Aptamer therapeutics advance

Current Opinion in Chemical Biology

Volumn 10, Issue 3, 2006, Pages 282-289

  Lee, Jennifer F ^a   Stovall, Gwendolyn M ^a   Ellington, Andrew D ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2' FLUOROPYRIMIDINE; 2' O METHYL RNA OLIGONUCLEOTIDE; ANTIDOTE; ANTIOBESITY AGENT; ANTITHROMBIN; APTAMER; ARC 183; GLYCOPROTEIN GP 120; HEMAGGLUTININ; LOCKED NUCLEIC ACID; OLIGONUCLEOTIDE; PEGAPTANIB; PYRIMIDINE DERIVATIVE; REG 1; SPIEGELMER; TENASCIN; UNCLASSIFIED DRUG; VASCULOTROPIN 165;

ANTIVIRAL ACTIVITY; BLEEDING; CAPILLARY ELECTROPHORESIS; CLINICAL TRIAL; CREUTZFELDT JAKOB DISEASE; DRUG DELIVERY SYSTEM; DRUG EFFICACY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; INFLUENZA; NONHUMAN; PRION DISEASE; RETINA MACULA DEGENERATION; REVIEW; VIRUS STRAIN;

ANIMALS; APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CLINICAL TRIALS; HUMANS;

ANIMALIA;

EID: 33744512608     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2006.03.015     Document Type: Review

References (73)

