RNA degrading agents and uses thereof

Abstract

The present invention includes compounds and compositions and methods of use thereof for regulating RNA transcripts, or precursors, isoforms, fragments, or variants thereof, by degradation of the RNA transcripts via recruitment or binding of one or more degradation factors (e.g., RNA binding proteins). The present invention also provides methods for preparing such compounds and compositions, and methods for treating RNA-mediated diseases, disorders, or conditions, comprising administering an effective amount of the disclosed compounds or compositions to a patient in need of treating an RNA-mediated disease, disorder, or condition. The present invention further provides compositions comprising RNA binders and ligands of RNA-binding proteins (RBPs), and methods of use thereof, including regulating the activity of RNA transcripts, or precursors, isoforms, fragments, or variants thereof, and treating diseases associated therewith.

Description

[Technical field]

[0001] The present invention relates to compounds and methods for their preparation and use for modulating the activity of an RNA transcript, as well as its isoforms, variants, and fragments, through modulating its degradation and / or otherwise modulating its activity. The present invention also provides methods for treating various diseases and conditions mediated by target RNA transcripts, such as those described herein.

[0002] (CROSS REFERENCE TO RELATED APPLICATIONS) This application claims the benefit of U.S. Provisional Patent Application No. 63 / 263,208, filed October 28, 2021, the entire contents of which are incorporated herein by reference. [Background technology]

[0003] Both coding or messenger RNA (mRNA), as well as non-coding RNA (ncRNA), play numerous important regulatory roles in cells. The sum of all RNAs transcribed from DNA (both coding and non-coding) comprises the transcriptome, and all cell biology originates from the transcriptome. All endogenous mammalian diseases ultimately originate from or are regulated by the transcriptome, either directly by RNA or through expressed proteins. Thus, there is the potential to intervene in all human diseases, whether protein- or RNA-mediated, by modulating the translational or regulatory functions of the corresponding mRNA or ncRNA.

[0004] RNA quality control (QC) mechanisms are diverse and ubiquitous. After transcription, RNA must undergo processing to produce its active form. RNA processing includes various endo- and exonuclease cleavage of sequences at either end of the initial transcript, cleavage of internal sequences (e.g., internal transcribed spacers and introns), nucleotide editing, and various types of functionalization via chemical modifications. In particular, most cellular RNAs undergo multiple processing reactions with alternative pathways (e.g., alternative splicing) that result in different products. Multiple RNAs from otherwise similar or identical RNA primary transcripts result in increased functional diversity of RNA and protein species encoded by individual genes.

[0005] mRNA degradation is a process that leads to programmed nucleolytic degradation of mRNA. This process is enabled by the association of mRNA with specific RNA-binding proteins (RBPs). Thus, mRNA degradation can directly affect the steady-state level of the translatable pool of mRNA in vivo. Eukaryotic mRNA degradation occurs primarily by enzymatic removal of nucleotides in the 5'-3' direction and is catalyzed by Xrn1. mRNAs are also degraded in the 3'-5' direction by multisubunit protein complexes called exosomes, whose catalytic subunit is Rrp44. The contribution of 3'-5' degradation to overall mRNA turnover is higher in metazoans compared to low in eukaryotes.

[0006] RNA QC machinery normally operates to eliminate incorrectly or incompletely processed RNA, however, if the normal activity of these nucleases and QC pathways could be harnessed to selectively degrade (or not degrade) disease-causing (or disease-treating) RNA targets, this would lead to new and novel ways to treat a variety of diseases.

[0007] Thus, there is a broad need for agents that selectively inhibit or eliminate target RNA.The present invention achieves this by using bifunctional or chimeric molecules and compositions that (i) bind to target RNA transcripts and (ii) recruit degradation factors, such as RNA-binding proteins (RBPs), that activate RNA degradation machinery to degrade the target RNA or otherwise interfere with the function of the target RNA (e.g., availability of RNA for translation into active protein).The compounds of the present invention and their pharmacologic acceptable compositions meet these requirements and provide other related benefits as described herein. Summary of the Invention [Means for solving the problem]

[0008] The approach to modulating RNA function described herein is to incorporate elements of endogenous RNA quality control (QC) machinery. As provided herein, compounds and compositions can be used that include ligands that recruit endogenous nucleic acid regulatory proteins, which when recruited, regulate, inhibit, or eliminate the RNA or its function. For example, RNA levels are frequently regulated by endonucleases or exonucleases in cells. There are ligands that, when tethered to RNA-targeting small molecules (rSMs) or RNA-targeting oligonucleotides, bring endonucleases or exonucleases into close proximity to the target RNA, thereby accelerating the degradation of the RNA and thus preventing its translation. Surprisingly, it has been found that certain RNA-binding proteins (RBPs), such as CNOT2, CNOT7, and YTHDF2, can degrade target nucleic acids at endogenous levels. RBPs do not need to be induced or dimerized to act on target RNAs.

[0009] In one aspect, we describe a chimeric molecule, shown below, that comprises three parts: (1) an RNA-binding small molecule (rSM) that binds to the target RNA and confers selectivity by specifically directing a degradation factor, e.g., an RBP such as a nuclease, to the RNA; (2) a degradation factor recruitment ligand, e.g., a small molecule ligand that binds to the degradation factor or associated protein but leaves its activity (e.g., its nuclease activity) intact (note that "nuclease" in this context encompasses endonucleases and exonucleases, as well as a wide variety of nucleic acid modifying proteins, described in more detail below); and (3) a linker that completes the chimera and brings the degradation factor (e.g., nucleic acid modifying protein) into proximity with the RNA bound by the rSM, thereby allowing the degradation factor (e.g., nucleic acid modifying protein) to act specifically on the target RNA. These elements together comprise a "NUTAC" (Nucleic Acid Targeting Chimera).

[0010] More specifically, in one aspect, the present invention provides a bifunctional compound of formula A: [ka] or a pharma- ceutically acceptable salt thereof, wherein: the rSM is an RNA-binding small molecule that binds to a target RNA transcript; DFL is a degrader recruiting ligand; L is a bivalent linker group that covalently attaches the rSM to the DFL; The DFL binds to or recruits one or more degradation factors that degrade the target RNA transcript.

[0011] In some embodiments, the DFL is a small molecule that binds to an RNA binding protein (RBP), and binding of the DFL to the RBP modulates the target RNA transcript.

[0012] In some embodiments, the DFL recruits the nuclease by binding to the nuclease or by binding to a protein that associates with or recruits the nuclease, thus bringing the nuclease into proximity with the target RNA.

[0013] In some embodiments, the DFL recruits an RBP that is part of a multi-component complex that has nuclease activity by binding to the nuclease or by binding to a protein of the multi-component complex, thus bringing the nuclease into close proximity to the target RNA. In some embodiments, the multi-component complex is a protein complex, a protein-nucleic acid complex, or a protein-metabolite complex.

[0014] In some embodiments, the recruited RBP is an RBP that can regulate (e.g., degrade) the target RNA transcript at endogenous levels. Thus, in some embodiments, no additional action (e.g., dimerization and / or induction of the RBP) is required to allow the RBP to act on the target RNA transcript.

[0015] In one aspect, the invention provides bifunctional compounds that affect the recruitment of a target RNA transcript (also referred to herein as an "RNA transcript," "target RNA," or "target transcript") to a nuclease that can degrade the target RNA, or to an RNA-binding protein (RBP) that destabilizes the target RNA transcript toward degradation by either the endogenous mechanisms of RNA degradation of a cell or tissue.

[0016] The present invention further provides methods of preparing and using the disclosed bifunctional compounds in treating a disease, disorder, or condition.

[0017] In some embodiments, the present invention provides bifunctional compounds useful as regulators of targeted degradation of various target RNA transcripts, which are then degraded and / or otherwise inhibited by the bifunctional compounds described herein.The advantage of the compounds provided herein is that they are capable of a broad range of pharmacological activity consistent with the degradation / inhibition of target RNA transcripts from virtually any RNA class or family.

[0018] In some embodiments, the present invention provides a bifunctional composition comprising an RNA binder and a DFL. In some embodiments, the RNA binder is an oligonucleotide. In some embodiments, the RNA binder is an oligonucleotide, a peptide, or an oligosaccharide. In some embodiments, the DFL binds to an RBP. In some embodiments, the present invention provides a bifunctional composition comprising an RNA binder and a DFL that is useful as a regulator of targeted degradation of various target RNA transcripts, which are then degraded and / or otherwise inhibited by the bifunctional composition described herein. An advantage of the compositions provided herein is that they are capable of a broad range of pharmacological activity consistent with the degradation / inhibition of target RNA transcripts from virtually any RNA class or family.

[0019] Additionally, the present invention provides methods of using effective amounts of the compounds and compositions described herein for the treatment or amelioration of diseases, disorders, or conditions, such as those described herein.

[0020] In another aspect, the invention provides a method of modulating the activity (e.g., availability of protein translation) of a target RNA transcript or an isoform, fragment, or variant thereof, the method comprising contacting the RNA transcript or an isoform, fragment, or variant thereof with a disclosed compound, or a pharma- ceutical acceptable salt thereof, that binds to the RNA transcript or an isoform, fragment, or variant thereof.

[0021] In another aspect, the invention provides a method for selectively degrading a target RNA transcript or an isoform, fragment, or variant thereof, the method comprising contacting the RNA transcript or an isoform, fragment, or variant thereof with a disclosed compound, or a pharma- ceutically acceptable salt thereof, that binds to the RNA transcript or an isoform, fragment, or variant thereof.

[0022] In another aspect, the present invention provides a method for identifying a bifunctional compound that binds to a target RNA transcript or an isoform, fragment, or variant thereof, comprising: i) contacting the target RNA transcript or an isoform, fragment, or variant thereof with a disclosed compound; and ii) analyzing the results by an assay as disclosed herein, optionally in combination with computational methods, and optionally including measuring degradation of the target RNA transcript or an isoform, fragment, or variant thereof.

[0023] In one aspect, the present disclosure provides a compound of formula A: [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is an RNA-binding small molecule that binds to a target RNA transcript, and DFL is a degrader recruiting ligand; L is a bivalent linker group that covalently links the rSM to the DFL, and the DFL binds to or recruits a degradation factor. In some embodiments of the compounds provided herein, the degradation factor is an RNA binding protein (RBP), and the binding of the DFL to the RBP results in the regulation of the target RNA transcript in vivo. In some embodiments of the compounds provided herein, the regulation of the target RNA transcript in vivo is the degradation of the target RNA transcript. In some embodiments of the compounds provided herein, the DFL binds to the RBP without interfering with the enzymatic activity of the RBP and / or the ability of the RBP to be part of a multi-component complex, such as a protein complex. In some embodiments of the compounds provided herein, the RBP is an endonuclease, exonuclease, deadenylase, or decapping protein, or the RBP is part of a multi-component complex that has endonuclease, exonuclease, deadenylase, or decapping activity. In some embodiments, the RBP destabilizes the three-dimensional structure of the target RNA transcript to make it more susceptible to degradation. In some embodiments of the compounds provided herein, the RBP is one of those listed in Table 1B. In some embodiments of the compounds provided herein, the RBP has enzymatic activity in vivo or is part of a multi-component complex that has enzymatic activity at endogenous levels sufficient to measurably regulate the target RNA transcript or destabilize its three-dimensional structure in a manner that makes it susceptible to degradation. In some embodiments, the multi-component complex is a protein complex, a protein-nucleic acid complex, or a protein-metabolite complex.

[0024] In some embodiments of the compounds provided herein, the modulation of the target RNA transcript is the degradation of the target RNA transcript. In some embodiments of the compounds provided herein, the RBP does not need to be induced to be active. In some embodiments of the compounds provided herein, the RBP does not need to dimerize to be active. In some embodiments of the compounds provided herein, the RBP is part of the CCR4-NOT (carbon catabolite repression negative in the absence of TATA) complex. In some embodiments of the compounds provided herein, the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1. In some embodiments of the compounds provided herein, the RBP is CNOT2. In some embodiments of the compounds provided herein, the RBP is CNOT7. In some embodiments of the compounds provided herein, the RBP is YTHDF2. In some embodiments of the compounds provided herein, the RBP is not RNase L. In some embodiments of the compounds provided herein, the DFL is one of those shown in Table 1C. In some embodiments of the compounds provided herein, the target RNA transcript is an mRNA or its precursor, isoform, unspliced ​​isoform, splicing intermediate, fragment, or variant. In some embodiments of the compounds provided herein, the target RNA transcript is selected from one of those listed in Table A, Table B, Table C, or Table D, or its precursor, isoform, unspliced ​​isoform, splicing intermediate, fragment, or variant.

[0025] In some embodiments of the compounds provided herein, L is a covalent bond or a divalent, saturated or unsaturated, linear or branched, optionally substituted C 1-50 is a hydrocarbon chain, wherein 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of L are -Cy 2-, -O-, -N(R)-, -S-, -OC(O)-, -C(O)O-, -C(O)-, -C(S)-, -S(O)-, -S(O) 2 -, -N(R)S(O) 2 -, -S(O) 2 N(R)-, -N(R)C(O)-, -C(O)N(R)-, -OC(O)N(R)-, -N(R)C(O)O-, -N(R)C(O)N(R)-, -N(R)C(S)N(R)-, -Si(R) 2 -, -Si(OH)(R)-, -Si(OH) 2 -, -P(O)(OR)-, -P(O)(R)-, -P(O)(NR 2 )-,amino acid, [ka] [ka] [ka] [ka] or [ka] and wherein Each-Cy 2- is an independently optionally substituted bivalent ring selected from phenylene, 8-12 membered bicyclic arylene, 3-8 membered saturated or partially unsaturated carbocyclylene, 8-12 membered bicyclic saturated or partially unsaturated carbocyclylene, 3-8 membered saturated or partially unsaturated heterocyclylene having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, 8-12 membered bicyclic saturated or partially unsaturated heterocyclylene having 1-5 heteroatoms independently selected from nitrogen, oxygen, and sulfur, 5-6 membered heteroarylenyl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or 8-10 membered bicyclic heteroarylenyl having 1-5 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and each q is independently 1, 2, or 3. In some embodiments of the compounds provided herein, L is selected from one of the compounds set forth in Table 2.

[0026] In some embodiments of the compounds provided herein, the rSM is selected from any one of those described in the section entitled Exemplary rSMs. In some embodiments of the compounds provided herein, the rSM is one of those shown in Table 1A.

[0027] In one aspect, the present disclosure provides a composition comprising an RNA binding agent that binds to a target RNA transcript and a degradation factor recruiting ligand (DFL), where the DFL binds to or recruits the degradation factor. In some embodiments of the compositions provided herein, the degradation factor is an RNA binding protein (RBP), and the binding of the DFL to the RBP results in the regulation of the target RNA transcript in vivo. In some embodiments of the compositions provided herein, the regulation of the target RNA transcript in vivo is the degradation of the target RNA transcript. In some embodiments of the compositions provided herein, the RNA binding agent is an oligonucleotide. In some embodiments of the compositions provided herein, the DFL binds to the RBP without interfering with the enzymatic activity of the RBP and / or the ability of the RBP to be part of a multi-component complex, such as a protein complex. In some embodiments of the compositions provided herein, the RBP is an endonuclease, exonuclease, deadenylase, or decapping protein, or the RBP is part of a multi-component complex that has endonuclease, exonuclease, deadenylase, or decapping activity. In some embodiments, the RBP destabilizes the three-dimensional structure of the target RNA transcript in a manner that makes it more susceptible to degradation. In some embodiments of the compositions provided herein, the RBP is one of those listed in Table 1B. In some embodiments of the compositions provided herein, the RBP has enzymatic activity in vivo or is part of a multi-component complex that has enzymatic activity at endogenous levels sufficient to measurably regulate the target RNA transcript or destabilize its three-dimensional structure in a manner that makes it more susceptible to degradation. In some embodiments, the multi-component complex is a protein complex, a protein-nucleic acid complex, or a protein-metabolite complex.

[0028] In some embodiments of the compositions provided herein, the modulation of the target RNA transcript is degradation of the target RNA transcript. In some embodiments of the compositions provided herein, the RBP does not need to be induced to be active. In some embodiments of the compositions provided herein, the RBP does not need to dimerize to be active. In some embodiments of the compositions provided herein, the RBP is part of the CCR4-NOT (carbon catabolite repression negative in the absence of TATA) complex. In some embodiments of the compositions provided herein, the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1. In some embodiments of the compositions provided herein, the RBP is CNOT2. In some embodiments of the compositions provided herein, the RBP is CNOT7. In some embodiments of the compositions provided herein, the RBP is YTHDF2. In some embodiments of the compounds provided herein, the RBP is not RNase L. In some embodiments of the compositions provided herein, the DFL is one of those shown in Table 1C. In some embodiments of the compositions provided herein, the target RNA transcript is an mRNA or a precursor, isoform, unspliced ​​isoform, splicing intermediate, fragment, or variant thereof. In some embodiments of the compositions provided herein, the target RNA transcript is selected from one of those listed in Table A, Table B, Table C, or Table D, or a precursor, isoform, unspliced ​​isoform, splicing intermediate, fragment, or variant thereof.

[0029] In one aspect, the disclosure provides a pharmaceutical composition comprising any one of the compounds provided herein, or a pharma- ceutically acceptable salt thereof, or any one of the compositions provided herein, and a pharma- ceutically acceptable carrier.

[0030] In one aspect, the present disclosure provides a method for modifying the amount of protein in a cell, the method comprising administering a compound or composition that acts on a target RNA transcript or its precursor, isoform, fragment, or variant in an amount sufficient to modify the amount of protein in a cell.In some embodiments of the methods provided herein, modifying the amount of protein in a cell reduces the amount of protein in a cell.In some embodiments of the methods provided herein, the method comprises administering any one of the compounds provided herein, or a pharma- ceutically acceptable salt thereof, or any one of the compositions provided herein, and a pharma- ceutically acceptable carrier.

[0031] In one aspect, the disclosure provides a method of modulating the availability of protein translation of a target RNA transcript or a precursor, isoform, fragment, or variant thereof, the method comprising contacting the target RNA transcript or a precursor, isoform, fragment, or variant thereof with any one of the compounds provided herein, or a pharma- ceutically acceptable salt thereof, or any one of the compositions provided herein, and a pharma- ceutically acceptable carrier.

[0032] In one aspect, the disclosure provides a method of modulating translation of a target protein or variant thereof, the method comprising contacting a target RNA transcript or a precursor, isoform, fragment, or variant thereof with any one of the compounds provided herein, or a pharma- ceutically acceptable salt thereof, or any one of the compositions provided herein, and a pharma- ceutically acceptable carrier.

[0033] In one aspect, the disclosure provides a method of decreasing the half-life or increasing the degradation of a target RNA transcript or precursor, isoform, fragment, or variant thereof, the method comprising contacting the target RNA transcript or precursor, isoform, fragment, or variant thereof with any one of the compounds provided herein, or a pharma- ceutically acceptable salt thereof, or any one of the compositions provided herein, and a pharma- ceutically acceptable carrier.

[0034] In one aspect, the disclosure provides a method of treating a disease, comprising administering to a subject in need of treating the disease any one of the compounds provided herein, or a pharma- ceutically acceptable salt thereof, or any one of the compositions provided herein, and a pharma- ceutically acceptable carrier. In some embodiments of the methods provided herein, the disease is characterized by abnormal levels of a protein in cells. In some embodiments of the methods provided herein, the disease is one of those listed in Table A, Table B, Table C, or Table D. In some embodiments of the methods provided herein, the disease is cancer. In some embodiments of the methods provided herein, the method induces proximity of an RNA binding protein (RBP) to a target RNA transcript, wherein the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1, and the target RNA transcript is a pre-mRNA, a mature mRNA, or a partially processed mRNA, or an isoform, fragment, or variant thereof.

[0035] In one aspect, the present disclosure provides a method for inducing degradation or decreasing half-life of a target RNA transcript or its isoform, fragment, or variant, comprising contacting the target RNA transcript or its isoform, fragment, or variant with an RNA binding moiety that induces the proximity of an RNA binding protein (RBP). In some embodiments of the methods provided herein, the RBP is one of those listed in Table 1B. In some embodiments of the methods provided herein, the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1. In some embodiments of the methods provided herein, the RBP is CNOT2, CNOT7, or YTHDF2. [Brief description of the drawings]

[0036] [Figure 1]Figure 1 shows an overview of the gene tethering assay to determine the RNA degradation activity of RBPs at endogenous activity levels. [Figure 2A] Figures 2A and 2B show bar graphs of gene tethering experiments demonstrating that RNA-binding proteins (RBPs) capable of degrading target RNAs can be degraded in a reporter system with a promoter expressing the reporter and RBP at endogenous (physiological) levels. Gene tethering assays identified multiple RNA-binding proteins (RBPs) with consistent activity at endogenous levels. Figure 2A shows various reporters and readouts for CNOT2, CNOT7 and ZFP36, while Figure 2B shows data for CNOT2, CNOT7, YTHDF2, DDX6, DCP1A, ZFP36 and PARN with endogenous levels of promoters. NCI-H1299 cells (ATCC), which provide a physiologically relevant model, were engineered to stably express various λN-tagged RBPs via lentivirus. Cells were then transfected with two plasmids, one encoding a reporter luciferase containing a BoxB site in either the 3' untranslated region (UTR) or 5' UTR, and the other encoding an alternative luciferase without any BoxB site for tethering, using Lipofectamine 3000 (Thermo Fisher). After 24 hours, expression of both luciferases was measured using a commercially available kit (Promega). Data are presented as the ratio of reporter expression (measured in relative light units (RLU)) to normalizer expression. [Figure 2B] Same as above. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0037] 1. General Description, Definitions of Certain Embodiments of the Invention Targeting RNA Transcripts with Compounds of the Invention It is known that RNA interference (RNAi) complexes recruit ribonucleases to cleave the bound target RNA. See, for example, Velagapudi, SP, et al., "Design of a small molecule against an oncogenic noncoding RNA," Proc Natl Acad Sci USA 2016 113 (21), 5898-903; Disney, MD, "Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine," J. Am. Chem. Soc. 2019 141 (17), 6776-6790; Ursu, A. et al., "Methods to identify and optimize small molecules interacting with RNA (SMIRNAs)," Drug Discovery Today 2019 Oct;24(10):2002-2016, each of which is incorporated herein by reference. Of course, for proteins, there is a burgeoning industry of protease-targeting chimeras (ProTacs) that consist of a ligand that binds to a target protein and (typically) recruits an E3-ligase machinery that ubiquitinates the target protein through linker-imposed proximity, thereby marking it for degradation by the proteasome system.

[0038] Different molecular properties protect mRNAs from structural degradation and are essential for mRNA stability. Mature eukaryotic mRNAs contain a 5' cap consisting of a 5'-methylguanosine residue linked to the mRNA in a 5'-5' linkage. The 5' cap is resistant to the activity of Xrn1 and protects the mRNA from 5'-3' mRNA degradation. The 3' end of the mRNA is protected by a series of adenosine residues, also called the polyA tail. The polyA residues are bound by polyA binding protein (PABP), which limits exosome access to the 3' end. Deadenylation, the successive removal of As from the polyA tail, occurs over the life of the mRNA. The resulting short polyA tail is no longer protected by PABP and instead the mRNA is exposed to 3'-5' degradation.

