Provided herein are methods, chemical library and simulation system for performing in situ patterned chemistry. Methods, systems and assays comprising the use of the synthesized chemical libraries, which increase explored protein space in a knowledge-based manner, are also provided for characterizing antibody-target interactions including: identifying target proteins of antibodies, characterizing antibody-binding regions in target proteins, identifying linear and structural epitopes in target proteins, and determining the propensity of antibody binding to target proteins.
G01N 33/68 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving proteins, peptides or amino acids
A61K 39/395 - AntibodiesImmunoglobulinsImmune serum, e.g. antilymphocytic serum
B01J 19/00 - Chemical, physical or physico-chemical processes in generalTheir relevant apparatus
C07K 16/32 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against translation products from oncogenes
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
2.
METHODS AND SYSTEMS FOR MASK ALIGNMENT IN MANUFACTURING PROCESS OF ARRAYS
Provided herein are molecules and salts thereof, arrays containing molecules and salts thereof, solid supports containing molecules and salts thereof, kits containing molecules or salts thereof, and methods of determining alignment of photolithographic masks comprising molecules or salts thereof.
C07D 233/02 - Heterocyclic compounds containing 1,3-diazole or hydrogenated 1,3-diazole rings, not condensed with other rings having no double bonds between ring members or between ring members and non-ring members
C07C 233/13 - Carboxylic acid amides having carbon atoms of carboxamide groups bound to hydrogen atoms or to acyclic carbon atoms having the nitrogen atom of at least one of the carboxamide groups bound to a carbon atom of a hydrocarbon radical substituted by halogen atoms or by nitro or nitroso groups with the substituted hydrocarbon radical bound to the nitrogen atom of the carboxamide group by an acyclic carbon atom
C07C 319/06 - Preparation of thiols, sulfides, hydropolysulfides or polysulfides of thiols from sulfides, hydropolysulfides or polysulfides
C07C 231/12 - Preparation of carboxylic acid amides by reactions not involving the formation of carboxamide groups
C07F 7/18 - Compounds having one or more C—Si linkages as well as one or more C—O—Si linkages
G03F 9/00 - Registration or positioning of originals, masks, frames, photographic sheets or textured or patterned surfaces, e.g. automatically
Molecules or salts thereof are provided, having the structure in Formula I,
Molecules or salts thereof are provided, having the structure in Formula I,
wherein n2 and n4 are the same or different and are independently 1, 2, or 3, and n3 is 1 to 20;
X is oxygen, nitrogen, or sulfur;
wherein R1, R2, R3, R4, R5, R6, and R7 are as described herein.
Molecules or salts thereof are provided, having the structure in Formula I,
wherein n2 and n4 are the same or different and are independently 1, 2, or 3, and n3 is 1 to 20;
X is oxygen, nitrogen, or sulfur;
wherein R1, R2, R3, R4, R5, R6, and R7 are as described herein.
Methods are also provided for the synthesis of and use of the provided molecules in applications for diagnostic testing.
C09D 183/08 - Polysiloxanes containing silicon bound to organic groups containing atoms other than carbon, hydrogen, and oxygen
B05D 1/00 - Processes for applying liquids or other fluent materials
C07F 7/08 - Compounds having one or more C—Si linkages
C08F 30/08 - Homopolymers or copolymers of compounds having one or more unsaturated aliphatic radicals, each having only one carbon-to-carbon double bond, and containing phosphorus, selenium, tellurium or a metal containing a metal containing silicon
C08G 77/26 - Polysiloxanes containing silicon bound to organic groups containing atoms other than carbon, hydrogen, and oxygen nitrogen-containing groups
C09D 143/04 - Homopolymers or copolymers of monomers containing silicon
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
C08G 65/336 - Polymers modified by chemical after-treatment with organic compounds containing silicon
C07F 7/18 - Compounds having one or more C—Si linkages as well as one or more C—O—Si linkages
4.
METHODS OF SELECTING FUNCTIONAL INTERFACE MIMICS, AND COMPOSITIONS THEREOF
Provided herein are functional interface mimics (FIMs), which mimic a functional interface of an interface protein. The FIMs comprise at least one peptide and at least one linking moiety, such as a linker or a cross-link. In some embodiments, the FIMs comprise at least two peptides connected by at least one linker. In some embodiments, the FIM is an immunogen. Also provided herein are methods of selected an FIM, and methods of producing an antibody using an FIM.
Provided herein are in situ generated conformationally constrained peptide arrays, methods for synthesizing such arrays, and methods, systems and assays comprising the use of the synthesized constrained peptide arrays for characterizing protein-target Interactions including: antibody-target interactions, receptor agonist interactions, receptor antagonist interactions, enzyme substrate interactions, enzyme inhibitor interactions, and other protein-protein interactions.
