regulation in at least
one effect marker. 63. The method of embodiment 61, wherein the
amount administered to the subject produces a greater than 89%,
greater than 88%, greater than 87%, greater than 86%, greater than
85%, greater than 80%, greater than 75%, or greater than 70%
down-regulation in at least one effect marker. 64. The method of
any one of embodiments 56-59, wherein at least two effect markers
are down-regulated.
TABLE-US-00001 TABLE 1 RET Point Mutations. Example RET Point
Mutation Example RET Point Mutation Amino acid position 2 Amino
acid position 665 (e.g., H665Q) Amino acid position 3 Amino acid
position 666 (e.g., K666E, K666M, or K666N) Amino acid position 4
Amino acid position 686 (e.g., S686N) Amino acid position 5 Amino
acid position 691 (e.g., G691S) Amino acid position 6 Amino acid
position 694 (e.g., R694Q) Amino acid position 7 Amino acid
position 700 (e.g., M700L) Amino acid position 8 Amino acid
position 706 (e.g., V706M or V706A) Amino acid position 11 Amino
acid position 713 splice variant (e.g., E713K) Amino acid position
12 Amino acid position 736 (e.g., G736R) Amino acid position 13
Amino acid position 748 (e.g., G748C) Amino acid position 20 Amino
acid position 750 (e.g., A750P) Amino acid position 32 (e.g., S32L)
Amino acid position 765 (e.g., S765P) Amino acid position 34 (e.g.,
D34S) Amino acid position 766 (e.g., P766S or P766M6) Amino acid
position 40 (e.g., L40P) Amino acid position 768 (e.g., E768Q or
E768D) Amino acid position 64 (e.g., P64L) Amino acid position 769
(e.g., L769L) Amino acid position 67 (e.g., R67H) Amino acid
position 770 (e.g., R770Q) Amino acid position 114 (e.g., R114H)
Amino acid position 771 (e.g., D771N) Amino acid position 136
(e.g., glutamic Amino acid position 777 (e.g., N777S) acid to stop
codon) Amino acid position 145 (e.g., V145G) Amino acid position
778 (e.g., V778I) Amino acid position 180 (e.g., arginine Amino
acid position 781 (e.g., Q781R) to stop codon) Amino acid position
200 Amino acid position 790 (e.g., L790F) Amino acid position 292
(e.g., V292M) Amino acid position 791 (e.g., Y791F or Y791N) Amino
acid position 294 Amino acid position 802 Amino acid position 321
(e.g., G321R) Amino acid position 804 (e.g., V804L, V804M, V804M,
or V804E) Amino acid position 330 (e.g., R330Q) Amino acid position
805 (e.g., E805K) Amino acid position 338 (e.g., T338I) Amino acid
position 806 (e.g., E806C, Y806E, Y806F, Y806S, Y806G, Y806H,
Y806N, or Y806C) Amino acid position 360 (e.g., R360W) Amino acid
position 818 (e.g., E818K) Amino acid position 373 (e.g., alanine
Amino acid position 819 (e.g., S819I) to frameshift) Amino acid
position 388 (e.g., V388A) Amino acid position 393 (e.g., F393L)
Amino acid position 823 (e.g., G823E) Amino acid position 432 Amino
acid position 826 (e.g., Y826M) .DELTA. Amino acid residues 505-506
(6- Amino acid position 833 (e.g., R833C) Base Pair In-Frame
Germline Deletion in Exon 7) Amino acid position 510 (e.g., A510V)
Amino acid position 841 (e.g., P841L or P841P) Amino acid position
511 (e.g., E511K) Amino acid position 843 (e.g., E843D) Amino acid
position 513 (e.g., A513D) Amino acid position 844 (e.g., R844W,
R844Q, or R844L) Amino acid position 515 (e.g., C515S, Amino acid
position 848 (e.g., M848T) C515W) Amino acid position 525 (e.g.,
R525W) Amino acid position 852 (e.g., 1852M) Amino acid position
531 (e.g., C531R, Amino acid position 866 (e.g., A866W) or 9 base
pair duplication) Amino acid position 532 (e.g., Amino acid
