Classifications

• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/535—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with at least one nitrogen and one oxygen as the ring hetero atoms, e.g. 1,2-oxazines
  • A61K31/5375—1,4-Oxazines, e.g. morpholine
  • A61K31/5377—1,4-Oxazines, e.g. morpholine not condensed and containing further heterocyclic rings, e.g. timolol
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/41—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having five-membered rings with two or more ring hetero atoms, at least one of which being nitrogen, e.g. tetrazole
  • A61K31/415—1,2-Diazoles
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/47—Quinolines; Isoquinolines
  • A61K31/4709—Non-condensed quinolines and containing further heterocyclic rings
• • A—HUMAN NECESSITIES
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  • A61K33/00—Medicinal preparations containing inorganic active ingredients
  • A61K33/24—Heavy metals; Compounds thereof
  • A61K33/243—Platinum; Compounds thereof
• • A—HUMAN NECESSITIES
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  • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
  • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
  • A61K47/06—Organic compounds, e.g. natural or synthetic hydrocarbons, polyolefins, mineral oil, petrolatum or ozokerite
  • A61K47/26—Carbohydrates, e.g. sugar alcohols, amino sugars, nucleic acids, mono-, di- or oligo-saccharides; Derivatives thereof, e.g. polysorbates, sorbitan fatty acid esters or glycyrrhizin
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
  • A61K47/30—Macromolecular organic or inorganic compounds, e.g. inorganic polyphosphates
  • A61K47/36—Polysaccharides; Derivatives thereof, e.g. gums, starch, alginate, dextrin, hyaluronic acid, chitosan, inulin, agar or pectin
  • A61K47/38—Cellulose; Derivatives thereof
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K9/00—Medicinal preparations characterised by special physical form
  • A61K9/0012—Galenical forms characterised by the site of application
  • A61K9/0053—Mouth and digestive tract, i.e. intraoral and peroral administration
• • 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
  • A61P35/00—Antineoplastic agents
• • 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
  • C07D401/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom
  • C07D401/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings
  • C07D401/04—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, at least one ring being a six-membered ring with only one nitrogen atom containing two hetero rings directly linked by a ring-member-to-ring-member bond
• • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
  • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
  • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
  • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
  • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Definitions

• Some aspects of the invention relate to identifying molecules that at least partially inhibit the activity of the Replication Protein A and these molecules can be used to treat hyper- proliferative diseases, including cancer.
• Replication protein A is a heterotrimeric single-stranded DNA (ssDNA) binding protein made up of 70, 34, and 14 kDa subunits (1).
• the ssDNA binding activity of RPA is required for several DNA metabolic pathways including DNA replication, recombination and repair.
• High affinity interactions with DNA are sustained by the numerous oligosaccharide/ oligonucleotide binding (OB)-folds present on each of the three subunits (2;3).
• OB oligosaccharide/ oligonucleotide binding
• the DNA binding pocket of a single OB-fold accommodates 3-4 bases of ssDNA (4;5).
• the main OB- folds, DNA binding domains A and B are present in the central region of the p70 subunit and contribute most of the binding energy for RPA-ssDNA interactions (2).
• Individual OB -folds are compact modular domains populated with hydrophobic and basic amino acids. These structural features make the OB -folds an attractive target for development of small molecule inhibitors (SMIs) of DNA binding activity. Given RPA's central role in cell growth and DNA repair, it is an attractive target for the development of compounds that can interfere with its activity.
• SMSIs small molecule inhibitors
• Various aspects of the invention include methods and compounds for reducing the activity of Replication Protein A, effecting eukaryotic cell proliferation, the cell cycle of eukaryotic cells and/or treating cancer by contacting Replication Protein A with a compound such as compound A or a metabolite thereof that includes the following core structure:
• eukaryotic cells contacted with a compound or metabolite thereof includes the core structure are further contacted with at least one compound that damage DNA directly or inhibits topoisomerase II.
