# Patent

## Title
Substituted quinobenzoxazine analogs

## Abstract

The present invention relates to quinobenzoxazines analogs having the general formula:




and pharmaceutically acceptable salts, esters and prodrugs thereof;

    
    
        wherein A, U, V, W, X and Z are substituents.
    
    


The present invention also relates to methods for using such compounds.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation-in-part of U.S. patent application Ser. No. 10/821,243, filed Apr. 7, 2004, now U.S. Pat. No. 7,141,565, which claims the benefit of U.S. provisional application 60/461,271, filed Apr. 7, 2003; U.S. provisional application 60/463,171, filed Apr. 15, 2003; U.S. provisional application 60/519,535, filed Nov. 12, 2003; and U.S. provisional application 60/532,727, filed Dec. 23, 2003. The contents of these documents are incorporated herein by reference.


FIELD OF THE INVENTION
The invention relates to substituted quinobenzoxazines analogs, and methods of using such compounds.
BACKGROUND
Quadruplexes can form in certain purine-rich strands of nucleic acids. In duplex nucleic acids, certain purine rich strands are capable of engaging in a slow equilibrium between a typical duplex helix structure and in unwound and non-B-form regions. These unwound and non-B forms can be referred to as “paranemic structures.” Some forms are associated with sensitivity to S1nuclease digestion, which can be referred to as “nuclease hypersensitivity elements” or “NHEs.” A quadruplex is one type of paranemic structure and certain NHEs can adopt a quadruplex structure. Considerable circumstantial evidence suggests that quadruplex structures can exist in vivo in specific regions of the genome, including the telomeric ends of chromosomes and oncogene regulatory regions. (Han, et al., Trends Pharm. Sci. (2000) 21:136-142). Thus, quadruplex forming regions of DNA may be used as molecular targets for anticancer agents.
SUMMARY OF THE INVENTION
Compounds described herein interact with regions of DNA that can form quadruplexes and act as tumor suppression agents with reduced side effects. Such compounds reduce expression of highly proliferate genes and are utilized for treating cancers. Furthermore, the compounds may also exhibit antibacterial or antiviral activity, and may be used for treating bacterial and viral infections.
Various embodiments of the present invention are described below. The present invention encompasses other compounds having formula 1, with substituents independently selected from compounds in Tables 1-3. Thus, the present invention is not limited to the specific combination of substituents described in various embodiments below.
The compounds have the general formula:




and pharmaceutically acceptable salts, esters and prodrugs thereof;

    
    
        wherein V is H, halo, or NR1R2;
        A is H, fluoro, or NR12;
        Z is O, S, NR1 or CH2;
        U is OR2 or NR1R2;
        X is OR2, NR1R2, halo, azido, or SR2;
        n is 1-3;
        wherein in NR1R2, R1 and R2 may form a double bound or a ring, each of which is optionally substituted;
        R1 is H or a C1-6 alkyl;
        R2 is H or a C1-10 alkyl or C2-10 alkenyl optionally containing one or more non-adjacent heteroatoms selected from N, O, and S, and optionally substituted with a carbocyclic or heterocyclic ring; or R2 is an optionally substituted heterocyclic ring, aryl or heteroaryl;
        W is selected from the group consisting of
    
    












wherein Q, Q1, Q2, and Q3 are independently CH or N;

    
    
        Y is independently O, CH, ═O or NR1;
        and R5 is a substituent at any position on the fused ring; and is H, OR2, Cl1-6 alkyl, C2-6 alkenyl, each optionally substituted by halo, ═O or one or more heteroatoms; or R5 is an inorganic substituent; or two adjacent R5 is linked to obtain a 5-6 membered substituted or unsubstituted carbocyclic or heterocyclic ring, optionally fused to an additional substituted or unsubstituted carbocyclic or heterocyclic ring;
        provided that U is not OR1 when X is pyrrolidinyl; A is F; Z is O; and W is naphthalenyl or phenylene;
        U is not morpholinyl or 2,4-difluoroaniline when X is F or pyrrolidinyl; A is F; Z is O; and W is phenylene; and
        further provided that if U is OH, then W represents multiple fused aromatic rings and X is not halo; and X is NH2, or a moiety that does not contain N, or contains more than 6 carbons.
    
    


In the above formula 1, A and X may independently be halo. In one example, A and X may independently be fluoro.
In the above formula, V may be H. Alternatively, V may be NH2 or a compound having the formula NR1—(CR12)n—NR3R4;

    
    
        wherein R1 and R3 are independently H or C1-6 alkyl;
        n is 1-6; and
        R4 is H, C1-6 alkyl optionally substituted with a carbocyclic or heterocyclic ring, or aryl; and
        wherein in NR3R4, R3 and R4 may form an optionally substituted ring.
    
    


In the above formula 1, U and X may independently be NR1R2. In one example, R1 is H and R2 is a C1-10 alkyl optionally containing one or more heteroatoms, and optionally substituted with a C3-6 cycloalkyl, aryl or a 5-14 membered heterocyclic ring containing one or more N, O or S. In another example, R1 is H and R2 is an aryl or a 5-14 membered heterocyclic ring containing one or more N, O or S, each optionally substituted with an amino or another heterocyclic ring. In yet another example, R1 and R2 in NR1R2 form an optionally substituted 5-14 membered ring containing one or more N, O or S. In particular examples, NR1R2 is morpholine, thiomorpholine, piperazine, piperidine or diazepine.
In the above formula 1, U and X may independently have the formula

NR1—(CR12)n—NR3R4  (2)

wherein R1 and R3 are independently H or C1-6 alkyl;

    
    
        n is 1-6; and
        R4 is H or a C1-10 alkyl or C2-10 alkenyl optionally containing one or more non-adjacent heteroatoms selected from N, O and S, and optionally substituted with a carbocyclic or heterocyclic ring; and
        wherein in NR3R4, R3 and R4 may form an optionally substituted ring.
    
    


In the above formula 2, n may be 2-3. In one example, NR3R4 is an acyclic amine, or guanidinyl or a tautomer thereof; or R3 and R4 optionally form a substituted ring containing one or more N, O or S. In particular examples, NR3R4 is morpholine, thiomorpholine, imidazole, pyrrolidine, piperazine, pyridine or piperidine.
In the above formula 1, X may be NR1R2; and U has the formula

NR1—(CR12)n—NR3R4  (2)

    
    
        wherein R1 and R2 are as defined in claim 1;
        R3 is H or C1-6 alkyl;
        n is 1-6; and
        
    
    


R4 is H or a C1-10 alkyl or C2-10 alkenyl optionally containing one or more non-adjacent heteroatoms selected from N, O and S, and optionally substituted with a carbocyclic or heterocyclic ring; and

    
    
        wherein in NR1R2 and NR3R4, R1 and R2, and R3 and R4 each independently may form a substituted ring.
    
    


In the above formula, where X is NR1R2 and U has the formula NR1—(CR12)n—NR3R4 (2), R1 and R2 in NR1R2, and R3 and R4 in NR3R4 each may independently form ring containing one or more N, O or S. For example, X is optionally substituted with amino, carbamate, a C1-10 alkyl containing one or more non-adjacent N, O or S, and optionally substituted with a heterocyclic ring; aryl or a saturated or unsaturated heterocyclic ring, each of which is optionally substituted. In one example, X and NR3R4 are independently morpholine, thiomorpholine, imidazole, pyrrolidine, piperazine, pyridine or piperidine. In one example, X and NR3R4 are independently pyrrolidine. In another example, X is pyrrolidine substituted with pyrazine. In this example, V is H; A is fluoro; and W is naphthalenyl.
Examples of 5-6 membered heterocyclic rings include but are not limited to tetrahydrofuran, 1,3-dioxolane, 2,3-dihydrofuran, tetrahydropyran, benzofuran, isobenzofuran, 1,3-dihydro-isobenzofuran, isoxazole, 4,5-dihydroisoxazole, piperidine, pyrrolidine, pyrrolidin-2-one, pyrrole, pyridine, pyrimidine, octahydro-pyrrolo[3,4-b]pyridine, piperazine, pyrazine, morpholine, thiomorpholine, imidazole, imidazolidine-2,4-dione, benzimidazole, 1,3-dihydrobenzimidazol-2-one, indole, thiazole, benzothiazole, thiadiazole, thiophene, tetrahydro-thiophene 1,1-dioxide, diazepine, triazole, guanidine, diazabicyclo[2.2.1]heptane, 2,5-diazabicyclo[2.2.1]heptane, and 2,3,4,4a,9,9a-hexahydro-1H-β-carboline.
In the above formula 1, W may be benzene, pyridine, biphenyl, naphthalene, phenanthrene, quinoline, isoquinoline, quinazoline, cinnoline, phthalazine, quinoxaline, indole, benzimidazole, benzoxazole, benzthiazole, benzofuran, anthrone, xanthone, acridone, fluorenone, carbazolyl, pyrimido[4,3-b]furan, pyrido[4,3-b]indole, pyrido[2,3-b]indole, dibenzofuran, acridine or acridizine.
In the above formula 1, U may be OR2 and R2 is a C1-6 alkyl optionally substituted with a carbocyclic or heterocyclic ring.
In the above formula 1, each optionally substituted moiety is substituted with one or more halo, OR2, NR1R2, carbamate, C1-10 alkyl, C2-10 alkenyl, each optionally substituted by halo, ═O, aryl or one or more heteroatoms; inorganic substituents, aryl, carbocyclic or a heterocyclic ring.
The compounds of the present invention may be chiral. As used herein, a chiral compound is a compound that is different from its mirror image, and has an enantiomer. Methods of synthesizing chiral compounds and resolving a racemic mixture of enantiomers are well known to those skilled in the art. See, e.g., March, “Advanced Organic Chemistry,” John Wiley and Sons, Inc., New York, (1985), which is incorporated herein by reference.
The present invention also provides pharmaceutical compositions comprising compounds having formula 1, and a pharmaceutically acceptable excipient. In one example, the pharmaceutical composition comprises about 2% w/w of a compound having formula (1), about 4% mannitol, and about 0.5% sucrose.
The present invention also provides a compound having formula (1A),




and pharmaceutically acceptable salts, esters and prodrugs thereof. The compound may be chiral. The present invention also provides a pharmaceutical composition comprising a compound having formula 1A and a pharmaceutically acceptable excipient.

The compounds and pharmaceutical compositions of the present invention may be formulated for any suitable route of administration. For example, the compounds and pharmaceutical compositions may be formulated for injection. Other suitable routes of administration include but are not limited to oral, parenteral, intravenous, intramuscular, topical, subcutaneous routes, and other routes known to the skilled person.
In one example, the pharmaceutical composition comprises about 2% w/w of the compound having formula 1A. The pharmaceutical composition may further comprise about 4% w/w mannitol, 0.5% sucrose, or both. In other examples, the pharmaceutical composition has a pH of about 3.5.
In one particular embodiment, the pharmaceutical composition comprises about 2% w/w of a compound having formula 1A, 4% w/w mannitol, and 0.5% sucrose. In one example, the pharmaceutical formulation may be aqueous, injectable or both. For injectable formulations, water may be added to the final weight.
The compounds and pharmaceutical compositions of the present invention may be administered with another therapeutic agent. For example, the compounds and pharmaceutical compositions of the present invention may be administered with a chemotherapeutic agent. Examples of chemotherapeutic agents include but are not limited to anti-infective agents, antihelmintics, antiprotozoal agents, antimalarial agents, antiamebic agents, sulfonamides, antimycobacterial drugs, or antiviral chemotherapeutics. Chemotherapeutic agents may also be antineoplastic agents or cytotoxic drugs, such as alkylating agents, plant alkaloids, antimetabolites, antibiotics, and other anticellular proliferative agents. In other examples, the compounds and pharmaceutical formulations of the present invention may be administered with hepatic enzyme inducers or inhibitors.
Furthermore, the present invention also provides methods for ameliorating a cell proliferative disorder, comprising administering to a subject in need thereof an effective amount of a compound having formula 1 or 1A, or pharmaceutical compositions thereof, thereby ameliorating said cell-proliferative disorder. In one example, the cell proliferative disorder is cancer. In another example, cell proliferation is reduced, or cell death is induced. The subject may be human or animal.
The present invention also provides methods for reducing cell proliferation or inducing cell death, comprising contacting a system with an effective amount of a compound having formula 1 or 1A, or pharmaceutical compositions thereof, thereby reducing cell proliferation or inducing cell death in said system. The system may be a cell or tissue.
The present invention further provides methods for reducing microbial titers, comprising contacting a system with an effective amount of a compound having formula 1 or 1A, or pharmaceutical compositions thereof, thereby reducing microbial titers. The system may be a cell or tissue. In one example, the microbial titers are viral, bacterial or fungal titers.
Further, the present invention provides methods for ameliorating a microbial infection, comprising administering to a subject in need thereof an effective amount of a compound formula 1 or 1A, or pharmaceutical compositions thereof, thereby ameliorating said microbial infection. The subject may be human or animal. In one example, the microbial infection is viral, bacterial or fungal.



DESCRIPTION OF THE FIGURES
FIG. 1 shows antitumor activity of a compound having formula 1 tested in a Ramos xenograft model.
FIG. 2 shows antitumor activity of a compound having formula 1 tested in HCT 116.
FIG. 3 shows a stop assay as a first pass screen for oncogene inhibitors.
FIG. 4 shows the electrophoretogram for CX-3543, mAMSA, distamycins, mithramycin, actinomycin D, and ciprofloxacin.
FIG. 5 shows the quadruplex/binding selectivity of CX-3543.
FIG. 6 shows the Quadrome footprint for CX-3543.
FIG. 7 shows the topoisomerase II assay for CX-3543.
FIG. 8 shows the pharmacokinetic profile of CX-3543.
FIG. 9 shows the antitumor activity of CX-3543 in HCT-116 colorectal cancer xenograft model.
FIG. 10 shows the antitumor activity of CX-3543 in PC3 prostate cancer xenograft model.



