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AML1 (RUNX1)-aptamer
Timeline
Report the 2.6 Å resolution crystal structure of the complex between the AML1 Runt domain and CBF, which represents a paradigm for the mode of interaction of this highly conserved family of transcription factors[1]
Indicate that a decrease in AML1 dosage resulting from chromosomal translocations or mutations contributes to leukemogenesis. Furthermore, dysregulated chromatin remodeling and transcriptional control appears to be a common pathway in AML1-associated leukemias that could be an important target for the development of new therapeutic agents[2]
Isolated high-affinity aptamers that alter the affinity of RUNX1 for DNA and investigated their effects on DNA binding and CBF complex formation. Identified minimal short stem-loop sequences from these consensus sequences which retain binding activity[3]
In development by Antisoma plc, AS-1411 is the first oligodeoxynucleotide aptamer to reach phase I and II clinical trials for the potential treatment of cancers, including acute myelogenous leukemia (AML)[4]
The motif contains the AHþC mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure[5]
Performed SELEX to obtain RNA aptamers that bind specifically to the AML1 protein to use as tools for better understanding AML1 and its potential utility for the diagnosis and treatment of AML1-related diseases. found that all the selected aptamers possessed a unique RNA motif and that one of these aptamers likely binds to the Runt domain in a manner similar to the DNA consensus binding sequence[6]
Demonstrated a pipeline approach for developing single stranded DNA aptamer probes, phenotyping AML cells in clinical specimens, and then identifying the aptamer-recognized target protein. The developed aptamer probes and identified Siglec-5 protein may potentially be used for leukemic cell detection and therapy in our future clinical practice[7]
Developed a single-strand DNA aptamer specific for the biomarker CD117, which is highly expressed on AML cells[8]
To evaluate an engineered nanostructure to silence five important oncogenes, including BAG1, MDM2, Bcl-2, BIRC5 (survivin) and XIAP, in acute myeloid leukemia subtype 2 (AML-M2)，using nanostructure consisted of gold nanoparticles functionalized with five AOs and one anti-CD33(+)/CD34(+) aptamer (functionalized gold nanoparticle (FGN))[9]
Obtained high-affinity RNA aptamers against RD under highly stringent conditions. Among the selected aptamers, S4 showed the highest binding affinity (Kd =0.044 ± 0.002 nM), whereas the Kd of the most frequently observed S1 was 0.27 ± 0.02 nM. It was previously reported that the most frequently observed aptamer showed fast association rather than high affinity[10]
In order to identify novel anticancer compounds, we applied peptide aptamers targeting translationally controlled tumor protein (TCTP), an interesting target protein overexpressed in many tumors and involved in various cancer-related pathways[11]
Identified high-affinity RNA aptamers that bind to RD by systematic evolution of ligands by exponential enrichment[12]
Developed the first CD123 (AML tumor marker) aptamers and designed a novel CD123-aptamer-mediated targeted drug train (TDT) with effective, economical, biocompatible and high drug-loading capacity[13]
Modified approach can rapidly screen reliable, stable and high binding affinity aptamers for precise cancer treatment. successfully obtained the CD33-targeting aptamer S30, which could highly recognize the C2 domain of the CD33 antigen in vitro and in vivo. Moreover, the optimized aptamer S30-T1 (i.e., core region of S30) was conjugated with doxorubicin (Dox) to synthesize S30-T1-Dox conjugates, which could specifically inhibit CD33 positive acute myeloid leukemia HL-60 cell proliferation by arresting the cell cycle at the G2 phase[14]
Description
In 2000, J. Warren et al reported the 2.6 AÊ resolution crystal structure of the complex between the AML1 Runt domain and CBF. In 2003, Asou et al infered that pathways in AML1-associated leukemias that could be an important target for the development of new therapeutic agents. In 2009, L. Barton et al Isolated high-affinity aptamers that alter the affinity of RUNX1 for DNA and investigated their effects on DNA binding and CBF complex formation. In 2013, Nomura et al., used nuclear magnetic resonance To understand the structural basis of recognition of the Runt domain by the aptamer motif; Fukunaga et al., Performed SELEX to obtain RNA aptamers that bind specifically to the AML1 protein to use as tools for better understanding AML1 and its potential utility for the diagnosis and treatment of AML1-related diseases.In 2016, Amano et al., Obtained high-affinity RNA aptamers against RD under highly stringent conditions. In 2019, Yang et al., modified approach can rapidly screen reliable, stable and high binding affinity aptamers for precise cancer treatment and successfully obtained the CD33-targeting aptamer S30, which could highly recognize the C2 domain of the CD33 antigen in vitro and in vivo[1,2,3,5,6,10,14].SELEX
In 2013，Junichi Fukunaga and his teammates obtained RNA aptamers that bind specifically to the AML1 protein to use as tools for better understanding AML1 and its potential utility for the diagnosis and treatment of AML1-related diseases performing SELEX.Following nine rounds of selection, the 30N and 40N random RNA pools converged into eight and four independent sequences, respectively. SPR assays was used to test the aptamer–Runt–CBFβ ternary complex formation[6].