[0039] The initiation of mRNA degradation is highly subdivided. Most mRNAs are metabolized through a process called "deadenylation-dependent degradation". Deadenylated (short polyA tail) mRNAs recruit translational repressors and decapping enhancer proteins, which then recruit the Dcp1-2 enzyme, which causes mRNA decapping. Deadenylation can therefore affect the rate of degradation of most mRNAs in vivo. This is supported by the observation that artificial tethering of deadenylating proteins to mRNAs significantly reduces their half-life. In some cases, mRNAs contain distinct cis elements that promote their degradation as part of an autoregulatory mechanism. Such cis elements, for example, AU-rich elements present at the mRNA 3' end, trigger the binding of regulatory RBPs that promote the deadenylation-dependent degradation mechanism by recruiting deadenylation factors to the mRNA. Finally, in some exceptional cases, decapping occurs independently of deadenylation. Such mechanisms are part of specialized mRNA degradation mechanisms.

[0040] In addition to normal mRNA turnover pathways, distinct quality control mechanisms have evolved to monitor mRNAs to ensure high-fidelity gene expression. mRNA surveillance systems ensure that mRNAs that may contain deleterious mutations that could cause defective protein production are identified and degraded at a rate significantly faster than their natural turnover rate. Different mRNA surveillance mechanisms identify specific types of abnormal mRNAs, such as mRNAs with premature stop codons, mRNAs that lack natural stop codons, and mRNAs that contain mutations that lead to prolonged pausing of the ribosome on the mRNA. Specialized mRNA degradation mechanisms, such as nonsense-mediated decay (NMD), nonstop decay, and no-go decay, respectively, allow for enhanced degradation of the abnormal mRNAs listed above.

[0041] RNA-binding proteins that promote the degradation of mRNA, whether at the end of the mRNA's natural lifespan or through quality control pathways, can be broadly classified as "mRNA destabilizing proteins." Upon stable association with an mRNA, most mRNA destabilizing proteins recruit deadenylating and / or decapping proteins to target the mRNA for degradation. The association of such mRNA destabilizing proteins with the mRNA is often dominant over other upstream RBP interactions and is penultimate to degradation. In some instances, mRNA destabilizing proteins also function by recruiting selected mRNA endonucleases (see below) to degrade the mRNA.

[0042] Finally, although the majority of mRNA degradation is initiated by 5'-3' and 3'-5' exonuclease mechanisms, endonucleolytic cleavage of target mRNAs is observed under some special circumstances. Select endonucleases such as SMG6, Cue2, RNase L, and IRE1 have been identified that cleave mRNAs internally as part of responses such as NMD, No-go degradation, viral defense, and the endoplasmic reticulum protein response (UPR), respectively. In some notable cases, endonucleolytic cleavage has been reported as part of the natural turnover of mRNAs such as c-myc, c-fos, and MITF.

[0043] The majority of molecular targets that are therapeutically addressed are proteins. However, it is understood that RNA plays an important regulatory role in both healthy and diseased cells. Bifunctional compounds that bind to target RNA transcripts, such as mRNA transcripts or mature mRNAs, can regulate the activity of the RNA transcript (e.g., its availability to be translated into functional proteins), for example, by increasing or decreasing the degradation rate of the RNA, increasing or decreasing its in vivo half-life. In some embodiments, the degradation rate is regulated through the recruitment or activation of RNA degradation machinery, such as nucleases and / or RNA destabilizing proteins. Such recruitment and / or activation occurs by binding a portion of the bifunctional compound to RBPs or other proteins involved in the RNA degradation process. Thus, for protein-coding RNAs, this process affects the expression level of the encoded protein.

[0044] Gene tethering assays are routinely employed to reveal the role of RBPs in mRNA destabilization and mRNA degradation. Gene tethering involves the artificial association of RBPs with reporter mRNAs using virus-derived high affinity RNA-protein interactions, such as MS2 RNA-MS2 protein and BoxB-λN. See, for example, Luo, E.-C. et al., Nature Structural & Molecular Biology volume 27, pages 989-1000 (2020), which is incorporated herein by reference. However, it should be understood that most gene tethering assays are designed to artificially maximize the "signal" of an experiment. Provided herein is a gene tethering assay that allows the identification of RBPs that are active in endogenous conditions.

[0045] In some embodiments, genetic tethering is used to assay the association of one or more mRNA destabilizing proteins with an mRNA target to induce its degradation. In some embodiments, genetic tethering is used to assay the association of one or more mRNA destabilizing proteins with an mRNA target to induce its degradation, and the one or more mRNA destabilizing proteins are present at endogenous levels.

[0046] In one aspect, the invention provides an mRNA destabilizing protein, such as a ribonuclease, tethered to a small molecule that binds to an mRNA target.

[0047] In one aspect, the present disclosure provides a bifunctional compound or composition that affects the recruitment of degradation factors to target RNA. In some embodiments, the degradation factors are mRNA destabilizing proteins, nucleases, and / or RNA binding proteins. However, the degradation factors are not so limited and include any proteins that interfere with the stability and / or activity of RNA. It should be further understood that some RNA binding proteins also have nuclease activity. In some embodiments, the present disclosure provides a bifunctional compound or composition that affects the recruitment of target RNA to nucleases (e.g., RBPs) that can degrade target RNA, or affects the recruitment of target RNA to RNA binding proteins (RBPs) that destabilize target RNA toward degradation by either the RNA degradation machinery of cells or tissues.

[0048] In one aspect, the present disclosure provides a bifunctional compound or composition that affects the recruitment of target RNA to degradation factors, and the degradation factors are present at endogenous levels.In some embodiments, the present disclosure provides a bifunctional compound or composition that affects the recruitment of target RNA to nucleases that can degrade target RNA, and the nucleases are present at endogenous levels, or affect the recruitment of target RNA to RNA binding proteins (RBPs) that destabilize target RNA toward degradation by either the RNA degradation machinery of cells or tissues, and the BPs that destabilize target RNA are present at endogenous levels.

[0049] In some embodiments, the compound or composition disclosed herein binds to mRNA transcript or mature mRNA.In some embodiments, the compound comprises rSM, and the compound binds to target RNA via its rSM.In general, rSM specifically binds to a specific target RNA, and causes selective degradation of the target RNA.

[0050] In some embodiments, the composition comprises an RNA binding agent such as an oligonucleotide, and the composition binds to RNA via the oligonucleotide. Oligonucleotides that bind to RNA are well known. In general, the oligonucleotides that bind to target RNA have a nucleic acid sequence that is complementary to the nucleic acid sequence in the target RNA. The binding of the oligonucleotides that have a complementary sequence to the target RNA sequence is stable and highly specific. In some embodiments, the composition that comprises an RNA binding agent such as an oligonucleotide is optimized for intracellular delivery. The optimization of oligonucleotides and compositions that comprise oligonucleotides for intracellular delivery has been well established.

[0051] In some embodiments, the composition comprises an RNA binder. In some embodiments, the RNA binder is an oligonucleotide. In some embodiments, the oligonucleotide can specifically bind to an RNA target. In some embodiments, the oligonucleotide comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotides. In some embodiments, the oligonucleotide is comprised of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotides. In some embodiments, the oligonucleotide is modified for therapeutic delivery.

[0052] In some embodiments, the target RNA transcript is a non-coding RNA, such as a microRNA (miRNA) or a long non-coding RNA (lncRNA). In some embodiments, such RNA transcripts regulate transcription, splicing, mRNA stability / degradation, or translation. In addition, non-coding regions of mRNA, such as the 5' untranslated region (5'UTR), 3'UTR, and introns, can play regulatory roles in influencing mRNA expression levels, alternative splicing, translation efficiency, and subcellular localization of mRNA and protein. Without wishing to be bound by theory, it is believed that the secondary and tertiary structures of RNA are important for these regulatory activities. Thus, the activity of the target RNA transcript or its isoforms, fragments, or variants can be modulated by binding the disclosed compounds at one or more binding sites.

[0053] In one aspect, the present disclosure provides a bifunctional compound of formula A: [ka] or a pharma- ceutically acceptable salt thereof, wherein: the rSM is an RNA-binding small molecule that binds to a target RNA transcript; DFL is degrader recruiting ligand; L is a bivalent linker group that covalently attaches the rSM to the DFL; The DFL binds to or recruits one or more degradation factors that degrade the target RNA transcript.

[0054] In some embodiments, the DFL is a small molecule that binds to an RNA binding protein (RBP), such that binding of the DFL to the RBP modulates the target RNA transcript (eg, modulates the half-life of the target RNA transcript).

[0055] In some embodiments, the DFL binds to a protein that associates with or recruits a nuclease. In some embodiments, the DFL recruits a nuclease by binding to the nuclease or by binding to a protein that associates with or recruits a nuclease, thus bringing the nuclease into close proximity to the target RNA.

[0056] In one aspect, the invention provides a method of modulating an activity of a target RNA transcript or an isoform, fragment, or variant thereof, the method comprising contacting the target RNA transcript or an isoform, fragment, or variant thereof with a disclosed compound, or a pharma- ceutically acceptable salt thereof, that binds to the target RNA transcript or an isoform, fragment, or variant thereof.

[0057] In another aspect, the invention provides a method of modulating the activity of a target protein, the method comprising contacting the corresponding target RNA transcript or an isoform, fragment, or variant thereof with a disclosed compound, or a pharma- ceutically acceptable salt thereof, that binds to the target RNA transcript or an isoform, fragment, or variant thereof.

[0058] In one aspect, the invention provides a method of decreasing the half-life or increasing the degradation of a target RNA transcript or an isoform, fragment, or variant thereof, the method comprising contacting the target RNA transcript or an isoform, fragment, or variant thereof with a disclosed compound that binds to the target RNA transcript or an isoform, fragment, or variant thereof.

[0059] In some embodiments, translation of the target RNA transcript is reduced or inhibited, for example, by reducing the half-life of the transcript, hi some embodiments, production of the corresponding functional protein or a variant thereof is reduced or inhibited.

[0060] In some embodiments, the target RNA transcript is a transcript that has a relatively long half-life in the body under normal physiological conditions or in a disease state treated by the compound of the present invention. In some embodiments, the half-life is at least 72 hours. In some embodiments, the half-life is at least 48, 24, 20, 18, 16, 14, 12, 10, 8, 6, 4, or 3 hours. In some embodiments, the half-life is about 24, 20, 18, 16, 14, 12, 10, 8, 6, 4, or 3 hours. In some embodiments, the half-life is about 3 to about 72 hours. In some embodiments, the half-life is about 4 to about 48 hours, or about 4 to 24, 4 to 18, 6 to 72, 6 to 48, 6 to 24, 6 to 18, 8 to 72, 8 to 48, 8 to 24, 8 to 18, 10 to 72, 10 to 48, 10 to 24, 10 to 18, 12 to 72, 12 to 48, 12-24, 12 to 18, 14 to 72, 14 to 48, 14 to 24, 14 to 18, 16 to 72, 16 to 48, 16 to 24, 16 to 18, 18 to 72, 18 to 48, 18 to 24, 20 to 72, 20 to 48, 20 to 24, 22 to 72, 22 to 48, 22 to 24, 24 to 72, 24 to 48, 30 to 72, or 30 to 48 hours.

[0061] In some embodiments, administration of a compound or composition provided herein results in a reduction or inhibition of production of a functional protein or variant thereof, hi some embodiments, production of the functional protein or variant thereof is reduced by at least 10%, at least 20%, at least 30%, at least 40%, at least 25%, at least 60%, at least 70%, at least 80%, at least 90%, or is not produced at detectable levels.

[0062] In some embodiments, the activity of the target RNA transcript or its isoform, fragment, or variant is inhibited or reduced. In some embodiments, the processing or splicing of the target RNA transcript or its isoform, fragment, or variant is inhibited.

[0063] In some embodiments, target RNA is mRNA, or its precursor, isoform, fragment or variant.In some embodiments, inhibiting processing or splicing leads to the reduction of mature mRNA and / or protein levels.In some embodiments, the activity of protein or its variant is inhibited or reduced, for example, due to the reduction of protein levels in cells.

[0064] In some embodiments, the target RNA transcript comprises a functionally relevant fragment of a disease-causing RNA. A target RNA transcript or an isoform, fragment, or variant thereof is "functionally relevant" if it comprises at least a portion of the target RNA transcript that is essential for ultimately transcribing and producing a corresponding disease-causing functional protein or variant thereof.

[0065] In some embodiments, the target RNA transcript is a pre-mRNA, a mature mRNA, or a partially processed mRNA, or an isoform, fragment, or variant thereof.

[0066] In some embodiments, the RNA transcript includes a 5' untranslated region (UTR).

[0067] In some embodiments, an RNA transcript comprises an open reading frame (ORF).

[0068] In some embodiments, the RNA transcript includes a 5' cap.

[0069] In some embodiments, the RNA transcript includes a 3' polyA tail (polyadenylation tail).

[0070] In some embodiments, the compound binds to the 5' untranslated region (5'UTR), 3'UTR, or introns present in the RNA transcript.

[0071] In some embodiments, the translation of RNA transcripts is reduced.In some embodiments, the level of the protein encoded by the RNA transcripts is reduced in biological samples such as cell cultures that are in contact with the disclosed compounds or compositions, or in patients that are treated with the disclosed compounds or compositions.In some embodiments, the degradation of RNA transcripts is increased.In some embodiments, the degradation of RNA transcripts is increased due to the binding of the disclosed compounds.

[0072] In one aspect, the present invention provides a method for identifying a compound that binds to a target RNA transcript or an isoform, fragment, or variant thereof, comprising: i) contacting the target RNA transcript or an isoform, fragment, or variant thereof with a disclosed compound; and ii) analyzing the results by an assay disclosed herein, optionally in combination with computational methods. In some embodiments, the method comprises the use of SEC-MS, SPR, or DEL screens to identify the compound.

[0073] In another aspect, the present invention provides a method of treating an RNA-mediated disease, disorder, or condition (including any protein-mediated disease, disorder, or condition) in a patient in need thereof, the method comprising administering to the patient an effective amount of a disclosed compound or a pharma- ceutically acceptable salt thereof. In some embodiments, the disease, disorder, or condition is a proliferative disease, such as cancer.

[0074] A variety of RNA transcripts are suitable as target RNA transcripts for use in the present invention. In some embodiments, the target RNA transcript is selected from any one of Tables A, B, C, or D below, or a precursor, isoform, unspliced ​​isoform, splice intermediate, fragment, or variant thereof.

[0075] In some embodiments, the target RNA transcript is single-stranded. In some embodiments, the target RNA transcript is double-stranded or partially double-stranded. In some embodiments, the target RNA is a pair of nucleic acids involved in an interaction, such as a miRNA-mRNA hybridized (or partially hybridized) pair. In some embodiments, the target RNA comprises one, two, or more miRNAs bound to an mRNA. In some embodiments, the target RNA is an mRNA, miRNA, premiRNA, or viral or fungal RNA.

[0076] In some embodiments, the target RNA transcript comprises at least some intramolecular base pairing, structural features such as junctions (e.g., cis or trans three-way junctions (3WJs)), quadruplexes, hairpins, triplexes, bulge loops, pseudoknots, or internal loops, and any transient form or structure adopted by a nucleic acid. In some embodiments, the target RNA transcript comprises a binding protein, such as a chaperone, an RNA binding protein (RBP), or other nucleic acid binding protein.

[0077] Target RNA transcripts of various lengths are within the scope of the present invention. For example, the target RNA may be 20 to 10,000 nucleotides long. In some embodiments, the target RNA is a relatively short sequence, for example, less than 250, less than 100, or less than 50 nucleotides long. In some embodiments, the target RNA is 100 or more nucleotides long. In some embodiments, the target RNA is 250 or more nucleotides long. In some embodiments, the target RNA is up to about 350, 450, 500, 600, 750, or 1,000, 2,000, 3,000, 4,000, 5,000, 7,500, 10,000, 15,000, 25,000, 50,000, or 50,000 or more nucleotides long. In some embodiments, the target RNA is about 30 to about 500 nucleotides long. In some embodiments, the target RNA is about 250 to about 1,000 nucleotides in length. In some embodiments, the target RNA is about 20 to 50, 30 to 60, 40 to 70, 50 to 80, 20 to 100, 30 to 100, 40 to 100, 50 to 100, 20 to 200, 30 to 200, 40 to 200, 50 to 200, 20 to 300, 50 to 300, 75 to 300, 100 to 300, 20 to 400, 50 to 400, 100 to 400, 200 to 400, 20 to 500, 50 to 500, 100 to 500, 250 to 500, 20 to 750, 50 to 750, 100-750, 250-750, 500-750, 20-1,000, 100-1,000, 250-1,000, 500-1,000, 20-2,000, 100-2,000, 500-2,000, 1,000-2,000, 20-5,000, 100-5,000, 1,000-5,000, 20-10,000, 100-10,000, 1,000-10,000, or 20-25,000 nucleotides in length.

[0078] When the target or other reference nucleic acid is RNA, "nucleotide" refers to ribonucleotides. When the target or other reference nucleic acid is DNA, "nucleotide" refers to 2'-deoxyribonucleotides. In some embodiments, the target RNA contains one or more nucleotide analogs (modified nucleotides) as defined herein and known in the art.

[0079] In some embodiments, the target RNA is a pre-mRNA, a pre-miRNA, a pre-transcript, a partially spliced ​​mRNA, a fully spliced ​​mRNA, a fully spliced ​​and partially processed mRNA, or a mature mRNA (i.e., a fully spliced ​​and processed mRNA).

[0080] In some embodiments, the RNA is non-coding RNA (ncRNA), messenger RNA (mRNA), microRNA (miRNA), ribozyme, riboswitch, lncRNA, lincRNA, snoRNA, snRNA, scaRNA, piRNA, rRNA, ceRNA, or pseudogene, each of the foregoing may be selected from human or non-human RNA, such as viral RNA, fungal RNA, or bacterial RNA.

[0081] mRNA targeting In some embodiments, the target RNA transcript is an mRNA, or a precursor of mature mRNA, or its isoform, fragment, or variant. Within mRNA, non-coding regions can affect the level of mRNA and protein expression. Briefly, these include internal ribosome entry sites (IRES) and upstream open reading frames (uORFs) that affect translation efficiency, intronic sequences that affect splicing efficiency and alternative splicing patterns, 3'UTR sequences that affect mRNA and protein localization, and elements that control mRNA degradation and half-life. Therapeutic modulation of these RNA elements can have beneficial effects. mRNA may also contain expansions of simple repetitive sequences, such as trinucleotide repeats. It has been observed that these repeat expansions containing RNA can be toxic and promote disease pathology, especially in certain neurological and musculoskeletal diseases (see Gatchel & Zoghbi, Nature Rev. Gen. 2005, 6, 743-755). Thus, in some embodiments, the invention provides a method of degrading an mRNA containing a toxic repeat expansion, or an isoform, fragment, or variant thereof, comprising contacting the mRNA with a disclosed compound. The invention further provides a method of treating a disease, disorder, or condition mediated by an mRNA containing a toxic repeat expansion, or an isoform, fragment, or variant thereof.

[0082] Furthermore, in some embodiments, the expression of target mRNA and its translation product is regulated by targeting non-coding sequences and structures in 5' and 3' UTR.For example, the RNA structure in 5' UTR can affect translation efficiency.It has been shown that the RNA structure in 5' UTR, such as hairpin, affects translation.In general, it is believed that RNA structure plays an important role in the translation of mRNA. One example of these is the internal ribosome entry site (IRES), which can affect the level of translation of the major open reading frame (Komar and Hatzoglou, Frontiers Oncol. 5: 233, 2015; Weingarten-Gabbay et al., Science 351, 4939, 2016; Calvo et al., Proc. Natl. Acad. Sci. USA 106: 7507-7512; Le Quesne et al., J. Pathol. 220:140-151, 2010; Barbosa et al., PLOS Genetics 9:e10035529, 2013). Small molecules that target these RNAs can be used to regulate specific protein levels for therapeutic benefit. In some embodiments, the small molecule rSM binding site is a 5'UTR, an internal ribosome entry site, or an upstream open reading frame.

[0083] Non-coding RNA transcripts Non-coding RNAs regulate cell biology directly through the function of RNA structures (e.g., ribonucleoproteins) as well as through the regulation of protein expression. These ncRNAs include (but are not limited to) miRNAs, lncRNAs, lincRNAs, snoRNAs, snRNAs, scaRNAs, piRNAs, ceRNAs, and pseudogenes. Agents that intervene at this level have the potential to regulate any cellular process.

[0084] In some embodiments, the target RNA transcript is an RNA that is transcribed but not translated into protein, and is referred to as a "non-coding RNA" or "ncRNA." Non-coding RNAs are highly conserved, and many types of non-coding RNAs perform a wide range of regulatory functions. As used herein, the term "non-coding RNA" includes, but is not limited to, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), long intergenic non-coding RNAs (lincRNAs), Piwi-interacting RNAs (piRNAs), competing endogenous RNAs (ceRNAs), and pseudogenes. Each of these subcategories of non-coding RNAs provides numerous RNA targets with significant therapeutic potential. Thus, in some embodiments, the present invention provides a method of treating a disease mediated by a non-coding transcript. In some embodiments, the disease is caused by a lncRNA, a lincRNA, a ceRNA, or a pseudogene. In another aspect, the present invention provides a method for producing a small molecule that modulates the activity of a target non-coding transcript to treat a disease or disorder, the method comprising screening one or more disclosed compounds for binding to or degradation of the target non-coding transcript and analyzing the results by an RNA binding assay disclosed herein. In some embodiments, the target non-coding transcript is a lncRNA, lincRNA, ceRNA, or pseudogene.

[0085] In some embodiments, the target RNA transcript is an miRNA. miRNAs are short double-stranded RNAs that regulate gene expression (Elliott & Ladomery, Molecular Biology of RNA, 2 nd(See Ed.). Each miRNA can affect the expression of many human genes. There are approximately 2,000 miRNAs in humans. These RNAs regulate many biological processes, including cell differentiation, cell fate, motility, survival, and function. miRNA expression levels vary among different tissues, cell types, and disease settings. They are often aberrantly expressed in tumors compared to normal tissues, and their activity may play an important role in cancer (for reviews, see Croce, Nature Rev. Genet. 10:704-714, 2009; Dykxhoorn Cancer Res. 70:6401-6406, 2010). miRNAs have been shown to regulate oncogenes and tumor suppressors and may themselves act as oncogenes or tumor suppressors. Some have been shown to promote epithelial-mesenchymal transition (EMT) and invasiveness and metastasis of cancer cells. In the case of cancerous miRNAs, their inhibition may be an effective anticancer treatment. Thus, in one aspect, the present invention provides a method for producing a small molecule that modulates the activity of a target miRNA to treat a disease or disorder, comprising screening one or more disclosed compounds for binding to or degradation of the target miRNA and analyzing the results by the RNA binding assay disclosed herein. In some embodiments, the miRNA regulates or acts as an oncogene or tumor suppressor. In some embodiments, the disease is cancer. In some embodiments, the cancer is a solid tumor.

[0086] Beyond oncology, miRNAs play a role in many other diseases, including cardiovascular and metabolic diseases (Quiant and Olson, J. Clin. Invest. 123:11-18, 2013; Olson, Science Trans. Med. 6: 239ps3, 2014; Baffy, J. Clin. Med. 4:1977-1988, 2015).