1. Ellington A.D., and Szostak J.W. In vitro selection of RNA molecules that bind specific ligands. Nature 346 (1990) 818-822
2. Tuerk C., and Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249 (1990) 505-510
3. Blank M., and Blind M. Aptamers as tools for target validation. Curr Opin Chem Biol 9 (2005) 336-342
4. Proske D., Blank M., Buhmann R., and Resch A. Aptamers-basic research, drug development, and clinical applications. Appl Microbiol Biotechnol 69 (2005) 367-374
5. Nimjee S.M., Rusconi C.P., and Sullenger B.A. Aptamers: an emerging class of therapeutics. Annu Rev Med 56 (2005) 555-583
6. Yan A.C., Bell K.M., Breeden M.M., and Ellington A.D. Aptamers: prospects in therapeutics and biomedicine. Front Biosci 10 (2005) 1802-1827
7. DeAnda Jr. A., Coutre S.E., Moon M.R., Vial C.M., Griffin L.C., Law V.S., Komeda M., Leung L.L., and Miller D.C. Pilot study of the efficacy of a thrombin inhibitor for use during cardiopulmonary bypass. Ann Thorac Surg 58 (1994) 344-350
8. Bless N.M., Smith D., Charlton J., Czermak B.J., Schmal H., Friedl H.P., and Ward P.A. Protective effects of an aptamer inhibitor of neutrophil elastase in lung inflammatory injury. Curr Biol 7 (1997) 877-880
9. Cunningham Jr. E.T., Adamis A.P., Altaweel M., Aiello L.P., Bressler N.M., D'Amico D.J., Goldbaum M., Guyer D.R., Katz B., Patel M., et al. A phase II randomized double-masked trial of pegaptanib, an anti-vascular endothelial growth factor aptamer, for diabetic macular edema. Ophthalmology 112 (2005) 1747-1757
10. Ng E.W., and Adamis A.P. Targeting angiogenesis, the underlying disorder in neovascular age-related macular degeneratio. Can J Ophthalmol 40 (2005) 352-368
11. Siddiqui M.A., and Keating G.M. Pegaptanib: in exudative age-related macular degeneration. Drugs 65 (2005) 1571-1577 discussion 1578-1579. A thorough paper describing in detail the pharmacological properties and the efficacy of the first FDA-approved aptamer-based therapy for treating age-related macular degeneration.
12. Ginsberg J.A., Crowther M.A., White R.H., and Ortel T.L. Anticoagulation therapy. Hematology (Am Soc Hematol Educ Program) (2001) 339-357
13. Bock L.C., Griffin L.C., Latham J.A., Vermaas E.H., and Toole J.J. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355 (1992) 564-566
14. Nimjee S.M., Rusconi C.P., Harrington R.A., and Sullenger B.A. The potential of aptamers as anticoagulants. Trends Cardiovasc Med 15 (2005) 41-45
15. Rusconi C.P., Scardino E., Layzer J., Pitoc G.A., Ortel T.L., Monroe D., and Sullenger B.A. RNA aptamers as reversible antagonists of coagulation factor IXa. Nature 419 (2002) 90-94
16. Rusconi C.P., Roberts J.D., Pitoc G.A., Nimjee S.M., White R.R., Quick Jr. G., Scardino E., Fay W.P., and Sullenger B.A. Antidote-mediated control of an anticoagulant aptamer in vivo. Nat Biotechnol 22 (2004) 1423-1428. A landmark paper showing how inhibition of aptamer activity can be modulated with an antisense sequence in vivo.
17. Klussmann S., Nolte A., Bald R., Erdmann V.A., and Furste J.P. Mirror-image RNA that binds d-adenosine. Nat Biotechnol 14 (1996) 1112-1115
18. Nolte A., Klussmann S., Bald R., Erdmann V.A., and Furste J.P. Mirror-design of l-oligonucleotide ligands binding to l-arginine. Nat Biotechnol 14 (1996) 1116-1119
19. Eulberg D., and Klussmann S. Spiegelmers: biostable aptamers. ChemBioChem 4 (2003) 979-983
20. Tschop M., Smiley D.L., and Heiman M.L. Ghrelin induces adiposity in rodents. Nature 407 (2000) 908-913
21. Shearman L.P., Wang S.P., Helmling S., Stribling D.S., Mazur P., Ge L., Wang L., Klussmann S., Macintyre D.E., Howard A.D., et al. Ghrelin neutralization by an RNA-spiegelmer ameliorates obesity in diet-induced obese mice. Endocrinology 147 (2006) 1517-1526