position 873 (e.g., R873W) duplication) Amino acid position 533
(e.g G533C or Amino acid position 876 (e.g., A876V) G533S) Amino
acid position 550 (e.g., G550E) Amino acid position 881 (e.g.,
L881V) Amino acid position 591 (e.g., V591I) Amino acid position
882 Amino acid position 593 (e.g., G593E) Amino acid position 883
(e.g., A883F, A883S, A883T, or A883T*) Amino acid position 600
(e.g., R600Q) Amino acid position 884 (e.g., E884K) Amino acid
position 602 (e.g., I602V) Amino acid position 886 (e.g., R886W)
Amino acid position 603 (e.g., K603Q Amino acid position 891 (e.g.,
S891A) or K603E2) Amino acid position 606 (e.g., Y606C) Amino acid
position 897 (e.g., R897Q) Amino acid position 609 (e.g., C609Y,
Amino acid position 898 (e.g., D898V) C609S, C609G, C609R, C609F,
or C609W) Amino acid position 611 (e.g., C611R, Amino acid position
901 (e.g., E901K) C611S, C611G, C611Y, C611F, or C611W) Amino acid
position 618 (e.g., C618S, Amino acid position 904 (e.g., S904F or
C618Y, C618R, C618Y, C618G, C618F, S904C2) C618W) Amino acid
position 619 (e.g., F619F) Amino acid position 907 (e.g., K907E or
K907M) Amino acid position 620 (e.g., C620S, Amino acid position
908 (e.g., R908K) C690W, C670R, C620G, C620L, C620Y, C620F) Amino
acid position 623 (e.g., E623K) Amino acid position 911 (e.g.,
G911D) Amino acid position 624 (e.g., D624N) Amino acid position
912 (e.g., R912P, R912Q) Amino acid position 629 (e.g., L629P)
Amino acid position 630 (e.g., C630A, Amino acid position 918
(e.g., M918T, M918V, C630R, C6305, C630Y, or C630F) or M918L6)
Amino acid position 631 (e.g., D631N, Amino acid position 919
(e.g., A919V) D631Y, D631A, D631G, D631V, or D631E,
D631_R635DELINSG) Amino acid position 632 (e.g., E632K Amino acid
position 921 (e.g., E921K) or E632G5) .DELTA. Amino acid residues
632-633 (6- Amino acid position 922 (e.g., S922P or S922Y) Base
Pair In-Frame Germline Deletion in Exon 11) Amino acid position 633
(e.g., 9 base Amino acid position 930 (e.g., T930M) pair
duplication) Amino acid position 634 (e.g., C634W, Amino acid
position 961 (e.g., F961L) C634Y, C634S, C634R, C634F, C634G,
C634L, C634A, or C634T, or an insertion ELCR2, or a 12 base pair
duplication) Amino acid position 635 (e.g., R6356) Amino acid
position 972 (e.g., R972G) Amino acid position 636 (e.g., T636P
Amino acid position 982 (e.g., R982C) or T636M4) Amino acid
position 637 (e.g., V637R) Amino acid position 640 (e.g., A640G)
Amino acid position 1009 (e.g., M1009V) Amino acid position 641
(e.g., A641S Amino acid position 1017 (e.g., Dl017N) or A641T8)
Amino acid position 648 (e.g., V6481) Amino acid position 1041
(e.g., V1041G) Amino acid position 649 (e.g., S649L) Amino acid
position 1064 (e.g., M1064T) Amino acid position 664 (e.g., A664D)
RET + 3 Amino acid position 629 (e.g., L629P) Amino acid position
637 (e.g., V637R)
[0067] Some of the RET point mutations in Table 1 are discussed in:
U.S. Patent Application Publication No. 2014/0272951; Krampitz et
al., Cancer 120:1920-31 (2014); Latteyer et al., J Clin.
Endocrinol. Metab. 101(3): 1016-22 (2016); Silva et al. Endocrine
49.2:366-72 (2015); Jovanovic et al., Prilozi 36(1):93-107 (2015);
Qi et al., Oncotarget 6(32):33993-4003 (2015); Kim et al. ACTA
ENDOCRINOLOGICA-BUCHAREST 11.2, 189-194, (2015); Cecchirini et al.
Oncogene, 14:2609-12 (1997); Karrasch et al., Eur. Thyroid J
5(1):73-77 (2016); Scollo et al., Endocr. J63:87-91 (2016); and
Wells et al., Thyroid 25:567-610(2015).
[0068] R525W and A513D may act in combination with S891A to enhance
oncogenic activity.
