Patent Application
20190374528
The Ubiquitin-Proteasome Pathway (UPP) is a critical pathway that regulates protein homeostasis and degrades misfolded or abnormal proteins. UPP is central to multiple cellular processes, and if defective or imbalanced, leads to pathogenesis of a variety of diseases. The covalent attachment of ubiquitin to specific protein substrates is achieved through the action of E3 ubiquitin ligases. These ligases comprise over 500 different proteins and are categorized into multiple classes defined by the structural element of their E3 functional activity. For example, cereblon (CRBN) interacts with damaged DNA binding protein 1 and forms an E3 ubiquitin ligase complex with Cullin 4 in which the proteins recognized by CRBN are ubiquitinated and degraded by proteasomes. Various immunomodulatory drugs (IMiDs), e.g., thalidomide and lenalidomide, binds to CRBN and modulates CRBN's role in the ubiquitination and degradation of proteins involved in maintaining regular cellular function.
Bifunctional compounds composed of a target protein-binding moiety and an E3 ubiquitin ligase-binding moiety have been shown to induce proteasome-mediated degradation of selected proteins. These drug-like molecules offer the possibility of temporal control over protein levels, and could be useful as biochemical reagents for the treatment of diseases.
Protein kinases are a class of enzymes that catalyze the transfer of the terminal phosphate of adenosine triphosphate to amino acid residues in protein substrates. Protein kinases are a large family of proteins which play a critical role in the regulation of a wide variety of cellular processes and functions. The protein kinase family includes, kinases such as abl, Akt, bcr-abl, Blk, Brk, c-kit, c-met, c-src, CDK1, CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, cRafl, CSK, EGFR, ErbB2, ErbB3, ErbB4, Erk, Pak, fes, FGFR1, FGFR2, FGFR3, FGFR4, FGFR5, Fgr, fit-1, Fps, Frk, Fyn, Hck, IGF-1R, INS-R, Jak, KDR, Lck, Lyn, MEK, p38, PDGFR, PIK, PKC, PYK2, ros, tie, tie2, TRK and Zap70. Abnormal protein kinase activity has been related to numerous disorders, including psoriasis, cancers, bone disorders, metabolic disorders, inflammatory disorders, and other diseases.
Compounds which inhibit the function of protein kinases via alternative strategies, such as through degradation of protein kinases, have the potential to be more potent than known inhibitors of protein kinases, and are needed. The present application addresses that need.
The present application relates to novel bifunctional compounds, which function to recruit targeted proteins to E3 ubiquitin ligase for ubiquitination and degradation, and methods of preparation and uses thereof. The bifunctional compound is of Formula X:
wherein:
the Targeting Ligand is capable of binding to at least one targeted protein, such as a protein kinase;
the Linker is a group that covalently binds to the Targeting Ligand and the Degron; and
the Degron is capable of binding to a ubiquitin ligase, such as an E3 ubiquitin ligase (e.g., cereblon).
The present application also relates to targeted degradation of proteins through the use of bifunctional compounds, including bifunctional compounds that link an E3 ubiquitin ligase-binding moiety to a ligand that binds the targeted proteins.
The present application also relates to a bifunctional compound of Formula I:
or an enantiomer, diastereomer, stereoisomer, or pharmaceutically acceptable salt thereof, wherein:
R1, R2, R3, R4, R5, Y1, n1, n2, n3, n4, and n5 are each as defined herein;
the Linker is a group that covalently binds to
the Degron is capable of binding to a ubiquitin ligase, such as an E3 ubiquitin ligase (e.g., cereblon); and
the Targeting Ligand is capable of binding to at least one targeted proteins, such a protein kinase.
The present application further relates to a Degron of Formula D1 or D2:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein Y, Z3, R28, R29, R30, R31, R32, R33, v, q, and q′ are each as defined herein, and the Degron covalently binds to a Linker via
The present application further relates to a Linker of Formula L1 or L2:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein p1, p2, p3, p4, p4′, p5, p6, W, W1, W2, W3, Q1, Q2, Z1, and Z2 are each as defined herein, the Linker is covalently bonded to a Degron via the
next to Q1 or Q2, and covalently bonded to a Targeting Ligand via the
next to Z1 or Z2.
The present application also relates to a pharmaceutical composition comprising a therapeutically effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
Another aspect of the present application relates to a method of inhibiting at least one protein kinase. The method comprises administering to a subject in need thereof an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application. In some embodiments, the bifunctional compound inhibits more than one protein kinase. In some embodiments, the protein kinase is Bcr-Abl.
Another aspect of the present application relates to a method of modulating (e.g., decreasing) the amount of at least one protein kinase. The method comprises administering to a subject in need thereof a therapeutically effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application. In some embodiments, the bifunctional compound modulates more than one protein kinase. In some embodiments, the protein kinase is Bcr-Abl.
Another aspect of the present application relates to a method of inhibiting Bcr-Abl. The method comprises administering to a subject in need thereof an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application.
Another aspect of the present application relates to a method of modulating (e.g., decreasing) the amount of Bcr-Abl. The method comprises administering to a subject in need thereof an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application.
Another aspect of the present application relates to a method of treating a disease (e.g., a disease in which one or more protein kinases (e.g., Bcr-Abl) play a role). The method comprises administering to a subject in need thereof an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application. In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In some embodiments, the method treats a disease in which Bcr-Abl plays a role.
Another aspect of the present application relates to a method of preventing a disease (e.g., a disease in which one or more protein kinases (e.g., Bcr-Abl) play a role). The method comprises administering to a subject in need thereof an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application. In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In some embodiments, the method prevents a disease in which Bcr-Abl plays a role.
Another aspect of the present application relates to a method of treating cancer in a subject, wherein the cancer cell comprises one or more activated protein kinases or wherein the subject is identified as being in need of inhibition of one more protein kinases for the treatment of cancer. The method comprises administering to the subject an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application. In some embodiments, the cell comprises more than one activated protein kinase. In some embodiments, the activated protein kinase is Bcr-Abl.
Another aspect of the present application relates to a method of preventing cancer in a subject, wherein the cancer cell comprises one or more activated protein kinases or wherein the subject is identified as being in need of inhibition of one more protein kinases for the prevention of cancer. The method comprises administering to the subject an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application. In some embodiments, the cell comprises more than one activated protein kinase. In some embodiments, the activated protein kinase is Bcr-Abl.
Another aspect of the present application relates to a method of treating cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment of cancer. The method comprises administering to the subject an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application.
Another aspect of the present application relates to a method of preventing cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the prevention of cancer. The method comprises administering to the subject an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application.
Another aspect of the present application relates to a kit comprising a bifunctional compound capable of inhibiting protein kinase activity of at least one protein kinase, selected from a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof. In some embodiments, the bifunctional compound inhibits more than one protein kinase. In some embodiments, the bifunctional compound inhibits Bcr-Abl.
Another aspect of the present application relates to a kit comprising a bifunctional compound capable of inhibiting Bcr-Abl activity, selected from a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof.
Another aspect of the present application relates to a kit comprising a bifunctional compound capable of modulating (e.g., decreasing) the amount of at least one protein kinase, selected from a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof. In some embodiments, the bifunctional compound modulates more than one protein kinase. In some embodiments, the bifunctional compound modulates Bcr-Abl.
Another aspect of the present application relates to a kit comprising a bifunctional compound capable of modulating (e.g., decreasing) the amount of Bcr-Abl, selected from a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for inhibiting at least one protein kinase or for modulating (e.g., decreasing) the amount of protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of more than one protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of Bcr-Abl.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting at least one protein kinase or for modulating (e.g., decreasing) the amount of protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of more than one protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of Bcr-Abl.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for inhibiting Bcr-Abl or for modulating (e.g., decreasing) the amount of Bcr-Abl.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting Bcr-Abl or for modulating (e.g., decreasing) the amount of Bcr-Abl.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for treating a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for preventing a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for treating a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for preventing a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for treating cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the treatment of cancer.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for preventing cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the prevention of cancer.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for treating cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the treatment of cancer.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for preventing cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the prevention of cancer.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for treating cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment of cancer.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for preventing cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the prevention of cancer.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for treating cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment of cancer.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for preventing cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the prevention of cancer.
Another aspect of the present application relates to the use of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for inhibiting at least one protein kinase or modulating (e.g., decreasing) the amount of at least one protein kinase.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting at least one protein kinase or modulating (e.g., decreasing) the amount of at least one protein kinase.
Another aspect of the present application relates to the use a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for inhibiting Bcr-Abl or modulating (e.g., decreasing) the amount of Bcr-Abl.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting Bcr-Abl or modulating (e.g., decreasing) the amount of Bcr-Abl.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for inhibiting at least one protein kinase or modulating (e.g., decreasing) the amount of at least one protein kinase.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for inhibiting Bcr-Abl or modulating (e.g., decreasing) the amount of Bcr-Abl.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for treating a disease (e.g., a disease in which one or more protein kinases plays a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In some embodiments, the protein kinase is Bcr-Abl.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for preventing a disease (e.g., a disease in which one or more protein kinases plays a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In some embodiments, the protein kinase is Bcr-Abl.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for treating cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the treatment of cancer.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for preventing cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the prevention of cancer.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for treating cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment of cancer.
Another aspect of the present application relates to a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for preventing cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the prevention of cancer.
The present application provides inhibitors of protein kinases that are therapeutic agents in the treatment of diseases such as cancer and metastasis.
The present application provides inhibitors of protein kinases that are therapeutic agents in the prevention of diseases such as cancer and metastasis.
The present application further provides compounds and compositions with an improved efficacy and/or safety profile relative to known protein kinase inhibitors. The present application also provides agents with novel mechanisms of action toward protein kinases in the treatment of various types of diseases including cancer and metastasis.
The compounds and methods of the present application address unmet needs in the treatment of diseases or disorders in which pathogenic or oncogenic endogenous proteins (e.g., protein kinases) play a role, such as cancer.
The details of the application are set forth in the accompanying description below. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present application, illustrative methods and materials are now described. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting. Other features, objects, and advantages of the application will be apparent from the description and from the claims. In the specification and the appended claims, the singular forms also include the plural unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this application belongs.
The contents of all references (including literature references, issued patents, published patent applications, and co-pending patent applications) cited throughout this application are hereby expressly incorporated herein in their entireties by reference. The references cited herein are not admitted to be prior art to the application.
The present application relates to bifunctional compounds having utility as modulators of ubiquitination and proteosomal degradation of targeted proteins, especially compounds comprising a moiety capable of binding to a polypeptide or a protein that is degraded and/or otherwise inhibited by the bifunctional compounds of the present application. In particular, the present application is directed to compounds which contain a moiety, e.g., a small molecule moiety (e.g., having a molecular weight of below 2,000, 1,000, 500, or 200 Daltons), such as a thalidomide-like moiety, which is capable of binding to an E3 ubiquitin ligase, such as cereblon, and a ligand that is capable of binding to a target protein, in such a way that the target protein is placed in proximity to the ubiquitin ligase to effect degradation (and/or inhibition) of that protein.
The compounds of the present application can be used in methods to treat a variety of diseases including, but not limited to, metabolic disorders, bone diseases (e.g., osteoporosis, Paget's Disease, etc.), inflammation (e.g., rheumatoid arthritis and other inflammatory disorders) and cancer (e.g., solid tumors and leukemias, mediated by one or more kinases (e.g., Src or kdr), or by dysregulation of a kinase (e.g., Abl and mutant variants thereof)), including, among others, advanced cases and cases which are resistant to one or more other treatments.
In one embodiment, the present application provides a bifunctional compound of Formula X:
wherein:
the Targeting Ligand is capable of binding to at least one targeted protein, such as a protein kinase;
the Linker is a group that covalently binds to the Targeting Ligand and the Degron; and
the Degron is capable of binding to a ubiquitin ligase, such as an E3 ubiquitin ligase (e.g., cereblon).
In one embodiment, the present application provides a compound of Formula I:
or an enantiomer, diastereomer, stereoisomer, or pharmaceutically acceptable salt thereof, wherein:
R1, R2, R3, R4, R5, Y1, n1, n2, n3, n4, and n5 are each as defined herein;
the Linker is a group that covalently binds to
the Degron is capable of binding to a ubiquitin ligase, such as an E3 ubiquitin ligase (e.g., cereblon); and
the Targeting Ligand is capable of binding to at least one targeted proteins, such a protein kinase.
The present application further relates to a Degron of Formula D1:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein Y, Z3, R28, R29, R30, R31, q, and
v are each as defined herein, and the Degron covalently binds to a Linker via
The present application further relates to a Degron of Formula D2:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein R32, R33, and q′ are each as defined herein, and the Degron covalently binds to a Linker via
The present application further relates to a Linker of Formula L1:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein p1, p2, p3, W, Q1, and Z1 are each as defined herein, the Linker is covalently bonded to a Degron via the
next to Q1, and covalently bonded to a Targeting Ligand via the
next to Z1.
The present application further relates to a Linker of Formula L2:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein p4, p4′, p5, p6, W1, W2, W3, Q2, and Z2 are each as defined herein, the Linker is covalently bonded to a Degron via the
next to Q2, and covalently bonded to the Targeting Ligand via the
next to Z2.
Targeting Ligand (TL) (or target protein moiety or target protein ligand or ligand) is a small molecule which is capable of binding to a target protein of interest, such a protein kinase.
In one embodiment, a Targeting Ligand is a compound of Formula TL-I:
or an enantiomer, diastereomer, stereoisomer, or pharmaceutically acceptable salt thereof, wherein:
Y1 is C(O)NR6 or NR6C(O);
each R1, each R3, and each R4 is independently (C1-C4) alkyl, (C1-C4) haloalkyl, (C1-C4) alkoxy, (C1-C4) haloalkoxy, halogen, OH, or NH2;
R2 is H, (C1-C4) alkyl, (C1-C4) haloalkyl, (C1-C4) alkoxy, or (C1-C4) haloalkoxy;
each R5 is independently (C1-C4) alkyl, (C1-C4) haloalkyl, (C1-C4) alkoxy, (C1-C4) haloalkoxy, halogen, C(O)(C1-C4) alkyl, or oxo;
R6 is H, (C1-C4) alkyl, or (C1-C4) haloalkyl;
n1, n2, n3, and n5 are each independently 0, 1, 2 or 3; and
n4 is 0, 1, or 2,
wherein the Targeting Ligand is bonded to the Linker via the
next to
In some embodiments, Y1 is C(O)NR6. In other embodiments, Y1 is NR6C(O).
In some embodiments, R6 is H, (C1-C3) alkyl, or (C1-C3) haloalkyl. In other embodiments, R6 is H or (C1-C4) alkyl. In other embodiments, R6 is H, methyl, ethyl, n-propyl, or i-propyl. In other embodiments, R6 is H, methyl or ethyl. In other embodiments, R6 is (C1-C4) alkyl. In other embodiments, R6 is methyl, ethyl, n-propyl, or i-propyl. In other embodiments, R6 is methyl or ethyl. In other embodiments, R6 is (C1-C4) alkyl or (C1-C4) haloalkyl. In other embodiments, R6 is H.
In some embodiments, each R1 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, (C1-C3) haloalkoxy, halogen, OH, or NH2. In other embodiments, each R1 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, or (C1-C3) haloalkoxy. In other embodiments, each R1 is independently halogen, OH, or NH2. In other embodiments, each R1 is independently (C1-C3) alkoxy or (C1-C3) haloalkoxy. In other embodiments, each R1 is independently (C1-C3) alkyl or (C1-C3) haloalkyl. In other embodiments, each R1 is independently methyl, ethyl, n-propyl, i-propyl, or (C1-C3) haloalkyl. In other embodiments, each R1 is independently methyl, ethyl, n-propyl, or i-propyl.
In some embodiments, R2 is H, (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, or (C1-C3) haloalkoxy. In other embodiments, R2 is (C1-C3) alkyl or (C1-C3) haloalkyl. In other embodiments, R2 is (C1-C3) alkoxy or (C1-C3) haloalkoxy. In other embodiments, R2 is (C1-C3) alkyl. In other embodiments, R2 is H or (C1-C3) alkyl. In other embodiments, R2 is methyl, ethyl, n-propyl, or i-propyl. In other embodiments, R2 is H, methyl, ethyl, n-propyl, or i-propyl. In other embodiments, R2 is H or methyl. In other embodiments, R2 is H.
In some embodiments, each R3 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, (C1-C3) haloalkoxy, halogen, OH, or NH2. In other embodiments, each R3 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, or (C1-C3) haloalkoxy. In other embodiments, each R3 is independently halogen, OH, or NH2. In other embodiments, each R3 is independently (C1-C3) alkoxy or (C1-C3) haloalkoxy. In other embodiments, each R3 is independently (C1-C3) alkyl or (C1-C3) haloalkyl. In other embodiments, each R3 is independently methyl, ethyl, n-propyl, i-propyl, or (C1-C3) haloalkyl. In other embodiments, each R3 is independently methyl, ethyl, n-propyl, or i-propyl. In other embodiments, each R3 is independently methyl or ethyl. In other embodiments, at least one R3 is methyl.
In some embodiments, each R4 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, (C1-C3) haloalkoxy, halogen, OH, or NH2. In other embodiments, each R4 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, or (C1-C3) haloalkoxy. In other embodiments, each R4 is independently halogen, OH, or NH2. In other embodiments, each R4 is independently (C1-C3) alkoxy or (C1-C3) haloalkoxy. In other embodiments, each R4 is independently (C1-C3) alkyl or (C1-C3) haloalkyl. In other embodiments, each R4 is independently methyl, ethyl, n-propyl, i-propyl, or (C1-C3) haloalkyl. In other embodiments, each R4 is independently (C1-C3) haloalkyl. In other embodiments, each R4 is independently CF3, CHCF2, CH2F, CH2CF3, or CF2CF3. In other embodiments, at least one R4 is CF3.
In some embodiments, each R5 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, (C1-C3) haloalkoxy, halogen, C(O)(C1-C4) alkyl, or oxo. In other embodiments, each R5 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, (C1-C3) alkoxy, or (C1-C3) haloalkoxy. In other embodiments, each R5 is independently halogen, C(O)(C1-C4) alkyl, or oxo. In other embodiments, each R5 is independently (C1-C3) alkoxy or (C1-C3) haloalkoxy. In other embodiments, each R5 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, halogen, C(O)(C1-C4) alkyl, or oxo. In other embodiments, each R5 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, C(O)(C1-C4) alkyl, or oxo. In other embodiments, each R5 is independently (C1-C3) alkyl, (C1-C3) haloalkyl, or oxo. In other embodiments, each R5 is independently (C1-C3) alkyl or (C1-C3) haloalkyl. In other embodiments, each R5 is independently methyl, ethyl, n-propyl, i-propyl, or (C1-C3) haloalkyl. In other embodiments, each R5 is independently methyl, ethyl, n-propyl, or i-propyl. In other embodiments, each R5 is independently methyl, ethyl, n-propyl, i-propyl, or oxo. In other embodiments, each R5 is independently methyl or oxo.
In some embodiments, n1 is 0. In other embodiments, n1 is 1. In other embodiments, n1 is 2. In other embodiments, n1 is 3. In other embodiments, n1 is 0 or 1. In other embodiments, n1 is 1 or 2. In other embodiments, n1 is 2 or 3. In other embodiments, n1 is 0, 1, or 2. In other embodiments, n1 is 1, 2, or 3.
In some embodiments, n2 is 0. In other embodiments, n2 is 1. In other embodiments, n2 is 2. In other embodiments, n2 is 3. In other embodiments, n2 is 0 or 1. In other embodiments, n2 is 1 or 2. In other embodiments, n2 is 2 or 3. In other embodiments, n2 is 0, 1, or 2. In other embodiments, n2 is 1, 2, or 3.
In some embodiments, n3 is 0. In other embodiments, n3 is 1. In other embodiments, n3 is 2. In other embodiments, n3 is 3. In other embodiments, n3 is 0 or 1. In other embodiments, n3 is 1 or 2. In other embodiments, n3 is 2 or 3. In other embodiments, n3 is 0, 1, or 2. In other embodiments, n3 is 1, 2, or 3.
In some embodiments, n4 is 0. In other embodiments, n4 is 1. In other embodiments, n4 is 2. In other embodiments, n4 is 0 or 1. In other embodiments, n4 is 1 or 2.
In some embodiments, n5 is 0. In other embodiments, n5 is 1. In other embodiments, n5 is 2. In other embodiments, n5 is 3. In other embodiments, n5 is 0 or 1. In other embodiments, n5 is 1 or 2. In other embodiments, n5 is 2 or 3. In other embodiments, n5 is 0, 1, or 2. In other embodiments, n5 is 1, 2, or 3.
