Kras-specific capture agents, compositions, and methods of making and using

Abstract

Disclosed are compounds, compositions, and methods involving cyclic peptides that can bind to KRAS (G12D) oncogenic protein. For example, disclosed are cyclic peptides that selectively bind KRAS (G12D) oncogenic protein. Also disclosed are methods of inhibiting KRAS (G12D) oncogenic protein in a cancer cell expressing KRAS (G12D) oncogenic protein. In some forms, the method comprises incubating the cancer cell with any one or more of the disclosed cyclic peptides. In some forms, the method comprises bringing into contact the cancer cell with any one or more of the disclosed cyclic peptides.

1 . A method of identifying, detecting, and/or quantifying KRAS (G12D) in a biological sample or in a subject, the method comprising bringing into contact the sample or the subject and a cyclic peptide that selectively binds KRAS (G12D) oncogenic protein, wherein binding of the cyclic peptide to KRAS (G12D) in the sample or in the subject facilitates identifying, detecting, and/or quantifying KRAS (G12D) in the sample or in the subject,
 wherein the cyclic peptide is represented by Formula I:   
       
         
           
           
               
               
           
         
         wherein: 
         Z1 and Z2 are each independently absent, aminoazidobutanoic acid (Az2), azidoornithine (OrnN3), L-azidolysine (Az4), or L-propargylglycine (Pra); 
         V1 is Q or L, V2 is Q or R, V3 is guanidinophenylalanine (Gnf) or G, V4 is absent or D, V5 is Gnf or bromophenylalanine (F-Br); 
         L is a linker; and 
         B m  is an optional group, wherein m is 0 or 1. 
       
     
     
         2 . The method of  claim 1 , wherein V1-V2-V3-V4-V5 is the sequence QQGnfGnf (SEQ ID NO:3), LRGGnf (SEQ ID NO:4), LRGDGnf (SEQ ID NO:5), LRGF-Br (SEQ ID NO:6), LQGnfGnf (SEQ ID NO:7), QRGnfGnf (SEQ ID NO:8), QQGGnf (SEQ ID NO:9), QQGnfF-Br (SEQ ID NO:10), QRGGnf (SEQ ID NO:11), LQGGnf (SEQ ID NO:12), LRGnfGnf (SEQ ID NO:13), QQGDGnf (SEQ ID NO:15), QRGDGnf (SEQ ID NO:16), LQGDGnf (SEQ ID NO:17), LRGnfDGnf (SEQ ID NO:18), LRGDF-Br (SEQ ID NO:19), QQGF-Br (SEQ ID NO:20), QRGF-Br (SEQ ID NO:21), LQGF-Br (SEQ ID NO:22), or LRGnfF-Br (SEQ ID NO:23). 
     
     
         3 . The method of  claim 1 , wherein Z1 and Z2 are both absent. 
     
     
         4 . The method of  claim 1 , wherein when Z1 is Az2, OrnN3, Az4, or Pra, Z2 is absent and when Z2 is Az2, OrnN3, Az4, or Pra, Z2 is absent. 
     
     
         5 . The method of  claim 1 , wherein Z1 is absent and Z2 is Az2. 
     
     
         6 . The method of  claim 1 , wherein Z1 is Pra and Z2 is Az2. 
     
     
         7 . The method of  claim 1 , wherein Z1 is absent and Z2 is OrnN3. 
     
     
         8 . The method of  claim 1 , wherein Z1 is Pra and Z2 is OrnN3. 
     
     
         9 . The method of  claim 1 , wherein Z1 is absent and Z2 is Az4. 
     
     
         10 . The method of  claim 1 , wherein Z1 is Pra and Z2 is Az4. 
     
     
         11 . The method of  claim 1 , wherein Z1 is Az2 and Z2 is absent. 
     
     
         12 . The method of  claim 1 , wherein Z1 is Az2 and Z2 is Pra. 
     
     
         13 . The method of  claim 1 , wherein Z1 is OrnN3 and Z2 is absent. 
     
     
         14 . The method of  claim 1 , wherein Z1 is OrnN3 and Z2 is Pra. 
     
     
         15 . The method of  claim 1 , wherein Z1 is Az4 and Z2 is absent. 
     
     
         16 . The method of  claim 1 , wherein Z1 is Az4 and Z2 is Pra. 
     
     
         17 . The method of  claim 1 , wherein L is 1,4-triazole or 1,5-triazole. 
     
