Polypeptide targeting aptamers for characterization, capture, and clinical management of circulating tumor cells

Abstract

Provided herein are new compositions and methods to target and deliver agents to pathological areas by utilizing multifunctional compounds. These compounds include three or more domains: (i) a vimentin-binding peptide, (ii) a linker, and (iii) a drug binding, a capturing reagent, or a detectable moiety. These compounds can be used to detect, isolate, and/or treat cancerous cells such as circulating tumor cells.

1 . A compound comprising:
 a first domain comprising a vimentin-binding peptide;   a second domain comprising a linker; and   a third domain selected from the group consisting of a detectable moiety, a capture reagent, and a drug binding domain, wherein the linker links the first domain and the third domain.   
     
     
         2 - 33 . (canceled) 
     
     
         34 . A compound comprising a sequence selected from the group consisting of: 
       
         
           
                 
               
                   (SEQ ID NO: 1) 
                 
                   acetyl- VNTANSTGGSGK(FITC)-amide; 
                 
                     
                 
                   (SEQ ID NO: 2) 
                 
                   acetyl- VNTANSTGGSGGVNTANSTGGSGK(FITC)-amide; 
                 
                     
                 
                   (SEQ ID NO: 3) 
                 
                   acetyl- VNTANSTGGSGK(Biotin)-amide; 
                 
                     
                 
                   (SEQ ID NO: 4) 
                 
                   acetyl- SAHGTSTGVPWPGGSGK(FITC)-amide; 
                 
                     
                 
                   (SEQ ID NO: 5) 
                 
                   acetyl- SAHGTSTGVPWPGGSGK(Biotin)-amide; 
                 
                     
                 
                   (SEQ ID NO: 6) 
                 
                   Biotin-Ahx)- SAHGTSTGVPWPGGS-amide; 
                 
                     
                 
                   (SEQ ID NO: 7) 
                 
                   acetyl - VNTANSTGGSGARRGVRVAWREPGRMELNMPHGGSGK 
                 
                     
                 
                   (FITC)-amide; 
                 
                     
                 
                   (SEQ ID NO: 8) 
                 
                   acetyl - VNTANSTGGSGARRGVRVAWREPGRMELNMPHGGSGK 
                 
                     
                 
                   (Biotin)-amide; 
                 
                     
                 
                   (SEQ ID NO: 9) 
                 
                   acetyl - STRSVSSSSYRRMFGGPGTASK(FITC) -amide; 
                 
                     
                 
                   (SEQ ID NO: 10) 
                 
                   acetyl - STRSVSSSSYRRMFGGPGTASK(Biotin) -amide; 
                 
                     
                 
                   (SEQ ID NO: 11) 
                 
                   acetyl - KMALDIEIATYRKLLEGEESRISGSGK(FITC) -amide; 
                 
                     
                 
                   (SEQ ID NO: 12) 
                 
                   acetyl - KMALDIEIATYRKLLEGEESRISGSGK(Biotin) - 
                 
                     
                 
                   amide; 
                 
                     
                 
                   (SEQ ID NO: 13) 
                 
                   acetyl - RRGVRVAWREPGRMELNIVIPHGGSGK(Biotin)- 
                 
                     
                 
                   amide; 
                 
                     
                 
                   (SEQ ID NO: 14) 
                 
                   acetyl - KVRFLEQQNKILLAELEQLKGQGK(FITC) -amide; 
                 
                     
                 
                   (SEQ ID NO: 15) 
                 
                   acetyl- KVRFLEQQNKILLAELEQLKGQGK(Biotin); 
                 
                     
                 
                   (SEQ ID NO: 16) 
                 
                   acetyl- RPKRNDGVVVPRLLDITLRAYDNRKSGK(FITC) -amide; 
                 
                     
                 
                   (SEQ ID NO: 53) 
                 
                   acetyl- RPKRNDGVVVPRLLDITLRAYDNRKSGK(Biotin) - 
                 
                     
                 
                   amide; 
                 
                     
                 
                   (SEQ ID NO: 17) 
                 
                   acetyl- TRKRIRIQRGPGRAFVTIGGK(FITC) -amide; 
                 
                     
                 
                   (SEQ ID NO: 54) 
                 
                   acetyl- TRKRIRIQRGPGRAFVTIGGK(Biotin) - amide; 
                 
                     
                 
                   (SEQ ID NO: 18) 
                 
                   acetyl- TRKSIHIGPGRAFYTTGGK(FITC)-amide; 
                 
                     
                 
                   (SEQ ID NO: 55) 
                 
                   acetyl- TRKSIHIGPGRAFYTTGGK(Biotin)-amide; 
                 
                     
                 
