Claims for Patent: 7,960,311

Summary for Patent: 7,960,311

Title:	Methods employing combinatorial artificial receptors
Abstract:	The present invention relates to methods employing artificial receptors, such as combinatorial artificial receptor arrays. The present receptors include heterogeneous and immobilized combinations of building block molecules. In certain embodiments, combinations of 2, 3, 4, or 5 distinct building block molecules immobilized near one another on a support provide molecular structures that can be employed in the present methods. The present methods can develop artificial receptors that can then be employed to detect the receptor\'s ligand. The present methods can find compounds that disrupt one or more binding interactions.
Inventor(s):	Carlson; Robert E. (Minnetonka, MN)
Assignee:	Receptors LLC (Chaska, MN)
Application Number:	10/934,977
Patent Claims:	1. A method of producing an affinity support, the method comprising: providing a plurality of candidate artificial receptors; the plurality of candidate artificial receptors independently comprising: at least 6 structural characteristics selected from the group consisting of positive charge, negative charge, acid, base, electron acceptor, electron donor, hydrogen bond donor, hydrogen bond acceptor, free electron pair, .pi. electrons, charge polarization, hydrophilicity, and hydrophobicity; a region on a solid support comprising 2, 3, 4, 5, or 6 different building block molecules; each of the building block molecules being independently covalently coupled to the region; a plurality of adjacent building block molecules forming a binding site; the region being a contiguous portion of the surface of the solid support with the different building block molecules distributed randomly throughout the contiguous region; contacting one or more candidate artificial receptors with a test ligand; identifying one or more artificial receptors that bind the test ligand as one or more working artificial receptors; selecting one or more of the working artificial receptors; producing an affinity support comprising the one or more selected working artificial receptors; wherein: each of the building block molecules comprises a framework and n recognition elements and is independently of the formula: framework-(recognition element).sub.n in which: n=1, 2, or 3; each recognition element is independently covalently coupled to the framework; and the framework comprises a functional group effective for covalent coupling to a support or a linker; the framework is alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, or heteroaryl alkyl; substituted with 1 to 4 functional groups; the functional groups independently being carboxyl, amine, hydroxyl, phenol, carbonyl, or thiol; each recognition element is independently a 1-12 carbon alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, or heteroaryl alkyl moiety; optionally, substituted with a group with a property of positive charge, negative charge, acid, base, electron acceptor, electron donor, hydrogen bond donor, hydrogen bond acceptor, free electron pair, .pi. electrons, charge polarization, hydrophilicity, or hydrophobicity; and when the building block molecule comprises an amino acid derivative, wherein amino acid derivatives are defined as a core feature having the chemical structure --NH--C--C(O)--, the building block molecule comprises a single derivatized amino acid and the framework is the amino acid derivative. 2. The method of claim 1, comprising contacting an array of candidate artificial receptors with the test ligand. 3. The method of claim 2, wherein the array comprises at least about 100 candidate artificial receptors. 4. The method of claim 1, wherein the artificial receptor is made up of building blocks that are naive to the test ligand. 5. The method of claim 1, wherein the affinity support comprises a chromatography support, a filtration membrane, or an electrophoresis medium. 6. The method of claim 5, wherein the affinity support comprises a chromatography support. 7. The method of claim 1, wherein the test ligand is a protein and the protein is a component of a mixture of individual proteins or a proteome. 