Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D498/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms
  • C07D498/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and oxygen atoms as the only ring hetero atoms in which the condensed system contains two hetero rings
  • C07D498/04—Ortho-condensed systems
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
  • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
  • C07D471/06—Peri-condensed systems
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/04—Antibacterial agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/10—Antimycotics
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
  • A61P35/02—Antineoplastic agents specific for leukemia
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D471/00—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00
  • C07D471/02—Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, at least one ring being a six-membered ring with one nitrogen atom, not provided for by groups C07D451/00 - C07D463/00 in which the condensed system contains two hetero rings
  • C07D471/04—Ortho-condensed systems
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07D—HETEROCYCLIC COMPOUNDS
  • C07D513/00—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for in groups C07D463/00, C07D477/00 or C07D499/00 - C07D507/00
  • C07D513/02—Heterocyclic compounds containing in the condensed system at least one hetero ring having nitrogen and sulfur atoms as the only ring hetero atoms, not provided for in groups C07D463/00, C07D477/00 or C07D499/00 - C07D507/00 in which the condensed system contains two hetero rings
  • C07D513/04—Ortho-condensed systems

Definitions

• V is H, halo, or NR ! R 2 ;
• A is H, fluoro, or NR J 2 ;
• Z is O, S, NR 1 or CH 2 ;
• X is OR 2 , NR'R 2 , halo, azido, or SR 2 ; n is 1-3; wherein in NR J R 2 , R 1 and R 2 may form a double bound or a ring, each of which is optionally substituted;
• R 1 is H or a C ⁇ -6 alkyl
• R is H or a C MO alkyl or C 2- ⁇ o alkenyl optionally containing one or more non-adjacent heteroatoms selected from N, O, and S, and optionally substituted with a carbocyclic or heteroc cyycclliicc rriinngg;; oorr RR 22 iiss aann ooppttiioonnaallllyy ssuubbssttiittuutteedd heterocyclic ring, aryl or heteroaryl; W is selected from the group consisting of
• Q, Q 1 , Q 2 , and Q 3 are independently CH or N;
• 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 NH 2 , or a moiety that does not contain N, or contains more than 6 carbons.
• a and X may independently be halo. In one example, A and X may independently be fluoro.
• V may be H.
• V may be NH 2 or a compound having the formula NR 1 - (CR 1 ⁇ - NR 3 R 4 ; wherein R 1 and R 3 are independently H or C ⁇ -6 alkyl; n is 1-6; and
• R 4 is H, Ci_ 6 alkyl optionally substituted with a carbocyclic or heterocyclic ring, or aryl; and wherein in NR 3 R 4 , R 3 and R 4 may form an optionally substituted ring.
• U and X may mdependently be NR ⁇ R 2 .
• R 1 is H and R 2 is a Ci.io alkyl optionally containing one or more heteroatoms, and optionally substituted with a C 3-6 cycloalkyl, aryl or a 5-14 membered heterocyclic ring containing one or more N, O or S.
• R 1 is H and R 2 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.
• R 1 and R 2 in NR R 2 form an optionally substituted
• NR 1 R 9 is morpholine, thiomorpholine, piperazine, piperidine or diazepine.
• U and X may independently have the formula NR 1 - (CR x 2 )n - NR 3 R 4 (2) wherein R 1 and R 3 are independently H or C ⁇ -6 alkyl; n is 1-6; and
• R is H or a C O alkyl or C 2-10 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 NR 3 R 4 , R 3 and R 4 may form an optionally substituted ring.
• n may be 2-3.
• NR 3 R 4 is an acyclic amine, or guanidinyl or a tautomer thereof; or R 3 and R 4 optionally form a substituted ring containing one or more N, O or S.
• NR 3 R 4 is morpholine, thiomorpholine, imidazole, pyrrolidine, piperazine, pyridine or piperidine.
• X may be NR'R 2 ; and U has the formula NR ⁇ CR ⁇ n -NR ⁇ 4 (2) wherein R 1 and R 2 are as defined in claim 1;
• R >3 is H or C 1-6 alkyl; n is 1-6; and
• R 4 is H or a .io alkyl or C 2- ⁇ o 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 NR*R 2 and NR 3 R 4 , R 1 and R 2 , and R 3 and R 4 each independently may form a substituted ring.
