Rna-based inhibitors of trna modifying enzymes

Abstract

The disclosure provides RNA molecules comprising at least one nucleotide capable of forming a covalent bond with a tRNA modifying enzyme, wherein formation of the covalent bond inhibits the tRNA modifying enzyme, and compositions comprising the RNA molecules. The disclosure further provides methods for killing cells, in particular cancer cells, and for treating or preventing cancer in a subject.

Description

Abstract This invention provides an RNA molecule comprising at least one nucleotide capable of forming a covalent bond with a tRNA-modifying enzyme, wherein the formation of the covalent bond inhibits the activity of the tRNA-modifying enzyme; the invention also provides a composition comprising the RNA molecule. The invention further provides methods for killing cells (particularly cancer cells) and methods for treating or preventing cancer in a subject.

Claims

CLAIMSWhat is claimed is:

1. An RNA molecule comprising at least one nucleotide capable of forming a covalent bond with a tRNA modifying enzyme, wherein formation of the covalent bond inhibits the tRNA modifying enzyme.

2. The RNA molecule of claim 1, wherein the RNA molecule is a tRNA molecule.

3. The RNA molecule of claim 1 or 2, wherein the at least one nucleotide comprises a nonnatural base.

4. The RNA molecule of claim 3, wherein the at least one nucleotide is 5-halouridine (5-haloU), 5-halocytidine (5-haloC), 5-aza-cytidine (5-azaC), 8-haloadenosine (8-haloA), 8-azanebularine, 8-aza-adenosine (8-azaA), or 8-haloguanosine (8-haloG).

5. The RNA molecule of any one of claims 1-4, wherein the tRNA modifying enzyme is a dihydrouridine synthase (DUS) or a pseudouridine synthase (PUS).

6. The RNA molecule of any one of claims 1-5, wherein the tRNA modifying enzyme is dihydrouridine synthase 1 (DUS1), dihydrouridine synthase 2 (DUS2), dihydrouridine synthase 3 (DUS3), dihydrouridine synthase 4 (DUS4), dihydrouridine synthase 1 -like (DUS1L), dihydrouridine synthase 3 like (DUS3L), dihydrouridine synthase 4 like (DUS4L), pseudouridine synthase 1 (PUS1), pseudouridine synthase like 1(PUSL1), pseudouridine synthase 3 (PUS3), TruB pseudouridine synthase family member 1 (TRUB1), TruB pseudouridine synthase family member 2 (TRUB2), dyskerin pseudouridine synthase 1 (DKC1), pseudouridine synthase 7 (PUS7), pseudouridine synthase 7 like (PUS7L), RNA pseudouridylate synthase domain containing 1 (RPUSD1), RNA pseudouridylate synthase domain containing 2 (RPUSD2), RNA pseudouridylate synthase domain containing 4 (RPUSD4), pseudouridine synthase 10 (PUS 10), tRNA methyltransferase 2 homolog A (TRMT2A), tRNA methyltransferase 2 homolog B (TRMT2B), NOP2 / Sun RNA methyltransferase 2 (NSUN2), NOP2 / Sun RNA methyltransferase3 (NSUN3), N0P2 / Sun RNA methyltransferase 6 (NSUN6), DNA ethyltransferase 2 (DNMT2), Methyltransferase-Like Protein 1 (METTL1), WD repeat domain 4 (WDR4), adenosine deaminase TRNA specific 1 (ADAT1), adenosine deaminase TRNA specific 2 (ADAT2), adenosine deaminase TRNA specific 2 (ADAT3), or ISCU.

7. The RNA molecule of any one of claims 1-6, wherein the non-natural base is 5-haloU, and the tRNA modifying enzyme is DUS2, DUS IL, DUS3L, DUS4L, ISCU, PUS1, PUS3, PUS7, PUS10, PUSL1, PUS7L, RPUSD1, RPUSD2, RPUSD4, TRMT2A, TRMT2B, TRUB1, or TRUB2; the nucleotide comprising the non-natural base is 5-azaC, and the tRNA modifying enzyme is DNMT2, NSUN2, NSUN3, or NSUN6; the nucleotide comprising the non-natural base is 8-halo-G, and the tRNA modifying enzyme is METTL1 or WDR4; or the nucleotide comprising the non-natural base is 8-azaA, and the tRNA modifying enzyme is ADAT1, ADAT2, or ADAT3.

8. The RNA molecule of any one of claims 3-7, wherein the at least one nucleotide is at a position corresponding to a natural position of a natural nucleotide of a natural tRNA that is modified by the tRNA modifying enzyme.

9. The RNA molecule of any one of claims 3-8, wherein the RNA molecule is a tRNA molecule, and wherein the non-natural modified base is a 5-halouracil in the D-loop, the t-psi-c loop, or the anticodon loop of the tRNA molecule.

10. The RNA molecule of any one of claims 1-9, wherein the RNA molecule comprises the sequence of any one of SEQ ID NOs: 1-53; or comprises at least about 80% sequence identity to the sequence of any one of SEQ ID NOs: 1-53.

11. The RNA molecule of any one of claims 1-10, wherein the RNA molecule is an isolated tRNA molecule.

12. The RNA molecule of any one of claims 1 -11 , wherein the RNA molecule comprises two or more non-natural bases, and wherein the two or more non-natural bases inhibit two or more different tRNA modifying enzymes.

13. A composition comprising the RNA molecule of any one of claims 1-12.

14. The composition of claim 13, further comprising a pharmaceutically acceptable carrier, wherein the composition is a pharmaceutical composition.

15. A method for killing a cell, the method comprising: contacting the RNA molecule of any one of claims 1-12 with the tRNA modifying enzyme in the cell, wherein formation of the covalent bond inhibits the tRNA modifying enzyme, thereby killing the cell .

16. The method of claim 15, wherein the cell is a brain cancer cell, a digestive tract cancer cell, a kidney cancer cell, a liver cancer cell, or a lung cancer cell.

17. The method of any one of claims 15-16, wherein the cell is a cancer cell in a culture.

18. A method for treating a cancer in a subject in need thereof, the method comprising: administering to the subject an effective amount of the pharmaceutical composition of claim 14, wherein the RNA molecule contacts the tRNA modifying enzyme in a cancer cell of the cancer, wherein formation of the covalent bond inhibits the tRNA modifying enzyme, thereby killing the cancer cell.

19. The method of claim 18, wherein the cancer is a lung cancer, a brain cancer, a digestive tract cancer, a kidney cancer, or a liver cancer.

20. The method of claim 18, wherein the cancer is a bladder cancer, a breast cancer, a cervix cancer, a bile duct cancer, a colon cancer, an esophageal cancer, a head / neck cancer, a kidney clear cancer, a kidney papillary cancer, a liver cancer, a lung non small cell cancer, a lung smallcell cancer, a prostate cancer, a rectum cancer, a sarcoma cancer, a stomach cancer, a uterine cancer, or a liquid tumor.

21. The method of any one of claims 18-20, further comprising administering a chemotherapy to the subject.

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