TABLE-US-00002 TABLE 2 RET Fusions. RET fusion partner Exemplary
cancers in which the fusion is found BCR Chronic Myelomonocytic
Leukemia (CMML) CLIP 1 Adenocarcinoma KIFSB NSCLC, Ovarian Cancer,
Spitzoid Neoplasm; Lung Adenocarcinoma, Adenosquamous Carcinomas
CCDC6 NSCLC, Colon Cancer, Papillary Thyroid Cancer; Adeno-
carcinoma; Lung Adenocarcinoma; Metastatic Colorectal Cancer;
Adenosquamous Carcinoma, Metastatic papillary thyroid cancer
PTClex9 Metastatic papillary thyroid cancer NCOA4 Papillary Thyroid
Cancer, NSCLC, Colon Cancer, Salivary Gland Cancer, Metastatic
Colorectal Cancer; Lung Adenocarcinoma, Adenosquamous Carcinomas;
Diffuse Sclerosing Variant of Papillary Thyroid Cancer TRIM33
NSCLC, Papillary Thyroid Cancer ERC1 Papillary Thyroid Cancer,
Breast Cancer FGFRIOP CMML, Primary Myelofibrosis with secondary
Acute Myeloid Leukemia MBD1 Papillary Thyroid Cancer RAB61P2
Papillary Thyroid Cancer PRKAR1A Papillary Thyroid Cancer TRIM24
Papillary Thyroid Cancer KTN1 Papillary Thyroid Cancer GOLGA5
Papillary Thyroid Cancer, Spitzoid Neoplasms HOOK3 Papillary
Thyroid Cancer KIAA1468 Papillary Thyroid Cancer, Lung
Adenocarcinoma TRIM27 Papillary Thyroid Cancer AKAP13 Papillary
Thyroid Cancer FKBP15 Papillary Thyroid Cancer SPECC1L Papillary
Thyroid Cancer, Thyroid Gland Carcinoma TBL1XR1 Papillary Thyroid
Cancer, Thyroid Gland Carcinoma CEP55 Diffuse Gastric Cancer CUX1
Lung Adenocarcinoma ACBD5 Papillary Thyroid Carcinoma MYH13
Medullary Thyroid Carcinoma PIBF1 Bronchiolus Lung Cell Carcinoma
KIAA1217 Papillary Thyroid Cancer, Lung Adenocarcinoma, NSCLC MPRIP
NSCLC
[0069] Some of the RET fusions in Table 2 are discussed in: Grubbs
et al., J Clin Endocrinol Metab, 100:788-93 (2015); Halkova et al.,
Human Pathology 46:1962-69 (2015); U.S. Pat. Nos. 9,297,011;
9,216,172; Le Rolle et al., Oncotarget 6(30):28929-37 (2015);
Antonescu et al., Am J Surg Pathol 39(7):957-67 (2015); U.S. Patent
Application Publication No. 2015/0177246; U.S. Patent Application
Publication No. 2015/0057335; Japanese Patent Application
Publication No. 2015/109806A; Chinese Patent Application
Publication No. 105255927A; Fang, et al., Journal of Thoracic
Oncology 11.2 (2016): S21-S22; European Patent Application
Publication No. EP3037547A1; Lee et al., Oncotarget DOI:
10.18632/oncotarget.9137, e-published ahead of printing, 2016;
Saito et al., Cancer Science 107:713-20 (2016); Pirker et al.,
Transl Lung Cancer Res, 4(6):797-800 (2015); and Joung et al.,
Histopathology 69(1):45-53 (2016).
[0070] A person of ordinary skill in the art may determine if a
subject possesses a RET-altered cell, cancer, gene, or gene
product, e.g., having a mutation, e.g., a fusion, deletion,
insertion, translocation, frameshift, duplication, point mutation,
and/or rearrangement, e.g., using a method selected from
hybridization-based methods, amplification-based methods,
microarray analysis, flow cytometry analysis, DNA sequencing,
next-generation sequencing (NGS), primer extension, PCR, in situ
hybridization, fluorescent in situ hybridization, dot blot, and
Southern blot.
[0071] To detect a fusion, primary tumor samples may be collected
from a subject. The samples are processed, the nucleic acids are
isolated using techniques known in the art, then the nucleic acids
are sequenced using methods known in the art. Sequences are then
mapped to individual exons, and measures of transcriptional
expression (such as RPKM, or reads per kilobase per million reads
mapped), are quantified. Raw sequences and exon array data are
available from sources such as TCGA, ICGC, and the NCBI Gene
Expression Omnibus (GEO). For a given sample, individual exon
coordinates are annotated with gene identifier information, and
exons belonging to kinase domains are flagged. The exon levels are
then z-score normalized across all tumors samples.
[0072] Next, genes in which 5' exons are expressed at significantly
different levels than 3' exons are identified. A sliding frame is
used to identify the breakpoint within an individual sample.