• R 1 and R 2 in NR*R 2 , and R 3 and R 4 in NR 3 R 4 each may independently form a substituted ring containing one or more N, O or S.
• X is optionally substituted with amino, carbamate, a .io 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.
• X and NR 3 R 4 are independently morpholine, thiomorpholine, imidazole, pyrrolidine, piperazine, pyridine or piperidine. In one example, X and NR 3 R 4 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, pynolidin-2-one, pyrrole, pyridine, pyrimidine, octahydro-pyrrolo[3,4- ⁇ ]pyridine, piperazine, pyrazine, morpholine, thiomorpholine, imidazole, imidazolidine-2,4-dione, benzimidazole, l,3-dihydrobenzimidazol-2-one, indole, thiazole, benzothiazole, thiadiazole, thiophene, tetrahydrofur
• W may be benzene, pyridine, biphenyl, naphthalene, phenanthrene, quinoline, isoquinoline, quinazol ne, cinnoline, phthalazine, quinoxaline, indole,
• U may be OR 2 and R 2 is a C ⁇ -6 alkyl optionally substituted with a carbocyclic or heterocyclic ring.
• each optionally substituted moiety is substituted with one or
• the compounds of the present invention may be chiral.
• 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.
• the present invention 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 a pharmaceutical composition thereof, thereby ameliorating said cell-proliferative disorder.
• the cell proliferative disorder is cancer.
• 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 a pharmaceutical composition 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 a pharmaceutical composition thereof, thereby reducing microbial titers.
• the system may be a cell or tissue.
• the microbial titers are viral, bacterial or fungal titers.
• the present invention provides methods for ameliorating a microbial infection, comprising administering to a subject in need thereof an effective amount of a compound having formula 1 or a pharmaceutical composition thereof, thereby ameliorating said
• the subject may be human or animal.
• the microbial infection is viral, bacterial or fungal.
• Figure 1 shows antitumor activity of a compound having formula 1 tested in a Ramos xenograft model.
• Figure 2 shows antitumor activity of a compound having formula 1 tested in HCT 116.
• the present invention relates to quinoline derivatives having formula 1, and pharmaceutically acceptable salts, esters, and prodrugs thereof.
• 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.
• 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.
• oncogenes include but are not limited to MYC, HIF, VEGF, ABL, TGF, PDGFA, MYB, SPARC, HUMTEL, HER, VAV, RET, H-RAS, EGF, SRC, BCLl, 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.
• 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.
• treatment refers 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.
• 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).
• 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).
• ALL acute lymphoblastic leukemia
• ALL includes B-lineage ALL and T-lineage ALL
• CLL chronic lymphocytic leukemia
• PLL prolymphocytic leukemia
• HLL hairy cell leukemia
• W Waldenstrom's macroglobulinemia
• 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
• 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).
• 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.
• 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.
• VEGF vascular endothelial growth factor
• alkyl refers to a carbon-containing compound, and encompasses compounds containing one or more heteroatoms.
• chain' refers to a cyclic compound containing only carbon atoms in the ring.
• heterocycle refers to a cyclic compound comprising a heteroatom, including monocyclic or bicyclic heterocycles.
• heteroatom refers to any atom that is not carbon or hydrogen, such as nitrogen, oxygen or sulfur.
• heterocycles include but are not limited to oxirane, oxetane, pyran, tetrahydropyran, dioxane, lactones, aziridine, azetidine, pyrrolidine, piperidine, morpholine, lactams, and tetrahydrofuran.
• 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.
• heteroaryl or “heteroaromatic” refer to an aromatic hetercycle.
• heteroaryls include but are not limited to furan, pynole, pyridine, pyrimidine, imidazole, or triazole.
• treat refers 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.
• microorganism include but are not limited to virus, bacterium and fungus.
• 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).
• DNA aptamers which are able to adopt either inter- or intramolecular quadruplex structures are able to inhibit viral replication.
• DNA aptamers are able to inhibit viral replication by targeting the envelope glycoprotein (putatively).
• DNA aptamers inhibit viral replication by targeting the HlV-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.
• 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.
• integrase 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 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.
• 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
• 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.