[0087] Many mature miRNAs are relatively short in length, and therefore may lack the three-dimensional structure that is fully folded to be targeted by small molecules.However, it is believed that the level of such miRNAs can be reduced by small molecules that bind to primary transcripts or miRNA precursors and block the biogenesis of mature miRNAs.Thus, in some embodiments of the above-mentioned method, the target miRNA is a primary transcript or miRNA precursor, and its corresponding mature miRNA affects oncogenes or tumor suppressors, or affects the level or activity of disease-causing RNA transcripts or proteins.

[0088] In some embodiments, the target RNA transcript is a lncRNA. lncRNAs are RNAs of more than 200 nucleotides (nt) that do not code for proteins (Rinn & Chang, Ann. Rev. Biochem. 2012, 81, 145-166; (for reviews, see Morris and Mattick, Nature Reviews Genetics 15:423-437, 2014; Mattick and Rinn, Nature Structural & Mol. Biol. 22:5-7, 2015; Iyer et al., Nature Genetics 47(:199-208, 2015)). They can affect the expression of protein-coding mRNAs at the level of transcription, splicing, and mRNA degradation. Considerable research has shown that lncRNAs can regulate transcription by recruiting epigenetic regulators that increase or decrease transcription by altering chromatin structure (e.g., Holoch and Moazed, Nature Reviews Genetics 16:71-84, 2015). lncRNAs are associated with human diseases including cancer, inflammatory diseases, neurological diseases and cardiovascular diseases (e.g., Presner and Chinnaiyan, Cancer Discovery 1:391-407, 2011; Johnson, Neurobiology of Disease 46:245-254, 2012; Gutscher and Diederichs, RNA Biology 9:703-719, 2012; Kumar et al., PLOS Genetics 9:e1003201, 2013; van de Vondervoort et al., Frontiers in Molecular Neuroscience, 2013; Li et al., Int. J. Mol. Sci. 14: 18790-18808, 2013). In general, lncRNAs are expressed at lower levels compared to mRNAs.Many lncRNAs are physically associated with chromatin (Werner et al., Cell Reports 12,1-10, 2015) and are transcribed close to protein-coding genes. They remain physically associated at the site of transcription and often act locally to regulate the expression of adjacent mRNAs in cis.

[0089] lncRNAs act at multiple different levels to regulate the expression of protein-coding genes and affect transcription, alternative splicing, and mRNA decay. For example, lncRNAs have been shown to bind to the epigenetic regulator PRC2 to facilitate its recruitment to genes whose transcription is then repressed via chromatin modifications. lncRNAs can form complex structures that mediate their association with various regulatory proteins. Small molecules that bind to these lncRNA structures can be used to regulate the expression of genes that are normally regulated by individual lncRNAs.

[0090] Targeting toxic RNA (repeat RNA) Simple repeats in mRNA are often associated with human diseases. These are often, but not limited to, repeats of three nucleotides, such as CAG ("triplet repeat") (for reviews, see Gatchel and Zoghbi, Nature Reviews Genetics 6:743-755, 2005; Krzyzosiak et al., Nucleic Acids Res. 40:11-26, 2012; Budworth and McMurray, Methods Mol. Biol.1010:3-17, 2013, which are incorporated herein by reference). Triplet repeats are abundant in the human genome and tend to grow over generations. About 40 human diseases are associated with the expansion of repetitive sequences. Diseases caused by triplet expansions are known as triplet repeat expansion diseases (TREDs). Healthy individuals have a variable number of triplet repeats, but there is a threshold above which higher repeat counts cause disease. The threshold varies with different disorders. The triplet repeat may be unstable. When the gene is inherited, the repeat number may increase and the condition may be more severe or have a faster onset across generations. If an individual has a repeat number within the normal range, it is not expected to expand when passed to the next generation. If the repeat number is in the premutation range (normal but unstable repeat number), the repeat may or may not expand upon transmission to the next generation. Normal individuals with the premutation do not have the condition, but are at risk of inheriting triplet repeats in the full mutation range and having affected children. TRED may be autosomal dominant, autosomal recessive, or X-linked. The more common triplet repeat disorders are autosomal dominant.

[0091] The repeats may be in the coding or non-coding part of the mRNA. In the case of repeats in non-coding regions, the repeats may be in the 5'UTR sequence, intron sequence, or 3'UTR sequence. Some examples of diseases caused by repeat sequences in coding regions are shown in Table A. [Table A]

[0092] In some embodiments, the target RNA is one of those listed in Table A, or a precursor, isoform, fragment, or variant thereof.

[0093] Some examples of diseases caused by repetitive sequences in non-coding regions of mRNA are shown in Table B. [Table B]

[0094] In some embodiments, the target RNA is one of those listed in Table B, or a precursor, isoform, fragment, or variant thereof.

[0095] Toxicity resulting from repeat sequences can be a direct consequence of the action of the toxic RNA itself, due to RNA and / or aberrant protein toxicity, or if the repeat expansion is within a coding sequence. Repeat-expansion RNAs can act by sequestering important RNA-binding proteins (RBPs) to a focal spot. One example of a sequestered RBP is the muscleblind family protein MBNL1. Sequestration of RBPs results in splicing defects and defects in nucleocytoplasmic transport of RNA and proteins. Sequestration of RBPs can also affect miRNA biogenesis. These perturbations in RNA biology can profoundly affect neuronal function and survival, resulting in a variety of neurological disorders.

[0096] Repeated sequences in RNA bind to RBPs and form secondary and tertiary structures that affect normal RNA biology. One specific disease example is myotonic dystrophy (DM1), a form of common inherited muscle disease characterized by muscle weakness and slow relaxation of muscle after contraction (Machuca-Tzili et al., Muscle Nerve 32:1-18, 2005, incorporated herein by reference). It is caused by a CUG expansion in the 3'UTR of the myotonic dystrophy protein kinase (DMPK) gene. RNA containing this repeat generates misregulation of alternative splicing of several developmentally regulated transcripts through its effect on splicing regulators MBNL1 and CUG repeat binding protein (CELF1) (Wheeler et al., Science 325:336-339, 2009, incorporated herein by reference). Small molecules that bind to the CUG repeats within the DMPK transcript alter the RNA structure, preventing focus formation and alleviating the effects on these spicing regulators. Fragile X syndrome (FXS), the most common inherited form of mental retardation, is the result of a CGG repeat expansion within the 5'UTR of the FMR1 gene (see Lozano et al., Intractable Rare Dis. Res. 3:134-146, 2014, which is incorporated herein by reference). FMRP is essential for regulating the translation of many mRNAs and protein trafficking, and is an essential protein for synapse development and neuroplasticity. Its deficiency therefore leads to neuropathology. Small molecules targeting this CGG repeat RNA could alleviate the repression of FMR1 mRNA and FMRP protein expression. Another TRED with a very high unmet medical need is Huntington's disease (HD). HD is a progressive neurological disorder with motor, cognitive, and psychiatric changes (Zuccato et al., Physiol Rev. 90:905-981, 2010, incorporated herein by reference).CAG repeats in the coding sequence of the HTT gene are characterized as polyglutamine or polyQ disorders because they result in proteins with polyglutamine repeats that have deleterious effects on transcription, vesicle transport, mitochondrial function, and proteasome activity. However, HTT CAG repeat RNA itself also exhibits toxicity, including sequestration of MBNL1 protein into nuclear inclusions. Another specific example is the GGGGCC repeat expansion in the C9orf72 (chromosome 9 open reading frame 72) gene, which is common in both familial frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) (Ling et al., Neuron 79:416-438, 2013; Haeusler et al., Nature 507:195-200, 2014, incorporated herein by reference). The repeat RNA structure forms nuclear foci that sequester important RNA-binding proteins. GGGGCC repeat RNA also binds and sequesters RanGAP1, impairing the nuclear-cytoplasmic transport of RNA and protein (Zhang et al., Nature 525:56-61, 2015, incorporated herein by reference).Selectively targeting any of these repeat-expanded RNAs may add therapeutic benefit to these neurological diseases.

[0097] The present invention includes a method for treating a disease or disorder in which the abnormal RNA itself causes a pathogenic effect, rather than acting through the regulation of protein expression or the regulation of protein expression. In some embodiments, the target RNA is a repeat RNA, such as those described herein or those described in Table A or Table B. In some embodiments, the repeat RNA mediates or is involved in a repeat expansion disease in which the repeat is present in the coding region of the mRNA. In some embodiments, the disease or disorder is a repeat expansion disease in which the repeat is present in the non-coding region of the mRNA. In some embodiments, the disease or disorder is selected from Huntington's disease (HD), dentatorubral-pallidal atrophy (DRPLA), spinal-bulbar muscular atrophy (SBMA), or spinocerebellar degeneration (SCA) selected from SCA1, SCA2, SCA3, SCA6, SCA7, or SCA17. In some embodiments, the disease or disorder is selected from fragile X syndrome, myotonic dystrophy (DM1 or myotonic dystrophy), Friedreich's ataxia (FRDA), a spinocerebellar degeneration (SCA) selected from SCA8, SCA10, or SCA12, or C9FTD (amyotrophic lateral sclerosis or ALS).

[0098] In some embodiments, the disease is amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), frontotemporal dementia (FTD), myotonic dystrophy (DM1 or myotonic dystrophy), or fragile X syndrome.

[0099] Also provided is a method of producing a small molecule that modulates the activity of a target repeat-expanded RNA to treat a disease or disorder, comprising screening one or more disclosed compounds for binding to the target repeat-expanded RNA and analyzing the results by an RNA binding assay disclosed herein. In some embodiments, the repeat-expanded RNA causes a disease or disorder selected from HD, DRPLA, SBMA, SCA1, SCA2, SCA3, SCA6, SCA7, or SCA17. In some embodiments, the disease or disorder is selected from fragile X syndrome, DM1, FRDA, SCA8, SCA10, SCA12, or C9FTD.

[0100] Target RNA and Diseases / Conditions There are known associations between numerous RNAs and diseases or conditions, some of which are shown in Tables C or D below. Thus, in some embodiments of the above-described methods, the target RNA transcript is selected from one of Tables C or D. In some embodiments, the target RNA mediates or is involved in a disease or disorder selected from one of Tables C or D. Thus, the present invention further provides a method of treating a disease, disorder, or condition selected from one of Tables C or D, comprising administering to a patient in need of treating the disease, disorder, or condition an effective amount of a disclosed compound. In some embodiments, the method upregulates or downregulates the target RNA transcript as shown in the "Desirability of Up / Downregulation" column of Tables C or D below, thus treating the disease, disorder, or condition. [Table C-1] [Table C-2] [Table C-3] [Table C-4] [Table C-5] [Table C-6] [Table C-7] [Table D]

[0101] 2. Compounds and Related Definitions The bifunctional compounds of the present invention, as well as their pharma- ceutically acceptable salts and compositions, have been found to be effective as regulators of the degradation of target RNA transcripts in biological samples or patients.Such compounds are also useful for treating RNA-mediated diseases, disorders, or conditions, such as those described herein.

[0102] As generally described above, the present invention provides a bifunctional compound of formula A [ka] or a pharma- ceutically acceptable salt thereof, wherein: the rSM is an RNA-binding small molecule that binds to a target RNA transcript; DFL is a degrader recruiting ligand; L is a bivalent linker group that covalently attaches the rSM to the DFL; The DFL binds to or recruits one or more degradation factors that degrade the target RNA transcript.

[0103] RNA-binding small molecules (rSM) In one aspect, the disclosure provides a bifunctional compound of formula A, the compound comprises an rSM. Various rSMs known in the art may be used in accordance with the present invention. In some embodiments, the rSM is modified from its known structure to covalently link the rSM to a linker L at any available modifiable C atom or heteroatom, such as N, O, S, or P atom of the rSM. In relation to a C atom, "modifiable" refers to a C atom having 1) a bonded H atom that can be replaced by a bond with L through a chemical reaction, such as oxidation, reduction, nucleophilic substitution, or crosslinking reaction, or 2) a C atom that can participate in a chemical reaction, such as oxidation, reduction, nucleophilic substitution, or crosslinking reaction, due to the presence of an unsaturation or a leaving group attached to the C atom. For example, a C=O group, a C=N group, or a C-Br group are "modifiable". Similarly, a modifiable heteroatom may be bonded to an H atom that can be replaced by a bond with L, or is modifiable due to the presence of a leaving group attached to the unsaturation or heteroatom.

[0104] In some embodiments, the rSM is a small molecule or a pharma- ceutically acceptable salt thereof. In some embodiments, the rSM has a molecular weight (MW) of 1000 or less. In some embodiments, the rSM has a MW of about 750 or less. In some embodiments, the rSM has a MW of about 600 or less. In some embodiments, the rSM has a MW of about 500 or less. In some embodiments, the rSM has a MW of about 100 to about 1000. In some embodiments, the rSM has a MW of about 150 to about 800, about 150 to about 600, about 150 to about 400, about 150 to about 350, about 200 to about 350, or about 200 to about 450.

[0105] In some embodiments, the rSM or compound of formula A has a K of 1 μM, 500 nM, 100 nM, 50 nM, 10 nM, 1 nM, 500 pM, 10 pM, or 1 pM under biological conditions. dor lower affinity to the target RNA transcript, or an isoform, fragment, or variant thereof. In some embodiments, the rSM or compound has a K of 0.1 nm to 500 nm, 10 nm to 250 nm, 0.001 to 25 μM, 0.01 to 25 μM, 0.1 to 25 μM, 0.1 to 15 μM, 0.01 to 10 μM, 0.001 to 1 μM, 0.001 to 0.1 μM, or 0.001 to 0.01 μM. d and binds to a target RNA transcript or an isoform, fragment, or variant thereof.

[0106] Exemplary rSM In some embodiments, the rSM is one of the following: [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C, N, or O atom.

[0107] In some embodiments, the rSM is one such as those described in Peng, W. et al., J. Med. Chem. 2018, 61, 6629-6646, which is incorporated herein by reference.

[0108] In some embodiments, the rSM is a compound described in Shi, Y. et al., Cell Chem. Biol. 2019, 26, 319-330, which is incorporated by reference herein, such as one of the following: [ka] [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom.

[0109] In some embodiments, the rSM is a compound disclosed, for example, in Velagapudi, SP et al. (2014), “Sequence-based design of bioactive small molecules that target precursor microRNAs,” Nat. Chem. Biol. 10, 291, which is incorporated herein by reference: [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C, N, or O atom.

[0110] In some embodiments, the rSM is a MALAT-1 binding agent, such as: [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C, N, or O atom.

[0111] In some embodiments, the rSM is a G-quadruplex binding agent, such as: [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C or N atom.

[0112] In some embodiments, the rSM is one of the following compounds: [ka] [ka] [ka] [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C, N, S or O atom.

[0113] In some embodiments, the rSM is a compound according to formula I from U.S. Pat. No. 8,729,263, which is incorporated herein by reference, or a compound according to formula I from U.S. Pat. No. 8,729,263, which is incorporated herein by reference. [ka] or a pharma- ceutically acceptable salt thereof, wherein each variable is defined therein, and rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom.

[0114] In some embodiments, the rSM is described in U.S. Patent No. 9,040,712, each of which is incorporated herein by reference. For example, in some embodiments, the rSM is a compound according to formula X from U.S. Patent No. 9,040,712: [ka] or a pharma- ceutically acceptable salt thereof, wherein each variable is defined therein, and rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom.

[0115] In some embodiments, the rSM is selected from one of those described in Angelbello, AJ, et al., "Small molecule targeting of RNA structures in neurological disorders," Annals of the New York Academy of Sciences, 2020 Jul;1471(1):57-71, which is incorporated herein by reference, or a pharma- ceutically acceptable salt thereof, and the rSM is covalently linked to the L at any available modifiable C, N, O, S, or P atom. In some embodiments, the rSM is one of the following: [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] or [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom.

[0116] In some embodiments, the rSM is [ka] [ka] or a pharma- ceutically acceptable salt thereof, where the rSM is covalently attached to L of Formula A at the shaded ball in the above structure. In some embodiments, the rSM binds to a miRNA, such as miR-21.

[0117] In some embodiments, the rSM is selected from one of those shown in Table 1A below, or a pharma- ceutically acceptable salt thereof, and the rSM is covalently bonded to L at any available modifiable C, N, O, S, or P atom.

[0118] In some embodiments, the rSM is a compound of formula IX: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Pat. No. 9,150,612, which is incorporated herein by reference in its entirety.

[0119] In some embodiments, the rSM is a compound of formula X [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 9,550,769, which is incorporated herein by reference in its entirety. In some embodiments, the variable L above is: [ka] where each variable is as defined in U.S. Pat. No. 9,550,769.

[0120] In some embodiments, the rSM is selected from one of those disclosed in U.S. Pat. No. 10,157,261, the entirety of which is incorporated herein by reference, and the rSM is covalently bonded to L at any available modifiable C, N, O, S, or P atom.

[0121] In some embodiments, the rSM is a compound of formula XI: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Pat. No. 9,586,944, which is incorporated herein by reference in its entirety.

[0122] In some embodiments, the rSM is a compound of formula XII: HYH XII where H is a group of the structure [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Pat. No. 9,795,687, which is incorporated herein by reference in its entirety.

[0123] In some embodiments, the rSM is a compound selected from one of the following: [ka] [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; or Another compound disclosed in WO2018 / 151810, the entirety of which is incorporated herein by reference.

[0124] In some embodiments, the rSM is a compound of the following structure: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently attached to L at any available modifiable C, N, O, S or P atom; or another compound disclosed in WO2018 / 152414, the entirety of which is incorporated herein by reference.

[0125] In some embodiments, the rSM is a compound of the following structure: [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; or Another compound disclosed in U.S. Patent No. 2018 / 0334678, the entirety of which is incorporated herein by reference.

[0126] In some embodiments, the rSM is a compound of formula XIII: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 2018 / 0296532, the entirety of which is incorporated herein by reference.

[0127] In some embodiments, the rSM is a compound of formula XIV: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2018 / 098297, the entire contents of which are incorporated herein by reference.

[0128] In some embodiments, the rSM is a compound of formula XV, XVI, or XVII: [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 2019 / 0152924, the entirety of which is incorporated herein by reference.

[0129] In some embodiments, the rSM is a compound of formula XVIII: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2019 / 005993, the entire contents of which are incorporated herein by reference.

[0130] In some embodiments, the rSM is a compound of formula XIX: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2018 / 232039, the entire contents of which are incorporated herein by reference.

[0131] In some embodiments, the rSM is a compound of formula XX: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2019 / 005980, the entire contents of which are incorporated herein by reference.

[0132] In some embodiments, the rSM is a compound of formula XXI: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2018 / 226622, the entire contents of which are incorporated herein by reference.

[0133] In some embodiments, the rSM is a compound of formula XXII: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom;

[0134] wherein each variable is as defined in WO 2018 / 098446, the entire contents of which are incorporated herein by reference.

[0135] In some embodiments, the rSM is a compound of formula XXIII: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2017 / 087364, the entire contents of which are incorporated herein by reference.

[0136] In some embodiments, the rSM is ataluren. [ka] or a deuterated analogue thereof or a pharma- ceutically acceptable salt thereof, as disclosed in U.S. Patent No. 2018 / 0333397 or WO2017 / 087364, each of which is incorporated herein by reference.

[0137] In some embodiments, the rSM is a compound of the following structure: [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom as described in U.S. Patent No. 2018 / 147228, the entirety of which is incorporated herein by reference.

[0138] In some embodiments, the rSM is a compound of formula XXIV: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Pat. No. 9,969,754, which is incorporated herein by reference in its entirety.

[0139] In some embodiments, the rSM is a compound of formula XXV-i: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 9,371,336, which is incorporated herein by reference in its entirety. In some embodiments, the rSM is a compound disclosed in U.S. Patent No. 9,371,336, or a pharma- ceutically acceptable salt thereof.

[0140] In some embodiments, the rSM is a compound of formula XXV-ii: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 9,617,268, which is incorporated herein by reference in its entirety. In some embodiments, the rSM is a compound disclosed in U.S. Patent No. 9,617,268, or a pharma- ceutically acceptable salt thereof.

[0141] In some embodiments, the rSM is a compound of formula XXVI: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 2019 / 0000844, which is incorporated herein by reference in its entirety. In some embodiments, the rSM is a compound disclosed in U.S. Patent No. 2019 / 0000844, or a pharma- ceutically acceptable salt thereof.

[0142] In some embodiments, the rSM is a compound of formula XXVII: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 2018 / 0161456, which is incorporated herein by reference in its entirety. In some embodiments, the rSM is a compound disclosed in U.S. Patent No. 2018 / 0161456, or a pharma- ceutically acceptable salt thereof.

[0143] In some embodiments, the rSM is a compound of formula XXVIII: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 10,195,202, which is incorporated herein by reference in its entirety. In some embodiments, the rSM is a compound disclosed in U.S. Patent No. 10,195,202, or a pharma- ceutically acceptable salt thereof.

[0144] In some embodiments, the rSM is a compound of formula XXIX-XXXIII: [ka] [ka] [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2019 / 028440, which is incorporated herein by reference in its entirety. In some embodiments, the rSM is a compound disclosed in WO 2019 / 028440, or a pharma- ceutically acceptable salt thereof.

[0145] In some embodiments, the rSM is a compound of formula XXXIV-XLXI: [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2019 / 060917, which is incorporated herein by reference in its entirety. In some embodiments, the rSM is a compound disclosed in WO 2019 / 060917, or a pharma- ceutically acceptable salt thereof.

[0146] In some embodiments, the rSM is a compound of formula XLXII or XLXIII: [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Pat. No. 9,879,007, which is incorporated herein by reference in its entirety.

[0147] In some embodiments, the rSM is a compound of formula XLXIV or XLXV: [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2019 / 191229, the entire contents of which are incorporated herein by reference.

[0148] In some embodiments, the rSM is a compound of formula XLXVI: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2019 / 191092, the entire contents of which are incorporated herein by reference.

[0149] In some embodiments, the rSM is a compound of formula XLXVII: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in U.S. Patent No. 2019 / 315773, the entire contents of which are incorporated herein by reference.

[0150] In some embodiments, the rSM is a compound of formula LVIII, LIX, or LX: [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2019 / 199972, the entirety of which is incorporated herein by reference. Such compounds are useful, for example, for regulating splicing of the FOXM1 gene for use in treating cancer.

[0151] In some embodiments, the rSM is a compound of formula LXI: [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in formula (I) of WO 2020 / 005873, the entirety of which is incorporated herein by reference. Such compounds are useful, for example, for regulating RNA targets that mediate Huntington's disease. In some embodiments, the compound is a compound of formula (Ibb1) as described herein. [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is covalently attached to L at any available modifiable C, N, O, S or P atom, and each variable is as defined therein.

[0152] In some embodiments, the rSM is a compound of formula LXII or LXIII [ka] [ka] or a pharma- ceutically acceptable salt thereof, in which rSM is covalently bonded to L at any available modifiable C, N, O, S or P atom; wherein each variable is as defined in WO 2020 / 005877, the entirety of which is incorporated herein by reference. Such compounds are useful, for example, for binding to HTT RNA transcripts for use in treating diseases such as Huntington's disease.

[0153] In some embodiments, the rSM is a compound of formula LXIV, LXV, LXVI, or LXVII: [ka] [ka] [ka] [ka] or a pharma- ceutically acceptable salt thereof, where rSM is covalently attached to L at any available modifiable C, N, O, S or P atom, and each variable is as defined in WO 2020 / 005882, the entirety of which is incorporated herein by reference. Such compounds are useful, for example, for binding to HTT RNA transcripts for use in treating diseases such as Huntington's disease.