Specifically, at each iteration, an incremental breakpoint divides
the gene into 5' and 3' regions, and a t-statistic is used to
measure the difference in expression (if any) between the two
regions. The breakpoint with the maximal t-statistic is chosen as
the likely fusion breakpoint. As used herein, "breakpoint" is the
boundary at which two different genes are fused. It is sometimes
referred to as a "fusion point." The location where the difference
in exon expression is maximal between 5' and 3' is the inferred
breakpoint of the fusion. Thousands of tumor samples can be rapidly
profiled in this manner, generating a list of fusion candidates
(ranked by t-statistic). High-ranking candidates can then be
validated, and fusion partners identified by examining the raw
RNA-seq data sets, and identifying chimeric pairs and/or split
reads which support the fusion. Candidate fusions can then be
experimentally confirmed as described below.
[0073] Alternatively, the methods described in Wang L et al., Genes
Chromosomes Cancer 51(2):127-39 (2012). doi: 10.1002/gcc.20937,
Epub 2011 Oct. 27; and Suehara Y et al., Clin Cancer Res.
18(24):6599-608 (2012). doi: 10.1158/1078-0432.CCR-12-0838, Epub
2012 Oct. 10 can also be used.
[0074] It has been proposed that the inclusion of a pharmacodynamic
assessment of molecularly targeted therapies in clinical trials can
streamline the drug development process (Tan D S et al., Cancer J
15(5):406-20 (2009); Sarker D & Workman P. Adv Cancer Res
96:213-68 (2007)). Pharmacodynamic biomarkers have been
successfully utilized for the clinical development of kinase
inhibitors, including imatinib and gefitinib (Sarker D &
Workman P. Adv Cancer Res 96:213-68 (2007); Baselga J et al., J
Clin Oncol 23(23):5323-33 (2005); Druker B J et al., N Engl J Med
344(14):1031-7 (2001)). As described herein, Compound 1
dose-dependently inhibited RET and SHC activation, which mirrored
the inhibition of DUSP6 and SPRY4 transcription across RET-driven
preclinical models, indicating that these transcripts can serve as
biomarkers for RET inhibitory activity. The translational
capability of these markers was established in this study in which
MTC tumor shrinkage induced by Compound 1 treatment was associated
with efficient inhibition of DUSP6 and SPRY4 expression within the
tumor tissue. To Applicant's knowledge, this represents the first
confirmation of RET target engagement by a small molecule
inhibitor, multi-targeted or selective, within the clinical
setting. These effect markers may be used to more precisely define
the optimal dose and schedule required for effective RET
inhibition.
[0075] While it is possible for Compound 1 to be administered
alone, in some embodiments, Compound 1 can be administered as a
pharmaceutical formulation, wherein Compound 1 is combined with one
or more pharmaceutically acceptable excipients or carriers.
Compound 1 may be formulated for administration in any convenient
way for use in human or veterinary medicine. In certain
embodiments, the compound included in the pharmaceutical
preparation may be active itself, or may be a prodrug, e.g.,
capable of being converted to an active compound in a physiological
setting.
[0076] The phrase "pharmaceutically acceptable" is employed herein
to refer to those compounds, materials, compositions, and/or dosage
forms which are, within the scope of sound medical judgment,
suitable for use in contact with the tissues of human beings and
animals without excessive toxicity, irritation, allergic response,
or other problem or complication, commensurate with a reasonable
benefit/risk ratio.
[0077] Examples of pharmaceutically acceptable carriers include:
(1) sugars, such as lactose, glucose, and sucrose; (2) starches,
such as corn starch and potato starch; (3) cellulose and its
derivatives, such as sodium carboxymethyl cellulose, ethyl
cellulose, and cellulose acetate; (4) powdered tragacanth; (5)
malt; (6) gelatin; (7) talc; (8) excipients, such as cocoa butter
and suppository waxes; (9) oils, such as peanut oil, cottonseed
oil, safflower oil, sesame oil, olive oil, corn oil, and soybean
oil; (10) glycols, such as propylene glycol; (11) polyols, such as
glycerin, sorbitol, mannitol, and polyethylene glycol; (12) esters,
such as ethyl oleate and ethyl laurate; (13) agar, (14) buffering
agents, such as magnesium hydroxide and aluminum hydroxide; (15)
alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18)
Ringer's solution; (19) ethyl alcohol; (20) phosphate buffer
solutions; (21) cyclodextrins such as Captisol.RTM.; and (22) other
non-toxic compatible substances employed in pharmaceutical
formulations.
