Compositions Containing a Pharmacophore with Selectivity to Diseased Tissue and Methods of Making Same

Abstract

Compositions and methods useful for delivery of targeted therapies for pulmonary arterial hypertension, sepsis, cancer and cachexia. The compositions and methods are based on peptide pharmacophores that selectively bind to and home to diseased tissue and enable targeted therapies to affect a beneficial therapeutic result. Peptide pharmacophores may selectively target tumor vasculature, regenerating tissue, wounded tissue, inflamed tissue, fibrotic tissue, remodeled tissue, tissue characterized by elevated heparanase levels, and have the ability to internalize into such diseased cells.

We claim: 
     
         1 . A method of identifying a pharmacophore of at least one therapeutically active molecule, the method comprising:
 a) performing permutations on the at least one therapeutically active molecule in order to synthesize analogues of the molecule;   b) performing cell binding and internalization assays for the therapeutically active molecule and synthesized analogues;   c) identifying any residues and sequence patterns from step b) which requires conservation for the molecule to retain therapeutic activity;   d) performing in silico modeling of the therapeutically active molecule and analogues in order to create a small compound library and further identify the conserved molecular features of the pharmacophore;   e) superimposing the analogue models onto the therapeutically active molecule model; and   f) analyzing the superimposed analogues for conserved structural patterns.   
     
     
         2 . The method of  claim 1 , wherein the at least one therapeutic molecule conveys a measurable therapeutic benefit to a disease by selectively target tumor vasculature, regenerating tissue, wounded tissue, inflamed tissue, fibrotic tissue, remodeled tissue, injured endothelium, tissue characterized by elevated heparanase levels, and has the ability to internalize into such diseased cells. 
     
     
         3 . The method of  claim 2 , wherein the disease is selected from the group consisting of pulmonary diseases, pulmonary hypertension, interstitial lung disease, acute lung injury, acute respiratory distress syndrome, asthma, sepsis, septic shock, infection, sarcoidosis of the lung, pulmonary manifestations of connective tissue diseases, including systemic lupus erythematosus, rheumatoid arthritis, scleroderma, and polymyositis, dennatomyositis, bronchiectasis, asbestosis, berylliosis, silicosis, Histiocytosis X, pneumonia, pneumotitis, smoker's lung, bronchiolitis obliterans, pulmonary fibrosis, other fibrotic diseases such as myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis, myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis, pneumoconiosis, nephrogenic systemic fibrosis, scar formation, keloid, arthrofibrosis, adhesive capsulitis, radiation fibrosis, fibrocystic breast condition, liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liver disease, acute liver failure, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes, or other organs; inflammatory bowel disease, Crohn's disease, cachexia, chronic kidney disease, acute kidney injury, acute renal failure, polycystic kidney disease, ulcerative colitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis, chronic obstructive pulmonary disease, atherosclerosis, ischemic heart disease, vasculitis, neoplastic/metastatic/oncological diseases (including cancer), pneumoconiosis, autoimmune diseases, angiogenic diseases, wound healing, infections, trauma injuries and systemic connective tissue diseases including systemic lupus erythematosus, rheumatoid arthritis scleroderma, polymyositis, dermatomyositis, cystic fibrosis, erectile dysfunction, α1-antitrypsin deficiency, diabetes, diseases characterized by high heparanase levels, neuroinflammatory conditions, stroke, CNS degenerative diseases, such as Alzheimer's Disease, Parkinson's disease (PD), Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, traumatic brain injury, hypoxia, aging brain, wet macular degeneration, neovascular age-related macular degeneration, diabetic retinopathy, glioblastoma, and senescence-related diseases. 
     
     
         4 . The method of  claim 3 , wherein the disease is selected from the group consisting of pulmonary arterial hypertension, sepsis, kidney disease, cancer and cachexia. 
     