DESCRIPTION OF THE INVENTION
The present invention relates to quinoline derivatives having formula 1, and pharmaceutically acceptable salts, esters, and prodrugs thereof. In particular embodiments, the compounds interact with regions of DNA that can form quadruplexes. The present invention also relates to methods for treating cancer, bacterial and viral infections using such compounds.
Because regions of DNA that can form quadruplexes are regulators of biological processes such as oncogene transcription, modulators of quadruplex biological activity can be utilized as cancer therapeutics. Molecules that interact with regions of DNA that can form quadruplexes can exert a therapeutic effect on certain cell proliferative disorders and related conditions. Particularly, abnormally increased oncogene expression can cause cell proliferative disorders and quadruplex structures typically down-regulate oncogene expression. Examples of oncogenes include but are not limited to MYC, HIF, VEGF, ABL, TGF, PDGFA, MYB, SPARC, HUMTEL, HER, VAV, RET, H-RAS, EGF, SRC, BCL1, BCL2, and other oncogenes known to one of skill in the art.
Molecules that bind to regions of DNA that can form quadruplexes can exert a biological effect according to different mechanisms, which include for example, stabilizing a native quadruplex structure, inhibiting conversion of a native quadruplex to duplex DNA by blocking strand cleavage, and stabilizing a native quadruplex structure having a quadruplex-destabilizing nucleotide substitution and other sequence specific interactions. Thus, compounds that bind to regions of DNA that can form quadruplexes described herein may be administered to cells, tissues, or organisms for the purpose of down-regulating oncogene transcription and thereby treating cell proliferative disorders. The terms “treatment” and “therapeutic effect” as used herein refer to reducing or stopping a cell proliferation rate (e.g., slowing or halting tumor growth) or reducing the number of proliferating cancer cells (e.g., removing part or all of a tumor).
Determining whether the biological activity of native DNA that can form quadruplexes is modulated in a cell, tissue, or organism can be accomplished by monitoring quadruplex biological activity. Quadruplex forming regions of DNA biological activity may be monitored in cells, tissues, or organisms, for example, by detecting a decrease or increase of gene transcription in response to contacting the quadruplex forming DNA with a molecule. Transcription can be detected by directly observing RNA transcripts or observing polypeptides translated by transcripts, which are methods well known in the art.
Molecules that interact with quadruplex forming DNA and quadruplex forming nucleic acids can be utilized to treat many cell proliferative disorders. Cell proliferative disorders include, for example, colorectal cancers and hematopoietic neoplastic disorders (i.e., diseases involving hyperplastic/neoplastic cells of hematopoietic origin such as those arising from myeloid, lymphoid or erythroid lineages, or precursor cells thereof). The diseases can arise from poorly differentiated acute leukemias, e.g., erythroblastic leukemia and acute megakaryoblastic leukemia. Additional myeloid disorders include, but are not limited to, acute promyeloid leukemia (APML), acute myelogenous leukemia (AML) and chronic myelogenous leukemia (CML) (Vaickus, Crit. Rev. in Oncol/Hemotol. 11:267-297 (1991)). Lymphoid malignancies include, but are not limited to acute lymphoblastic leukemia (ALL), which includes B-lineage ALL and T-lineage ALL, chronic lymphocytic leukemia (CLL), prolymphocytic leukemia (PLL), hairy cell leukemia (HLL) and Waldenstrom's macroglobulinemia (WM). Additional forms of malignant lymphomas include, but are not limited to non-Hodgkin lymphoma and variants thereof, peripheral T cell lymphomas, adult T cell leukemia/lymphoma (ATL), cutaneous T-cell lymphoma (CTCL), large granular lymphocytic leukemia (LGF), Hodgkin's disease and Reed-Sternberg disease. Cell proliferative disorders also include cancers of the colorectum, breast, lung, liver, pancreas, lymph node, colon, prostate, brain, head and neck, skin, liver, kidney, and heart. Compounds that interact with regions of DNA that can form quadruplexes also can be utilized to target cancer related processes and conditions, such as increased angiogenesis, by inhibiting angiogenesis in a subject.
The present invention provides a method for reducing cell proliferation or for treating or alleviating cell proliferative disorders, comprising contacting a system having a DNA capable of forming a quadruplex with a compound having formula 1. The system may be a group of cells or one or more tissues. In one embodiment, the system is a subject in need of a treatment of a cell proliferative disorder (e.g., a mammal such as a mouse, rat, monkey, or human). The present invention also provides a method for treating colorectal cancer by administering a compound that interacts with a c-MYC quadruplex forming region to a subject in need thereof, thereby reducing the colorectal cancer cell proliferation. Furthermore, the present invention provides a method for inhibiting angiogenesis and optionally treating a cancer associated with angiogenesis, comprising administering a compound that interacts with a vascular endothelial growth factor (VEGF) quadruplex forming region to a subject in need thereof, thereby reducing angiogenesis and optionally treating a cancer associated with angiogenesis.
As used herein, the term “alkyl” refers to a carbon-containing compound, and encompasses compounds containing one or more heteroatoms. The term “alkyl” also encompasses compounds substituted with one or more non-interfering substituents. Examples of non-interfering substituents include but are not limited to OR1, amino, amido, halo, ═O, aryl, heterocyclic groups, or inorganic substituents, and other substituents that do not interfere with the activity of the compound.
As used herein, the term “carbocycle” refers to a cyclic compound containing only carbon atoms in the ring.
As used herein, the term “heterocycle” refers to a cyclic compound comprising a heteroatom, including monocyclic or bicyclic heterocycles. As used herein, the term “heteroatom” refers to any atom that is not carbon or hydrogen, such as nitrogen, oxygen or sulfur. Examples of heterocycles include but are not limited to oxirane, oxetane, pyran, tetrahydropyran, dioxane, lactones, aziridine, azetidine, pyrrolidine, piperidine, morpholine, lactams, and tetrahydrofuran.
As used herein, the term “bicyclic compound” refers to a compound having two rings which share a pair of bridgehead carbon atoms. Examples of bicyclic compounds include but are not limited to decalin, norbornane, camphor, and diazabicyclo[2.2.1]heptane.
As used herein, the terms “heteroaryl” or “heteroaromatic” refer to an aromatic heterocycle. Examples of heteroaryls include but are not limited to furan, pyrrole, pyridine, pyrimidine, imidazole, or triazole.
The terms “treat,” “treatment” and “therapeutic effect” as used herein refer to reducing or stopping a cell proliferation rate (e.g., slowing or halting tumor growth) or reducing the number of proliferating cancer cells (e.g., removing part or all of a tumor). These terms also are applicable to reducing a titre of a microorganism in a system (i.e., cell, tissue, or subject) infected with a microorganism, reducing the rate of microbial propagation, reducing the number of symptoms or an effect of a symptom associated with the microbial infection, and/or removing detectable amounts of the microbe from the system. Examples of microorganism include but are not limited to virus, bacterium and fungus.
Compounds that interact with quadruplex forming regions of DNA can also be used to reduce a microbial infection, such as a viral infection. Retroviruses offer a wealth of potential targets for G-quadruplex targeted therapeutics. G-quadruplex structures have been implicated as functional elements in at least two secondary structures formed by either viral RNA or DNA in HIV, the dimer linker structure (DLS) and the central DNA flap (CDF). Additionally, DNA aptamers which are able to adopt either inter- or intramolecular quadruplex structures are able to inhibit viral replication. In one example, DNA aptamers are able to inhibit viral replication by targeting the envelope glycoprotein (putatively). In another example, DNA aptamers inhibit viral replication by targeting the HIV-integrase respectively, suggesting the involvement of native quadruplex structures in interaction with the integrase enzyme.
Dimer linker structures, which are common to all retroviruses, serve to bind two copies of the viral genome together by a non-covalent interaction between the two 5′ ends of the two viral RNA sequences. The genomic dimer is stably associated with the gag protein in the mature virus particle. In the case of HIV, the origin of this non-covalent binding may be traced to a 98 base-pair sequence containing several runs of at least two consecutive guanines (e.g., the 3′ for the formation of RNA dimers in vitro). An observed cation (potassium) dependence for the formation and stability of the dimer in vitro, in addition to the failure of an antisense sequence to effectively dimerize, has revealed the most likely binding structure to be an intermolecular G-quadruplex.
Prior to integration into the host genome, reverse transcribed viral DNA forms a pre-integration complex (PIC) with at least two major viral proteins, integrase and reverse transcriptase, which is subsequently transported into the nucleus. The Central DNA Flap (CDF) refers to 99-base length single-stranded tail of the +strand, occurring near the center of the viral duplex DNA, which is known to a play a role in the nuclear import of the PIC. Oligonucleotide mimics of the CDF have been shown to form intermolecular G-quadruplex structures in cell-free systems.
Thus, compounds that recognize quadruplex forming regions can be used to stabilize the dimer linker structure and thus prevent de-coupling of the two RNA strands. Also, by binding to the quadruplex structure formed by the CDF, protein recognition and/or binding events for nuclear transport of the PIC may be disrupted. In either case, a substantial advantage can exist over other anti-viral therapeutics. Current Highly Active Anti-Retroviral Therapeutic (HAART) regimes rely on the use of combinations of drugs targeted towards the HIV protease and HIV integrase. The requirement for multi-drug regimes is to minimize the emergence of resistance, which will usually develop rapidly when agents are used in isolation. The source of such rapid resistance is the infidelity of the reverse transcriptase enzyme which makes a mutation approximately once in every 10,000 base pairs. An advantage of targeting viral quadruplex structures over protein targets, is that the development of resistance is slow or is impossible. A point mutation of the target quadruplex can compromise the integrity of the quadruplex structure and lead to a non-functional copy of the virus. A single therapeutic agent based on this concept may replace the multiple drug regimes currently employed, with the concomitant benefits of reduced costs and the elimination of harmful drug/drug interactions.
The present invention provides a method for reducing a microbial titer in a system, comprising contacting a system having a native DNA quadruplex forming region with a compound having formula 1. The system may be one or more cells or tissues. Examples of microbial titers include but are not limited to viral, bacterial or fungal titers. In a particular embodiment, the system is a subject in need of a treatment for a viral infection (e.g., a mammal such as a mouse, rat, monkey, or human). Examples of viral infections include infections by a hepatitis virus (e.g., hepatitis B or C), human immunodeficiency virus (HIV), rhinovirus, herpes-zoster virus (VZV), herpes simplex virus (e.g., HSV-1 or HSV-2), cytomegalovirus (CMV), vaccinia virus, influenza virus, encephalitis virus, hantavirus, arbovirus, West Nile virus, human papilloma virus (HPV), Epstein-Barr virus, and respiratory syncytial virus. The present invention also provides a method for treating HIV infection by administering a compound having formula 1 to a subject in need thereof, thereby reducing the HIV infection.
Identifying Compounds That Can Bind to Quadruplex Forming Regions of DNA
Compounds described herein are identified as compounds that can bind to quadruplex forming regions of DNA where a biological activity of this region, often expressed as a “signal,” produced in a system containing the compound is different than the signal produced in a system not containing the compound. While background signals may be assessed each time a new molecule is probed by the assay, detecting the background signal is not required each time a new molecule is assayed.
Examples of quadruplex forming nucleic acid sequences are set forth in the following Table A:










TABLE A






SEQ




SEQUENCE
ID NO
ORIGIN


















TG4AG3TG4AG3TG4AAGG
1
CMYC



GGGGGGGGGGGGGCGGGGGCGGGGGCGGGGGAGGGGC
2
PDGFA


G8ACGCG3AGCTG5AG3CTTG4CCAG3CG4CGCTTAG5
3
PDGFB/c




-sis


AGGAAGGGGAGGGCCGGGGGGAGGTGGC
4
CABL


AGGGGCGGGGCGGGGCGGGGGC
5
RET


GGGAGGAAGGGGGCGGGAGCGGGGC
6
BCL-2


GGGGGGCGGGGGCGGGCGCAGGGGGAGGGGGC
7
Cyclin




D1/BCL-1


CGGGGCGGGGCGGGGGCGGGGGC
8
H-RAS


AGAGGAGGAGGAGGTCACGGAGGAGGAGGAGAAGGAGGAGGAGGAA
9
CMYB


(GGA)4
10
VAV


AGAGAAGAGGGGAGGAGGAGGAGGAGAGGAGGAGGCGC
11
HMGA2


GGAGGGGGAGGGG
12
CPIM


AGGAGAAGGAGGAGGTGGAGGAGGAGG
13
HER2/neu


AGGAGGAGGAGAATGCGAGGAGGAGGGAGGAGA
14
EGFR


GGGGCGGGCCGGGGGCGGGGTCCCGGCGGGGCGGAG
15
VEGF


CGGGAGGAGGAGGAAGGAGGAAGCGCG
16
CSRC









In addition to determining whether a test molecule or test nucleic acid gives rise to a different signal, the affinity of the interaction between the nucleic acid and the compound may be quantified. IC50, Kd, or Ki threshold values may be compared to the measured IC50 or Kd values for each interaction, and thereby identify a test molecule as a quadruplex interacting molecule or a test nucleic acid as a quadruplex forming nucleic acid. For example, IC50 or Kd threshold values of 10 μM or less, 1 μM or less, and 100 nM or less are often utilized. In another example, threshold values of 10 nM or less, 1 nM or less, 100 pM or less, and 10 pM or less may be utilized to identify quadruplex interacting molecules and quadruplex forming nucleic acids.
Many assays are available for identifying compounds that have affinity for quadruplex forming regions of DNA. In some of these assays, the biological activity is the quadruplex nucleic acid binding to a compound and binding is measured as a signal. In other assays, the biological activity, is a polymerase arresting function of a quadruplex and the degree of arrest is measured as a decrease in a signal. In certain assays, the biological activity is transcription and transcription levels can be quantified as a signal. In another assay, the biological activity is cell death and the number of cells undergoing cell death is quantified. Another assay monitors proliferation rates of cancer cells. Examples of assays are fluorescence binding assays, gel mobility shift assays (see, e.g., Jin & Pike, Mol. Endocrinol. (1996)10:196-205), polymerase arrest assays, transcription reporter assays, cancer cell proliferation assays, and apoptosis assays (see, e.g., Amersham Biosciences (Piscataway, N.J.)), and embodiments of such assays are described hereafter. Also, topoisomerase assays can be utilized to determine whether the quadruplex interacting molecules have a topoisomerase pathway activity (see, e.g. TopoGEN, Inc. (Columbus, Ohio)).
Gel Electrophoretic Mobility Shift Assay (EMSA)
An EMSA is useful for determining whether a nucleic acid forms a quadruplex and whether a nucleotide sequence is quadruplex-destabilizing. EMSA is conducted as described previously (Jin & Pike, Mol. Endocrinol. 10: 196-205 (1996)) with minor modifications. Generally, synthetic single-stranded oligonucleotides are labeled in the 5′-terminus with T4-kinase in the presence of [γ32P] ATP (1,000 mCi/mmol, Amersham Life Science) and purified through a sephadex column. 32P-labeled oligonucleotides ( ̃30,000 cpm) are then incubated with or without various concentrations of a testing compound in 20 μl of a buffer containing 10 mM Tris pH 7.5, 100 mM KCl, 5 mM dithiothreitol, 0.1 mM EDTA, 5 mM MgCl2, 10% glycerol, 0.05% Nonedit P-40, and 0.1 mg/ml of poly(dI-dC) (Pharmacia). After incubation for 20 minutes at room temperature, binding reactions are loaded on a 5% polyacrylamide gel in 0.25× Tris borate-EDTA buffer (0.25×TBE, 1×TBE is 89 mM Tris-borate, pH 8.0, 1 mM EDTA). The gel is dried and each band is quantified using a phosphoimager.
DMS Methylation Protection Assay
Chemical footprinting assays are useful for assessing quadruplex structure. Quadruplex structure is assessed by determining which nucleotides in a nucleic acid are protected or unprotected from chemical modification as a result of being inaccessible or accessible, respectively, to the modifying reagent. A DMS methylation assay is an example of a chemical footprinting assay. In such an assay, bands from EMSA are isolated and subjected to DMS-induced strand cleavage. Each band of interest is excised from an electrophoretic mobility shift gel and soaked in 100 mM KCl solution (300 μl) for 6 hours at 4° C. The solutions are filtered (microcentrifuge) and 30,000 cpm (per reaction) of DNA solution is diluted further with 100 mM KCl in 0.1×TE to a total volume of 70 μl (per reaction). Following the addition of 1 μl salmon sperm DNA (0.1 μg/μl), the reaction mixture is incubated with 1 μl DMS solution (DMS:ethanol; 4:1; v:v) for a period of time. Each reaction is quenched with 18 μl of stop buffer (b-mercaptoethanol:water:NaOAc (3 M); 1:6:7; v:v:v). Following ethanol precipitation (twice)-and piperidine cleavage, the reactions are separated on a preparative gel (16%) and visualized on a phosphoimager.
Polymerase Arrest Assay
An arrest assay includes a template nucleic acid, which may comprise a quadruplex forming sequence, and a primer nucleic acid which hybridizes to the template nucleic acid 5′ of the quadruplex-forming sequence. The primer is extended by a polymerase (e.g., Taq polymerase), which advances from the primer along the template nucleic acid. In this assay, a quadruplex structure can block or arrest the advance of the enzyme, leading to shorter transcription fragments. Also, the arrest assay may be conducted at a variety of temperatures, including 45° C. and 60° C., and at a variety of ion concentrations.
An example of the Taq polymerase stop assay is described in Han, et al., Nucl. Acids Res. (1999) 27:537-542, which is a modification of that used by Weitzmann, et al., J. Biol. Chem. (1996) 271:20958-20964. Briefly, a reaction mixture of template DNA (50 nM), Tris-HCl (50 mM), MgCl2 (10 mM), DTT (0.5 mM), EDTA (0.1 mM), BSA (60 ng), and 5′-end-labeled quadruplex nucleic acid ( ̃18 nM) is heated to 90° C. for 5 minutes and allowed to cool to ambient temperature over 30 minutes. Taq Polymerase (1 μl) is added to the reaction mixture, and the reaction is maintained at a constant temperature for 30 minutes. Following the addition of 10 μl stop buffer (formamide (20 ml), 1 M NaOH (200 μl), 0.5 M EDTA (400 μl), and 10 mg bromophenol blue), the reactions are separated on a preparative gel (12%) and visualized on a phosphoimager. Adenine sequencing (indicated by “A” at the top of the gel) is performed using double-stranded DNA Cycle Sequencing System from Life Technologies. The general sequence for the template strands is TCCAACTATGTATAC (SEQ ID NO:17)-INSERT-TTAGCGACACGCAATTGCTATAGTGAGTCGTATTA (SEQ ID NO:18), where “INSERT” refers to a nucleic acid sequence comprising a quadruplex forming sequence (See e.g., Table A). Bands on the gel that exhibit slower mobility are indicative of quadruplex formation.
High Throughput Polymerase Arrest Assay
A high throughput polymerase arrest assay has been developed. The assay comprises contacting a template nucleic acid, often DNA, with a primer, which also is often DNA; contacting the primer/template complex with a compound described herein (also referred to as a “test compound”); contacting the primer/template complex with a polymerase; and separating reaction products. The assay often includes the step of denaturing the primer/template complex mixture and then renaturing the complex, which often is carried out before a test molecule is added to the system. Multiple assays often are carried out using varying concentrations of a test compound, such that an IC50 value can be obtained, for example. The reaction products often include extended primers of different lengths. Where a test compound does not significantly interact with a quadruplex structure in the template, the primer often is extended to the end of the template.
Where a test compound significantly interacts with a quadruplex structure in the template, the primer often is extended only to the quadruplex structure in the template and no further. Thus, the reaction mixture often includes at least two reaction products when a test compound interacts with a quadruplex structure in the template, one having a completely extended primer and one having an incompletely extended primer, and these two reaction products are separated. The products may be separated using any convenient separation method, such as mass spectrometry and in one embodiment, capillary electrophoresis.
The reaction products often are identified by detecting a detectable label linked to the primer. The detectable label may be non-covalently linked to the 5′ end of the primer (e.g., a biotin molecule covalently linked to the 5′ end of the primer which is non-covalently linked to an avidin molecule joined to a detectable label). The detectable label may be joined to the primer at any stage of the assay, sometimes before the primer is added to the system, after the primer is extended, or after the products are separated. The detectable label often is covalently linked to the primer using a procedure selected based upon the nature of the chemical groups in the detectable label.
Many methods for covalently linking detectable labels to nucleic acids are available, such as chemically coupling an allylamine-derivatized nucleotide to a succinimidyl-ester derivative of a detectable label, and then generating a primer using the labeled nucleotide. (See, e.g., Nature Biotech (2000) 18:345-348 and http address info.med.yale.edu/genetics/ward/tavi/n_coupling.html). A spacer (often between 5-16 carbon atoms long) sometimes is incorporated between the detectable label and the nucleotide. Any convenient detectable label may be utilized, including but not limited to a radioactive isotope (e.g., 125I, 131I, 35S, 32p, 14C or 3H); a light scattering label (e.g., a spherical gold or silver label; Genicon Sciences Corporation, San Diego, Calif. and U.S. Pat. No. 6,214,560); an enzymic or protein label (e.g., GFP or peroxidase); or another chromogenic label or dye sometimes is utilized. Often, a fluorescent label is utilized (e.g., amino-methyl coumarin (AMCA); diethyl aminomethyl coumarin (DEAC); cascade blue (CB); fluorescein isothiocyanate (FITC); Oregon green (OG); Alexa 488 (A488); rhodamine green (RGr); lanthanide chelate (e.g., europium), carboxy-rhodamine 6G (R6G); tetramethyl rhodamine (TAMRA); Texas Red (TxR); Cy3; Cy3.5; Cy5, Cy5.5 and carboxynaphtofluorescein (CNF), digoxigenin (DIG); and 2,4-dinitrophenyl (DNP)). Other fluorophores and attendant excitation and emission wavelengths are described in Anantha, et al., Biochemistry (1998) 37:2709-2714 and Qu & Chaires, Methods Enzymol (2000) 321:353-369).
In an embodiment, a primer oligonucleotide covalently linked to a fluorescent label is contacted with template DNA. The resulting complex is contacted with a test molecule and then contacted with a polymerase capable of extending the primer. The reaction products then are separated and detected by capillary electrophoresis. A longer primer sequence was used for practicing this embodiment as compared to embodiments where the primer includes no covalently-linked fluorophore or where capillary electrophoresis is not utilized for separation. Deoxynucleotides are added at any stage of the assay before the separation, often when the primer is contacted with the template DNA. The template DNA/primer complex often is denatured (e.g., by increasing the temperature of the system) and then renatured (e.g., by cooling the system) before a test compound is added).
The following is a specific example of the assay embodiment. A 5′-fluorescent-labeled (FAM) primer (P45, 15 nM) was mixed with template DNA (15 nM) in a Tris-HCL buffer (15 mM Tris, pH 7.5) containing 10 mM MgCl2, 0.1 mM EDTA and 0.1 mM mixed deoxynucleotide triphosphates (dNTP's). The FAM-P45 primer (5′-6FAM-AGTCTGAC TGACTGTACGTAGCTAATACGACTCACTATAGCAATT-3′) (SEQ ID NO:19) and the template DNA (5′-TCCAACTATGTATACTGGGGAGGGTGGGGAGGGTGGGGAAGGTT AGCGACACGCAATTGCTATAGTGAGTCGTATTAGCTACGTACAGTCAGTCAGACT-3′) (SEQ ID NO:20) were synthesized and HPLC purified by Applied Biosystems. The mixture was denatured at 95° C. for 5 minutes and, after cooling down to room temperature, was incubated at 37° C. for 15 minutes.
After cooling down to room temperature, 1 mM KCl2 and the test compound (various concentrations) were added and the mixture incubated for 15 minutes at room temperature. The primer extension was performed by adding 10 mM KCl and Taq DNA Polymerase (2.5 U/reaction, Promega) and incubating at 70° C. for 30 minutes. The reaction was stopped by adding 1 μl of the reaction mixture to 10 μl Hi-Di Formamide mixed and 0.25 μl LIZ 120 size standard. Hi-Di Formamide and LIZ120 size standard were purchased from Applied Biosystems. The partially extended quadruplex arrest product was between 61 or 62 bases long and the full-length extended product was 99 bases long. The products were separated and analyzed using capillary electrophoresis. Capillary electrophoresis was performed using an ABI PRISM 3100-Avant Genetic Analyzer. The assay was performed using compounds described above and results are shown in Table 1. μM concentrations reported in Table 1 are concentrations at which 50% of the DNA was arrested in the assay (i.e., the ratio of shorter partially extended DNA (arrested DNA) to fill-length extended DNA is 1:1).
Transcription Reporter Assay
In a transcription reporter assay, test quadruplex DNA is coupled to a reporter system, such that a formation or stabilization of a quadruplex structure can modulate a reporter signal. An example of such a system is a reporter expression system in which a polypeptide, such as luciferase or green fluorescent protein (GFP), is expressed by a gene operably linked to the potential quadruplex forming nucleic acid and expression of the polypeptide can be detected. As used herein, the term “operably linked” refers to a nucleotide sequence which is regulated by a sequence comprising the potential quadruplex forming nucleic acid. A sequence may be operably linked when it is on the same nucleic acid as the quadruplex DNA, or on a different nucleic acid. An exemplary luciferase reporter system is described herein.
A luciferase promoter assay described in He, et al., Science (1998) 281:1509-1512 often is utilized for the study of quadruplex formation. Specifically, a vector utilized for the assay is set forth in reference 11 of the He, et al., document. In this assay, HeLa cells are transfected using the lipofectamin 2000-based system (Invitrogen) according to the manufacturer's protocol, using 0.1 μg of pRL-TK (Renilla luciferase reporter plasmid) and 0.9 μg of the quadruplex-forming plasmid. Firefly and Renilla luciferase activities are assayed using the Dual Luciferase Reporter Assay System (Promega) in a 96-well plate format according to the manufacturer's protocol.
Circular Dichroism Assay
Circular dichroism (CD) is utilized to determine whether another molecule interacts with a quadruplex nucleic acid. CD is particularly useful for determining whether a PNA or PNA-peptide conjugate hybridizes with a quadruplex nucleic acid in vitro. PNA probes are added to quadruplex DNA (5 μM each) in a buffer containing 10 mM potassium phosphate (pH 7.2) and 10 or 250 mM KCl at 37° C. and then allowed to stand for 5 minutes at the same temperature before recording spectra. CD spectra are recorded on a Jasco J-715 spectropolarimeter equipped with a thermoelectrically controlled single cell holder. CD intensity normally is detected between 220 nm and 320 nm and comparative spectra for quadruplex DNA alone, PNA alone, and quadruplex DNA with PNA are generated to determine the presence or absence of an interaction (see, e.g., Datta, et al., JACS (2001) 123:9612-9619). Spectra are arranged to represent the average of eight scans recorded at 100 nm/min.
Fluorescence Binding Assay
An example of a fluorescence binding assay is a system that includes a quadruplex nucleic acid, a signal molecule, and a test molecule. The signal molecule generates a fluorescent signal when bound to the quadruplex nucleic acid (e.g., N-methylmesoporphyrin IX (NMM)), and the signal is altered when a test compound competes with the signal molecule for binding to the quadruplex nucleic acid. An alteration in the signal when test molecule is present as compared to when test compound is not present identifies the test compound as a quadruplex interacting compound.
50 μl of quadruplex nucleic acid or a nucleic acid not capable of forming a quadruplex is added in 96-well plate. A test compound also is added in varying concentrations. A typical assay is carried out in 100 μl of 20 mM HEPES buffer, pH 7.0, 140 mM NaCl, and 100 mM KCl. 50 μl of the signal molecule NMM then is added for a final concentration of 3 μM. NMM is obtained from Frontier Scientific Inc, Logan, Utah. Fluorescence is measured at an excitation wavelength of 420 nm and an emission wavelength of 660 nm using a FluroStar 2000 fluorometer (BMG Labtechnologies, Durham, N.C.). Fluorescence often is plotted as a function of concentration of the test compound or quadruplex-targeted nucleic acid and maximum fluorescent signals for NMM are assessed in the absence of these molecules.
Cell Proliferation Assay
In a cancer cell proliferation assay, cell proliferation rates are assessed as a function of different concentrations of test compounds added to the cell culture medium. Any cancer cell type can be utilized in the assay. In one embodiment, colon cancer cells are cultured in vitro and test compounds are added to the culture medium at varying concentrations. A useful colon cancer cell line is colo320, which is a colon adenocarcinoma cell line deposited with the National Institutes of Health as accession number JCRB0225. Parameters for using such cells are available at the http address cellbank.nihs.go.jp/cell/data/jcrb0225.htm.
Formulation of Compounds
As used herein, the term “pharmaceutically acceptable salts, esters and amides” includes but are not limited to carboxylate salts, amino acid addition salts, esters and amides of the compounds, as well as the zwitterionic forms thereof, which are known to those skilled in the art as suitable for use with humans and animals. (See, e.g., Gerge, S. M., et al., “Pharmaceutical Salts,” J. Pharm. Sci. (1977) 66:1-19, which is incorporated herein by reference.)
Any suitable formulation of the compounds described herein can be prepared. In cases where compounds are sufficiently basic or acidic to form stable nontoxic acid or base salts, administration of the compounds as salts may be appropriate. Examples of pharmaceutically acceptable salts are organic acid addition salts formed with acids that form a physiological acceptable anion, for example, tosylate, methanesulfonate, acetate, citrate, malonate, tartarate, succinate, benzoate, ascorbate, a-ketoglutarate, and a-glycerophosphate. Suitable inorganic salts may also be formed, including hydrochloride, sulfate, nitrate, bicarbonate, and carbonate salts. Pharmaceutically acceptable salts are obtained using standard procedures well known in the art. For example, pharmaceutically acceptable salts may be obtained by reacting a sufficiently basic compound such as an amine with a suitable acid affording a physiologically acceptable anion. Alkali metal (e.g., sodium, potassium or lithium) or alkaline earth metal (e.g., calcium) salts of carboxylic acids also are made.
A compound may be formulated as a pharmaceutical composition and administered to a mammalian host in need of such treatment. In one embodiment, the mammalian host is human. Any suitable route of administration may be used, including but not limited to oral, parenteral, intravenous, intramuscular, topical and subcutaneous routes.
In one embodiment, a compound is administered systemically (e.g., orally) in combination with a pharmaceutically acceptable vehicle such as an inert diluent or an assimilable edible carrier. They may be enclosed in hard or soft shell gelatin capsules, compressed into tablets, or incorporated directly with the food of the patient's diet. For oral therapeutic administration, the active compound may be combined with one or more excipients and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, wafers, and the like. Such compositions and preparations should contain at least 0.1% of active compound. The percentage of the compositions and preparations may be varied and may conveniently be between about 2 to about 60% of the weight of a given unit dosage form. The amount of active compound in such therapeutically useful compositions is such that an effective dosage level will be obtained.
Tablets, troches, pills, capsules, and the like also may contain the following: binders such as gum tragacanth, acacia, corn starch or gelatin; excipients such as dicalcium phosphate; a disintegrating agent such as corn starch, potato starch, alginic acid and the like; a lubricant such as magnesium stearate; and a sweetening agent such as sucrose, fructose, lactose or aspartame or a flavoring agent such as peppermint, oil of wintergreen, or cherry flavoring may be added. When the unit dosage form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier, such as a vegetable oil or a polyethylene glycol. Various other materials may be present as coatings or to otherwise modify the physical form of the solid unit dosage form. For instance, tablets, pills, or capsules may be coated with gelatin, wax, shellac or sugar and the like. A syrup or elixir may contain the active compound, sucrose or fructose as a sweetening agent, methyl and propylparabens as preservatives, a dye and flavoring such as cherry or orange flavor. Any material used in preparing any unit dosage form is pharmaceutically acceptable and substantially non-toxic in the amounts employed. In addition, the active compound may be incorporated into sustained-release preparations and devices.
The active compound also may be administered intravenously or intraperitoneally by infusion or injection. Solutions of the active compound or its salts may be prepared in a buffered solution, often phosphate buffered saline, optionally mixed with a nontoxic surfactant. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, triacetin, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms. The compound is sometimes prepared as a polymatrix-containing formulation for such administration (e.g., a liposome or microsome). Liposomes are described for example in U.S. Pat. No. 5,703,055 (Felgner, et al.) and Gregoriadis, Liposome Technology vols. I to III (2nd ed. 1993).
The pharmaceutical dosage forms suitable for injection or infusion can include sterile aqueous solutions or dispersions or sterile powders comprising the active ingredient that are adapted for the extemporaneous preparation of sterile injectable or infusible solutions or dispersions, optionally encapsulated in liposomes. In all cases, the ultimate dosage form should be sterile, fluid and stable under the conditions of manufacture and storage. The liquid carrier or vehicle can be a solvent or liquid dispersion medium comprising, for example, water, ethanol, a polyol (for example, glycerol, propylene glycol, liquid polyethylene glycols, and the like), vegetable oils, nontoxic glyceryl esters, and suitable mixtures thereof. The proper fluidity can be maintained, for example, by the formation of liposomes, by the maintenance of the particle size in the case of dispersions or by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars, buffers or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions are prepared by incorporating the active compound in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filter sterilization. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and the freeze drying techniques, which yield a powder of the active ingredient plus any additional desired ingredient present in the previously sterile-filtered solutions.
For topical administration, the present compounds may be applied in liquid form. Compounds often are administered as compositions or formulations, in combination with a dermatologically acceptable carrier, which may be a solid or a liquid. Examples of useful dermatological compositions used to deliver compounds to the skin are known (see, e.g., Jacquet, et al. (U.S. Pat. No. 4,608,392), Geria (U.S. Pat. No. 4,992,478), Smith, et al. (U.S. Pat. No. 4,559,157) and Wortzman (U.S. Pat. No. 4,820,508).
Compounds may be formulated with a solid carrier, which include finely divided solids such as talc, clay, microcrystalline cellulose, silica, alumina and the like. Useful liquid carriers include water, alcohols or glycols or water-alcohol/glycol blends, in which the present compounds can be dissolved or dispersed at effective levels, optionally with the aid of non-toxic surfactants. Adjuvants such as fragrances and additional antimicrobial agents can be added to optimize the properties for a given use. The resultant liquid compositions can be applied from absorbent pads, used to impregnate bandages and other dressings, or sprayed onto the affected area using pump-type or aerosol sprayers. Thickeners such as synthetic polymers, fatty acids, fatty acid salts and esters, fatty alcohols, modified celluloses or modified mineral materials can also be employed with liquid carriers to form spreadable pastes, gels, ointments, soaps, and the like, for application directly to the skin of the user.
Generally, the concentration of the compound in a liquid composition often is from about 0.1 wt % to about 25 wt %, sometimes from about 0.5 wt % to about 10 wt %. The concentration in a semi-solid or solid composition such as a gel or a powder often is about 0.1 wt % to about 5 wt %, sometimes about 0.5 wt % to about 2.5 wt %. A compound composition may be prepared as a unit dosage form, which is prepared according to conventional techniques known in the pharmaceutical industry. In general terms, such techniques include bringing a compound into association with pharmaceutical carrier(s) and/or excipient(s) in liquid form or finely divided solid form, or both, and then shaping the product if required.
In a particular example, the pharmaceutical composition comprises about 2% w/w of a compound having formula (1), about 4% mannitol, and about 0.5% sucrose. In particular examples, the formulation has a pH of about 3.5. For injectable formulations, water may be added to the final weight.
The compound composition may be formulated into any dosage form, such as tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions also may be formulated as suspensions in aqueous, non aqueous, or mixed media. Aqueous suspensions may further contain substances which increase viscosity, including for example, sodium carboxymethylcellulose, sorbitol, and/or dextran. The suspension may also contain one or more stabilizers.
The amount of the compound, or an active salt or derivative thereof, required for use in treatment will vary not only with the particular salt selected but also with the route of administration, the nature of the condition being treated and the age and condition of the patient and will be ultimately at the discretion of the attendant physician or clinician.
A useful compound dosage often is determined by assessing its in vitro activity in a cell or tissue system and/or in vivo activity in an animal system. For example, methods for extrapolating an effective dosage in mice and other animals to humans are known to the art (see, e.g., U.S. Pat. No. 4,938,949). Such systems can be used for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population) of a compound. The dose ratio between a toxic and therapeutic effect is the therapeutic index and it can be expressed as the ratio ED50/LD50. The compound dosage often lies within a range of circulating concentrations for which the ED50 is associated with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any compounds used in the methods described herein, the therapeutically effective dose can be estimated initially from cell culture assays. A dose sometimes is formulated to achieve a circulating plasma concentration range covering the IC50 (i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in in vitro assays, as such information often is used to more accurately determine useful doses in humans. Levels in plasma may be measured, for example, by high performance liquid chromatography.
Another example of effective dose determination for a subject is the ability to directly assay levels of “free” and “bound” compound in the serum of the test subject. Such assays may utilize antibody mimics and/or “biosensors” generated by molecular imprinting techniques. The compound is used as a template, or “imprinting molecule”, to spatially organize polymerizable monomers prior to their polymerization with catalytic reagents. Subsequent removal of the imprinted molecule leaves a polymer matrix which contains a repeated “negative image” of the compound and is able to selectively rebind the molecule under biological assay conditions (see, e.g., Ansell, et al., Current Opinion in Biotechnology (1996) 7:89-94 and in Shea, Trends in Polymer Science (1994) 2:166-173). Such “imprinted” affinity matrixes are amenable to ligand-binding assays, whereby the immobilized monoclonal antibody component is replaced by an appropriately imprinted matrix (see, e.g., Vlatakis, et al., Nature (1993) 361:645-647). Through the use of isotope-labeling, “free” concentration of compound can be readily monitored and used in calculations of IC50. Such “imprinted” affinity matrixes can also be designed to include fluorescent groups whose photon-emitting properties measurably change upon local and selective binding of compound. These changes can be readily assayed in real time using appropriate fiberoptic devices, in turn allowing the dose in a test subject to be quickly optimized based on its individual IC50. An example of such a “biosensor” is discussed in Kriz, et al., Analytical Chemistry (1995) 67:2142-2144.
Exemplary doses include milligram or microgram amounts of the compound per kilogram of subject or sample weight, for example, about 1 microgram per kilogram to about 500 milligrams per kilogram, about 100 micrograms per kilogram to about 5 milligrams per kilogram, or about 1 microgram per kilogram to about 50 micrograms per kilogram. It is understood that appropriate doses of a small molecule depend upon the potency of the small molecule with respect to the expression or activity to be modulated. When one or more of these small molecules is to be administered to an animal (e.g., a human) in order to modulate expression or activity of a polypeptide or nucleic acid described herein, a physician, veterinarian, or researcher may, for example, prescribe a relatively low dose at first, subsequently increasing the dose until an appropriate response is obtained. In addition, it is understood that the specific dose level for any particular animal subject will depend upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, gender, and diet of the subject, the time of administration, the route of administration, the rate of excretion, any drug combination, and the degree of expression or activity to be modulated.
The following examples are offered to illustrate but not to limit the invention.
EXAMPLES
The following are exemplary procedures for synthesizing substituted quinobenzoxazines analogs.
Example 1
Preparation of Substituted Quinobenzoxazine Analogs
The general synthetic scheme for the preparation of substituted quinobenzoxazines analogs is shown in Scheme 1.