[0078] Examples of pharmaceutically acceptable antioxidants
include: (1) water soluble antioxidants, such as ascorbic acid,
cysteine hydrochloride, sodium bisulfate, sodium metabisulfite,
sodium sulfite, and the like; (2) oil-soluble antioxidants, such as
ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated
hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol,
and the like; and (3) metal chelating agents, such as citric acid,
ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid,
phosphoric acid, and the like.
[0079] Solid dosage forms (e.g., capsules, tablets, pills, dragees,
powders, granules, and the like) can include one or more
pharmaceutically acceptable carriers, such as sodium citrate or
dicalcium phosphate, and/or any of the following: (1) fillers or
extenders, such as starches, lactose, sucrose, glucose, mannitol,
and/or silicic acid; (2) binders, such as, for example,
carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone,
sucrose, and/or acacia; (3) humectants, such as glycerol; (4)
disintegrating agents, such as agar-agar, calcium carbonate, potato
or tapioca starch, alginic acid, certain silicates, and sodium
carbonate; (5) solution retarding agents, such as paraffin; (6)
absorption accelerators, such as quaternary ammonium compounds; (7)
wetting agents, such as, for example, cetyl alcohol and glycerol
monostearate; (8) absorbents, such as kaolin and bentonite clay;
(9) lubricants, such a talc, calcium stearate, magnesium stearate,
solid polyethylene glycols, sodium lauryl sulfate, and mixtures
thereof; and (10) coloring agents.
[0080] Liquid dosage forms can include pharmaceutically acceptable
emulsions, microemulsions, solutions, suspensions, syrups, and
elixirs. In addition to the active ingredient, the liquid dosage
forms may contain inert diluents commonly used in the art, such as,
for example, water or other solvents, solubilizing agents and
emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl
carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate,
propylene glycol, 1,3-butylene glycol, oils (in particular,
cottonseed, groundnut, corn, germ, olive, castor and sesame oils),
glycerol, tetrahydrofuryl alcohol, polyethylene glycols, and fatty
acid esters of sorbitan, and mixtures thereof.
[0081] Suspensions, in addition to the active compounds, may
contain suspending agents as, for example, ethoxylated isostearyl
alcohols, polyoxyethylene sorbitol and sorbitan esters,
microcrystalline cellulose, aluminum metahydroxide, bentonite,
agar-agar and tragacanth, and mixtures thereof.
[0082] Ointments, pastes, creams, and gels may contain, in addition
to an active compound, excipients, such as animal and vegetable
fats, oils, waxes, paraffins, starch, tragacanth, cellulose
derivatives, polyethylene glycols, silicones, bentonites, silicic
acid, talc, and zinc oxide, or mixtures thereof.
[0083] Powders and sprays can contain, in addition to an active
compound, excipients such as lactose, talc, silicic acid, aluminum
hydroxide, calcium silicates, and polyamide powder, or mixtures of
these substances. Sprays can additionally contain customary
propellants, such as chlorofluorohydrocarbons and volatile
unsubstituted hydrocarbons, such as butane and propane.
[0084] Dosage forms for the topical or transdermal administration
of Compound 1 include powders, sprays, ointments, pastes, creams,
lotions, gels, solutions, patches, and inhalants. The active
compound may be mixed under sterile conditions with a
pharmaceutically acceptable carrier, and with any preservatives,
buffers, or propellants that may be required.
[0085] When Compound 1 is administered as a pharmaceutical, to
humans and animals, it can be given per se or as a pharmaceutical
composition containing, for example, 0.1 to 99.5% (such as 0.5 to
90%) of active ingredient in combination with a pharmaceutically
acceptable carrier.
[0086] The formulations can be administered topically, orally,
transdermally, rectally, vaginally, parentally, intranasally,
intrapulmonary, intraocularly, intravenously, intramuscularly,
intraarterially, intrathecally, intracapsularly, intradermally,
intraperitoneally, subcutaneously, subcuticularly, or by
inhalation.
[0087] The present disclosure is further illustrated by the
following examples which should not be construed as further
limiting. The contents of all references cited throughout this
application are expressly incorporated herein by reference.
EXAMPLES
Example 1: DUSP6 and SPRY4 Expression Analysis
[0088] Cells were treated with the indicated compounds for 7 hours
before lysis with Buffer RLT (QIAGEN, Hilden, Germany) containing
1% .beta.-mercaptoethanol. Total RNA was isolated using the Rneasy
Plus Mini kit (QIAGEN, Hilden, Germany) according to the
manufacturer's instructions. First-strand cDNA was synthesized
using the SuperScript VILO Master Mix (Thermo Fisher Scientific,
Waltham, Mass.) according to the manufacturer's instructions.