• Such compounds include, but are not limited to, Cisplatin, Etoposide, Busulfan, Bendamustine, Carboplatin, Carmustine, Chlorambucil Cisplatin, Cyclophosphamide, dacarbazine, Daunorubicin, Decitabine, Doxorubicin, Epirubicin, Etoposide, Idarubicin, Ifosfamide, Irinotecan, Lomustine, Mechlorethamine, Melphalan, Mitomycin C, Mitoxantrone, Oxaliplatin, Temozolomide, Topotecan and the like.
• Some aspects of the invention include methods of reducing the activity of a Replication Protein A, comprising the steps of: providing a compound A, wherein the compound A binds to Replication Protein A or is metabolized into a chemical that binds to Replication Protein A, compound have the following formula:
• R ⁇ is selected from the group consisting of: substituted quinolins, thiophenes and phenyls; including 5-(7-chloro-2,3-dihydro-[l,4]dioxino[2,3-g]quinolin-8-yl);5- (quinoxalin-6-yl); and 6-chloro-[l,3]dioxolo[4,5-g]quinolin-7-yl
• R 2 is selected from the group consisting of: hydrogen, halogens, methyl groups, nitro groups; wherein compound A or a
• ketobutyric acids consisting of: ketobutyric acids, and
• n 1 , 2, 3,4, or 5.
• the quinolin or the phenyl in compound A is substituted with at least one moiety selected from the group consisting of: halogens, methyl groups, ethyl groups, amino groups and pyrazole.
• R ⁇ in compound A is selected from the group consisting of: 2-chloro-7-ethoxyquinolin, 5(quinoxalin-6-yl), 2-chloro- 6,7-dimethoxyquinolin, 2-chloro-6-ethoxyquinolin, 4-Bromophenyl, 4-fluorophenyl, 4- chlorophenyl, 2-chlorophenyl, 2-methoxyphenyl, 4-ethylphenyl, 4-Diethylaminophenyl, 4- dimethylaminophenyl, Thiophene, 4-methoxyphenyl, p-tolyl, 2,5-dimethoxyphenyl, 3,4- dimethoxyphenyl, 4-ethylphenyl; and l-phenyl-3-p-tolyl-lH- pryazole; and R 2 in compound A is selected from the groups consisting of: 4-bromo, 4-chloro, 4-nitro, 4-methyl, 4-methoxy, H, 3,4
• the molecule that binds to Replication Protein A is a derivative of compound A or a metabolite thereof. And in some embodiments the molecule that binds to Replication Protein A is the compound TDLR-505, the compound TDLR-506, or a metabolite thereof.
• the step of contacting either compound A or a metabolite thereof and the at least one isoform of Replication Protein A occurs in vivo. In still other embodiments the step of contacting compound A or a metabolite thereof and the at least one isoform of Replication Protein A occurs in vitro.
• aspects of the invention include methods of inhibiting cell proliferation via altering the eukaryotic cell cycle-progression, comprising the steps of: providing a compound A that interferes with eukaryotic cell cycle-progression or that is metabolized into a chemical that interferes with eukaryotic cell cycle-progression, wherein compound A has the following formula:
• Ri is selected from the group consisting of: substituted quinolins, thiophenes and phenyls; including 5-(7-chloro-2,3-dihydro-[l,4]dioxino[2,3-g]quinolin-8-yl);5-(quinoxalin-6- yl); and 6-chloro-[l,3]dioxolo[4,5-g]quinolin-7-yl; R 2 is selected from the group consisting of: hydrogen, halogens, methyl groups, nitro groups; wherein compound A or a metabolite of compound A binds to Replication Protein A; and R 3 is selected from the group consisting of:
• n 1, 2, 3,4, or 5.
• the quinolin or the phenyl in compound A is substituted with at least one moiety selected from the group consisting of: halogens, methyl groups, ethyl groups, amino groups and pyrazole.