Ethyl-(2′,3′,4′,5′-tetrafluorobenzoyl)-ethanoate




Potassium ethyl malonate (3.66 g, 21.5 mmol), MgCl2 (2.44 g, 25.7 mmol) and TEA (2.05 g, 20.3 mmol) were mixed in acetonitrile (70 ml) at 10-15° C for 2.5 hr. 2,3,4,5-tetrafluorobenzoyl chloride (2.00 g, 10.3 mmol) in acetonitrile (10 ml) was added at 0° C. over 15 min followed by a second addition of TEA (0.23 g, 2.3 mmol). After allowing to warm to RT, the mixture was stirred for 16 hr. After removal of volatiles in vacuo Toluene (30 ml) was added and removed in vacuo. Following the addition of toluene (60 ml), HCl 1.5 M (40 ml) was added cautiously, ensuring the temperature did not exceed 25° C. The organic fraction was washed with HCl 1.5 M (2×25 ml) and water (2×25 ml), dried over MgSO4 and reduced to a light orange oil in vacuo ([M+1]+ 265, 98%).
Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(dimethylamino)-prop-2-enoate




Dimethyl acetal dimethyl formamide (0.61 g, 5.1 mmol) was added dropwise to ethyl-(2′,3′,4′,5′-tetrafluorobenzoyl)-ethanoate (0.9 g, 3.41 mmol) dissolved in acetic anhydride (2 ml), under argon. After 30 min solvent was removed in vacuo to leave the product as an orange oil in a quantitative yield ([M+1+] 320).
Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-phenyl-phenoxazine-5-carboxylate




Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(dimethylamino)-prop-2-enoate (3.4 g, 8.0 mmol) and 2-amino-4-phenyl-phenol (1.5 g, 8.0 mmol) in 20 DMSO (20 ml) was stirred under vacuum at 60° C. for 30 min. K2CO3 (5 g) and MeCN (20 ml) was added and the suspension was heated at 80° C. for 1 hr. After cooling to RT, the mixture was poured into a slight excess of dilute sulfuric acid and filtered. The product was recovered as a yellow-brown solid ([M+1]+ 420, 65%).
Example 2
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-phenyl-phenoxazine-5-carboxylic acid




Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-phenyl-phenoxazine-5-carboxylate (2.2 g, 5.3 mmol) was refluxed in a mixture of conc. HCl and acetic acid (20 ml each) for 2 hr. After cooling to room temperature cold water (40 ml) was added to the reaction mixture and the resulting precipitate filtered and washed with ether to afford the product as a yellow-brown solid 90% ([M+1]+ 392).
Example 3
Preparation of Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(napthyl-2′′,3′′-diamino)-prop-2-enoate




Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(dimethylamino)-prop-2-enoate (10.53 g, 33 mmol) in acetonitrile (50 ml) was added to a solution of 2,3-diaminonapthalene (5.22 g, 33 mmol) in acetonitrile (150 ml), maintained at 50° C. under argon. After 3 hours, volatiles were removed in vacuo and the residue was subjected to chromatography over silica (15% EtOAc/Hexane) to yield the product as a yellow solid ([M+1]+ 433) (55%).
Example 4
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phendiazine-5-carboxylate




Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(napthyl-2′′,3′′diamino)-prop-2-enoate (600 mg 1.4 mmol) was dissolved in a slurry of K2CO3 in DMF (500 ml), The mixture was stirred vigorously at 100° C. for 1 hour, then allowed to cool to RT. The K2CO3 was removed by filtration and the DMF removed in vacuo to leave a yellow-brown solid in quantitative yield. ([M+1]+ 393).
Example 5
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phendiazine-5-carboxylic acid




KOH solution (1N, 2.54 ml, 2.56 mmol) was added to a solution of ethyl 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phendiazine-5-carboxylate (500 mg, 1.28 mmol) in ethanol (400 ml), heated under reflux. After 2 hours the reaction mixture was allowed to cool to RT, then neutralized with HCl solution (1N). The product was collected by filtration as a yellow solid, 89%. ([M+1]+ 365).
Example 6
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-phenthiazine-5-carboxylate
Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(N-aminobenzyldisulfide)-prop-2-enoate




Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(dimethylamino)-prop-2-enoate (17.7 g, 55.3 mmol) in acetonitrile (10 ml) was added to a solution of 1,2-aminothiophenol dimer (5.22 g, 33 mmol) in acetonitrile (100 ml). After 3 hours, volatiles were removed in vacuo and the residue was subjected to chromatography over silica (1% MeOH/DCM) to yield the product as a yellow solid ([M+1]+ 523) (50%).
Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-phenthiazine-5-carboxylate




Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(N-aminobenzyldisulfide)-prop-2-enoate (2.5 g 3.2 mmol) was dissolved in DMF (120 ml) and heated under reflux for six hours. Removal of DMF in vacuo gave the product as a yellow solid 90% ([M+1]+ 360).
Example 7
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-phenthiazine-5-carboxylic acid




KOH solution (1N, 3.0, 3.0 mmol) was added to a solution of ethyl 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]-phenthiazine-5-carboxylate (1000 mg, 2.5 mmol) in ethanol (400 ml), heated under reflux. After 2 hours the reaction mixture was allowed to cool to RT, then neutralized with HCl solution (1N). The product was collected by filtration as a yellow solid, ([M+1]+ 332, 95%)
Example 8
Preparation of 5,6-Difluoro-9-hydroxy-3-oxo-3H-pyrido[3,2,1-kl]-pyrimido[g]phenoxazine-2-carboxylic acid
7-nitroquinazoline-4,6-diol




To a solution containing 20 ml of 48% aqueous HBr and 20 ml of AcOH was added 6-methoxy-7-nitro-3,4-dihydroquinazolin-4-one (1.4 g, 6.3 mmol) and the mixture was refluxed overnight. The resulting solution was evaporated to afford the crude phenol as a residue and was used without further purification (1.2 g, 5.8 mmol) (M+1, 208).
7-aminoquinazoline-4,6-diol




The crude product from above (1.0 g, 5.8 mmol) was diluted with 40 ml water and 3 g of Tin II chloride dihydrate was added and the reaction was stirred at room temperature. After 1 h the reaction was neutralized with K2CO3, and extracted with EtOAc (3×50 mL). The combined organic extracts were dried over sodium sulfate and the solvent was removed in vacuo to afford the crude amino alcohol (1.0 g, 5.6 mmol) (M+1, 178).
Ethyl; 5,6-difluoro-9-hydroxy-3-oxo-3H-pyrido[3,2,1-kl]pyrimido[g]phenoxazine-2-carboxylate




To a solution of the tetrafluoroenamine (2.2 g, 6.9 mmol) in DMSO (3 mL) was added the aminophenol (1.0 g, 5.6 mmol) and the reaction mixture was stirred under vacuum (rotary evaporator) at 60° C. for 20 minutes. The reaction mixture was allowed to cool to room temperature and was diluted with acetonitrile (200 mL) and potassium carbonate was added. The mixture was heated to reflux for 5 hours and poured into dilute HOAc/water. The solid product was collected by vacuum filtration and dried to afford the difluoroester as a tan solid (1.3 g, 3.2 mmol) (M+1, 412).
5,6-Difluoro-9-hydroxy-3-oxo-3H-pyrido[3,2,1-kl]pyrimido[g]phenoxazine-2-carboxylic acid




The difluoroester (1.3 g, 3.2 mmol) was dissolved in a 1:1 mixture of glacial acetic acid and 12 M HCl (20 mL) and refluxed for 30 min. The mixture was then cooled to room temperature and poured into water. The solid product was then collected by vacuum filtration and dried to afford the difluoroacid as a tan solid (0.98 g, 2.5 mmol) ([M+1]+ 392).
Example 9
Preparation of 2-(2-(Ethoxycarbonyl)-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazin-9-yloxy)acetic acid
Ethyl 5,6-difluoro-9-hydroxy-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylate




To a solution of the tetrafluoroenamine (5.8 g, 18.2 mmol), dissolved in DMSO (12 mL), was added 2,4-dihydroxyaniline hydrochloride (2.5 g, 15.5 mmol) and the mixture was heated to 60° C. under vacuum (rotary evaporator) for 20 minutes. The reaction mixture was then diluted with acetonitrile (100 mL) and potassium carbonate (3 g) was added and the mixture was refluxed overnight. The mixture was allowed to cool to room temperature and the solvent was removed in vacuo. A slight excess of 2 M HCl was added to rapidly dissolve the carbonate, and the solid precipitate was filtered and dried to afford the difluoroester as a tan solid (5.0 g, 13.9 mmol) (M+1, 360).
2-(2-(Ethoxycarbonyl)-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazin-9-yloxy)acetic acid




To a solution of the difluoroester (2.1 g, 5.8 mmol) and tert-butylbromoacetate (2.0 g, 10.3 mmol) in DMF (30 mL) was added potassium carbonate (2.0 g) and the mixture was heated to 60° C. for 1 hour. The reaction was allowed to cool and poured into water (500 mL) and extracted with ethyl acetate (3×100 mL),washed with brine, dried over magnesium sulfate and filtered over a pad of silica gel (30×50 mm), eluting with ethyl acetate. The solvent was removed in vacuo and the resulting material was triturated with hexanes and dried to afford the tert-butyl ester as a tan solid (2.8 g, 5.8 mmol). This material was dissolved in trifluoroacetic acid (40 mL) and stirred at room temperature for 30 minutes. The solvent was removed in vacuo to afford the acid as a tan solid (2.4 g, 5.7 mmol) (M+1, 418).
Example 10
Preparation of 9-(Carboxymethoxy)-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylic acid




The difluoroester (2.4 g, 5.7 mmol) was dissolved in a 1:1 mixture of glacial acetic acid and 12 M HCl (40 mL) and refluxed for 1 hour. The mixture was then cooled to room temperature and poured into water. The solid product was then collected by vacuum filtration and dried to afford the difluoroacid as a tan solid (2.0 g, 5.1 mmol) (M+1, 390).
Example 11
Preparation of Ethyl 1,2,3-trifluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phenoxazine-5-carboxylate




To a solution of pentafluoroenamine (8 g, 23.7 mmol), prepared by a similar procedure as for the tetrafluoroenamine dissolved in DMSO (12 mL) was added 3-amino-2-naphthol (3.5 g, 21.9 mmol) and the mixture was heated to 60° C. under vacuum (rotary evaporator) for 2 hours. The reaction mixture was then diluted with acetonitrile (200 mL) and potassium carbonate (8.0 g) was added and the mixture was refluxed overnight. The mixture was allowed to cool to room temperature and the solvent was removed in vacuo. A slight excess of 2 M HCl was added to rapidly dissolve the carbonate, and the solid precipitate was filtered and dried to afford the difluoroester as a tan solid (1.3 g, 3.2 mmol) (M+1, 412).
Example 12
Preparation of 1,2,3-Trifluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phenoxazine-5-carboxylic acid




The trifluoroester (1.3 g, 3.2 mmol) was dissolved in acetic acid (5 mL) and 12 M HCl was added (5 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the trifluoroacid as a pale solid (1.0 g, 2.6 mmol) (M+1, 384).
Example 13
Preparation of Ethyl 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phenoxazine-5-carboxylate




To a solution of the enamine (30 g, 94 mmol) in ethyl acetate (100 mL) was added 3-amino-2-naphthol (10 g, 63 mmol) at room temperature and the mixture was immediately placed on a rotary evaporator and the solvent was removed over 2 hours at a temperature below 0° C. (ice formed on the flask) to produce a yellow solid. To this solid was added ether (200 mL) and the slurry was filtered to afford a yellow solid. This solid was then dissolved in DMF (200 mL) and potassium carbonate was added (16.5 g, 120 mmol) and the mixture was heated to 90° C. for 1 hour. The mixture was allowed to cool to room temperature and water was added (500 mL) and the resulting solid was filtered, washed with water and dried to afford the difluoroester as a tan solid (12.2 g, 30.8 mmol) (M+1, 394).
Example 14
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phenoxazine-5-carboxylic acid




The difluoroester (5 g, 12.7 mmol) was dissolved in methanol (50 mL) and conc HCl was added (20 mL) and the mixture was refluxed for 12 hours. The mixture was allowed to cool to room temperature and the solid was collected by vacuum filtration, washing with methanol to afford the difluoroacid as a light tan powder (3.6 g, 9.9 mmol) (M+1, 366).
Example 15
Preparation of Ethyl 1-fluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phenoxazine-5-carboxylate




To a solution of the enamine, similarly prepared as the tetrafluoroenamine (14 g, 46.3 mmol) in ethyl acetate (100 mL) was added 3-Amino-2-naphthol (5.0 g, 31.2 mmol) at room temperature and the mixture was immediately placed on a rotary evaporator and the solvent was removed over 2 hours at a temperature below 0° C. (ice formed on the flask) to produce a yellow solid. To this solid was added methanol (200 mL) and the slurry was filtered to afford a yellow solid. This solid was then dissolved in acetonitrile (200 mL) and potassium carbonate was added (10.0 g, 72.5 mmol) and the mixture was heated to 80° C. for 1 hour. The mixture was allowed to cool to room temperature and water was added (500 mL) and the resulting solid was filtered, washed with water and dried to afford the fluoroester as a tan solid (6.0 g, 16.0 mmol) (M+1, 376).
Example 16
Preparation of 1-Fluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[g]-phenoxazine-5-carboxylic acid