Real-time qPCR was run on ViiA 7 Real Time PCR System (Thermo
Fisher Scientific). For qRT-PCR, the expression of the reference
gene glucuronidase beta (GUSB) was used to normalize expression of
the target genes DUSP6, SPRY4, and glycogen synthase kinase 3 beta
(GSK3B). Replicate qRT-PCR reactions were analyzed for each sample,
and QuantStudio Real-Time PCR software (Life Technologies,
Carlsbad, Calif.) normalized the average expression of DUSP6,
SPRY4, or GSK3B to the average expression of the reference gene
GUSB in each sample. FIGS. 1A-1C show relative transcript
expression of RET pathway targets DUSP6 and SPRY4 and AKT-pathway
target GSK3B 7 hours after treatment of L2C/ad cells (FIG. 1A),
MZ-CRC-1 cells (FIG. 1B), or TT MTC cells (FIG. 1C) with Compound 1
or cabozantinib. FIG. 2 shows relative transcript expression of
DUSP6, SPRY4 and GSK3B from KIF5B-RET NSCLC PDX. Tumors collected
at the indicated times (hours) after administration of last dose.
Data are the mean+SD. *P<0.05, **P<0.01, ***P<0.001,
2-sided Student's t-test. SD, standard deviation.
Example 2: Generation of KIF5B-RET Ba/F3 Cells and ENU Mutagenesis
Assays
[0089] The DNA encoding the amino acid sequence of human KIF5B-RET
variant 1 was placed in a lentivirus vector under a
doxycycline-inducible promoter to maximize expression with a
carboxyl-terminal FLAG epitope to facilitate immunodetection of the
fusion by anti-FLAG antibodies. Lentiviral-mediated gene
transduction was used to express KIF5B-RET in Ba/F3 cells,
KIF5B-RET dependent cells were selected by IL-3 withdrawal and
confirmed to express the KIF5B-RET fusion protein by immunoblot
analysis. To generate Ba/F3 cells carrying V804 substitutions, WT
KIF5B-RET Ba/F3 cells were mutagenized overnight with ENU and
plated in 96-well plates for a period of 2 weeks in the presence of
6 concentrations of MKIs (ponatinib, regorafenib, cabozantinib, or
vandetanib). The concentrations chosen ranged from
2.times.-64.times. the proliferation IC.sub.50 for each compound:
125 nM to 4 .mu.mol/L cabozantinib, 20 to 640 nM ponatinib, and 250
nM to 8 .mu.mol/L vandetanib. Genomic DNA was isolated from
resistant clones, and Sanger sequencing was used to identify those
that harbored substitutions. FIG. 3 shows antitumor activity of
Compound 1 compared with cabozantinib in KIF5B-RET V804L Ba/F3
allografts.
Example 3: Phase I Study
[0090] A phase I, first-in-human study (NCT03037385) to define the
maximum tolerated dose, safety profile, pharmacokinetics, and
preliminary anti-tumor activity of Compound 1 in advanced,
RET-altered NSCLC, MTC and other solid tumors was initiated. Prior
to study entry, written informed consent was obtained from all
patients for treatment with Compound 1 and collection of blood and
tumor samples for exploratory biomarker analyses to characterize
potential predictive biomarkers of safety and efficacy. Adult
patients (18 years of age) must have had advanced, unresectable
solid tumors, with an Eastern Cooperative Oncology Group
performance status of 0 to 2, and adequate bone marrow, hepatic,
renal, and cardiac function. Compound 1 was administered orally,
once daily, on a 4-week cycle using a Bayesian Optimal Interval
Design. At dose levels .gtoreq.120 mg, documented RET-alteration
was additionally required for study entry. Adverse events were
graded per Common Terminology Criteria for Adverse Events (CTCAE).
Radiographic response by computed tomography was evaluated RECIST
version 1.1 (European Journal of Cancer 45: 228-247 (2009)). Levels
of ctDNA in plasma were assessed using the PlasmaSELECT.TM.-R64 NGS
panel (Personal Genome Diagnostics, Baltimore, Md.). Serum
calcitonin levels in MTC patients were measured by ELISA (Medpace,
Cincinnati, Ohio). Tumor DUSP6/SPRY4 levels were analyzed by
qRT-PCR (Molecular MD, Portland, Oreg.).