Detailed information are accessible on SELEX page.
Structure
2D representation
Here we use ribodraw to complete the figure, through the 3D structure information[5].
5'-GGACCCACCACGGCGAGGUCCA-3'
3D visualisation
Nomura and his colleague determined the solution structure of a 22-mer RNA (AML1 (RUNX1)-aptamer) using nuclear magnetic resonance. Although structure of the Runt domain-aptamer complex could not be determined, comparison of the aptamer structure with RDE and dsRNA suggested that the aptamer motif binds to the Runt domain by mimicking the RDE sequence and structure. Therefore, we chose the complex structure of double-stranded DNA element(RDE) and AML1 to show it. His structural ID is 1HJC[5].Additional available structures that have been solved and detailed information are accessible on Structures page.
(Clicking the "Settings/Controls info" to turn Spin off)
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Binding pocket
AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N- terminal Runt domain. Left: Surface representation of the binding pocket. TetR (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the DNA element bound with TetR.
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Ligand information
SELEX ligand
Fukunaga and his colleagues performed SELEX to obtain RNA aptamers against the Runt domain of AML1[6].
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| APt1 | 5'-GGGACGCAAUGGACGACCCACCACGGCGAGGUAUCCCAUUGCCCCUAACGGCCGACAUGAGAG-3' | AML1–Runt | 3.6nM |
| Apt1-S | 5'-GGGAUGGACGACCCACCACGGCGAGGUAUCCCAUCCCA-3' | AML1–Runt | 0.99nM |
| RDE | 5'-TCCCCAAACCGCAAACGAC-3' 3'-GTCGTTTGCGGTTTGGGGA-5' |
AML1–Runt | 9.6nM |
Structure ligand
Runx1 is required for definitive hematopoiesis and is well-known for its frequent chromosomal translocations and point mutations in leukemia. Runx1 regulates a variety of genes via Ets1 activation on an Ets1•Runx1 composite DNA sequence.
| Uniprot ID | Pfam | MW | Amino acids sequences | PDB ID | GenBank |
|---|---|---|---|---|---|
| Q03347 | IPR013524 | 53.26 kDa | MRIPVDASTSRRFTPPSTALSPGKMSEALPLGAPDAGAALAGKLRSGDRSMVEVLADHPGELVRTDSPNFLCSVLPTHWRCNKTLPIAFKVVALGDVPDGTLVTVMAGNDENYSAELRNATAAMKNQVARFNDLRFVGRSGRGKSFTLTITVFTNPPQVATYHRAIKITVDGPREPRRHRQKLDDQTKPGSLSFSERLSELEQLRRTAMRVSPHHPAPTPNPRASLNHSTAFNPQPQSQMQDPNHKPKGTFKDYVRDRADLNKDKPVIPAAALAGYTGSGPIQLWQFLLELLTDKSCQSFISWTGDGWEFKLSDPDEVARRWGKRKNKPKMNYEKLSRGLRYYYDKNIIHKTAGKRYVYRFVCDLQSLLGYTPEELHAMLDVKPDADE | 4L0Y | 10090 |
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Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
| PDB | Z-score | RMSD | Description |
|---|---|---|---|
| 4L0Z-A | 24.7 | 0.8 | Runt-related transcription factor 1 |
| 1UUS-A | 8.6 | 3 | Stat protein |
| 1YVL-B | 7.6 | 3.2 | Signal transducer and activator of transcription |
| 7XDI-E | 7.5 | 3.9 | Vp1 |
| 5I5K-B | 7.2 | 3.1 | Complement c5 |
| 8OQ3-D | 7.2 | 2.5 | Complement c3 |
| 4KH9-A | 7.2 | 3.2 | Hypothetical protein |
| 7PTP-A | 7.1 | 2.7 | Cell surface glycoprotein |
| 5J72-A | 7 | 3.4 | Putative n-acetylmuramoyl-l-alanine amidase,autol |
| 3TP4-B | 7 | 3.3 | Computational design of enzyme |
References
[1] Structural basis for the heterodimeric interaction between the acute leukaemia-associated transcription factors AML1 and CBFbeta.Warren, A. J., Bravo, J., Williams, R. L., & Rabbitts, T. H
The EMBO journal, 19(12), 3004–3015. (2000)
[2] The role of a Runt domain transcription factor AML1/RUNX1 in leukemogenesis and its clinical implications.