8. The method of claim 1, wherein the test ligand is a protein and the protein is a component of an antibody or a component of a mixture of antibodies. 9. The method of claim 1, wherein each recognition element is independently unsubstituted or substituted with a moiety selected from the group consisting of amine, quaternary ammonium, carboxylate, phenol, phosphate, phosphonate, phosphinate, sulphate, sulphonate, thiocarboxylate, hydroxamic acid, sulfoxide, betaine, amine oxide, amide, carboxyl, alcohol, ether, thiol, thioether, ester, thio ester, borane, borate, metal complex, alkyl, alkene, alkyne, aromatic moiety, and plurality thereof. 10. The method of claim 1, wherein the recognition element is substituted with or to form: protonated phosphate, protonated phosphonate, protonated phosphinate, protonated sulphate, or protonated sulphinate; alkyl amine, alkyl diamine, heteroalkyl amine, aryl amine, heteroaryl amine, aryl alkyl amine, heterocyclic amine, amidine, hydrazine, urea, trimethyl alkyl quaternary ammonium, dimethyl ethyl alkyl quaternary ammonium, dimethyl alkyl quaternary ammonium, aryl alkyl quaternary ammonium, or pyridinium quaternary ammonium; alkyl carboxylate, aryl carboxylate, aryl alkyl carboxylate, or thiocarboxylate; phosphonate or phosphinate; primary alcohol, secondary alcohol, tertiary alcohol, or aromatic alcohol; lower alkyl, substituted alkyl, cycloalkyl, aryl alkyl, heteroaryl alkyl, lower alkene, aryl alkene, unsubstituted aryl, heteroaryl, substituted aryl, aryl alkyl, heteroaryl alkyl, alkyl substituted aryl, or polyaromatic hydrocarbon; or a plurality thereof. 11. The method of claim 1, wherein the framework has the formula: ##STR00007## in which: R.sub.1 is 1-12 carbon alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, or heteroaryl alkyl; F.sub.1 and F.sub.2 are independently carboxyl, amine, hydroxyl, phenol, carbonyl, or thiol group; or are independently 1-12 carbon alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, heteroaryl alkyl, or inorganic group substituted with carboxyl, amine, hydroxyl, phenol, carbonyl, or thiol group; F.sub.3 and F.sub.4 are independently absent, carboxyl, amine, hydroxyl, phenol, carbonyl, or thiol group; or are independently absent, or 1-12 carbon alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, heteroaryl alkyl, or inorganic group substituted with carboxyl, amine, hydroxyl, phenol, carbonyl, or thiol group. 12. The method of claim 11, wherein: R.sub.1 is 1-6 carbon alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, or heteroaryl alkyl; F.sub.1, F.sub.2, F.sub.3, or F.sub.4 are independently 1-6 carbon alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, heteroaryl alkyl, or inorganic group substituted with carboxyl, amine, hydroxyl, phenol, carbonyl, or thiol group. F.sub.3 is absent; or F.sub.3 and F.sub.4 are absent. 13. The method of claim 1, wherein the framework is: a natural or synthetic amino acid, an .alpha.-hydroxy acid, or a thioic acid; or a .beta.-amino acid or homo or .beta. analog of a natural amino acid. 14. The method of claim 1, wherein the framework is an amino acid with an amine, hydroxyl, phenol, carboxyl, thiol, thioether, or amidino group on its side chain. 15. The method of claim 14, wherein the framework is a serine, threonine, tyrosine, aspartic acid, glutamic acid, asparagine, glutamine, cysteine, lysine, arginine, or histidine moiety. 16. The method of claim 1, wherein one or more of the building block molecules further comprises a linker and independently has the formula: linker-framework-(first recognition element) (second recognition element) in which the linker, first recognition element, and second recognition element are independently covalently coupled to the framework. 17. The method of claim 16, wherein the framework is of the formula of an amino acid. 18. The method of claim 17, wherein the amino acid is serine, threonine, or tyrosine. 19. The method of claim 18, wherein the amino acid is tyrosine. 20. The method of claim 16, wherein the linker is of the formula (CH.sub.2).sub.nC(O)--, with n=1-16. 