Case Studies
[0091] Patient 1 was a 27-year-old patient with sporadic MTC
harboring multiple RET mutations (L629P, D631_R635DELINSG, and
V637R). The patient was tyrosine kinase inhibitor naive prior to
the start of Compound 1 treatment with highly invasive disease that
required emergent tracheostomy and extensive surgery, including
total thyroidectomy, central neck dissection, bilateral levels 1
through 4 neck dissection, total thymectomy, and median sternotomy.
The postoperative course was complicated by chylothorax.
Multidisciplinary medical consensus was against radiotherapy to the
neck, and restaging scans showed left paratracheal disease with
tracheal and esophageal invasion as well as metastatic disease to
the lungs and liver. The two FDA approved multi-kinase drugs for
MTC (vandetanib and cabozantinib) were not considered appropriate
for this patient given the associated risk of VEGFR-related
toxicities that can include impaired wound healing, and increase
the risk of fistula formation and hemorrhage (CAPRELSA (vandetanib)
[package insert]. Cambridge, Mass.: Sanofi Genzyme; 2016; COMETRIQ
(cabozantinib) [package insert]. South San Francisco, Calif.:
Exelixix, Inc.; 2018). Therefore, the patient was enrolled on the
Compound 1 clinical trial and began treatment at the second dose
level (60 mg, QD). Remarkably, after 28 days of Compound 1 therapy,
there was a >90% reduction in the serum tumor marker calcitonin
(FIG. 4A). After 8 weeks, target lesions were reduced by 19%. After
successive dose escalations of Compound 1 to 200 mg QD, the patient
achieved partial response with >30% tumor reduction per Response
Evaluation Criteria in Solid Tumors (RECIST) version 1.1 (FIG. 4B).
This patient subsequently escalated to 300 mg QD Compound 1 and
achieved a confirmed partial response (47% maximal reduction) at 10
months. Overall, carcinoembryonic antigen (CEA) levels decreased by
57% over this period. Improved health status with Compound 1
treatment allowed for removal of the patient's tracheostomy tube
and a return to baseline body weight after several kilograms of
weight loss prior to treatment. Compound 1 has been well tolerated
throughout II months of continuous treatment with the only
drug-related adverse event being transient grade 1 decrease in
white blood cells, which resolved without drug interruption or dose
modification. As of Apr. 13, 2018, the patient remains on
therapy.
[0092] Patient 2 was a 56-year-old with sporadic RET M918T-mutant
MTC, who had responded and then progressed on vandetanib, initiated
therapy with Compound 1, 300 mg QD. Early signals of clinical
activity emerged within the first few weeks of Compound 1
treatment: serum calcitonin decreased >90% and CEA decreased by
75% after 28 days (FIG. 4C). RET M918T circulating tumor DNA
(ctDNA) decreased by 47% after 28 days and was not detectable after
56 days. Paired tumor biopsies collected pretreatment and 28 days
post-treatment demonstrated a 93% reduction in DUSP6 and an 86%
reduction in SPRY4 mRNA expression, confirming RET-pathway
inhibition within the tumor (FIG. 4E). Importantly, these
indications of activity were confirmed by radiographic response
(-35%) per RECIST 1.1 after 8 weeks (FIG. 4D). The patient
tolerated Compound 1 treatment well without dose interruption;
drug-related adverse events were grade 1 nausea and
hyperphosphatemia. The patient continues on therapy at 8 months
with a confirmed partial response (maximum 47% reduction) as of
Apr. 13, 2018.
[0093] Patient 3 was a 37-year-old patient with metastatic
RET-altered NSCLC, who had progressed on cisplatin, pemetrexed, and
bevacizumab, had tumor tissue test positive for a RET fusion via
FISH analysis. The patient initiated treatment with 200 mg QD
Compound 1, and ctDNA analysis at baseline revealed a canonical
KIF5B-RET fusion and co-occurring TP53 mutation. Tumor reduction
(-25%) was noted at first radiographic assessment after 8 weeks of
treatment and correlated with a concomitant decline in KIF5B-RET
and TP53 ctDNA levels (FIG. 5A). The patient achieved a partial
response on the second radiographic assessment after 16 weeks (FIG.
5B) and continues on treatment through 10 months with a confirmed
partial response as of Apr. 13, 2018. As observed with the MTC
patients described above, Compound 1 has been well tolerated, with
all drug-related adverse events being grade 1 and including
constipation (resolved), dry skin, rash, and leukopenia.