     
         5 . A method of treating an individual suffering from a disease, the method comprising:
 a) providing a targeting peptide comprising a sequence substantially identical to a CAR pharmacophore, the sequence selected from the group consisting of SEQ ID NO:16-SEQ ID NO:33, or a variant thereof;   (b) providing at least one therapeutic molecule which conveys a measureable therapeutic benefit to a disease selected from the group consisting of pulmonary diseases, pulmonary hypertension, interstitial lung disease, acute lung injury, acute respiratory distress syndrome, asthma, sepsis, septic shock, infection, sarcoidosis of the lung, pulmonary manifestations of connective tissue diseases, including systemic lupus erythematosus, rheumatoid arthritis, scleroderma, and polymyositis, dennatomyositis, bronchiectasis, asbestosis, berylliosis, silicosis, Histiocytosis X, pneumonia, pneumotitis, smoker's lung, bronchiolitis obliterans, pulmonary fibrosis, other fibrotic diseases such as myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis, myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis, pneumoconiosis, nephrogenic systemic fibrosis, scar formation, keloid, arthrofibrosis, adhesive capsulitis, radiation fibrosis, fibrocystic breast condition, liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liver disease, acute liver failure, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes, or other organs; inflammatory bowel disease, Crohn's disease, cachexia, chronic kidney disease, acute kidney injury, acute renal failure, polycystic kidney disease, ulcerative colitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis, chronic obstructive pulmonary disease, atherosclerosis, ischemic heart disease, vasculitis, neoplastic/metastatic/oncological diseases (including cancer), pneumoconiosis, autoimmune diseases, angiogenic diseases, wound healing, infections, trauma injuries and systemic connective tissue diseases including systemic lupus erythematosus, rheumatoid arthritis scleroderma, polymyositis, dermatomyositis, cystic fibrosis, erectile dysfunction, α1-antitrypsin deficiency, diabetes, diseases characterized by high heparanase levels, neuroinflammatory conditions, stroke, CNS degenerative diseases, such as Alzheimer's Disease, Parkinson's disease (PD), Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, traumatic brain injury, hypoxia, aging brain, wet macular degeneration, neovascular age-related macular degeneration, diabetic retinopathy, glioblastoma, and senescence-related diseases;   c) co-administering a composition comprising a) and b) to an individual in need thereof; and   d) measuring a therapeutic benefit to the individual.   
     
     
         6 . The method of  claim 5 , wherein the composition is co-administered orally, parenterally, by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, or topically. 
     
     
         7 . The method of  claim 5 , wherein the disease is selected from the group consisting of pulmonary arterial hypertension, sepsis, kidney disease, cancer and cachexia. 
     
     
         8 . The method of  claim 5 , wherein the at least one therapeutic molecule is selected from the group consisting of imatinib, sivelestat, paclitaxel, antithrombin III, hydrocortisone. 
     
     
         9 . A conjugate for treating an individual suffering from a disease, wherein the peptide is comprised of:
 a) at least one peptide containing an amino acid segment with the sequence of SEQ ID NOs: 1-8, 12, and 16-33, related amino acid sequences, or the CAR pharmacophore; and   b) a moiety linked to the peptide of a).   
     
     
         10 . The conjugate of  claim 9 , wherein the amino acid sequence contains one or more conservative amino acid substitutions. 
     
     
         11 . The conjugate of  claim 9 , wherein the moiety is selected from the group consisting of an anti-angiogenic agent, a pro-angiogenic agent, a cancer chemotherapeutic agent, a cytotoxic agent, an anti-inflammatory agent, an anti-arthritic agent, a polypeptide, a nucleic acid molecule, a small molecule, a fluorophore, fluorescein, rhodamine, a radionuclide, indium-111, technetium-99, carbon-11, carbon-13, or a combination. The moiety can be a therapeutic agent, a detectable agent, a virus, or a phage. 
     