[0154] In some embodiments, the rSM is selected from one of those set forth in U.S. Patent Nos. 8,729,263, 9,545,404, 9,856,474, or 7,838,657, each of which is incorporated herein by reference.

[0155] In some embodiments, the rSM is selected from one of those shown in Table 1A below, or a pharma- ceutically acceptable salt thereof, and the rSM is covalently bonded to L at any available modifiable C, N, O, S, or P atom. [Table 1A-1] [Table 1A-2] [Table 1A-3] [Table 1A-4] [Table 1A-5] [Table 1A-6] [Table 1A-7] [Table 1A-8] [Table 1A-9] [Table 1A-10] [Table 1A-11] [Table 1A-12] [Table 1A-13] [Table 1A-14] [Table 1A-15]

Table 1A-16

Table 1A-17

Table 1A-18

Table 1A-19

Table 1A-20

Table 1A-21

Table 1A-22

Table 1A-23

Table 1A-24

Table 1A-25

Table 1A-26

Table 1A-27

Table 1A-28

Table 1A-29

Table 1A-30

Table 1A-31

Table 1A-32

[0156] Degraders and RNA-binding proteins (RBPs) In one aspect, the present disclosure provides a compound of formula A: [ka] or a pharma- ceutically acceptable salt thereof, wherein rSM is an RNA-binding small molecule that binds to a target RNA transcript, DFL is a degradator recruitment ligand, and L is a bivalent linker group that covalently links rSM to the DFL, and DFL binds to or recruits the degradator.

[0157] In one aspect, the disclosure provides a composition comprising an RNA binding agent that binds to a target RNA transcript and a degradator recruiting ligand (DFL), where the DFL binds to or recruits a degradator.

[0158] The degradation factor provided herein is any protein, polypeptide, or biological molecule present in a cell that modulates a target RNA when brought in the vicinity of the target RNA. Modulating RNA provided herein includes destabilizing RNA, stabilizing RNA, degrading RNA, or acting on RNA in any other capacity. Degradation factors include any protein that interferes with the stability and / or activity of RNA. In some embodiments, the degradation factor is an RNA destabilizing protein, a nuclease, or an RNA binding protein. It should be understood that nucleases and RNA binding proteins are not mutually exclusive, e.g., some RNA binding proteins also have nuclease activity. In some embodiments, the present disclosure provides bifunctional compounds or compositions that affect the recruitment of target RNA to nucleases that can degrade the target RNA, or affect the recruitment of target RNA to RNA binding proteins (RBPs) that destabilize the target RNA toward degradation by either the RNA degradation machinery of the cell or tissue.

[0159] In one aspect, the present invention provides compounds and compositions that act on RNA without the need to induce RBP. Of course, some RBPs need to be induced, dimerized, or otherwise modified to be active. For example, RNase L needs to be induced to dimerize and be active. Activation of RBPs is often not a desirable process, as it results in the induction of undesirable elements. For example, some RBPs are activated by inducing immune response. Furthermore, RBPs often cannot be activated in cells where activation is desirable. As disclosed herein, in some embodiments, the present invention provides compounds and compositions that act on RNA without the need to induce RBP. In some embodiments, the RBP is not RNase L.

[0160] In some embodiments, the degradation factor (e.g., nuclease or RBP) can regulate the target RNA while the degradation factor is at endogenous levels. In some embodiments, the RBP does not need to be induced to be active. In some embodiments, the RBP does not need to dimerize to be active. In some embodiments, the RBP is not RNase L.

[0161] In some embodiments, the RBP or degradation factor does not have a nuclease or other RNA degrading or RNA destabilizing activity, but can bind to or recruit a second protein or multi-component complex that has nuclease, RNA degrading and / or RNA destabilizing activity.

[0162] In one aspect, the present disclosure provides a bifunctional compound or composition that affects the recruitment of target RNA to degradation factors, and the degradation factors are present at endogenous levels.In some embodiments, the present disclosure provides a bifunctional compound or composition that affects the recruitment of target RNA to nucleases that can degrade target RNA, and the nucleases are present at endogenous levels, or affect the recruitment of target RNA to RNA binding proteins (RBPs) that destabilize target RNA toward degradation by either the RNA degradation machinery of cells or tissues, and the BPs that destabilize target RNA are present at endogenous levels.

[0163] In some embodiments, the DFL binds to or attracts a complex of proteins that can degrade or otherwise regulate RNA function (e.g., availability of protein translation). In some embodiments, the protein complex is the CCR4-NOT (carbon catabolite repression negative in the absence of TATA) complex.

[0164] CCR4-NOT complex In some embodiments, DFL binds to or attracts a complex of proteins that can degrade or otherwise regulate RNA function. In some embodiments, DFL binds to a protein complex. In some embodiments, DFL binds to one or more RBPs that are part of a protein complex. Binding of one or more RBPs is expected to bring the complete protein complex into proximity with the target RNA. In some embodiments, DFL binds to the CCR4-NOT (carbon catabolite repression negative in the absence of TATA) complex, or an RBP that is a member of the CCR4-NOT complex. The CCR4-NOT complex is a large, highly conserved, multifunctional assembly of proteins involved in different aspects of mRNA metabolism. Without wishing to be bound by theory, it is believed that the CCR4-NOT complex plays a role in deadenylation-dependent mRNA turnover. RBPs that are part of the CCR4-NOT complex include CNOT1, CNOT2, CNOT3, CNOT6, CNOT6L, CNOT7, CNOT8, CNOT9, CNOT10, and CNOT11. The functions of the CCR4-NOT complex and each RBP that constitutes the complex are discussed, for example, in Shirai et al. Multifunctional roles of the mammalian CCR4-NOT complex in physiological phenomena, Frontiers in Genetics, 2014, 5, Article 286, which is incorporated by reference.

[0165] In some embodiments, the RBP is one of those listed in Table 1B. In some embodiments, the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1. In some embodiments, the DFL is a small molecule ligand of an RBP listed in Table 1B, such as CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1. In some embodiments, the RBP is CNOT2, CNOT7, or YTHDF2.

[0166] CNOT2 In some embodiments, the RBP is CNOT2. In some embodiments, the disclosed compound or composition comprises a small molecule CNOT2 ligand as DFL. CNOT2 is a member of the CCR4-NOT complex. Without wishing to be bound by theory, it is believed that CNOT2 interacts with other RBPs (e.g., RBPs of the CCR4-NOT complex) to cause deadenylation of target RNA. CNOT2 is widely expressed in the human body.

[0167] CNOT7 In some embodiments, the RBP is CNOT7. In some embodiments, the disclosed compound or composition comprises a small molecule CNOT7 ligand as DFL. CNOT7 is a member of the CCR4-NOT complex. Without wishing to be bound by theory, CNOT7 is believed to act as an exonuclease. It is believed to induce the degradation of target RNA (e.g., via deadenylation) directly or in conjunction with other members of the CCR4-NOT complex. CNOT7 is widely expressed in the human body.

[0168] CNOT6 In some embodiments, the RBP is CNOT6. In some embodiments, the disclosed compound or composition comprises a small molecule CNOT6 ligand as the DFL. Without wishing to be bound by theory, it is believed that CNOT6 is a mammalian homologue of yeast CCR4 protein and is part of the mammalian CCR4-NOT complex. CNOT6 protein has 3'-5' exoribonuclease activity and shows a preference for removing A residues from mRNA 3'-polyA tails. Without wishing to be bound by theory, it is believed that CNOT6 shows a) 3'-5' RNase activity that causes rapid destabilization of mRNA, b) ubiquitous expression, and c) broad substrate specificity.

[0169] In some embodiments, the RBP is CNOT2, CNOT7, YTHDF2, DDX6, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1.

[0170] YTHDF2 YTHDF2 stands for YTH N6-methyladenosine RNA binding protein 2. In some embodiments, the RBP is YTHDF2. In some embodiments, the disclosed compound or composition comprises a small molecule YTHDF2 ligand as a DFL. Without wishing to be bound by theory, it is believed that YTHDF2 specifically recognizes and binds N6-methyladenosine (m6A)-containing RNA, thereby regulating RNA stability. It may also be said that, depending on the circumstances, it acts as a regulator of mRNA stability by promoting the degradation of m6A-containing RNA through interaction with CCR4-NOT and ribonuclease P / MRP complex.

[0171] DDX6 In some embodiments, RBP is DDX6. In some embodiments, the disclosed compound or composition comprises small molecule DDX6 ligand as DFL. DDX6 is a member of DEAD box protein family. Without wishing to be bound by theory, DDX6 is an RNA helicase, found in P body and stress granule, and functions in translation repression and mRNA degradation.

[0172] ZFP36 In some embodiments, the RBP is ZFP36. In some embodiments, the disclosed compound or composition comprises a small molecule ZFP36 ligand as DFL. Without wishing to be bound by theory, ZFP36 is believed to suppress the abundance and translation of mRNA targets, particularly through novel AU-rich sites in coding sequences. ZFP36 binds to AU-rich elements (AREs) in the 3'-untranslated region (UTR) of some cytokine mRNAs and promotes their degradation. For example, TTP is a component of a negative feedback loop that prevents TNF-α production by destabilizing its mRNA.

[0173] DCP1, DCP1A, or DCP2 In some embodiments, the RBP is DCP1, DCP1A, or DCP2. In some embodiments, the disclosed compounds or compositions include a small molecule DCP2 ligand as a DFL. Without wishing to be bound by theory, DCP2 is believed to be the catalytic subunit of the DCP1-DCP2 complex of proteins. By using a DFL for either DCP1 (DCP1A) or DCP2, the DCP1-DCP2 complex can be brought into proximity of the target RNA. DCP2 catalyzes the removal of the mRNA 5-cap, which inhibits mRNA translation and promotes mRNA degradation by the 5'-'3' ribonuclease, Xrn1. The DCP1-DCP2 complex functions on all mRNAs in vivo. Without wishing to be bound by theory, DCP1-DCP2 is believed to exhibit a) rapid destabilization of mRNA by decapping, b) ubiquitous expression, and c) broad substrate specificity.

[0174] ZC3H12A(Regnase-1) In some embodiments, the RBP is ZC3H12A (Regnase-1). In some embodiments, the disclosed compounds or compositions include a small molecule ZC3H12A (Regnase-1) ligand as a DFL. Without wishing to be bound by theory, ZC3H12A (Regnase-1) is believed to function as an endoribonuclease involved in mRNA degradation.

[0175] PARN In some embodiments, the RBP is PARN. In some embodiments, the disclosed compounds or compositions include small molecule PARN ligands. Without wishing to be bound by theory, PARN protein is believed to be a 3'-exoribonuclease similar to the RNase D family of 3'-exoribonucleases. It prefers poly(A) as a substrate, and therefore efficiently degrades the poly(A) tail of mRNA. Exonucleolytic degradation of poly(A) tails is often the first step in the degradation of eukaryotic mRNAs. PARN is also involved in the silencing of certain maternal mRNAs during oocyte maturation and early embryonic development, as well as nonsense-mediated decay (NMD) of mRNAs containing premature stop codons.

[0176] MARF1 MARF1 is an abbreviation for meiosis arrest factor 1, and is an mRNA destabilizing protein. In some embodiments, the RBP is MARF1. In some embodiments, the disclosed compound or composition comprises a small molecule MARF1 ligand. Without wishing to be bound by theory, it is believed that MARF1 interacts with Dcp1-Dcp2 proteins, which promotes mRNA degradation. MARF1 is also further believed to have intrinsic endonuclease activity. Artificial tethering of MARF1 to a reporter mRNA causes degradation of the mRNA, and this activity is independent of interaction with Dcp1-Dcp2. Without wishing to be bound by theory, it is believed that MARF1 provides a) ribonuclease activity and destabilization of mRNA via Dcp1-Dcp2 recruitment, and b) broad substrate specificity as demonstrated by gene tethering.

[0177] IRE1 In some embodiments, the RBP is IRE1. In some embodiments, the disclosed compounds or compositions include a small molecule IRE1 ligand as a DFL. Without wishing to be bound by theory, IRE / ERN1 is an endoplasmic reticulum (ER) associated protein, which is believed to function downstream of the endoplasmic reticulum protein response (UPR). IRE1 is a transmembrane protein that exists as a monomer on the ER membrane. When ER stress is detected, the protein undergoes phosphorylation, which leads to oligomerization and activation of RNase activity. The primary target of IRE1 RNase activity is XBP1 mRNA, although some reports suggest that IRE1 cleaves several mRNAs. It is further believed that IRE1 exhibits a) RNase activity and b) ubiquitous expression.

[0178] In some embodiments, the RBP is SMG7, KSRP, or SMG6.

[0179] SMG7 In some embodiments, the RBP is SMG7. In some embodiments, the disclosed compound or composition comprises a small molecule SMG7 ligand as the DFL. SMG7 is part of the nonsense-mediated decay (NMD) pathway and is recruited to defective mRNAs via interaction with Upf1. In gene tethering experiments, SMG7 has been shown to function in a manner that is dominant over upstream mRNA surveillance proteins, causing a severe reduction in reporter mRNA levels via the deadenylation-dependent mRNA decay pathway. Without wishing to be bound by theory, it is believed that SMG7 exhibits a) broad substrate specificity, b) no activation step (activity is limited by mRNA recruitment), c) no directional bias for activity (tethered to the 5' or 3' end of target mRNAs for mRNA destabilization), and d) high to moderate expression in most cell and tissue types.

[0180] KSRP In some embodiments, the RBP is KSRP. In some embodiments, the disclosed compound or composition comprises a small molecule KSRP ligand as the DFL. KSRP (also known as KHSRP) is a KH domain-containing protein that functions in mRNA degradation of specific mRNA targets in vivo. KSRP is an AU-rich element-binding protein. Without wishing to be bound by theory, it is believed that upon binding to AU-rich elements (AREs), it promotes mRNA degradation via deadenylation and the 3'-5' degradation pathway. KSRP is further believed to exhibit a) broad substrate specificity, b) no activation step (activity is limited by mRNA recruitment), c) rapid kinetics of mRNA degradation, and d) ubiquitous expression in cell and tissue types.

[0181] SMG6 In some embodiments, the RBP is SMG6. In some embodiments, the disclosed compound or composition comprises a small molecule SMG6 ligand as the DFL. Without wishing to be bound by theory, it is believed that SMG6 is a PIN domain containing endonuclease associated with the NMD pathway. SMG6 is recruited to NMD substrate mRNA via activated Upf1 protein. Once recruited, SMG6 endonucleolytically cleaves the mRNA. Experiments involving SMG6 tethering to mRNA have revealed that it can cleave reporter mRNA but still requires assembly of NMD-associated protein complexes on the mRNA. Without wishing to be bound by theory, it is believed that SMG6 exhibits a) RNase activity, b) ubiquitous expression, and c) broad substrate specificity.

[0182] In some embodiments, the RBP is selected from one of those in Table 1B below: In some embodiments, the DFL is a ligand of an RBP listed in Table 1B. [Table 1B-1] [Table 1B-2] [Table 1B-3]

[0183] Degradation factor ligand In one embodiment, the present disclosure provides a bifunctional compound of formula A, the compound comprises a degrader ligand. The degrader ligand is a chemical moiety that can bind to a degrader, such as a nuclease or an RBP. The degrader ligand is not limited to such, as long as it can bind to the degrader and / or the degrader can act on the target RNA transcript.

[0184] In some embodiments, the DFL is a small molecule or a pharma- ceutically acceptable salt thereof. In some embodiments, the DFL has a molecular weight (MW) of 1000 or less. In some embodiments, the DFL has a MW of about 750 or less. In some embodiments, the DFL has a MW of about 600 or less. In some embodiments, the DFL has a MW of about 500 or less. In some embodiments, the DFL has a MW of about 100 to about 1000. In some embodiments, the DFL has a MW of about 150 to about 800, about 150 to about 600, about 150 to about 400, about 150 to about 350, about 200 to about 350, or about 200 to about 450.

[0185] Methods for identifying DFLs for an RBP of interest are well established (eg, DNA-encoded library screening).

[0186] In some embodiments, the DFL is selected from one of those shown in Table 1C below. [Table 1C-1] [Table 1C-2] [Table 1C-3] [Table 1C-4] [Table 1C-5] [Table 1C-6] [Table 1C-7] [Table 1C-8] [Table 1C-9] [Table 1C-10] [Table 1C-11] [Table 1C-12] [Table 1C-13]

[0187] Linker As generally defined above, the linker L in the formulas described herein is a divalent group that connects the rSM to the ligand of the decomposition factor ligand (DFL). In some embodiments, L is a covalent bond or a divalent, saturated or unsaturated, linear or branched, optionally substituted C 1-50 is a hydrocarbon chain, wherein 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of L are -Cy 2 -, -O-, -N(R)-, -S-, OC(O)-, -C(O)O-, -C(O)-, -C(S)-, -S(O)-, -S(O) 2 -, -N(R)S(O) 2 -, -S(O) 2 N(R)-, -N(R)C(O)-, -C(O)N(R)-, -OC(O)N(R)-, -N(R)C(O)O-, -N(R)C(O)N(R)-, -N(R)C(S)N(R)-, -Si(R) 2 -, -Si(OH)(R)-, -Si(OH) 2 -, -P(O)(OR)-, -P(O)(R)-, -P(O)(NR 2 )-,amino acid, [ka] [ka] [ka] [ka] or [ka] and wherein Each-Cy 2 - is an independently optionally substituted bivalent ring selected from phenylenyl, 8-12-membered bicyclic arylenyl, 3-8-membered saturated carbocyclylene or partially unsaturated carbocyclylenyl, 8-12-membered bicyclic saturated carbocyclylenyl or partially unsaturated carbocyclylenyl, 3-8-membered saturated heterocyclylenyl or partially unsaturated heterocyclylenyl having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, 8-12-membered bicyclic saturated heterocyclylenyl or partially unsaturated heterocyclylenyl having 1-5 heteroatoms independently selected from nitrogen, oxygen, and sulfur, 5-6-membered heteroarylenyl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, and 8-10-membered bicyclic heteroarylenyl having 1-5 heteroatoms independently selected from nitrogen, oxygen, and sulfur; Each q is independently 1, 2, or 3.

[0188] In some embodiments, L is a covalent bond. In some embodiments, L is a bivalent, saturated or unsaturated, linear or branched, optionally substituted C 1-50 is a hydrocarbon chain, wherein 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of L are -Cy 2 -, -O-, -N(R)-, -S-, -OC(O)-, -C(O)O-, -C(O)-, -C(S)-, -S(O)-, -S(O) 2 -, -N(R)S(O) 2 -, -S(O) 2 N(R)-, -N(R)C(O)-, -C(O)N(R)-, -OC(O)N(R)-, -N(R)C(O)O-, -N(R)C(O)N(R)-, -N(R)C(S)N(R)-, -Si(R) 2-, -Si(OH)(R)-, -Si(OH) 2 -, -P(O)(OR)-, -P(O)(R)-, -P(O)(NR 2 )-,amino acid, [ka] [ka] [ka] [ka] or [ka] and wherein

[0189] In some embodiments, L is a divalent, saturated or unsaturated, linear or branched, optionally substituted C 1-50 , C 1~40 , C 1~30 , C 1~20 , C 1~15 , C 1~10 , C 1~5 , C 2~50 , C 2~40 , C 2~30 , C 2~20 , C 2~15 , C 2~10 , C 3~50 , C 3~40 , C 3~30 , C 3~20 , C 3~15 , C 3~10 , C 4~50 , C 4~40 , C 4~30 , C 4~20 , C 4~15 , C 4~10 , C 5~50 , C 5~40 , C 5~30 , C 5~20 , C 5~15 , C 5~10 , C 6~50 , C 6~40 , C6~30 , C 6~20 , C 6~15 , C 7~50 , C 7~40 , C 7~30 , C 7~20 , C 7~15 , C 8~50 , C 8~40 , C 8~30 , C 8~20 , C 8~15 , C 10~50 , C 10~40 , C 10~30 , C 10~20 , C 10~15 , C 12~50 , C 12~40 , C 12~30 , C 12~20 , C 15~50 , C 15~40 , C 15~30 , C 15~20 , C 20~50 , C 20~40 , or C 20-30 is a hydrocarbon chain, wherein 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of L are -Cy 2 -, -O-, -N(R)-, -S-, -OC(O)-, -C(O)O-, -C(O)-, -C(S)-, -S(O)-, -S(O) 2 -, -N(R)S(O) 2 -, -S(O) 2 N(R)-, -N(R)C(O)-, -C(O)N(R)-, -OC(O)N(R)-, -N(R)C(O)O-, -N(R)C(O)N(R)-, -N(R)C(R)-, -N(R)C(R)C(R)-, amino acids, [ka] [ka] [ka] [ka] or [ka] are independently substituted by:

[0190] In some embodiments, L is a divalent, saturated or unsaturated, linear or branched, optionally substituted C 1-50 , C 1-40 , C 1-30 , C 1-20 , C 1-15 , C 1-10 , C 1-5、 C 2-50 , C 2-40 , C 2-30 , C 2-20 , C 2-15 , C 2-10 , C 3-50 , C 3-40 , C 3-30 , C 3-20 , C 3-15 , C 3-10 , C 4-50 , C 4-40 , C 4-30 , C 4-20 , C 4-15 , C 4-10 , C 5-50 , C 5-40 , C 5-30 , C 5-20 , C 5-15 , C 5-10 , C 6-50 , C 6-40 , C 6-30 , C 6-20 , C 6-15 , C 7-50 , C 7-40 , C 7-30 , C 7-20 , C 7-15 , C 8-50 , C 8-40 , C 8-30 , C 8-20 , C 8-15 , C 10-50 , C 10-40 , C 10-30 , C 10-20 , C 10-15 , C 12-50 , C 12-40 , C 12-30 , C 12-20 , C 15-50 , C 15-40 , C 15-30 , C15-20 , C 20-50 , C 20-40 , or C 20-30 a hydrocarbon chain, wherein 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of L are -Cy2-, -O-, -N(R)-, -S-, -OC(O)-, -C(O)O-, -C(O)-, -C(S)-, -S(O)-, -S(O)2-, -N(R)S(O)2-, -S(O)2N(R)-, -N(R)C(O)-, -C(O)N(R)-, -OC(O)N(R)-, -N(R)C(O)O-, -N(R)C(O)N(R)-, -N(R)C(R)-, -N(R)C(R)C(R)-, amino acids, [ka] [ka] [ka] [ka] [ka] [ka] [ka] [ka] or [ka] are independently substituted by:

[0191] In some embodiments, L is a divalent, saturated or unsaturated, linear or branched, optionally substituted C 1-50 , C 1-40 , C 1-30 , C1-20 , C 1-15 , C 1-10 , C 1-5、 C 2-50 , C 2-40 , C 2-30 , C 2-20 , C 2-15 , C 2-10 , C 3-50 , C 3-40 , C 3-30 , C 3-20 , C 3-15 , C 3-10 , C 4-50 , C 4-40 , C 4-30 , C 4-20 , C 4-15 , C 4-10 , C 5-50 , C 5-40 , C 5-30 , C 5-20 , C 5-15 , C 5-10 , C 6-50 , C 6-40 , C 6-30 , C 6-20 , C 6-15 , C 7-50 , C 7-40 , C 7-30 , C 7-20 , C 7-15 , C 8-50 , C 8-40 , C 8-30 , C 8-20 , C 8-15 , C 10-50 , C 10-40 , C 10-30 , C 10-20 , C 10-15 , C 12-50 , C 12-40 , C 12-30 , C 12-20 , C 15-50 , C 15-40 , C 15-30 , C 15-20 , C 20-50 , C 20-40 , or C 20-30 a hydrocarbon chain, wherein 0, 1, 2, 3, 4, 5, 6, 7, or 8 methylene units of L are -Cy2-, -O-, -N(R)-, -S-, -OC(O)-, -C(O)O-, -C(O)-, -C(S)-, -S(O)-, -S(O)2-, -N(R)C(O)-, [ka] -C(O)N(R)-, -OC(O)N(R)-, -N(R)C(O)O-, amino acids, [ka] [ka] [ka] [ka] or [ka] are independently substituted by:

[0192] In some embodiments, L is 1, 2, 3, 4, 5, or 6 PEG units, [ka] or [ka] In some embodiments, L comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 PEG units. In some embodiments, L comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 units, or 1, 2, 3, 4, 5, or 6 units. [ka] [ka] [ka] [ka] [ka] or [ka] Includes.

