Platform using dna-encoded small molecule libraries and rna selection to design small molecules that target rna
AssigneeUniversity of Florida Research
InventorsMatthew D. Disney, Brian M. Paegel
Life of this patent
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Abstract
A dual screen technique using DEL and 2DCS screens with libraries of synthesized small molecules and synthesized RNA structures (4,096 targets) delivers bona fide ligand-RNA 3D fold target pairs. One of the newly discovered ligands bound a 5′GAG/3′CCC internal loop that is present in pri-miR-27a, the oncogenic precursor of microRNA-27a. The DEL-derived pri-miR-27a ligand is cell-active, potently and selectively inhibits pri-miR-27a processing to reprogram gene expression and halt an otherwise invasive phenotype in triple-negative breast cancer cells.
Claims32
A DEL method for screening compounds by DNA encoded labeling, comprising:
- Forming an immobilized library of compounds having DNA labels wherein each of the compounds is bound to an individual solid microsupport and each microsupport also carries a unique DNA sequence that describes both the microsupport and the synthesis history of the individual compound immobilized on the microsupport;
- Contacting the immobilized compound library with a first RNA library comprising synthesized RNA constructs with fluorescent labels wherein the synthesized RNA constructs display a randomized region in a discrete structural motif pattern, and simultaneously contacting the immobilized compound library with a non-selective RNA counter construct labeled with tetramethylrhodamine wherein the non-selective RNA counter construct comprises the synthesized RNA library construct in which the randomized region is replaced with base paired nucleotides, to produce a first subgroup of the immobilized compound library bound to the first RNA library, a second subgroup of the immobilized compound library bound to the second non-selective RNA counter construct, and a third unbound subgroup;
- Sorting and isolating the first, second and third subgroups by flow cytometry using fluorescent detection;
- Amplifying the DNA labels of each of compounds of the first subgroup;
- Reading the amplified DNA labels to identify each of the compounds of the first subgroup.
A method for targeting primary microRNA-27a (pri-miR-27a) or microRNA-409 (miR-409) comprising contacting pri-miR-27a or miR-409 with a peptide compound of Formula I
- wherein
- R6 is hydrogen, C1-C3 alkyl or propargyl;
- R1 is CHR7 wherein R7 is phenyl, butyl, isobutyl, 2-cyanophenyl, CH2CH (CH2 (3-indolyl)) or R7 and R4 together form an azetidine ring;
- R4 is hydrogen or together with R7 forms the azetidine ring;
- R5 is a bond between carbonyl and the pyrrolidine ring or is CHR8NHCO— wherein R8 and R4 together form a pyrrolidinone ring provided that R4 cannot be both of the azetidine ring and the pyrrolidinone ring;
- R3 is hydrogen or —CO—R9 wherein R9 is 5-trifluoromethylbenzothiophen-2-yl, 5-chloroindol-3-yl or 2-(4-morpholinylcarbonyl)phenyl provided that R3 is hydrogen when R1 is CHR7 and R7 is 2-cyanophenyl or CH2CH (CH2(3-indolyl));
- R2 is hydrogen or COR10 wherein R10 is tetrahydrofuran-2-yl, or quinazolindion-3-ylmethylenyl, provided that R2 is not hydrogen when R3 is hydrogen;
- and, the asterisk indicates the position of the diastereomeric R and S forms of Formula I.
A composition comprising a peptide compound of Formula I
- wherein
- R6 is hydrogen, C1-C3 alkyl or propargyl;
- R1 is CHR7 wherein R7 is phenyl, butyl, isobutyl, 2-cyanophenyl, CH2CH (CH2 (3-indolyl)) or R7 and R4 together form an azetidine ring;
- R4 is hydrogen or together with R7 forms the azetidine ring;
- R5 is a bond between carbonyl and the pyrrolidine ring or is CHR8NHCO— wherein R8 and R4 together form a pyrrolidinone ring provided that R4 cannot be both of the azetidine ring and the pyrrolidinone ring;
- R3 is hydrogen or —CO—R9 wherein R9 is 5-trifluoromethylbenzothiophen-2-yl, 5-chloroindol-3-yl or 2-(4-morpholinylcarbonyl)phenyl provided that R3 is hydrogen when R1 is CHR7 and R7 is 2-cyanophenyl or CH2CH (CH2 (3-indolyl));
- R2 is hydrogen or COR10 wherein R10 is tetrahydrofuran-2-yl, or quinazolindion-3-ylmethylenyl, provided that R2 is not hydrogen when R3 is hydrogen;
- and,
- the asterisk indicates the position of the diastereomeric R and S forms of Formula I.
Dependencies are inferred from the claim text.