• microbial titers include but are not limited to viral, bacterial or fungal titers.
• 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).
• viral infections include infections by a hepatitis virus (e.g., hepatitis B or C), human immunodeficiency virus (HIV), rhino virus, 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-Ban 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.
• the affinity of the interaction between the nucleic acid and the compound may be quantified.
• IC 50 , K d , or K; threshold values may be compared to the measured IC 50 or K d 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.
• IC 50 or K d threshold values 10 ⁇ M or less, 1 ⁇ M or less, and 100 nM or less are often utilized.
• 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.
• the biological activity is a polymerase anesting function of a quadruplex and the degree of arrest is measured as a decrease in a signal.
• the biological activity is transcription and transcription levels can be quantified as a signal.
• 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.
• topoisomerase assays can be utilized to determine whether the quadruplex interacting molecules have a topoisomerase pathway activity (see, e.g., TopoGEN, Inc. (Columbus, Ohio)).
• EMSA Gel Electrophoretic Mobility Shift Assay
• 32 P-labeled oligonucleotides ( ⁇ 30,000 cpm) are then incubated with or without various concentrations of a testing compound in 20 ⁇ l of a buffer containing 10 mM Tris pH 7.5, 100 mM KCl, 5 mM dithiothreitol, 0.1 mM EDTA, 5 mM MgCl 2 , 10% glycerol, 0.05% Nonedit P-40, and 0.1 mg/ml of poly(dl-dC) (Pharmacia).
• binding reactions are loaded on a 5% polyacrylamide gel in 0.25 x Tris borate-EDTA buffer (0.25 x TBE, 1 x 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
• reaction mixture is incubated with 1 ⁇ l DMS solution (DMS: ethanol; 4: 1; v:v) for a period of time.
• DMS DMS solution
• stop buffer b-mercaptoathanol:water:NaOAc (3 M); 1:6:7; v:v:v.
• An anest 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.
• a quadruplex structure can block or anest the advance of the enzyme, leading to shorter transcription fragments.
• the anest assay may be conducted at a variety of temperatures, including 45°C and 60°C, and at a variety of ion concentrations.
• Taq polymerase stop assay 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), MgCl 2 (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 ⁇ l) is added to the reaction mixture, and the reaction is maintained at a constant temperature for 30 minutes. Following the addition of 10 ⁇ l stop buffer (formamide (20 ml), 1 M NaOH (200 ⁇ l), 0.5 M EDTA (400 ⁇ l), 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-INSERT- TTAGCGACACGCAATTGCTATAGTGAGTCGTATTA, where "INSERT" refers to a nucleic
• a high throughput polymerase anest 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 refened 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 IC5 0 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.
• the primer often is extended only to the quadruplex structure in the template and no further.
• 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 linlced to the primer using a procedure selected based upon the nature of the chemical groups in the detectable label.
• a spacer 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., 125 1, 131 1, 35 S, 32 P, 14 C or 3 H); a light scattering label (e.g., a spherical gold or silver label; Genicon Sciences Corporation, San Diego, CA and U.S. Patent No.
• an enzymic or protein label e.g., GFP or peroxidase
• another chromogenic label or dye sometimes is utilized.
• a fluorescent label 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, Biol, et
• 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).
• 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 MgCl 2 , 0.1 mM EDTA and 0.1 mM mixed deoxynucleotide triphosphates (dNTP's).
• FAM fluorescent-labeled
• the FAM-P45 primer (5'-6FAM-AGTCTGAC TGACTGTACGTAGCTAATACGACTCACTATAGCAATT-3') and the template DNA (5'-TCCAACTATGTATACTGGGGAGGGTGGGGAGGGTGGGGAAGGTTAGCGACACG CAATTGCTATAGTGAGTCGTATTAGCTACGTACAGTCAGTCAGACT-3 ') were
• test quadruplex DNA is coupled to a reporter system, such that a formation or stabilization of a quadruplex structure can modulate a reporter signal.
• 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.
• GFP green fluorescent protein
• 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 vector utilized for the assay is set forth in reference 11 of the He, et al, document.
