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NOX-E36 L-aptamer
Timeline
Ccl2 blockade with mNOX-E36–3′PEG effectively blocks macrophage recruitment into the glomerular and interstitial compartments of the kidney[2]
Ccl2 mediates the recruitment of glomerular and interstitial macrophages but this mechanism does not contribute to the progression of Alport nephropathy in Col4a3-deficient mice[3]
Inhibition of monocyte infiltration by targeting the chemokine CCL2 prevented fibrosis-associated angiogenesis, but not fibrosis progression[5]
Pharmacological inhibition of Ly-6C(+) monocyte recruitment using the CCL2-inhibitor, mNOX-E36, accelerates regression from toxic and metabolic liver fibrosis[6]
Spiegelmer-based inhibition of MCP-1/CCR2 with the compound mNOX-E36 results in moderate but statistically significant improvements for graft survival[8]
Inhibition of the CCL2/CCL2 receptor axis with NOX-E36 was generally safe and well tolerated[9]
Description
In 2014, Oberthuer, D and Achenbach, J chemically synthesized NOX-E36 L-aptamer and the structure was solved applying single-wavelength anomalous diffraction (SAD) and refined to 2.05 Å[7].SELEX
In 2015, Dominik Oberthür and John Achenbach firstly selected aptamers from oligonucleotide libraries to bind to the non-natural, mirror-image form of an intended target molecule by an evolutionary screening technique called SELEX. Then, they selected the aptamer sequence from non-natural L-nucleotides by chemical synthesis, an exact mirror image of the aptamer is produced, the Spiegelmer, which consequently binds to L-CCL2[7].
Detailed information are accessible on SELEX page.
Structure
2D representation
Here we use ribodraw to complete the figure, through the 3D structure information[7].
5'-GCACGUCCCUCACCGGUGCAAGUGAAGCCGAGGCUCUGCG-3'
3D visualisation
Oberthuer, D and Achenbach, J. sovled the crystal structure, at 2.05 A resolution, of an RNA aptamer bound to L-CCL2 has been determined. The PDB ID of this structure is 4R8I[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)
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Binding pocket
Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 4R8I. L-CCL2 (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the aptamer bound with L-CCL2.
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Ligand information
SELEX ligand
Oberthuer, D and Achenbach, J investigated the ion dependence of L-aptamer binding using surface plasmon resonance (SPR), revealing a strong dependence on Ca2+ , which appears to be important for proper folding of the L-aptamer and will likely occupy the position of Sr2+ observed in the structure. And they also studied the effect of the mutations on L-aptamer afffinity and measured the L-aptamer’s affinity using SPR[7].| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| NOX-E36 L-aptamer | 5'-GCACGUCCCUCACCGGUGCAAGUGAAGCCGAGGCUCUGCG-3' | L-CCL2 | 1.40±0.16nM |
Structure ligand
Acts as a ligand for C-C chemokine receptor CCR2. Signals through binding and activation of CCR2 and induces a strong chemotactic response and mobilization of intracellular calcium ions. Exhibits a chemotactic activity for monocytes and basophils but not neutrophils or eosinophils. May be involved in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis.-----from uniprot
| Uniprot ID | Pfam | MW | Amino acids sequences | PDB ID | GenBank |
|---|---|---|---|---|---|
| P13500 | P13500 | 8.82 kDa | MQPDAINAPVTCCYNFTNRKISVQRLASYRRITSSKCPKEAVIFKTIVAKEICADPKQKWVQDSMDHLDKQTQTPKT | 1DOK | 9606 |
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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 |
|---|---|---|---|
| 7SO0-B | 12 | 0.7 | Evasin p974 |
| 2VXW-A | 12 | 1.5 | C-C motif chemokine 5 |
| 1NR4-E | 11.3 | 1.5 | Thymus and activation-regulated chemokine |
| 5EKI-E | 10.4 | 1.5 | C-C motif chemokine 21 |
| 2JYO-A | 9.4 | 2.1 | C-C motif chemokine 20 (small-inducible cytokine) |
| 1B2T-A | 8.7 | 3.5 | Protein (fractalkine) |
| 2MP1-A | 8.3 | 2.0 | C-C motif chemokine 19 |
| 1O80-A | 7.9 | 2.4 | Small inducible cytokine b10 |
| 1F9P-A | 7.4 | 1.6 | Connective tissue activating peptide-iii |
| 4HED-A | 6.8 | 2.2 | Uncharacterized protein |
References
[1] Physicochemical stability of NOX-E36, a 40mer L-RNA (Spiegelmer) for therapeutic applications.Maasch, C., Buchner, K., Eulberg, D., Vonhoff, S., & Klussmann, S.