Any of the groups described herein for any of Y1, R1, R2, R3, R4, R5, R6, n1, n2, n3, n4, and n5 can be combined with any of the groups described herein for one or more of the remainder of Y1, R1, R2, R3, R4, R5, R6, n1, n2, n3, n4, and n5, and may further be combined with any of the groups described herein for the Linker.
For a Targeting Ligand of Formula TL-I:
In one embodiment, the compound of Formula TL-I is of Formula TL-Ia, TL-Ib, TL-Ic, or TL-Id:
wherein R1, R2, R3, R4, R5, R6, n1, n2, n3, n4, and n5 are each as defined above in Formula TL-I, and each can be selected from any of the groups described above in Formula TL-I.
For a Targeting Ligand of Formula TL-Ia, TL-Ib, TL-Ic, or TL-Id:
R1, R2, R3, R4, R5, R6, n1, n2, n3, n4, and n5 can each be selected from any of the groups and combined as described above in Formula TL-I, TL-Ia, TL-Ib, TL-Ic, or TL-Id.
In other embodiments, the compound of Formula TL-I is of Formula TL-Ie:
wherein R1, R2, R3, R4, R5, R6, n1, n3, n4, and n5 are each as defined above in Formula TL-I, and each can be selected from any of the groups described above in Formula TL-I.
For a Targeting Ligand of Formula TL-Ie:
R1, R2, R3, R4, R5, R6, n1, n3, n4, and n5 can each be selected from any of the groups and combined as described above in Formula TL-I or TL-Ie.
In other embodiments, the compound of Formula TL-I is of Formula TL-If:
wherein R1, R2, R3, R4, R5, R6, n1, n4, and n5 are each as defined above in Formula TL-I, and each can be selected from any of the groups described above in Formula TL-I.
For a Targeting Ligand of Formula TL-If:
R1, R2, R3, R4, R5, R6, n1, n4, and n5 can each be selected from any of the groups and combined as described above in Formula TL-I or TL-If.
In other embodiments, the compound of Formula TL-I is of Formula TL-Ig:
wherein R3, R4, R6, and n4 are each as defined above in Formula TL-I, and each can be selected from any of the groups described above in Formula TL-I.
For a Targeting Ligand of Formula TL-Ig:
R3, R4, R6, and n4 can each be selected from any of the groups and combined as described above in Formula TL-I or TL-Ig.
In other embodiments, the compound of Formula TL-I is of Formula TL-Ih:
The Degron serves to link a targeted protein, through a Linker and a Targeting Ligand, to a ubiquitin ligase for proteosomal degradation. In one embodiment, the Degron is capable of binding to a ubiquitin ligase, such as an E3 ubiquitin ligase. In one embodiment, the Degron is capable of binding to cereblon.
In one embodiment, the Degron is of Formula D1:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein:
Y is a bond, (CH2)1-6, (CH2)0-6—O, (CH2)0-6—C(O)NR26, (CH2)0-6—NR2C(O), (CH2)0-6—NH, or (CH2)0-6—NR27;
Z3 is C(O) or C(R28)2;
R26 is H or C1-C6 alkyl;
R27 is C1-C6 alkyl or C(O)—C1-C6 alkyl;
each R28 is independently H or C1-C3 alkyl;
each R29 is independently C1-C3 alkyl;
R30 is H, deuterium, C1-C3 alkyl, F, or Cl;
each R31 is independently halogen, OH, C1-C6 alkyl, or C1-C6 alkoxy;
q is 0, 1, or 2; and
v is 0, 1, 2, or 3,
wherein the Degron is covalently bonded to the Linker via
In one embodiment, Z3 is C(O).
In one embodiment, Z3 is C(O) or CH2.
In one embodiment, Z3 is C(R28)2; and each R28 is H. In one embodiment, Z3 is C(R28)2; and one of R28 is H, and the other is C1-C3 alkyl selected from methyl, ethyl, and propyl. In one embodiment, Z3 is C(R28)2; and each R28 is independently selected from methyl, ethyl, and propyl.
In one embodiment, Y is a bond.
In one embodiment, Y is a bond, O, or NH.
In one embodiment, Y is (CH2)1, (CH2)2, (CH2)3, (CH2)4, (CH2)5, or (CH2)6. In one embodiment, Y is (CH2)1, (CH2)2, or (CH2)3. In one embodiment, Y is (CH2)1 or (CH2)2.
In one embodiment, Y is O, CH2—O, (CH2)2—O, (CH2)3—O, (CH2)4—O, (CH2)5—O, or (CH2)6—O. In one embodiment, Y is O, CH2—O, (CH2)2—O, or (CH2)3—O. In one embodiment, Y is O or CH2—O. In one embodiment, Y is O.
In one embodiment, Y is C(O)NR26, CH2—C(O)NR26, (CH2)2—C(O)NR26, (CH2)3—C(O)NR26, (CH2)4—C(O)NR26, (CH2)5—C(O)NR26, or (CH2)6—C(O)NR26. In one embodiment, Y is C(O)R26, CH2—C(O)NR26, (CH2)2—C(O)NR26, or (CH2)3—C(O)NR26. In one embodiment, Y is C(O)NR26 or CH2—C(O)NR26. In one embodiment, Y is C(O)NR26.
In one embodiment, Y is NR26C(O), CH2—NR26C(O), (CH2)2—NR26C(O), (CH2)3—NR26C(O), (CH2)4—NR26C(O), (CH2)5—NR26C(O), or (CH2)6—NR26C(O). In one embodiment, Y is NR26C(O), CH2—NR26C(O), (CH2)2—NR26C(O), or (CH2)3—NR26C(O). In one embodiment, Y is NR26C(O) or CH2—NR26C(O). In one embodiment, Y is NR26C(O).
In one embodiment, R26 is H. In one embodiment, R26 is selected from methyl, ethyl, propyl, butyl, i-butyl, t-butyl, pentyl, i-pentyl, and hexyl. In one embodiment, R26 is C1-C3 alkyl selected from methyl, ethyl, and propyl.
In one embodiment, Y is NH, CH2—NH, (CH2)2—NH, (CH2)3—NH, (CH2)4—NH, (CH2)5—NH, or (CH2)6—NH. In one embodiment, Y is NH, CH2—NH, (CH2)2—NH, or (CH2)3—NH. In one embodiment, Y is NH or CH2—NH. In one embodiment, Y is NH.
In one embodiment, Y is NR27, CH2—NR27, (CH2)2—NR27, (CH2)3—NR27, (CH2)4—NR27, (CH2)5—NR27, or (CH2)6—NR27. In one embodiment, Y is NR27, CH2—NR27, (CH2)2—NR27, or (CH2)3—NR27. In one embodiment, Y is NR27 or CH2—NR27. In one embodiment, Y is NR27.
In one embodiment, R27 is selected from methyl, ethyl, propyl, butyl, i-butyl, t-butyl, pentyl, i-pentyl, and hexyl. In one embodiment, R27 is C1-C3 alkyl selected from methyl, ethyl, and propyl.
In one embodiment, R27 is selected from C(O)-methyl, C(O)-ethyl, C(O)-propyl, C(O)-butyl, C(O)-i-butyl, C(O)-t-butyl, C(O)-pentyl, C(O)-i-pentyl, and C(O)-hexyl. In one embodiment, R27 is C(O)—C1-C3 alkyl selected from C(O)-methyl, C(O)-ethyl, and C(O)-propyl.
In one embodiment, R28 is H.
In one embodiment, R28 is C1-C3 alkyl selected from methyl, ethyl, and propyl. In one embodiment, R28 is methyl.
In one embodiment, q is 0.
In one embodiment, q is 1.
In one embodiment, q is 2.
In one embodiment, each R29 is independently C1-C3 alkyl selected from methyl, ethyl, and propyl.
In one embodiment, v is 0.
In one embodiment, v is 1.
In one embodiment, v is 2.
In one embodiment, v is 3.
In one embodiment, each R31 is independently selected from halogen (e.g., F, Cl, Br, and I), OH, C1-C6 alkyl (e.g., methyl, ethyl, propyl, butyl, i-butyl, t-butyl, pentyl, i-pentyl, and hexyl), and C1-C6 alkoxy (e.g., methoxy, ethoxy, propoxy, butoxy, i-butoxy, t-butoxy, and pentoxy). In a further embodiment, each R31 is independently selected from F, Cl, OH, methyl, ethyl, propyl, butyl, i-butyl, t-butyl, methoxy, and ethoxy.
In one embodiment, R30 is H, deuterium, or C1-C3 alkyl. In other embodiments, R30 is H or C1-C3 alkyl. In a further embodiment, R30 is in the (S) or (R) configuration. In a further embodiment, R30 is in the (S) configuration. In one embodiment, the compound comprises a racemic mixture of (S)—R30 and (R)—R30.
In one embodiment, R30 is H.
In one embodiment, R30 is deuterium.
In one embodiment, R30 is C1-C3 alkyl selected from methyl, ethyl, and propyl. In one embodiment, R30 is methyl.
In one embodiment, R30 is F or Cl. In a further embodiment, R30 is in the (S) or (R) configuration. In a further embodiment, R30 is in the (R) configuration. In one embodiment, the compound comprises a racemic mixture of (S)—R30 and (R)—R30. In one embodiment, R30 is F.
Any of the groups described herein for any of Y, Z3, R26, R27, R28, R29, R30, R31, q and v can be combined with any of the groups described herein for one or more of the remainder of Y, Z3, R26, R27, R28, R29, R30, R31, q and v, and may further be combined with any of the groups described herein for the Linker.
For a Degron of Formula D1:
In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein Y, R29, R31, q, and v are each as defined above in Formula D1, and can be selected from any moieties or combinations thereof described above.
In one embodiment, Y is a bond, O, or NH. In one embodiment, Y is a bond. In one embodiment, Y is O. In one embodiment, Y is NH.
In one embodiment, the Degron is of Formula D2:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein:
each R32 is independently C1-C3 alkyl;
q′ is 0, 1, 2, 3 or 4; and
R33 is H or C1-C3 alkyl,
wherein the Degron is covalently bonded to another moiety (e.g., a compound, or a Linker) via
In one embodiment, q′ is 0.
In one embodiment, q′ is 1.
In one embodiment, q′ is 2.
In one embodiment, q′ is 3.
In one embodiment, each R32 is independently C1-C3 alkyl selected from methyl, ethyl, and propyl.
In one embodiment, R33 is methyl, ethyl, or propyl. In one embodiment, R33 is methyl.
In one embodiment, the Degron is of Formula D2a:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein:
each R32 is independently C1-C3 alkyl;
q′ is 0, 1, 2, 3 or 4; and
R33 is H or C1-C3 alkyl,
wherein the Degron is covalently bonded to another moiety (e.g., a compound, or a Linker) via
In one embodiment, q′ is 0.
In one embodiment, q′ is 1.
In one embodiment, q′ is 2.
In one embodiment, q′ is 3.
In one embodiment, each R32 is independently C1-C3 alkyl selected from methyl, ethyl, and propyl.
In one embodiment, R33 is methyl, ethyl, or propyl. In one embodiment, R33 is methyl.
In one embodiment, the Degron is of Formula D2b:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein:
R33 is H or C1-C3 alkyl,
wherein the Degron is covalently bonded to another moiety (e.g., a compound, or a Linker) via
In one embodiment, q′ is 0.
In one embodiment, q′ is 1.
In one embodiment, q′ is 2.
In one embodiment, q′ is 3.
In one embodiment, each R32 is independently C1-C3 alkyl selected from methyl, ethyl, and propyl.
In one embodiment, R33 is methyl, ethyl, or propyl. In one embodiment, R33 is methyl.
In one embodiment, the Degron is of Formula D2c:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein:
wherein the Degron is covalently bonded to another moiety (e.g., a compound, or a Linker) via
In one embodiment, the Degron is of Formula D2d:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein:
wherein the Degron is covalently bonded to another moiety (e.g., a compound, or a Linker) via
The Linker is a bond, a carbon chain, carbocyclic ring, or heterocyclic ring that serves to link a Targeting Ligand with a Degron. In one embodiment, the carbon chain optionally comprises one, two, three, or more heteroatoms selected from N, O, and S. In one embodiment, the carbon chain comprises only saturated chain carbon atoms. In one embodiment, the carbon chain optionally comprises two or more unsaturated chain carbon atoms (e.g., CC or C
C). In one embodiment, one or more chain carbon atoms in the carbon chain are optionally substituted with one or more substituents (e.g., oxo, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C1-C3 alkoxy, OH, halogen, NH2, NH(C1-C3 alkyl), N(C1-C3 alkyl)2, CN, C3-C8 cycloalkyl, heterocyclyl, phenyl, and heteroaryl).
In one embodiment, the Linker comprises at least 5 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises less than 25 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises less than 20 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, or 24 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 5, 7, 9, 11, 13, 15, 17, or 19 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 5, 7, 9, or 11 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 11, 13, 15, 17, or 19 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 11, 13, 15, 17, 19, 21, or 23 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 6, 8, 10, 12, 14, 16, 18, 20, 22, or 24 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 6, 8, 10, 12, 14, 16, 18, or 20 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 6, 8, 10, or 12 chain atoms (e.g., C, O, N, and S). In one embodiment, the Linker comprises 12, 14, 16, 18, or 20 chain atoms (e.g., C, O, N, and S).
In one embodiment, the Linker comprises from 11 to 19 chain atoms (e.g., C, O, N, and S).
In one embodiment, the Linker is a carbon chain optionally substituted with non-bulky substituents (e.g., oxo, C1-C6 alkyl, C2-C6 alkenyl, C2-C6 alkynyl, C1-C3 alkoxy, OH, halogen, NH2, NH(C1-C3 alkyl), N(C1-C3 alkyl)2, and CN). In one embodiment, the non-bulky substitution is located on the chain carbon atom proximal to the Degron (e.g., the carbon atom is separated from the carbon atom to which the Degron is bonded by at least 3, 4, or 5 chain atoms in the Linker). In one embodiment, the non-bulky substitution is located on the chain carbon atom proximal to the Targeting Ligand (e.g., the carbon atom is separated from the carbon atom to which the Degron is bonded by at least 3, 4, or 5 chain atoms in the Linker).
In one embodiment, the Linker is of Formula L1:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein
p1 is an integer selected from 0 to 12;
p2 is an integer selected from 0 to 12;
p3 is an integer selected from 1 to 6;
each W is independently absent, CH2, O, S, or NR24;
Z1 is absent, C(O), CH2, O, (CH2)jNR24, O(CH2)jC(O)NR24, C(O)NR24, (CH2)jC(O)NR24, NR24C(O), (CH2)jNR24C(O), (CH2)kNR24(CH2)jC(O)NR24, or NR24(CH2)jC(O)NR24;
each R24 is independently H or C1-C3 alkyl;
j is 1, 2, or 3;
k is 1, 2, or 3; and
Q1 is absent, C(O), NHC(O)CH2, OCH2C(O), or O(CH2)1-2;
wherein the Linker is covalently bonded to a Degron via the
next to Q1, and covalently bonded to a Targeting Ligand via the
next to Z1.
In one embodiment, the total number of chain atoms in the Linker is less than 30. In a further embodiment, the total number of chain atoms in the Linker is less than 20.
For a Linker of Formula L1:
In one embodiment, the Linker-Targeting Ligand (TL) has the structure selected from Table L:
wherein Z1, W, Q1, TL, p1, p2, and p3 are each as described above.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L1a-L1q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L1a-L1c. In one embodiment, the Degron is of Formula D1, and the Linker is selected from L1d-L1f. In one embodiment, the Degron is of Formula D1, and the Linker is selected from L1g. In one embodiment, the Degron is of Formula D1, and the Linker is L1h-L1j. In one embodiment, the Degron is of Formula D1, and the Linker is L1k-L1m. In one embodiment, the Degron is of Formula D1, and the Linker is L1n. In one embodiment, the Degron is of Formula D1, and the Linker is L1o-L1q. In one embodiment, the Degron is of Formula D1, and the Linker is L1e, L1f, or L1q. In one embodiment, the Degron is of Formula D1, and the Linker is L1e or L1f. In one embodiment, the Degron is of Formula D1, and the Linker is L1q.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L1a-L1q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L1a-L1c. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L1d-L1f. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L1g. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is L1h-L1j. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is L1k-L1m. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is L1n. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is L1o-L1q. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is L1e, L1f, or L1q. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is L1e or L1f. In one embodiment, the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is L1q.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L1a-L1q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L1a-L1c. In one embodiment, the Degron is of Formula D2, and the Linker is selected from L1d-L1f. In one embodiment, the Degron is of Formula D2, and the Linker is selected from L1g. In one embodiment, the Degron is of Formula D2, and the Linker is L1h-L1j. In one embodiment, the Degron is of Formula D2, and the Linker is L k-L1 m. In one embodiment, the Degron is of Formula D2, and the Linker is L1 n. In one embodiment, the Degron is of Formula D2, and the Linker is L1o-L1q. In one embodiment, the Degron is of Formula D2, and the Linker is L1e, L1f, or L1q. In one embodiment, the Degron is of Formula D2, and the Linker is L1e or L1f. In one embodiment, the Degron is of Formula D2, and the Linker is L1q.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L1a-L1q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L1a-L1c. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is selected from L1d-L1f. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is selected from L1g. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is L1h-L1j. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is L1k-L1m. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is L1n. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is L1o-L1q. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is L1e, L1f, or L1q. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is L1e or L1f. In one embodiment, the Degron is of Formula D2a or D2b, and the Linker is L1q.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L1a-L1q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L1a-L1c. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is selected from L1d-L1f. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is selected from L1g. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is L1h-L1j. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is L1k-L1m. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is L1n. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is L1o-L1q. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is L1e, L1f, or L1q. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is L1e or L1f. In one embodiment, the Degron is of Formula D2c or D2d, and the Linker is L1 q.
In one embodiment, the Linker is of Formula L2:
or an enantiomer, diastereomer, or stereoisomer thereof, wherein
p4 and p4′ are each independently an integer selected from 0 to 12;
p5 is an integer selected from 0 to 12;
p6 is an integer selected from 1 to 6;
each W1 is independently absent, CH2, O, S, or NR25;
W2 is NR25C(O) or NR25C(O)(CH2)1-3C(O)NR25(CH2)1-4;
each W3 is independently absent, CH2, O, S, or NR25;
Z2 is absent, C(O), CH2, O, (CH2)j1NR25, O(CH2)j1C(O)NR25, C(O)NR25, (CH2)j1C(O)NR25, NR25C(O), (CH2)j1NR25C(O), (CH2)kNR25(CH2)j1C(O)NR25, or NR25(CH2)j1C(O)NR25;
each R25 is independently H or C1-C3 alkyl;
j1 is 1, 2, or 3;
k1 is 1, 2, or 3; and
Q2 is absent, C(O), NHC(O)CH2, or O(CH2)1-2;
wherein the Linker is covalently bonded to a Degron via the
next to Q2, and covalently bonded to a Targeting Ligand via the
next to Z2.
For a Linker of Formula L2:
In one embodiment, the Linker-Targeting Ligand (TL) has the structure selected from Table M:
wherein Z2, W1, W3, Q2, TL, R25, p4, p4′, p5, and p6 are each as described above.
Any one of the Degrons described herein can be covalently bound to any one of the Linkers described herein. Any one of the Targeting Ligands described herein can be covalently bound to any one of the Linkers described herein.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2a-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2a-L2c. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2d-L2f. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2g-L2i. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2j-L2l. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2m or L2n. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2o-L2q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2r-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1, and the Linker is selected from L2l, L2p, L2q, L2s, or L2t.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L2a-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L2a-L2c. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L2d-L2f. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D11, and the Linker is selected from L2g-L2i. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D11, and the Linker is selected from L2j-L2l. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L2m or L2n. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L2o-L2q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L2r-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D1a, D1b, D1c, D1d, D1e, D1f, D1g, D1h, D1i, D1j, D1k, or D1l, and the Linker is selected from L2l, L2p, L2q, L2s, or L2t.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2a-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2a-L2c. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2d-L2f. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2g-L2i. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2j-L2l. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2m or L2n. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2o-L2q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2r-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2, and the Linker is selected from L2l, L2p, L2q, L2s, or L2t.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2a-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2a-L2c. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2d-L2f. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2g-L2i. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2j-L2l. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2m or L2n. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2o-L2q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2r-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2a or D2b, and the Linker is selected from L2l, L2p, L2q, L2s, or L2t.
In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2a-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2a-L2c. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2d-L2f. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2g-L2i. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2j-L2l. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2m or L2n. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2o-L2q. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2r-L2t. In one embodiment, the present application relates to the Degron-Linker (DL), wherein the Degron is of Formula D2c or D2d, and the Linker is selected from L2l, L2p, L2q, L2s, or L2t.
