Project

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Ligands for the modulation of microRNA biogenesis and function

Applicant Hall Jonathan
Number 144123
Funding scheme Project funding (Div. I-III)
Research institution Institut für Pharmazeutische Wissenschaften ETH Zürich
Institution of higher education ETH Zurich - ETHZ
Main discipline Organic Chemistry
Start/End 01.01.2013 - 31.12.2015
Approved amount 200'000.00
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All Disciplines (2)

Discipline
Organic Chemistry
Biochemistry

Keywords (5)

polyamine; microRNA; miR-122; antimiR; oligonucleotide

Lay Summary (English)

Lead
Efforts to develop man-made drugs which target ribonucleic acids (RNA) have in the past been unsuccessful. The discovery of a new class of small RNAs which contribute to a number of mechanisms of disease represents an opportunity to investigate new routes to drugs, including short oligonucleotides. In this project we will explore the targeting of one such RNA found in human liver - miR-122. The results may be of value for the development of inhibitors of hepatitis C virus.
Lay summary
Drugs which target ribonucleic acids (RNA) make incremental progress in the clinic. This is to be expected for new classes of compounds targeting untested classes of macromolecular targets which cannot be addressed by the usual small molecule drugs. In this context, therapeutic oligonucleotides (oligomers composed of 15-20 nucleotide units), an experimental class of drug molecule, have a tremendous potential in medicine, yet are not pursued by the mainstream pharmaceutical industry because of the outstanding technical challenges associated with developing large and complex drug molecules. The recent discovery of a new class of natural small RNAs (microRNAs or miRNAs) which contribute to a number of mechanisms of disease represents a new class of RNA target for drugs and has fueled motivation to overcome these challenges, especially in the academia and biotech sectors. For example, mir-122 is a human microRNA which is abundant in the liver and is used by the hepatitis C viral RNA during viral replication. It is the target for an oligonucleotide (miravirsen) in late-phase clinical trials. The research plan in this application is aligned with a principal objective of our group which is generally to make oligonucleotide drugs more tractable. Current dogma states that oligonucleotide drugs need to be large in order to have high binding affinity and high selectivity for their targets in cells. In the current project we are attempting to decrease the length of oligonucleotide drugs indirectly by identifying optimal binding sites on the precursor of miRNA-122 which are structurally pre-disposed such that oligonucleotide drugs bind with high affinity. We have established novel methods (in vitro and cellular assays) to identify such sites in the first stage of the project. Targeting miRNA precursors is a novel high-risk approach rarely pursued by other groups. To date, we have succeeded to show using in vitro enzymatic assays and cellular assays that oligonucleotides composed of “standard” ribonucleotides targeting these “favored” sites can inhibit their target. However, they only show low efficiency in cells. In this proposed extension of the project we propose to build on this foundation with a new approach to directly increase the binding affinity of the oligonucleotides. We believe that this will in turn increase efficiency in cellular assays. This comprises the design, synthesis and incorporation of non-natural nucleotide building blocks into the drugs. Briefly, we will append small functional groups to certain nucleotides of the oligonucleotide which will endow the drug with additional binding affinity without adding unduly to their size. We estimate to be able to synthesize and test approximately 100-200 new molecules against miRNA-122 in dedicated assays which we developed during the currently funded project. The fragments will be attached to the nucleotides such that they protrude into two types of binding pocket or “groove” on the target pre-miRNA-122 and increase the binding affinity of the overall interaction, for example electrostatically. Fragments will be selected from those which have previously been reported in literature to bind to RNA structures. We will determine the source of increased (or decreased) binding affinities with respect to the rates of association and dissociation of the molecules with the target using surface plasmon resonance spectroscopy. The investigation will demonstrate the suitability of the “major groove” and the “minor groove” in general as a favored binding site for small molecule fragments providing guidance for further unrelated projects with other miRNAs or alternative classes of the numerous RNA targets in cells.
Direct link to Lay Summary Last update: 04.12.2012