The fluoroester (6.0 g, 16.0 mmol) was dissolved in acetic acid (10 mL) and 12 M HCl was added (10 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the fluoroacid as a pale solid (4.8 g, 13.8 mmol) (M+1, 348).
Example 17
Preparation of Ethyl 9-chloro-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylate




To a solution of the enamine (14.4 g, 45.3 mmol) in ethyl acetate (200 mL) was added 5-chloro-2-aminophenol (5.0 g, 34.8 mmol) and the solvent was removed in vacuo with a rotary evaporator over 2 hours without heating. Methanol was added and the resulting phenolic enamine was isolated by vacuum filtration. The resulting solid (7.0 g) was dissolved in acetonitrile and potassium carbonate was added and the resulting mixture was heated to reflux for 2 hours. The mixture was then allowed to cool to room temperature and poured into Dilute HCl. The resulting solid was collected by vacuum filtration and dried to afford the difluoroester as a pale yellow solid (5.0 g, 13.3 mmol) (M+1, 378).
Example 18
Preparation of 9-Chloro-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylic acid




The difluoroester (5.0 g, 13.3 mmol) was dissolved in acetic acid (45 mL) and 12 M HCl was added (30 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluoroacid as a pale solid (4.0 g, 10.6 mmol) (M+1, 350).
Example 19
Preparation of Ethyl 10-chloro-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylate




To a solution of the enamine (14.4 g, 45.3 mmol) in ethyl acetate (200 mL) was added 4-chloro-2-aminophenol (5.0 g, 34.8 mmol) and the solvent was removed in vacuo with a rotary evaporator over 2 hours without heating. Methanol was added and the resulting phenolic enamine was isolated by vacuum filtration. The resulting solid (7.5 g) was dissolved in acetonitrile and potassium carbonate was added and the resulting mixture was heated to reflux for 2 hours. The mixture was then allowed to cool to room temperature and poured into Dilute HCl. The resulting solid was collected by vacuum filtration and dried to afford the difluoroester as a pale yellow solid (5.0 g, 13.3 mmol) (M+1, 378).
Example 20
Preparation of 10-Chloro-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylic acid




The difluoroester (2.5 g) was dissolved in acetic acid (25 mL) and 12 M HCl was added (20 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluoroacid as a pale solid (2.0 g, 5.3 mmol) (M+1, 350).
Example 21
Preparation of Ethyl 5,6-Difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylate




To a solution of the enamine (5.7 g, 17.9 mmol) in ethyl acetate (50 mL) was added 2-aminophenol (1.9 g, 17.43 mmol) at room temperature and the mixture was immediately placed on a rotary evaporator and the solvent was removed over 2 hours at a temperature below 0° C. (ice formed on the flask) to produce a yellow solid. To this solid was added ether (25 mL) and the slurry was filtered to afford a yellow solid. This solid was then dissolved in DMF (20 mL) and potassium carbonate was added (2.9 g, 21 mmol) and the mixture was heated to 90° C. for 1 hour. The mixture was allowed to cool to room temperature and water was added (200 mL) and the resulting solid was filtered, washed with water and dried to afford the phenoxazine as a tan solid (2.9 g, 8.45 mmol) (M+1, 344).
Example 22
Preparation of 5,6-Difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylic acid




The difluoroester (5.0 g, 14 mmol) was dissolved in methanol (50 mL) and conc HCl was added (20 mL) and the mixture was refluxed for 2 hours. The mixture was allowed to cool to room temperature and the solid was collected by vacuum filtration, washing with methanol to afford the difluoroacid as a light tan powder (4.2 g, 13.3 mmol, 91%) (M+1,316).
Example 23
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[h]-phenoxazine-5-carboxylate




To a solution of the enamine (14.0 g, 45.3 mmol) in ethyl acetate (200 mL) was added 1-amino-2-naphthol (5.0 g, 31.3 mmol) and the solvent was removed in vacuo with a rotary evaporator over 2 hours without heating. Methanol was added and the resulting phenolic enamine was isolated by vacuum filtration. The solid was dissolved in acetonitrile and potassium carbonate (10 g) was added and the mixture was heated to reflux for 2 hours. The mixture was then allowed to cool to room temperature and poured into Dilute HCl. The resulting solid was collected by vacuum filtration and dried to afford the difluoroester as a pale yellow solid (5.0 g, 13.3 mmol) (M+1, 376).
Example 24
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[h]-phenoxazine-5-carboxylic acid




The difluoroester (5.5 g) was dissolved in acetic acid (25 mL) and 12 M HCl was added (20 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluoroacid as a pale solid (5.0 g, 14.4 mmol) (M+1, 348).
Example 25
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[f]-phenoxazine-5-carboxylate




To a solution of the enamine (45 g, 141 mmol) in ethyl acetate (500 mL) was added 2-amino-1-naphthol (15.0 g, 93.8 mmol) and the solvent was removed in vacuo with a rotary evaporator over 2 hours without heating. Methanol was added and the phenolic enamine was isolated by vacuum filtration. The resulting solid was dissolved in acetonitrile (400 mL) and potassium carbonate (25 g) was added and the mixture was heated to reflux for 2.5 hours. The mixture was then allowed to cool to room temperature and poured into Dilute HCl. The resulting solid was collected by vacuum filtration and dried to afford the difluoroester as a pale yellow solid (19.69 g, 50.1 mmol) (M+1, 394).
Example 26
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[f]-phenoxazine-5-carboxylic acid




The difluoroester (15.0 g, 38.1 mmol) was dissolved in acetic acid (60 mL) and 12M HCl was added (60 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluoroacid as a pale solid (11.7 g, 32 mmol) (M+1, 366).
Example 27
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[b]furan[2,3-g]-phenoxazine-5-carboxylate
3-Aminodibenzofuran-2-ol




To a solution of the dibenzofuran (15 g, 70.4 mmol) dissolved in methylene chloride (500 mL) at 0° C. was added BBr3 (200 mL, 1 M in CH2Cl2) via addition funnel. After the addition was complete, the mixture was allowed to come to room temperature over 1 hour and then quenched with water followed by potassium carbonate (40 g). The resulting solid was recovered by vacuum filtration and dried to afford the hydroxyl dibenzofuran as a white solid (13.2 g, 199 mmol) (M+1, 200).
Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[b]furan[2,3-g]-phenoxazine-5-carboxylate




To a solution of the tetrafluoroenamine (15.0 g, 47 mmol) dissolved in DMSO (30 mL) was added the hydroxyl dibenzofuran (12.0 g, 60 mmol) and the mixture was heated to 60° C. under vacuum (rotary evaporator) for 20 minutes. The reaction mixture was then diluted with acetonitrile (200 mL) and potassium carbonate (17 g) was added and the mixture was refluxed for 2.5 hours. The mixture was allowed to cool to room temperature and the solvent was removed in vacuo. A slight excess of 2 M HCl was added to rapidly dissolve the carbonate, and the solid precipitate was filtered and dried to afford the difluoroester as a tan solid (15.0 g, 34.6 mmol) (M+1, 434).
Example 28
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]benzo[b]furan[2.3-g]-phenoxazine-5-carboxylic acid




The difluoroester (15.0 g, 34.6 mmol) was dissolved in acetic acid (60 mL) and 12 M HCl was added (60 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluoroacid as a pale solid (13.7 g, 34 mmol) (M+1, 406).
Example 29
Preparation of Ethyl 2-(ethoxycarbonyl)-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-10-carboxylate




To a solution of the tetrafluoroenamine (7.0 g, 21.9 mmol) dissolved in DMSO (25 mL) was added 4-hydroxy-3-amino benzoic acid (3.0 g, 19.6 mmol) and the mixture was heated to 60° C. under vacuum (rotary evaporator) for 2 hours. The reaction mixture was then diluted with acetonitrile (200 mL) and potassium carbonate (8.0 g) was added and the mixture was refluxed overnight. The mixture was allowed to cool to room temperature and the solvent was removed in vacuo. A slight excess of 2 M HCl was added to rapidly dissolve the carbonate, and the solid precipitate was filtered and dried to afford the difluoroester as a tan solid (6.2 g, 16.0 mmol) (M+1, 388).
Example 30
Preparation of 2-(Ethoxycarbonyl)-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-10-carboxylic acid




The difluoroester (6.2, 16.0 mmol g) was dissolved in acetic acid (25 mL) and 12 M HCl was added (20 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluorodi-acid as a pale solid (5.3 g, 14.8 mmol) (M+1, 360).
Example 31
Preparation of Ethyl 5,6-difluoro-10-nitro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylate




A solution of the enamine (6.0 g, 18.7 mmol) and 2-amino-4-nitrophenol (3.5 g, 23.3 mmol) in acetonitrile was heated to 80° C. for 15 minutes. Potassium carbonate was then added (8.0 g) and the mixture was heated to reflux overnight. The reaction mixture was then filtered hot and the solvent was removed in vacuo to afford the crude nitroester (5.0 g, 12.8 mmol) (M+1, 389).
Example 32
Preparation of 5,6-Difluoro-10-nitro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylic acid




The crude difluoroester (5.0 g, 12.8 mmol) was dissolved in acetic acid (25 mL) and 12 M HCl was added (20 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluoroacid as a pale solid (2.0 g, 5.5 mmol) (M+1, 361).
Example 33
Preparation of Ethyl 5,6-difluoro-3-oxo-10-phenyl-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylate




A solution of the enamine (5.4 g, 16.9 mmol) and 3-amino-4-hydroxybiphenyl (3.5 g, 18.9 mmol) in acetonitrile was heated to 80° C. for 90 minutes. Potassium carbonate was then added (8.0 g) and the mixture was heated to reflux overnight. The reaction mixture was then filtered hot and the solvent was removed in vacuo to afford the crude difluoroester (3.9 g, 9.3 mmol) (M+1, 420).
Example 34
Preparation of 5,6-Difluoro-3-oxo-10-phenyl-3H-pyrido[3,2,1-kl]phenoxazine-2-carboxylic acid




The crude difluoroester (3.6 g, 8.6 mmol) was dissolved in acetic acid (10 mL) and 12 M HCl was added (10 mL) and the reaction mixture was heated to reflux for 2 hours. The mixture was then cooled to room temperature, poured into water and the solid product was collected by vacuum filtration and dried to afford the difluoroacid as a pale solid (2.6 g, 6.6 mmol) (M+1,392).
Example 35
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-11-sulfonic-acid-pyrido[3,2,1-kl]benzo[h]-phenoxazine-5-carboxylate




To a solution of the tetrafluoroenamine (5.4 g, 16.9 mmol) dissolved in DMSO (30 mL) was added 1-amino-2-hydroxy-4-naphthalenesulfonic acid (4.8 g, 20 mmol) and the mixture was heated to 60° C. under vacuum (rotary evaporator) for 2 hours. To the reaction mixture was added potassium carbonate (10.0 g) and the mixture was heated to 60° C. for 1 hour. The mixture was allowed to cool to room temperature and a slight excess of 2 M HCl was added to rapidly dissolve the carbonate. The aqueous layer was decanted and the remaining organic residue was dissolved in methanol (100 mL) and precipitated with ethyl acetate (200 mL) and the solid precipitate was filtered and dried to afford the sulfonic acid as a brown solid (3.1 g, 6.5 mmol) (M+1, 474).
Example 36
Preparation of 1,2-Difluoro-4-oxo-4H-11-sulfonic-pyrido[3,2,1-kl]benzo[h]-phenoxazine-5-carboxylic acids




The crude difluoroester (1.5 g, 3.2 mmol) was dissolved in acetic acid (10 mL) and 12 M HCl was added (10 mL) and the reaction mixture was heated to reflux for 30 minutes. The solvent was removed in vacuo to afford the sulfonic acid as a brown solid (1.1 g, 2.5 mmol) (M+1, 446)
Example 37
Preparation of 2-(Ethoxycarbonyl)-5,6-difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-9-carboxylic acid




A solution of the difluoroenamine (5.2 g, 16.3 mmol) and 4-amino-3-hydroxybenzoic acid (4.0 g, 26.1 mmol) in DMSO was stirred at room temperature for 1.5 hours. Potassium carbonate (8 g) was then added and the reaction mixture was stirred under vacuum (rotary evaporator) for 1 hour. The mixture was then heated to 100° C. for 1 hour and then allowed to cool to room temperature. The reaction mixture was then poured into 1 M H2SO4 (500 mL) and the solids were recovered by vacuum filtration. The resulting solid was dried to afford the crude difluoroacid as a tan solid (5.0 g, 12.9 mmol) (M+1, 388).
Example 38
Preparation of 5,6-Difluoro-3-oxo-3H-pyrido[3,2,1-kl]phenoxazine-2,9-dicarboxylic acid




The crude difluoroester (5.0 g, 12.9 mmol) was dissolved in acetic acid (20 mL) and 12 M HCl was added (20 mL) and the reaction mixture was heated to reflux for 1 hour. The reaction was allowed to cool to room temperature and water was added. The resulting solid was collected by vacuum filtration and dried overnight to afford the di-acid as a tan solid (1.9 g, 5.3 mmol) (M+1, 360).
Example 39
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-fluorenone-5-carboxylate
3-Nitro-2-hydroxyfluorenone




A solution of NO2BF4 (3.52 g, 25.5 mmol) in acetonitrile (100 ml) was added dropwise to a solution of 2-hydroxyfluorenone (5 g, 25.5 mmol) in acetonitrile (400 ml) at ambient temperature. The reaction mixture was then cooled to 0° C. and water (100 ml) was added to precipitate impurities. After filtration, water (200 ml) was added and the precipitate filtered off as a red solid (68%) (M+1, 242).
3-amino-2-hydroxyfluorenone




A mixture of 3-nitro-2-hydroxyfluorenone (1.6 g, 6.6 mmol) and SnCl2 (3 g, 6.6 mmol was refluxed in 100 ml acetic acid:conc. HCl (1:1) for 1 hour. The mixture was allowed to cool to room temperature and neutralized with ammonium hydroxide. After extracting with EtOAc (3×100 ml), combined organic fractions were dried over magnesium sulfate and evaporated to leave the product as a brown solid (65%) (M+1, 212).
Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-fluorenone-5-carboxylate




A mixture of 3-amino-2-hydroxyfluorenone (0.9 g, 4.26 mmol) and ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(dimethylamino)-prop-2-enoate (1.36 g, 4.26 m heated in DMSO (50 ml) under vacuum for 18 hr. The product was extracted using EtOAc/Brine and the organic layers combined and dried to give the product as a red solid. The solid was dissolved in DMSO (40 ml) containing a large excess of K2CO3 and heated at 100° C. for 30 min. After cooling to room temperature, brine (30 ml) was added and the precipitated product collected as a yellow solid (60% over two steps) (M+1, 446).
Example 40
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-fluorenone-5-carboxylic acid




A mixture of ethyl 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-fluorenone-5-carboxyl in acetic acid:conc. HCl (1:1) (50 ml each) was heated at reflux for 2 hr. After cooling to room temperature, water (50 ml) was added and the product collected as yellow solid (94%) (M+1, 418).
Example 41
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-anthraquinone-5-carboxylate




A mixture of 3-amino-2-hydroxyanthraquinone (5.54 g, 23.2 mmol) and ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(dimethylamino)-prop-2-enoate (8.7 g, 34.8 mm heated in a minimum of DMSO ( ̃10 ml) under vacuum for 24 hr. The product was precipitated by the addition of water (50 ml). The solid was dried overnight in a vacuum oven and dissolved in DMSO (40 ml) containing a large excess of K2CO3 and heated at 100° C. for 30 min. After cooling to room temperature, brine (30 ml) was added and the precipitated product collected as a yellow solid (60% over two steps) (M+1, 474).
Example 42
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-anthraquinone-5-carboxylic acid




A mixture of ethyl 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-anthraquinonenone-5-carboxylate (3.5 g, 6.8 mmol) in acetic acid:conc. HCl (1:1) (50 ml each) was heated at reflux for 2 hr. After cooling to room temperature, water (50 ml) was added and the product collected as yellow solid (94%) (M+1, 446).
Example 43
Preparation of Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-phenyl-phenoxazole-5-carboxylate
2-amino(t-butoxy carbonyl)-5-amino hydroquinone




