A blood-brain penetrant RNA-targeted small molecule triggers elimination of r(GC) in c9ALS/FTD via the nuclear RNA exosome.

A hexanucleotide repeat expansion in intron 1 of the gene is the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia, or c9ALS/FTD. The RNA transcribed from the expansion, r(GC), causes various pathologies, including intron retention, aberrant translation that produces toxic dipeptide repeat proteins (DPRs), and sequestration of RNA-binding proteins (RBPs) in RNA foci. Here, we describe a small molecule that potently and selectively interacts with r(GC) and mitigates disease pathologies in spinal neurons differentiated from c9ALS patient-derived induced pluripotent stem cells (iPSCs) and in two c9ALS/FTD mouse models.

Study of an RNA-Focused DNA-Encoded Library Informs Design of a Degrader of a r(CUG) Repeat Expansion.

A solid-phase DNA-encoded library (DEL) was studied for binding the RNA repeat expansion r(), the causative agent of the most common form of adult-onset muscular dystrophy, myotonic dystrophy type 1 (DM1). A variety of uncharged and novel RNA binders were identified to selectively bind r() by using a two-color flow cytometry screen. The cellular activity of one binder was augmented by attaching it with a module that directly cleaves r().

Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(GC) repeat expansion in vitro and in vivo ALS models.

The most common cause of amyotrophic lateral sclerosis and frontotemporal dementia (c9ALS/FTD) is an expanded GC RNA repeat [r(GC)] in chromosome 9 open reading frame 72 (), which elicits pathology through several mechanisms. Here, we developed and characterized a small molecule for targeted degradation of r(GC). The compound was able to selectively bind r(GC)’s structure and to assemble an endogenous nuclease onto the target, provoking removal of the transcript by native RNA quality control mechanisms.

A structure-specific small molecule inhibits a miRNA-200 family member precursor and reverses a type 2 diabetes phenotype.

MicroRNA families are ubiquitous in the human transcriptome, yet targeting of individual members is challenging because of sequence homology. Many secondary structures of the precursors to these miRNAs (pri- and pre-miRNAs), however, are quite different. Here, we demonstrate both in vitro and in cellulis that design of structure-specific small molecules can inhibit a particular miRNA family member to modulate a disease pathway.

Small molecule recognition of disease-relevant RNA structures.

Targeting RNAs with small molecules represents a new frontier in drug discovery and development. The rich structural diversity of folded RNAs offers a nearly unlimited reservoir of targets for small molecules to bind, similar to small molecule occupancy of protein binding pockets, thus creating the potential to modulate human biology. Although the bacterial ribosome has historically been the most well exploited RNA target, advances in RNA sequencing technologies and a growing understanding of RNA structure have led to an explosion of interest in the direct targeting of human pathological RNAs.

Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing.

Approximately 95% of human genes are alternatively spliced, and aberrant splicing events can cause disease. One pre-mRNA that is alternatively spliced and linked to neurodegenerative diseases is tau (microtubule-associated protein tau), which can cause frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) and can contribute to Alzheimer's disease. Here, we describe the design of structure-specific lead small molecules that directly target tau pre-mRNA from sequence.

Targeted Degradation of the Oncogenic MicroRNA 17-92 Cluster by Structure-Targeting Ligands.

Many RNAs are processed into biologically active transcripts, the aberrant expression of which can contribute to disease phenotypes. For example, the primary microRNA-17-92 (pri-miR-17-92) cluster contains six microRNAs (miRNAs) that collectively act in several disease settings. Herein, we used sequence-based design of structure-specific ligands to target a common structure in the Dicer processing sites of three miRNAs in the cluster, miR-17, miR-18a, and miR-20a, thereby inhibiting their biogenesis.

Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer.

As the area of small molecules interacting with RNA advances, general routes to provide bioactive compounds are needed as ligands can bind RNA avidly to sites that will not affect function. Small-molecule targeted RNA degradation will thus provide a general route to affect RNA biology. A non-oligonucleotide-containing compound was designed from sequence to target the precursor to oncogenic microRNA-21 (pre-miR-21) for enzymatic destruction with selectivity that can exceed that for protein-targeted medicines.