Responsible applicant and co-applicants

Employees

Name Institute

Publications

Publication
Towards Improved Oligonucleotide Therapeutics Through Faster Target Binding Kinetics
Menzi M Wild B Pradere U Malinowska A Brunschweiger A Lightfoot HLL Hall J (2017), Towards Improved Oligonucleotide Therapeutics Through Faster Target Binding Kinetics, in Chemistry - A European Journal, 23, 14221-14230.
A Small-Molecule Inhibitor of Lin28.
Roos M Pradère U Ngondo RP Behera A Allegrini S Civenni G Zagalak JA Menzi M Hall J (2016), A Small-Molecule Inhibitor of Lin28., in ACS Chemical Biology, 11, 2773-2781.
Site-Specific Labeling of MicroRNA Precursors: A Structure–Activity Relationship Study
Menzi M Pradère U Wang Y Fischer M Baumann F Bigatti M Hall J (2016), Site-Specific Labeling of MicroRNA Precursors: A Structure–Activity Relationship Study, in ChemBioChem, 17, 2012-2017.
Polyamine–oligonucleotide conjugates: a promising direction for nucleic acid tools and therapeutics
Menzi M Lightfoot H.L. Hall J (2015), Polyamine–oligonucleotide conjugates: a promising direction for nucleic acid tools and therapeutics, in Future Medicinal Chemistry, 7(13), 1733-1749.
Properties of short double-stranded RNAs carrying randomized base pairs: toward better controls for RNAi experiments.
Zagalak JA Menzi M Schmich F Jahns H Dogar AM Wullschleger F Towbin H Hall J (2015), Properties of short double-stranded RNAs carrying randomized base pairs: toward better controls for RNAi experiments., in RNA, 21((12)), 2132-2142.

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
RNPnet RNA and disease Poster Polyamine-conjugation to RNA looptomirs for enhanced target binding affinity. 14.10.2015 Marrakech, Morocco Menzi Mirjam;
XXI Round Table on Nucleosides, Nucleotides and Nucleic Acids Poster Spermine conjugation to C-5 of Uracil within Antisense Oligonucleotides. 24.08.2015 Poznan, Poland Menzi Mirjam;
Swiss Pharma Science Day Poster Polyamine-conjugation to RNA looptomirs for enhanced target binding affinity. 19.08.2015 Bern, Switzerland Menzi Mirjam;


Associated projects

Number Title Start Funding scheme
124720 Chemical biology in microRNA pathways 01.01.2010 Project funding (Div. I-III)

Abstract

Drugs which target ribonucleic acids (RNA) make incremental progress in the clinic. This is to be expected for new classes of compounds targeting untested classes of macromolecular targets which cannot be addressed by the usual small molecule drugs. In this context, therapeutic oligonucleotides (oligomers composed of 15-20 nucleotide units), an experimental class of drug molecule, have a tremendous potential in medicine, yet are not pursued by the mainstream pharmaceutical industry because of the outstanding technical challenges associated with developing large and complex drug molecules. The recent discovery of a new class of natural small RNAs (microRNAs or miRNAs) which contribute to a number of mechanisms of disease represents a new class of RNA target for drugs and has fueled motivation to overcome these challenges, especially in the academia and biotech sectors. One particular miRNA, mir-122, a human miRNA expressed in the liver which is used by the hepatitis C viral RNA during viral replication, is the target for an oligonucleotide (miravirsen) in late-phase clinical trials. The research plan in this application represents a proposed extension of funded work currently ongoing which expires at the end of 2012, the principal objective of which is generally to make oligonucleotide drugs more tractable.Current dogma states that oligonucleotide drugs need to be large in order to have high binding affinity and high selectivity for their targets in cells. In the current project we are attempting to decrease the length of oligonucleotide drugs indirectly by identifying optimal binding sites on the target (pre-mir-122: a precursor of mir-122) which are structurally pre-disposed such that oligonucleotide drugs bind with high affinity. We hypothesized that such sites are present amongst the three-dimensional structures of pre-miRNAs, and we have established novel methods (in vitro and cellular assays) to identify these sites during the current project. Targeting miRNA precursors is a novel high-risk approach rarely pursued by other groups. To date, we have succeeded to show using in vitro enzymatic assays and cellular assays that oligonucleotides composed of “standard” ribonucleotides targeting these “favored” sites can inhibit their target. However, they only show low efficiency in cells. In this proposed extension of the project we propose to build on this foundation with a new approach to directly increase the binding affinity of the oligonucleotides. We believe that this will in turn increase efficiency in cellular assays. This comprises the design, synthesis and incorporation of non-natural nucleotide building blocks into the drugs. Briefly, we will append small functional groups to certain nucleotides of the oligonucleotide which will endow the drug with additional binding affinity without adding unduly to their size. We estimate to be able to synthesize and test approximately 100-200 new molecules against mir-122 in dedicated assays which we developed during the currently funded project. The fragments will be attached to the nucleotides such that they protrude into two types of binding pocket or “groove” on the target pre-mir-122 and increase the binding affinity of the overall interaction, for example electrostatically. Fragments will be selected from those which have previously been reported in literature to bind to RNA structures. We will determine the source of increased (or decreased) binding affinities with respect to the rates of association and dissociation (kon and koff, respectively) of the molecules with the target using surface plasmon resonance. The investigation will demonstrate the suitability of the “major groove” and the “minor groove” in general as a favored binding site for small molecule fragments providing guidance for further unrelated projects with other miRNAs or alternative classes of the numerous RNA targets in cells. The research plan is designed for two PhD students however the content of the proposal contains numerous possibilities for additional research projects.
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