     
         12 . The conjugate of  claim 9 , wherein the disease is selected from the group consisting of pulmonary diseases, pulmonary hypertension, interstitial lung disease, acute lung injury, acute respiratory distress syndrome, asthma, sepsis, septic shock, infection, sarcoidosis of the lung, pulmonary manifestations of connective tissue diseases, including systemic lupus erythematosus, rheumatoid arthritis, scleroderma, and polymyositis, dennatomyositis, bronchiectasis, asbestosis, berylliosis, silicosis, Histiocytosis X, pneumonia, pneumotitis, smoker's lung, bronchiolitis obliterans, pulmonary fibrosis, other fibrotic diseases such as myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis, myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis, pneumoconiosis, nephrogenic systemic fibrosis, scar formation, keloid, arthrofibrosis, adhesive capsulitis, radiation fibrosis, fibrocystic breast condition, liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liver disease, acute liver failure, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes, or other organs; inflammatory bowel disease, Crohn's disease, cachexia, chronic kidney disease, acute kidney injury, acute renal failure, polycystic kidney disease, ulcerative colitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis, chronic obstructive pulmonary disease, atherosclerosis, ischemic heart disease, vasculitis, neoplastic/metastatic/oncological diseases (including cancer), pneumoconiosis, autoimmune diseases, angiogenic diseases, wound healing, infections, trauma injuries and systemic connective tissue diseases including systemic lupus erythematosus, rheumatoid arthritis scleroderma, polymyositis, dermatomyositis, cystic fibrosis, erectile dysfunction, α1-antitrypsin deficiency, diabetes, diseases characterized by high heparanase levels, neuroinflammatory conditions, stroke, CNS degenerative diseases, such as Alzheimer's Disease, Parkinson's disease (PD), Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, traumatic brain injury, hypoxia, aging brain, wet macular degeneration, neovascular age-related macular degeneration, diabetic retinopathy, glioblastoma, and senescence-related diseases. 
     
     
         13 . A conjugate for diagnosing an individual suffering from a disease, wherein the peptide is comprised of:
 a) at least one peptide containing an amino acid segment with the sequence of SEQ ID NOs: 1-8, 12, and 16-33, related amino acid sequences, or the CAR pharmacophore; and   b) a moiety linked to the peptide of a).   
     
     
         14 . The conjugate of  claim 13 , wherein the amino acid sequence contains one or more conservative amino acid substitutions. 
     
     
         15 . The conjugate of  claim 13 , wherein the moiety is selected from the group consisting of an anti-angiogenic agent, a pro-angiogenic agent, a cancer chemotherapeutic agent, a cytotoxic agent, an anti-inflammatory agent, an anti-arthritic agent, a polypeptide, a nucleic acid molecule, a small molecule, a fluorophore, fluorescein, rhodamine, a radionuclide, gadolinium, iron oxide, iodine containing contrast medium, barium sulfate, gallium, 18F-fluorodeoxyglucose. Cupryrnina, 3′-deoxy-3′-[18]fluorothymidine, indium-111, technetium-99, carbon-11, carbon-13, a therapeutic agent, a detectable agent, a virus, or a phage. 
     
     
         16 . The conjugate of  claim 13 , wherein the disease is selected from the group consisting of pulmonary diseases, pulmonary hypertension, interstitial lung disease, acute lung injury, acute respiratory distress syndrome, asthma, sepsis, septic shock, infection, sarcoidosis of the lung, pulmonary manifestations of connective tissue diseases, including systemic lupus erythematosus, rheumatoid arthritis, scleroderma, and polymyositis, dennatomyositis, bronchiectasis, asbestosis, berylliosis, silicosis, Histiocytosis X, pneumonia, pneumotitis, smoker's lung, bronchiolitis obliterans, pulmonary fibrosis, other fibrotic diseases such as myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis, myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis, pneumoconiosis, nephrogenic systemic fibrosis, scar formation, keloid, arthrofibrosis, adhesive capsulitis, radiation fibrosis, fibrocystic breast condition, liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liver disease, acute liver failure, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes, or other organs; inflammatory bowel disease, Crohn's disease, cachexia, chronic kidney disease, acute kidney injury, acute renal failure, polycystic kidney disease, ulcerative colitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis, chronic obstructive pulmonary disease, atherosclerosis, ischemic heart disease, vasculitis, neoplastic/metastatic/oncological diseases (including cancer), pneumoconiosis, autoimmune diseases, angiogenic diseases, wound healing, infections, trauma injuries and systemic connective tissue diseases including systemic lupus erythematosus, rheumatoid arthritis scleroderma, polymyositis, dermatomyositis, cystic fibrosis, erectile dysfunction, α1-antitrypsin deficiency, diabetes, diseases characterized by high heparanase levels, neuroinflammatory conditions, stroke, CNS degenerative diseases, such as Alzheimer's Disease, Parkinson's disease (PD), Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, traumatic brain injury, hypoxia, aging brain, wet macular degeneration, neovascular age-related macular degeneration, diabetic retinopathy, glioblastoma, and senescence-related diseases. 
     