[0193] In some embodiments, L is a saturated chain. In some embodiments, L contains at least one unsaturated pair of carbon atoms, i.e., at least one double or triple carbon-carbon bond. In some embodiments, L contains 1, 2, 3, 4, or 5 double or triple carbon-carbon bonds. In some embodiments, L is a linear hydrocarbon chain, where the methylene units of L are optionally replaced or substituted as described above. In some embodiments, L is a saturated and linear hydrocarbon chain, where the methylene units of L are optionally replaced or substituted as described above.

[0194] In some embodiments, L is substituted with 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 "optional substituents" as defined herein. In some embodiments, each substituent is selected from the group consisting of deuterium, halogen, -CN, -OR, -NR 2 , -SR, 3-8 membered saturated or partially unsaturated monocyclic carbocyclic ring, one or more C 1-4 Alkyl, -CO 2 R, -OR, -CONR 2 , -NR 2or phenyl optionally substituted with halogen; an 8-10 membered bicyclic aromatic carbocyclic ring; a 4-8 membered saturated or partially unsaturated monocyclic heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; a 5-6 membered monocyclic heteroaromatic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; an 8-10 membered bicyclic heteroaromatic ring having 1-5 heteroatoms independently selected from nitrogen, oxygen, or sulfur; nitrogen, oxygen, or sulfur; or -CN, -OR, -NR 2 , C optionally substituted with -SR 1-6 Aliphatic groups, 3-8 membered saturated or partially unsaturated monocyclic carbocyclic rings, one or more C 1-4 Alkyl, -CO 2 R, -OR, -CONR 2 , -NR 2 or phenyl optionally substituted with halogen, an 8-10 membered bicyclic aromatic carbocyclic ring, a 4-8 membered saturated or partially unsaturated monocyclic heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, a 5-6 membered monocyclic heteroaromatic ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, an 8-10 membered bicyclic heteroaromatic ring having 1-5 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or C 1-6 Aliphatic groups are optionally substituted, together with the carbon atom to which they are attached, with 1, 2, 3, 4, 5, or 6 deuterium or halogen atoms, or two substituents attached to the same carbon atom to form a 3- to 6-membered saturated monocyclic carbocyclic or 3- to 6-membered saturated heterocyclic ring having 1 to 2 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0195] As mentioned above, in some embodiments, the methylene unit of L is replaced with an amino acid. The amino acid may be naturally occurring or non-naturally occurring. In some embodiments, the amino acid is selected from non-polar or branched chain amino acids (BCAAs). In some embodiments, the amino acid is selected from valine, isoleucine, leucine, methionine, alanine, proline, glycine, phenylalanine, tyrosine, tryptophan, histidine, asparagine, glutamine, serine threonine, lysine, arginine, histidine, aspartic acid, glutamic acid, cysteine, selenocysteine, or tyrosine. In some embodiments, the amino acid is an L-amino acid. In some embodiments, the amino acid is a D-amino acid.

[0196] In some embodiments, L is [ka] or [ka] It is.

[0197] In some embodiments, L is selected from one of those shown in Table 2 below. [Table 2-1] [Table 2-2] [Table 2-3] [Table 2-4] [Table 2-5] [Table 2-6] [Table 2-7]

Table 2-8

Table 2-9

Table 2-10

Table 2-11

Table 2-12

Table 2-13

Table 2-14

Table 2-15

Table 2-16

Table 2-17

Table 2-18

Table 2-19

Table 2-20

Table 2-21

Table 2-22

Table 2-23

Table 2-24

[0198] In some embodiments, L is selected from those shown in Table 2 above.

[0199] In some embodiments, the compound is not selected from one of those described in WO2019 / 209975.

[0200] In some embodiments, the compound of formula A is not selected from the following: [ka] [ka] [ka] [ka] [ka]

[0201] definition As used herein, "nucleoside" refers to a molecule consisting of a guanine (G), adenine (A), thymine (T), uridine (U), or cytidine (C) base covalently linked to a pentose sugar, while "nucleotide" or "mononucleotide" refers to a nucleoside phosphorylated at one of the hydroxyl groups of the pentose sugar. "Nucleoside" also encompasses analogs of G, A, T, C, or U, as well as natural or unnatural nucleic acid building blocks in which the base, sugar, and / or phosphate backbone have been modified or substituted. Nucleoside analogs are known in the art and include those described herein. Also included are endogenously post-transcriptionally modified nucleosides, such as methylated nucleosides.

[0202] A linear nucleic acid molecule is said to have a "5' end" (5' terminus) and a "3' end" (3' terminus) because mononucleotides are joined unidirectionally via a phosphodiester bond (or analogue) to make an oligonucleotide, such that the phosphate (or analogue) on the 5' carbon of one mononucleotide sugar is attached to the oxygen on the 3' carbon of the adjacent mononucleotide sugar, except as described elsewhere herein for adenylation. Thus, an end of an oligonucleotide is referred to as the "5' end" if its 5' phosphate (or analogue) is not attached to the oxygen of the 3' carbon of the mononucleotide sugar, and as the "3' end" if its 3' oxygen is not attached to the 5' phosphate (or analogue) of the subsequent mononucleotide sugar. As used herein, a "terminal nucleotide" is the nucleotide at the terminal position of the 3' end or 5' end. The 3' end or 5' end may alternatively terminate with a 3'-OH or 5'-OH if the terminal nucleotide is not phosphorylated.

[0203] As used herein, the term "nucleic acid" refers to a covalently linked sequence of nucleotides in which the 3' position of the sugar of one nucleotide is linked to the 5' position of the sugar of the next nucleotide by a phosphodiester bond (i.e., a 3' to 5' phosphodiester bond), and the nucleotides are linked in a specific sequence, i.e., the linear order of the nucleotides. "Nucleic acid" includes analogs of the above, in which one or more nucleotides are modified at the base, sugar, or phosphodiester. Such analogs are known in the art and include those described elsewhere herein. As used herein, "polynucleotide" or "polynucleic acid" refers to a long nucleic acid sequence of many nucleotides (or analogs thereof). For example, a polynucleotide (or polynucleic acid) can be, but is not limited to, 60, 61-1,000, or more than 201-1,000, or more than 1,000 nucleotides long. As used herein, an "oligonucleotide" or "oligonucleic acid" is a short polynucleotide or portion of a polynucleotide. For example, but not limited to, oligonucleotides can be 5-10, 10-60, or 10-200 nucleotides in length.

[0204] In some embodiments, the nucleic acid, oligonucleotide, or polynucleotide consists primarily of, or consists primarily of, or is mostly 2'-deoxyribonucleotides (DNA) or ribonucleotides (RNA). In some embodiments, the oligonucleotide consists of, or comprises, 2'-deoxyribonucleotides (DNA). In some embodiments, the oligonucleotide consists of, or comprises, ribonucleotides (RNA). In some embodiments, the oligonucleotide is a DNA sequence of consecutive nucleotides linked to an RNA sequence of consecutive nucleotides, or a DNA-RNA hybrid having some regions of RNA and some regions of DNA.

[0205] As used herein, the term "RNA-mediated" with respect to RNA-mediated disorders, diseases, and / or conditions means any disease or other deleterious condition in which RNA is known to play a role, such as overexpressed, underexpressed, mutant, misfolded, expanded, pathogenic, or oncogenic RNA.

[0206] The compounds of the present invention include those generally described herein, and are further exemplified by the classes, subclasses, and species disclosed herein. As used herein, the following definitions shall apply unless otherwise indicated. For purposes of this invention, chemical elements are defined as defined in the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75 th In addition, the general principles of organic chemistry are specified in Organic Chemistry, Thomas Sorrell, University Science Books, Sausalito: 1999, and March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, MB Smith and J. March, 7 th Edition, John Wiley & Sons: 2013, the entire contents of each of which are incorporated herein by reference.

[0207] The term "aliphatic" or "aliphatic group", as used herein, means a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is fully saturated or contains one or more units of unsaturation, or a monocyclic or bicyclic hydrocarbon that is fully saturated or contains one or more units of unsaturation, but is not aromatic with a single point of attachment to the rest of the molecule (also referred to herein as "carbocycle", "alicyclic" or "cycloalkyl"). Unless otherwise specified, an aliphatic group contains 1-6 aliphatic carbon atoms. In some embodiments, an aliphatic group contains 1-5 aliphatic carbon atoms. In other embodiments, an aliphatic group contains 1-4 aliphatic carbon atoms. In still other embodiments, an aliphatic group contains 1-3 aliphatic carbon atoms, and in still other embodiments, an aliphatic group contains 1-2 aliphatic carbon atoms. In some embodiments, an "alicyclic" (or "carbocycle" or "cycloalkyl") refers to a monocyclic C ring that is fully saturated or contains one or more units of unsaturation, but is not aromatic with a single point of attachment to the rest of the molecule. 3 -C 6 "a" refers to a hydrocarbon. Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkenyl, alkynyl groups, and hybrids thereof, such as (cycloalkyl)alkyl, and (cycloalkenyl)alkyl or (cycloalkyl)alkenyl.

[0208] As used herein, the term "bicyclic ring" or "bicyclic ring system" refers to any bicyclic ring system, i.e., any bicyclic ring system that is carbocyclic or heterocyclic, saturated, or has one or more unsaturated units with one or more atoms in common between the two rings of the ring system. Thus, the term includes any permissible ring fusion, such as ortho-fused or spirocyclic. As used herein, the term "heterobicyclic" is a subset of "bicyclic" which requires that one or more heteroatoms are present in one or both rings of the bicycle. Such heteroatoms may be present at the ring junction, may be optionally substituted, and may be selected from nitrogen (including N-oxides), oxygen, sulfur (including oxidized forms such as sulfones and sulfonates), phosphorus (including oxidized forms such as phosphates), boron, and the like. In some embodiments, the bicyclic group has 7-12 ring members and 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. As used herein, the term "bridged bicyclic" refers to any bicyclic ring system having at least one bridge, i.e., carbocyclic or heterocyclic, saturated or partially unsaturated. As defined by IUPAC, a "bridge" is an unbranched chain or valence bond of atoms connecting two bridgeheads, and a "bridgehead" is any skeletal atom of the ring system that is bonded to three or more skeletal atoms (except hydrogen). In some embodiments, the bridged bicyclic group has 7-12 ring members and 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Such bridged bicyclic groups are well known in the art and include the groups described below, in which each group is attached to the remainder of the molecule at any substitutable carbon or nitrogen atom. Unless otherwise specified, bridged bicyclic groups are optionally substituted with one or more of the substituents described for aliphatic groups. Additionally or alternatively, any substitutable nitrogen of the bridged bicyclic group is optionally substituted. Exemplary bicyclic rings include: [ka]

[0209] Examples of bridged bicyclic rings include: [ka] [ka]

[0210] The term lower alkyl means C 1-4 It refers to a straight chain or branched alkyl group. Exemplary lower alkyl groups are methyl, ethyl, propyl, isopropyl, butyl, isobutyl, and tert-butyl.

[0211] The term "lower haloalkyl" refers to a C substituted with one or more halogen atoms. 1-4 It refers to a straight chain or branched alkyl group.

[0212] The term "heteroatom" refers to oxygen, sulfur, nitrogen, phosphorus, or silicon (including any oxidized form of nitrogen, sulfur, phosphorus, or silicon, the quaternized form of any basic nitrogen, or a substitutable nitrogen of a heterocycle, e.g., N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl), or NR + (similar to N-substituted pyrrolidinyl).

[0213] The term "unsaturated," as used herein, means that a moiety has one or more units of unsaturation.

[0214] As used herein, "divalent C 1-8 (or C 1-6 The term "saturated or unsaturated, straight or branched hydrocarbon chain" refers to divalent alkylene, alkenylene, and alkynylene chains that are straight or branched as defined herein.

[0215] The term "alkylene" refers to a divalent alkyl group. An "alkylene chain" is a polymethylene group, i.e., -(CH 2 ) n-, where n is a positive integer, preferably 1 to 6, 1 to 4, 1 to 3, 1 to 2, or 2 to 3. A substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for substituted aliphatic groups.

[0216] The term "alkenylene" refers to a divalent alkenyl group. A substituted alkenylene chain is a polymethylene group containing at least one double bond in which one or more hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for substituted aliphatic groups.

[0217] The term "halogen" means F, Cl, Br, or I.

[0218] The term "aryl" used alone or as part of a larger moiety such as "aralkyl", "aralkoxy", or "aryloxyalkyl" refers to a monocyclic or bicyclic ring system having a total of 5 to 14 ring members, in which at least one ring in the system is aromatic and each ring in the system contains 3 to 7 ring members. The term "aryl" may be used interchangeably with the term "aryl ring". In certain embodiments of the invention, "aryl" refers to an aromatic ring system, including, but not limited to, phenyl, biphenyl, naphthyl, anthracyl, and the like, which may bear one or more substituents. Also included within the scope of the term "aryl" as used herein are groups in which an aromatic ring is fused to one or more non-aromatic rings, such as indanyl, phthalimidyl, naphthymidyl, phenanthridinyl, or tetrahydronaphthyl.

[0219] The terms "heteroaryl" and "heteroar-", used alone or as part of a larger moiety, e.g., "heteroaralkyl" or "heteroaralkoxy", refer to groups having 5 to 10 ring atoms, preferably 5, 6, or 9 ring atoms, with 6, 10, or 14 π electrons shared in a cyclic array, and having 1 to 5 heteroatoms in addition to the carbon atoms. The term "heteroatom" refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of basic nitrogen. Heteroaryl groups include, but are not limited to, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl. As used herein, the terms "heteroaryl" and "heteroar-" also include groups in which a heteroaromatic ring is fused to one or more aryl, alicyclic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring. Non-limiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, 4H-quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and pyrido[2,3-b]-1,4-oxazin-3(4H)-one. Heteroaryl groups may be monocyclic or bicyclic. The term "heteroaryl" may be used interchangeably with the terms "heteroaryl ring," "heteroaryl group," or "heteroaromatic," any of which terms include rings that are optionally substituted. The term "heteroaralkyl" refers to an alkyl group substituted with a heteroaryl, where the alkyl and heteroaryl portions independently are optionally substituted.

[0220] As used herein, the terms "heterocycle," "heterocyclyl," "heterocyclic radical," and "heterocycle" are used interchangeably and refer to a stable 5- to 7-membered monocyclic or 7- to 10-membered bicyclic heterocyclic moiety that is either saturated or partially unsaturated as defined above and has, in addition to carbon atoms, one or more, preferably one to four heteroatoms. When used in reference to a ring atom of a heterocycle, the term "nitrogen" includes substituted nitrogen. As an example, in a saturated or partially unsaturated ring having 0-3 heteroatoms selected from oxygen, sulfur, or nitrogen, the nitrogen can be N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl), or . + It may also be NR (similar to N-substituted pyrrolidinyl).

[0221] A heterocycle can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure, and any of the ring atoms can be substituted as required. Examples of such saturated or partially unsaturated heterocyclic radicals include, but are not limited to, tetrahydrofuranyl, tetrahydrothiophenyl, pyrrolidinyl, piperidinyl, pyrrolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and quinuclidinyl. The terms "heterocycle", "heterocyclyl", "heterocyclyl ring", "heterocyclic group", "heterocyclic moiety", and "heterocyclic radical" are used interchangeably herein and also include groups in which a heterocyclyl ring is fused to one or more aryl, heteroaryl, or alicyclic rings, such as indolinyl, 3H-indolyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl. Heterocyclyl groups may be monocyclic or bicyclic.The term "heterocyclylalkyl" refers to an alkyl group substituted with a heterocyclyl, where the alkyl and heterocyclyl portions independently are optionally substituted.

[0222] As used herein, the term "partially unsaturated" refers to a ring moiety that contains at least one double or triple bond. The term "partially unsaturated" is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aryl or heteroaryl moieties as defined herein.

[0223] As described herein, the compounds of the invention may contain "optionally substituted" moieties. In general, the term "substituted", whether preceded by the term "optionally" or not, means that one or more hydrogens of the specified moiety are replaced with a suitable substituent. Unless otherwise indicated, an "optionally substituted" group may have a suitable substituent ("optionally substituent") at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be the same or different at each position. The combinations of substituents envisioned by the present invention are preferably those that result in the formation of stable or chemically feasible compounds. As used herein, the term "stable" refers to compounds that are substantially unchanged when subjected to conditions to enable their production, detection, and in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein.

[0224] Suitable monovalent substituents on a substitutable carbon atom of an "optionally substituted" group are independently halogen, -(CH 2 ) 0-4 R 〇 , -(CH 2 ) 0-4 OR 〇 , -O(CH 2 ) 0-4 R o , -O-(CH 2 ) 0-4 C(O)OR°, -(CH 2 ) 0-4 CH(OR 〇 ) 2 , -(CH 2 ) 0-4 S.R. 〇, which may be substituted with R° -(CH 2 ) 0-4 Ph, R° may be substituted with -(CH 2 ) 0-4 O(CH 2 ) 0-1 Ph, R° may be substituted with -CH=CHPh, R° may be substituted with -(CH 2 ) 0-4 O(CH 2 ) 0-1 -Pyridyl, -NO 2 , -CN, -N 3 , -(CH 2 ) 0-4 N(R 〇 ) 2 , -(CH 2 ) 0-4 N(R 〇 )C(O)R 〇 , -N(R 〇 )C(S)R 〇 , -(CH 2 ) 0-4 N(R 〇 )C(O)NR 〇 2 , -N(R 〇 )C(S)NR 〇 2 , -(CH 2 ) 0-4 N(R 〇 )C(O)OR 〇 , -N(R 〇 )N(R 〇 )C(O)R 〇 , -N(R 〇 )N(R 〇 )C(O)NR 〇 2 , -N(R 〇 )N(R 〇 )C(O)OR 〇 , -(CH 2 ) 0-4 C(O)R 〇 , -C(S)R 〇 , -(CH 2 ) 0-4 C(O)OR 〇 , -(CH 2 ) 0-4 C(O)SR 〇 , -(CH 2 ) 0-4C(O)OSiR 〇 3 、-(CH 2 ) 0-4 OC(O)R 〇 、-OC(O)(CH 2 ) 0-4 SR-、SC(S)SR°、-(CH 2 ) 0-4 SC(O)R 〇 、-(CH 2 ) 0-4 C(O)NR 〇 2 、-C(S)NR 〇 2 、-C(S)SR°、-SC(S)SR°、-(CH 2 ) 0-4 OC(O)NR 〇 2 、-C(O)N(OR 〇 )R 〇 、-C(O)C(O)R 〇 、-C(O)CH 2 C(O)R 〇 、-C(NOR 〇 )R 〇 、-(CH 2 ) 0-4 SSR 〇 、-(CH 2 ) 0-4 S(O) 2 R 〇 、-(CH 2 ) 0-4 S(O) 2 OR 〇 、-(CH 2 ) 0-4 OS(O) 2 R 〇 、-S(O) 2 NR 〇 2 、-(CH 2 ) 0-4 S(O)R 〇 、-N(R 〇 )S(O) 2 NR 〇 2 、-N(R 〇 )S(O) 2 R 〇 、-N(OR 〇 )R 〇 、-C(NH)NR〇 2 , -P(O) 2 R 〇 , -P(O)R 〇 2 , -OP(O)R 〇 2 , -OP(O)(OR 〇 ) 2 , SiR 〇 3 , -(C 1-4 Linear or branched alkylene)ON(R 〇 ) 2 , or -(C 1-4 Linear or branched alkylene)C(O)ON(R 〇 ) 2 where each R 〇 are optionally substituted as defined below and independently represent hydrogen, C 1~6 Aliphatic, -CH 2 Ph, -O(CH 2 ) 0~1 Ph, -CH 2 -(5-6 membered heteroaryl ring), or a 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, together with their intervening atoms, R 〇 two independent occurrences of form a 3-12 membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below.

[0225] R 〇 The preferred monovalent substituents (or R 〇 (a ring formed by taking two independent occurrences of together with their intervening atoms) are independently halogen, -(CH 2 ) 0-2 R ● , -(Halo R ● ), -(CH 2 ) 0-2 OH, -(CH 2 ) 0-2 OR ● , -(CH 2 ) 0-2CH(OR ● ) 2 , -O(HaloR ● ), -CN, -N 3 , -(CH 2 ) 0-2 C(O)R ● , -(CH 2 ) 0-2 C(O)OH, -(CH 2 ) 0-2 C(O)OR ● , -(CH 2 ) 0-2 S.R. ● , -(CH 2 ) 0-2 SH, -(CH 2 ) 0-2 NH 2 , -(CH 2 ) 0-2 NHR ● , -(CH 2 ) 0-2 NR ● 2 , -NO 2 , -SiR ● 3 , -OSiR ● 3 , -C(O)SR ● 、 -(C 1-4 Linear or branched alkylene)C(O)OR ● , or -SSR ● where each R ● is unsubstituted or, if preceded by "halo", is substituted only with one or more halogens; C 1-4 Aliphatic, -CH 2 Ph, -O(CH 2 ) 0-1 R is independently selected from Ph, or a 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. 〇 Suitable divalent substituents on a saturated carbon atom of include ═O and ═S.