[0094] Patient 4 was a 69-year-old patient with NSCLC, who had
prior lung resection nephrectomy, and pleural drainage. The patient
initiated treatment with 400 mg QD Compound 1. Tumor reduction was
noted against KIF5B-RET NSCLC brain metastases (FIG. 9).
Specifically, evidence of intracranial anti-tumor activity was
observed in the patient. At baseline, the patient had an
approximately 6 mm metastatic lesion in the brain, which appeared
to resolve after 8 weeks on treatment. At the time of the 8-week
assessment, the patient was determined to have stable disease.
[0095] Patient 5 was a 74-year-old former smoker with locally
advanced KIF5B-RET NSCLC. The patient's CT scans are shown in FIGS.
11A-11D. The patient had received concurrent chemoradiation with
cisplatin and pemetrexed, was then treated with carboplatin and
nab-paclitaxel and eventually progressed. Next generation
sequencing of the tumor tissue, along with FISH, revealed a
KIF5B-RET fusion, and the patient was enrolled on a clinical trial
testing a combination regimen of vandetanib and everolimus
(NCT01582191). The patient achieved a partial response, but
restaging scans performed after 11 cycles showed progressive
disease, which was associated with clinical symptoms of increasing
dyspnea and worsening performance status. The patient was then
enrolled on the phase 1 trial of Compound 1. After 16 weeks of
treatment with Compound 1 (300 mg QD), the patient had a partial
response with 34% reduction of tumor volume (FIGS. 11C and 11D) and
improvement of dyspnea and performance status. Compound 1 has been
well tolerated throughout treatment, and the patient has not
experienced drug-related adverse events as of Apr. 13, 2018.
[0096] Patient 6 was a 23-year old woman with PTC, sclerosing
variant (CCDC6-RET fusion), who presented 6 years ago with
symptomatic diffuse lung metastases requiring supplemental oxygen,
since diagnosis. She had progressed on sorafenib and lenvatinib.
She initiated treatment with Compound 1 at 400 mg once daily. FIG.
13 shows tumor reduction after 5 months of treatment with Compound
1. Within 5 months, she was weaned to room air.
Measuring ctDNA Levels
[0097] Levels of one example effect marker, ctDNA in plasma (e.g.,
KIF5B or TP53 ctDNA), may be assessed using the
PlasmaSELECT.TM.-R64 NGS panel (Personal Genome Diagnostics,
Baltimore, Md.). PlasmaSELECT.TM. 64 analyzes circulating tumor DNA
for genetic alterations in cancer. Specifically, PlasmaSELECT.TM.
64 evaluates a targeted panel of 64 well-characterized cancer
genes. Cell-free DNA is extracted from plasma and prepared using
proprietary methods that accommodate low abundance sample DNA.
Samples are then processed using a proprietary capture process and
high coverage next-generation sequencing.
Steady State Plasma Concentration, RET IC.sub.90 and Brain
IC.sub.90 (Predicted)
[0098] Blood samples were collected at pre-determined time points
from patients dosed with 30 to 600 mg Compound 1 orally once daily.
Plasma samples were analyzed for Compound 1 using a validated
liquid chromatography-tandem mass spectrometry (LC-MS/MS) method.
The plasma Compound 1 concentration-time data were graphed using
Phoenix WinNonlin.COPYRGT. (Version 6.4, Certara L. P.) or Graphpad
Prism (Version 7.02). FIG. 6A shows the plasma concentration-time
profile of Compound 1 at steady state. The RET IC.sub.90 and brain
IC.sub.90 (predicted) are based on projections and extrapolations
based on PK and PD data in animals.
[0099] A twice a day (BID) dosing schedule was also explored as
part of the phase I clinical trial. The BID dosing schedule started
at a 300 mg total daily dose (200 mg in the morning, 100 mg in the
evening). A total of 9 patients were enrolled into the BID dose
escalation: 4 patients at 300 mg total daily dose (200 mg in the
morning, 100 mg in the evening) and 5 patients at 200 mg total
daily dose (100 mg BID). Of the first 4 patients enrolled at the
300 mg total daily dose, 2 patients experienced dose limiting
toxicities (DLTs) of Grade 3 hypertension and the dose was
subsequently de-escalated to 100 mg BID. Two of 5 patients at 100
mg BID experienced DLTs, including 1 patient with Grade 3
hypertension and 1 patient with Grade 3 tumor lysis syndrome. Based
on overall safety, exposure, and tolerability, QD was the superior
dosing schedule and chosen for the dose expansion.
[0100] All publications and patents mentioned herein are hereby
incorporated by reference in their entirety.
* * * * *
References