• compound A is selected from the group consisting of: 2-chloro-7-ethoxyquinolin, 5(quinoxalin-6-yl), 2-chloro- 6,7-dimethoxyquinolin, 2-chloro-6-ethoxyquinolin, 4-Bromophenyl, 4-fluorophenyl, 4- chlorophenyl, 2-chlorophenyl, 2-methoxyphenyl, 4-ethylphenyl, 4-Diethylaminophenyl, 4- dimethylaminophenyl, Thiophene, 4-methoxyphenyl, p-tolyl, 2,5-dimethoxyphenyl, 3,4- dimethoxyphenyl, 4-ethylphenyl; and l-phenyl-3 -p-tolyl- 1H- pryazole; and R 2 in compound A is selected from the groups consisting of: 4-bromo, 4-chloro, 4-nitro, 4-methyl, 4-methoxy, H, 3,4- di
• the compound that at least partially interferes with the eukaryotic cell cycle-progression is the compound A or a metabolite thereof.
• the compound that interferes with eukaryotic cell cycle-progression is the compound TDLR-505, TDLR-506, or metabolite thereof.
• the contacting step between compound A or a metabolite thereof and the Replication Protein A occurs in vivo.
• Still other embodiments include methods for treating human or animal patients comprising the step of supplying or providing at least one therapeutically active amount of at
• BDDB01 6 5 29599vl 4 least one compound that inhibits the activity of RPA or a pharmaceutically acceptable salt thereof.
• Some embodiments include the step of administering a dose of the compound to a patient wherein the dose is about 50 mg of said compound per kg "1 of the patient's body weight or about 100 mg of said compound per kg "1 of the patient's body weight or about 200 mg of said compound per kg " of the patient's body weight.
• the contacting step between said compound A or a metabolite thereof and the Replication Protein A occurs in vitro.
• Still other aspects of the invention include a method treating cancer, comprising the steps of: providing a compound wherein the compound interferes with the cell cycle of a cancer cell or is metabolized into a chemical that interferes with the cell cycle of a cancer cell, and the compound has the following formula:
• R ⁇ is selected from the group consisting of: substituted quinolins, thiophenes and phenyls
• R 2 in compound A is selected from the group consisting of: halogens, methyl groups, nitro groups; wherein compound A binds to Replication Protein A; and contacting said compound A with at least one cancer cell.
• the quinolin or the phenyl in compound A is substituted with at least one moiety selected from the group consisting of:
• Rj in compound A is selected from the group consisting of: 2-chloro-7-ethoxy quinolin, 5(quinoxalin- 6-yl), 2-chloro-6,7-dimethoxyquinolin, 2-chloro-6-ethoxyquinolin, 4-Bromophenyl, 4- fluorophenyl, 4-chlorophenyl, 2-chlorophenyl, 2-methoxyphenyl, 4-ethylphenyl, 4- Diethylaminophenyl, 4-dimethylaminophenyl, Thiophene, 4-methoxyphenyl, p-tolyl, 2,5- dimethoxyphenyl, 3,4-dimethoxyphenyl, 4-ethylphenyl; and l-phenyl-3 -p-tolyl- 1H- pryazole; and R 2 in compound A is selected from the groups consisting of
• the compound that is contacted with the cancer cell is compound A or a metabolite thereof.
• the compound that is contacted with the cancer cell is the compound TDLR-505, TDLR-506, or metabolite thereof.
• the contacting step between said compound A or a metabolite thereof and the cancer cell occurs in vitro.
• the cancer cell is found in a solid tumor selected from the group consisting of: lung cancer, non-small cell, small cell, epithelial ovarian cancer, cervical cancer, colon cancer and breast cancer.
• Some embodiments of the invention further include the step of contacting the cancer cell with at least one chemotherapeutic reagent that binds to or damages DNA directly or reduces the activity of topoisomerase II.
• the chemotherapeutic reagent is selected from the group consisting of but not limited to: cisplatin and etoposide.