[0226] Suitable divalent substituents on a saturated carbon atom of an "optionally substituted" group include: ═O, ═S, ═NNR * 2, =NNHC(O)R * , =NNHC(O)OR * , =NNHS(O) 2 R * , =NR * , =NOR * , -O(C(R * 2 )) 2-3 O-, or -S(C(R * 2 )) 2-3 S-, where R * Each independent occurrence of may be substituted with hydrogen, as defined below. 1-6 Aliphatic or unsubstituted 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents attached to adjacent substitutable carbons of an "optionally substituted" group include: -O(CR * 2 ) 2-3 O-, where R * Each independent occurrence of may be substituted with hydrogen, as defined below. 1-6 It is selected from aliphatic or unsubstituted 5-6 membered saturated, partially unsaturated, or aryl rings having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0227] R * Suitable substituents on the aliphatic group include halogen, -R ● ,-(Halo R ● ), -OH, -OR ● , -O(HaloR ● ), -CN, -C(O)OH, -C(O)OR ● , -NH 2 , -NHR ● , -NR ● 2 , or -NO 2 In the formula, each R ● is unsubstituted or, if preceded by "halo", is substituted with one or more halogens only, and independently represents C 1-4 Aliphatic, -CH 2 Ph, -O(CH 2 )0-1 Ph, or a 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0228] Suitable substituents on a substitutable nitrogen of an "optionally substituted" group include -R † , -NR † 2 , -C(O)R † , -C(O)OR † , -C(O)C(O)R † , -C(O)CH 2 C(O)R † , -S(O) 2 R † , -S(O) 2 NR † 2 , -C(S)NR † 2 , -C(NH)NR † 2 , or -N(R † )S(O) 2 R † In the formula, each R † are independently hydrogen, and C may be substituted as defined below. 1~6 an aliphatic, unsubstituted -OPh, or an unsubstituted 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur; or, notwithstanding the above definitions, R † two independent occurrences of together with their intervening atoms form an unsubstituted 3-12 membered saturated, partially unsaturated, or aryl monocyclic or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0229] R † Suitable substituents on the aliphatic groups are independently halogen, -R ● , -(Halo R ● ), -OH, -OR ● , -O(haloR ● ), -CN, -C(O)OH, -C(O)OR ● , -NH 2 , -NHR● , -NR ● 2 , or -NO 2 wherein each R is unsubstituted or, if preceded by "halo", is substituted with one or more halogens only, and independently represents 1-4 Aliphatic, -CH 2 Ph, -O(CH 2 ) 0-1 Ph, or a 5-6 membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

[0230] As used herein, the term "pharmaceutical acceptable salt" refers to a salt that is suitable for use in contact with the tissues of humans and lower animals without excessive toxicity, irritation, allergic reactions, etc., within the scope of sound medical judgment, and is commensurate with a reasonable benefit / risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, SM Berge et al. describe pharmaceutical acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, which is incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of the present invention include salts derived from suitable inorganic and organic acids and bases. Examples of pharmaceutical acceptable non-toxic acid addition salts are salts of amino groups formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid, and perchloric acid, or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid, or malonic acid, or by using other methods used in the art, such as ion exchange. Other pharma- ceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecyl sulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydrogen iodide, 2-hydroxy-ethanesulfonate, and the like. Examples of salts that can be used include, but are not limited to, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, and valerate.

[0231] Salts derived from appropriate bases include alkali metal salts, alkaline earth metal salts, ammonium salts, and N + (C 1-4 Alkyl)4 Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, etc. Further pharma- ceutically acceptable salts include non-toxic ammonium, quaternary ammonium, and amine cations, formed where appropriate using counterions such as halides, hydroxides, carboxylates, sulfates, phosphates, nitrates, lower alkylsulfonates, and arylsulfonates.

[0232] Unless otherwise stated, structures depicted herein are also intended to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure, such as the R and S configurations for each asymmetric center, Z and E double bond isomers, and Z and E conformers. Accordingly, single stereoisomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention. Additionally, unless otherwise stated, structures depicted herein are also intended to include compounds which differ only in the presence of one or more isotopically enriched atoms. For example, replacement of hydrogen by deuterium or tritium, or 13 C or 14 Compounds having this structure including the replacement of a carbon with a C-enriched carbon are within the scope of this invention. Such compounds are useful, for example, as analytical tools, as probes in biological assays, or as therapeutic agents according to the present invention.

[0233] As used herein, the term "binding agent" or "ligand" is defined as a compound that binds to a target RNA transcript or a degradation factor (e.g., a nuclease) or an RBP with a measurable affinity. In certain embodiments, a binding agent has an IC of less than about 50 μM, less than about 1 M, less than about 500 μM, less than about 100 nM, less than about 10 nM, or less than about 1 nM. 50 and / or has a binding constant.

[0234] The compounds of the present invention may be tethered to a detectable moiety. It will be appreciated that such compounds are useful as imaging agents. Those skilled in the art will recognize that the detectable moiety may be attached to the provided compound via a suitable substituent. As used herein, the term "suitable substituent" refers to a moiety capable of covalent attachment to a detectable moiety. Such moieties are well known to those skilled in the art and include, for example, groups containing a carboxylate moiety, an amino moiety, a thiol moiety, or a hydroxyl moiety, to name just a few. It will be appreciated that such moieties may be attached directly to the provided compound or may be attached via a tethering group, such as a bivalent saturated or unsaturated hydrocarbon chain. In some embodiments, such moieties may be attached via click chemistry. In some embodiments, such moieties may be attached via 1,3-cycloaddition of an azide with an alkyne, optionally in the presence of a copper catalyst. Methods using click chemistry are known in the art and are described in Rostovtsev et al., Angew. Chem. Int. Ed. 2002, 41 , 2596-99 and Sun et al., Bioconjugate Chem., 2006, 17 , 52-57.

[0235] As used herein, the term "detectable moiety" is used interchangeably with the term "label" and refers to any moiety that is detectable, such as primary labels and secondary labels. Radioisotopes (e.g., tritium, 32 P, 33 P, 35 S, or 14 C), primary labels, such as mass tags and fluorescent labels, are signal-generating reporter groups that can be detected without further modification. Detectable moieties also include luminescent and phosphorescent groups.

[0236] As used herein, the term "secondary label" refers to moieties such as biotin and various protein antigens that require the presence of a second intermediate to produce a detectable signal. For biotin, the secondary intermediate may include a streptavidin enzyme conjugate. For antigen labels, the secondary intermediate may include an antibody-enzyme conjugate. Some fluorescent groups transfer energy to another group in the process of non-radiative fluorescence resonance energy transfer (FRET), and the second group generates the detected signal, thus acting as a secondary label.

[0237] As used herein, the terms "fluorescent label," "fluorescent dye," and "fluorophore" refer to a moiety that absorbs light energy at a defined excitation wavelength and emits light energy at a different wavelength. Examples of fluorescent labels include, but are not limited to, the following: Alexa Fluor dyes (Alexa Fluor 350, Alexa Fluor 488, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 660 and Alexa Fluor 680), AMCA, AMCA-S, BODIPY dyes (BODIPY FL, BODIPY R6G, BODIPY TMR, BODIPY TR, BODIPY 530 / 550, BODIPY 558 / 568, BODIPY 564 / 570, BODIPY 576 / 589, BODIPY 581 / 591, BODIPY 630 / 650, BODIPY 650 / 665), Carboxyrhodamine 6G, Carboxy-X-rhodamine (ROX), Cascade Blue, Cascade Yellow, Coumarin 343, Cyanine dyes (Cy3, Cy5, Cy3.5, Cy5.5), Dansyl, Dapoxyl, Dialkylaminocoumarin, 4',5'-Dichloro-2',7'-Dimethoxy-Fluorescein, DM-NERF, Eosin, Erythrosine, Fluorescein, FAM, Hydroxycoumarin, IRDye (IRD40, IRD700, IRD800), JOE, Lissamine Rhodamine B, Marina Blue, Methoxycoumarin, Naphthofluorescein, Oregon Green 488, Oregon Green 500, Oregon Green 514, Pacific Blue, PyMPO, Pyrene, Rhodamine B, Rhodamine 6G, Rhodamine Green, Rhodamine Red, Rhodol Green, 2',4',5',7'-tetra-bromosulfone-fluorescein, tetramethyl-rhodamine (TMR), carboxytetramethylrhodamine (TAMRA), Texas Red, Texas Red-X.

[0238] As used herein, the term "mass tag" refers to any moiety that can be uniquely detected by its mass using mass spectrometry (MS) detection techniques. Examples of mass tags include electrophoretic release tags such as N-[3-[4'-[(p-methoxytetrafluorobenzyl)oxy]phenyl]-3-methylglyceronyl]isonipecotic acid, 4'-[2,3,5,6-tetrafluoro-4-(pentafluorophenoxyl)]methylacetophenone, and derivatives thereof. The synthesis and utility of these mass tags are described in U.S. Patent Nos. 4,650,750, 4,709,016, 5,360,8191, 5,516,931, 5,602,273, 5,604,104, 5,610,020, and 5,650,270. Other examples of mass tags include, but are not limited to, nucleotides, dideoxynucleotides, oligonucleotides of various lengths and base compositions, oligopeptides, oligosaccharides, and other synthetic polymers of various lengths and monomer compositions. A wide variety of organic molecules, both neutral and charged (biomolecules or synthetic compounds), in the appropriate mass range (100-2000 Daltons) can also be used as mass tags.

[0239] As used herein, the term "RNA" (ribonucleic acid) refers to any nucleic acid that is capable of being synthesized or synthesized without regard to source (e.g., RNA may be produced from humans, animals, plants, viruses, or bacteria, or may be of synthetic origin), biological context (e.g., RNA may be in the nucleus, circulating in the blood, in vitro, in a cell lysate, or in isolated or pure form), or physical form (e.g., RNA may be a natural or synthetic oligonucleotide or polyribonucleotide in single-stranded, double-stranded, or triple-stranded form (including RNA-DNA hybrids), and may be subject to epigenetic modifications). The RNA may contain natural post-transcriptional modifications, artificial modifications (e.g., obtained by chemical or in vitro modifications), or other modifications, may be bound to, for example, metal ions, small molecules, protein chaperones, or cofactors, or may be in a denatured, partially denatured, or folded state, including any natural or non-natural iridescent or tertiary structure of junctions (e.g., cis or trans three-way junctions (3WJs)), tetraplexes, hairpins, triplexes, hairpins, bulge loops, pseudoknots, internal loops, etc., and transient forms or structures adopted by RNA). In some embodiments, the RNA is 100 or more nucleotides in length. In some embodiments, the RNA is 250 or more nucleotides in length. In some embodiments, the RNA is 350, 450, 500, 600, 750, or 1,000, 2,000, 3,000, 4,000, 5,000, 7,500, 10,000, 15,000, 25,000, 50,000, or more nucleotides in length. In some embodiments, the RNA is 250-1,000 nucleotides in length. In some embodiments, the RNA is a precursor RNA, a precursor miRNA, or a precursor transcript. In some embodiments, the RNA is a non-coding RNA (ncRNA), messenger RNA (mRNA), microRNA (miRNA), ribozyme, riboswitch, lncRNA, lincRNA, snoRNA, snRNA, scaRNA, piRNA, ceRNA, pseudogene, viral RNA, or bacterial RNA.As used herein, the term "target RNA" refers to any type of RNA that has or can adopt a secondary or tertiary structure that is capable of binding to a small molecule ligand as described herein. The target RNA may be in a cell, in a cell lysate, or in an isolated form prior to contact with a small molecule.

[0240] 3. General Method of Providing the Compounds

[0241] The compounds of the invention may generally be prepared or isolated by synthetic and / or semi-synthetic methods known to those skilled in the art for similar compounds, as well as by the methods detailed in the Examples and Figures herein.

[0242] In the schemes and chemical reactions depicted in the Detailed Description, Examples, and Figures where a particular protecting group ("PG"), leaving group ("LG"), or transformation condition is indicated, one of skill in the art will recognize that other protecting groups, leaving groups, and transformation conditions are suitable and contemplated. Such groups and transformations are described in detail in March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, MB Smith and J. March, 7 th Edition, John Wiley & Sons, 2013, Comprehensive Organic Transformations, RC Larock, 3 rd Edition, John Wiley & Sons, 2018, and Protective Groups in Organic Synthesis, PGM Wuts, 5 th edition, John Wiley & Sons, 2014, each of which is incorporated by reference herein in its entirety.

[0243] As used herein, the phrase "leaving group" (LG) includes, but is not limited to, halogen (e.g., fluoride, chloride, bromide, iodide), sulfonate (e.g., mesylate, tosylate, benzenesulfonate, brosylate, nosylate, triflate), diazonium, and the like.

[0244] As used herein, the phrase "oxygen protecting group" includes, for example, carbonyl protecting groups, hydroxyl protecting groups, and the like. Hydroxyl protecting groups are well known in the art and are described in Protective Groups in Organic Synthesis, PGM Wuts, 5 thIncluding those described in detail in "Protecting Groups", John Wiley & Sons, 2014 edition, and Philip Kocienski, in Protecting Groups, Georg Thieme Verlag Stuttgart, New York, 1994, which are incorporated herein by reference in their entirety. Examples of suitable hydroxyl protecting groups include, but are not limited to, ester, allyl ether, ether, silyl ether, alkyl ether, aryl alkyl ether, and alkoxy alkyl ether. Examples of such esters include formate, acetate, carbonate, and sulfonate. Specific examples include formate, benzoyl formate, chloroacetate, trifluoroacetate, methoxyacetate, triphenylmethoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate, 4-oxopentanoate, 4,4-(ethylenedithio)pentanoate, pivalate (trimethylacetyl), crotonate, 4-methoxy-crotonate, benzoate, p-benzylbenzoate, 2,4,6-trimethylbenzoate, methyl, 9-fluorenylmethyl, ethyl, 2,2,2-trichloroethyl, 2-(trimethylsilyl)ethyl, 2-(phenylsulfonyl)ethyl, vinyl, allyl, and p-nitrobenzyl carbonates. Examples of such silyl ethers include trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triisopropylsilyl, and other trialkylsilyl ethers. Alkyl ethers include methyl, benzyl, p-methoxybenzyl, 3,4-dimethoxybenzyl, trityl, t-butyl, allyl, and allyloxycarbonyl ethers or derivatives.Alkoxyalkyl ethers include acetals such as methoxymethyl, methylthiomethyl, (2-methoxyethoxy)methyl, benzyloxymethyl, beta-(trimethylsilyl)ethoxymethyl, and tetrahydropyranyl ethers.Examples of arylalkyl ethers include benzyl, p-methoxybenzyl (MPM), 3,4-dimethoxybenzyl, O-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl, p-cyanobenzyl, and 2- and 4-picolyl.

[0245] Amino protecting groups are well known in the art and are described in Protective Groups in Organic Synthesis, PGM Wuts, 5 th edition, John Wiley & Sons, 2014, and Philip Kocienski, in Protecting Groups, Georg Thieme Verlag Stuttgart, New York, 1994, which are incorporated herein by reference in their entirety. Suitable amino-protecting groups include, but are not limited to, aralkylamines, carbamates, cyclic imides, allylamines, amides, and the like. Examples of such groups include t-butyloxycarbonyl (Boc), ethyloxycarbonyl, methyloxycarbonyl, trichloroethyloxycarbonyl, allyloxycarbonyl (Alloc), benzyloxocarbonyl (Cbz), allyl, phthalimide, benzyl (Bn), fluorenylmethylcarbonyl (Fmoc), formyl, acetyl, chloroacetyl, dichloroacetyl, trichloroacetyl, phenylacetyl, trifluoroacetyl, benzoyl, and the like.

[0246] Those skilled in the art will appreciate that the various functional groups present in the compounds of the present invention, such as aliphatic groups, alcohols, carboxylic acids, esters, amides, aldehydes, halogens, and nitriles, may be interconverted by techniques well known in the art, including, but not limited to, reduction, oxidation, esterification, hydrolysis, partial oxidation, partial reduction, halogenation, dehydration, partial hydration, and hydration. See, for example, March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, MB Smith and J. March, 7 th Edition, John Wiley & Sons, 2013, Comprehensive Organic Transformations, RC Larock, 3 rd Edition, John Wiley & Sons, 2018, each of which is incorporated herein by reference in its entirety. Such interconversions may require one or more of the techniques described above, and specific methods for synthesizing the compounds of the invention are described below.

[0247] Those skilled in the art will appreciate that the various functional groups present in the compounds of the present invention, such as aliphatic groups, alcohols, carboxylic acids, esters, amides, aldehydes, halogens, and nitriles, may be interconverted by techniques well known in the art, including, but not limited to, reduction, oxidation, esterification, hydrolysis, partial oxidation, partial reduction, halogenation, dehydration, partial hydration, and hydration. Such groups and transformations are described in detail in March's Advanced Organic Chemistry: Reactions, Mechanisms, and Structure, MB Smith and J. March, 7 th Edition, John Wiley & Sons, 2013, Comprehensive Organic Transformations, RC Larock, 3 rdEdition, John Wiley & Sons, 2018, and Protective Groups in Organic Synthesis, PGM Wuts, 5 th edition, John Wiley & Sons, 2014, each of which is incorporated herein by reference in its entirety. Such interconversions may require one or more of the techniques described above, and specific methods for synthesizing the compounds of the invention are described below in the Examples and Figures.

[0248] 4. Use, Formulation, and Administration Pharmaceutically acceptable compositions In one aspect, the disclosure provides a composition comprising a compound of the present invention or a pharma- ceutically acceptable derivative thereof and a pharma- ceutically acceptable carrier, adjuvant, or vehicle. The amount of the compound in the composition of the present invention is an amount that is effective to measurably modulate (e.g., inhibit or degrade) a target RNA transcript, or its isoform, variant, or fragment, in a biological sample or in a patient. In certain embodiments, the amount of the compound in the composition of the present invention is an amount that is effective to measurably inhibit or modulate a target RNA transcript in a biological sample or in a patient. In certain embodiments, the composition of the present invention is formulated for administration to a patient in need of such a composition. In some embodiments, the composition of the present invention is formulated for oral administration to a patient.

[0249] The term "pharmaceutically acceptable carrier, adjuvant, or vehicle" refers to a non-toxic carrier, adjuvant, or vehicle that does not destroy the pharmacological activity of the compound in which it is formulated.The pharmaceutically acceptable carrier, adjuvant, or vehicle that can be used in the composition of the present invention includes, but is not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins such as human serum albumin, buffer substances such as phosphoric acid, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, electrolytes such as salts or protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, and polyvinylpyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene block polymers, polyethylene glycol, and wool fat.

[0250] "Pharmaceutically acceptable derivative" means any non-toxic salt, ester, salt of an ester, or other derivative of a compound of the invention which, upon administration to a recipient, is capable of providing, directly or indirectly, a compound of the invention, or an inhibitory active metabolite, or residue thereof.

[0251] The compositions of the present invention may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, bucally, vaginally, or via an implanted reservoir. As used herein, the term "parenteral" includes subcutaneous, intravenous, intramuscular, intra-articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional, and intracranial injection or infusion techniques. The compositions are preferably administered orally, intraperitoneally, or intravenously. Sterile injectable forms of the compositions of the present invention may be aqueous or oily suspensions. These suspensions may be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparations may also be sterile injectable solutions or suspensions in a non-toxic and parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Acceptable vehicles and solvents that may be used include water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile fixed oils are conventionally used as solvents or suspending agents.

[0252] For this purpose, any non-irritating fixed oil may be used, including synthetic mono- or diglycerides. Fatty acids such as oleic acid and its glyceride derivatives, especially in their polyoxyethylated form, are useful for the preparation of injections, as are natural pharmaceutically acceptable oils such as olive oil or castor oil. These oil solutions or suspensions may also contain long-chain alcohol diluents or dispersants, such as carboxymethylcellulose or similar dispersants, which are commonly used in the preparation of pharmaceutically acceptable dosage forms, including emulsions and suspensions. Other commonly used surfactants, such as Tweens®, Spans and other emulsifiers or bioavailability enhancers, which are commonly used in the manufacture of pharmaceutically acceptable solid, liquid, or other dosage forms, may also be used for formulation purposes.

[0253] The pharma- ceutically acceptable composition of the present invention may be orally administered in any orally acceptable dosage form, including but not limited to capsules, tablets, aqueous suspensions, or solutions.For tablets for oral use, commonly used carriers include lactose and corn starch.Lubricants such as magnesium stearate are also typically added.For oral administration in capsule form, useful diluents include lactose and dried corn starch.When aqueous suspensions are required for oral use, active ingredient is combined with emulsifying and suspending agents.If necessary, certain sweeteners, flavors, or colorants may also be added.

[0254] Alternatively, the pharma- ceutically acceptable composition of the present invention may be administered in the form of suppositories for rectal administration.These can be prepared by mixing the drug with a suitable non-irritating excipient that is solid at room temperature but liquid at rectal temperature, and therefore will melt in the rectum and release the drug.Such materials include cocoa butter, beeswax, and polyethylene glycol.

[0255] The pharma- ceutically acceptable compositions of the present invention may also be administered topically, particularly when the target of treatment includes areas or organs readily accessible by topical application, including diseases of the eye, the skin, or the lower gastrointestinal tract. Suitable topical formulations are readily prepared for each of these areas or organs.

[0256] Topical application for the lower intestinal tract can be effected in a rectal suppository formulation (see above) or in a suitable enema formulation. Topical-transdermal patches may also be used.

[0257] For topical application, the provided pharma- ceutically acceptable composition may be formulated in a suitable ointment containing the active ingredient suspended or dissolved in one or more carriers.Carriers for topical administration of the compounds of the present invention include, but are not limited to, mineral oil, liquid petrolatum, white petrolatum, propylene glycol, polyoxyethylene, polyoxypropylene compounds, emulsifying wax, and water.Alternatively, the provided pharma-ceutically acceptable composition may be formulated in a suitable lotion or cream containing the active ingredient suspended or dissolved in one or more pharma-ceutically acceptable carriers.Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol, and water.

[0258] For ophthalmic applications, the provided pharma- ceutically acceptable compositions may be formulated as a micronized suspension in isotonic, pH-adjusted sterile saline, or preferably as a solution in isotonic, pH-adjusted sterile saline, with or without a preservative, such as benzylalkonium chloride. Alternatively, for ophthalmic applications, the pharma-ceutically acceptable compositions may be formulated in an ointment, such as petrolatum.

[0259] The pharma- ceutically acceptable compositions of the invention may also be administered by nasal aerosol or inhalation.Such compositions are prepared according to techniques well known in the art of pharmaceutical formulation and may be prepared as a solution in saline using benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and / or other conventional solubilizing or dispersing agents.

[0260] Most preferably, the pharma- ceutically acceptable composition of the present invention is formulated for oral administration. Such formulations may be administered with or without food. In some embodiments, the pharma- ceutically acceptable composition of the present invention is administered without food. In other embodiments, the pharma- ceutically acceptable composition of the present invention is administered with food.

[0261] The amount of the compounds of the present invention that can be combined with carrier materials to produce a composition in a single dosage form will vary depending on the host to be treated, the particular mode of administration. Preferably, the compositions provided should be formulated so that a dosage of 0.01-100 mg / kg body weight / day of the inhibitor can be administered to a patient receiving these compositions.

[0262] It should also be understood that the specific dosage and treatment regimen for any particular patient will depend on a variety of factors, including the activity of the particular compound used, age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, and the judgment of the treating physician, as well as the severity of the particular disease being treated. The amount of a compound of the invention in a composition will also depend on the particular compound in the composition.

[0263] Those skilled in the art may refer to general reference texts for detailed descriptions of known techniques discussed herein or equivalent techniques. These texts include Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Inc. (2005); Sambrook et al., Molecular Cloning, A Laboratory Manual (3 rd edition), Cold Spring Harbor Press, Cold Spring Harbor, New York (2000), Colligan et al., Current Protocols in Immunology , John Wiley & Sons, NY; Enna et al., Current Protocols in Pharmacology, John Wiley & Sons,NY, Fingl et al., The Pharmacological Basis of Therapeutics(1975), and Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, PA,18th edition (1990), each of which is incorporated herein by reference in its entirety. These texts may of course also be referred to when making or using the embodiments of the present disclosure. The present disclosure also provides pharmaceutical compositions comprising a compound of the present disclosure, or a pharma- ceutical acceptable salt thereof, and one or more other therapeutic agents disclosed herein, mixed with a pharma- ceutical suitable carrier or excipient, in a dose for treating or preventing a disease or condition described herein. The pharmaceutical compositions of the present disclosure may also be administered in combination with other therapeutic agents or treatment methods, either simultaneously, sequentially, or alternatingly.