Provided herein are methods, assays and devices for the differential diagnosis and detection of disease progression of autoimmune diseases. The methods, assays and devices provided herein produce and analyze binding patterns of peripheral-blood antibodies on mimetic peptide arrays that differentiate autoimmune diseases, and identify patients progressing to internal organ complications such as interstitial lung disease (ILD), and gastric antral vascular ectasia (GAVE), or renal involvement.
The disclosed embodiments concern methods, devices, and systems for identifying candidate biomarkers useful for the diagnosis, prognosis, monitoring and screening and/or as targets for the treatment of diseases and conditions in subjects, in particular autoimmune and infectious diseases. The identification of candidate biomarkers is predicated on identifying discriminating peptides present on a peptide array, which can distinguish samples from different subjects having different health conditions by the binding patterns of antibodies present in the samples.
The disclosed embodiments concern methods, apparatus, and systems for providing differential diagnosis of autoimmune diseases including, Systemic Lupus Erythematosus (SLE) and Rheumatoid Arthritis (RA). The disclosed embodiments provide for differentially diagnosing autoimmune diseases from each other, from other autoimmune diseases, and from mimic disease conditions that are not classified as autoimmune, but that present with symptoms that are often associated with the autoimmune diseases.
G01N 33/564 - ImmunoassayBiospecific binding assayMaterials therefor for pre-existing immune complex or autoimmune disease
C07K 14/47 - Peptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from animalsPeptides having more than 20 amino acidsGastrinsSomatostatinsMelanotropinsDerivatives thereof from humans from vertebrates from mammals
C07C 323/67 - Thiols, sulfides, hydropolysulfides or polysulfides substituted by halogen, oxygen or nitrogen atoms, or by sulfur atoms not being part of thio groups containing thio groups and sulfur atoms, not being part of thio groups, bound to the same carbon skeleton containing sulfur atoms of sulfonamide groups, bound to the carbon skeleton
A61P 1/04 - Drugs for disorders of the alimentary tract or the digestive system for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants
A61P 19/02 - Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
A61P 29/00 - Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agentsNon-steroidal antiinflammatory drugs [NSAID]
A61P 31/00 - Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
C09D 183/08 - Polysiloxanes containing silicon bound to organic groups containing atoms other than carbon, hydrogen, and oxygen
B05D 1/00 - Processes for applying liquids or other fluent materials
C07F 7/08 - Compounds having one or more C—Si linkages
C08F 30/08 - Homopolymers or copolymers of compounds having one or more unsaturated aliphatic radicals, each having only one carbon-to-carbon double bond, and containing phosphorus, selenium, tellurium or a metal containing a metal containing silicon
C08G 77/26 - Polysiloxanes containing silicon bound to organic groups containing atoms other than carbon, hydrogen, and oxygen nitrogen-containing groups
C09D 143/04 - Homopolymers or copolymers of monomers containing silicon
G01N 33/543 - ImmunoassayBiospecific binding assayMaterials therefor with an insoluble carrier for immobilising immunochemicals
C08G 65/336 - Polymers modified by chemical after-treatment with organic compounds containing silicon
C07F 7/18 - Compounds having one or more C—Si linkages as well as one or more C—O—Si linkages
11.
Methods for diagnosis and treatment of autoimmune diseases
Provided herein are methods, assays and devices for the detection and diagnosis of autoimmune diseases, including systemic lupus erythematosus. The methods, assays and devices provided herein analyzes binding patterns of peripheral-blood antibodies on peptide array that correlates well with current systemic lupus erythematosus clinical assessment standards.
Provided herein are molecules and salts thereof, arrays containing molecules and salts thereof, solid supports containing molecules and salts thereof, kits containing molecules or salts thereof, and methods of determining alignment of photolithographic masks comprising molecules or salts thereof.
C07D 233/02 - Heterocyclic compounds containing 1,3-diazole or hydrogenated 1,3-diazole rings, not condensed with other rings having no double bonds between ring members or between ring members and non-ring members
C07C 233/13 - Carboxylic acid amides having carbon atoms of carboxamide groups bound to hydrogen atoms or to acyclic carbon atoms having the nitrogen atom of at least one of the carboxamide groups bound to a carbon atom of a hydrocarbon radical substituted by halogen atoms or by nitro or nitroso groups with the substituted hydrocarbon radical bound to the nitrogen atom of the carboxamide group by an acyclic carbon atom
C07F 7/18 - Compounds having one or more C—Si linkages as well as one or more C—O—Si linkages
G03F 9/00 - Registration or positioning of originals, masks, frames, photographic sheets or textured or patterned surfaces, e.g. automatically
C07C 319/06 - Preparation of thiols, sulfides, hydropolysulfides or polysulfides of thiols from sulfides, hydropolysulfides or polysulfides
C07C 231/12 - Preparation of carboxylic acid amides by reactions not involving the formation of carboxamide groups
patents