• Such compounds include, but are not limited to, Busulfan, Bendamustine, Carboplatin, Carmustine, Chlorambucil, Cisplatin, Cyclophosphamide, dacarbazine, Daunorubicin, Decitabine,
• Doxorubicin Epirubicin, Etoposide, Idarubicin, Ifosfamide, Irinotecan, Lomustine,
• FIG. 1A Compound 3.
• FIG. IB EMS A of compound 3 inhibition of RPA binding to DNA.
• FIG. 1C Plot of EMSA data of compound 3 inhibition of RPA binding to DNA.
• FIG. 2A A ketobutyric acid derivative of compound A.
• FIG. 2B Compound TDLR-505.
• FIG. 2C EMSA of compound TDLR-505 inhibition of RPA binding to DNA.
• Fig. 2D Plot of EMSA data of TDRL-505 inhibition of RPA binding to DNA.
• FIG. 4A Dot plots of H460 cells stained with Annexin V/PI measuring cell death induced by TDRL-505.
• FIG. 4B Plot of cell death data measured at different concentrations of compound TDLR-505.
• FIG. 4C Immuno-fluorescence of RPA cellular localization probed with an anti- RPA antibody and visualized with an AlexaFlour antibody.
• FIG. 4D Western blots of the of the p34 subunit of RPA as a function of treatment with compound TDRL-505.
• FIG. 5A Cell cycle distribution of H460 NSCLC cells treated with compound TDLR-505.
• FIG. 5B Cell cycle distribution of H460cells treated with Nocodazole and then compound TDLR-505 for 4, 8 or 12 hours.
• FIG. 6 Analysis of synergy in H460 cells co-treated with compound TDLR-505 and either cisplatin (open circles) or etoposide (closed circles).
• FIG. 7B In vivo anticancer activity of TDRL-505 versus non-small cell lung cancer in an individual mouse assessed in the xenograft model.
• 'about' as used herein means plus or minus 10 percent.
• 'about 1.0' encompasses the range of 0.9 to 1.1.
• a therapeutically effective amount is an amount of a biologically active compound that has a single or cumulative beneficial effect on the health or well being of a patient.
• RPA inhibition has the potential to impact numerous differentially regulated pathways in cancer cells.
• RPA inhibition can be used to exploit the highly proliferative nature of cancer cells which is characterized by a large population of cells in S-phase.
• RPA is also essential for several DNA repair pathways in the cell including nucleotide excision repair (NER).
• NER nucleotide excision repair
• Cisplatin a common chemotherapeutic used in the treatment of various cancers, induces its cytotoxic effect by forming intrastrand covalent DNA adducts that are repaired primarily by the NER pathway (6). Consequently, cisplatin treatment, in conjunction with decreased RPA ssDNA binding activity, would be expected to result in decreased efficiency of cellular repair of cisplatin-DNA adducts and increased cytotoxicity.
• targeting RPA has the potential not only for single agent activity but also to sensitize cancer cells to therapies that induce DNA damage and genetic instability, such as cisplatin, etoposide and ionizing radiation (IR).
• therapies that induce DNA damage and genetic instability such as cisplatin, etoposide and ionizing radiation (IR).
• Busulfan Bendamustine, Carboplatin, Carmustine, Chlorambucil, Cisplatin, Cyclophosphamide, dacarbazine, Daunorubicin, Decitabine, Doxorubicin, Epirubicin, Etoposide, Idarubicin, Ifosfamide, Irinotecan, Lomustine, Mechlorethamine, Melphalan, Mitomycin C, Mitoxantrone, Oxaliplatin, Temozolomide, Topotecan and the like.
• small molecules that inhibits the ssDNA binding activity of RPA have been identified.
• Cellular RPA inhibition results in the inability to enter S phase, induction of cell death and synergistic activity with the chemotherapeutic reagents cisplatin and etoposide.