[0264] The mixtures of the compositions of the present disclosure can also be administered to a patient as simple mixtures or in suitable formulated pharmaceutical compositions. For example, some aspects of the present disclosure relate to pharmaceutical compositions that include a therapeutically effective dose of a compound of the present disclosure, or a pharma- ceutically acceptable salt, hydrate, enantiomer, or stereoisomer thereof, one or more other therapeutic agents, and a pharma- ceutically acceptable diluent or carrier.

[0265] A "pharmaceutical composition" is a formulation containing a compound of the present disclosure in a form suitable for administration to a subject. The compounds of the present disclosure and one or more other therapeutic agents described herein can each be formulated individually or in multiple pharmaceutical compositions of any combination of active ingredients.

[0266] Therefore, one or more administration routes may be appropriately selected based on the dosage form of each pharmaceutical composition. Alternatively, the compound of the present disclosure and one or more other therapeutic agents described herein may be formulated as one pharmaceutical composition.

[0267] Uses of the Compounds and Pharmaceutically Acceptable Compositions

[0268] The compounds and compositions described herein are generally useful for regulating target RNA transcripts to treat RNA-mediated disease or condition.It should be understood that RNA-mediated disease includes all protein-mediated diseases and conditions.

[0269] The activity of the compound utilized in the present invention to modulate (e.g., degrade) target RNA transcript can be assayed in vitro, in vivo, ex vivo, or in cell line. In vitro assays include assays that determine the modulation of target RNA transcript. Alternative in vitro assays quantify the ability of a compound to bind to target RNA transcript. Detailed conditions for assaying the compound utilized in the present invention to modulate target RNA transcript are described in the following examples.

[0270] The term "patient" or "subject", as used herein, means an animal, preferably a mammal, and most preferably a human.

[0271] As used herein, the terms "treatment," "treating," and "treating" refer to reversing, alleviating, delaying the onset, or inhibiting the progression of a disease or disorder described herein, or one or more symptoms thereof. In some embodiments, treatment may be administered after one or more symptoms have developed. In other embodiments, treatment may be administered in the absence of symptoms. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and / or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, e.g., to prevent or delay recurrence.

[0272] The present disclosure provides therapeutic methods, methods, strategies, compositions, combinations, and dosage forms for the treatment of RNA-mediated diseases, disorders, and conditions.

[0273] The compounds provided are regulators of target RNA transcripts and are therefore useful for treating one or more disorders associated with or affected by (e.g., downstream of) the target RNA transcript.Thus, in certain embodiments, the present invention provides a method for treating an RNA-mediated disorder, comprising administering a compound of the present invention or a pharma-ceutically acceptable composition thereof to a patient in need of treating the RNA-mediated disorder.

[0274] In one aspect, the present disclosure provides selective modulators of a target RNA transcript. For example, in some embodiments, a selective modulator (e.g., an inhibitor or antagonist) has an IC50 of a non-target RNA transcript. 50 IC of the target RNA transcript that is at least 40 percent lower than 50 In some embodiments, the selective modulator (e.g., inhibitor or antagonist) has an IC 50 IC of the target RNA transcript that is at least 50 percent lower than 50 In some embodiments, the selective modulator (e.g., inhibitor or antagonist) has an IC 50 IC of the target RNA transcript that is at least 60, 70, 80, 90, or 95 percent lower than 50 In some embodiments, a selective modulator (e.g., an antagonist or inhibitor) of a target RNA transcript has essentially no inhibitory effect on a non-target RNA transcript.

[0275] In some embodiments, a selective regulator (e.g., an inhibitor or antagonist) modulates the activity of a target RNA transcript at least 2-fold more efficiently than a non-target RNA transcript. In some embodiments, a selective regulator (e.g., an inhibitor or antagonist) modulates the activity of a target RNA transcript at least 5-fold more efficiently than a non-target RNA transcript. In some embodiments, a selective regulator (e.g., an inhibitor or antagonist) modulates the activity of a target RNA transcript at least 10-fold, 20-fold, 50-fold, 100-fold, 1000-fold, 10000-fold, or 100000-fold more efficiently than a non-target RNA transcript.

[0276] The disclosed compounds can be used to treat a variety of diseases, disorders, and conditions. In some embodiments, the present invention provides methods of treating one or more diseases, disorders, and conditions, where the disorder, disease, or condition includes, but is not limited to, a cell proliferative disorder.

[0277] Cell Proliferative Disorders In one aspect, the present invention provides methods and compositions for the diagnosis and prognosis of cell proliferation disease (e.g., cancer) and the treatment of these disorders by regulating (e.g., degrading) target RNA transcripts.Cell proliferation disease described herein includes, for example, cancer, obesity, and proliferation-dependent disease.Such disorders can be diagnosed using methods known in the art.

[0278] In one aspect, the present invention provides methods and compositions for treating cancer by modulating (e.g., degrading) target RNA transcripts. In some embodiments, cancer is driven or characterized by overexpression of a protein (e.g., an oncogenic protein), and the cancer is treated by modulating (e.g., degrading) a target RNA transcript that corresponds to the overexpressed protein.

[0279] In one aspect, the invention provides methods and compositions for treating cancer. In one embodiment, cancer includes leukemia (e.g., acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroid leukemia, chronic leukemia, chronic myelogenous leukemia, chronic lymphocytic leukemia), polycythemia vera, lymphoma (e.g., Hodgkin's disease or non-Hodgkin's disease), Waldenstrom's hypergammaglobulinemia, multiple myeloma, heavy chain disease, and solid tumors such as sarcomas and carcinomas (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chondroma, angiosarcoma, endothelial sarcoma, lymphangiosarcoma, lymphoma ... The cancers include, but are not limited to, lymphangiosarcoma, synovium, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon cancer, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinoma, cystic adenocarcinoma, medullary carcinoma, bronchial carcinoma, renal cell carcinoma, hepatoma, cholangiocarcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, uterine cancer, testicular cancer, lung cancer, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, schwannoma, meningioma, melanoma, neuroblastoma, and retinoblastoma. In some embodiments, the cancer is melanoma or breast cancer.

[0280] In another embodiment, the cancer includes mesothelioma, hepatobiliary (liver and bile duct) cancer, bone cancer, pancreatic cancer, skin cancer, head and neck cancer, cutaneous or intraocular melanoma, ovarian cancer, colon cancer, rectal cancer, anal region cancer, stomach cancer, digestive system (stomach, colorectal, and duodenum) cancer, uterine cancer, fallopian tube cancer, endometrial cancer, cervical cancer, vaginal cancer, vulvar cancer, Hodgkin's disease, esophageal cancer, small intestine cancer, endocrine system cancer, thyroid cancer, parathyroid cancer, adrenal cancer, soft tissue sarcoma, urethral cancer, including, but not limited to, penile cancer, prostate cancer, testicular cancer, chronic or acute leukemia, chronic myeloid leukemia, lymphocytic lymphoma, bladder cancer, kidney or ureter cancer, renal cell carcinoma, renal pelvic cancer, non-Hodgkin's lymphoma, spinal axis tumor, brain stem glioma, pituitary adenoma, adrenal cortical carcinoma, gallbladder cancer, multiple myeloma, cholangiocarcinoma, fibrosarcoma, neuroblastoma, retinoblastoma, or a combination of one or more of the foregoing cancers.

[0281] In some embodiments, the present invention provides a method for treating a tumor in a patient in need thereof, the method comprising administering to the patient any of the compounds, salts, or pharmaceutical compositions described herein. In some embodiments, the tumor comprises any of the cancers described herein. In some embodiments, the tumor comprises melanoma cancer. In some embodiments, the tumor comprises breast cancer. In some embodiments, the tumor comprises lung cancer. In some embodiments, the tumor comprises small cell lung cancer (SCLC). In some embodiments, the tumor comprises non-small cell lung cancer (NSCLC).

[0282] Exemplary cancers include adrenocortical carcinoma, AIDS-related cancer, AIDS-related lymphoma, anal cancer, rectal cancer, anal canal cancer, appendix cancer, pediatric cerebellar astrocytoma, pediatric cerebral astrocytoma, basal cell carcinoma, skin cancer (non-melanoma), biliary tract cancer, extrahepatic bile duct cancer, intrahepatic bile duct cancer, bladder cancer, urinary bladder cancer, bone and joint cancer, osteosarcoma, and malignant fibrous histiocytoma, brain cancer, brain tumor, brain stem glioma, cerebellar astrocytoma, brain astrocytoma / malignant glioma, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumor. , visual pathway and hypothalamic glioma, breast cancer, bronchial adenoma / carcinoid, carcinoid tumor, gastrointestinal cancer, nervous system cancer, nervous system lymphoma, central nervous system cancer, central nervous system lymphoma, cervical cancer, childhood cancer, chronic lymphocytic leukemia, chronic myeloid leukemia, chronic myeloproliferative disorder, colon cancer, colorectal cancer, cutaneous T-cell lymphoma, lymphoid neoplasms, mycosis, Sézary syndrome, endometrial cancer, esophageal cancer, extracranial germ cell tumor, extragonadal germ cell tumor, extrahepatic bile duct cancer, eye cancer, intraocular melanoma tumor, retinoblastoma, gallbladder cancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor (GIST), germ cell tumor, ovarian germ cell tumor, gestational trophoblastic tumor glioma, head and neck cancer, hepatocellular (liver) cancer, Hodgkin's lymphoma, hypopharyngeal cancer, intraocular melanoma, eye cancer, islet cell tumor (endocrine pancreas), Kaposi's sarcoma, kidney cancer, renal cancer, kidney cancer, pharyngeal cancer, acute lymphoblastic leukemia, acute myeloid leukemia, chronic lymphocytic leukemia, chronic myeloid leukemia, hairy cell leukemia , lip and oral cavity cancer, liver cancer, lung cancer, non-small cell lung cancer, small cell lung cancer, AIDS-related lymphoma, non-Hodgkin's lymphoma, primary central nervous system lymphoma, Waldens layer hypergammaglobulinemia, medulloblastoma, melanoma, intraocular (eye) melanoma, Merkel cell carcinoma, malignant mesothelioma, mesothelioma, metastatic squamous cell neck cancer, oral cancer, tongue cancer, multiple endocrine neoplasia syndrome, mycosis, myelodysplastic syndrome, myelodysplastic / myeloproliferative disorders, chronic myeloid leukemia, acute myeloid leukemia, multiple myelomaChronic myeloproliferative disorders, nasopharyngeal carcinoma, neuroblastoma, oral cavity cancer, oral cancer, oropharyngeal cancer, ovarian cancer, ovarian epithelial cancer, ovarian low malignant potential tumor, pancreatic cancer, islet cell carcinoma, paranasal sinus and nasal cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pinoblastoma and supratentorial primitive neuroectodermal tumor, pituitary tumor, plasma cell neoplasm / multiple myeloma, pleuropulmonary blastoma, prostate cancer, rectal cancer, renal pelvis and ureter, transitional cell carcinoma, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, Ewing's sarcoma family of tumors, Kaposi's sarcoma These include, but are not limited to, melanoma, soft tissue sarcoma, uterine cancer, uterine sarcoma, skin cancer (non-melanoma), skin cancer (melanoma), Merkel cell skin cancer, small intestine cancer, soft tissue sarcoma, squamous cell carcinoma, gastric (stomach) cancer, supratentorial primitive neuroectodermal tumor, testicular cancer, pharyngeal cancer, thymoma, thymoma and thymic carcinoma, thyroid cancer, transitional cell carcinoma of the renal pelvis and ureter and other urinary organs, gestational trophoblastic neoplasm, urethral cancer, endometrial uterine cancer, uterine sarcoma, uterine somatic cell carcinoma, vaginal cancer, vulvar cancer, and Wilms' tumor.

[0283] In some embodiments, the disease, disorder, or condition is a cell proliferative disorder of the blood system. A "cell proliferative disorder of the blood system" is a cell proliferative disorder involving cells of the blood system. Cell proliferative disorders of the blood system include lymphoma, leukemia, myeloid neoplasm, mast cell neoplasm, myelodysplasia, benign monoclonal gammapathies, lymphomatoid granulomatosis, lymphomatoid body-papular disease, polycythemia vera, chronic myelocytic leukemia, ankylosing myeloblastoma, and essential thrombocythemia. Cell proliferative disorders of the blood system include hyperplasia, dysplasia, and metaplasia of cells of the blood system. In some embodiments, the cancer is selected from a hematological cancer disclosed herein or a blood cell proliferative disorder disclosed herein. Hematologic cancers include multiple myeloma, lymphomas (including Hodgkin's lymphoma, non-Hodgkin's lymphoma, childhood lymphoma, and lymphomas of lymphocytic and cutaneous origin), leukemias (including childhood leukemia, hairy cell leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, chronic lymphocytic leukemia, chronic myelocytic leukemia, chronic myelogenous leukemia, and mast cell leukemia), myeloid tumors, and mast cell neoplasms.

[0284] In some embodiments, treating cancer results in a decrease in tumor volume. In some embodiments, after treatment, the tumor volume is reduced by 5% or more compared to the size before treatment, the tumor volume is reduced by 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, or 75% or more. Tumor volume may be measured by any reproducible means of measurement.

[0285] In some embodiments, treating cancer results in a decrease in tumor number. In some embodiments, after treatment, tumor number is reduced by 5% or more compared to the number before treatment, or tumor number is reduced by 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, or 75% or more. Tumor number may be measured by any reproducible measurement means. Tumor number may be measured by counting tumors visible to the naked eye or at a specified magnification. For example, the specified magnification is selected from 2x, 3x, 4x, 5x, 10x, or 50x.

[0286] In some embodiments, treating cancer results in a reduction in the number of metastatic lesions in other tissues or organs distant from the primary tumor site. In some embodiments, after treatment, the number of metastatic lesions is reduced by 5% or more, or by 10% or more, 20% or more, 30% or more, 40% or more, 50% or more, or by 75% or more, compared to the number before treatment. The number of metastatic lesions may be measured by any reproducible measurement means. The number of metastatic lesions may be measured by counting the metastatic lesions visible to the naked eye or at a specified magnification. The specified magnification is preferably 2x, 3x, 4x, 5x, 10x, or 50x.

[0287] In some embodiments, treating cancer results in an increase in the average survival time in a population of treated subjects compared to a population receiving carrier alone. In some embodiments, the average survival time is increased by more than 30 days, or more than 60 days, or more than 90 days, or more than 120 days.

[0288] In some embodiments, treating cancer results in an increase in the average survival time of a population of treated subjects compared to a population of untreated subjects. In some embodiments, the average survival time is increased by more than 30 days, or more than 60 days, or more than 90 days, or more than 120 days.

[0289] In some embodiments, treating cancer may result in an increase in the average survival time of a population of treated subjects compared to a population receiving monotherapy with a drug that is not a compound of the present disclosure, or a pharma- ceutically acceptable salt, solvate, analog, or derivative thereof. In some embodiments, the average survival time is increased by more than 30 days, or more than 60 days, or more than 90 days, or more than 120 days.

[0290] The increase in the average survival time of a population can be measured by any reproducible means. The increase in the average survival time of a population can be measured, for example, by calculating the average length of survival for a population after the start of treatment with an active compound. The increase in the average survival time of a population can also be measured, for example, by calculating the average length of survival for a population after the completion of initial treatment with an active compound.

[0291] In some embodiments, treating cancer results in a reduction in mortality in a population of treated subjects compared to a population receiving carrier alone. In some embodiments, treating cancer results in a reduction in mortality in a population of treated subjects compared to an untreated population. In some embodiments, treating cancer results in a reduction in mortality in a population of treated subjects compared to a population receiving monotherapy with a drug that is not a compound of the present disclosure, or a pharma- ceutically acceptable salt, solvate, analog, or derivative thereof. In some embodiments, the mortality rate is reduced by more than 2%, more than 5%, more than 10%, or more than 25%. The reduction in mortality in a population of treated subjects can be measured by any reproducible means. The reduction in mortality in a population can be measured, for example, by calculating the average number of disease-related deaths per unit time for a population after initiating treatment with an active compound. The reduction in mortality in a population can also be measured, for example, by calculating the average number of disease-related deaths per unit time for a population after completing initial treatment with an active compound.

[0292] In some embodiments, treating cancer results in a decrease in tumor growth rate. In some embodiments, after treatment, tumor growth rate is reduced by at least 5% compared to the number before treatment, or reduced by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 50%, or at least 75%. Tumor growth rate may be measured by any reproducible measurement means. Tumor growth rate can be measured according to the change in tumor diameter per unit time.

[0293] In some embodiments, treating cancer can result in a reduction in tumor regrowth. In some embodiments, after treatment, tumor regrowth is less than 5%, less than 10%, less than 20%, less than 30%, less than 40%, less than 50%, less than 50%, or less than 75%. Tumor regrowth may be measured by any reproducible means of measurement. Tumor regrowth is measured, for example, by measuring the increase in tumor diameter after a previous tumor shrinkage after treatment. A reduction in tumor regrowth is indicated by the tumor not recurring after treatment is stopped.

[0294] In some embodiments, treating or preventing cell proliferation disease results in a reduction in cell proliferation rate. In some embodiments, after treatment, cell proliferation rate is reduced by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 50%, or at least 75%. Cell proliferation rate may be measured by any reproducible measuring means. Cell proliferation rate is measured, for example, by measuring the number of dividing cells in a tissue sample per unit time.

[0295] In some embodiments, treating or preventing cell proliferation disorder results in a reduction in the percentage of proliferating cells. In some embodiments, after treatment, the percentage of proliferating cells is reduced by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 50%, or at least 75%. The percentage of proliferating cells may be measured by any reproducible measurement means. Preferably, the percentage of proliferating cells is measured, for example, by quantifying the number of dividing cells relative to the number of non-dividing cells in a tissue sample. The percentage of proliferating cells may be equivalent to the mitotic index.

[0296] In some embodiments, treating or preventing a cell proliferation disorder results in a reduction in the size of the area or zone of cell proliferation. In some embodiments, after treatment, the size of the area or zone of cell proliferation is reduced by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 50%, or at least 75% compared to its size before treatment. The size of the area or zone of cell proliferation can be measured by any reproducible measuring means. The size of the area or zone of cell proliferation can be measured as the diameter or width of the area or zone of cell proliferation.

[0297] In some embodiments, treating or preventing a cell proliferative disorder results in a reduction in the number or percentage of cells with abnormal appearance or morphology. In some embodiments, after treatment, the number of cells with abnormal morphology is reduced by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 50%, or at least 75% compared to their size before treatment. Abnormal cell appearance or morphology can be measured by any reproducible means of measurement. Abnormal cell morphology can be measured using a microscope, for example, an inverted tissue culture microscope. Abnormal cell morphology can take the form of nuclear pleomorphism.

[0298] In some embodiments, the tumor is treated by stopping further growth of the tumor. In some embodiments, the tumor is treated by reducing the size (e.g., volume or mass) of the tumor by at least 5%, 10%, 25%, 50%, 75%, 90%, or 99% relative to the size of the tumor before treatment. In some embodiments, the tumor is treated by reducing the tumor mass in the patient by at least 5%, 10%, 25%, 50%, 75%, 90%, or 99% relative to the tumor mass before treatment.

[0299] In some embodiments, the subject in need thereof has a refractory or resistant cancer. "Refractory or resistant cancer" refers to a cancer that does not respond to established lines of therapy. In some embodiments, the cancer is resistant at the start of treatment or becomes resistant during treatment. In some embodiments, the subject in need thereof has cancer recurrence after remission of the most recent therapy. In some embodiments, the subject in need thereof has undergone all known effective therapies for cancer treatment without success. In some embodiments, the subject in need thereof has undergone at least one previous treatment. In some embodiments, the previous treatment is a monotherapy. In some embodiments, the previous treatment is a combination therapy.

[0300] In some embodiments, a subject in need thereof has a secondary cancer as a result of a previous therapy. By "secondary cancer" is meant a cancer that arises from or results from a previous oncogenic therapy, such as chemotherapy.

[0301] As used herein, the term "responsive" is interchangeable with the terms "responsive," "susceptible," and "susceptibility," and means that a subject exhibits a therapeutic response when administered a composition of the present disclosure, e.g., the subject's tumor cells or tumor tissue undergo apoptosis and / or necrosis and / or exhibit reduced growth, division, or proliferation. In some embodiments, "response" means that the probability that a subject exhibits a therapeutic response to a disclosed compound, e.g., when the subject's tumor cells or tumor tissue undergo apoptosis and / or necrosis and / or exhibit reduced growth, division, or proliferation, is high or increased compared to a population.

[0302] As used herein, "sample" means any biological sample derived from a subject, including, but not limited to, cell, tissue samples, bodily fluids (including, but not limited to, mucus, blood, plasma, serum, urine, saliva, and semen), tumor cells, and tumor tissue.

[0303] In some embodiments, the sample is selected from bone marrow, peripheral blood cells, blood, plasma, and serum. The sample can be provided by the subject during treatment or testing. Alternatively, the sample can be obtained by a physician according to routine practice in the art.

[0304] As used herein, a "normal cell" is a cell that cannot be classified as part of a "cell proliferative disorder". A normal cell is free of uncontrolled or abnormal growth, or both, that can lead to the development of an undesirable condition or disease. Typically, a normal cell has a normally functioning cell cycle checkpoint control mechanism.

[0305] As used herein, "contacting a cell" refers to a compound or other composition of matter being in direct contact with a cell or sufficiently close to induce a desired biological effect in the cell.

[0306] In one aspect, the present invention provides methods and compositions for the diagnosis and prognosis of cell proliferation diseases that are not generally characterized as cancer, and the treatment of these disorders, by regulating (e.g., degrading) target RNA transcripts.Other proliferation diseases include, for example, obesity, benign prostatic hyperplasia, psoriasis, abnormal keratosis, lymphoproliferative diseases (e.g., disorders with abnormal proliferation of lymphatic cells), rheumatoid arthritis, arteriosclerosis, restenosis, and diabetic retinopathy.Proliferative diseases that are incorporated herein by reference include those described in U.S. Patent Nos. 5,639,600 and 7,087,648.

[0307] As used herein, the term "selectivity" means that it tends to occur more frequently in one population than in another. The compared population can be a cell population. In some embodiments, the disclosed compound, or its pharmaceutically acceptable salt or solvate, acts selectively on cancer or precancerous cells, but does not act on normal cells. In some embodiments, the disclosed compound, or its pharmaceutically acceptable salt or solvate, acts selectively to modulate one molecular target, but does not significantly modulate another molecular target. The present invention also provides a method for selectively inhibiting the activity of target RNA.

[0308] In some embodiments, treating cancer or cell proliferation disease results in cell death. In some embodiments, cell death results in at least 10% reduction in cell number in a population. In some embodiments, cell death refers to at least 20%, at least 30%, at least 40%, at least 50%, or at least 75% reduction. The number of cells in a population may be measured by any reproducible means. The number of cells in a population can be measured by fluorescence activated cell sorting (FACS), immunofluorescence microscopy, and light microscopy. Methods for measuring cell death are as shown in Li et al., Proc Natl Acad Sci USA, 100(5): 2674-8, 2003. In some aspects, cell death occurs by apoptosis.

[0309] In some embodiments, the disclosed compound or its pharmaceutically acceptable salt or solvate is not significantly cytotoxic to normal cells.The therapeutically effective amount of the compound is not significantly cytotoxic to normal cells if the administration of the compound in a therapeutically effective amount does not induce cell death in more than 10% of normal cells.The therapeutically effective amount of the compound does not significantly affect the viability of normal cells if the administration of the compound in a therapeutically effective amount does not induce cell death in more than 10% of normal cells.In some aspects, cell death occurs by apoptosis.