22. Labrijn A.F., Poignard P., Raja A., Zwick M.B., Delgado K., Franti M., Binley J., Vivona V., Grundner C., Huang C.C., et al. Access of antibody molecules to the conserved coreceptor binding site on glycoprotein gp120 is sterically restricted on primary human immunodeficiency virus type 1. J Virol 77 (2003) 10557-10565
23. Dey A.K., Khati M., Tang M., Wyatt R., Lea S.M., and James W. An aptamer that neutralizes R5 strains of human immunodeficiency virus type 1 blocks gp120-CCR5 interaction. J Virol 79 (2005) 13806-13810
24. Dey A.K., Griffiths C., Lea S.M., and James W. Structural characterization of an anti-gp120 RNA aptamer that neutralizes R5 strains of HIV-1. RNA 11 (2005) 873-884. An interesting example of the advantages of aptamers relative to antibodies as potential therapeutic agents. The ability of the aptamer to target many different viral strains is also notable.
25. Jeon S.H., Kayhan B., Ben-Yedidia T., and Arnon R. A DNA aptamer prevents influenza infection by blocking the receptor binding region of the viral hemagglutinin. J Biol Chem 279 (2004) 48410-48419
26. Misono T.S., and Kumar P.K. Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance. Anal Biochem 342 (2005) 312-317
27. Sc formation. Chem Bio Chem 3 (2002) 717-725
28. Rhie A., Kirby L., Sayer N., Wellesley R., Disterer P., Sylvester I., Gill A., Hope J., James W., and Tahiri-Alaoui A. Characterization of 2′-fluoro-RNA aptamers that bind preferentially to disease-associated conformations of prion protein and inhibit conversion. J Biol Chem 278 (2003) 39697-39705
29. Sekiya S., Nishikawa F., Noda K., Kumar P.K.R., Yokoyama T., and Nagashima S. In vitro selection of RNA aptamers against cellular and abornormal isoform of mouse prion protein. Nucleic Acids Symp Ser 49 (2005) 361-362
30. Sayer N.M., Cubin M., Rhie A., Bullock M., Tahiri-Alaoui A., and James W. Structural determinants of conformationally selective, prion-binding aptamers. J Biol Chem 279 (2004) 13102-13109
31. Gschwind A., Fischer O.M., and Ullrich A. The discovery of receptor tyrosine kinases: targets for cancer therapy. Nat Rev Cancer 4 (2004) 361-370
32. Hansford J.R., and Mulligan L.M. Multiple endocrine neoplasia type 2 and RET: from neoplasia to neurogenesis. J Med Genet 37 (2000) 817-827
33. Ichihara M., Murakumo Y., and Takahashi M. RET and neuroendocrine tumors. Cancer Lett 204 (2004) 197-211
34. Cerchia L., Duconge F., Pestourie C., Boulay J., Aissouni Y., Gombert K., Tavitian B., de Franciscis V., and Libri D. Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol 3 (2005) e123. This article describes a selection strategy against a cell target that yielded aptamers against a particular RTK; it is a particularly good example of the use of negative selection techniques.
35. Petitclerc E., Stromblad S., von Schalscha T.L., Mitjans F., Piulats J., Montgomery A.M., Cheresh D.A., and Brooks P.C. Integrin alpha(v)beta3 promotes M21 melanoma growth in human skin by regulating tumor cell survival. Cancer Res 59 (1999) 2724-2730
36. Mi J., Zhang X., Giangrande P.H., McNamara II J.O., Nimjee S.M., Sarraf-Yazdi S., Sullenger B.A., and Clary B.M. Targeted inhibition of alphavbeta3 integrin with an RNA aptamer impairs endothelial cell growth and survival. Biochem Biophys Res Commun 338 (2005) 956-963
37. Burke D.H., Scates L., Andrews K., and Gold L. Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase. J Mol Biol 264 (1996) 650-666
38. Schneider D.J., Feigon J., Hostomsky Z., and Gold L. High-affinity ssDNA inhibitors of the reverse transcriptase of type 1 human immunodeficiency virus. Biochemistry 34 (1995) 9599-9610
39. Tuerk C., MacDougal S., and Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci USA 89 (1992) 6988-6992
40. Fisher T.S., Darden T., and Prasad V.R. Mutations proximal to the minor groove-binding track of human immunodeficiency virus type 1 reverse transcriptase differentially affect utilization of RNA versus DNA as template. J Virol 77 (2003) 5837-5845