     
         17 . A pharmacophore for administration to an individual suffering from a disease, wherein the pharmacophore is comprised of a peptide containing an amino acid sequence selected from the group consisting of SEQ ID NOs: 1-8, 12, and 16-33. 
     
     
         18 . The pharmacophore of  claim 16 , wherein the pharmacophore is a therapeutic agent for a disease selected from the group consisting of pulmonary diseases, pulmonary hypertension, interstitial lung disease, acute lung injury, acute respiratory distress syndrome, asthma, sepsis, septic shock, infection, sarcoidosis of the lung, pulmonary manifestations of connective tissue diseases, including systemic lupus erythematosus, rheumatoid arthritis, scleroderma, and polymyositis, dennatomyositis, bronchiectasis, asbestosis, berylliosis, silicosis, Histiocytosis X, pneumonia, pneumotitis, smoker's lung, bronchiolitis obliterans, pulmonary fibrosis, other fibrotic diseases such as myocardial infarction, endomyocardial fibrosis, mediastinal fibrosis, myelofibrosis, retroperitoneal fibrosis, progressive massive fibrosis, pneumoconiosis, nephrogenic systemic fibrosis, scar formation, keloid, arthrofibrosis, adhesive capsulitis, radiation fibrosis, fibrocystic breast condition, liver cirrhosis, hepatitis, liver fibrosis, nonalcoholic fatty liver disease, acute liver failure, nonalcoholic steatohepatitis, sarcoidosis of the lymph nodes, or other organs; inflammatory bowel disease, Crohn's disease, cachexia, chronic kidney disease, acute kidney injury, acute renal failure, polycystic kidney disease, ulcerative colitis, primary biliary cirrhosis, pancreatitis, interstitial cystitis, chronic obstructive pulmonary disease, atherosclerosis, ischemic heart disease, vasculitis, neoplastic/metastatic/oncological diseases (including cancer), pneumoconiosis, autoimmune diseases, angiogenic diseases, wound healing, infections, trauma injuries and systemic connective tissue diseases including systemic lupus erythematosus, rheumatoid arthritis scleroderma, polymyositis, dermatomyositis, cystic fibrosis, erectile dysfunction, α1-antitrypsin deficiency, diabetes, diseases characterized by high heparanase levels, neuroinflammatory conditions, stroke, CNS degenerative diseases, such as Alzheimer's Disease, Parkinson's disease (PD), Huntington's disease, amyotrophic lateral sclerosis, multiple sclerosis, traumatic brain injury, hypoxia, aging brain, wet macular degeneration, neovascular age-related macular degeneration, diabetic retinopathy, glioblastoma, and senescence-related diseases. 
     
     
         19 . The pharmacophore of  claim 17 , wherein the disease is selected from the group consisting of pulmonary arterial hypertension, sepsis, kidney disease, cancer and cachexia. 
     
     
         20 . The pharmacophore of  claim 16 , wherein the pharmacophore selectively homes to tumor vasculature, regenerating tissue, wounded tissue, inflamed tissue, fibrotic tissue, remodeled tissue, injured endothelium, tissue characterized by elevated heparanase levels, and has the ability to internalize into such diseased cells.