A solution of Boc anhydride (7.17 g, 33 mmol) and DIEA (17 ml, 99 mmol) in DMSO (20 ml) was added dropwise at room temperature to stirred solution of 1,4-dihydroxy-2,5-diaminobenzene (7 g, 33 mmol). After stirring for 18 hr, the product was separated between EtOAc and brine and the organic layers combined and dried over MgSO4. After removal of solvent the residue was subjected to column chromatography on silica eluting with 25-50% EtOAc in hexane to give pure product (45%) (M+1,239).
4-hydroxy-3-amino(t-butoxy carbonyl)-phenoxazole




To solution of 2-amino(t-butoxy carbonyl)-5-amino hydroquinone (4.69 g, 23.3 mmol) dissolved in acetonitrile/water (1:1; 20 ml) was added Na hydrosulfite (large excess) and the mixture stirred at room temp. for 15 min. The acetonitrile was removed in vacuo and the aqueous mixture extracted with EtOAc (3×20 ml). Combined organic layers were dried over MgSO4 and solvent removed in vacuo. The residue was taken up in neat triethyl orthoformate (100 ml), left to stir for 16 hr then heated to reflux for 10 min. The product was precipitated following cooling to room temp. by the addition of water (83%)(M+1, 251).
4-hydroxy-2-amino phenoxazole




4-Hydroxy-3-amino(t-butoxy carbonyl)-phenoxazole (3 g, 12 mmol) was dissolved in neat TFA (100 ml) and allowed to stir at room temperature for 1 hour. TFA was removed in vacuo to leave the final product as a TFA salt (quant.) (M−1, 149)
Ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(N-(4-hydroxy-2-amino phenoxazole))-prop-2-enoate




A solution of ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(dimethylamino)-prop-2-enoate (7.34 g, 23 mmol) and 2-amino-4-phenyl-phenol (3.45 g, 23 mmol) in EtOAc (20 ml) containing triethylamine (10 ml) was stirred under vacuum on the rotary evaporator for 3 hours. The EtOAc was removed in vacuo and the residue subjected to column chromatography on silica eluting with 50% EtOAc in hexane to give pure product (72%) (M+1, 425).
Ethyl 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-phenyl-phenoxazole-5-carboxylate




A solution of ethyl-2-(2′,3′,4′,5′-tetrafluorobenzoyl-)-3-(N-(4-hydroxy-2-amino phenoxazole))-prop-2-enoate (3.5 g, 8.25 mmol) in DMSO (50 m) containing K2CO3 (large excess) was heated at 80° C. for 10 min. After cooling to room temperature, water was added to precipitate the product as a yellow sold (82%) (M+1, 385).
Example 44
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(3′-hydroxy-4′-amino phenyl)-5-carboxylic  acid




A mixture of ethyl 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-phenyl-phenoxazole-5-carboxylate (2.3 g, 6 mmol) in acetic acid:conc. HCl (1:1; 100 ml) was heated to reflux for 30 min. After cooling to room temp., volatiles were removed in vacuo to leave the product as a brown solid (82%) (M+1, 347).
Example 45
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(nitro-phenoxazine)-5-carboxylic acid
1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(3′-hydroxy-4′-amino-(N-2′′-fluoro-4′′-nitro phenyl)-phenyl))-5-carboxylic acid




A solution of 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(3′-hydroxy-4′-amino phenyl)-5-carboxylic acid (0.5 g, 1.44 mmol), 3,4-difluoro-nitro benzene (0.5 ml, 4.3 mmol) and DIEA (1 ml) was heated to 90° C. in NMP (50 ml) for 30 min. After cooling to room temp. the product was precipitated by the addition of water and filtered (63%) (M+1, 486).
1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(nitro-phenoxazine)-5-carboxylic acid




A solution of 2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(3′-hydroxy-4′-amino phenyl)-5-carboxylic acid (0.3 g, 0.6 mmol) in DMSO (50 ml) containing an excess of K2CO3 was stirred and heated to 110° C. for 1 hr. After cooling to room temp. the product was precipitated by the addition of 3M HCl and filtered (71%) (M+1, 465).
Example 46
Preparation of 1,2-Difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(amino-phenoxazine)-5-carboxylic acid




A mixture of 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-kl]-8-(nitro-phenoxazine)-5-carboxyl acid (0.1 g, 0.2 mmol) and Tin (II) chloride (0.15 g, 0.6 mmol) in acetic acid:conc. HCl (1:1; 50 ml) was heated to reflux for four hr. After cooling to room temp. the product was precipitated by the addition of water and filtered (72%) (M+1,435).
Example 47
Preparation of Preparation of Amide Derivatives of Substituted Quinobenzoxazine Analogs




To a series of solutions of the fluoroacid (0.5 mmol) in NMP (3.6 mL) was added the amines NHR1R2 (0.5-2.0 mmol) at room temperature. The vessels were sealed and heated on a 90° C. hotplate with constant stirring for 1-2 hours until the reactions were determined to be complete by HPLC/MS analysis. The reaction mixtures were allowed to cool to room temperature and water was added (20 mL). The resulting precipitates were collected by vacuum filtration and dried under vacuum. In cases where 1.0 equivalent of amine was used, the resulting reaction mixtures were used in the next step “as is.” The resulting solids or solutions were treated with HBTU (2.5 eq.) and DIEA in 3.6 mL NMP and allowed to stir for 30 minutes at room temperature under an inert atmosphere. These solutions were added to a series of amines NHR3R4 (2.5 equivalents) in a 96 well format (Whatman Uniplate, 2 mL) and allowed to react for 2 hours. Methanol was then added (50-100 μL) and the plate was filtered (Whatman Unifilter Polypropylene). The resulting liquids were directly chromatographed on reverse HPLC (Waters Xterra 19×50 mm) with mass directed collection (Micromass ZQ, Waters FCII). The fractions were analyzed for purity (MS TIC, UV) and dried by vacuum evaporation (Savant) with an average yield of 5-10 mg). Tables 1 and 2 list exemplary ester-substituted and amide-substituted quinobenzoxazines analogs, respectively.
Example 48
Antitumor Data
Two xenograft models for inoculation were harvested and diluted to a concentration of 50×106 cells/ml or 100×106 cells/ml. Four to six week old nude mice were injected with 0.1 ml of the cell suspension which contains between 5×106 and 10×106 cells. When tumors are of a suitable size compound dosing is commenced. Tumor sizes are measured throughout the treatment period with calipers and body weights also measured.
Antitumor activities for compounds CX-3092 (1204) and CX-1535 (148) are shown in FIGS. 1 and 2, indicating efficacy (slow tumor weight gain) and a lack of toxicity (little body weight change). FIG. 1 shows the antitumor activity of compound 494 in Ramos, a model for fatal childhood leukemia. FIG. 2 shows the antitumor activity of compound 516 in HCT-116, a model of colorectal cancer.
Example 49
Cell Proliferation and/or Cytotoxicity Assay
Cell culture. Human cervical epithelial cells (HeLa cells) were obtained from American Type Culture Collection (Manassas, Va.). Cells were grown in Eagle's minimum essential medium (MEM, Hyclone, Utah) supplemented with 2 mM Glutamine, 0.1 mM nonessential amino acid, 1 mM Na Pyruvate, 1.5 g/L NaHCO3, 50 mg/L gentamicin, and 10% fetal bovine serum (Hyclone, USA) in a humidified atmosphere of 5% CO2 at 37° C.
MTS assays. Antiproliferative effects of anticancer drugs were tested by the CellTiter 96 AQueous assay (Promega, WI), which is a calorimetric assay for determining the number of viable cells. (See, e.g., Wang, L., et al., Methods Cell Sci (1996) 18:249-255).
Cells (4,500 cells/well) were seeded on 96 well flat bottom plates (Corning, N.Y.) in 100 μl of culture medium without any anticancer drug on day 0, and the culture medium was exchanged for that contained anticancer drugs at various concentrations on day 1. After incubation for 3 days under normal growth conditions (on day 4), the monolayers were washed once in PBS, and the medium was switched to 100 μl of PBS in each of the 96 well plate. After mixing MTS and PMS at the ratio of 20:1, 20 μl of MTS/PMS solution was added to each of the 96 well plate and incubated for 4 hours in a humidified atmosphere of 5% CO2 at 37° C. The absorbance was read at 490 nm using FLUOstar Galaxy 96 well plate reader (BMG Labtechnologies, Germany). μM concentrations (MTS data) reported in Tables 1-2 are concentrations at which 50% of antiproliferative cell response is seen. Compounds whose IC50 values were greater than 5 μM were not reported.
Example 50
Measurement of mRNA Values in Cell Assays
Real-time quantitative PCR (QPCR) method was used to detect accurately the changes of the target c-myc and the endogenous reference GAPDH gene copies in the same tube. Cells (15,000 cells/well) were seed on 96 well flat bottom plates (Corning, N.Y.) and incubated under normal growth conditions for overnight. The next day, the culture medium was exchanged for that contained anticancer drugs at various concentrations and incubate for 4 hrs in a humidified atmosphere of 5% CO2 at 37° C. Total RNA (tRNA) was extracted using the RNeasy 96 Kit (QIAGEN, CA). The concentration of the tRNA was determined by the RiboGreen RNA Quantitation Reagent (Molecular Probes, OR).
Reverse-transcription (RT) reaction was occurred using 50 ng of tRNA from each well in a 25 μl reaction containing 1× TaqMan RT buffer, 2.5 uM random hexamers, 5.5 mM MgCl2, 0.5 mM each deoxynucleoside triphosphate (dNTP), 30 U MultiScribe Reverse Transcriptase, and 10 U RNase inhibitor. RT reactions were incubated for 10 min at 25° C., reverse-transcribed for 30 min at 48° C., inactivated for 5 min at 95° C., and placed at 4° C. All RT reagents were purchased from Applied Biosystems, CA.
Real-Time QPCR reaction was performed in a 50 μl reaction containing the 5 μl of cDNA, 1× Universal PCR Master Mix, 1×c-myc Pre-Developed Primers and Probe set, and 0.8×GAPDH Pre-Developed Primers and Probe set. Because of the relative abundance of GAPDH gene in Hela, GAPDH primers and probe concentration were adjusted to get accurate threshold cycles (CT) for both genes in the same tube. The threshold cycle (CT) indicates the fractional cycle number at which the amount of amplified target reaches a fixed threshold. By doing so, the GAPDH amplification was stopped before it can limit the common reactants available for amplification of the c-myc, resulted in a reduction in ? Rn value of GAPDH, but no effect on its CT value, and equal amplification efficiency for both genes. The ? Rn value represents the normalized reporter signal minus the baseline signal. ? Rn increases during PCR as amplicon copy number increases until the reaction approaches a plateau.
The c-myc probe was labeled with 6FAMTM dye-MGB and the GAPDH probe was labeled with VICTM dye-MGB. Preincubation was performed for 2 min at 50° C. to activate AmpErase UNG enzyme and then for 10 min at 95° C. to activate AmpliTaq DNA Polymerase. DNA was amplified for 40 cycles of 15 sec at 95° C. and 1 min at 60° C. Human c-myc and GAPDH cDNA were amplified, detected, and quantitated in real time using the ABI Prism 7000 Sequence Detection system (Applied Biosystems, CA), which was set to detect both 6-FAM and VIC reporter dyes simultaneously.
The data was analyzed by using the ABI PRISM Sequence Detection System and Microsoft Excel. Relative quantitation was done using the standard curve and comparative CT method at the same time, and both methods gave equivalent results. The cycle at which the amplification plot crosses the CT is known to accurately reflect relative mRNA values. (See, Heid, et al., Genome Res. (1996) 6:986-994; Gibson, et al., Genome Res. (1996) 6:995-1001). QPCR reactions were set up in triplicate at each cDNA sample and the triplicate CT values were averaged. All reagents including Pre-Developed Primers and probe set were purchased from Applied Biosystems, CA. μM concentrations (STOP data) reported in Tables 1-2 are concentrations at which 50% inhibition of c-myc mRNA levels are seen. Compounds whose IC50 values were greater than 5 μM were not reported.
Example 51
Synthesis of CX-3092 and CX-3543
One method for synthesizing CX-3543 is shown below. As shown in Scheme 2, CX-3543 is synthesized in a convergent manner, assembling the substructures 1, 1A and 2A in the final two synthetic steps (Scheme 2), to form CX-3543 having a 50:50 ratio of RS and SS isomers. CX-3092 may be synthesized in a similar manner using a non-chiral form of 1A.




In more detail, pyrazinopyrrolidine 1A is synthesized via a [3+2] cycloaddition chemistry. Conversion of L-proline 7 to cyano-1-aminopyrrolidine 8 without loss of stereochemistry, followed by reduction provides the chiral 2-aminoethyl-1-methyl pyrrolidine 2A in high yield. CX-3543 was found to have a formulated solubility of approximately 20 mg/mL.
Example 52
In vitro Characterization for CX-3543
Various methods were used for in vitro characterization of the compounds of the present invention, including but not limited to i) stop assays; ii) quadruplex/duplex selectivity screens; and iii) quadrome footprints.
Stop Assays. FIG. 3 represents a stop assay, a high throughput, first-pass screen for detecting drugs that bind to and stabilize the target G-quadruplex. As shown in FIG. 3, DNA template oligonucleotide is created, which contains the nucleotide sequence of the “target” quadruplex against which drug screening is desired. A fluorescently labeled primer DNA is then annealed to the 3′ end of the template DNA. A DNA polymerase such as Taq polymerase is then introduced to synthesize a complementary strand of DNA by extending from the fluorescently labeled primer. When the progress of the Taq polymerase is unhindered, it synthesizes a full-length copy of the template. Addition of a test drug that merely binds to duplex DNA but does not bind selectively the quadruplex region results in a decrease in synthesis of full length product and a concomitant increase in variable-length DNA copies. If, however, the test drug selectively binds to and stabilizes the quadruplex, the progress of polymerase arrests only at the quadruplex, and a characteristic “Stop Product” is synthesized.
In one aspect, the present invention provides compounds that will selectively target oncogenes regulated by the propeller/chair type of quadruplex, such as c-myc. Compounds are initially screened at a single concentration, and “hits” are re-assayed over a range of doses to determine an IC50 value (i.e., the concentration of drug required to produce an arrest product/full-length product ratio of 1:1). These products are visualized by capillary electrophoresis.
FIG. 4 shows the electrophoretogram for CX-3543 as well as for other types of drugs, including DNA interactive drugs such as the topo-II poison m-AMSA; the antibiotics distamycin, actinomycin D (a non-specific transcription inhibitor), and mithramycin; and the antibiotic fluoroquinolone ciprofloxacin. CX-3543 demonstrated an IC50 value of 1.0 μM in the stop assay, while none of the other DNA interactive drugs bound to the quadruplex at concentrations up to 100 μM. Thus, the first pass screen effectively identified agents having at least a 100-fold selectivity for the propeller/chair type quadruplex.
Quadruplex/Duplex Selectivity Screens. The selectivity of CX-3543 for the target quadruplex sequence relative to duplex DNA was measured using a proprietary direct competition assay (i.e., “selectivity screen”). This selectivity screen uses the stop assay as a reporter system to measure the relative ability of an externally added DNA sequence to compete with the target quadruplex structure formed in the DNA template for binding of the drug. In one example, the competitors are the c-myc quadruplex sequence, which is identical to the quadruplex sequence present in the template DNA; or a plasmid DNA which mimics complex genomic duplex DNA. The degree to which each competitor successfully “soaks up” drug in solution is reflected by the quantitative decrease in synthesis of the stop product. In this manner, the relative binding affinities of drug to both the target quadruplex and duplex DNA are determined.
FIG. 5 shows the quadruplex/duplex binding selectivity of CX-3543. As shown in FIG. 5, the free c-myc quadruplex (myc27) competes more effectively for the drug than does the plasmid DNA. The ratio of the competitor IC50 values indicates relative binding affinities of the drug for the quadruplex or duplex DNA. For CX-3543, this selectivity ratio for myc-quadruplex/plasmid DNA is around 400.
Quadrome Footprints. CX-3543 was also evaluated for its ability to bind to other native quadruplex structures of biological relevance, including quadruplex control elements that regulate a range of different oncogenes. The resulting data are used to create the Quadrome footprint.
FIG. 6 shows the Quadrome footprint for CX-3543. In FIG. 6, the primary IC50 data (upper panel) derived from different quadruplexes are inverted and displayed in column chart format to identify affected oncogenes (second panel). This chart reveals that CX-3543 selectively binds to those quadruplexes that are capable of adopting the chair/propeller conformation (see, boxed oncogene cluster in Quadrome).
In vitro range of antitumor activity. The antitumor range of action of CX-3543 was tested in vitro using a panel of cancer cell-lines. Cells were exposed to CX3543 at various concentrations over a four day period, and IC50 values were calculated (Table 4). In particular examples, IC50 values (i.e., concentrations of test drug required to induce 50% cell death) were measured by Alamar Blue. As shown in Table 4, CX-3543 demonstrates a broad range of antitumor action.


