Expanding chemical space of DNA-binding molecules with three base-binding units.

A new molecule NC3-3 designed to expand chemical space of parent molecule NCD by adding the third base-binding unit was reported. NC3-3 bound to the G-G mismatch in the 5'-CGG-3'/5'-CGG-3' motif but not to that in 5'-GGC-3'/5'-GGC-3'. This binding selectivity is similar to that reported for NCD.

Development and validation of a cell-based assay system to assess human immunodeficiency virus type 1 integrase multimerization.

Multimerization of HIV-1 integrase (IN) subunits is required for the concerted integration of HIV-1 proviral DNA into the host genome. Thus, the disruption of IN multimerization represents a new avenue for intervening HIV-1 infection. Here, we generated a cell-based assay system to assess IN multimerization using a newly constructed bimolecular fluorescence complementation (BiFC-IN) system.

Exploration of labeling by near infrared dyes of the polyproline linker for bivalent-type CXCR4 ligands.

We have previously used poly-L-proline linkers for the development of bivalent-type ligands for the chemokine receptor, CXCR4. The bivalent ligands with optimum linkers showed specific binding to CXCR4, suggesting the existence of CXCR4 possibly as a dimer on the cell membrane, and enabled definition of the amount of CXCR4 expressed. This paper reports the synthesis by a copper-catalyzed azide-alkyne cycloaddition reaction as the key reaction, of bivalent CXCR4 ligands with near infrared (NIR) dyes at the terminus or the center of the poly-L-proline linker.

Exploratory Study on the RNA-Binding Structural Motifs by Library Screening Targeting pre-miRNA-29 a.

The metabolic stream of microRNA (miRNA) production, the so-called maturation process of miRNAs, became one of important metabolic paths for drug-targeting to modulate the expression of genes related to a number of diseases. We carried out discovery studies on small molecules binding to the precursor of miR-29a (pre-miR-29a) from a chemical library containing 41,119 compounds (AQ library) by the fluorescent indicator displacement (FID) assay using the xanthone derivative X2SdiMe as a fluorescent indicator. The FID assay provided 1075 compounds, which showed an increase of fluorescence.

Cell-permeable stapled peptides based on HIV-1 integrase inhibitors derived from HIV-1 gene products.

HIV-1 integrase (IN) is an enzyme which is indispensable for the stable infection of host cells because it catalyzes the insertion of viral DNA into the genome and thus is an attractive target for the development of anti-HIV agents. Earlier, we found Vpr-derived peptides with inhibitory activity against HIV-1 IN. These Vpr-derived peptides are originally located in an α-helical region of the parent Vpr protein.

Low-molecular-weight CXCR4 ligands with variable spacers.

Low-molecular-weight CXCR4 ligands based on known lead compounds including the 14-mer peptide T140, the cyclic pentapeptide FC131, peptide mimetics, and dipicolylamine-containing compounds were designed and synthesized. Three types of aromatic spacers, 1,4-phenylenedimethanamine, naphthalene-2,6-diyldimethanamine, and [1,1'-biphenyl]-4,4'-diyldimethanamine, were used to build four pharmacophore groups. As pharmacophore groups, 2-pyridylmethyl and 1-naphthylmethyl are present in all of the compounds, and several aromatic groups and a cationic group from 1-propylguanidine and 1,1,3,3-tetramethyl-2-propylguanidine were also used.

Stereoselective formation of trisubstituted (Z)-chloroalkenes adjacent to a tertiary carbon stereogenic center by organocuprate-mediated reduction/alkylation.

A robust and efficient method for the synthesis of trisubstituted (Z)-chloroalkenes is described. A one-pot reaction of γ,γ-dichloro-α,β-enoyl sultams involving organocuprate-mediated reduction/asymmetric alkylation affords α-chiral (Z)-chloroalkene derivatives in moderate to high yields with excellent diastereoselectivity, and allylic alkylation of internal allylic gem-dichlorides is also demonstrated. This study provides the first examples of the use of allylic gem-dichlorides adjacent to the chiral center for novel 1,4-asymmetric induction.

Pharmacophore-based small molecule CXCR4 ligands.