In one embodiment, the Linker is designed and optimized based on SAR (structure-activity relationship) and X-ray crystallography of the Targeting Ligand with regard to the location of attachment for the Linker.
In one embodiment, the optimal Linker length and composition vary by the Targeting Ligand and can be estimated based upon X-ray structure of the Targeting Ligand bound to its target. Linker length and composition can be also modified to modulate metabolic stability and pharmacokinetic (PK) and pharmacodynamics (PD) parameters.
Some embodiments of present application relate to the bifunctional compounds having one of the following structures in Table A:
Some of the foregoing compounds can comprise one or more asymmetric centers, and thus can exist in various isomeric forms, e.g., stereoisomers and/or diastereomers. Accordingly, compounds of the application may be in the form of an individual enantiomer, diastereomer or geometric isomer, or may be in the form of a mixture of stereoisomers. In one embodiment, the compounds of the application are enantiopure compounds. In other embodiments, mixtures of stereoisomers or diastereomers are provided.
Furthermore, certain compounds, as described herein, may have one or more double bonds that can exist as either the Z or E isomer, unless otherwise indicated. The application additionally encompasses the compounds as individual Z/E isomers substantially free of other E/Z isomers and alternatively, as mixtures of various isomers.
In one embodiment, the present application relates to compounds that target proteins, such as protein kinases for degradation, which have numerous advantages over inhibitors of protein function (e.g., protein activity) and can a) overcome resistance in certain cases; b) prolong the kinetics of drug effect by destroying the protein, thus requiring resynthesis of the protein even after the compound has been metabolized; c) target all functions of a protein at once rather than a specific catalytic activity or binding event; d) expand the number of drug targets by including all proteins that a ligand can be developed for, rather than proteins whose activity (e.g., protein activity) can be affected by a small molecule inhibitor, antagonist or agonist; and e) have increased potency compared to inhibitors due to the possibility of the small molecule acting catalytically.
Some embodiments of the present application relate to degradation or loss of 30% to 100% of the target protein. Some embodiments relate to the loss of 50-100% of the target protein. Other embodiments relate to the loss of 75-95% of the targeted protein.
A bifunctional compound of the present application (e.g., a bifunctional compound of any of the formulae described herein, or selected from any bifunctional compounds described herein) is capable of modulating (e.g., decreasing) the amount of a targeted protein (e.g., a protein kinase). A bifunctional compound of the present application (e.g., a bifunctional compound of any of the formulae described herein, or selected from any bifunctional compounds described herein) is also capable of degrading a targeted protein (e.g., a protein kinase) through the UPP pathway. Accordingly, a bifunctional compound of the present application (e.g., a bifunctional compound of any of the formulae described herein, or selected from any bifunctional compounds described herein) is capable of treating or preventing a disease or disorder in which a protein kinase plays a role. A bifunctional compound of the present application (e.g., a bifunctional compound of any of the formulae described herein, or selected from any bifunctional compounds described herein) is also capable of treating or preventing a disease or disorder in which a protein kinase plays a role or in which a protein kinase is deregulated (e.g., overexpressed).
A bifunctional compound of the present application can be used for treating or ameliorating diseases in which kinases may be involved, symptoms of such disease, or the effect of other physiological events mediated by kinases. In some embodiments, bifunctional compound of the present application is capable of modulating and/or inhibiting the tyrosine kinase activity of Src and Abl, among other tyrosine kinases which are believed to mediate the growth, development and/or metastasis of cancer. In other embodiments, the bifunctional compound of the present application is capable of modulating and/or inhibiting the tyrosine kinase activity of Bcr-Abl.
Modulation of a protein kinase through UPP-mediated degradation by a bifunctional compound of the application, such as those described herein, provides a novel approach to the treatment, prevention, or amelioration of diseases or disorders in which a protein kinase plays a role including, but not limited to, cancer and metastasis, inflammation, arthritis, systemic lupus erthematosus, skin-related disorders, pulmonary disorders, cardiovascular disease, ischemia, neurodegenerative disorders, liver disease, gastrointestinal disorders, viral and bacterial infections, central nervous system disorders, Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, spinal cord injury, and peripheral neuropathy. Further, modulation of a protein kinase through UPP-mediated degradation by a bifunctional compound of the application, such as those described herein, also provides a new paradigm for treating, preventing, or ameliorating diseases or disorders in which a protein kinase is deregulated.
In one embodiment, a bifunctional compound of the present application (e.g., a bifunctional compound of any of the formulae described herein, or selected from any bifunctional compounds described herein) is more efficacious in treating a disease or condition (e.g., cancer) than, or is capable of treating a disease or condition resistant to, the Targeting Ligand, when the Targeting Ligand is administered alone (e.g., not bonded to a Linker and a Degron). In one embodiment, a bifunctional compound of the present application (e.g., a bifunctional compound of any of the formulae described herein, or selected from any bifunctional compounds described herein) is capable of modulating (e.g., decreasing) the amount of a protein kinase, and thus is useful in treating a disease or condition (e.g., cancer) in which a protein kinase plays a role.
In one embodiment, the bifunctional compound of the present application that is more efficacious in treating a disease or condition than, or is capable of treating a disease or condition resistant to, the Targeting Ligand, when the Targeting Ligand is administered alone (e.g., not bonded to a Linker and a Degron), is more potent in inhibiting the growth of cells (e.g., cancer cells) or decreasing the viability of cells (e.g., cancer cells), than the Targeting Ligand, when the Targeting Ligand is administered alone (e.g., not bonded to a Linker and a Degron). In one embodiment, the bifunctional compound inhibits the growth of cells (e.g., cancer cells) or decreases the viability of cells (e.g., cancer cells) at an IC50 that is lower than the IC50 of the Targeting Ligand (when the Targeting Ligand is administered alone (e.g., not bonded to a Linker and a Degron)) for inhibiting the growth or decreasing the viability of the cells. In one embodiment, the IC50 of the bifunctional compound is at most 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 8%, 5%, 4%, 3%, 2%, 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of the IC50 of the Targeting Ligand. In one embodiment, the IC50 of the bifunctional compound is at most 50%, 40%, 30%, 20%, 10%, 8%, 5%, 4%, 3%, 2%, 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of the IC50 of the Targeting Ligand. In one embodiment, the IC50 of the bifunctional compound is at most 30%, 20%, 10%, 8%, 5%, 4%, 3%, 2%, 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of the IC50 of the Targeting Ligand. In one embodiment, the IC50 of the bifunctional compound is at most 10%, 8%, 5%, 4%, 3%, 2%, 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of the IC50 of the Targeting Ligand. In one embodiment, the IC50 of the bifunctional compound is at most 5%, 4%, 3%, 2%, 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of the IC50 of the Targeting Ligand. In one embodiment, the IC50 of the bifunctional compound is at most 2%, 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of the IC50 of the Targeting Ligand. In one embodiment, the IC50 of the bifunctional compound is at most 1%, 0.8%, 0.5%, 0.4%, 0.3%, 0.2%, or 0.1% of the IC50 of the Targeting Ligand. In one embodiment, the bifunctional compound inhibits the growth of cells (e.g., cancer cells) or decreases the viability of cells (e.g., cancer cells) at an Emax that is lower than the Emax of the Targeting Ligand (when the Targeting Ligand is administered alone (e.g., not bonded to a Linker and a Degron)) for inhibiting the growth or decreasing the viability of the cells. In one embodiment, the Emax of the bifunctional compound is at most 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, 10%, 8%, 5%, 4%, 3%, 2%, or 1% of the Emax of the Targeting Ligand. In one embodiment, the Emax of the bifunctional compound is at most 50%, 40%, 30%, 20%, 10%, 8%, 5%, 4%, 3%, 2%, or 1% of the Emax of the Targeting Ligand. In one embodiment, the Emax of the bifunctional compound is at most 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, or 10% of the Emax of the Targeting Ligand.
In some embodiments, the inhibition of a protein kinase (e.g., Bcr-Abl) activity is measured by IC50.
In some embodiments, the inhibition of a protein kinase (e.g., Bcr-Abl) activity is measured by EC50.
Potency of the inhibitor can be determined by EC50 value. A compound with a lower EC50 value, as determined under substantially similar conditions, is a more potent inhibitor relative to a compound with a higher EC50 value. In some embodiments, the substantially similar conditions comprise determining protein kinase-dependent cell proliferation, in vitro or in vivo (e.g., in cells expressing a protein kinase).
Potency of the inhibitor can also be determined by IC50 value. A compound with a lower IC50 value, as determined under substantially similar conditions, is a more potent inhibitor relative to a compound with a higher IC50 value. In some embodiments, the substantially similar conditions comprise determining protein kinase-dependent cell proliferation, in vitro or in vivo (e.g., in cells expressing a protein kinase).
In one embodiment, the bifunctional compounds of the present application are useful as anticancer agents, and thus may be useful in the treatment of cancer, by effecting tumor cell death or inhibiting the growth of tumor cells. In certain exemplary embodiments, the disclosed anticancer agents are useful in the treatment of cancers and other proliferative disorders, including, but not limited to breast cancer, cervical cancer, colon and rectal cancer, leukemia, lung cancer (e.g., non-small cell lung cancer), melanoma, multiple myeloma, non-Hodgkin's lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, gastric cancer, leukemias (e.g., myeloid, lymphocytic, myelocytic and lymphoblastic leukemias), malignant melanomas, and T-cell lymphoma.
A “selective protein kinase inhibitor,” can be identified, for example, by comparing the ability of a compound to inhibit one protein kinase activity to its ability to inhibit other kinases. For example, a substance may be assayed for its ability to inhibit one protein kinase activity, as well as another protein kinase or other kinase. In some embodiments, the selectivity can be identified by measuring the EC50 or IC50 of the compounds.
The bifunctional compounds of the present application can modulate and/or inhibit one of more kinases. In some embodiments, the bifunctional compounds of the present application modulate and/or inhibit one protein kinase. In other embodiment, the bifunctional compounds of the present application modulate and/or inhibit more than one kinase. In some embodiments, the bifunctional compounds of the present application modulate and/or inhibit wild-type kinase. In other embodiments, the bifunctional compounds of the present application modulate and/or inhibit a mutant protein kinase. In other embodiments, the bifunctional compounds of the present application modulate and/or inhibit both a wild-type and mutant variant of a kinase.
Resistance to various anticancer agents can arise from one or more mutations in a mediator or effector of the cancer (e.g., mutation in a kinase such as Src or Abl) which correlate with alteration in the protein's drug binding properties, phosphate binding properties, protein binding properties, autoregulation or other characteristics. Mutation of BCR-Abl, for example, has associated with chronic myeloid leukemia. In addition, resistance to Gleevec has been mapped to a variety of BCR/Abl mutations which are linked to a variety of functional consequences, including among others, steric hindrance of drug occupancy at the kinase's active site, alteration in deformability of the phosphate binding P loop, effects on the conformation of the activation loop surrounding the active site, and others. The bifunctional compounds of this application can be used to treat leukemias and other cancers, including those which are resistant in whole or part to other anticancer agents, specifically including Gleevec and other kinase inhibitors, and specifically including leukemias involving one or more mutations in BCR-Abl, within or outside the kinase domain, including but not limited to those noted in any of the foregoing publications.
In one aspect, the application provides a bifunctional compound comprising a protein kinase inhibitor (e.g., Bcr-Abl inhibitor), wherein the bifunctional compound is a more potent inhibitor of a drug-resistant protein kinase mutant relative to a wild type protein kinase. For example, the compound can be at least about 2-fold, 3-fold, 5-fold, 10-fold, 25-fold, 50-fold or about 100-fold more potent at inhibiting the kinase activity of the drug-resistant protein kinase mutant relative to the compound's inhibition of wild type protein kinase activity. In some embodiments, the drug-resistant protein kinase mutant is resistant to Gleevec and other protein kinase inhibitor drugs. In some embodiments, the drug-resistant protein mutant comprises an activating mutation. In another aspect, the application provides a compound comprising a protein kinase inhibitor, wherein the bifunctional compound inhibits protein kinase activity of a drug-resistant protein kinase mutant harboring an activating mutation and a drug-resistance mutation with less than a 10-fold difference in potency relative to a protein kinase mutant harboring the activating mutation but not the drug-resistance mutation. In some embodiments, the difference in potency is less than about 9-fold, 8-fold, 7-fold, 6-fold, 5-fold, 4-fold, 3-fold or 2-fold.
Listed below are definitions of various terms used in this application. These definitions apply to the terms as they are used throughout this specification and claims, unless otherwise limited in specific instances, either individually or as part of a larger group.
The term “alkyl,” as used herein, refers to saturated, straight or branched-chain hydrocarbon radicals containing, in certain embodiments, between one and six carbon atoms. For example C1-C3 alkyl includes methyl, ethyl, n-propyl, and isopropyl. Examples of C1-C6 alkyl radicals include, but are not limited to, methyl, ethyl, propyl, isopropyl, n-butyl, tert-butyl, neopentyl, and n-hexyl radicals.
The term “alkoxy” refers to an —O-alkyl radical. For example C1-C3 alkoxy includes methoxy, ethoxy, n-propoxy, and isopropoxy. Examples of C1-C6 alkyl radicals include, but are not limited to, methoxy, ethoxy, propoxy, isopropoxy, n-butoxy, tert-butoxy, neopentoxy, and n-hexoxy radicals.
The terms “hal,” “halo,” and “halogen,” as used herein, refer to an atom selected from fluorine, chlorine, bromine and iodine.
The term “aryl,” as used herein, refers to a mono- or poly-cyclic carbocyclic ring system having one or more aromatic rings, fused or non-fused, including, but not limited to, phenyl, naphthyl, tetrahydronaphthyl, indanyl, indenyl and the like.
The term “aralkyl,” as used herein, refers to an alkyl residue attached to an aryl ring. Examples include, but are not limited to, benzyl, phenethyl and the like.
The term “cycloalkyl,” as used herein, denotes a monovalent group derived from a monocyclic or polycyclic saturated or partially unsaturated carbocyclic ring compound.
Examples of C3-C8 cycloalkyl include, but not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cyclopentyl and cyclooctyl; and examples of C3-C12-cycloalkyl include, but not limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, bicyclo [2.2.1] heptyl, and bicyclo [2.2.2] octyl. Also contemplated is a monovalent group derived from a monocyclic or polycyclic carbocyclic ring compound having at least one carbon-carbon double bond by the removal of a single hydrogen atom. Examples of such groups include, but are not limited to, cyclopropenyl, cyclobutenyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, cyclooctenyl, and the like.
The term “heteroaryl,” as used herein, refers to a mono- or poly-cyclic (e.g., bi-, or tri-cyclic or more) fused or non-fused, radical or ring system having at least one aromatic ring, having from five to ten ring atoms of which one ring atoms is selected from S, O, and N; zero, one, or two ring atoms are additional heteroatoms independently selected from S, O, and N; and the remaining ring atoms are carbon. Heteroaryl includes, but is not limited to, pyridinyl, pyrazinyl, pyrimidinyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl, isooxazolyl, thiadiazolyl, oxadiazolyl, thiophenyl, furanyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzooxazolyl, quinoxalinyl, and the like.
The term “heteroaralkyl,” as used herein, refers to an alkyl residue attached to a heteroaryl ring. Examples include, but are not limited to, pyridinylmethyl, pyrimidinylethyl and the like.
The term “heterocyclyl,” or “heterocycloalkyl,” as used herein, refers to a non-aromatic 3-, 4-, 5-, 6- or 7-membered ring or a bi- or tri-cyclic group fused of non-fused system, where (i) each ring contains between one and three heteroatoms independently selected from oxygen, sulfur and nitrogen, (ii) each 5-membered ring has 0 to 1 double bonds and each 6-membered ring has 0 to 2 double bonds, (iii) the nitrogen and sulfur heteroatoms may optionally be oxidized, and (iv) the nitrogen heteroatom may optionally be quaternized. Representative heterocycloalkyl groups include, but are not limited to, [1,3]dioxolane, pyrrolidinyl, pyrazolinyl, pyrazolidinyl, imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl, isothiazolidinyl, and tetrahydrofuryl.
The term “alkylamino” refers to a group having the structure —NH(C1-C12 alkyl), e.g., —NH(C1-C6 alkyl), where C1-C12 alkyl is as previously defined.
The term “dialkylamino” refers to a group having the structure —N(C1-C12 alkyl)2, e.g., —NH(C1-C6 alkyl), where C1-C12 alkyl is as previously defined.
The term “acyl” includes residues derived from acids, including but not limited to carboxylic acids, carbamic acids, carbonic acids, sulfonic acids, and phosphorous acids. Examples include aliphatic carbonyls, aromatic carbonyls, aliphatic sulfonyls, aromatic sulfinyls, aliphatic sulfinyls, aromatic phosphates and aliphatic phosphates. Examples of aliphatic carbonyls include, but are not limited to, acetyl, propionyl, 2-fluoroacetyl, butyryl, 2-hydroxy acetyl, and the like.
In accordance with the application, any of the aryls, substituted aryls, heteroaryls and substituted heteroaryls described herein, can be any aromatic group. Aromatic groups can be substituted or unsubstituted.
As described herein, compounds of the application may optionally be substituted with one or more substituents, such as are illustrated generally above, or as exemplified by particular classes, subclasses, and species of the application. It will be appreciated that the phrase “optionally substituted” is used interchangeably with the phrase “substituted or unsubstituted.” In general, the term “substituted”, whether preceded by the term “optionally” or not, refers to the replacement of hydrogen radicals in a given structure with the radical of a specified substituent. Unless otherwise indicated, an optionally substituted group may have a substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. The terms “optionally substituted”, “optionally substituted alkyl,” “optionally substituted” “optionally substituted alkenyl,” “optionally substituted alkynyl”, “optionally substituted cycloalkyl,” “optionally substituted cycloalkenyl,” “optionally substituted aryl”, “optionally substituted heteroaryl,” “optionally substituted aralkyl”, “optionally substituted heteroaralkyl,” “optionally substituted heterocycloalkyl,” and any other optionally substituted group as used herein, refer to groups that are substituted or unsubstituted by independent replacement of one, two, or three or more of the hydrogen atoms thereon with substituents including, but not limited to:
—F, —CI, —Br, —I, —OH, protected hydroxy, —NO2, —CN, —NH2, protected amino, —NH—C1-C12-alkyl, —NH—C2-C12-alkenyl, —NH—C2-C12-alkenyl, —NH—C3-C12-cycloalkyl, —NH-aryl, —NH-heteroaryl, —NH-heterocycloalkyl, -dialkylamino, -diarylamino, -diheteroarylamino, —O—C1-C12-alkyl, —O—C2-C12-alkenyl, —O—C2-C12-alkenyl, —O−C3-C12-cycloalkyl, —O-aryl, —O-heteroaryl, —O-heterocycloalkyl, —C(O)—C1-C12-alkyl, —C(O)—C2-C12-alkenyl, —C(O)—C2-C12-alkenyl, —C(O)—C3-C12-cycloalkyl, —C(O)-aryl, —C(O)-heteroaryl, —C(O)-heterocycloalkyl, —CONH2, —CONH—C1-C12-alkyl, —CONH—C2-C12-alkenyl, —CONH—C2-C12-alkenyl, —CONH—C3-C12-cycloalkyl, —CONH-aryl, —CONH-heteroaryl, —CONH-heterocycloalkyl, —OCO2—C1-C12-alkyl, —OCO2—C2-C12-alkenyl, —OCO2—C2-C12-alkenyl, —OCO2—C3-C12-cycloalkyl, —OCO2-aryl, —OCO2-heteroaryl, —OCO2-heterocycloalkyl, —OCONH2, —OCONH—C1-C12-alkyl, —OCONH—C2-C12-alkenyl, —OCONH—C2-C12-alkenyl, —OCONH—C3-C12-cycloalkyl, —OCONH-aryl, —OCONH-heteroaryl, —OCONH-heterocycloalkyl, —NHC(O)—C1-C12-alkyl, —NHC(O)—C2-C12-alkenyl, —NHC(O)—C2-C12-alkenyl, —NHC(O)—C3-C12-cycloalkyl, —NHC(O)-aryl, —NHC(O)-heteroaryl, —NHC(O)-heterocycloalkyl, —NHCO2—C1-C12-alkyl, —NHCO2—C2-C12-alkenyl, —NHCO2—C2-C12-alkenyl, —NHCO2—C3-C12-cycloalkyl, —NHCO2-aryl, —NHCO2-heteroaryl, —NHCO2-heterocycloalkyl, NHC(O)NH2, —NHC(O)NH—C1-C12-alkyl, —NHC(O)NH—C2-C12-alkenyl, —NHC(O)NH—C2-C12-alkenyl, —NHC(O)NH—C1-C12-cycloalkyl, —NHC(O)NH-aryl, —NHC(O)NH-heteroaryl, NHC(O)NH-heterocycloalkyl, —NHC(S)NH2, —NHC(S)NH—C1-C12-alkyl, —NHC(S)NH—C2-C12-alkenyl, —NHC(S)NH—C2-C12-alkenyl, —NHC(S)NH—C3-C12-cycloalkyl, —NHC(S)NH-aryl, —NHC(S)NH-heteroaryl, —NHC(S)NH-heterocycloalkyl, —NHC(NH)NH2, —NHC(NH)NH— C1-C12-alkyl, —NHC(NH)NH—C2-C12-alkenyl, —NHC(NH)NH—C2-C12-alkenyl, —NHC(NH)NH—C3-C12-cycloalkyl, —NHC(NH)NH-aryl, —NHC(NH)NH-heteroaryl, —NHC(NH)NH-heterocycloalkyl, —NHC(NH)—C1-C12-alkyl, —NHC(NH)—C2-C12-alkenyl, —NHC(NH)—C2-C12-alkenyl, —NHC(NH)—C3-C12-cycloalkyl, —NHC(NH)-aryl, —NHC(NH)-heteroaryl, —NHC(NH)-heterocycloalkyl, —C(NH)NH—C1-C12-alkyl, —C(NH)NH—C2-C12-alkenyl, —C(NH)NH—C2-C12-alkenyl, C(NH)NH—C3-C12-cycloalkyl, —C(NH)NH-aryl, —C(NH)NH-heteroaryl, —C(NH)NH-heterocycloalkyl, —S(O)—C1-C12-alkyl, —S(O)—C2-C12-alkenyl, —S(O)—C2-C12-alkenyl, —S(O)—C3-C12-cycloalkyl, —S(O)-aryl, —S(O)-heteroaryl, —S(O)-heterocycloalkyl —SO2NH2, —SO2NH—C1-C12-alkyl, —SO2NH—C2-C12-alkenyl, —SO2NH—C2-C12-alkenyl, —SO2NH—C3-C12-cycloalkyl, —SO2NH-aryl, —SO2NH-heteroaryl, —SO2NH-heterocycloalkyl, —NHSO2—C1-C12-alkyl, —NHSO2—C2-C12-alkenyl, —NHSO2—C2-C12-alkenyl, —NHSO2—C3-C12-cycloalkyl, —NHSO2-aryl, —NHSO2-heteroaryl, —NHSO2-heterocycloalkyl, —CH2NH2, —CH2SO2CH3, -aryl, -arylalkyl, -heteroaryl, -heteroarylalkyl, -heterocycloalkyl, —C3-C12-cycloalkyl, polyalkoxyalkyl, polyalkoxy, -methoxymethoxy, -methoxyethoxy, —SH, —S—C1-C12-alkyl, —S—C2-C12-alkenyl, —S—C2-C12-alkenyl, —S—C3-C12-cycloalkyl, —S-aryl, —S-heteroaryl, —S-heterocycloalkyl, or methylthiomethyl.