41. Fisher T.S., Joshi P., and Prasad V.R. HIV-1 reverse transcriptase mutations that confer decreased in vitro susceptibility to anti-RT DNA aptamer RT1t49 confer cross resistance to other anti-RT aptamers but not to standard RT inhibitors. AIDS Res Ther 2 (2005) 8
42. Mendonsa S.D., and Bowser M.T. In vitro selection of high-affinity DNA ligands for human IgE using capillary electrophoresis. Anal Chem 76 (2004) 5387-5392
43. Mendonsa S.D., and Bowser M.T. In vitro evolution of functional DNA using capillary electrophoresis. J Am Chem Soc 126 (2004) 20-21. One of the first demonstrations of the power of capillary electrophoresis for selection experiments.
44. Drabovich A., Berezovski M., and Krylov S.N. Selection of smart aptamers by equilibrium capillary electrophoresis of equilibrium mixtures (ECEEM). J Am Chem Soc 127 (2005) 11224-11225
45. Berezovski M., Drabovich A., Krylova S.M., Musheev M., Okhonin V., Petrov A., and Krylov S.N. Nonequilibrium capillary electrophoresis of equilibrium mixtures: a universal tool for development of aptamers. J Am Chem Soc 127 (2005) 3165-3171. Another early example of the use of CE-SELEX, whereby aptamers are isolated in only a single round of selection.
46. Mosing R.K., Mendonsa S.D., and Bowser M.T. Capillary electrophoresis-SELEX selection of aptamers with affinity for HIV-1 reverse transcriptase. Anal Chem 77 (2005) 6107-6112
47. Guo K., Wendel H.P., Scheideler L., Ziemer G., and Scheule A.M. Aptamer-based capture molecules as a novel coating strategy to promote cell adhesion. J Cell Mol Med 9 (2005) 731-736
48. Homann M., and Goringer H.U. Combinatorial selection of high affinity RNA ligands to live African trypanosomes. Nucleic Acids Res 27 (1999) 2006-2014
49. Lorger M., Engstler M., Homann M., and Goringer H.U. Targeting the variable surface of African trypanosomes with variant surface glycoprotein-specific, serum-stable RNA aptamers. Eukaryot Cell 2 (2003) 84-94
50. Fitter S., and James R. Deconvolution of a complex target using DNA aptamers. J Biol Chem 280 (2005) 34193-34201
51. Uhlmann E., Peyman A., Ryte A., Schmidt A., and Budecke E. Use of minimally modified antisense oligonucleotides for specific inhibition of gene expression. Methods Enzymol 313 (2000) 268-284
52. Burmeister P.E., Lewis S.D., Silva R.F., Preiss J.R., Horwitz L.R., Pendergrast P.S., McCauley T.G., Kurz J.C., Epstein D.M., Wilson C., et al. Direct in vitro selection of a 2′-O-methyl aptamer to VEGF. Chem Biol 12 (2005) 25-33. The complete incorporation of 2′-O-methyl nucleotides during selection was a tour de force.
53. Padilla R., and Sousa R. A Y639F/H784A T7 RNA polymerase double mutant displays superior properties for synthesizing RNAs with non-canonical NTPs. Nucleic Acids Res 30 (2002) e138
54. Chelliserrykattil J., and Ellington A.D. Evolution of a T7 RNA polymerase variant that transcribes 2′-O-methyl RNA. Nat Biotechnol 22 (2004) 1155-1160
55. Somasunderam A., Ferguson M.R., Rojo D.R., Thiviyanathan V., Li X., O'Brien W.A., and Gorenstein D.G. Combinatorial selection, inhibition, and antiviral activity of DNA thioaptamers targeting the RNase H domain of HIV-1 reverse transcriptase. Biochemistry 44 (2005) 10388-10395
56. Yang X., Fennewald S., Luxon B.A., Aronson J., Herzog N.K., and Gorenstein D.G. Aptamers containing thymidine 3′-O-phosphorodithioates: synthesis and binding to nuclear factor-kappaB. Bioorg Med Chem Lett 9 (1999) 3357-3362
57. Bassett S.E., Fennewald S.M., King D.J., Li X., Herzog N.K., Shope R., Aronson J.F., Luxon B.A., and Gorenstein D.G. Combinatorial selection and edited combinatorial selection of phosphorothioate aptamers targeting human nuclear factor-kappaB RelA/p50 and RelA/RelA. Biochemistry 43 (2004) 9105-9115