21. The method of claim 1, wherein one or more of the building block molecules further comprises a linker and independently is of formula: ##STR00008## in which: X is absent or C.dbd.O; Y is absent, NH, or O; Z is O; R.sub.2 is H or CH.sub.3; R.sub.3 is CH.sub.2 or CH.sub.2-phenyl; RE.sub.1 is B1, B2, B3, B4, B5, B69, B7, B8, B9, A1, A2, A3, A4, A5, A69, A7, A8, or A9; RE.sub.2 is A1, A2, A3, A4, A5, A69, A7, A8, A9, B1, B2, B3, B4, B5, B69, B7, B8, or B9; L is (CH.sub.2).sub.nCOOH, with n=1-16; A1 is CH.sub.2 CH.sub.3; A2 is CH.sub.2CH(CH.sub.3).sub.2; A3 is ##STR00009## A4 is ##STR00010## A5 is ##STR00011## A6 is CH.sub.2CH.sub.2--O--CH.sub.3; A7 is CH.sub.2CH.sub.2--OH.sub.; A8 is CH.sub.2CH.sub.2--NH--C(O)CH.sub.3; A9 is ##STR00012## B1 is CH.sub.3; B2 is ##STR00013## B3 is ##STR00014## B4 is ##STR00015## B5 is ##STR00016## B6 is CH.sub.2--S--CH.sub.3; B7 is CH.sub.2CH(OH)CH.sub.3; B8 is CH.sub.2CH.sub.2C(O)--NH.sub.2; and B9 is CH.sub.2CH.sub.2CH.sub.2--N--(CH.sub.3).sub.2. 22. The method of claim 1, wherein the building block molecule further comprises a linker, and the linker is a alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, heteroaryl alkyl, ethoxy or propoxy oligomer, or glycoside moiety; substituted with a carboxyl, alcohol, phenol, thiol, amine, carbonyl, or maleimide group. 23. The method of claim 1, wherein the building block molecules coupled to the support are in proximity to one another. 24. The method of claim 1, wherein the test ligand comprises an antibody or mixture of antibodies. 25. The method of claim 1, wherein the test ligand comprises a protein or a mixture of proteins. 26. The method of claim 25, wherein the protein or mixture of proteins comprises a prion. 27. The method of claim 25, wherein the protein or mixture of proteins comprises a .beta.-amyloid. 28. The method of claim 25, wherein the protein or mixture of proteins comprises a cholera toxin. 29. The method of claim 25, wherein the protein or mixture of proteins comprises at least one protein of a cancer cell. 30. The method of claim 29, wherein the cancer comprises bladder cancer, breast cancer, colon cancer, kidney cancer, liver cancer, lung cancer, esophageal cancer, gall-bladder cancer, ovarian cancer, pancreatic cancer, stomach cancer, cervical cancer, thyroid cancer, prostate cancer, skin cancer, a hematopoietic tumor of lymphoid lineage, a hematopoietic tumor of myeloid lineage, a tumor of mesenchymal origin, a tumor of the central nervous system, a tumor of the peripheral nervous system, melanoma, seminoma, teratocarcinoma, osteosarcoma, xeroderoma pigmentosum, keratoctanthoma, thyroid follicular cancer, or Kaposi's sarcoma. 31. The method of claim 30, wherein the cancer comprises small cell lung cancer, squamous cell carcinoma, leukemia, acute lymphocytic leukemia, acute lymphoblastic leukemia, B-cell lymphoma, T-cell-lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, hairy cell lymphoma, Burkett's lymphoma, acute myelogenous leukemia, chronic myelogenous leukemia, myelodysplastic syndrome, promyelocytic leukemia, fibrosarcoma, rhabdomyosarcoma, astrocytoma, neuroblastoma, glioma, or schwannoma. 32. The method of claim 25, wherein a sample from cells or tissues suspected of being cancerous or including a tumor comprises the protein or mixture of proteins. 33. The method of claim 25, wherein serum comprises the protein or mixture of proteins. 34. The method of claim 1, wherein the test ligand comprises a microbe. 35. The method of claim 34, wherein the microbe comprises Vibrio cholerae. 36. The method of claim 34, wherein the microbe comprises a bacterium, a mycoplasma, a fungus, a rickettsia, or a virus. 