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WO 2014/004376 A2 3 January 2014 (03.01.2014) P O P C T

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WO 2014/004376 A2 3 January 2014 (03.01.2014) P O P C T (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2014/004376 A2 3 January 2014 (03.01.2014) P O P C T (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every A61K 31/047 (2006.01) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (21) International Application Number: BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, PCT/US20 13/047320 DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, (22) International Filing Date: HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KN, KP, KR, 24 June 2013 (24.06.2013) KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, (25) Filing Language: English OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SC, (26) Publication Language: English SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: 61/664,279 26 June 2012 (26.06.2012) (84) Designated States (unless otherwise indicated, for every 61/824,672 17 May 2013 (17.05.2013) kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, (71) Applicant: DEL MAR PHARMACEUTICALS UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, [CA/CA]; 999 West Broadway, Suite 720, Vancouver, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, British Columbia V57 1K5 (CA). EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, FT, LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, (72) Inventors; and TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, (71) Applicants : BROWN, Dennis M. [US/US]; 3475 Edison KM, ML, MR, NE, SN, TD, TG). Way, Suite R, Menlo Park, California 94025 (US). BACHA, Jeffrey A. [CA/CA]; c/o Del Mar Pharmaceutic Published: als, Suite 115, Vancouver, British Columbia V5T 4T5 — without international search report and to be republished (CA). GARNER, William J. [US/US]; 1701 Jackson upon receipt of that report (Rule 48.2(g)) Street, #102, San Francisco, California 94109 (US). (74) Agents: DITTHAVONG MORI & STEINER P.C. et al; 44 Canal Center Plaza, Suite 322, Alexandria, Virginia 22314 (US). < (54) Title: METHODS FOR TREATING TYROSINE-KINASE-INHIBITOR-RESISTANT MALIGNANCIES IN PATIENTS WITH GENETIC POLYMORPHISMS OR AHIl DYSREGULATIONS OR MUTATIONS EMPLOYING DIANHYDROGALACTITOL, DIACETYLDIANHYD ROGALACTITOL, DIBROMODULCITOL, OR ANALOGS OR DERIVATIVES THEREOF o (57) Abstract: Methods and compositions suitable for the treatment of malignancies in subjects with a germline deletion polymorph o ism that blocks the activity of thymidine kinase inhibitors in triggering apoptosis in tumor cells or in subjects having a mutation in or a dysregulation of the AHIl gene are disclosed. These methods employ an alkylating hexitol derivative such as dianhydrogalactitol, a derivative or analog of dianhydrogalactitol, diacetyldianhydrogalactitol, a derivative or analog of diacetyldianhydrogalactitol, dibro - modulcitol, and a derivative or analog of dibromodulcitol. The compositions can include such alkylating hexitol derivatives. The methods can further include administration of a BH3 mimetic, and the compositions can further include a BH3 mimetic. In subjects having a dysregulation of the AHIl gene, the methods can further include the administration of an agent modulating the expression or activity of the AHIl gene or AHIl protein, and the compositions can further include such an agent. METHODS FOR TREATING TYROSINE-KINASE-INHIBITOR-RESISTANT MALIGNANCIES IN PATIENTS WITH GENETIC POLYMORPHISMS OR AHI1 DYSREGULATIONS OR MUTATIONS EMPLOYING DIANHYDROGALACTITOL, DIACETYLDIANHYDROGALACTITOL, DIBROMODULCITOL, OR ANALOGS OR DERIVATIVES THEREOF CROSS-REFERENCES [0001] This application claims the benefit of Provisional Application Serial No. 61/824,672 by D.M. Brown et al., entitled "Methods for Treating Tyrosine-Kinase- Inhibitor-Resistant Malignancies in Patients with Genetic Polymorphisms Employing Dianhydrogalactitol, Diacetyldianhydrogalactitol, Dibromodulcitol or Analogs or Derivatives Thereof," and filed on May 17, 2013, the contents of which are hereby incorporated by this reference, and of Provisional Application Serial No. 61/664,279 by D.M. Brown et al., entitled "Methods for Treating Tyrosine-Kinase-lnhibitor-Resistant Malignancies in Patients with Genetic Polymorphisms Employing Dianhydrogalactitol, Diacetyldianhydrogalactitol, Dibromodulcitol or Analogs or Derivatives Thereof," and filed on June 26, 2012, the contents of which are hereby incorporated by this reference. FIELD OF THE INVENTION [0002] The present invention is directed to methods for treating tyrosine-kinase- inhibitor resistant malignancies in patients with genetic