• These small molecules which are able to inhibit the ssDNA binding activity of RPA are active both as single agents and in conjunction with commonly used chemotherapeutics for killing cancer cells.
• the compounds can be safely administered up to 200 mg/mg in mice IP and via oral gavage with not signs of overt toxicity and possess anticancer activity versus human non-small cell lung cancer in mouse xenograft model.
• TDRL-506 was prepared from TDRL-505 and 3- morpholinopropan-1 -amine (2) via EDC coupling.
• H460 cells were analyzed for apoptosis using an Annexin V-FITC/Propidium iodide (PI) Vybrant Apoptosis Assay Kit (Invitrogen), according to manufacturer's instructions. Cells were plated at a density of 1 x 10 4 cells per cm 2 and allowed to adhere for 24 hours and then treated with compound TDLR-505 for 48 hours. Following plating and treatment of H460 cells as described above, adherent and non-adherent cells were collected, processed, and analyzed on a BD F AC Scan flow cytometer. Data was analyzed using WinMDI software (http://facs.scripps.edu/software.html). Cell cycle analysis was performed by PI staining.
• PI Annexin V-FITC/Propidium iodide
• cells were plated and treated with compound collected and then washed twice with PBS- EDTA supplemented with 1% BSA. Cells were fixed in 70% EtOH at -20 °C while vortexing followed by incubation on ice for 30 minutes. Cells were then collected and stained with PI solution (10 ⁇ g/mL PI and 25 ⁇ g/mL RNaseA in PBS-EDTA supplemented with 1% BSA). Cells were analyzed on a Becton Dickinson FACScan flow cytometer. Cells were gated and analyzed on a histogram with events plotted against the FL2-A parameter. Cell cycle distribution was analyzed using ModFit software.
• G2 arrest was induced by treatment with 0.8 ⁇ ⁇ , nocodazole for 12 hours (10). Cells were then washed with PBS and treated with either vehicle or compound TDLR-505 (100 ⁇ ). Cells were harvested and analyzed for cell cycle distribution as described above.
• H460 cells were plated on chamber slides (LabTek) as described above. Cells were then treated for 3 hours with either 50 ⁇ of compound TDLR-505 or vehicle as indicated and following treatment, cells were fixed in 4% paraformaldehyde at 25 °C for 3 minutes followed by washing in 0.2% Triton X-100 for 2 minutes at 4 °C. The slides were then blocked in 15% FBS in PBS for 1 hour at 25 °C and then incubated with anti-RPA 34 primary antibody (Neomarkers)
• BDDB01 6 5 29 5 99vl 10 at a dilution of 1 :500 in 15% FBS for 1 hour. Slides were then washed 3 x 10 minutes with 15% FBS and then incubated with Alexa Fluor-594 goat-anti-mouse secondary antibody (Invitrogen) at a dilution of 1 :300 for 1 hour. Slides were again washed and stained with 300 nM DAPI diluted in PBS-EDTA for five minutes. Slides were then mounted and images captured using a Zeiss fluorescent microscope and images were captured using filters for Texas Red to visualize RPA staining and DAPI for visualizing DNA. Slides were visualized and images analyzed and quantified using Image J software.
• H460 cells were plated and treated with either vehicle or 100 ⁇ compound TDLR- 505 in the presence or absence of 25 ⁇ etoposide for 6 hours and then processed for western blot analysis using a RIPA lysis and extraction procedure.
• RPA was detected with an anti-RPA p34 antibody (Neomarkers) and goat anti-mouse-HRP secondary (Santa Cruz). Bands were visualized using chemiluminescence detection.
• TDRL-505 was administered to mice at 200 mg/kg either ip or po and blood drawn at 1, 2, 4, 8, 24 and 48 hours post treatment. Serum concentration of TDRL-505 was measured using a HPLC MS/MS protocol and PK parameters analysis using on- compartmental analysis.