It is understood that the aryls, heteroaryls, alkyls, and the like can be substituted.
The term “cancer” includes, but is not limited to, the following cancers: epidermoid Oral: buccal cavity, lip, tongue, mouth, pharynx; Cardiac: sarcoma (angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma), myxoma, rhabdomyoma, fibroma, lipoma, and teratoma; Lung: bronchogenic carcinoma (squamous cell or epidermoid, undifferentiated small cell, undifferentiated large cell, adenocarcinoma), alveolar (bronchiolar) carcinoma, bronchial adenoma, sarcoma, lymphoma, chondromatous hamartoma, mesothelioma; Gastrointestinal: esophagus (squamous cell carcinoma, larynx, adenocarcinoma, leiomyosarcoma, lymphoma), stomach (carcinoma, lymphoma, leiomyosarcoma), pancreas (ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumors, vipoma), small bowel or small intestines (adenocarcinoma, lymphoma, carcinoid tumors, Karposi's sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), large bowel or large intestines (adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma), colon, colon-rectum, colorectal, rectum; Genitourinary tract: kidney (adenocarcinoma, Wilm's tumor (nephroblastoma), lymphoma, leukemia), bladder and urethra (squamous cell carcinoma, transitional cell carcinoma, adenocarcinoma), prostate (adenocarcinoma, sarcoma), testis (seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, interstitial cell carcinoma, fibroma, fibroadenoma, adenomatoid tumors, lipoma); Liver: hepatoma (hepatocellular carcinoma), cholangiocarcinoma, hepatoblastoma, angiosarcoma, hepatocellular adenoma, hemangioma, biliary passages; Bone: osteogenic sarcoma (osteosarcoma), fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticulum cell sarcoma), multiple myeloma, malignant giant cell tumor chordoma, osteochronfroma (osteocartilaginous exostoses), benign chondroma, chondroblastoma, chondromyxofibroma, osteoid osteoma and giant cell tumors; Nervous system: skull (osteoma, hemangioma, granuloma, xanthoma, osteitis deformans), meninges (meningioma, meningiosarcoma, gliomatosis), brain (astrocytoma, medulloblastoma, glioma, ependymoma, germinoma (pinealoma), glioblastoma multiform, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors), spinal cord neurofibroma, meningioma, glioma, sarcoma); Gynecological: uterus (endometrial carcinoma), cervix (cervical carcinoma, pre-tumor cervical dysplasia), ovaries (ovarian carcinoma (serous cystadenocarcinoma, mucinous cystadenocarcinoma, unclassified carcinoma), granulosa-thecal cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignant teratoma), vulva (squamous cell carcinoma, intraepithelial carcinoma, adenocarcinoma, fibrosarcoma, melanoma), vagina (clear cell carcinoma, squamous cell carcinoma, botryoid sarcoma (embryonal rhabdomyosarcoma), fallopian tubes (carcinoma), breast; Hematologic: blood (myeloid leukemia (acute and chronic), acute lymphoblastic leukemia, chronic lymphocytic leukemia, myeloproliferative diseases, multiple myeloma, myelodysplastic syndrome), Hodgkin's disease, non-Hodgkin's lymphoma (malignant lymphoma) hairy cell; lymphoid disorders, Skin: malignant melanoma, basal cell carcinoma, squamous cell carcinoma, Karposi's sarcoma, keratoacanthoma, moles dysplastic nevi, lipoma, angioma, dermatofibroma, keloids, psoriasis, Thyroid gland: papillary thyroid carcinoma, follicular thyroid carcinoma; medullary thyroid carcinoma, undifferentiated thyroid cancer, multiple endocrine neoplasia type 2A, multiple endocrine neoplasia type 2B, familial medullary thyroid cancer, pheochromocytoma, paraganglioma; and Adrenal glands: neuroblastoma. Thus, the term “cancerous cell” as provided herein, includes a cell afflicted by any one of the above-identified conditions.
The term “subject” as used herein refers to a mammal. A subject therefore refers to, for example, dogs, cats, horses, cows, pigs, guinea pigs, and the like. Preferably the subject is a human. When the subject is a human, the subject may be referred to herein as a patient.
“Treat”, “treating” and “treatment” refer to a method of alleviating or abating a disease and/or its attendant symptoms.
As used herein, “preventing” or “prevent” describes reducing or eliminating the onset of the symptoms or complications of the disease, condition or disorder.
The term “targeted protein(s)” is used interchangeably with “target protein(s)”, unless the context clearly dictates otherwise. In some embodiments, a “targeted protein” is a protein kinase. In other embodiments, a targeted protein is one or more protein kinases. In other embodiments, the “targeted protein” is Bcr-Abl.
The terms “disease(s)”, “disorder(s)”, and “condition(s)” are used interchangeably, unless the context clearly dictates otherwise.
The term “therapeutically effective amount” of a bifunctional compound or pharmaceutical composition of the application, as used herein, means a sufficient amount of the bifunctional compound or pharmaceutical composition so as to decrease the symptoms of a disorder in a subject. As is well understood in the medical arts a therapeutically effective amount of a bifunctional compound or pharmaceutical composition of this application will be at a reasonable benefit/risk ratio applicable to any medical treatment. It will be understood, however, that the total daily usage of the compounds and compositions of the present application will be decided by the attending physician within the scope of sound medical judgment. The specific inhibitory dose for any particular patient will depend upon a variety of factors including the disorder being treated and the severity of the disorder, the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed; and like factors well known in the medical arts.
As used herein, the term “pharmaceutically acceptable salt” refers to those salts of the compounds formed by the process of the present application which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge, et al. describes pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 66: 1-19 (1977). The salts can be prepared in situ during the final isolation and purification of the compounds of the application, or separately by reacting the free base or acid function with a suitable acid or base.
Examples of pharmaceutically acceptable salts include, but are not limited to, nontoxic acid addition salts: salts formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid, or with organic acids such as acetic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid. Other pharmaceutically acceptable salts include, but are not limited to, adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, picrate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, alkyl having from 1 to 6 carbon atoms, sulfonate and aryl sulfonate.
As used herein, the term “pharmaceutically acceptable ester” refers to esters of the bifunctional compounds formed by the process of the present application which hydrolyze in vivo and include those that break down readily in the human body to leave the parent compound or a salt thereof. Suitable ester groups include, for example, those derived from pharmaceutically acceptable aliphatic carboxylic acids, particularly alkanoic, alkenoic, cycloalkanoic and alkanedioic acids, in which each alkyl or alkenyl moiety advantageously has not more than 6 carbon atoms. Examples of particular esters include, but are not limited to, formates, acetates, propionates, butyrates, acrylates and ethylsuccinates.
The term “pharmaceutically acceptable prodrugs” as used herein, refers to those prodrugs of the bifunctional compounds formed by the process of the present application which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals with undue toxicity, irritation, allergic response, and the like, commensurate with a reasonable benefit/risk ratio, and effective for their intended use, as well as the zwitterionic forms, where possible, of the compounds of the present application. “Prodrug”, as used herein, means a compound which is convertible in vivo by metabolic means (e.g., by hydrolysis) to afford any compound delineated by the formulae of the instant application. Various forms of prodrugs are known in the art, for example, as discussed in Bundgaard, (ed.), Design of Prodrugs, Elsevier (1985); Widder, et al. (ed.), Methods in Enzymology, vol. 4, Academic Press (1985); Krogsgaard-Larsen, et al., (ed). “Design and Application of Prodrugs, Textbook of Drug Design and Development, Chapter 5, 113-191 (1991); Bundgaard, et al., Journal of Drug Deliver Reviews, 8:1-38 (1992); Bundgaard, J. of Pharmaceutical Sciences, 77:285 et seq. (1988); Higuchi and Stella (eds.) Prodrugs as Novel Drug Delivery Systems, American Chemical Society (1975); and Bernard Testa & Joachim Mayer, “Hydrolysis In Drug And Prodrug Metabolism: Chemistry, Biochemistry And Enzymology,” John Wiley and Sons, Ltd. (2002).
This application also encompasses pharmaceutical compositions containing, and methods of treating disorders through administering, pharmaceutically acceptable prodrugs of bifunctional compounds of the application. For example, compounds of the application having free amino, amido, hydroxy or carboxylic groups can be converted into prodrugs. Prodrugs include compounds wherein an amino acid residue, or a polypeptide chain of two or more (e.g., two, three or four) amino acid residues is covalently joined through an amide or ester bond to a free amino, hydroxy or carboxylic acid group of compounds of the application. The amino acid residues include but are not limited to the 20 naturally occurring amino acids commonly designated by three letter symbols and also includes 4-hydroxyproline, hydroxylysine, demosine, isodemosine, 3-methylhistidine, norvalin, beta-alanine, gamma-aminobutyric acid, citrulline, homocysteine, homoserine, ornithine and methionine sulfone. Additional types of prodrugs are also encompassed. For instance, free carboxyl groups can be derivatized as amides or alkyl esters. Free hydroxy groups may be derivatized using groups including but not limited to hemisuccinates, phosphate esters, dimethylaminoacetates, and phosphoryloxymethyloxy carbonyls, as outlined in Advanced Drug Delivery Reviews, 1996, 19, 1 15. Carbamate prodrugs of hydroxy and amino groups are also included, as are carbonate prodrugs, sulfonate esters and sulfate esters of hydroxy groups. Derivatization of hydroxy groups as (acyloxy)methyl and (acyloxy)ethyl ethers wherein the acyl group may be an alkyl ester, optionally substituted with groups including but not limited to ether, amine and carboxylic acid functionalities, or where the acyl group is an amino acid ester as described above, are also encompassed. Prodrugs of this type are described in J. Med. Chem. 1996, 39, 10. Free amines can also be derivatized as amides, sulfonamides or phosphonamides. All of these prodrug moieties may incorporate groups including but not limited to ether, amine and carboxylic acid functionalities.
The application also provides for a pharmaceutical composition comprising a therapeutically effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, stereoisomer, or pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier.
In another aspect, the application provides a kit comprising a bifunctional compound capable of inhibiting protein kinase activity of at least one protein kinase selected from one or more compounds disclosed herein, or a pharmaceutically acceptable salt, hydrate, solvate, prodrug, stereoisomer, or tautomer thereof, optionally in combination with a second agent and instructions for use in treating cancer. In one embodiment, the bifunctional compound in the kit inhibits more than one protein kinase
In another aspect, the application provides a method of synthesizing a bifunctional compound disclosed herein.
The synthesis of the bifunctional compounds of the application can be found herein and in the Examples below.
Other embodiments are a method of making a bifunctional compound of any of the formulae herein using any one, or combination of, reactions delineated herein. The method can include the use of one or more intermediates or chemical reagents delineated herein.
Another aspect is an isotopically labeled bifunctional compound of any of the formulae delineated herein. Such compounds have one or more isotope atoms which may or may not be radioactive (e.g., 3H, 2H, 14C, 3C, 18F, 35S, 32P, 125I, and 131I) introduced into the bifunctional compound. Such compounds are useful for drug metabolism studies and diagnostics, as well as therapeutic applications.
A bifunctional compound of the application can be prepared as a pharmaceutically acceptable acid addition salt by reacting the free base form of the compound with a pharmaceutically acceptable inorganic or organic acid. Alternatively, a pharmaceutically acceptable base addition salt of a bifunctional compound of the application can be prepared by reacting the free acid form of the bifunctional compound with a pharmaceutically acceptable inorganic or organic base.
Alternatively, the salt forms of the bifunctional compounds of the application can be prepared using salts of the starting materials or intermediates.
The free acid or free base forms of the bifunctional compounds of the application can be prepared from the corresponding base addition salt or acid addition salt from, respectively. For example, a bifunctional compound of the application in an acid addition salt form can be converted to the corresponding free base by treating with a suitable base (e.g., ammonium hydroxide solution, sodium hydroxide, and the like). A bifunctional compound of the application in a base addition salt form can be converted to the corresponding free acid by treating with a suitable acid (e.g., hydrochloric acid, etc.).
Prodrugs of the bifunctional compounds of the application can be prepared by methods known to those of ordinary skill in the art (e.g., for further details see Saulnier et al., (1994), Bioorganic and Medicinal Chemistry Letters, Vol. 4, p. 1985). For example, appropriate prodrugs can be prepared by reacting a non-derivatized bifunctional compound of the application with a suitable carbamoylating agent (e.g., 1,1-acyloxyalkylcarbanochloridate, para-nitrophenyl carbonate, or the like).
Protected derivatives of the bifunctional compounds of the application can be made by means known to those of ordinary skill in the art. A detailed description of techniques applicable to the creation of protecting groups and their removal can be found in T. W. Greene, “Protecting Groups in Organic Chemistry”, 3rd edition, John Wiley and Sons, Inc., 1999.
Compounds of the present application can be conveniently prepared or formed during the process of the application, as solvates (e.g., hydrates). Hydrates of bifunctional compounds of the present application can be conveniently prepared by recrystallization from an aqueous/organic solvent mixture, using organic solvents such as dioxin, tetrahydrofuran or methanol.
Acids and bases useful in the methods herein are known in the art. Acid catalysts are any acidic chemical, which can be inorganic (e.g., hydrochloric, sulfuric, nitric acids, aluminum trichloride) or organic (e.g., camphorsulfonic acid, p-toluenesulfonic acid, acetic acid, ytterbium triflate) in nature. Acids are useful in either catalytic or stoichiometric amounts to facilitate chemical reactions. Bases are any basic chemical, which can be inorganic (e.g., sodium bicarbonate, potassium hydroxide) or organic (e.g., triethylamine, pyridine) in nature. Bases are useful in either catalytic or stoichiometric amounts to facilitate chemical reactions.
Combinations of substituents and variables envisioned by this application are only those that result in the formation of stable compounds. The term “stable”, as used herein, refers to compounds which possess stability sufficient to allow manufacture and which maintains the integrity of the compound for a sufficient period of time to be useful for the purposes detailed herein (e.g., therapeutic or prophylactic administration to a subject).
When any variable (e.g., R3) occurs more than one time in any constituent or formula for a compound, its definition at each occurrence is independent of its definition at every other occurrence. Thus, for example, if a group is shown to be substituted with one or more R3 moieties, then R3 at each occurrence is selected independently from the definition of R3. Also, combinations of substituents and/or variables are permissible, but only if such combinations result in stable compounds within a designated atom's normal valency.
In addition, some of the compounds of this application have one or more double bonds, or one or more asymmetric centers. Such compounds can occur as racemates, racemic mixtures, single enantiomers, individual diastereomers, diastereomeric mixtures, and cis- or trans- or E- or Z-double isomeric forms, and other stereoisomeric forms that may be defined, in terms of absolute stereochemistry, as (R)- or (S)-, or as (D)- or (L)- for amino acids. When the compounds described herein contain olefinic double bonds or other centers of geometric asymmetry, and unless specified otherwise, it is intended that the compounds include both E and Z geometric isomers. The configuration of any carbon-carbon double bond appearing herein is selected for convenience only and is not intended to designate a particular configuration unless the text so states; thus a carbon-carbon double bond depicted arbitrarily herein as trans may be cis, trans, or a mixture of the two in any proportion. All such isomeric forms of such compounds are expressly included in the present application.
Optical isomers may be prepared from their respective optically active precursors by the procedures described herein, or by resolving the racemic mixtures. The resolution can be carried out in the presence of a resolving agent, by chromatography or by repeated crystallization or by some combination of these techniques which are known to those skilled in the art. Further details regarding resolutions can be found in Jacques, et al., Enantiomers, Racemates, and Resolutions (John Wiley & Sons, 1981).
“Isomerism” means compounds that have identical molecular formulae but differ in the sequence of bonding of their atoms or in the arrangement of their atoms in space. Isomers that differ in the arrangement of their atoms in space are termed “stereoisomers”. Stereoisomers that are not mirror images of one another are termed “diastereoisomers”, and stereoisomers that are non-superimposable mirror images of each other are termed “enantiomers” or sometimes optical isomers. A mixture containing equal amounts of individual enantiomeric forms of opposite chirality is termed a “racemic mixture”.
A carbon atom bonded to four non-identical substituents is termed a “chiral center”.
“Chiral isomer” means a compound with at least one chiral center. Compounds with more than one chiral center may exist either as an individual diastereomer or as a mixture of diastereomers, termed “diastereomeric mixture”. When one chiral center is present, a stereoisomer may be characterized by the absolute configuration (R or S) of that chiral center. Absolute configuration refers to the arrangement in space of the substituents attached to the chiral center. The substituents attached to the chiral center under consideration are ranked in accordance with the Sequence Rule of Cahn, Ingold and Prelog. (Cahn et al., Angew. Chenm. Inter. Edit. 1966, 5, 385; errata 511; Cahn et al., Angew. Chem. 1966, 78, 413; Cahn and Ingold, J. Chem. Soc. 1951 (London), 612; Cahn et al., Experientia 1956, 12, 81; Cahn, J. Chenr. Educ. 1964, 41, 116).
“Geometric isomer” means the diastereomers that owe their existence to hindered rotation about double bonds. These configurations are differentiated in their names by the prefixes cis and trans, or Z and E, which indicate that the groups are on the same or opposite side of the double bond in the molecule according to the Cahn-Ingold-Prelog rules.
Furthermore, the structures and other compounds discussed in this application include all atropic isomers thereof. “Atropic isomers” are a type of stereoisomer in which the atoms of two isomers are arranged differently in space. Atropic isomers owe their existence to a restricted rotation caused by hindrance of rotation of large groups about a central bond. Such atropic isomers typically exist as a mixture, however as a result of recent advances in chromatography techniques; it has been possible to separate mixtures of two atropic isomers in select cases.