Low molecular weight CXCR4 ligands were developed based on the peptide T140, which has previously been identified as a potent CXCR4 antagonist. Some compounds with naphthyl, fluorobenzyl and pyridyl moieties as pharmacophore groups in the molecule showed significant CXCR4-binding activity and anti-HIV activity. Structure-activity relationships were studied and characteristics of each of these three moieties necessary for CXCR4 binding were defined.

Evaluation of a synthetic C34 trimer of HIV-1 gp41 as AIDS vaccines.

An artificial antigen forming the C34 trimeric structure targeting membrane-fusion mechanism of HIV-1 has been evaluated as an HIV vaccine. The C34 trimeric molecule was previously designed and synthesized using a novel template with C3-symmetric linkers by us. The antiserum produced by immunization of the C34 trimeric form antigen showed 23-fold higher binding affinity for the C34 trimer than for the C34 monomer and showed significant neutralizing activity.

Gold-catalyzed alkylation of silyl enol ethers with ortho-alkynylbenzoic acid esters.

Unprecedented alkylation of silyl enol ethers has been developed by the use of ortho-alkynylbenzoic acid alkyl esters as alkylating agents in the presence of a gold catalyst. The reaction probably proceeds through the gold-induced in situ construction of leaving groups and subsequent nucleophilic attack on the silyl enol ethers. The generated leaving compound abstracts a proton to regenerate the silyl enol ether structure.

Synthesis of 1,8-di(1-adamantyl)naphthalenes as single enantiomers stable at ambient temperatures.

Single enantiomers of 1,8-di(1-adamantyl)naphthalenes were synthesized by the [4+2]cycloaddition reaction of 6-adamantylbenzyne and 2-adamantylfuran. The enantiomers were resolved by conversion into diastereomeric ketopinic acid esters. The absolute configuration was determined by X-ray analysis.

Gold-catalyzed etherification and Friedel-Crafts alkylation using ortho-alkynylbenzoic acid alkyl ester as an efficient alkylating agent.

A gold-catalyzed alkylation of alcohols and aromatic compounds is described. The reaction of ortho-alkynylbenzoic acid alkyl esters with alcohols or aromatic compounds occurs in the presence of catalytic amounts of Ph3PAuCl and AgOTf under mild conditions to produce corresponding ethers or Friedel-Crafts alkylation products in good to high yields. The reaction likely proceeds through the gold-induced in situ construction of leaving groups and subsequent nucleophilic attack of alcohols or aromatic compounds.

Lewis acid-catalyzed [4 + 2] benzannulation between enynal units and enols or enol ethers: novel synthetic tools for polysubstituted aromatic compounds including indole and benzofuran derivatives.

The reaction of enynals 1, including o-(alkynyl)benzaldehydes, and carbonyl compounds 2, such as aldehydes and ketones, in the presence of a catalytic amount of AuBr3 in 1,4-dioxane at 100 degrees C gave the functionalized aromatic compounds 3 in high yields. Similarly, the AuBr3-catalyzed reactions of 1 with acetal compounds 5 afforded the corresponding aromatic compounds 3 in good yields. On the other hand, when the reaction was carried out in the presence of a catalytic amount of Cu(NTf2)2 and 1 equiv of H2O in (CH2Cl)2 at 100 degrees C, the decarbonylated naphthalene products 4 were obtained selectively over 3.

AuBr(3)-catalyzed [4 + 2] benzannulation between an enynal unit and enol.

The reaction of enynals 1, including o-alkynylbenzaldehydes, and carbonyl compounds 2 in the presence of a catalytic amount of AuBr3 in 1,4-dioxane at 100 degrees C gave the functionalized aromatic compounds 3 in high yields. The AuBr3-catalyzed formal [4 + 2] benzannulation proceeds most probably through the coordination of the triple bond of 1 to AuBr3, the formation of a pyrylium auric ate complex via the nucleophilic addition of the carbonyl oxygen atom, the reverse electron demand-type Diels-Alder addition of the enols, derived from 2, to the auric ate complex, and subsequent dehydration and bond rearrangement. Similarly, the AuBr3-catalyzed reactions of 1 with acetal compounds afforded the corresponding aromatic compounds in good yields.