• FIG. 2A and B In view of the high level of in vitro inhibition of RPA observed using compounds in the core structure of compound A, the core structure was substituted with dihydropyrazole with a 4-oxo-butanoic acid at the Nl position and a phenyl substituent at the C3 to initiate analysis of structure activity relationships (SAR) and search for other compounds with cellular activity. Eighty-one analogs were identified and obtained from the ChemDiv library with differing substitutions off the phenyl ring (R 2 ) and varying substituents at position C5 on the dihydropyrazole ring (R ⁇ ) (data not shown). Among the compounds analyzed, compound TDRL-505 (FIG.
• BDDB01 6529 5 99vl 12 and in vitro inhibitory activity of the compound 3 analogs showed that compound TDLR-505 displayed the lowest in vitro ICs 0 value and was the most potent compound of those examined in cells. Accordingly, the compound was selected for further investigation, including studying its mechanism of action and the cellular effects that result from inhibition of RPA-ssDNA interactions using a comprehensive series of in vitro, cell based and in vivo assays.
• the in vitro IC 50 was determined by EMSA analysis as described in FIG. 1A.
• the cellular IC 50 value was determined by treating H460 cells with the indicated compounds and analyzing annexinV/PI staining as described in Methods.
• the in vitro and cellular data was analyzed using standard 4 parameter logistic-curve.
• the ICs 0 values and standard error of the fit were determined from this analysis.
• FIG. 2D quantification of the gel presented in FIG. 2C.
• TDRL-506 was synthesized and purified and assessed for in vitro RPA inhibitory activity.
• TDRL-506 was assessed for RPA inhibitory activity against both full length RPA heterotrimer Lanes 1-7 and the DBD-A/B construct (lanes 8-12).
• the concentrations used were 25, 50, 75 and 100 DM TDRL-506.
• the data demonstrate that the TDRL-506 compound containing the morpholino modification retains full RPA inhibitory activity.
• TDRL-505 is capable of inducing cell death in NSCLC cells.
• a crystal violet staining assay was used and gave an IC50 value of 64 ⁇ (data not shown).
• a similar result was also observed in treatment of the A549 NSCLC cell line with compound TDLR-505 while analysis using freshly isolated peripheral blood mononuclear cells (PBMCs) revealed minimal cytotoxic activity (data not shown).
• PBMCs peripheral blood mononuclear cells
• compound TDLR-505 shows significant cytotoxic effects in NSCLC cell lines and only modest activity in non-cancerous cells, indicating that there is a therapeutic treatment window for these molecules.
• Lane 1 is a positive control with RPA purified from an E. coli expression system.
• the position of un-phosphorylated RPA p34 and hyper-phosphorylated RPA p34 are indicated by the arrows, These data demonstrate that RPA is not degraded or reduced in expression as a function of TDRL-505 treatment.
• Compound TDLR-505 induces a Gl arrest in H460 cell lines.
• the compound TDLR-505 was tested to assess its affect on cell cycle progression. Knockdown of RPA by siRNA has been demonstrated to induce a Gl cell cycle arrest consistent with the essential role of RPA in the initiation of S-phase DNA replication (19). In order to determine if this is the same mechanism of action displayed by compound TDLR-505, its affect on H460 cell cycle progression was measured. As illustrated by the data presented in FIG. 5, synchronized H460 cells show an inability to re-enter S-phase when treated with TDRL-505.
• FIG. 5A H460 NSCLC cells were treated with 0 and 75 ⁇ of compound TDLR-505 for 48 hours and then analyzed for cell cycle distribution using flow cytometry.
• FIG. 5B H460 cells were treated with 0.8 ⁇ g/mL nocodazole for 12 hours, washed then treated with either vehicle or 100 ⁇ MTDLR-505 for 4, 8 and 12 hours. Cells were then harvested and analyzed for cell cycle distribution using flow cytometry.