“Tautomer” is one of two or more structural isomers that exist in equilibrium and is readily converted from one isomeric form to another. This conversion results in the formal migration of a hydrogen atom accompanied by a switch of adjacent conjugated double bonds. Tautomers exist as a mixture of a tautomeric set in solution. In solid form, usually one tautomer predominates. In solutions where tautomerization is possible, a chemical equilibrium of the tautomers will be reached. The exact ratio of the tautomers depends on several factors, including temperature, solvent and pH. The concept of tautomers that are interconvertible by tautomerizations is called tautomerism.
Of the various types of tautomerism that are possible, two are commonly observed. In keto-enol tautomerism a simultaneous shift of electrons and a hydrogen atom occurs. Ring-chain tautomerism arises as a result of the aldehyde group (—CHO) in a sugar chain molecule reacting with one of the hydroxy groups (—OH) in the same molecule to give it a cyclic (ring-shaped) form as exhibited by glucose. Common tautomeric pairs are: ketone-enol, amide-nitrile, lactam-lactim, amide-imidic acid tautomerism in heterocyclic rings (e.g., in nucleobases such as guanine, thymine and cytosine), amine-enamine and enamine-enamine. The compounds of this application may also be represented in multiple tautomeric forms, in such instances, the application expressly includes all tautomeric forms of the compounds described herein (e.g., alkylation of a ring system may result in alkylation at multiple sites, the application expressly includes all such reaction products).
In the present application, the structural formula of the bifunctional compound represents a certain isomer for convenience in some cases, but the present application includes all isomers, such as geometrical isomers, optical isomers based on an asymmetrical carbon, stereoisomers, tautomers, and the like. In the present specification, the structural formula of the compound represents a certain isomer for convenience in some cases, but the present application includes all isomers, such as geometrical isomers, optical isomers based on an asymmetrical carbon, stereoisomers, tautomers, and the like.
Additionally, the compounds of the present application, for example, the salts of the bifunctional compounds, can exist in either hydrated or unhydrated (the anhydrous) form or as solvates with other solvent molecules. Non-limiting examples of hydrates include monohydrates, dihydrates, etc. Non-limiting examples of solvates include ethanol solvates, acetone solvates, etc.
“Solvate” means solvent addition forms that contain either stoichiometric or non stoichiometric amounts of solvent. Some compounds have a tendency to trap a fixed molar ratio of solvent molecules in the crystalline solid state, thus forming a solvate. If the solvent is water the solvate formed is a hydrate; and if the solvent is alcohol, the solvate formed is an alcoholate. Hydrates are formed by the combination of one or more molecules of water with one molecule of the substance in which the water retains its molecular state as H2O.
The synthesized bifunctional compounds can be separated from a reaction mixture and further purified by a method such as column chromatography, high pressure liquid chromatography, or recrystallization. As can be appreciated by the skilled artisan, further methods of synthesizing the bifunctional compounds of the formulae herein will be evident to those of ordinary skill in the art. Additionally, the various synthetic steps may be performed in an alternate sequence or order to give the desired compounds. In addition, the solvents, temperatures, reaction durations, etc. delineated herein are for purposes of illustration only and one of ordinary skill in the art will recognize that variation of the reaction conditions can produce the desired bridged macrocyclic products of the present application. Synthetic chemistry transformations and protecting group methodologies (protection and deprotection) useful in synthesizing the compounds described herein are known in the art and include, for example, those such as described in R Larock, Comprehensive Organic Transformations, VCH Publishers (1989); T. W. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 2d. Ed., John Wiley and Sons (1991); L. Fieser and M. Fieser, Fieser and Fieser's Reagents for Organic Synthesis, John Wiley and Sons (1994); and L. Paquette, ed., Encyclopedia of Reagents for Organic Synthesis, John Wiley and Sons (1995), and subsequent editions thereof.
The compounds of this application may be modified by appending various functionalities via any synthetic means delineated herein to enhance selective biological properties. Such modifications are known in the art and include those which increase biological penetration into a given biological system (e.g., blood, lymphatic system, central nervous system), increase oral availability, increase solubility to allow administration by injection, alter metabolism and alter rate of excretion.
The compounds of the application are defined herein by their chemical structures and/or chemical names. Where a compound is referred to by both a chemical structure and a chemical name, and the chemical structure and chemical name conflict, the chemical structure is determinative of the compound's identity.
The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
Compounds of the present application can be prepared in a variety of ways using commercially available starting materials, compounds known in the literature, or from readily prepared intermediates, by employing standard synthetic methods and procedures either known to those skilled in the art, or which will be apparent to the skilled artisan in light of the teachings herein. Standard synthetic methods and procedures for the preparation of organic molecules and functional group transformations and manipulations can be obtained from the relevant scientific literature or from standard textbooks in the field. Although not limited to any one or several sources, classic texts such as Smith, M. B., March, J., March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, 5th edition, John Wiley & Sons: New York, 2001; and Greene, T. W., Wuts, P. G. M, Protective Groups in Organic Synthesis, 3rd edition, John Wiley & Sons: New York, 1999, incorporated by reference herein, are useful and recognized reference textbooks of organic synthesis known to those in the art. The following descriptions of synthetic methods are designed to illustrate, but not to limit, general procedures for the preparation of compounds of the present application. The processes generally provide the desired final compound at or near the end of the overall process, although it may be desirable in certain instances to further convert the compound to a pharmaceutically acceptable salt, ester or prodrug thereof. Suitable synthetic routes are depicted in the schemes below.
Those skilled in the art will recognize if a stereocenter exists in the compounds disclosed herein. Accordingly, the present application includes both possible stereoisomers (unless specified in the synthesis) and includes not only racemic compounds but the individual enantiomers and/or diastereomers as well. When a compound is desired as a single enantiomer or diastereomer, it may be obtained by stereospecific synthesis or by resolution of the final product or any convenient intermediate. Resolution of the final product, an intermediate, or a starting material may be affected by any suitable method known in the art. See, for example, “Stereochemistry of Organic Compounds” by E. L. Eliel, S. H. Wilen, and L. N. Mander (Wiley-Interscience, 1994).
The compounds of the present application can be prepared in a number of ways well known to those skilled in the art of organic synthesis. By way of example, compounds of the present application can be synthesized using the methods described below, together with synthetic methods known in the art of synthetic organic chemistry, or variations thereon as appreciated by those skilled in the art. Preferred methods include but are not limited to those methods described below.
Compounds of the present application can be synthesized by following the steps outlined in General Scheme 1 and 2 which comprise different sequences of assembling intermediates. Starting materials are either commercially available or made by known procedures in the reported literature or as illustrated.
wherein R28, R29, R30, R31, W, p1, q, and v are as defined herein above.
The general way of preparing representative compounds of the present application (e.g., Compound of formula (I) shown above) using intermediates 1a, 1b, 1c, 1d, 1e, 1f, and 1g is outlined in General Scheme 1. Reaction of 1a with 1b in the presence of potassium acetate (KOAc), and in an acid, e.g., acetic acid (ACOH), optionally at elevated temperature provides intermediate 1c. Reaction of 1d with fluoride 1c provides intermediate 1e. Deprotection of the 1e in the presence of TFA in a solvent, e.g., dichloromethane (DCM) or methanol (MeOH), provides 1f. Coupling of 1f and Target Ligand (TL) 1g under standard coupling conditions using a coupling reagent, e.g., 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDCI) and hydroxybenzotriazole (HOBt) or 1-[Bis(dimethylamino)methylene]-1H-1,2,3-triazolo[4,5-b]pyridinium 3-oxide hexafluorophosphate (HATU), and a base (i.e., triethylamine (TEA) or N,N-Diisopropylethylamine (DIPEA)) in a solvent, e.g., DCM or DMF, provides bifunctional compound of formula (I).
The general way of preparing representative compounds of the present application (e.g., Compound of formula (II) shown above) using intermediates 3a, 3b, 3c, and 3d is outlined in General Scheme 2. Reaction of 3a with 3b in the presence of potassium iodide (KI), a base, e.g., potassium carbonate (K2CO3), and in a solvent, e.g., acetone), followed by Boc deprotection in the presence of strong acid (e.g., hydrochloric acid (HCl) or trifluoroacetic acid (TFA)) in a solvent, e.g., dichloromethane (DCM) or methanol (MeOH) provides intermediate 3c. Coupling of amine 3d and Target Ligand 3c under standard coupling conditions using a coupling reagent, e.g., EDCI and (HOBt) or HATU, and a base (i.e., triethylamine (TEA) or N,N-Diisopropylethylamine (DIPEA)) in a solvent, e.g., DCM or DMF, provides bifunctional compound of formula (II) in shown in General Scheme 2.
Cells are treated with various concentrations of a bifunctional compound of the application and incubated. Cells are then assayed to determine cell viability by measuring the amount of ATP content in the cell, which is an indicator of cell metabolic activity. Results are graphed as relative luminescent values.
In another aspect, the application provides a method of modulating a kinase, comprising contacting the kinase with a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, or with a pharmaceutical composition disclosed herein. In some embodiments, the kinase is a protein kinase. In other embodiments, the kinase is a tyrosine kinase. In other embodiments, the kinase is Bcr-Abl.
In another aspect, the application provides a method of modulating at least one kinase, comprising contacting the kinase with a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, or with a pharmaceutical composition disclosed herein. In some embodiments, the kinase is a protein kinase. In other embodiments, the kinase is a tyrosine kinase. In other embodiments, the kinase is Bcr-Abl. In some embodiments, the bifunctional compound modulates one protein kinase. In other embodiments, the bifunctional compound modulates more than one protein kinase.
In another aspect, the application provides a method of inhibiting a kinase, comprising contacting the kinase with a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, or with a pharmaceutical composition disclosed herein. In some embodiments, the kinase is a protein kinase. In other embodiments, the kinase is a tyrosine kinase. In other embodiments, the kinase is Bcr-Abl.
In still another aspect, the application provides a method of inhibiting a protein kinase, the method comprising administering to a subject in need thereof an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof. In some embodiments, the protein kinase is a tyrosine kinase. In some embodiments, the protein kinase is Bcr-Abl. In some embodiments, the bifunctional compound modulates one protein kinase. In other embodiments, the bifunctional compound modulates more than one protein kinase.
In still another aspect, the application provides a method of inhibiting Bcr-Abl, the method comprising administering to a subject in need thereof an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof.
In still another aspect, the application provides a method of inhibiting a protein kinase, the method comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier. In some embodiments, the protein kinase is a tyrosine kinase. In some embodiments, the protein kinase is Bcr-Abl.
In still another aspect, the application provides a method of inhibiting Bcr-Abl, the method comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier.
Another aspect of the application provides a method of treating or preventing a disease, the method comprising administering to a subject in need thereof an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof. In some embodiments, the disease is mediated by a kinase. In some embodiments, the kinase is a protein kinase. In other embodiments, the kinase is a tyrosine kinase. In further embodiments, the kinase is Bcr-Abl.
Another aspect of the application provides a method of treating or preventing a disease, the method comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier. In some embodiments, the disease is mediated by a kinase. In some embodiments, the kinase is a protein kinase. In other embodiments, the kinase is a tyrosine kinase. In further embodiments, the kinase is Bcr-Abl.
In some embodiments, the disease is mediated by Bcr-Abl (e.g., Bcr-Abl plays a role in the initiation or development of the disease).
In certain embodiments, the disease or disorder is cancer or a proliferation disease.
In further embodiments, the disease or disorder is lung cancer, colon cancer, breast cancer, prostate cancer, liver cancer, pancreas cancer, brain cancer, kidney cancer, ovarian cancer, stomach cancer, skin cancer, bone cancer, gastric cancer, breast cancer, pancreatic cancer, glioma, glioblastoma, hepatocellular carcinoma, papillary renal carcinoma, head and neck squamous cell carcinoma, leukemias, lymphomas, myelomas, or solid tumors.
In further embodiments, the disease or disorder is sarcoma. In further embodiments, the disease or disorder is sarcoma of the bones, muscles, tendons, cartilage, nerves, fat, or blood vessels. In further embodiments, the disease or disorder is soft tissue sarcoma, bone sarcoma, or osteosarcoma. In further embodiments, the disease or disorder is angiosarcoma, fibrosarcoma, liposarcoma, leiomyosarcoma, Karposi's sarcoma, osteosarcoma, gastrointestinal stromal tumor, Synovial sarcoma, Pleomorphic sarcoma, chondrosarcoma, Ewing's sarcoma, reticulum cell sarcoma, meningiosarcoma, botryoid sarcoma, rhabdomyosarcoma, or embryonal rhabdomyosarcoma.
In further embodiments, the disease or disorder is multiple myeloma.
In other embodiments, the disease or disorder is inflammation, arthritis, rheumatoid arthritis, spondyiarthropathies, gouty arthritis, osteoarthritis, juvenile arthritis, and other arthritic conditions, systemic lupus erthematosus (SLE), skin-related conditions, psoriasis, eczema, burns, dermatitis, neuroinflammation, allergy, pain, neuropathic pain, fever, pulmonary disorders, lung inflammation, adult respiratory distress syndrome, pulmonary sarcoisosis, asthma, silicosis, chronic pulmonary inflammatory disease, and chronic obstructive pulmonary disease (COPD), cardiovascular disease, arteriosclerosis, myocardial infarction (including post-myocardial infarction indications), thrombosis, congestive heart failure, cardiac reperfusion injury, as well as complications associated with hypertension and/or heart failure such as vascular organ damage, restenosis, cardiomyopathy, stroke including ischemic and hemorrhagic stroke, reperfusion injury, renal reperfusion injury, ischemia including stroke and brain ischemia, and ischemia resulting from cardiac/coronary bypass, neurodegenerative disorders, liver disease and nephritis, gastrointestinal conditions, inflammatory bowel disease, Crohn's disease, gastritis, irritable bowel syndrome, ulcerative colitis, ulcerative diseases, gastric ulcers, viral and bacterial infections, sepsis, septic shock, gram negative sepsis, malaria, meningitis, HIV infection, opportunistic infections, cachexia secondary to infection or malignancy, cachexia secondary to acquired immune deficiency syndrome (AIDS), AIDS, ARC (AIDS related complex), pneumonia, herpes virus, myalgias due to infection, influenza, autoimmune disease, graft vs. host reaction and allograft rejections, treatment of bone resorption diseases, osteoporosis, multiple sclerosis, cancer, leukemia, lymphoma, colorectal cancer, brain cancer, bone cancer, epithelial call-derived neoplasia (epithelial carcinoma), basal cell carcinoma, adenocarcinoma, gastrointestinal cancer, lip cancer, mouth cancer, esophageal cancer, small bowel cancer, stomach cancer, colon cancer, liver cancer, bladder cancer, pancreas cancer, ovarian cancer, cervical cancer, lung cancer, breast cancer, skin cancer, squamous cell and/or basal cell cancers, prostate cancer, renal cell carcinoma, and other known cancers that affect epithelial cells throughout the body, chronic myelogenous leukemia (CML), acute myeloid leukemia (AML) and acute promyelocytic leukemia (APL), angiogenesis including neoplasia, metastasis, central nervous system disorders, central nervous system disorders having an inflammatory or apoptotic component, Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, spinal cord injury, and peripheral neuropathy, or B-Cell Lymphoma.
In some embodiments, the disease or disorder is CML.
In further embodiments, the disease or disorder is inflammation, arthritis, rheumatoid arthritis, spondylarthropathies, gouty arthritis, osteoarthritis, juvenile arthritis, and other arthritic conditions, systemic lupus erthematosus (SLE), skin-related conditions, psoriasis, eczema, dermatitis, pain, pulmonary disorders, lung inflammation, adult respiratory distress syndrome, pulmonary sarcoisosis, asthma, chronic pulmonary inflammatory disease, and chronic obstructive pulmonary disease (COPD), cardiovascular disease, arteriosclerosis, myocardial infarction (including post-myocardial infarction indications), congestive heart failure, cardiac reperfusion injury, inflammatory bowel disease, Crohn's disease, gastritis, irritable bowel syndrome, leukemia or lymphoma.
Another aspect of the application provides a method of treating a kinase mediated disorder, the method comprising administering to a subject in need thereof an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof. In some embodiments, the bifunctional compound is an inhibitor of a protein kinase. In other embodiments, the bifunctional compound is an inhibitor of a tyrosine kinase. In other embodiments, the bifunctional compound is an inhibitor of Bcr-Abl. In other embodiments, the subject is administered an additional therapeutic agent. In other embodiments, the bifunctional compound and the additional therapeutic agent are administered simultaneously or sequentially.
Another aspect of the application provides a method of treating a kinase mediated disorder, the method comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier. In some embodiments, the bifunctional compound is an inhibitor of a protein kinase. In other embodiments, the bifunctional compound is an inhibitor of a tyrosine kinase. In other embodiments, the bifunctional compound is an inhibitor of Bcr-Abl. In other embodiments, the subject is administered an additional therapeutic agent. In other embodiments, the pharmaceutical composition comprising a bifunctional compound and the additional therapeutic agent are administered simultaneously or sequentially.
In other embodiments, the disease or disorder is cancer. In further embodiments, the cancer is lung cancer, colon cancer, breast cancer, prostate cancer, liver cancer, pancreas cancer, brain cancer, kidney cancer, ovarian cancer, stomach cancer, skin cancer, bone cancer, gastric cancer, breast cancer, pancreatic cancer, glioma, glioblastoma, hepatocellular carcinoma, papillary renal carcinoma, head and neck squamous cell carcinoma, leukemias, lymphomas, myelomas, or solid tumors.
Another aspect of the present application relates to a method of treating or preventing a proliferative disease. The method comprises administering to a subject in need thereof an effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof.
Another aspect of the present application relates to a method of treating or preventing a proliferative disease. The method comprises administering to a subject in need thereof an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier.
In another aspect, the application provides a method of treating or preventing cancer, wherein the cancer cell comprises activated protein kinase, comprising administering to a subject in need thereof an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof. In some embodiments, the cell comprises one activated protein kinase. In other embodiments, the cell comprises more than one activated protein kinase. In other embodiments, the cell comprises an activated tyrosine kinase. In other embodiments, the cell comprises more than one activated tyrosine kinase. In other embodiments, the cell comprises activated Bcr-Abl.
In another aspect, the application provides a method of treating or preventing cancer, wherein the cancer cell comprises activated Bcr-Abl, comprising administering to a subject in need thereof an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof.
In another aspect, the application provides a method of treating or preventing cancer, wherein the cancer cell comprises activated protein kinase, comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier. In some embodiments, the cell comprises one activated protein kinase. In other embodiments, the cell comprises more than one activated protein kinase. In other embodiments, the cell comprises an activated tyrosine kinase. In other embodiments, the cell comprises more than one activated tyrosine kinase. In other embodiments, the cell comprises activated Bcr-Abl.
In another aspect, the application provides a method of treating or preventing cancer, wherein the cancer cell comprises activated Bcr-Abl, comprising administering to a subject in need thereof an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier.
In certain embodiments, the Bcr-Abl activation is selected from mutation of Bcr-Abl, amplification of Bcr-Abl, expression of Bcr-Abl, and ligand mediated activation of Bcr-Abl.
Another aspect of the application provides a method of treating or preventing cancer in a subject, wherein the subject is identified as being in need of inhibition of at least one protein kinase for the treatment of cancer, comprising administering to the subject an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof. In some embodiments, the protein kinase is a tyrosine kinase. In some embodiments, the protein kinase is Bcr-Abl.
Another aspect of the application provides a method of treating or preventing cancer in a subject, wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment of cancer, comprising administering to the subject an effective amount of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof.
Another aspect of the application provides a method of treating or preventing cancer in a subject, wherein the subject is identified as being in need of inhibition of at least one protein kinase for the treatment of cancer, comprising administering to the subject an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
Another aspect of the application provides a method of treating or preventing cancer in a subject, wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment of cancer, comprising administering to the subject an effective amount of a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier.
In certain embodiments, the application provides a method of treating any of the disorders described herein, wherein the subject is a human. In certain embodiments, the application provides a method of preventing any of the disorders described herein, wherein the subject is a human.
In another aspect, the present application relates to the use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for treating or preventing a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for treating or preventing a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
In another aspect, the present application relates to the use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for inhibiting at least one protein kinase or for modulating (e.g., decreasing) the amount of protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of more than one protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of Bcr-Abl.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting at least one protein kinase or for modulating (e.g., decreasing) the amount of protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of more than one protein kinase. In some embodiments, the bifunctional compound inhibits or modulates (e.g., decreases) the amount of Bcr-Abl.
In another aspect, the present application relates to the use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for inhibiting Bcr-Abl or for modulating (e.g., decreasing) the amount of Bcr-Abl.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting Bcr-Abl or for modulating (e.g., decreasing) the amount of Bcr-Abl.