TABLE 4










MDA-
MDA-







Cell

HCT-

HT-
MB-
MB-


Line
A549
116
HeLa
29
231
468
MiaPaca
PC3
Ramos
HepG2
786-O







IC50
2.9
3.3
3.3
5.5
2.4
1.5
2.8
3.2
0.3
2.5
2.1


(μM)









Furthermore, CX-3543 was evaluated for potential inhibitory activity against topoisomerase I and topoisomerase II enzymes, and was determined not to be an inhibitor or poison of either enzyme. FIG. 7 illustrates data from a toposiomerase-II poison assay, using VP-16 (Etoposide) as a control Topoisomerase-II poison. In the presence of 1 μM VP-16, topoisomerase-II mediates the formation of double-strand breaks within the supercoiled DNA, giving rise to linear DNA product. CX-3543 did not induce topoisomerase dependent strand breaks at concentrations as high as 100 μM.
Example 53
Drug Metabolism and Pharmacokinetics of CX-3543
CX-3543 was evaluated for i) potential inhibitory activity against cytochrome P450 isoenzymes; and ii) metabolic stability with human hepatocytes. The pharmacokinetics of CX-3543 was also evaluated.
Cytochrome P450 (CYP450) Inhibition Assay. CX-3543 was tested in an in vitro inhibition assay with five CYP450 isoenzymes: CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4. No significant inhibition was apparent with four of the five isoenzymes: CYP1A2, CYP2C9, CYP2C19 and CYP2D6. In the case of the remaining isoenzyme, CYP3A4, only minor and partial inhibition in the 1-3 μM range was evident. These results suggest that at clinical levels of drug exposure, there is a low likelihood of drug-drug interactions with the liver metabolism of co-administered drugs. It should not, therefore, be necessary to adjust the doses of co-administered anticancer cancer drugs that are principally metabolized by the CYP450 isoenzyme system (e.g., docetaxel).
Metabolic Stability Assay and Metabolite Profiling. The metabolic stability of CX-3543 with human hepatocytes was evaluated following incubation at 0, 30, 60, and 120 minutes at 1 and 20 μM. Consumption of the parent compound and the appearance of metabolites were carefully monitored, and mass spectrometer product ion scans were conducted on potential metabolite peaks to define the metabolite fragmentation pattern. The consumption of CX-3543 was noted to be moderate or slow, and no major metabolite peaks from hepatic biotransformation were observed. These results suggest that hepatic clearance of CX-3543 will be moderate to low, and the minor role of hepatic elimination minimizes the likelihood of drug-drug interactions with co-administered compounds that are inducers or inhibitors of liver enzymes.
Pharmacokinetic Study. A pharmacokinetic study to determine the time course of CX-3543 disposition was conducted in mice following intravenous administered of 25 mg/kg of CX-3543. Regular sampling was undertaken throughout a 24 hour period after IV dose administration, and the key derived pharmacokinetic parameters were derived. FIG. 8 provides the graphical representation of the pharmacokinetic profile of CX-3543 from which key parameters (Table 5) were obtained.
In FIG. 8, Cmax is the maximum CX-3543 plasma concentration attained (expressed in ng/ml); AUC0-inf is the area under the CX-3543 plasma concentration versus time curve, extrapolated from time zero to infinity (expressed in ng.hr/ml); T1/2 is the terminal half life of CX-3543 (expressed in hr); Vdss is the volume of distribution of CX-3543 at steady state (expressed in L/kg); and ClS is the systemic clearance of CX-3543 (expressed in L/hr/kg). As shown in FIG. 8, CX-3543 has a Cmax of about 5353 ng/mL; an AUC0-inf of about 20332.5 ng.hr/ml; and a T1/2 of about 4.6 hr.











TABLE 5







PARAMETER
VALUE
UNITS




















Cmax
4353.0
ng/mL



AUC0-inf
20322.5
ng · hr/mL



T1/2
4.6
hr



Vdss
7.26
L/kg



ClS
1.23
L/hr/kg










Example 54
In vivo Evaluation in Xenograft Models
CX-3543 was tested against a number of cancer xenograft models to determine the in vivo efficacy. In-house testing for activity in nude mice was first conducted using the HCT-116 colorectal xenograft model, followed by the PC3 prostate cancer xenograft model in which both c-myc and VEGF oncogenic proteins are highly over-expressed. As shown in FIG. 9, CX-3543 inhibits tumor growth in HCT-116 colorectal cancer xenograft model. As shown in FIG. 10, CX-3543 inhibits tumor growth in PC3 prostate cancer xenograft model. Thus, representative tumor volume graphs from both tumor models show suppression of cancer growth when tumor bearing mice are administered intraperitoneal doses of CX-3453.
It is understood that the foregoing detailed description and accompanying examples are merely illustrative, and are not to be taken as limitations upon the scope of the invention. Various changes and modifications to the disclosed embodiments will be apparent to those skilled in the art. Such changes and modifications, including without limitation those relating to the chemical structures, substituents, derivatives, intermediates, syntheses, formulations and/or methods of use of the invention, may be made without departing from the spirit and scope thereof. U.S. patents and publications referenced herein are incorporated by reference.











TABLE 1








Stop Data
MTS Data



Structure
c-Myc μM
Hella μM



















1




4


 


2




2.5


 


3




2.5


 


4




1.76


 


5




1.75
7.20


 


6




1.75


 


7




1.75


 


8




1.75


 


9




1.75


 


10




1.75


 


11




1.75


 


12




1.75


 


13




1.75


 


14




1.75


 


15




1.75


 


16




0.9


 


17




0.75


 


18




0.75


 


19




0.75


 


20




0.75


 


21




0.75


 


22




0.75


 


23




0.75


 


24




0.5
7.00


 


25




0.25
0.20




















TABLE 2








Stop Data
MTS Data



Structure
c-Myc μM
Hella μM



















 26




4
0.73


 


 27




3
3.80


 


 28




3
2.50


 


 29




3
2.00


 


 30




3
1.80


 


 31




3
1.40


 


 32




3
0.60


 


 33




3
0.29


 


 34




3
0.28


 


 35




3
0.21


 


 36




3
0.16


 


 37




2.5
2.80


 


 38




2.5
0.26


 


 39




2.5


 


 40




2.5


 


 41




2.5


 


 42




2.5


 


 43




2.5


 


 44




2.5


 


 45




2.5


 


 46




2.5


 


 47




2.5


 


 48




2.5


 


 49




2.5


 


 50




2.5


 


 51




2.5


 


 52




2.5


 


 53




2.5


 


 54




2.5


 


 55




2.5


 


 56




2.5


 


 57




2.5


 


 58




2.5


 


 59




2.5


 


 60




2.5


 


 61




2.5


 


 62




2.5


 


 63




2.5


 


 64




2.5


 


 65




2.5


 


 66




2.5


 


 67




2.5


 


 68




2.5


 


 69




2.5


 


 70




2.5


 


 71




2.5


 


 72




2.5


 


 73




2.5


 


 74




2.5


 


 75




2.5


 


 76




2.5


 


 77




2.5


 


 78




2.5


 


 79




2.5


 


 80




2.5


 


 81




2.5


 


 82




2.5


 


 83




2.5


 


 84




2.5


 


 85




2.5


 


 86




2.5


 


 87




2.5


 


 88




2.5


 


 89




2.5


 


 90




2.5


 


 91




2.5


 


 92




2.5


 


 93




2.5


 


 94




2.5


 


 95




2.5


 


 96




2.5


 


 97




2.5


 


 98




2.5


 


 99




2.5


 


 100




2.5


 


 101




2.25


 


 102




1.8
2.20


 


 103




1.8


 


 104




1.75
2.80


 


 105




1.75
2.80


 


 106




1.75
2.50


 


 107




1.75
1.80


 


 108




1.75
0.46


 


 109




1.75
0.31


 


 110




1.75
0.25


 


 111




1.75
0.22


 


 112




1.75
0.22


 


 113




1.75


 


 114




1.75


 


 115




1.75


 


 116




1.75


 


 117




1.75


 


 118




1.75


 


 119




1.75


 


 120




1.75


 


 121




1.75


 


 122




1.75


 


 123




1.75


 


 124




1.75


 


 125




1.75


 


 126




1.75


 


 127




1.75


 


 128




1.75


 


 129




1.75


 


 130




1.75


 


 131




1.75


 


 132




1.75


 


 133




1.75


 


 134




1.75


 


 135




1.75


 


 136




1.75


 


 137




1.75


 


 138




1.75


 


 139




1.75


 


 140




1.75


 


 141




1.75


 


 142




1.75


 


 143




1.75


 


 144




1.75


 


 145




1.75


 


 146




1.75


 


 147




1.75


 


 148




1.75


 


 149




1.75


 


 150




1.75

























Stop Data
MTS Data



Structure
c-Myc μM
Hella μM



















 151




1.75


 


 152




1.75


 


 153




1.75


 


 154




1.75


 


 155




1.75


 


 156




1.75


 


 157




1.75


 


 158




1.75


 


 159




1.75


 


 160




1.75


 


 161




1.75


 


 162




1.75


 


 163




1.75


 


 164




1.75


 


 165




1.75


 


 166




1.75


 


 167




1.75


 


 168




1.75


 


 169




1.75


 


 170




1.75


 


 171




1.75


 


 172




1.75


 


 173




1.75


 


 174




1.75


 


 175




1.75


 


 176




1.75


 


 177




1.75


 


 178




1.75


 


 179




1.75


 


 180




1.75


 


 181




1.75


 


 182




1.75


 


 183




1.75


 


 184




1.75


 


 185




1.75


 


 186




1.75


 


 187




1.75


 


 188




1.75


 


 189




1.75


 


 190




1.75


 


 191




1.75


 


 192




1.75


 


 193




1.75


 


 194




1.75


 


 195




1.75


 


 196




1.75


 


 197




1.75


 


 198




1.75


 


 199




1.75


 


 200




1.75


 


 201




1.75


 


 202




1.75


 


 203




1.75


 


 204




1.75


 


 205




1.75


 


 206




1.75


 


 207




1.75


 


 208




1.75


 


 209




1.75


 


 210




1.75


 


 211




1.75


 


 212




1.75


 


 213




1.75


 


 214




1.75


 


 215




1.75


 


 216




1.75


 


 217




1.75


 


 218




1.75


 


 219




1.75


 


 220




1.75


 


 221




1.75


 


 222




1.75


 


 223




1.75


 


 224




1.75


 


 225




1.75


 


 226




1.75


 


 227




1.75


 


 228




1.75


 


 229




1.75


 


 230




1.75


 


 231




1.75


 


 232




1.75


 


 233




1.75


 


 234




1.75


 


 235




1.75


 


 236




1.75


 


 237




1.75


 


 238




1.75


 


 239




1.75


 


 240




1.75


 


 241




1.75


 


 242




1.75


 


 243




1.75


 


 244




1.75


 


 245




1.75


 


 246




1.75


 


 247




1.75


 


 248




1.75


 


 249




1.75


 


 250




1.75


 


 251




1.75


 


 252




1.75


 


 253




1.75


 


 254




1.75


 


 255




1.75


 


 256




1.75


 


 257




1.75


 


 258




1.75


 


 259




1.75


 


 260




1.75


 


 261




1.75


 


 262




1.75


 


 263




1.75


 


 264




1.75


 


 265




1.75


 


 266




1.75


 


 267




1.75


 


 268




1.75


 


 269




1.75


 


 270




1.75


 


 271




1.75


 


 272




1.75


 


 273




1.75


 


 274




1.75


 


 275




1.75


 


 276




1.75


 


 277




1.75


 


 278




1.75


 


 279




1.75


 


 280




1.75


 


 281




1.75


 


 282




1.75


 


 283




1.75


 


 284




1.75


 


 285




1.75


 


 286




1.75


 


 287




1.75


 


 288




1.75


 


 289




1.75


 


 290




1.75


 


 291




1.75


 


 292




1.75


 


 293




1.75


 


 294




1.75


 


 295




1.75


 


 296




1.75


 


 297




1.75


 


 298




1.75


 


 299




1.75


 


 300




1.75

























Stop Data
MTS Data



Structure
c-Myc μM
Hella μM



















 301




1.75



 


 302




1.75



 


 303




1.5
2.10


 


 304




1.13



 


 305




1.05



 


 306




1
3.20


 


 307




1
3.10


 


 308




1
3.10


 


 309




1
3.00


 


 310




1
2.30


 


 311




1
2.10


 


 312




1
1.90


 


 313




1



 


 314




1



 


 315




1



 


 316




1



 


 317




1



 


 318




1



 


 319




1



 


 320




1



 


 321




1



 


 322




1



 


 323




1



 


 324




1



 


 325




1



 


 326




1



 


 327




1



 


 328




1



 


 329




1



 


 330




1



 


 331




1



 


 332




1



 


 333




1



 


 334




1



 


 335




1



 


 336




1



 


 337




1



 


 338




1



 


 339




0.94



 


 340




0.9
8.50


 


 341




0.9
0.28


 


 342




0.9



 


 343




0.9



 


 344




0.9



 


 345




0.9



 


 346




0.9



 


 347




0.9



 


 348




0.9



 


 349




0.9



 


 350




0.9



 


 351




0.9



 


 352




0.9



 


 353




0.9



 


 354




0.9



 


 355




0.89



 


 356




0.85



 


 357




0.75
8.60


 


 358




0.75
5.70


 


 359




0.75
4.80


 


 360




0.75
4.50


 


 361




0.75
4.20


 


 362




0.75
4.00


 


 363




0.75
3.80


 


 364




0.75
3.80


 


 365




0.75
3.80


 


 366




0.75
3.70


 


 367




0.75
3.70


 


 368




0.75
3.60


 


 369




0.75
3.50


 


 370




0.75
3.50


 


 371




0.75
3.50


 


 372




0.75
3.40


 


 373




0.75
3.30


 


 374




0.75
3.30


 


 375




0.75
2.70


 


 376




0.75
2.40


 


 377




0.75
2.20


 


 378




0.75
2.10


 


 379




0.75
1.90


 


 380




0.75
1.80


 


 381




0.75
1.80


 


 382




0.75
1.80


 


 383




0.75
0.37


 


 384




0.75
0.37


 


 385




0.75
0.36


 


 386




0.75
0.34


 


 387




0.75
0.33


 


 388




0.75
0.31


 


 389




0.75
0.29


 


 390




0.75
0.24


 


 391




0.75
0.24


 


 392




0.75
0.19


 


 393




0.75



 


 394




0.75



 


 395




0.75



 


 396




0.75



 


 397




0.75



 


 398




0.75



 


 399




0.75



 


 400




0.75



 


 401




0.75



 


 402




0.75



 


 403




0.75



 


 404




0.75



 


 405




0.75



 


 406




0.75



 


 407




0.75



 


 408




0.75



 


 409




0.75



 


 410




0.75



 


 411




0.75



 


 412




0.75



 


 413




0.75



 


 414




0.75



 


 415




0.75



 


 416




0.75



 


 417




0.75



 


 418




0.75



 


 419




0.75



 


 420




0.75



 


 421




0.75



 


 422




0.75



 


 423




0.75



 


 424




0.75



 


 425




0.75



 


 426




0.75



 


 427




0.75



 


 428




0.75



 


 429




0.75



 


 430




0.75



 


 431




0.75



 


 432




0.75



 


 433




0.75



 


 434




0.75



 


 435




0.75



 


 436




0.75



 


 437




0.75



 


 438




0.75



 


 439




0.75



 


 440




0.75



 


 441




0.75



 


 442




0.75



 


 443




0.75



 


 444




0.75



 


 445




0.75



 


 446




0.75



 


 447




0.75



 


 448




0.75



 


 449




0.75



 


 450




0.75



 


 451




0.75



 


 452




0.75



 


 453




0.75



 


 454




0.75



 


 455




0.75



 


 456




0.75



 


 457




0.75



 


 458




0.75



 


 459




0.75



 


 460




0.75



 


 461




0.75



 


 462




0.75



 


 463




0.75



 


 464




0.75



 


 465




0.75



 


 466




0.75



 


 467




0.75



 


 468




0.74



 


 469




0.73



 


 470




0.64



 


 471




0.64



 


 472




0.62
3.30


 


 473




0.62



 


 474




0.58
0.37


 


 475




0.58
0.24


 


 476




0.58



 


 477




0.55
2.10


 


 478




0.53



 


 479




0.5
7.40


 


 480




0.5
3.70

























Stop Data
MTS Data



Structure
c-Myc μM
Hella μM



















 481




0.5
3.60


 