• RPA is required for the repair of bulky DNA adducts as well as DNA breaks induced by various types of exogenous and
• BDDB01 6_29 5 99vl 17 endogenous agents The association of RPA with ssDNA is a critical feature of all of these pathways, indicating that inhibition of this activity would increase the cytotoxic effects induced by DNA damage.
• the combination index (CI) (20) was measured. Referring now to FIG. 6. As illustrated in this experiment, compound TDLR-505 acts synergistically with both cisplatin and etoposide in H460 cells. H460 cells were treated with increasing fractions of the 1 ⁇ 2 0 concentration of either cisplatin or etoposide with compound TDLR-505 for 48 hours.
• TDRL-505 demonstrating reasonable IC 50 values against NSCLC prompted the assessment in vivo of the effect of RPA inhibition on lung cancer tumor growth.
• the safety of administration of TDRL-505 in naive mice was determined Additional data demonstrated that IP administration of compound TDLR-505 in a formulation of 25% DMSO in 0.75% Tween 80 to NOD/SCID mice is well tolerated up to 400 mg/kg. Oral dosing in 0.1% Tween 80/methylcellulose was also well tolerated up to 800 mg/kg.
• mice that had been implanted with a human NSCLC tumor cells were subjected to a regime of oral dosing.
• the tumors were allowed to grow to 100 mm3 after which treatment with TDRL-505 or vehicle was commenced.
• the results presented in (FIG. 7) demonstrate a reduction in tumor growth in mice treated with TDRL-505 compared to the vehicle control.
• FIG. 7B analysis of individual mice reveal significant reduction in tumor growth compared to vehicle treated controls.
• Gl arrest may also induce cell death after prolonged periods of time, explaining why the degree of cell death after 48 hours of treatment is greater than the number of cells that are in S-phase. This illustrates the existence of a therapeutic window for specifically targeting actively dividing cells in the context of cancer treatment using SMIs to block the cellular activity of RPA.
• RPA DNA repair protein
• the role of RPA in DNA repair also allows for inhibition of its activity to increase the efficacy of current chemotherapeutics that induce DNA damage in the context of combination therapy.
• the inhibition of DNA repair is anticipated to result in persistent DNA damage which would increase cytotoxicity.
• the indispensable role of RPA in the recognition and verification steps of NER is well characterized and, in addition, RPA participates in the re-synthesis step following excision of the damaged oligonucleotide (25).
• Previous studies have shown that cells with decreased levels of NER proteins demonstrate increased sensitivity to cisplatin treatment (26). Consistent with this, our data reveal a synergistic interaction between compound TDLR- 505 and cisplatin at high fractions of cells affected.
• BDDB01 6 5 29599vl 20 be subject to cisplatin induced G2 arrest.
• compound TDLR-505 toxicity stems from an extended Gl arrest
• the G2 checkpoint induced by cisplatin would result in less cell death as a result of treatment.
• this effect is mitigated by the interaction at the level of DNA repair with RPA inhibition increasing cisplatin toxicity and overcoming the antagonistic signaling interaction.
• BDDB01 6 5 29 5 99vl 21 of RPA will have broad spectrum utility as the reliance on RPA for increased cell proliferation and repair of chemotherapeutic DNA damaging agents is not unique to any single cancer.
• Targeting the DNA binding activity of RPA with small, drug-like molecules as disclosed herein illustrates that this class of proteins can be targeted to produce therapeutic compounds.
• Bochkarev A Bochkareva E. From RPA to BRCA2: lessons from single-stranded DNA binding by the OB-fold. Current Opinion in Structural Biology 2004 Feb;14(l):36-42.
• Bochkarev A Pfuetzner RA, Edwards AM, Frappier L. Structure of the single-stranded- DNA-binding domain of replication protein A bound to DNA. Nature
• Bochkareva E Belegu V, Korolev S, Bochkarev A. Structure of the major single-stranded DNA-binding domain of replication protein A suggests a dynamic mechanism for DNA binding. EMBO J 2001;20(3):612-8.

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