Abstract
microRNAs (miRNAs) have been identified as high-value drug targets. A widely applied strategy in miRNA inhibition is the use of antisense agents. However, it has been shown that oligonucleotides are poorly cell permeable because of their complex chemical structure and due to their negatively charged backbone. Consequently, the general application of oligonucleotides in therapy is limited. Since miRNAs’ functions are executed exclusively by the Argonaute 2 protein, we therefore describe a protocol for the design of a novel miRNA inhibitor class: antagonists of the miRNA-Argonaute 2 protein complex, so-called anti-miR-AGOs, that not only block the crucial binding site of the target miRNA but also bind to the protein’s active site. Due to their lower molecular weight and, thus, more drug-like chemical structure, the novel inhibitor class may show better pharmacokinetic properties than reported oligonucleotide inhibitors, enabling them for potential therapeutic use.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Dykxhoorn DM, Novina CD, Sharp PA (2003) Killing the messenger: short RNAs that silence gene expression. Nat Rev Mol Cell Biol 4:457–467
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Fabian MR, Sonenberg N (2012) The mechanisms of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat Struct Mol Biol 19:586–593
Schmidt MF (2014) Drug target miRNA: chances and challenges. Trends Biotechnol 32:578–585
Krützfeld J, Rajewsky N, Braich R, Rajeev KG, Tuschl T, Manoharan M, Stoffel M (2005) Silencing of microRNAs in vivo with antagomirs. Nature 438:685–689
Kole R, Krainer AR, Altman S (2012) RNA therapeutics: beyond RNA interference and antisense oligonucleotides. Nat Rev Drug Discov 11:125–140
Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233
Koshkin AA, Singh SK, Nielsen P, Rajwanshi VK, Kumar R, Meldgaard M, Olsen CE, Wengel J (1998) LNA (locked nucleic acid): synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition. Tetrahedron 54:3607–3630
Obad S, dos Santos CO, Petri A, Heidenblad M, Broom O, Ruse C, Fu C, Lindow M, Stenvang J, Staarup EM, Hanssen HF, Koch T, Pappin D, Hannon GJ, Kauppinen S (2011) Silencing of microRNA families by seed-targeting tiny LNAs. Nat Genet 43:371–378
Schmidt MF, Korb O, Abell C (2013) MicroRNA-specific argonaute 2 protein inhibitors. ACS Chem Biol 8:2122–2126
Schmidt MF, Rademann J (2009) Dynamic template-assisted strategies in fragment-based drug discovery. Trends Biotechnol 27:512–521
Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P (2005) Modulation of hepatitis C virus RNA abundance by a liver-specific microRNA. Science 309:1577–1581
DeLano WL (2006) The PyMOL molecular graphics system, v.0.99rc6. DeLano Scientific LLC, San Carlos, CA
Gasteiger J, Rudolph C, Sadowski J (1990) Automatic generation of 3D atomic coordinates for organic molecules. Tetrahedron Comput Methodol 3:537–547
Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245:43–53
Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009) Nucleation, propagation, and cleavage of target RNAs in Ago silencing complexes. Nature 461:754–761
Schirle NT, MacRae IJ (2012) The crystal structure of human Argonaute 2. Science 336:1037–1040
Korb O, Stützle T, Exner TE (2009) Empirical scoring functions for advanced protein-ligand docking with PLANTS. J Chem Inf Model 49:84–96
Acknowledgment
We acknowledge Dr Rajavel Srinivasan for proofreading the manuscript. Work at CCDC was performed using Darwin Supercomputer of the University of Cambridge High Performance Computing Service (http://www.hpc.cam.ac.uk/), provided by Dell Inc. using Strategic Research Infrastructure Funding from the Higher Education Funding Council for England and funding from the Science and Technology Facilities Council. Work at the University Chemical Laboratory Cambridge was funded by the European Commission FP7 PEOPLE-GA-2010-275765 (Marie Curie Intra-European-Fellowship to M.F.S.).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Schmidt, M.F., Korb, O., Abell, C. (2017). Antagonists of the miRNA-Argonaute 2 Protein Complex: Anti-miR-AGOs. In: Schmidt, M. (eds) Drug Target miRNA. Methods in Molecular Biology, vol 1517. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6563-2_17
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6563-2_17
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6561-8
Online ISBN: 978-1-4939-6563-2
eBook Packages: Springer Protocols