Transcriptome-wide design of selective, bioactive small molecules targeting RNA
AssigneeUniversity of Florida Research Foundation, Inc.
InventorsMatthew D. Disney, Sai Velagapudi
Life of this patent
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Abstract
Methods and computer systems are described herein for identifying small molecules that bind to selected RNA structural features (e.g., to RNA secondary structures). Also described are compounds and compositions that modulate RNA function and/or activity.
Claims23
A method for identifying a compound that binds to an RNA, comprising:
- (a) generating a query dataset of RNA secondary structures from one or more sequences of the RNA alone;
- (b) comparing the query dataset of RNA secondary structures with a dataset of identified bound RNA motif-small molecule pairs, to generate an output listing of pairs of identified RNA secondary structures and the identified small molecule that binds thereto;
- (c) obtaining an RNA with an identified RNA secondary structure and the identified small molecule that binds thereto;
- (d) determining a binding affinity of the identified RNA secondary structure with the identified small molecule that binds thereto by mixing an RNA having the RNA secondary structure with the identified small molecule and measuring the binding affinity, and/or determining whether the identified small molecule reduces or increases amounts of an RNA having the RNA secondary structure in a mammalian cell;
- to thereby identify a compound that binds to the RNA.
A computer system for identifying a molecule that binds to an RNA comprising:
- one or more computer processors;
- and
- storage having computer-useable instructions embodied thereon;
- wherein the computer-useable instructions are configured to generate a structured query dataset describing RNA secondary structures from one or more sequences of the RNA alone;
- and compare the structured query dataset describing RNA secondary structures with a structured dataset of identified RNA motif-small molecule pairs, to thereby identify the molecule that binds to the RNA.
One or more computer-readable hardware storage having computer-useable instructions embodied thereon and configured for performing a method of generating a structured query dataset describing RNA secondary structures from one or more sequences of the RNA alone;
- and comparing the structured query dataset describing RNA secondary structures with a structured dataset of identified RNA motif-small molecule pairs to identify a molecule that binds to the RNA.
Dependencies are inferred from the claim text.