Nucleic acids symposium series, (52), 61–62. (2008)
[2] Late onset of Ccl2 blockade with the Spiegelmer mNOX-E36-3'PEG prevents glomerulosclerosis and improves glomerular filtration rate in db/db mice.
Ninichuk, V., Clauss, S., Kulkarni, O., Schmid, H., Segerer, S., Radomska, E., Eulberg, D., Buchner, K., Selve, N., Klussmann, S., & Anders, H. J
The American journal of pathology, 172(3), 628–637. (2008)
[3] Ccl2/Mcp-1 blockade reduces glomerular and interstitial macrophages but does not ameliorate renal pathology in collagen4A3-deficient mice with autosomal recessive Alport nephropathy.
Clauss, S., Gross, O., Kulkarni, O., Avila-Ferrufino, A., Radomska, E., Segerer, S., Eulberg, D., Klussmann, S., & Anders, H. J.
The Journal of pathology, 218(1), 40–47. (2009)
[4] Pharmacological inhibition of the chemokine CCL2 (MCP-1) diminishes liver macrophage infiltration and steatohepatitis in chronic hepatic injury.
Baeck, C., Wehr, A., Karlmark, K. R., Heymann, F., Vucur, M., Gassler, N., Huss, S., Klussmann, S., Eulberg, D., Luedde, T., Trautwein, C., & Tacke, F.
Gut,61(3), 416–426. (2012)
[5] CCL2-dependent infiltrating macrophages promote angiogenesis in progressive liver fibrosis.
Ehling, J., Bartneck, M., Wei, X., Gremse, F., Fech, V., Möckel, D., Baeck, C., Hittatiya, K., Eulberg, D., Luedde, T., Kiessling, F., Trautwein, C., Lammers, T., & Tacke, F.
Gut,63(12), 1960–1971. (2014)
[6] Pharmacological inhibition of the chemokine C-C motif chemokine ligand 2 (monocyte chemoattractant protein 1) accelerates liver fibrosis regression by suppressing Ly-6C(+) macrophage infiltration in mice.
Baeck, C., Wei, X., Bartneck, M., Fech, V., Heymann, F., Gassler, N., Hittatiya, K., Eulberg, D., Luedde, T., Trautwein, C., & Tacke, F.
Hepatology (Baltimore, Md.), 59(3), 1060–1072. (2014)
[7] Crystal structure of a mirror-image L-RNA aptamer (Spiegelmer) in complex with the natural L-protein target CCL2.
Oberthür D, Achenbach J, Gabdulkhakov A, Buchner K, Maasch C, Falke S, Rehders D, Klussmann S, Betzel C.
Nat Commun, 6:6923 (2015)
[8] Spiegelmer Inhibition of MCP-1/CCR2--Potential as an Adjunct Immunosuppressive Therapy in Transplantation.
Kalnins, A., Thomas, M. N., Andrassy, M., Müller, S., Wagner, A., Pratschke, S., Rentsch, M., Klussmann, S., Kauke, T., Angele, M. K., Bazhin, A. V., Fischereder, M., Werner, J., Guba, M., & Andrassy, J.
Scandinavian journal of immunology, 82(2), 102–109. (2015)
[9] C-C motif-ligand 2 inhibition with emapticap pegol (NOX-E36) in type 2 diabetic patients with albuminuria.
Menne, J., Eulberg, D., Beyer, D., Baumann, M., Saudek, F., Valkusz, Z., Więcek, A., Haller, H., & Emapticap Study Group
Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association, 32(2), 307–315. (2017)
[10] Systemic Monocyte Chemotactic Protein-1 Inhibition Modifies Renal Macrophages and Restores Glomerular Endothelial Glycocalyx and Barrier Function in Diabetic Nephropathy.
Boels, M. G. S., Koudijs, A., Avramut, M. C., Sol, W. M. P. J., Wang, G., van Oeveren-Rietdijk, A. M., van Zonneveld, A. J., de Boer, H. C., van der Vlag, J., van Kooten, C., Eulberg, D., van den Berg, B. M., IJpelaar, D. H. T., & Rabelink, T. J.
The American journal of pathology, 187(11), 2430–2440. (2017)