58. Ohbayashi T., Kuwahara M., Hasegawa M., Kasamatsu T., Tamura T., and Sawai H. Expansion of repertoire of modified DNAs prepared by PCR using KOD Dash DNA polymerase. Org Biomol Chem 3 (2005) 2463-2468
59. Kuwahara M., Hanawa K., Ohsawa K., Kitagata R., Ozaki H., and Sawai H. Direct PCR amplification of various modified DNAs having amino acids: Convenient preparation of DNA libraries with high-potential activities for in vitro selection. Bioorg Med Chem 14 (2006) 2518-2526
60. Masud M.M., Kuwahara M., Ozaki H., and Sawai H. Sialyllactose-binding modified DNA aptamer bearing additional functionality by SELEX. Bioorg Med Chem 12 (2004) 1111-1120
61. Kawai R., Kimoto M., Ikeda S., Mitsui T., Endo M., Yokoyama S., and Hirao I. Site-specific fluorescent labeling of RNA molecules by specific transcription using unnatural base pairs. J Am Chem Soc 127 (2005) 17286-17295
62. Tucker C.E., Chen L.S., Judkins M.B., Farmer J.A., Gill S.C., and Drolet D.W. Detection and plasma pharmacokinetics of an anti-vascular endothelial growth factor oligonucleotide-aptamer (NX1838) in rhesus monkeys. J Chromatogr B Biomed Sci Appl 732 (1999) 203-212
63. Watson S.R., Chang Y.F., O'Connell D., Weigand L., Ringquist S., and Parma D.H. Anti-l-selectin aptamers: binding characteristics, pharmacokinetic parameters, and activity against an intravascular target in vivo. Antisense Nucleic Acid Drug Dev 10 (2000) 63-75
64. Reyderman L., and Stavchansky S. Pharmacokinetics and biodistribution of a nucleotide-based thrombin inhibitor in rats. Pharm Res 15 (1998) 904-910
65. Marro M.L., Daniels D.A., McNamee A., Andrew D.P., Chapman T.D., Jiang M.S., Wu Z., Smith J.L., Patel K.K., and Gearing K.L. Identification of potent and selective RNA antagonists of the IFN-gamma-inducible CXCL10 chemokine. Biochemistry 44 (2005) 8449-8460
66. Healy J.M., Lewis S.D., Kurz M., Boomer R.M., Thompson K.M., Wilson C., and McCauley T.G. Pharmacokinetics and biodistribution of novel aptamer compositions. Pharm Res 21 (2004) 2234-2246. An incredibly thorough study of aptamer pharmacokinetics that will serve as a standard for comparison.
67. Boomer R.M., Lewis S.D., Healy J.M., Kurz M., Wilson C., and McCauley T.G. Conjugation to polyethylene glycol polymer promotes aptamer biodistribution to healthy and inflamed tissues. Oligonucleotides 15 (2005) 183-195
68. de Smidt P.C., Le Doan T., de Falco S., and van Berkel T.J. Association of antisense oligonucleotides with lipoproteins prolongs the plasma half-life and modifies the tissue distribution. Nucleic Acids Res 19 (1991) 4695-4700
69. Farokhzad O.C., Khademhosseini A., Jon S., Hermmann A., Cheng J., Chin C., Kiselyuk A., Teply B., Eng G., and Langer R. Microfluidic system for studying the interaction of nanoparticles and microparticles with cells. Anal Chem 77 (2005) 5453-5459
70. Schmidt K.S., Borkowski S., Kurreck J., Stephens A.W., Bald R., Hecht M., Friebe M., Dinkelborg L., and Erdmann V.A. Application of locked nucleic acids to improve aptamer in vivo stability and targeting function. Nucleic Acids Res 32 (2004) 5757-5765
71. Theis M.G., Knorre A., Kellersch B., Moelleken J., Wieland F., Kolanus W., and Famulok M. Discriminatory aptamer reveals serum response element transcription regulated by cytohesin-2. Proc Natl Acad Sci USA 101 (2004) 11221-11226
72. Farokhzad O.C., Jon S., Khademhosseini A., Tran T.N., Lavan D.A., and Langer R. Nanoparticle-aptamer bioconjugates: a new approach for targeting prostate cancer cells. Cancer Res 64 (2004) 7668-7672. The use of aptamers for nanoparticle delivery is novel and has many potential applications.
73. Tereshko V., Skripkin E., and Patel D.J. Encapsulating streptomycin within a small 40-mer RNA. Chem Biol 10 (2003) 103-104