In another aspect, the present application relates to the use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for treating or preventing a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for treating or preventing a disease (e.g., a disease in which one or more protein kinases play a role). In one aspect, the disease is protein kinase mediated disorder. In one aspect, the disease is a proliferative disease (e.g., a proliferative disease in which one or more protein kinases play a role). In another aspect, the disease is Bcr-Abl mediated disorder.
In another aspect, the present application relates to the use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for treating or preventing cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the treatment or prevention of cancer.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for treating or preventing cancer in a subject, wherein the cancer cell comprises at least one activated protein kinase or wherein the subject is identified as being in need of inhibition of at least one protein kinase for the treatment or prevention of cancer.
In another aspect, the present application relates to the use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for treating or preventing cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment or prevention of cancer.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for treating or preventing cancer in a subject, wherein the cancer cell comprises activated Bcr-Abl or wherein the subject is identified as being in need of Bcr-Abl inhibition for the treatment or prevention of cancer.
In another aspect, the present application relates to the use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for inhibiting at least one protein kinase or modulating (e.g., decreasing) the amount of at least one protein kinase.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting at least one protein kinase or modulating (e.g., decreasing) the amount of at least one protein kinase.
In another aspect, the present application relates to use of a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, in the manufacture of a medicament for inhibiting Bcr-Abl or modulating (e.g., decreasing) the amount of Bcr-Abl.
Another aspect of the present application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer, or pharmaceutically acceptable salt thereof, or a pharmaceutical composition of the application, for use in the manufacture of a medicament for inhibiting Bcr-Abl or modulating (e.g., decreasing) the amount of Bcr-Abl.
In another aspect, the application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, for use in the manufacture of a medicament for treating a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
Another aspect of the application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, for use in the manufacture of a medicament for preventing a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
In still another aspect, the application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, for use in the manufacture of a medicament for treating a disease in which Bcr-Abl plays a role.
In still another aspect, the application provides a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, for use in the manufacture of a medicament for preventing a disease in which Bcr-Abl plays a role.
In another aspect, the application provides a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof for use in treating a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
In another aspect, the application provides a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof for use in preventing a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
In still another aspect, the application provides a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof for use in treating a disease in which Bcr-Abl plays a role.
In still another aspect, the application provides a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof for use in preventing a disease in which Bcr-Abl plays a role.
In another aspect, the application provides a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier, for use in the manufacture of a medicament for treating a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
In another aspect, the application provides a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier, for use in the manufacture of a medicament for preventing a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
In another aspect, the application provides a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier, for use in the manufacture of a medicament for treating a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
In another aspect, the application provides a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier, for use in the manufacture of a medicament for preventing a disease in which a protein kinase plays a role. In some embodiments, the protein kinase is a tyrosine kinase. In other embodiments, the protein kinase is Bcr-Abl.
In still another aspect, the application provides a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier, for use in treating a disease in which Bcr-Abl plays a role.
In still another aspect, the application provides a pharmaceutical composition comprising a bifunctional compound disclosed herein, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof and a pharmaceutically acceptable carrier, for use in preventing a disease in which Bcr-Abl plays a role.
As inhibitors of protein kinases (e.g., Bcr-abl), the bifunctional compounds and compositions of this application are particularly useful for treating or lessening the severity of a disease, condition, or disorder where a protein kinase is implicated in the disease, condition, or disorder. In one aspect, the present application provides a method for treating or lessening the severity of a disease, condition, or disorder where a protein kinase is implicated in the disease state. In another aspect, the present application provides a method for treating or lessening the severity of a protein kinase mediated disease, condition, or disorder where inhibition of enzymatic activity is implicated in the treatment of the disease. In another aspect, this application provides a method for treating or lessening the severity of a disease, condition, or disorder with bifunctional compounds that inhibit enzymatic activity by binding to the protein kinase. Another aspect provides a method for treating or lessening the severity of a protein kinase mediated disease, condition, or disorder by inhibiting enzymatic activity of the protein kinase with a protein kinase inhibitor.
In some embodiments, said method is used to treat or prevent a condition selected from autoimmune diseases, inflammatory diseases, proliferative and hyperproliferative diseases, immunologically-mediated diseases, bone diseases, metabolic diseases, neurological and neurodegenerative diseases, cardiovascular diseases, hormone related diseases, allergies, asthma, and Alzheimer's disease. In other embodiments, said condition is selected from a proliferative disorder and a neurodegenerative disorder.
One aspect of this application provides bifunctional compounds that are useful for the treatment of diseases, disorders, and conditions characterized by excessive or abnormal cell proliferation. Such diseases include, but are not limited to, a proliferative or hyperproliferative disease, and a neurodegenerative disease. Examples of proliferative and hyperproliferative diseases include, without limitation, cancer. The term “cancer” includes, but is not limited to, the following cancers: breast; ovary; cervix; prostate; testis, genitourinary tract; esophagus; larynx, glioblastoma; neuroblastoma; stomach; skin, keratoacanthoma; lung, epidermoid carcinoma, large cell carcinoma, small cell carcinoma, lung adenocarcinoma; bone; colon; colorectal; adenoma: pancreas, adenocarcinoma; thyroid, follicular carcinoma, undifferentiated carcinoma, papillary carcinoma; seminoma; melanoma; sarcoma; bladder carcinoma; liver carcinoma and biliary passages; kidney carcinoma; myeloid disorders; lymphoid disorders, Hodgkin's, hairy cells; buccal cavity and pharynx (oral), lip, tongue, mouth, pharynx; small intestine; colonrectum, large intestine, rectum, brain and central nervous system; chronic myeloid leukemia (CML), and leukemia. The term “cancer” includes, but is not limited to, the following cancers: myeloma, lymphoma, or a cancer selected from gastric, renal, or and the following cancers: head and neck, oropharyngeal, non-small cell lung cancer (NSCLC), endometrial, hepatocarcinoma, Non-Hodgkins lymphoma, and pulmonary.
The term “cancer” refers to any cancer caused by the proliferation of malignant neoplastic cells, such as tumors, neoplasms, carcinomas, sarcomas, leukemias, lymphomas and the like. For example, cancers include, but are not limited to, mesothelioma, leukemias and lymphomas such as cutaneous T-cell lymphomas (CTCL), noncutaneous peripheral T-cell lymphomas, lymphomas associated with human T-cell lymphotrophic virus (HTLV) such as adult T-cell leukemia/lymphoma (ATLL), B-cell lymphoma, acute nonlymphocytic leukemias, chronic lymphocytic leukemia, chronic myelogenous leukemia, acute myelogenous leukemia, lymphomas, and multiple myeloma, non-Hodgkin lymphoma, acute lymphatic leukemia (ALL), chronic lymphatic leukemia (CLL), Hodgkin's lymphoma, Burkitt lymphoma, adult T-cell leukemia lymphoma, acute-myeloid leukemia (AML), chronic myeloid leukemia (CML), or hepatocellular carcinoma. Further examples include myelodisplastic syndrome, childhood solid tumors such as brain tumors, neuroblastoma, retinoblastoma, Wilms' tumor, bone tumors, and soft-tissue sarcomas, common solid tumors of adults such as head and neck cancers (e.g., oral, laryngeal, nasopharyngeal and esophageal), genitourinary cancers (e.g., prostate, bladder, renal, uterine, ovarian, testicular), lung cancer (e.g., small-cell and non-small cell), breast cancer, pancreatic cancer, melanoma and other skin cancers, stomach cancer, brain tumors, tumors related to Gorlin's syndrome (e.g., medulloblastoma, meningioma, etc.), and liver cancer. Additional exemplary forms of cancer which may be treated by the subject bifunctional compounds include, but are not limited to, cancer of skeletal or smooth muscle, stomach cancer, cancer of the small intestine, rectum carcinoma, cancer of the salivary gland, endometrial cancer, adrenal cancer, anal cancer, rectal cancer, parathyroid cancer, and pituitary cancer.
Additional cancers that the bifunctional compounds described herein may be useful in preventing, treating and studying are, for example, colon carcinoma, familiarly adenomatous polyposis carcinoma and hereditary non-polyposis colorectal cancer, or melanoma. Further, cancers include, but are not limited to, labial carcinoma, larynx carcinoma, hypopharynx carcinoma, tongue carcinoma, salivary gland carcinoma, gastric carcinoma, adenocarcinoma, thyroid cancer (medullary and papillary thyroid carcinoma), renal carcinoma, kidney parenchyma carcinoma, cervix carcinoma, uterine corpus carcinoma, endometrium carcinoma, chorion carcinoma, testis carcinoma, urinary carcinoma, melanoma, brain tumors such as glioblastoma, astrocytoma, meningioma, medulloblastoma and peripheral neuroectodermal tumors, gall bladder carcinoma, bronchial carcinoma, multiple myeloma, basalioma, teratoma, retinoblastoma, choroidea melanoma, seminoma, rhabdomyosarcoma, craniopharyngeoma, osteosarcoma, chondrosarcoma, myosarcoma, liposarcoma, fibrosarcoma, Ewing sarcoma, and plasmocytoma. In one aspect of the application, the present application provides for the use of one or more bifunctional compounds of the application in the manufacture of a medicament for the treatment of cancer, including without limitation the various types of cancer disclosed herein.
In some embodiments, the bifunctional compounds of this application are useful for treating cancer, such as colorectal, thyroid, breast, and lung cancer; and myeloproliferative disorders, such as polycythemia vera, thrombocythemia, myeloid metaplasia with myelofibrosis, chronic myelogenous leukemia, chronic myelomonocytic leukemia, hypereosinophilic syndrome, juvenile myelomonocytic leukemia, and systemic mast cell disease. In some embodiments, the bifunctional compounds of this application are useful for treating hematopoietic disorders, in particular, acute-myelogenous leukemia (AML), chronic-myelogenous leukemia (CML), acute-promyelocytic leukemia, and acute lymphocytic leukemia (ALL).
This application further embraces the treatment or prevention of cell proliferative disorders such as hyperplasias, dysplasias and pre-cancerous lesions. Dysplasia is the earliest form of pre-cancerous lesion recognizable in a biopsy by a pathologist. The subject bifunctional compounds may be administered for the purpose of preventing said hyperplasias, dysplasias or pre-cancerous lesions from continuing to expand or from becoming cancerous. Examples of pre-cancerous lesions may occur in skin, esophageal tissue, breast and cervical intra-epithelial tissue.
Another aspect of this application provides a method for the treatment or lessening the severity of a disease selected from a proliferative or hyperproliferative disease, or a neurodegenerative disease, comprising administering an effective amount of a bifunctional compound, or a pharmaceutically acceptable composition comprising a bifunctional compound, to a subject in need thereof.
As inhibitors of a protein kinase (e.g., Bcr-Abl), the compounds and compositions of this application are also useful in biological samples. One aspect of the application relates to inhibiting protein kinase activity in a biological sample, which method comprises contacting said biological sample with a bifunctional compound of the application or a composition comprising said bifunctional compound. The term “biological sample”, as used herein, means an in vitro or an ex vivo sample, including, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof. Inhibition of protein kinase activity in a biological sample is useful for a variety of purposes that are known to one of skill in the art. Examples of such purposes include, but are not limited to, blood transfusion, organ-transplantation, and biological specimen storage.
Another aspect of this application relates to the study of protein kinases (e.g., Bcr-Abl) in biological and pathological phenomena; the study of intracellular signal transduction pathways mediated by such protein kinases; and the comparative evaluation of new protein kinase inhibitors. Examples of such uses include, but are not limited to, biological assays such as enzyme assays and cell-based assays.
The activity of the compounds and compositions of the present application as protein kinase (e.g., Bcr-Abl) inhibitors may be assayed in vitro, in vivo, or in a cell line. In vitro assays include assays that determine inhibition of either the enzyme activity or ATPase activity of the activated kinase. Alternate in vitro assays quantitate the ability of the inhibitor to bind to the protein kinase and may be measured either by radio labelling the inhibitor prior to binding, isolating the inhibitor/protein kinase complex or inhibitor Bcr-Abl kinase complex and determining the amount of radio label bound, or by running a competition experiment where new inhibitors are incubated with the kinase bound to known radioligands. Detailed conditions for assaying a compound utilized in this application as an inhibitor of various kinases are set forth in the Examples below.
In accordance with the foregoing, the present application further provides a method for preventing or treating any of the diseases or disorders described above in a subject in need of such treatment, which method comprises administering to said subject a therapeutically effective amount of a bifunctional compound of the application, or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof. For any of the above uses, the required dosage will vary depending on the mode of administration, the particular condition to be treated and the effect desired.
In another aspect, the application provides a pharmaceutical composition comprising a therapeutically effective amount of a bifunctional compound of the present application or an enantiomer, diastereomer, or stereoisomer thereof, or pharmaceutically acceptable salt, hydrate, solvate, or prodrug thereof, and a pharmaceutically acceptable carrier.
Bifunctional compounds of the application can be administered as pharmaceutical compositions by any conventional route, in particular enterally, e.g., orally, e.g., in the form of tablets or capsules, or parenterally, e.g., in the form of injectable solutions or suspensions, or topically, e.g., in the form of lotions, gels, ointments or creams, or in a nasal or suppository form. Pharmaceutical compositions comprising a compound of the present application in free form or in a pharmaceutically acceptable salt form in association with at least one pharmaceutically acceptable carrier or diluent can be manufactured in a conventional manner by mixing, granulating or coating methods. For example, oral compositions can be tablets or gelatin capsules comprising the active ingredient together with a) diluents, e.g., lactose, dextrose, sucrose, mannitol, sorbitol, cellulose and/or glycine; b) lubricants, e.g., silica, talcum, stearic acid, its magnesium or calcium salt and/or polyethyleneglycol; for tablets also c) binders, e.g., magnesium aluminum silicate, starch paste, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose and or polyvinylpyrrolidone; if desired d) disintegrants, e.g., starches, agar, alginic acid or its sodium salt, or effervescent mixtures; and/or e) absorbents, colorants, flavors and sweeteners. Injectable compositions can be aqueous isotonic solutions or suspensions, and suppositories can be prepared from fatty emulsions or suspensions. The compositions may be sterilized and/or contain adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure and/or buffers. In addition, they may also contain other therapeutically valuable substances. Suitable formulations for transdermal applications include an effective amount of a compound of the present application with a carrier. A carrier can include absorbable pharmacologically acceptable solvents to assist passage through the skin of the host. For example, transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin. Matrix transdermal formulations may also be used. Suitable formulations for topical application, e.g., to the skin and eyes, are preferably aqueous solutions, ointments, creams or gels well-known in the art. Such may contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.
The pharmaceutical compositions of the present application comprise a therapeutically effective amount of a compound of the present application formulated together with one or more pharmaceutically acceptable carriers. As used herein, the term “pharmaceutically acceptable carrier” means a non-toxic, inert solid, semi-solid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type. Some examples of materials which can serve as pharmaceutically acceptable carriers include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, or potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, polyacrylates, waxes, polyethylenepolyoxy propylene-block polymers, wool fat, sugars such as lactose, glucose and sucrose; starches such as corn starch and potato starch; cellulose and its derivatives such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients such as cocoa butter and suppository waxes, oils such as peanut oil, cottonseed oil; safflower oil; sesame oil; olive oil; corn oil and soybean oil; glycols such a propylene glycol or polyethylene glycol; esters such as ethyl oleate and ethyl laurate, agar; buffering agents such as magnesium hydroxide and aluminum hydroxide; alginic acid; pyrogen-free water, isotonic saline; Ringer's solution; ethyl alcohol, and phosphate buffer solutions, as well as other non-toxic compatible lubricants such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, releasing agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the composition, according to the judgment of the formulator.
The pharmaceutical compositions of this application can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), buccally, or as an oral or nasal spray.
Liquid dosage forms for oral administration include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, 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, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.
Injectable preparations, for example, sterile injectable aqueous, or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.
In order to prolong the effect of a drug, it is often desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.
Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this application with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.
Solid compositions of a similar type may also be employed as fillers in soft and hard filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like.
The active compounds can also be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents.
Dosage forms for topical or transdermal administration of a compound of this application include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches.
The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, ear drops, eye ointments, powders and solutions are also contemplated as being within the scope of this application.
The ointments, pastes, creams and gels may contain, in addition to an active compound of this application, 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.
Powders and sprays can contain, in addition to the compounds of this application, 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.
Transdermal patches have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms can be made by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.
Compounds and compositions of the application can be administered in therapeutically effective amounts in a combinational therapy with one or more therapeutic agents (pharmaceutical combinations) or modalities, e.g., an anti-proliferative, anti-cancer, immunomodulatory or anti-inflammatory agent. Where the compounds of the application are administered in conjunction with other therapies, dosages of the co-administered compounds will of course vary depending on the type of co-drug employed, on the specific drug employed, on the condition being treated and so forth. Compounds and compositions of the application can be administered in therapeutically effective amounts in a combinational therapy with one or more therapeutic agents (pharmaceutical combinations) or modalities, e.g., anti-proliferative, anti-cancer, immunomodulatory or anti-inflammatory agent, and/or non-drug therapies, etc. For example, synergistic effects can occur with anti-proliferative, anti-cancer, immunomodulatory or anti-inflammatory substances. Where the compounds of the application are administered in conjunction with other therapies, dosages of the co-administered compounds will of course vary depending on the type of co-drug employed, on the specific drug employed, on the condition being treated and so forth.
Combination therapy includes the administration of the subject compounds in further combination with one or more other biologically active ingredients (such as, but not limited to, a second Bcr-Abl inhibitor, a second and different antineoplastic agent, a kinase inhibitor and non-drug therapies (such as, but not limited to, surgery or radiation treatment). For instance, the compounds of the application can be used in combination with other pharmaceutically active compounds, preferably compounds that are able to enhance the effect of the compounds of the application. The compounds of the application can be administered simultaneously (as a single preparation or separate preparation) or sequentially to the other drug therapy or treatment modality. In general, a combination therapy envisions administration of two or more drugs during a single cycle or course of therapy.
In another aspect of the application, the compounds may be administered in combination with one or more separate pharmaceutical agents, e.g., a chemotherapeutic agent, an immunotherapeutic agent, or an adjunctive therapeutic agent.
All reactions are monitored on a Waters Acquity UPLC/MS system (Waters PDA eλ Detector, QDa Detector, Sample manager—FL, Binary Solvent Manager) using Acquity UPLC® BEH C18 column (2.1×50 mm, 1.7 μm particle size): solvent gradient=90% A at 0 min, 1% A at 1.8 min; solvent A=0.1% formic acid in Water; solvent B=0.1% formic acid in Acetonitrile; flow rate: 0.6 mL/min. Reaction products are purified by flash column chromatography using CombiFlash® Rf with Teledyne Isco RediSep® Rf High Performance Gold or Silicycle SiliaSep™ High Performance columns (4 g, 12 g, 24 g, 40 g, or 80 g), Waters HPLC system using SunFire™ Prep C18 column (19×100 mm, 5 μm particle size): solvent gradient=80% A at 0 min, 5% A at 25 min; solvent A=0.035% TFA in Water; solvent B=0.035% TFA in MeOH; flow rate: 25 mL/min (Method A), and Waters Acquity UPLC/MS system (Waters PDA eλ Detector, QDa Detector, Sample manager—FL, Binary Solvent Manager) using Acquity UPLC® BEH C18 column (2.1×50 mm, 1.7 m particle size): solvent gradient=80% A at 0 min, 5% A at 2 min; solvent A=0.1% formic acid in Water; solvent B=0.1% formic acid in Acetonitrile; flow rate: 0.6 mL/min (method B). The purity of all compounds is over 95% and is analyzed with Waters LC/MS system. 1H NMR is obtained using a 500 MHz Bruker Avance III. Chemical shifts are reported relative to dimethyl sulfoxide (δ=2.50), chloroform (δ=7.26) or methanol (δ=3.35) for 1H NMR. Data are reported as (b=broad, s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet).
Abbreviations used in the following examples and elsewhere herein are:
To a solution of 4-nitro-2-(trifluoromethyl)benzaldehyde (2a, 300 mg, 1.37 mmol, 1 equiv) in CH2Cl2 (5.48 mL, 0.25 M) was added tert-butyl (3-(piperazin-1-yl)propyl)-carbamate (400 mg, 1.64 mmol, 1.2 equiv), NaBH(OAc)3 (435 mg, 2.05 mmol, 1.5 equiv) and AcOH (118 μL, 2.05 mmol, 1.5 equiv). The reaction mixture was stirred under an atmosphere of nitrogen overnight, whereupon it was taken up in CH2Cl2 (25 mL) and NaHCO3 (25 mL). The organic layer was then washed with water (25 mL) and brine (2×25 mL). The combined organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 10% MeOH in CH2Cl2) to afford compound 2b as a colorless thick oil (414 mg, 68%). 1H NMR (500 MHz, CDCl3) δ 8.50 (d, J=2.3 Hz, 1H), 8.37 (dd, J=8.6, 2.4 Hz, 1H), 8.10 (d, J=8.6 Hz, 1H), 5.43 (s, 1H), 3.74 (s, 2H), 3.24-3.15 (m, 2H), 2.58-2.40 (m, 10H), 1.66 (p, J=6.6 Hz, 2H), 1.44 (s, 9H). MS (ESI) [M+H]+: 447.9.