polymorphisms, methods for treating malignancies where resistance is mediated by expression of the AHI1 gene, or methods for treating triple-negative breast cancer, employing dianhydrogalactitol, diacetyldianhydrogalactitol, dibromodulcitol, or analogs or derivatives thereof, as well as pharmaceutical compositions for treating tyrosine-kinase-inhibitor resistant malignancies in patients with genetic polymorphisms, malignancies where resistance is mediated by expression of the AHI1 gene, or triple-negative breast cancer. BACKGROUND OF THE INVENTION [0003] The use of tyrosine kinase inhibitors (TKIs) has been responsible for effective therapeutic responses in patients presenting with a range of malignancies believed to be driven by the activity of oncogenic kinases (P.A. Janne et al., "Factors Underlying Sensitivity of Cancers to Small-Molecule Kinase Inhibitors," Nat. Rev. Drug Discov. 8 : 709-723 (2009), incorporated herein by this reference). However, before the use of TKIs, such malignancies were generally regarded as highly chemoresistant, as exemplified by breakpoint cluster region (BCR)-c-abl oncogene 1, non-receptor tyrosine kinase (ABL1 ) kinase-driven chronic myelocytic leukemia (CML) and EGFR non-small- cell lung carcinoma (NSCLC) (A.M. Carella et al., "New Insights in Biology and Current Therapeutic Options for Patients with Chronic Myelogenous Leukemia," Haematologica 82: 478-495 (1997) and J.H. Schiller et al., "Comparison of Four Chemotherapy Regimens for Advanced Non-Small-Cell Lung Cancer," New Engl. J. Med. 346: 92-98 (2002), both of which are incorporated herein by this reference). After the advent and clinical use of TKIs, treatment responses in both of these malignancies typically approached 80% (V.L. Keedy et al., "American Society of Clinical Oncology Provisional Clinical Opinion: Epidermal Growth Factor Receptor (EGFR) Mutation Testing for Patients with Advanced Non-Small-Cell Lung Cancer Considering First-Line EGFR Tyrosine Kinase Inhibitor Therapy," J. Clin. Oncol. 29: 2121-2127 (201 1) and M . Baccarani et al., "Chronic Myeloid Leukemia: An Update of Concepts and Management Recommendations of European LeukemiaNet" J. Clin. Oncol. 27: 6041-6051 (2009), both of which are incorporated herein by this reference). [0004] However, as effective as TKIs have proven to be in treating a number of types of malignancy that had previously been considered untreatable by chemotherapy, there is a significant proportion of patients that is resistant to TKI chemotherapy. Many of these patients are of East Asian ancestry, suggesting the existence of genetic variations that may cause resistance to TKI chemotherapy. [0005] Therefore, there is an urgent need for therapeutic methods and pharmaceutical compositions that can treat malignancies in patients resistant to TKI chemotherapy. [0006] Additionally, there are other malignancies, particularly, but not limited to, chronic lymphocytic leukemia, that are associated with the AHI1 gene, particularly with mutation or dysregulation of the AHI1 gene. The AHI1 gene is a gene that encodes a modular protein with WD40 repeat and SH3 domains. Insertion of provirus at the genomic location of this gene is associated with the development of malignancy, possibly by the expression of truncated forms of the gene (X. Jiang et al., "Ahi-1, a Novel Gene Encoding a Modular Protein with WD40-Repeat and SH3 Domains, Is Targeted by the Ahi-1 and Mis-2 Provirus Insertions," J. Virol. 76: 9046-9059 (2002), incorporated herein by this reference). Human leukemias that are Philadelphia chromosome-positive (Ph+) also show deregulated expression of the AHI1 gene (X. Jiang et al., "Deregulated Expression in Ph+ Human Leukemias of AHI-1, a Gene Activated by Insertional Mutagenesis in Mouse Models of Leukemia," Blood 103: 3897- 3904 (2004), incorporated herein by this reference. [0007] Therefore, there is an urgent need for improved methods to treat malignancies associated with mutation or dysregulation of the AHI1 gene, particularly leukemias. [0008] Additionally, triple-negative breast cancer is a form of breast cancer that is characterized by tumors that do not express estrogen receptor (ER), progesterone receptor (PR), or HER-2 genes. This form of breast cancer represents an important clinical challenge because these cancers do not respond to endocrine therapy or a number of targeted agents. Current treatment strategies for triple-negative breast cancer include many chemotherapy agents, such as the anthracyclines, taxanes, ixabepilone, and platinum agents, as well as selected biologic agents and possibly anti- EGFR drugs. [0009] However, there is also an urgent need for improved methods to treat
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