PSMA aptamer

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Timeline

2002

Lupold et al. used the extracellular part of PSMA to select an aptamer, termed A9, capable of inhibiting PSMA enzymatic activity and binding to PSMA-positive cells with low nanomolar affinity[2]

2006

The A9 aptamer, stabilized by the incorporation of 2′-fluor-pyrimidines bases, has since been used in a variety of functional studies, including the A9-mediated delivery of therapeutic siRNA to PCa cells[3]

2010

A9 apatmer is used in A9-targeted gold nanoparticles for PCa imaging and delivery of doxorubicin payloads[4]

2011

A9 aptamer was modified to prepare a minimal functional part, giving rise to A9g, its truncated 43-nucleotide variant[5]

2014

A9 apatmer is used in generation of A9-bound drug-loaded liposomes[6]

2020

Crystal structure of human PSMA in complex with A9g, a 43-bp PSMA-specific RNA aptamer, that was determined to the 2.2 Å resolution limit[7]

Description

In 2002, Lupold et al. used the extracellular part of PSMA to select an aptamer, termed A9. In 2006, The A9 aptamer, stabilized by the incorporation of 2′-fluor-pyrimidines bases, has since been used in a variety of functional studies, including the A9-mediated delivery of therapeutic siRNA to PCa cells. In 2014, A9 apatmer is used in generation of A9-bound drug-loaded liposomes. In 2020, Barinka C et al. published on the crystal structure of human prostate-specific membrane antigen (PSMA) in complex with A9g, a 43-bp PSMA-specific RNA aptamer. This structure was determined to a resolution limit of 2.2 Å[2,3,6].



SELEX

In 2002, Lupold et al. used the extracellular moiety of PSMA as a target to isolate for RNA aptamer A9 that can inhibit PSMA enzyme activity and bind to PSMA-positive cells by SELEX technology. The aptamer underwent multiple rounds of screening and amplification to obtain a binding molecule with high affinity and specificity. Two specific aptamers were selected from an initial 40-mer library of approximately 6 × 10¹⁴ random-sequence RNA molecules for their ability to bind to a recombinant protein representing the extracellular 706 amino acids of prostate-specific membrane antigen (PSMA), termed xPSM. Six rounds of in vitro selection were conducted, enriching for xPSM binding as monitored by the aptamers' inhibition of xPSM's N-acetyl-alpha-linked acid dipeptidase (NAALADase) enzymatic activity. By the sixth round, 95% of the aptamer pool consisted of just two sequences. These two aptamers, designated xPSM-A9 and xPSM-A10, were cloned and found to be unique, sharing no consensus sequences[2].

Detailed information are accessible on SELEX page.



Structure

2D representation

Here we utilized RiboDraw to complete the figure, based the 3D structure information. A9g aptamer was named by Paloma H Giangrande et al. in the 2011 article[7].

5'-GGGACCGAAAAAGACCUGACUUCUAUACUAAGUCUACGUUCCC-3'

drawing

3D visualisation

The complex is the crystal structure of human PSMA in complex with A9g, a 43-bp PSMA-specific RNA aptamer, that was determined to the 2.2 Å resolution limit. GCPII is a close homology of PSMA. A9g aptamer inhibits the enzyme activity of PSMA residing in the central/peripheral nervous system (also known as glutamate carboxypeptidase II, GCPII). The experimentally determined fold of the 43-nucleotide A9g aptamer in its PSMA-bound state is a relatively simple stem-loop structure that includes two stems termed S1 (7-base pairs) and S2 (4-base pairs), a 4 × 1 internal loop 1 (L1; 4 unpaired adenines A8–A11 on the 5′-side and an unpaired nucleotide A36 on the 3′-side) and a 16-nucleotide long hairpin loop 2 The PDB ID of this structure is 6RTI[7].

Additional available structures that have been solved and detailed information are accessible on Structures page.

(Clicking the "Settings/Controls info" to turn Spin off)      

drawing PDBe Molstar




Binding pocket

Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 6MSF. GCPII (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the aptamer bound with GCPII.

drawing drawing


Ligand information

SELEX ligand

For surface plasmon resonance (SPR) measurements using the BIACore 3000 device, the KD value was calculated by global fitting of six concentrations of PSMA on a constant density A9g aptamer. The data were fitted 1:1 with the mass transfer model to calculate the kinetic parameters. The binding parameter KD of A9 aptamer was determined by filtration membrane binding assay[5].