To a solution of tert-butyl (3-(4-(4-nitro-2-(trifluoromethyl)benzyl)piperazin-1-yl)propyl)carbamate (2b, 414 mg, 0.927 mmol, 1 equiv) in THF:water (8:1) (0.1 M) was added KF (108 mg, 1.86 mmol, 2 equiv) and Pd(OAc)2 (21 mg, 0.0927 mmol, 0.1 equiv), followed by the slow addition of Et3SiH (592 μL, 3.71 mmol, 4 equiv). The reaction was stirred at room temperature for 30 min, whereupon it was filtered through a pad of celite, which was washed with EtOAc (25 mL). The combined organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. The residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2) to afford compound 2-1 as a grey oil (119 mg, 31%). (See Rahaim et al., Org. Lett. 2005, 7, 5087-5090.) 1H NMR (500 MHz, CDCl3) δ 7.47 (d, J=8.3 Hz, 1H), 6.91 (d, J=2.5 Hz, 1H), 6.79 (dd, J=8.4, 2.5 Hz, 1H), 5.59 (s, 1H), 3.76 (s, 2H), 3.52 (d, J=1.6 Hz, 2H), 3.19 (q, J=6.1 Hz, 2H), 2.60-2.33 (m, 10H), 1.70-1.58 (m, 2H), 1.44 (s, 9H). MS (ESI) [M+H]+: 417.4.
A solution of 6-aminohexanoic acid (3a, 300 mg, 2.29 mmol, 1 equiv) in SOCl2 (1595 μL, 22.9 mmol, 10 equiv) was stirred at room temperature for 1.5 hours, whereupon excess SOCl2 was removed in vacuo. A solution of NaHCO3 (423 mg, 5.03 mmol, 2.2 equiv) in tBuOH (5 mL) was then added to the residue, and the resulting mixture was stirred overnight at room temperature. The volatiles were removed in vacuo, and the resulting residue was taken up in EtOAc (30 mL) and NaOH (1M, aq) (20 mL). The combined organic layers were washed with water (30 mL) and brine (3×20 mL), dried over Na2SO4, filtered, and concentrated in vacuo, to give compound 3b as a colorless oil (258 mg, 60%), which was used in the next step without further purification. 1H NMR (400 MHz, CDCl3) δ 2.69 (t, J=7.0 Hz, 1H), 2.21 (t, J=7.4 Hz, 1H), 1.63-1.54 (m, 1H), 1.50-1.45 (m, 2H), 1.44 (s, 6H), 1.39-1.31 (m, 1H).
To a stirred solution of 2-(2,6-dioxopiperidin-3-yl)-4-fluoroisoindoline-1,3-dione (3c, 50 mg, 0.181 mmol, 1 equiv) in NMP (905 μL, 0.2 M) was added DIPEA (63.1 μL, 0.724 mmol, 2 equiv) and tert-butyl 6-aminohexanoate (3b, 37.3 mg, 0.199 mmol, 1.1 equiv). The reaction mixture was then heated to 90° C. overnight, and then cooled to room temperature. EtOAc (20 mL) was added and the organic layer was washed with water (20 mL) and brine (3×20 mL), dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2) to give compound 3d as a yellow solid (52 mg, 65%). 1H NMR (400 MHz, CDCl3) δ 8.80 (s, 1H), 7.44 (dd, J=8.5, 7.1 Hz, 1H), 7.03 (d, J=7.1 Hz, 1H), 6.83 (d, J=8.5 Hz, 1H), 6.19 (t, J=5.6 Hz, 1H), 4.90-4.83 (m, 1H), 3.28-3.18 (m, 2H), 2.87-2.58 (m, 3H), 2.24-2.13 (m, 4H), 2.12-2.04 (m, 1H), 1.70-1.51 (m, 4H), 1.39 (s, 9H). MS (ESI) [M+H]+: 444.3.
To tert-butyl 6-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)hexanoate (3d, 22 mg, 0.0496 mmol, 1 equiv) was added HCl (4M, dioxane) (300 μL). The reaction mixture was stirred at room temperature for 1 h, and then concentrated in vacuo to give compound 3-1 as a white solid (23 mg, quantitative), that was used in the next step without further purification. MS (ESI) [M+H]+: 388.2.
A solution of 4-nitro-2-(trifluoromethyl)benzaldehyde (4a, 200 mg, 0.913 mmol, 1 equiv) in CH2Cl2 (4.50 mL, 0.2 M) was added tert-butyl piperazine-1-carboxylate (204 mg, 1.10 mmol, 1.2 equiv), NaBH(OAc)3 (290 mg, 1.37 mmol, 1.5 equiv) and AcOH (78 μL, 1.37 mmol, 1.5 equiv). The reaction was stirred under an atmosphere of N2 overnight, whereupon it was taken up in CH2Cl2 (25 mL) and NaHCO3 (25 mL). The organic layer was washed with water (25 mL) and brine (2×25 mL). The organic layers were dried over Na2SO4 and concentrated in vacuo. The residue was purified by flash column chromatography on silica gel (eluting with 0 to 100% EtOAc in hexanes) to afford compound 4b as a colorless thick oil (246 mg, 69%). 1H NMR (500 MHz, CDCl3) δ 8.51 (d, J=2.3 Hz, 1H), 8.38 (dd, J=8.6, 2.4 Hz, 1H), 8.11 (d, J=8.6 Hz, 1H), 3.75 (s, 2H), 3.46 (t, J=5.1 Hz, 4H), 2.45 (t, J=5.1 Hz, 4H), 1.46 (s, 9H). MS (ESI) [M+H]+: 390.4.
To a solution of tert-butyl 4-(4-nitro-2-(trifluoromethyl)benzyl)piperazine-1-carboxylate (4b, 219 mg, 0.562 mmol, 1 equiv) in THF:water (8:1) (0.1 M) was added KF (65 mg, 1.13 mmol, 2 equiv) and Pd(OAc)2 (12.6 mg, 0.0562 mmol, 0.1 equiv), followed by the slow addition of Et3SiH (359 μL, 2.25 mmol, 4 equiv). The reaction was stirred at room temperature for 30 min, and then filtered through a pad of celite. The celite was washed with EtOAc (25 mL). The combined organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2 to afford compound 4-1 as a grey oil (107 mg, 50%). 1H NMR (500 MHz, CDCl3) δ 7.47 (d, J=8.2 Hz, 1H), 6.92 (d, J=2.5 Hz, 1H), 6.79 (dd, J=8.3, 2.5 Hz, 1H), 3.77 (s, 2H), 3.52 (d, J=1.6 Hz, 2H), 3.41 (t, J=5.1 Hz, 4H), 2.38 (t, J=5.0 Hz, 4H), 1.45 (s, 9H). MS (ESI) [M+H]+: 360.1.
To a stirred solution of 2-(2,6-dioxopiperidin-3-yl)-5-fluoroisoindoline-1,3-dione (5a, 74 mg, 0.268 mmol, 1 equiv) in NMP (1.3 mL, 0.2 M) was added DIPEA (93.3 μL, 0.536 mmol, 2 equiv) and tert-butyl 6-aminohexanoate (3b, 55.2 mg, 0.295 mmol, 1.1 equiv). The reaction mixture was heated to 90° C. overnight, and then cooled to room temperature. EtOAc (20 mL) was added. The organic layer was washed with water (20 mL) and brine (3×20 mL), dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2) to give compound 5b as a yellow solid (18 mg, 15%). 1H NMR (400 MHz, CDCl3) δ 8.31 (s, 1H), 7.57 (d, J=8.3 Hz, 1H), 6.91 (d, J=2.2 Hz, 1H), 6.70 (dd, J=8.3, 2.2 Hz, 1H), 4.92 (dd, J=12.3, 5.3 Hz, 1H), 4.71 (t, J=5.4 Hz, 1H), 3.46-3.31 (m, 2H), 3.20 (td, J=7.0, 5.4 Hz, 2H), 2.94-2.63 (m, 3H), 2.25-2.19 (m, 2H), 2.15-2.06 (m, 1H), 1.69-1.55 (m, 4H), 1.44 (s, 9H). MS (ESI) [M+H]+: 444.3.
To tert-butyl 6-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)amino)hexanoate (5b, 18 mg, 0.0406 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h, and then concentrated in vacuo to give compound 5-1 as a white solid (18 mg, quantitative), which was used in the next step without further purification. MS (ESI) [M+H]+: 388.3.
A solution of 8-aminooctanoic acid (6a, 300 mg, 1.88 mmol, 1 equiv) in SOCl2 (1313 μL, 18.1 mmol, 10 equiv) was stirred at room temperature for 1.5 hours and then concentrated in vacuo to remove excess SOCl2. A solution of NaHCO3 (348 mg, 4.15 mmol, 2.2 equiv) in tBuOH (5 mL) was added to the residue, and the reaction mixture was stirred overnight at room temperature. The volatiles were removed in vacuo, and the resulting residue was taken up in EtOAc (30 mL) and NaOH (1M, aq) (20 mL). The organic layer was washed with water (30 mL) and brine (3×20 mL), dried over Na2SO4, filtered, and concentrated in vacuo, to give compound 6b as a colorless oil (330 mg, 81%). The product was used in the next step without further purification. 1H NMR (500 MHz, CDCl3) δ 2.67 (t, J=7.0 Hz, 2H), 2.19 (t, J=7.5 Hz, 2H), 1.57 (p, J=7.2, 6.7 Hz, 2H), 1.43 (s, 9H), 1.30 (d, J=4.0 Hz, 10H). 13C NMR (126 MHz, CDCl3) δ 173.4, 80.1, 42.3, 35.7, 33.8, 29.3, 29.2, 28.3, 26.9, 25.2.
To a stirred solution of 2-(2,6-dioxopiperidin-3-yl)-4-fluoroisoindoline-1,3-dione (3c, 100 mg, 0.362 mmol, 1 equiv) in NMP (1.8 mL, 0.2 M) was added DIPEA (126.1 μL, 0.724 mmol, 2 equiv) and tert-butyl 8-aminooctanoate (6b, 78 mg, 0.362 mmol, 1 equiv). The reaction mixture was heated to 90° C. overnight, then cooled to room temperature and taken up in EtOAc (20 mL). The organic layer was washed with water (20 mL) and brine (3×20 mL), and then dried over Na2SO4, filtered, and concentrated in vacuo. The residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2) to give compound 6c as a yellow solid (69 mg, 41%). 1H NMR (500 MHz, CDCl3) δ 8.05 (s, 1H), 7.49 (dd, J=8.5, 7.1 Hz, 1H), 7.08 (d, J=7.0 Hz, 1H), 6.87 (d, J=8.5 Hz, 1H), 6.22 (s, 1H), 4.95-4.86 (m, 1H), 3.25 (t, J=7.1 Hz, 2H), 3.00-2.68 (m, 3H), 2.20 (t, J=7.5 Hz, 2H), 2.17-2.08 (m, 1H), 1.70-1.53 (m, 4H), 1.44 (s, 9H), 1.38-1.30 (m, 6H).
Tert-butyl 8-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)octanoate (6c, 53 mg, 0.0857 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo to give compound 6-1 as a white solid (38 mg, quantitative yield), which was used in the next step without further purification. MS (ESI) [M+H]+: 416.3.
To a stirred solution of 2-(2,6-dioxopiperidin-3-yl)-5-fluoroisoindoline-1,3-dione (5a, 100 mg, 0.362 mmol, 1 equiv) in NMP (1.8 mL, 0.2 M) was added DIPEA (126.1 μL, 0.724 mmol, 2 equiv) and tert-butyl 8-aminooctanoate (6b, 78 mg, 0.362 mmol, 1 equiv). The reaction mixture was heated to 90° C. overnight and then cooled to room temperature and taken up in EtOAc (20 mL). The organic layer was washed with water (20 mL) and brine (3×20 mL), then dried over Na2SO4, filtered and concentrated in vacuo. The residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2) to give compound 7a as a yellow solid (56 mg, 33%). 1H NMR (500 MHz, CDCl3) δ 8.27 (s, 1H), 7.58 (d, J=8.3 Hz, 1H), 6.93 (d, J=2.1 Hz, 1H), 6.71 (dd, J=8.3, 2.2 Hz, 1H), 4.94-4.88 (m, 1H), 4.59 (s, 1H), 3.19 (t, J=7.2 Hz, 2H), 2.94-2.66 (m, 3H), 2.24-2.17 (m, 2H), 2.16-2.03 (m, 1H), 1.68-1.53 (m, 4H), 1.43 (s, 9H), 1.40-1.27 (m, 6H).
To tert-butyl 8-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)amino)octanoate (7a, 30.1 mg, 0.0490 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo to give compound 7-1 as a white solid (25 mg, quantitative yield), which was used in the next step without further purification. MS (ESI) [M+H]+: 416.3.
To a stirred solution of 2-(2,6-dioxopiperidin-3-yl)-4-fluoroisoindoline-1,3-dione (3c, 172 mg, 0.623 mmol, 1 equiv) in NMP (3.1 mL, 0.2 M) was added DIPEA (325 μL, 1.87 mmol, 3 equiv) and 8-aminooctanol (99 mg, 0.684 mmol, 1 equiv). The reaction mixture was heated to 90° C. overnight and then cooled to room temperature. EtOAc (20 mL) was added. The organic layer was washed with water (20 mL) and brine (3×20 mL), dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2) to give the title compound 8a, as a yellow oil (69 mg, 28%). MS (ESI) [M+H]+: 402.4.
To a stirred solution of 2-(2,6-dioxopiperidin-3-yl)-4-((8-hydroxyoctyl)amino) isoindoline-1,3-dione (8a, 60 mg, 0.150 mmol, 1 equiv) in CH2Cl2 (747 μL, 0.2 M) was added Et3N (18 μL, 0.224 mmol, 1.5 equiv). TsCl (35 mg, 0.179 mmol, 1.2 equiv) in CH2Cl2 (0.9 mL, 0.2 M) was then added dropwise, and the resulting mixture was heated to 40° C. for three days. The reaction mixture was taken up in CH2Cl2 (20 mL), washed with saturated NaHCO3 (aq) (20 mL), water (20 mL) and brine (3×20 mL), dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 100% EtOAc in hexanes) to give the title compound 8b as a yellow oil (17 mg, 20%). MS (ESI) [M+H]+: 419.3.
To a stirred solution of 4-((8-chlorooctyl)amino)-2-(2,6-dioxopiperidin-3-yl)isoindoline-1,3-dione (8b, 37 mg, 0.0881 mmol, 1 equiv) in acetone (881 μL, 0.1 M) was added KI (70.2 mg, 0.423 mmol, 4.8 equiv) and the reaction was heated to 70° C. for three days. The reaction mixture was concentrated in vacuo and then EtOAc (15 mL) and water were added. The organic layer was isolated, dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 5% MeOH in CH2Cl2) to give the title compound 8-1 as a yellow oil (12 mg, 27%). MS (ESI) [M+H]+: 512.5.
A solution of 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzoic acid (9a, 95 mg, 0.343 mmol, 1 equiv) in SOCl2 was heated to 50° C. for 4.5 h and then concentrated in vacuo to remove excess SOCl2. The resulting residue was dispersed in EtOAc (2 mL) and cooled to 0° C. A solution of tert-butyl (3-(4-(4-amino-2-(trifluoromethyl)benzyl)piperazin-1-yl)propyl) carbamate (2-1, 119 mg, 0.285 mmol, 0.83 equiv) and DIPEA (298 μL, 1.71 mmol, 5 equiv) in EtOAc (2 mL) was then added. The reaction mixture was warmed to ambient temperature and NaHCO3 (20 mL) was added, followed by CH2Cl2 (50 mL) to dissolve the precipitate. The aqueous phase was extracted with CH2Cl2 (20 mL) and the combined organic layers were washed with brine (2×30 mL), dried over Na2SO4, filtered, and concentrated in vacuo. The residue was purified by flash column chromatography on silica gel (eluting with 0 to 10% MeOH in CH2Cl2) to afford compound 9b as a grey solid (144 mg, 62%). 1H NMR (500 MHz, CDCl3) δ 8.49 (dd, J=4.4, 1.7 Hz, 1H), 8.08 (s, 1H), 8.06 (d, J=2.1 Hz, 2H), 8.00 (dd, J=9.2, 1.6 Hz, 1H), 7.93-7.88 (m, 2H), 7.83 (dd, J=8.0, 2.0 Hz, 1H), 7.78 (s, 1H), 7.41 (d, J=8.0 Hz, 1H), 7.15 (dd, J=9.2, 4.4 Hz, 1H), 5.54 (s, 1H), 3.64 (s, 2H), 3.25-3.14 (m, 2H), 2.65 (s, 3H), 2.59 (s, 10H), 1.69 (s, 2H), 1.44 (s, 9H). MS (ESI) [M+H]+: 673.5.
Tert-butyl (3-(4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl)benzyl)piperazin-1-yl)propyl)carbamate (9b, 50 mg, 0.074 mmol, 1 equiv) was dissolved in CH2Cl2 (0.8 mL) and TFA (0.8 mL) was added. The resulting mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The residue was triturated with ice cold ether to afford compound 9c as a colorless oil (76 mg, quantitative yield), which was used in the next step without further purification. MS (ESI) [M+H]+: 573.5.
To a solution of N-(4-((4-(3-aminopropyl)piperazin-1-yl)methyl)-3-(trifluoromethyl) phenyl)-3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamide (9c, 64 mg, 0.074 mmol, 1 equiv) in DMF (0.06 M) was added succinic anhydride (11 mg, 0.111 mmol, 1.5 equiv), Et3N (62 μL, 0.443 mmol, 6 equiv) and DMAP (13.5 mg, 0.111 mmol, 1 equiv). The reaction mixture was stirred at room temperature overnight, then diluted with MeOH (3 mL) and filtered. The filtrate was purified via preparative HPLC to afford compound 9-1 as a white solid (56 mg, 88%). 1H NMR (500 MHz, Methanol-d4) δ 8.70 (dd, J=4.5, 1.3 Hz, 1H), 8.21-8.10 (m, 4H), 7.94 (dd, J=8.5, 2.2 Hz, 1H), 7.85 (dd, J=8.0, 2.0 Hz, 1H), 7.70 (d, J=8.5 Hz, 1H), 7.47 (dd, J=9.2, 4.5 Hz, 1H), 7.42 (d, J=8.1 Hz, 1H), 3.77 (s, 2H), 3.33-3.20 (m, 9H), 3.12 (t, J=7.4 Hz, 2H), 2.63-2.56 (m, 6H), 2.44 (dd, J=7.3, 5.7 Hz, 2H), 1.98-1.84 (m, 2H). MS (ESI) [M+H]+: 676.4.
To a solution of N-(4-aminobutyl)-2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)oxy)acetamide (10a, 10.4 mg, 0.02 mmol, 1 equiv) in DMF (200 μL, 0.1 M) in a 4 mL vial was added 4-((3-(4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl)benzyl)piperazin-1-yl)propyl)amino)-4-oxobutanoic acid (9-1, 17.6 mg, 0.02 mmol, 1 equiv), HATU (7.7 mg, 0.02 mmol, 1 equiv) and DIPEA (21.1 μL, 0.06 mmol, 6 equiv). The reaction mixture was stirred at room temperature overnight and EtOAc (15 mL) and NaHCO3 (15 mL) were then added. The organic layers were washed with water (10 mL) and brine (3×15 mL), dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting with 0 to 10% MeOH in CH2Cl2) to afford compound I-2 as a colorless oil (4.3 mg, 16%). 1H NMR (500 MHz, Methanol-d4) δ 8.65 (dd, J=4.4, 1.6 Hz, 1H), 8.19-8.15 (m, 2H), 8.12 (dt, J=9.2, 1.6 Hz, 1H), 8.10-8.07 (m, 1H), 7.96 (dd, J=8.4, 2.3 Hz, 1H), 7.90 (dd, J=8.1, 2.1 Hz, 1H), 7.82-7.75 (m, 2H), 7.54-7.47 (m, 2H), 7.44-7.35 (m, 2H), 5.15 (dd, J=12.7, 5.5 Hz, 1H), 4.75 (s, 2H), 3.70 (s, 2H), 3.35-3.31 (m, 2H), 3.28-3.15 (m, 4H), 2.95-2.55 (m, 13H), 2.66 (s, 3H), 2.53-2.42 (m, 4H), 2.20-2.12 (m, 1H), 1.83-1.73 (m, 2H), 1.65-1.50 (m, 4H). MS (ESI) [M+H]+: 1060.5.