37. The method of claim 36, wherein the bacteria or mycoplasma comprises Escherichia coli, Vibrio cholerae, Acinetobacter caicoaceticus, Haemophilus influenzae, Actinobacillus actinoides, Haemophilus parahaemolyticus, Actinobacillus lignieresii, Haemophilus parainfluenzae, Actinobacillus suis, Legionella pneumophila, Actinomyces bovis, Leptospira interrogans, Actinomyces israelli, Mima polymorphs, Aeromonas hydrophile, Moraxella lacunata, Arachnia propionica, Burkholderia mallei, Burkholderia pseudomallei, Moraxella osioensis, Arizona hinshawii, Mycobacterium osioensis, Bacillus cereus, Mycobacterium leprae, Bacteroides spp, Mycobacterium spp, Bartonella bacilliformis, Plesiomonas shigelloides, Bordetella bronchiseptica, Proteus spp, Clostridium difficile, Pseudomonas aeruginosa, Clostridium sordellii, Salmonella cholerasuis, Clostridium tetani, Salmonella enteritidis, Corynebacterium diphtheriae, Salmonella typhi, Edwardsiella tarda, Serratia marcescens, Enterobacter aerogenes, Shigella spp, Staphylococcus epidermidis, Francisella novicida, Vibrio parahaemolyticus, Haemophilus ducreyi, Haemophilus gallinarum, Haemophilus haemolyticus, Bacillus anthracis, Mycobacterium bovis, Bordetella pertussis, Mycobacterium tuberculosis, Borrella burgdorfii, Mycoplasma pneumoniae, Borrella spp, Neisseria gonorrhoeae, Campylobacter, Neisseria meningitides, Chlamydia psittaci, Nocardia asteroids, Chlamydia trachomatis, Nocardia brasillensis, Clostridium botulinum, Pasteurella haemolytica, Clostridium chauvoei, Pasteurelia multocida, Clostridium haemolyticus, Pasteurella pneumotropica, Clostridium histolyticum, Pseudomonas pseudomallei, Clostridium novyl, Staphylococcus aureus, Clostridium perfringens, Streptobacillus moniliformis, Clostridium septicum, Cyclospora cayatanensis, Streptococcus agalacetiae, Erysipelothrix insidiosa, Streptococcus pneumoniae, Klebsiella pneumoniae, Streptococcus pyogenes, Listeria manocytogenes, Yersinia pestis, Yersinia pseudotuberculosis, Yersinia enterocolitica, Brucella abortus, Brucella canis, Brucella melitensis, Brucella suis, or Francisella tularensis. 38. The method of claim 36, wherein the bacteria or mycoplasma comprises E. coli H157:O7. 39. The method of claim 36, wherein the fungus comprises Absidia, Piedraia hortae, Aspergillus, Prototheca, Candida, Paecilomyces, Cryptococcus neoformans, Cryptosporidium parvum, Phialaphora, Dermatophilus congolensis, Rhizopus, Epidermophyton, Scopulariopsis, Exophiala, Sporothrix schenkii, Fusarium, Trichophyton, Madurella mycetomi, Toxoplasma, Trichosporon, Microsporum, Microsporidia, Wangiella dermatitidis, Mucor, Blastomyces dermatitidis, Giardia lamblia, Entamoeba histolytica, Coccidioides immitis, or Histoplasma capsulatum. 40. The method of claim 36, wherein the rickettsia or virus comprises a Coronavirus, a Hepatitis virus, Myxovirus, Paramyxovirus, Picornavirus, Rickettsia akari, Rochalimaea Quintana, Rochalimaea vinsonii, Norwalk Agent, an Adenovirus, an Arenavirus, a Herpesvirus, a Human Immunodeficiency Virus, a Parainfluenza virus, a Poxvirus, Papovaviruses, a Spongiform Encephalopathy Virus, a Rhabdoviruses, a Togavirus, Coxiella burnetii, Rickettsia canada, Rickettsia prowazekii, Rickettsia rickettsii, Rickettsia Tsutsugamushi, Rickettsia typhi, a Spotted Fever Group Agent, a Vesicular Stomatitis Virus, a Toga virus, an Arena virus, a Bunya virus, a Flaviruses, a Filovirus, a Nipah virus, a viral encephalitis agent, a LaCrosse virus, a Kyasanur Forest virus, a Yellow fever, and a West Nile virus. 41. The method of claim 36, wherein the rickettsia or virus comprises an Influenza virus, a Measles virus, a Mumps virus, a Newcastle disease virus, a Coxsackie virus, an Echoviruses, a Poliomyelitis virus, a Herpesvirus hominis, a Cytomegalovirus, an Epstein-Barr virus, a Caliciviruses, a Pseudo-rabies virus, a Varicella virus, a Respiratory syncytial virus, a Subsclerosing panencephalitis virus, a Variola virus, a Cowpox virus, a Molluscum contagiosum virus, a Monkeypox virus, an Orf virus, a Paravaccinia virus, a Tanapox virus, a Vaccinia virus, a Yabapox virus, an SV 40 virus, a B-K-virus, Creutzfeld-Jacob agent, Kuru agent, BSE, a Rabies virus, a Rubella virus, R. mooseri, a LCM virus, a Junin virus, a Lassa virus, a Marchupo virus, a Guanarito virus, a hantavirus, a Rift Valley Fever virus, a Dengue virus, an Ebola virus, or a Marburg virus. 42. The method of claim 34, wherein the microbe comprises a Variola Virus, a Congo-Crimean hemorrhagic fever virus, a Tick-borne encephalitis virus complex, a Marburg virus, an Ebola virus, a Junin virus, a Lassa virus, a Machupo virus, a Herpesvirus simiae, a Bluetongue virus, a Louping III virus, a Rift Valley fever virus, a Wesselsbron virus, a Foot and Mouth Disease virus, a Newcastle Disease virus, an African Swine Fever virus, a Vesicular exanthema virus, a Swine vesicular disease virus, a Rinderpest virus, an African horse sickness virus, an Avian influenza virus, a Sheep pox virus. 