Name Sequence Ligand Affinity
A9g RNA aptamer 5'-GGGACCGAAAAAGACCUGACUUCUAUACUAAGUCUACGUUCCC-3' Human PSMA protein 5-30 nM
A9 RNA aptamer 5'-GGGAGGACGAUGCGGACCGAAAAAGACCUGACUUCUAAGUCUACGUUCCCAGACGACUCGCCCGA-3' Human PSMA protein 110 nM

Structure ligand

Glutamate carboxypeptidase II, also known as N-acetyl-L-aspartyl-L-glutamate peptidase I (NAALADase I), NAAG peptidase, or prostate-specific membrane antigen (PSMA) is an enzyme that in humans is encoded by the FOLH1 (folate hydrolase 1) gene. Human GCPII contains 750 amino acids and weighs approximately 84 kDa.-----From Wiki

UniProt ID: uniquely identifies protein sequences in the UniProt database, a resource for protein information.

Pfam: a widely recognised database of protein families and domains.

GenBank: maintained by NCBI(National Center for Biotechnology Information), is a database of nucleotide sequences from various organisms, vital for genetic and molecular biology research.

Mass: an intrinsic property of a body.

Uniprot ID Pfam Mass Protein sequence PDB ID GenBank
Q04609 CD08022 84.33 KDa
MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIKSSNEAT ...... MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIKSSNEATNITPKHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGLDSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSPQGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAGAKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEYAYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFTGNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSGAAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVAYINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEFSGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVEKFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHPQEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAFIDPLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVAAFTVQAAAETLSEVA
2OOT AAA60209.1
drawing

Similar compound

We used the Dail server website to compare the structural similarities of ligand proteins, and selected the previous information with high 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).

Dail server website: a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB).

Z-score: 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) is used to measure the degree to which atoms deviate from the alignment position.

PDB: PDB ID+ chain name.

PDB Z-score RMSD Description
6RTI-A 64.5 0 Glutamate carboxypeptidase 2
3BI0-A 64.7 0.5 Glutamate carboxypeptidase 2
3FF3-A 60.9 0.8 Glutamate carboxypeptidase iii
4TWE-B 53.7 1.8 N-acetylated-alpha-linked acidic dipeptidase-like
6WRX-B 43.8 2.5 Transferrin receptor protein 1
1DE4-I 42.9 2.5 Hemochromatosis protein
3S9L-A 42.5 2.5 Transferrin receptor protein 1
3KAS-A 40.7 2.7 Transferrin receptor protein 1
1CX8-A 40.7 2.7 Transferrin receptor protein
2NSU-A 40.6 2.7 Transferrin receptor protein 1


References

[1] Three small ribooligonucleotides with specific arginine sites.
Connell, G. J., Illangesekare, M., & Yarus, M.
Biochemistry, 32(21), 5497–5502. (1993)
[2] Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen.
Lupold, S. E., Hicke, B. J., Lin, Y., & Coffey, D. S.
Cancer research, 62(14), 4029–4033. (2002)
[3] Aptamer mediated siRNA delivery.
Chu, T. C., Twu, K. Y., Ellington, A. D., & Levy, M.
Nucleic acids research, 34(10), e73. (2006)
[4] A drug-loaded aptamer-gold nanoparticle bioconjugate for combined CT imaging and therapy of prostate cancer.
Kim, D., Jeong, Y. Y., & Jon, S.
ACS nano, 4(7), 3689–3696. (2010)
[5] Rational truncation of an RNA aptamer to prostate-specific membrane antigen using computational structural modeling.
Rockey, W. M., Hernandez, F. J., Huang, S. Y., Cao, S., Howell, C. A., Thomas, G. S., Liu, X. Y., Lapteva, N., Spencer, D. M., McNamara, J. O., Zou, X., Chen, S. J., & Giangrande, P. H.
Nucleic acid therapeutics, 21(5), 299–314. (2011)
[6] RNA aptamer-conjugated liposome as an efficient anticancer drug delivery vehicle targeting cancer cells in vivo.
Baek, S. E., Lee, K. H., Park, Y. S., Oh, D. K., Oh, S., Kim, K. S., & Kim, D. E.
Journal of controlled release : official journal of the Controlled Release Society, 196, 234–242. (2014)
[7] Structural basis of prostate-specific membrane antigen recognition by the A9g RNA aptamer.
Ptacek, J., Zhang, D., Qiu, L., Kruspe, S., Motlova, L., Kolenko, P., Novakova, Z., Shubham, S., Havlinova, B., Baranova, P., Chen, S. J., Zou, X., Giangrande, P., & Barinka, C.
Nucleic acids research, 48(19), 11130–11145. (2020)