Asou N.
Critical reviews in oncology/hematology, 45(2), 129–150. (2003)
[3] Characterization of RNA aptamers that disrupt the RUNX1-CBFbeta/DNA complex.
Barton, J. L., Bunka, D. H., Knowling, S. E., Lefevre, P., Warren, A. J., Bonifer, C., & Stockley, P. G
Nucleic acids research, 37(20), 6818–6830. (2009)
[4] AS-1411, a guanosine-rich oligonucleotide aptamer targeting nucleolin for the potential treatment of cancer, including acute myeloid leukemia.
Mongelard, F., & Bouvet, P
Current opinion in molecular therapeutics, 12(1), 107–114 (2010)
[5] Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain.
Nomura, Y., Tanaka, Y., Fukunaga, J., Fujiwara, K., Chiba, M., Iibuchi, H., Tanaka, T., Nakamura, Y., Kawai, G., Kozu, T., & Sakamoto, T
Journal of biochemistry, 154(6), 513–519 (2013)
[6] The Runt domain of AML1 (RUNX1) binds a sequence-conserved RNA motif that mimics a DNA element.
Fukunaga, J., Nomura, Y., Tanaka, Y., Amano, R., Tanaka, T., Nakamura, Y., Kawai, G., Sakamoto, T., & Kozu, T
RNA (New York, N.Y.), 19(7), 927–936 (2013)
[7] Developing aptamer probes for acute myelogenous leukemia detection and surface protein biomarker discovery.
Yang, M., Jiang, G., Li, W., Qiu, K., Zhang, M., Carter, C. M., Al-Quran, S. Z., & Li, Y
Journal of hematology & oncology, 7, 5 (2014)
[8] Oligonucleotide aptamer-drug conjugates for targeted therapy of acute myeloid leukemia.
Zhao, N., Pei, S. N., Qi, J., Zeng, Z., Iyer, S. P., Lin, P., Tung, C. H., & Zu, Y
Biomaterials, 67, 42–51. (2015)
[9] Coinhibition of overexpressed genes in acute myeloid leukemia subtype M2 by gold nanoparticles functionalized with five antisense oligonucleotides and one anti-CD33(+)/CD34(+) aptamer.
Zaimy, M. A., Jebali, A., Bazrafshan, B., Mehrtashfar, S., Shabani, S., Tavakoli, A., Hekmatimoghaddam, S. H., Sarli, A., Azizi, H., Izadi, P., Kazemi, B., Shojaei, A., Abdalaian, A., & Tavakkoly-Bazzaz, J
Cancer gene therapy, 23(9), 315–320 (2016)
[10] Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein.
Amano, R., Takada, K., Tanaka, Y., Nakamura, Y., Kawai, G., Kozu, T., & Sakamoto, T
Biochemistry, 55(45), 6221–6229 (2016)
[11] Peptide aptamer identified by molecular docking targeting translationally controlled tumor protein in leukemia cells.
Kadioglu, O., & Efferth, T
Investigational new drugs, 34(4), 515–521 (2016)
[12] Kinetic and Thermodynamic Analyses of Interaction between a High-Affinity RNA Aptamer and Its Target Protein.
Amano, R., Takada, K., Tanaka, Y., Nakamura, Y., Kawai, G., Kozu, T., & Sakamoto, T
Biochemistry, 55(45), 6221–6229 (2016)
[13] Novel CD123-aptamer-originated targeted drug trains for selectively delivering cytotoxic agent to tumor cells in acute myeloid leukemia theranostics.
Wu, H., Wang, M., Dai, B., Zhang, Y., Yang, Y., Li, Q., Duan, M., Zhang, X., Wang, X., Li, A., & Zhang, L
Drug delivery, 24(1), 1216–1229 (2017)
[14] Rapid identification of specific DNA aptamers precisely targeting CD33 positive leukemia cells through a paired cell-based approach.
Yang, C., , Wang, Y., , Ge, M. H., , Fu, Y. J., , Hao, R., , Islam, K., , Huang, P., , Chen, F., , Sun, J., , Hong, F., , & Naranmandura, H.,
Biomaterials science, 7(3), 938–950 (2019)
[15] Nucleic Acid Aptamer: A Novel Potential Diagnostic and Therapeutic Tool for Leukemia.
Tan, Y., Li, Y., & Tang, F
OncoTargets and therapy, 12, 10597–10613 (2019)