[0310] In some embodiments, the present invention provides methods of treating or preventing cancer by administering an effective amount of a disclosed compound, or a pharma- ceutically acceptable salt or solvate thereof, to a subject in need thereof, where administration of the compound, or a pharma- ceutically acceptable salt or solvate thereof, results in one or more of the following: prevention of cancer cell proliferation by accumulation of cells in one or more stages of the cell cycle (e.g., Gl, Gl / S, G2 / M), or induction of cellular senescence, or promotion of tumor cell differentiation; promotion of cell death in cancer cells via cytotoxicity, necrosis, or apoptosis without significant amounts of cell death in normal cells; anti-tumor activity in animals with a therapeutic index of at least 2. As used herein, "therapeutic index" is the maximum tolerated dose divided by the effective dose.

[0311] Formulation and route of administration According to the method of the present invention, the compounds and compositions may be administered using any amount and any route of administration effective for treating or reducing the severity of cancer or other diseases, disorders, or conditions disclosed herein. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular agent, its mode of administration, and the like. The compounds of the present invention are preferably formulated in unit dosage form for ease of administration and uniformity of dose. As used herein, the expression "unit dosage form" refers to a physically discrete unit of agent appropriate for the patient to be treated. However, it will be understood that the total daily usage of the compounds and compositions of the present invention will be determined by the attending physician within the scope of sound medical judgment. The specific effective dosage level for any particular patient or organism will depend on a variety of factors, including the disorder and severity of the disorder being treated, the activity of the particular compound employed, the particular composition employed, the age, weight, general health, sex, and diet of the patient, the time of administration, the route of administration, and the excretion rate of the particular compound employed, the duration of treatment, the agents used in combination with or simultaneously with the particular compound, and similar factors well known in the medical arts. The term "patient" or "subject", as used herein, means an animal, preferably a mammal, and most preferably a human.

[0312] The pharma- ceutically acceptable compositions of the present invention may be administered to humans and other animals orally, rectally, parenterally, intravesically, intravaginally, intraperitoneally, topically (by powder, ointment, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated. In certain embodiments, the compounds of the present invention may be administered orally or parenterally at dosage levels of about 0.01 mg / kg to about 50 mg / kg, preferably about 1 mg / kg to about 25 mg / kg of the subject's body weight, one or more times per day to obtain the desired therapeutic effect.

[0313] Liquid dosage forms for oral administration include, but are not limited to, pharma- ceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and elixirs.In addition to active compounds, liquid dosage forms include, for example, water or other solvents, solubilizers and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (especially cottonseed oil, peanut oil, corn oil, germ oil, olive oil, castor oil, and sesame oil), glycerol, tetrahydrofuryl alcohol, polyethylene glycol and fatty acid esters of sorbitan, and mixtures thereof.In addition to inert diluents, oral compositions can also include adjuvants, such as wetting agents, emulsifiers and suspending agents, sweeteners, flavorings, and aromatics.

[0314] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions, may be formulated according to known techniques using suitable dispersing or wetting agents and suspending agents. Sterile injectable preparations may also be sterile injectable solutions, suspensions or emulsions in non-toxic and parenterally acceptable diluents or solvents, for example, as a solution in 1,3-butanediol. Acceptable vehicles and solvents that may be used include water, Ringer's solution, USP, and isotonic sodium chloride solution. In addition, sterile fixed oils are conventionally used as solvents or suspending agents. For this purpose, any non-irritating fixed oil may be used, including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

[0315] Injectable preparations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

[0316] In order to prolong the effect of the compounds of the present invention, it is often desirable to slow the absorption of the compound from subcutaneous or intramuscular injection. This can be accomplished by using a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the compound then depends on its rate of dissolution, which may depend on crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered compound form is accomplished by dissolving or suspending the compound in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the compound in biodegradable polymers such as polylactide-polyglycolide. Depending on the ratio of compound to polymer and the nature of the particular polymer used, the compound release rate can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the compound in liposomes or microemulsions that are compatible with body tissues.

[0317] Compositions for rectal or vaginal administration are preferably suppositories which may be prepared by mixing a compound of the invention with a suitable non-irritating excipient or carrier, such as cocoa butter, polyethylene glycol, or a suppository wax, which is solid at ambient temperature but liquid at body temperature and thus will melt in the rectum or vaginal cavity and release the active compound.

[0318] Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert pharma- ceutically acceptable excipient or carrier, such as sodium citrate or dicalcium phosphate, and / or a) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and silicic acid; b) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, acacia; c) humectants, such as glycerol; d) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, sodium carbonate; e) solution retarding agents, such as paraffin; f) absorption accelerators, such as quaternary ammonium compounds; g) wetting agents, such as, for example, cetyl alcohol and glycerol monostearate; h) absorbents, such as kaolin and bentonite clay; i) lubricants, such as, for example, talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents.

[0319] Similar types of solid compositions may also be used as fillers in soft and hard filled gelatin capsules, using excipients such as lactose or milk sugar and high molecular weight polyethylene glycols. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical formulation art. They may optionally contain opacifying agents, and may also be of a composition that releases the active ingredient only, or selectively, in a certain part of the intestinal tract, optionally in a delayed manner. Examples of embedding compositions that may be used include polymeric substances and waxes. Similar types of solid compositions may also be used as fillers in soft and hard filled gelatin capsules, using excipients such as lactose or milk sugar and high molecular weight polyethylene glycols.

[0320] The active compound may also be in microencapsulated form with one or more excipients as described above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells, such as enteric coatings, release-controlling coatings, and other coatings well known in the pharmaceutical formulation art. In these solid dosage forms, the active compound may be mixed with at least one inert diluent, such as sucrose, lactose, or starch. These dosage forms may also contain additional substances other than the inert diluent, as is common practice, such as tableting lubricants and other tableting aids, such as magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets, and pills, the dosage forms may also contain buffering agents. They may optionally contain opacifying agents, and may be of a composition that releases the active ingredient only, or selectively, in a certain part of the intestinal tract, optionally in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.

[0321] The dosage forms for topical or transdermal administration of the compounds of the present invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants, or patches. The active ingredient is mixed under sterile conditions with a pharma- ceutically acceptable carrier and any necessary preservatives or buffers as necessary. Ophthalmic preparations, ear drops, and eye drops are also contemplated within the scope of the present invention. In addition, the present invention contemplates the use of transdermal patches, which have the additional advantage of providing controlled delivery of the compound into the body. Such dosage forms can be made by dissolving or dispensing the compound in a suitable medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.

[0322] In one embodiment, the invention relates to a method for modulating the activity of a target RNA transcript in a biological sample, the method comprising the step of contacting the biological sample with a compound of the invention, or a composition comprising said compound.

[0323] In another embodiment, the present invention relates to a method of modulating the activity of a target RNA transcript in a biological sample, the method comprising contacting the biological sample with a compound of the present invention, or a composition comprising said compound. In a particular embodiment, the present invention relates to a method of irreversibly inhibiting the activity of a target RNA transcript in a biological sample, the method comprising contacting the biological sample with a compound of the present invention, or a composition comprising the compound.

[0324] As used herein, the term "biological sample" includes, but is not limited to, cell cultures or extracts thereof, biopsies obtained from mammals or extracts thereof, as well as blood, saliva, urine, feces, semen, tears, cerebrospinal fluid, or other bodily fluids or extracts.

[0325] Another embodiment of the invention relates to a method of modulating the activity of a target RNA transcript in a patient, the method comprising administering to said patient a compound of the invention, or a composition comprising said compound.

[0326] In another embodiment, the present invention relates to a method for inhibiting the activity of a target RNA transcript in a patient, the method comprising administering to the patient a compound of the present invention, or a composition comprising said compound. In a particular embodiment, the present invention relates to a method for irreversibly inhibiting the activity of a target RNA transcript in a patient, the method comprising administering to the patient a compound of the present invention, or a composition comprising said compound. In another embodiment, the present invention provides a method for treating a disorder mediated by a target RNA transcript in a patient in need of such treatment, the method comprising administering to the patient a compound of the present invention, or a pharma- ceutically acceptable composition thereof. Such disorders are described in detail herein. EXAMPLES

[0327] As shown in the following examples, exemplary compounds are prepared according to the following general procedures and used in biological assays and other procedures generally described herein.It is understood that while the general methods show the synthesis of specific compounds of the present invention, the following general methods and other methods known to those skilled in the art can be applied to all compounds and subclasses and species of each of these compounds as described herein.Similarly, assays and other analyses can be adapted according to the knowledge of those skilled in the art.

[0328] Example 1: Gene tethering assay General description of gene tethering A human non-small cell lung carcinoma cell line (ATCC), NCI-H1299, was engineered to stably express various λN-tag RNA-binding proteins (RBPs) via lentivirus. Cells were then transfected using Lipofectamine 3000 (Thermo Fisher) with two plasmids: one encoding a reporter luciferase containing a BoxB site in either the 3' untranslated region (UTR) or 5' UTR, and the other a normalizer plasmid encoding an alternative luciferase that does not have any BoxB sites for tethering. After 24 hours, expression of both luciferases was measured using a commercially available kit (Promega). Data are expressed as the ratio of reporter expression (measured in relative light units (RLU)) to normalizer expression. An overview of the assay is shown in Figure 1.

[0329] Transfection NCI-H1299 cells were seeded on day 0 in 96-well plates at 5000 cells per well in Roswell Park Memorial Institute medium (RPMI) 1640 medium containing 10% fetal bovine serum and incubated in 5% carbon dioxide (CO 2 ) at 37 degrees Celsius overnight. On day 1, transfection mixtures were prepared with reporter and normalizer constructs containing BoxB sites for gene tethering, or constructs without BoxB sites. Transfections were performed according to the manufacturer's instructions for Lipofectamine 3000 (Thermo Fisher). After approximately 24 hours, luciferase activity was measured using the Dual Luciferase Reporter Assay System (Promega).

[0330] Lentivirus production and cell transduction Lentiviruses encoding λN-tagged RNA-binding proteins (RBPs) were prepared using ViraPower Lentiviral Packaging Mix (Thermo Fisher) according to the manufacturer's protocol. On day 0, cells were transduced via centrifugation with polybrene at 1000 relative centrifugal force (RCF) for 1 h. After centrifugation, cells were incubated at 37 °C, 5% CO 2 The cells were then grown in standard tissue culture flasks under puromycin selection pressure. The cells were passaged in appropriate cell culture medium for downstream applications.

[0331] Quantification of RNA-binding protein (RBP) expression Protein expression of RBPs was measured using an automated in-capillary electrophoresis assay according to the manufacturer's protocol (ProteinSimple, Inc.). Appropriate antibodies targeting either the RBPs or the hemagglutinin (HA) tag were purchased from commercial vendors (i.e., Sigma Aldrich, Inc.).

[0332] Development and optimization of quantitative polymerase chain reaction (qPCR) assays qPCR assay reagents were ordered based on manufacturer specifications (Applied Biosystems). Standard software such as Primer BLAST was used to generate optimal qPCR amplification primers and probes specific for firefly and luciferase complementary deoxyribonucleic acid (cDNA). PCR primers were ordered from Integrated DNA Technologies (IDT). Gene-specific probes were generated using 5-carboxyfluorescein (5'FAM), a nonfluorescent quencher (NFQ), and a minor groove binder (MGB).

[0333] qPCR assays for cDNA quantification and primer validation were performed using Taqman Fast Advanced Master Mix (Life Technologies). Gene quantification and plotting were performed using Excel and Prism software, respectively.

[0334] Vector design and synthesis The desired RBP and reporter gene expression constructs were generated using Geneious Primer software. The preferred RBP isoform sequences and luciferase sequences were obtained from the National Center for Biotechnology Information (NCBI).

[0335] Vector cloning and transfection grade plasmid preparation were performed in Genscript. Base mammalian expression vectors for cloning were obtained from the Arrakis Therapeutics vector database.

[0336] Having described several embodiments of the invention, it will be apparent that the basic examples may be modified to provide other embodiments which utilize the compounds and methods of the invention. It will therefore be appreciated that the scope of the invention is to be defined by the appended claims rather than by the specific embodiments which have been represented by way of example.

Claims

1. A compound of formula A, 【Chemistry 158】 or a pharmaceutically acceptable salt thereof, wherein: the rSM is an RNA-binding small molecule that binds to a target RNA transcript; DFL is a degrader-recruiting ligand; L is a divalent linker group covalently linking the rSM to the DFL; A compound or a pharmaceutically acceptable salt thereof, wherein the DFL binds to or recruits a degrading factor.

2. 2. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the degradation factor is an RNA-binding protein (RBP) and binding of the DFL to the RBP results in modulation of the target RNA transcript in vivo.

3. 3. The compound of claim 2 or a pharmaceutically acceptable salt thereof, wherein the modulation of the target RNA transcript in vivo is degradation of the target RNA transcript.

4. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the DFL binds to the RBP without interfering with the enzymatic activity of the RBP and / or the ability of the RBP to be part of a multi-component complex.

5. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP is an endonuclease, exonuclease, deadenylase, or decapping protein, or the RBP is part of a multi-component complex that has endonuclease, exonuclease, deadenylase, or decapping activity, or the RBP destabilizes the three-dimensional structure of the target RNA transcript, making it more susceptible to degradation.

6. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP is one of those listed in Table 1B.

7. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP has in vivo enzymatic activity, or is part of a multi-component complex having enzymatic activity, at endogenous levels sufficient to measurably regulate the target RNA transcript or destabilize its three-dimensional structure in a manner that renders it susceptible to degradation.

8. 8. The compound of claim 7 or a pharmaceutically acceptable salt thereof, wherein the modulation of the target RNA transcript is degradation of the target RNA transcript.

9. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP does not need to be induced to be active.

10. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP does not need to dimerize to be active.

11. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP is part of a CCR4-NOT (carbon catabolite repression negative in the absence of TATA) complex.

12. 3. The compound according to claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1.

13. 13. The compound of claim 12, or a pharmaceutically acceptable salt thereof, wherein the RBP is CNOT2.

14. 13. The compound of claim 12, or a pharmaceutically acceptable salt thereof, wherein the RBP is CNOT7.

15. 13. The compound of claim 12, or a pharmaceutically acceptable salt thereof, wherein the RBP is YTHDF2.

16. 3. The compound of claim 2, or a pharmaceutically acceptable salt thereof, wherein the RBP is not RNase L.

17. 2. The compound of claim 1, or a pharmaceutically acceptable salt thereof, wherein the DFL is one of those shown in Table 1C.

18. 18. The compound of any one of claims 1 to 17, or a pharmaceutically acceptable salt thereof, wherein the target RNA transcript is mRNA, or a precursor, isoform, unspliced ​​isoform, splicing intermediate, fragment, or variant thereof.

19. 20. The compound of claim 18, or a pharmaceutically acceptable salt thereof, wherein the target RNA transcript is selected from one of those listed in Table A, Table B, Table C, or Table D, or a precursor, isoform, unspliced ​​isoform, splice intermediate, fragment, or variant thereof.

20. 19. The compound of claim 18, or a pharmaceutically acceptable salt thereof, wherein L is a covalent bond or a divalent, saturated or unsaturated, linear or branched, optionally substituted C １－５０ a hydrocarbon chain, wherein 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 methylene units of L are -Cy ２ -, -O-, -N(R)-, -S-, -OC(O)-, -C(O)O-, -C(O)-, -C(S)-, -S(O)-, -S(O) ２ -, -N(R)S(O) ２ -, -S(O) ２ N(R)-, -N(R)C(O)-, -C(O)N(R)-, -OC(O)N(R)-, -N(R)C(O)O-, -N(R)C(O)N(R)-, -N(R)C(S)N(R)-, -Si(R) ２ -, -Si(OH)(R)-, -Si(OH) ２ -, -P(O)(OR)-, -P(O)(R)-, -P(O)(NR ２ )-,amino acid, 【Chemistry 159】 [Chemical 160] 【Chemistry 161】 【Chemistry 162】 or 【Chemical 163】 and wherein Each -Cy ２ - is an independently optionally substituted bivalent ring selected from phenylene, 8- to 12-membered bicyclic arylene, 3- to 8-membered saturated carbocyclylene or partially unsaturated carbocyclylene, 8- to 12-membered bicyclic saturated carbocyclylene or partially unsaturated carbocyclylene, 3- to 8-membered saturated heterocyclylene or partially unsaturated heterocyclylene having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, 8- to 12-membered bicyclic saturated heterocyclylene or partially unsaturated heterocyclylene having 1-5 heteroatoms independently selected from nitrogen, oxygen, and sulfur, 5- to 6-membered heteroarylenyl having 1-4 heteroatoms independently selected from nitrogen, oxygen, and sulfur, or 8- to 10-membered bicyclic heteroarylenyl having 1-5 heteroatoms independently selected from nitrogen, oxygen, or sulfur; A compound or a pharmaceutically acceptable salt thereof, wherein each q is independently 1, 2, or 3.

21. 21. The compound of claim 20, or a pharmaceutically acceptable salt thereof, wherein L is selected from one of those shown in Table 2.

22. 21. The compound of claim 20, or a pharmaceutically acceptable salt thereof, wherein the rSM is selected from any one of those listed in the section entitled Exemplary rSMs.

23. 22. The compound of claim 21, or a pharmaceutically acceptable salt thereof, wherein the rSM is one of those shown in Table 1A.

24. A composition comprising an RNA binding agent that binds to a target RNA transcript and a degradator recruiting ligand (DFL), wherein the DFL binds to or recruits a degradator.

25. 25. The composition of claim 24, wherein the degradation factor is an RNA-binding protein (RBP), and binding of the DFL to the RBP results in modulation of the target RNA transcript in vivo.

26. 26. The composition of claim 25, wherein the modulation of the target RNA transcript in vivo is degradation of the target RNA transcript.

27. 25. The composition of claim 24, wherein the RNA-binding agent is an oligonucleotide, a peptide, or an oligosaccharide.

28. 26. The composition of claim 25, wherein the DFL binds to the RBP without interfering with the enzymatic activity of the RBP and / or the ability of the RBP to be part of a multi-component complex.

29. 26. The composition of claim 25, wherein the RBP is an endonuclease, exonuclease, deadenylase, or decapping protein, or the RBP is part of a multi-component complex that has endonuclease, exonuclease, deadenylase, or decapping activity, or the RBP destabilizes the three-dimensional structure of the target RNA transcript making it more susceptible to degradation.

30. 26. The composition of claim 25, wherein the RBP is one of those listed in Table 1B.

31. 26. The composition of claim 25, wherein the RBP has enzymatic activity in vivo, or is part of a multi-component complex with enzymatic activity, at endogenous levels sufficient to measurably regulate the target RNA transcript or destabilize its three-dimensional structure in a manner that renders it susceptible to degradation.

32. 32. The composition of claim 31, wherein the modulation of the target RNA transcript is degradation of the target RNA transcript.

33. 26. The composition of claim 25, wherein the RBP does not need to be induced to be active.

34. 26. The composition of claim 25, wherein the RBP does not need to dimerize to be active.

35. 26. The composition of claim 25, wherein the RBP is part of a CCR4-NOT (carbon catabolite repression negative in the absence of TATA) complex.

36. 26. The composition of claim 25, wherein the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1.

37. 37. The composition of claim 36, wherein the RBP is CNOT2.

38. 37. The composition of claim 36, wherein the RBP is CNOT7.

39. 37. The composition of claim 36, wherein the RBP is YTHDF2.

40. 26. The composition of claim 25, wherein the RBP is not RNase L.

41. 26. The composition of claim 25, wherein the DFL is one of those shown in Table 1C.

42. 42. The composition of any one of claims 24 to 41, wherein the target RNA transcript is an mRNA, or a precursor, isoform, unspliced ​​isoform, splice intermediate, fragment, or variant thereof.

43. 43. The composition of claim 42, wherein the target RNA transcript is selected from one of those listed in Table A, Table B, Table C, or Table D, or a precursor, isoform, unspliced ​​isoform, splice intermediate, fragment, or variant thereof.

44. A pharmaceutical composition comprising a compound according to any one of claims 1 to 17, or a pharmaceutically acceptable salt thereof, or a composition according to any one of claims 24 to 41, and a pharmaceutically acceptable carrier.

45. A composition or compositions comprising a compound that acts on a target RNA transcript or a precursor, isoform, fragment, or variant thereof for use in a method of altering the amount of a protein in a cell, said method comprising administering said composition in an amount sufficient to alter said amount of said protein in said cell.

46. 46. ​​The composition of claim 45, wherein modifying the amount of a protein in a cell reduces the amount of a protein in the cell.

47. 46. ​​The composition of claim 45, wherein the method comprises administering a compound of any one of claims 1 to 17, or a pharmaceutically acceptable salt thereof, or a composition of any one of claims 24 to 41.

48. 42. A composition comprising the compound of any one of claims 1 to 17, or a pharmaceutically acceptable salt thereof, for use in a method of modulating the availability for protein translation of a target RNA transcript, or a precursor, isoform, fragment, or variant thereof, said method comprising contacting said target RNA transcript, or a precursor, isoform, fragment, or variant thereof, with said composition, which binds to said target RNA transcript, or an isoform, fragment, or variant thereof.

49. 42. A composition comprising the compound of any one of claims 1 to 17, or a pharmaceutically acceptable salt thereof, or the composition of any one of claims 24 to 41, for use in a method of modulating translation of a target protein or variant thereof, said method comprising contacting a target RNA transcript or precursor, isoform, fragment, or variant thereof with said composition.

50. 42. A composition comprising the compound of any one of claims 1 to 17, or a pharmaceutically acceptable salt thereof, for use in a method of decreasing the half-life or increasing the degradation of a target RNA transcript, or precursor, isoform, fragment, or variant thereof, wherein the method comprises contacting the target RNA transcript, or the precursor, isoform, fragment, or variant thereof, with the composition.

51. A composition comprising a compound according to any one of claims 1 to 17, or a pharmaceutically acceptable salt thereof, or a composition according to any one of claims 24 to 41, for use in a method of treating a disease in a subject.

52. 52. The composition of claim 51, wherein the disease is characterized by abnormal levels of a protein in a cell.

53. 53. The composition of claim 52, wherein the disease is one of those listed in Table A, Table B, Table C, or Table D.

54. 53. The composition of claim 52, wherein the disease is cancer.

55. 52. The composition of claim 51 , wherein the method induces proximity of an RNA binding protein (RBP) to the target RNA transcript, wherein the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1, and the target RNA transcript is a pre-mRNA, mature mRNA, or partially processed mRNA, or an isoform, fragment, or variant thereof.

56. 1. A composition comprising an RNA-binding moiety that induces the proximity of an RNA-binding protein (RBP) for use in a method of inducing degradation or decreasing the half-life of a target RNA transcript or an isoform, fragment, or variant thereof, the method comprising contacting the target RNA transcript or the isoform, fragment, or variant thereof with the RNA-binding moiety.

57. 57. The composition of claim 56, wherein the RBP is one of those listed in Table 1B.

58. 57. The composition of claim 56, wherein the RBP is CNOT2, CNOT7, DDX6, YTHDF2, ZFP36, DCP1A, ZC3H12A (Regnase-1), PARN, MARF, or IRE-1.

59. 59. The composition of claim 58, wherein the RBP is CNOT2, CNOT7, or YTHDF2.

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