     
         18 . The method of  claim 1 , wherein L is 1,4-substituted-1,2,3-triazole (Tz4) or a 1,5-substituted-1,2,3-triazole (Tz5). 
     
     
         19 . The method of  claim 18 , wherein L is 1,4-substituted-1,2,3-triazole residue (Tz4). 
     
     
         20 . The method of  claim 18 , wherein L is 1,5-substituted-1,2,3-triazole residue (Tz5). 
     
     
         21 . The method of  claim 1 , wherein when m is 1, B is a spacer group, a detection tag, or a combination of a spacer group and a detection tag. 
     
     
         22 . The method of  claim 21 , wherein the spacer group is polyethylene glycol (PEG) or 6-aminohexanoic acid (Ahx). 
     
     
         23 . The method of  claim 21 , wherein the detection tag is an affinity tag, a fluorescent tag, or a fluorescently labeled affinity tag. 
     
     
         24 . The method of  claim 21 , wherein the detection tag is selected from the group consisting of biotin, streptavidin, poly-histidine, poly-arginine, FLAG, cyclodextrin, adamantane, copper-DOTA, biotin-PEG3, aminooxyacetate,  19 FB,  18 FB, FITC-PEG 3 ,  64 Cu DOTA,  68 Ga DOTA,  68 Ga NOTA,  18 F, Al 18 F NOTA,  64 Cu,  68 Ga,  89 Zr,  124 I,  86 Y,  94m Tc,  110m In,  11 C,  76 Br, and combinations thereof. 
     
     
         25 . The method of  claim 21 , wherein the spacer group is PEG and the detection tag is biotin. 
     
     
         26 . The method of  claim 1 , wherein V1-V2-V3-V4-V5 is not the sequence LRGDGnf (SEQ ID NO:5) or LRGDF-Br. 
     
     
         27 . The method of  claim 1 , wherein V1-V2-V3-V4-V5 is not the sequence LRGDGnf (SEQ ID NO:5), LRGDF-Br (SEQ ID NO:19), NDETY (SEQ ID NO:25), PSEEG (SEQ ID NO:26), SEEGG (SEQ ID NO:27), EGTGT (SEQ ID NO:28), YEQGE (SEQ ID NO:29), YGEQE (SEQ ID NO:30), LRGDR (SEQ ID NO:31), QEKPP (SEQ ID NO:32), ELTFG (SEQ ID NO:33), VRGDR (SEQ ID NO:34), LRGPR (SEQ ID NO:35), LRGER (SEQ ID NO:36), L(homoR)GDR (SEQ ID NO:37), LRGD(homoR) (SEQ ID NO:38), LGnfGDR (SEQ ID NO:41), LRGAGnf (SEQ ID NO:42), LRGNR (SEQ ID NO:43), LRGQR (SEQ ID NO:44), or LRGAR (SEQ ID NO:45). 
     
     
         28 - 30 . (canceled) 
     
     
         31 . The method of  claim 1 , wherein the identifying, detecting, and/or quantifying KRAS (G12D) in the sample or in the subject involves an assay analogous to an immunoassay with the cyclic peptide replacing the antibody or its equivalent in the immunoassay. 
     
     
         32 . The method of  claim 31 , wherein the immunoassay is a Western blot, pull-down assay, dot blot, or ELISA. 
     
     
         33 . The method of  claim 31 , wherein the sample is a biological sample, wherein the biological sample is be selected from the group consisting of organs, tissue, bodily fluids, and cells. 
     
     
         34 . The method of  claim 33 , wherein the biological sample is a bodily fluid, wherein the fluid is selected from the group consisting of blood, serum, plasma, urine, sputum, saliva, stool, spinal fluid, cerebral spinal fluid, lymph fluid, skin secretions, respiratory secretions, intestinal secretions, genitourinary tract secretions, tears, and milk. 
     
     
         35 . The method of  claim 33 , wherein the organ is selected form the group consisting of adrenal glands, bladder, bones, brain, breasts, cervix, esophagus, eyes, gall bladder, genitals, heart, kidneys, large intestine, liver, lungs, lymph nodes, ovaries, pancreas, pituitary gland, prostate, salivary glands, skeletal muscles, skin, small intestine, spinal cord, spleen, stomach, thymus gland, trachea, thyroid, testes, ureters, and urethra. 
     
     
         36 . The method of  claim 33 , wherein the issue is selected from the group consisting of epithelial tissues, connective tissues, nervous system tissues, and muscle tissues.