                   (SEQ ID NO: 19) 
                 
                   acetyl- RRGVHVGWREPSFMALSMPHGGSGK(FITC)-amide; 
                 
                     
                 
                   (SEQ ID NO: 20) 
                 
                   acetyl- RRGVRVAWREPGRMELNMPHGGSGK(FITC) -amide; 
                 
                     
                 
                   (SEQ ID NO: 21) 
                 
                   acetyl- RRGVRVAWREPGRMELNMPHGGSGK(Biotin)-amide; 
                 
                     
                 
                   (SEQ ID NO: 49) 
                 
                   (FITC-Ahx)AGKKPRVTVTNVFLYNRPLNSTE -free acid; 
                 
                     
                 
                   (SEQ ID NO: 50) 
                 
                   (Biotin-Ahx)AGKKPRVTVTNVFLYNRPLNSTE -free acid; 
                 
                     
                 
                   (SEQ ID NO: 51) 
                 
                   (FITC-Ahx)AGKKPSVTVTNVFLYNRPLNSTE -free acid; 
                 
                   and 
                 
                     
                 
                   (SEQ ID NO: 52) 
                 
                   (Biotin-Ahx)AGKKPSVTVTNVFLYNRPLNSTE -free acid. 
                 
             
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
                
               
            
           
         
       
     
     
         35 - 37 . (canceled) 
     
     
         38 . A method of detecting cancer, a tumor, or circulating tumor cells (CTSs) in a sample, the method comprising:
 contacting the sample with a compound, wherein the compound comprises (i) a first domain comprising a vimentin-binding peptide; (ii) a second domain comprising a linker; and (iii) a third domain comprising a detectable moiety; and   detecting the compound, to thereby detect cancer, a tumor, or circulating tumor cells CTCs) in the sample.   
     
     
         39 - 46 . (canceled) 
     
     
         47 . A method of diagnosing cancer in a subject, the method comprising:
 contacting a sample with a compound, wherein the compound comprises:
 a first domain comprising a vimentin-binding peptide; 
 a second domain comprising a linker; and 
 a third domain comprising a detectable moiety; 
   detecting the compound in the sample; and   diagnosing the subject as having cancer when the levels of the compound in the sample are increased when compared to a reference sample.   
     
     
         48 . A method of determining the stage of a cancer, the method comprising:
 contacting a sample with a compound, wherein the compound comprises:
 a first domain comprising a vimentin-binding peptide; 
 a second domain comprising a linker; and 
 a third domain comprising a detectable moiety; 
   detecting the compound in the sample;   comparing the levels of the compound to those of a reference sample; and   determining the stage of the cancer based on the comparison to the reference sample.   
     
     
         49 . A method of determining the efficacy of a cancer treatment, the method comprising:
 detecting levels of CTCs in a first sample taken from a subject before administering the cancer treatment, wherein detecting comprises contacting the first sample with a compound and detecting the compound, wherein the compound comprises: (i) a first domain comprising a vimentin-binding peptide; (ii) a second domain comprising a linker; and (iii) a third domain comprising a detectable moiety;   detecting levels of CTCs in a second sample taken from the subject after administering the cancer treatment, wherein detecting comprises contacting the second sample with the compound and detecting the compound; and   determining the efficacy of the cancer treatment by comparison of the levels of CTCs in the first and second samples.   
     
     
         50 - 62 . (canceled) 
     
     
         63 . A method of diagnosing and/or treating a viral infection gf white blood cells in a sample, the method comprising:
 contacting a sample with a compound, wherein the compound comprises:
 a first domain comprising a vimentin-binding peptide; 
 a second domain comprising a linker; and 
 a third domain comprising a detectable moiety; 
   detecting the compound in the sample; and   diagnosing the sample as having a viral infection when the level of compound in the sample is increased as compared to a reference level.   
     
     
         64 - 66 . (canceled) 
     
     
         67 . A method of isolating CTCs from a sample, the method comprising:
 contacting the sample with a compound, wherein the compound comprises: (i) a first domain comprising a vimentin-binding peptide; (ii) a second domain comprising a linker; and (iii) a third domain comprising a capture reagent, thereby forming a mixture; and   contacting the mixture with an immobilizing agent, wherein the immobilizing agent binds to the capture reagent; thereby isolating the CTCs from the sample.   
     
     
         68 - 86 . (canceled) 
     
     
         87 . A method of removing CTCs from a subject's blood, the method comprising:
 contacting the subject's blood to a solid support comprising one of the following immobilized thereon:   (a) a vimentin-binding peptide; or   (b) a compound, wherein the compound comprises a vimentin-binding peptide linked to a capture reagent, and wherein the capture reagent is immobilized on the solid support; to thereby remove CTCs from the subject's blood.   
     
     
         88 - 95 . (canceled)