43. The method of claim 1, wherein the test ligand comprises drug of abuse, peptide, polypeptide, oligonucleotide, polynucleotide, microbe, or mixture thereof 44. The method of claim 1, wherein the test ligand comprises isomer, conformation of protein, or proteome. 45. The method of claim 1, wherein the test ligand comprises a cell. 46. The method of claim 45 wherein the cell comprises a hapatocyte. 47. The method of claim 1, wherein the test ligand comprises an oligosaccharide or polysaccharide. 48. The method of claim 1, wherein the support comprises a dish, a tube, a well, a bead, a chromatography support, or a microchannel. 49. A method of producing a working artificial receptor, the method comprising: providing a plurality of candidate artificial receptors; the plurality of candidate artificial receptors independently comprising: at least 6 structural characteristics selected from the group consisting of positive charge, negative charge, acid, base, electron acceptor, electron donor, hydrogen bond donor, hydrogen bond acceptor, free electron pair, .pi. electrons, charge polarization, hydrophilicity, and hydrophobicity; a region on a solid support comprising 2, 3, 4, 5, or 6 different building block molecules; each of the building block molecules being independently covalently coupled to the region; a plurality of adjacent building block molecules forming a binding site; the region being a contiguous portion of the surface of the solid support with the different building block molecules distributed randomly throughout the contiguous region; contacting one or more candidate artificial receptors with a test ligand; identifying one or more artificial receptors that bind the test ligand as one or more working artificial receptors; selecting one or more of the working artificial receptors for use on an affinity support for binding the test ligand; wherein: each of the building block molecules comprises a framework and n recognition elements and is independently of the formula: framework-(recognition element).sub.n in which: n=1, 2, or 3; each recognition element is independently covalently coupled to the framework; and the framework comprises a functional group effective for covalent coupling to a support or a linker; the framework is alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, or heteroaryl alkyl; substituted with 1 to 4 functional groups; the functional groups independently being carboxyl, amine, hydroxyl, phenol, carbonyl, or thiol; each recognition element is independently a 1-12 carbon alkyl, substituted alkyl, cycloalkyl, heterocyclic, substituted heterocyclic, aryl alkyl, aryl, heteroaryl, or heteroaryl alkyl moiety; substituted with a group with a property of positive charge, negative charge, acid, base, electron acceptor, electron donor, hydrogen bond donor, hydrogen bond acceptor, free electron pair, .pi. electrons, charge polarization, hydrophilicity, or hydrophobicity; and when the building block molecule comprises an amino acid derivative, wherein amino acid derivatives are defined as a core feature having the chemical structure --NH--C--C(O)--, the building block molecule comprises a single derivatized amino acid and the framework is the amino acid derivative. 50. The method of claim 49, further comprising producing the affinity support comprising the one or more selected working artificial receptors. 51. The method of claim 49, wherein the affinity support comprises a chromatography support, a filtration membrane, or an electrophoresis medium. 52. The method of claim 41, wherein the affinity support comprises a chromatography support. 53. The method of claim 49, wherein the support comprises a dish, a tube, a well, a bead, a chromatography support, or a microchannel.

Details for Patent 7,960,311

Applicant	Tradename	Biologic Ingredient	Dosage Form	BLA	Approval Date	Patent No.	Expiredate
Emergent Biodefense Operations Lansing Llc	BIOTHRAX	anthrax vaccine adsorbed	Injection	103821	11/12/1998		2023-02-19