 482




0.5
3.40


 


 483




0.5
3.20


 


 484




0.5
3.10


 


 485




0.5
0.50


 


 486




0.5
0.39


 


 487




0.5
0.18


 


 488




0.5


 


 489




0.5


 


 490




0.5


 


 491




0.45


 


 492




0.45


 


 493




0.44
0.40


 


 494




0.44
0.19


 


 495




0.42


 


 496




0.41
4.00


 


 497




0.41
2.10


 


 498




0.41


 


 499




0.4


 


 500




0.375
5.60


 


 501




0.375
4.20


 


 502




0.375
4.00


 


 503




0.375
4.00


 


 504




0.375
3.40


 


 505




0.375
3.40


 


 506




0.375
3.40


 


 507




0.375
3.30


 


 508




0.375
3.20


 


 509




0.375
3.10


 


 510




0.375
3.10


 


 511




0.375
3.10


 


 512




0.375
3.10


 


 513




0.375
3.10


 


 514




0.375
2.90


 


 515




0.375
2.50


 


 516




0.375
2.30


 


 517




0.375
2.20


 


 518




0.375
2.20


 


 519




0.375
2.10


 


 520




0.375
1.90


 


 521




0.375
1.70


 


 522




0.375
1.70


 


 523




0.375
1.60


 


 524




0.375
1.50


 


 525




0.375
1.,2


 


 526




0.375
0.90


 


 527




0.375
0.79


 


 528




0.375
0.75


 


 529




0.375
0.75


 


 530




0.375
0.72


 


 531




0.375
0.48


 


 532




0.375
0.44


 


 533




0.375
0.40


 


 534




0.375
0.40


 


 535




0.375
0.31


 


 536




0.375
0.31


 


 537




0.375
0.29


 


 538




0.375
0.28


 


 539




0.375
0.28


 


 540




0.375
0.27


 


 541




0.375
0.27


 


 542




0.375
0.23


 


 543




0.375
0.20


 


 544




0.375
0.20


 


 545




0.375
0.15


 


 546




0.375
0.10


 


 547




0.375
0.10


 


 548




0.375
0.10


 


 549




0.375


 


 550




0.375


 


 551




0.375


 


 552




0.375


 


 553




0.375


 


 554




0.375


 


 555




0.375


 


 556




0.375


 


 557




0.375


 


 558




0.375


 


 559




0.375


 


 560




0.37


 


 561




0.34


 


 562




0.32
0.85


 


 563




0.25
0.31


 


 564




0.25
0.29


 


 565




0.25
0.20


 


 566




0.25
0.03


 


 567




0.25


 


 568




0.22
4.10


 


 569




0.18
7.80


 


 570




0.18
6.80


 


 571




0.18
4.80


 


 572




0.18
4.80


 


 573




0.18
4.50


 


 574




0.18
4.00


 


 575




0.18
2.10


 


 576




0.18
2.10


 


 577




0.18
1.10


 


 578




0.18
0.58


 


 579




0.18
0.49


 


 580




0.18
0.30


 


 581




0.18
0.30


 


 582




0.18
0.28


 


 583




0.18
0.25


 


 584




0.18
0.19


 


 585




0.18


 


 586




0.18


 


 587




0.18


 


 588




0.18


 


 589




0.18


 


 590




0.18


 


 591




0.13
3.30


 


 592




0.1
3.80


 


1467




0.25
0.35


 


1468




0.375
0.35


 


1469




1.75


 


1470




1.75


 


1471




5




















TABLE 3








Stop Data
MTS Data



Structure
e-mye μM
Helia μM


















1472






 


1473






 


1474






 


1475






 


1476






 


 593






 


 594






 


 595






 


 596






 


 597






 


 598






 


 599






 


 600






 


 601






 


 602






 


 603






 


 604






 


 605






 


 606






 


 607






 


 608






 


 609






 


 610






 


 611






 


 612






 


 613






 


 614






 


 615






 


 616






 


 617






 


 618






 


 619






 


 620






 


 621






 


 622






 


 623






 


 624






 


 625






 


 626






 


 627






 


 628






 


 629






 


 630






 


 631






 


 632






 


 633






 


 634






 


 635






 


 636






 


 637






 


 638






 


 639






 


 640






 


 641






 


 642






 


 643






 


 644






 


 645






 


 646






 


 647






 


 648






 


 649






 


 650






 


 651






 


 652






 


 653






 


 654






 


 655






 


 656






 


 657






 


 658






 


 659






 


 660






 


 661






 


 662






 


 663






 


 664






 


 665






 


 666






 


 667






 


 668






 


 669






 


 670






 


 671






 


 672






 


 673






 


 674






 


 675






 


 676






 


 677






 


 678






 


 679






 


 680






 


 681






 


 682






 


 683






 


 684






 


 685






 


 686






 


 687






 


 688






 


 689






 


 690






 


 691






 


 692






 


 693






 


 694






 


 695






 


 696






 


 697






 


 698






 


 699






 


 700






 


 701






 


 702






 


 703






 


 704






 


 705






 


 706






 


 707






 


 708






 


 709






 


 710






 


 711






 


 712






 


 713






 


 714






 


 715






 


 716






 


 717






 


 718






 


 719






 


 720






 


 721






 


 722






 


 723






 


 724






 


 725






 


 726






 


 727






 


 728






 


 729






 


 730






 


 731






 


 732






 


 733






 


 734






 


 735






 


 736






 


 737





























Stop Data
MTS Data



Structure
c-Myc μM
Hella μM


















 738






 


 739






 


 740






 


 741






 


 742






 


 743






 


 744






 


 745






 


 746






 


 747






 


 748






 


 749






 


 750






 


 751






 


 752






 


 753






 


 754






 


 755






 


 756






 


 757






 


 758






 


 759






 


 760






 


 761






 


 762






 


 763






 


 764






 


 765






 


 766






 


 767






 


 768






 


 769






 


 770






 


 771






 


 772






 


 773






 


 774






 


 775






 


 776






 


 777






 


 778






 


 779






 


 780






 


 781






 


 782






 


 783






 


 784






 


 785






 


 786






 


 787






 


 788






 


 789






 


 790






 


 791






 


 792






 


 793






 


 794






 


 795






 


 796






 


 797






 


 798






 


 799






 


 800






 


 801






 


 802






 


 803






 


 804






 


 805






 


 806






 


 807






 


 808






 


 809






 


 810






 


 811






 


 812






 


 813






 


 814






 


 815






 


 816






 


 817






 


 818






 


 819






 


 820






 


 821






 


 822






 


 823






 


 824






 


 825






 


 826






 


 827






 


 828






 


 829






 


 830






 


 831






 


 832






 


 833






 


 834






 


 835






 


 836






 


 837






 


 838






 


 839






 


 840






 


 841






 


 842






 


 843






 


 844






 


 845






 


 846






 


 847






 


 848






 


 849






 


 850






 


 851






 


 852






 


 853






 


 854






 


 855






 


 856






 


 857






 


 858






 


 859






 


 860






 


 861






 


 862






 


 863






 


 864






 


 865






 


 866






 


 867






 


 868






 


 869






 


 870






 


 871






 


 872






 


 873






 


 874






 


 875






 


 876






 


 877






 


 878






 


 879






 


 880






 


 881






 


 882






 


 883






 


 884






 


 885






 


 886






 


 887






 


 888






 


 889






 


 890






 


 891





























Stop Data
MTS Data



Structure
c-Myc μM
Hella μM


















 892






 


 893






 


 894






 


 895






 


 896






 


 897






 


 898






 


 899






 


 900






 


 901






 


 902






 


 903






 


 904






 


 905






 


 906






 


 907






 


 908






 


 909






 


 910






 


 911






 


 912






 


 913






 


 914






 


 915






 


 916






 


 917






 


 918






 


 919






 


 920






 


 921






 


 922






 


 923






 


 924






 


 925






 


 926






 


 927






 


 928






 


 929






 


 930






 


 931






 


 932






 


 933






 


 934






 


 935






 


 936






 


 937






 


 938






 


 939






 


 940






 


 941






 


 942






 


 943






 


 944






 


 945






 


 946






 


 947






 


 948






 


 949






 


 950






 


 951






 


 952






 


 953






 


 954






 


 955






 


 956






 


 957






 


 958






 


 959






 


 960






 


 961






 


 962






 


 963






 


 964






 


 965






 


 966






 


 967






 


 968






 


 969






 


 970






 


 971






 


 972






 


 973






 


 974






 


 975






 


 976






 


 977






 


 978






 


 979






 


 980






 


 981






 


 982






 


 983






 


 984






 


 985






 


 986






 


 987






 


 988






 


 989






 


 990






 


 991






 


 992






 


 993






 


 994






 


 995






 


 996






 


 997






 


 998






 


 999






 


1000






 


1001






 


1002






 


1003






 


1004






 


1005






 


1006






 


1007






 


1008






 


1009






 


1010






 


1011






 


1012






 


1013






 


1014






 


1015






 


1016






 


1017






 


1018






 


1019






 


1020






 


1021






 


1022






 


1023






 


1024






 


1025






 


1026






 


1027






 


1028






 


1029






 


1030






 


1031






 


1032






 


1033






 


1034






 


1035






 


1036






 


1037






 


1038






 


1039






 


1040






 


1041





























Stop Data
MTS Data



Structure
c-Myc μM
Hella μM


















1042






 


1043






 


1044






 


1045






 


1046






 


1047






 


1048






 


1049






 


1050






 


1051






 


1052






 


1053






 


1054






 


1055






 


1056






 


1057






 


1058






 


1059






 


1060






 


1061






 


1062






 


1063






 


1064






 


1065






 


1066






 


1067






 


1068






 


1069






 


1070






 


1071






 


1072






 


1073






 


1074






 


1075






 


1076






 


1077






 


1078






 


1079






 


1080






 


1081






 


1082






 


1083






 


1084






 


1085






 


1086






 


1087






 


1088






 


1089






 


1090






 


1091






 


1092






 


1093






 


1094






 


1095






 


1096






 


1097






 


1098






 


1099






 


1100






 


1101






 


1102






 


1103






 


1104






 


1105






 


1106






 


1107






 


1108






 


1109






 


1110






 


1111






 


1112






 


1113






 


1114






 


1115






 


1116






 


1117






 


1118






 


1119






 


1120






 


1121






 


1122






 


1123






 


1124






 


1125






 


1126






 


1127






 


1128






 


1129






 


1130






 


1131






 


1132






 


1133






 


1134






 


1135






 


1136






 


1137






 


1138






 


1139






 


1140






 


1141






 


1142






 


1143






 


1144






 


1145






 


1146






 


1147






 


1148






 


1149






 


1150






 


1151






 


1152






 


1153






 


1154






 


1155






 


1156






 


1157






 


1158






 


1159






 


1160






 


1161






 


1162






 


1163






 


1164






 


1165






 


1166






 


1167






 


1168






 


1169






 


1170






 


1171






 


1172






 


1173






 


1174






 


1175






 


1176






 


1177






 


1178






 


1179






 


1180






 


1181






 


1182






 


1183






 


1184






 


1185






 


1186






 


1187






 


1188






 


1189






 


1190






 


1191





























Stop Data
MTS Data



Structure
c-Myc μM
Hella μM


















1192






 


1193






 


1194






 


1195






 


1196






 


1197






 


1198






 


1199






 


1200






 


1201






 


1202






 


1203






 


1204






 


1205






 


1206






 


1207






 


1208






 


1209






 


1210






 


1211






 


1212






 


1213






 


1214






 


1215






 


1216






 


1217






 


1218






 


1219






 


1220






 


1221






 


1222






 


1223






 


1224






 


1225






 


1226






 


1227






 


1228






 


1229






 


1230






 


1231






 


1232






 


1233






 


1234






 


1235






 


1236






 


1237






 


1238






 


1239






 


1240






 


1241






 


1242






 


1243






 


1244






 


1245






 


1246






 


1247






 


1248






 


1249






 


1250






 


1251






 


1252






 


1253






 


1254






 


1255






 


1256






 


1257






 


1258






 


1259






 


1260






 


1261






 


1262






 


1263






 


1264






 


1265






 


1266






 


1267






 


1268






 


1269






 


1270






 


1271






 


1272






 


1273






 


1274






 


1275






 


1276






 


1277






 


1278






 


1279






 


1280






 


1281






 


1282






 


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Stop Data
MTS Data



Structure
c-Myc λM
Hella αM


















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1466

## Claims

1. A compound having formula (1A),




and pharmaceutically acceptable salts thereof.

2. The compound of claim 1, wherein said compound is chiral.

3. A pharmaceutical composition comprising the compound of claim 1 and a pharmaceutically acceptable excipient.

4. The pharmaceutical composition of claim 3, comprising 2% w/w of the compound of claim 1.

5. The pharmaceutical composition of claim 4, further comprising 4% w/w mannitol.

6. The pharmaceutical composition of claim 4, further comprising 0.5% sucrose.

7. The pharmaceutical composition of claim 3, wherein said formulation is aqueous.

8. The pharmaceutical composition of claim 3, wherein said formulation has a pH of about 3.5.

9. The pharmaceutical composition of claim 3, wherein said formulation is suitable for injection, oral, parenteral, intravenous, intramuscular, topical or subtopical administration.

10. The pharmaceutical composition of claim 3, comprising 2% w/w of the compound of claim 1, 4% w/w mannitol, and 0.5% sucrose.

11. The pharmaceutical composition of claim 10, wherein said composition is aqueous.

12. The pharmaceutical composition of claim 10, wherein said composition has a pH of about 3.5.

13. The pharmaceutical composition of claim 10, wherein said composition is suitable for injection.

14. A method for ameliorating a cell proliferative disorder selected from the group consisting of colorectal cancer, prostate cancer and leukemia, comprising administering to a subject in need thereof an effective amount of the compound of claim 1 or a pharmaceutical composition thereof, thereby ameliorating said cell-proliferative disorder.

15. The method of claim 14, wherein cell proliferation is reduced, or cell death is induced.

16. The method of claim 14, wherein said subject is human or an animal.

17. A method for reducing cell proliferation or inducing cell death in a colorectal cancer cell, prostate cancer cell, or leukemia cancer cell, comprising contacting a system with an effective amount of the compound of claim 1 or a pharmaceutical composition thereof, thereby reducing cell proliferation or inducing cell death in said system.

18. The method of claim 17, wherein said system is a cell or tissue.

19. A method for reducing bacterial or fungal titers, comprising contacting a system with an effective amount of the compound of claim 1 or a pharmaceutical composition thereof, thereby reducing bacterial or fungal titers.

20. The method of claim 19, where the system is a cell or tissue.

21. The method of claim 19, wherein the microbial titers are bacterial titers.

22. A method for ameliorating a bacterial or fungal infection, comprising administering to a subject in need thereof an effective amount of the compound of claim 1 or a pharmaceutical composition thereof, thereby ameliorating said bacterial or fungal infection.

23. The method of claim 22, where the subject is a human or an animal.

24. The method of claim 22, wherein said microbial infection is bacterial.

25. The method of claim 14, further comprising administering a chemotherapeutic agent selected from the group consisting of anti-infective agents, antihelmintics, antiprotozoal agents, antimalarial agents, antiamebic agents, sulfonamides, antimycobacterial drugs, and antiviral chemotherapeutics.

26. The method of claim 17, further comprising administering a chemotherapeutic agent.

27. The compound of claim 1, which is an acid addition salt having a pharmaceutically acceptable counterion.

28. The compound of claim 27, wherein the pharmaceutically acceptable counterion is selected from tosylate, methanesulfonate, acetate, citrate, malonate, tartrate, succinate, benzoate, ascorbate, a-ketoglutarate, a-glycerophosphate, chloride, sulfate, nitrate, bicarbonate and carbonate.

29. The pharmaceutical composition of claim 3, wherein the compound of claim 1 is an acid addition salt having a pharmaceutically acceptable counterion.

30. The pharmaceutical composition of claim 29, wherein the pharmaceutically acceptable counterion is selected from tosylate, methanesulfonate, acetate, citrate, malonate, tartrate, succinate, benzoate, ascorbate, a-ketoglutarate, a-glycerophosphate, chloride, sulfate, nitrate, bicarbonate and carbonate.

31. The compound of claim 1, having the formula:



or a pharmaceutically acceptable salt thereof.

32. The compound of claim 1, having the formula:



or a pharmaceutically acceptable salt thereof.

33. The compound of claim 1, having the formula:



or a pharmaceutically acceptable salt thereof.

34. The compound of claim 1, having the formula:



or a pharmaceutically acceptable salt thereof.

35. The compound of claim 1, which has a 50:50 ratio of RS and SS isomers.