• HeLa cells are transfected using the lipofectamin 2000-based system (Invitrogen) according to the manufacturer's protocol, using 0.1 ⁇ g of pRL-TK (Renilla luciferase reporter plasmid) and 0.9 ⁇ g of the quadruplex-forming plasmid. Firefly and Renilla luciferase activities are assayed
• Circular dichroism 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 ⁇ M 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 ananged to represent the average of eight scans recorded at 100 nm/min.
• 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.
• NMM N-methylmesoporphyrin IX
• 50 ⁇ l 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 ⁇ l of 20 mM HEPES buffer, pH 7.0, 140 mM NaCl, and 100 mM KCl.
• 50 ⁇ l of the signal molecule NMM then is added for a final concentration of 3 ⁇ M.
• 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, NC). 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.
• 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.
• 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.
• 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 inco ⁇ orated herein by reference.)
• any suitable formulation of the compounds described herein can be prepared.
• administration of the compounds as salts may be appropriate.
• 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.
• salts are obtained using standard procedures well known in the art, for example by reacting a sufficiently basic compound such as an amine with a suitable acid affording a physiologically acceptable anion.
• a sufficiently basic compound such as an amine
• a suitable acid affording a physiologically acceptable anion.
• Alkali metal e.g., sodium, potassium or lithium
• alkaline earth metal e.g., calcium
• a compound may be formulated as a pharmaceutical composition and administered to a mammalian host in need of such treatment.
• 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.
• a compound is administered systemically (e.g., orally) in combination with a pharmaceutically acceptable vehicle such as an inert diluent or an
• 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.
• a liquid carrier such as a vegetable oil or a polyethylene glycol.
• any material may be present as coatings or to otherwise modify the physical form of the solid unit dosage form.
• 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.
• the active compound may be incorporated into sustained-release preparations and devices.
• the active compound also may be administered intravenously or rntraperitoneally 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. Patent No. 5,703,055 (Feigner, et ⁇ l) 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 hposomes.
• 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.
• the prefened 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.
• 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.
• a dermatologically acceptable carrier which may be a solid or a liquid.
• 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.
• 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.
• 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.
• 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 LD 50 (the dose lethal to 50% of the population) and the ED 50 (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 ED 50 /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 IC 50 (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.
• 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 admimstered 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,
• 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.
• Ethyl-2-(2',3 ',4',5'-tetrafluorobenzoyl-)-3-(napthyl-2", 3 ' 'diamino)-pro ⁇ -2-enoate 600 mg 1.4 mmol was dissolved in a slurry of K 2 CO 3 in DMF (500 ml), The mixture was stirred vigorously at 100°C for 1 hour, then allowed to cool to RT. The K 2 CO 3 was removed by filtration and the DMF removed in vacuo to leave a yellow-brown solid in quantitative yield.
• 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 (0.98g, 2.5 mmol) ([M+lf 392).
• 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+l, 390).
• Two xenograft models for inoculation were harvested and diluted to a concentration of 50 x 10 6 cells/ml or 100 x 10 cells/ml.
• Four to six week old nude mice were injected with 0.1 ml of the cell suspension which contains between 5 x 10 and 10 x 10 6 cells.
• 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.
• Figure 2 shows the antitumor activity of compound 516 in HCT-116, a model of colorectal cancer.
• HeLa cells Human cervical epithelial cells
• MEM Eagle's minimum essential medium
• Glutamine 2 mM Glutamine
• 0.1 mM nonessential amino acid 2 mM Na Pyruvate
• 1.5 g L NaHCO 3 50 mg/L gentamicin
• fetal bovine serum 10% fetal bovine serum
• RNA Total RNA
• tRNA Total RNA
• RT reaction Reverse-transcription (RT) reaction was occuned using 50 ng of tRNA from each well in a 25 ⁇ l reaction containing lx TaqMan RT buffer, 2.5 uM random hexamers, 5.5 mM MgCl 2 , 0.5 mM each deoxynucleoside triphosphate (dNTP), 30 U MultiScribe Reverse Transcriptase, and 10 U RNase inhibitor.
• dNTP deoxynucleoside triphosphate
• dNTP deoxynucleoside triphosphate
• dNTP deoxynucleoside triphosphate
• dNTP deoxynucleoside triphosphate
• RNase inhibitor 10 U RNase inhibitor
• Rn value of GAPDH but no effect on its Cp 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.

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