To a solution of N-(8-aminooctyl)-2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)oxy)acetamide (11a, 11.6 mg, 0.02 mmol, 1 equiv) in DMF (200 μL, 0.1 M) in a 4 mL vial was added 4-((3-(4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl) benzyl)piperazin-1-yl)propyl)amino)-4-oxobutanoic acid (9-1, 17.6 mg, 0.02 mmol, 1 equiv), HATU (7.7 mg, 0.0200 mmol, 1 equiv) and DIPEA (21.1 μL, 0.06 mmol, 6 equiv). The resulting mixture was stirred at room temperature overnight, then diluted with MeOH (3 mL) and filtered. The filtrate was purified by preparative HPLC to afford compound I-3 as a colorless oil (7.6 mg, 30%). 1H NMR (500 MHz, Methanol-d4) δ 8.77 (d, J=4.4 Hz, IH), 8.27-8.20 (m, 2H), 8.15 (t, J=1.6 Hz, 2H), 8.00 (dd, J=8.4, 2.3 Hz, 1H), 7.89 (dd, J=8.0, 2.0 Hz, 1H), 7.77-7.70 (m, 2H), 7.55 (d, J=7.9 Hz, 1H), 7.45 (dd, J=7.7, 5.4 Hz, 2H), 7.34 (d, J=8.4 Hz, 1H), 5.10 (dd, J=12.6, 5.4 Hz, 1H), 4.67 (s, 2H), 3.79 (s, 2H), 3.35-3.21 (m, 17H), 3.19 (t, J=7.3 Hz, 2H), 3.08 (t, J=7.2 Hz, 2H), 2.91-2.80 (m, 3H), 2.77-2.64 (m, 3H), 2.62 (s, 3H), 2.55-2.40 (m, 4H), 2.17-2.08 (m, 1H), 1.93 (d, J=6.5 Hz, 2H), 1.56-1.46 (m, 2H), 1.47-1.38 (m, 2H). MS (ESI) [M+H]+: 1116.6.
To a solution of N-(3-(2-(2-(3-aminopropoxy)-ethoxy)ethoxy)propyl)-2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)oxy)acetamide (12a, 0.7 mg, 0.0200 mmol, 1 equiv) in DMF (200 μL, 0.1 M) in a 4 mL vial was added 4-((3-(4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl)benzyl)pipera-zin-1-yl)propyl)amino)-4-oxobutanoic acid (9-1, 17.6 mg, 0.02 mmol, 1 equiv), HATU (7.7 mg, 0.02 mmol, 1 equiv) and DIPEA (21.1 μL, 0.06 mmol, 6 equiv). The reaction mixture was stirred at room temperature overnight, whereupon it was diluted with MeOH (3 mL) and filtered. The filtrate was purified by preparative HPLC to afford compound I-4 as a colorless oil (9.3 mg, 32%). 1H NMR (500 MHz, Methanol-d4) δ 8.77 (dd, J=4.5, 1.4 Hz, 1H), 8.28-8.21 (m, 2H), 8.16 (dd, J=6.4, 2.2 Hz, 2H), 8.00 (dd, J=8.5, 2.3 Hz, 1H), 7.90 (dd, J=8.0, 2.0 Hz, 1H), 7.78-7.72 (m, 2H), 7.55 (dd, J=9.2, 4.5 Hz, 1H), 7.50-7.46 (m, 2H), 7.37 (d, J=8.4 Hz, 1H), 5.10 (dd, J=12.5, 5.5 Hz, 1H), 4.71 (s, 2H), 3.80 (s, 2H), 3.61-3.48 (m, 13H), 3.45 (t, J=6.1 Hz, 2H), 3.37 (t, J=6.7 Hz, 4H), 3.33-3.30 (m, 4H), 3.19 (t, J=7.0 Hz, 4H), 2.91-2.81 (m, 2H), 2.77-2.67 (m, 2H), 2.64 (s, 3H), 2.55-2.41 (m, 4H), 2.18-2.08 (m, 1H), 1.98-1.89 (m, 2H), 1.78 (p, J=6.4 Hz, 2H), 1.69 (p, J=6.5 Hz, 2H). MS (ESI) [M+H]+: 1192.6.
A solution of 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzoic acid (9a, 95 mg, 0.343 mmol, 1 equiv) in SOCl2 was heated to 50° C. for 4.5 h and then concentrated in vacuo to remove the excess SOCl2. The resulting residue was dispersed in EtOAc (2 mL) and cooled to 0° C. A solution of tert-butyl 4-(4-amino-2-(trifluoromethyl)benzyl)piperazine-1-carboxylate (4-1, 103 mg, 0.285 mmol, 0.83 equiv) and DIPEA (298 μL, 1.71 mmol, 5 equiv) in EtOAc (2 mL) was then added. The reaction mixture was warmed to ambient temperature and NaHCO3 (20 mL) and CH2Cl2 (50 mL) were then added to dissolve the precipitate. The aqueous phase was extracted with CH2Cl2 (20 mL) and the combined organic layers were washed with brine (2×30 mL), dried over Na2SO4, filtered, and concentrated in vacuo. The resulting residue was purified by flash column chromatography on silica gel (eluting 0 to 10% MeOH in CH2Cl2) to afford compound 13-1 as a grey solid (114 mg, 49%). 1H NMR (500 MHz, CDCl3) δ 8.93 (s, 1H), 8.45 (dd, J=4.4, 1.6 Hz, 1H), 8.09 (s, 1H), 8.03 (d, J=2.0 Hz, 1H), 7.99-7.94 (m, 2H), 7.88 (dd, J=9.2, 1.6 Hz, 1H), 7.82 (dd, J=8.0, 2.0 Hz, 1H), 7.75 (d, J=9.1 Hz, 1H), 7.33 (d, J=8.1 Hz, 1H), 7.09 (dd, J=9.2, 4.4 Hz, 1H), 3.61 (s, 2H), 3.42 (t, J=5.0 Hz, 4H), 2.59 (s, 3H), 2.39 (t, J=5.0 Hz, 4H), 1.45 (s, 9H). MS (ESI) [M+H]+: 619.3.
To tert-butyl 4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl)benzyl)piperazine-1-carboxylate (13-1, 15.4 mg, 0.0248 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The resulting residue was taken up in DMF (248 μL), and 6-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)hexanoic acid (3-1, 9.6 mg, 0.0248 mmol, 1 equiv), HATU (9.4 mg, 0.0248 mmol, 1 equiv) and DIPEA (21.6 μL, 0.124 mmol, 5 equiv) were added. The reaction mixture was stirred at room temperature overnight and then diluted with MeOH and filtered. The filtrate was purified by preparative HPLC to give compound I-5 as a bright green solid (6.5 mg, 26%). 1H NMR (500 MHz, DMSO-d6) δ 11.09 (s, 1H), 10.74 (s, 1H), 8.73 (dd, J=4.5, 1.6 Hz, 1H), 8.32 (s, 1H), 8.30-8.21 (m, 4H), 7.97 (dd, J=8.0, 2.0 Hz, 1H), 7.90-7.84 (m, 1H), 7.62-7.56 (m, 2H), 7.41 (dd, J=9.2, 4.4 Hz, 1H), 7.10 (d, J=8.7 Hz, 1H), 7.03 (d, J=7.0 Hz, 1H), 6.53 (s, 1H), 5.05 (dd, J=12.8, 5.5 Hz, 1H), 4.63-4.33 (m, 4H), 3.51-3.34 (m, 4H), 3.30 (s, 2H), 2.96-2.82 (m, 1H), 2.66-2.59 (m, 2H), 2.62 (s, 3H), 2.59-2.55 (m, 2H), 2.42-2.32 (m, 2H), 2.07-1.98 (m, 1H), 1.65-1.51 (m, 4H), 1.44-1.32 (m, 2H). MS (ESI) [M+H]+: 888.5.
To tert-butyl (3-(4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl)benzyl)piperazin-1-yl)propyl)carbamate (9b, 50 mg, 0.074 mmol, 1 equiv) was dissolved in CH2Cl2 (0.8 mL) and TFA (0.8 mL) was added. The resulting mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The resulting residue was dissolved in in DMF (248 μL) and N-(4-((4-(3-aminopropyl)piperazin-1-yl)methyl)-3-(trifluoromethyl) phenyl)-3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamide (9c, 0.0248 mmol) was added 6-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)hexanoic acid (3-1, 9.6 mg, 0.0248 mmol, 1 equiv), HATU (9.4 mg, 0.0248 mmol, 1 equiv) and DIPEA (21.6 μL, 0.124 mmol, 5 equiv). The resulting mixture was stirred at room temperature overnight and then diluted with MeOH and filtered. The filtrate was purified by preparative HPLC to give the title compound I-6 as a bright green solid (12.5 mg, 48%). 1H NMR (500 MHz, DMSO-d6) δ 11.09 (s, 1H), 10.60 (s, 1H), 9.35 (s, 1H), 8.73 (dd, J=4.4, 1.6 Hz, 1H), 8.27 (dd, J=9.2, 1.6 Hz, 1H), 8.25 (s, 1H), 8.22 (dd, J=6.0, 2.1 Hz, 1H), 8.13 (dd, J=8.6, 2.2 Hz, 1H), 7.98-7.93 (m, 2H), 7.72 (d, J=8.6 Hz, 1H), 7.60-7.54 (m, 2H), 7.41 (dd, J=9.2, 4.5 Hz, 1H), 7.08 (d, J=8.6 Hz, 1H), 7.02 (d, J=7.0 Hz, 1H), 6.51 (s, 1H), 5.04 (dd, J=12.8, 5.5 Hz, 1H), 3.70 (s, 2H), 3.53-3.40 (m, 2H), 3.32-3.24 (m, 2H), 3.15-2.98 (m, 6H), 2.98-2.82 (m, 3H), 2.65-2.59 (m, 2H), 2.61 (s, 3H), 2.47-2.37 (m, 2H), 2.09 (t, J=7.5 Hz, 2H), 2.06-1.98 (m, 1H), 1.81-1.71 (m, 2H), 1.63-1.49 (m, 4H), 1.37-1.28 (m, 2H). MS (ESI) [M+H]+: 945.6.
To tert-butyl (3-(4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoro-methyl)benzyl)piperazin-1-yl)propyl)carbamate (9b, 13.4 mg, 0.02 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The resulting mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The resulting residue was dissolved in DMF (200 μL, 0.2 M), and 6-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)amino)hexanoic acid (5-1, 7.7 mg, 0.02 mmol, 1 equiv), HATU (7.6 mg, 0.02 mmol, 1 equiv) and DIPEA (17.3 μL, 0.0994 mmol, 5 equiv) were added. The reaction mixture was stirred at room temperature overnight and then diluted with MeOH and filtered. The filtrate was purified by preparative HPLC to give compound I-8 as a bright green solid (9.7 mg, 46%). 1H NMR (500 MHz, DMSO-d6) δ 11.05 (s, 1H), 10.60 (s, 1H), 9.28 (s, 1H), 8.73 (dd, J=4.4, 1.5 Hz, 1H), 8.28 (dd, J=9.2, 1.6 Hz, 1H), 8.25 (s, 1H), 8.22 (dd, J=5.1, 2.1 Hz, 1H), 8.13 (dd, J=8.5, 2.2 Hz, 1H), 7.98-7.93 (m, 2H), 7.72 (d, J=8.5 Hz, 1H), 7.56 (dd, J=8.3, 2.7 Hz, 2H), 7.41 (dd, J=9.2, 4.4 Hz, 1H), 7.09 (s, IH), 6.93 (d, J=2.2 Hz, 1H), 6.84 (dd, J=8.4, 2.2 Hz, 1H), 5.02 (dd, J=12.7, 5.4 Hz, 1H), 3.70 (s, 2H), 3.50-3.40 (m, 2H), 3.20-2.97 (m, 8H), 2.97-2.82 (m, 3H), 2.64-2.60 (m, 2H), 2.62 (s, 3H), 2.45-2.36 (m, 2H), 2.09 (t, J=7.4 Hz, 2H), 2.02-1.94 (m, 1H), 1.80-1.72 (m, 2H), 1.64-1.48 (m, 4H), 1.40-1.30 (m, 2H). MS (ESI) [M+H]+: 945.6.
To tert-butyl 4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl)benzyl)piperazine-1-carboxylate (13-1, 12.3 mg, 0.02 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The resulting residue was dissolved in DMF (200 μL, 0.2 M), and 6-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)amino)hexanoic acid (5-1, 7.7 mg, 0.02 mmol, 1 equiv), HATU (7.6 mg, 0.02 mmol, 1 equiv) and DIPEA (17.3 μL, 0.0994 mmol, 5 equiv) were added. The reaction mixture was stirred at room temperature overnight and then diluted with MeOH and filtered. The filtrate was purified by preparative HPLC to give compound I-7 as a bright green solid (2.9 mg, 15%). 1H NMR (500 MHz, DMSO-d6) δ 11.05 (s, 1H), 10.58 (s, 1H), 8.73 (dd, J=4.5, 1.6 Hz, 1H), 8.27 (dd, J=9.2, 1.6 Hz, 1H), 8.25 (s, 1H), 8.22 (dd, J=3.6, 2.1 Hz, 2H), 8.09 (dd, J=8.6, 2.2 Hz, 1H), 7.95 (dd, J=8.0, 2.0 Hz, 1H), 7.74 (d, J=8.5 Hz, 1H), 7.56 (dd, J=8.4, 1.3 Hz, 2H), 7.40 (dd, J=9.2, 4.4 Hz, 1H), 7.10 (t, J=5.4 Hz, 1H), 6.94 (d, J=2.1 Hz, 1H), 6.84 (dd, J=8.4, 2.2 Hz, 1H), 5.02 (dd, J=12.7, 5.4 Hz, 1H), 3.59 (s, 2H), 3.51-3.41 (m, 4H), 3.15 (q, J=6.6 Hz, 2H), 2.87 (ddd, J=16.5, 13.7, 5.3 Hz, 1H), 2.61 (s, 3H), 2.64-2.51 (m, 2H), 2.41-2.26 (m, 6H), 2.03-1.94 (m, 1H), 1.63-1.49 (m, 4H), 1.43-1.33 (m, 2H). MS (ESI) [M+H]+: 888.5.
To tert-butyl 4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromethyl)benzyl)piperazine-1-carboxylate (13-1, 40.4 mg, 0.0857 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The residue was dissolved in DMF (428 μL, 0.2 M), and 8-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)octanoic acid (6-1, 38 mg, 0.0857 mmol, 1 equiv), HATU (33 mg, 0.0857 mmol, 1 equiv) and DIPEA (74.6 μL, 0.428 mmol, 5 equiv) were added. The reaction mixture was stirred at room temperature overnight, diluted with EtOAc (20 mL) and washed with NaHCO3 (20 mL) water (20 mL) and brine (3×20 mL). The organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. The residue was purified by was purified by flash column chromatography on silica gel (eluting with 0 to 10% MeOH in CH2Cl2) to afford compound I-11 as a bright green solid (35 mg, 45%). 1H NMR (500 MHz, CDCl3) δ 8.65 (s, 1H), 8.50 (s, 1H), 8.47 (dd, J=4.4, 1.6 Hz, 1H), 8.08 (s, 1H), 8.06 (d, J=2.0 Hz, 1H), 8.03-7.91 (m, 3H), 7.83 (dd, J=8.0, 2.0 Hz, 1H), 7.78 (s, 1H), 7.47 (dd, J=8.5, 7.1 Hz, 1H), 7.37 (d, J=8.1 Hz, 1H), 7.12 (dd, J=9.2, 4.4 Hz, 1H), 7.05 (d, J=7.0 Hz, 1H), 6.85 (d, J=8.5 Hz, 1H), 6.20 (t, J=5.6 Hz, 1H), 4.93-4.84 (m, 1H), 3.68 (s, 4H), 3.50 (s, 2H), 3.23 (q, J=6.6 Hz, 2H), 2.91-2.67 (m, 3H), 2.62 (s, 3H), 2.48 (s, 4H), 2.31 (t, J=7.6 Hz, 2H), 2.17-2.07 (m, 1H), 1.72-1.56 (m, 4H), 1.46-1.29 (m, 6H). MS (ESI) [M+H]+: 916.6.
To tert-butyl 4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromet-hyl)benzyl)piperazine-1-carboxylate (13-1, 23.1 mg, 0.0490 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The residue was dissolved in DMF (490 μL, 0.1 M), and 8-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)amino)octanoic acid (7-1, 25 mg, 0.0490 mmol, 1 equiv), HATU (91 mg, 0.0490 mmol, 1 equiv) and DIPEA (74.6 μL, 0.196 mmol, 5 equiv) were added. The reaction mixture was stirred at room temperature overnight and then diluted with EtOAc (20 mL) and washed with NaHCO3 (20 mL), water (20 mL), and brine (3×20 mL). The organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. The residue was purified by was purified by flash column chromatography on silica gel (eluting with 0 to 10% MeOH in CH2Cl2) to afford compound I-12 as a bright green solid (17.4 mg, 40%). 1H NMR (500 MHz, CDCl3) δ 8.58 (s, 1H), 8.52-8.40 (m, 2H), 8.09-8.04 (m, 2H), 8.01-7.91 (m, 3H), 7.83 (dd, J=8.0, 2.0 Hz, 1H), 7.75 (s, 1H), 7.56 (d, J=8.3 Hz, 1H), 7.37 (d, J=8.0 Hz, 1H), 7.13 (dd, J=9.1, 4.4 Hz, 1H), 6.91 (d, J=2.1 Hz, 1H), 6.70 (dd, J=8.4, 2.2 Hz, 1H), 4.91 (dd, J=12.2, 5.4 Hz, 1H), 4.72 (t, J=5.4 Hz, 1H), 3.78-3.55 (m, 4H), 3.47 (s, 2H), 3.18 (td, J=7.1, 5.3 Hz, 2H), 2.91-2.67 (m, 3H), 2.62 (s, 3H), 2.53-2.37 (m, 4H), 2.32 (t, J=7.5 Hz, 2H), 2.14-2.06 (m, 1H), 1.63 (m, 4H), 1.47-1.27 (m, 6H). MS (ESI) [M+H]+: 916.6.
To tert-butyl 4-(4-(3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methylbenzamido)-2-(trifluoromet-hyl)benzyl)piperazine-1-carboxylate (13-1, 10.7 mg, 0.0172 mmol, 1 equiv) was added HCl (300 μL, 4 M in dioxane). The reaction mixture was stirred at room temperature for 1 h and then concentrated in vacuo. The residue was dissolved in DMF (400 μL, 0.04 M), and 2-(2,6-dioxopiperidin-3-yl)-4-((8-iodooctyl)amino)isoindoline-1,3-dione (8-1, 8.8 mg, 0.0172 mmol, 1 equiv) and DIPEA (9.0 μL, 0.0516 mmol, 3 equiv) were added. The reaction mixture was heated to 50° C. for 10 days, then taken up in EtOAc (15 mL) and washed with water (15 mL) and brine (15 mL). The organic layers were dried over Na2SO4, filtered, and concentrated in vacuo. The residue was purified by was purified by flash column chromatography on silica gel (eluting with 0 to 10% MeOH in CH2Cl2) to afford compound I-10 as a bright green solid (4 mg, 26%). MS (ESI) [M+H]+: 902.7.
Dose-ranging viability assays were been performed using cellular ATP content as a proxy for cellular viability (ATPlite assay, Promega®). Bifunctional compounds of the application were incubated for 72 hours in DNA41, HBP-ALL, HSB2, JURKAT, KOPTK1, MOLT4, MOLT4-CRBN−/−, MOLT16, CCRF-CEM, P12-ICHIKAWA, RF382, RPMI-8402, SKW3, and SUPT11 cells. All experiments were conducted in quadruplicates and the resulting data was then converted to represent a single value per replicate (area under the curve, AUC) and shown as a heatmap. (
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments and methods described herein. Such equivalents are intended to be encompassed by the scope of the present application.
All patents, patent applications, and literature references cited herein are hereby expressly incorporated by reference.
This application claims priority to, and the benefit of, U.S. Ser. No. 62/420,136, filed on Nov. 10, 2016, the entire contents of which are incorporated herein by reference.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2017/061004 | 11/10/2017 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62420136 | Nov 2016 | US |
