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A solid-phase DNA-encoded library (DEL) was studied for binding the RNA repeat expansion r( CUG ) exp , 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( CUG ) exp 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( CUG ) exp . In DM1 patient-derived muscle cells, the compound specifically bound r( CUG ) exp and allele-specifically eliminated r( CUG ) exp , improving disease-associated defects. The approaches herein can be used to identify and optimize ligands and bind RNA that can be further augmented for functionality including degradation.

Ribonuclease targeting chimeras (RiboTACs) induce degradation of an RNA target by facilitating an interaction between an RNA and a ribonuclease (RNase). We describe the screening of a DNA-encoded library (DEL) to identify binders of monomeric RNase L to provide a compound that induced dimerization of RNase L, activating its ribonuclease activity. This compound was incorporated into the design of a next-generation RiboTAC that targeted the microRNA-21 (miR-21) precursor and alleviated a miR-21-associated cellular phenotype in triple-negative breast cancer cells. The RNA-binding module in the RiboTAC is Dovitinib, a known receptor tyrosine kinase (RTK) inhibitor, which was previously identified to bind miR-21 as an off-target. Conversion of Dovitinib into this RiboTAC reprograms the known drug to selectively affect the RNA target. This work demonstrates that DEL can be used to identify compounds that bind and recruit proteins with effector functions in heterobifunctional compounds.

RNA is challenging to target with bioactive small molecules, particularly those of low molecular weight that bind with sufficient affinity and specificity. In this report, we developed a platform to address this challenge, affording a novel bioactive interaction. An RNA-focused small-molecule fragment collection ( n = 2500) was constructed by analyzing features in all publicly reported compounds that bind RNA, the largest collection of RNA-focused fragments to date. The RNA-binding landscape for each fragment was studied by using a library-versus-library selection with an RNA library displaying a discrete structural element, probing over 12.8 million interactions, the greatest number of interactions between fragments and biomolecules probed experimentally. Mining of this dataset across the human transcriptome defined a drug-like fragment that potently and specifically targeted the microRNA-372 hairpin precursor, inhibiting its processing into the mature, functional microRNA and alleviating invasive and proliferative oncogenic phenotypes in gastric cancer cells. Importantly, this fragment has favorable properties, including an affinity for the RNA target of 300 ± 130 nM, a molecular weight of 273 Da, and quantitative estimate of drug-likeness (QED) score of 0.8. (For comparison, the mean QED of oral medicines is 0.6 ± 0.2). Thus, these studies demonstrate that a low-molecular weight, fragment-like compound can specifically and potently modulate RNA targets.

The interactions between cellular RNAs in MDA-MB-231 triple negative breast cancer cells and a panel of small molecules appended with a diazirine cross-linking moiety and an alkyne tag were probed transcriptome-wide in live cells. The alkyne tag allows for facile pull-down of cellular RNAs bound by each small molecule, and the enrichment of each RNA target defines the compound's molecular footprint. Among the 34 chemically diverse small molecules studied, six bound and enriched cellular RNAs. The most highly enriched interaction occurs between the novel RNA-binding compound F1 and a structured region in the 5' untranslated region of quiescin sulfhydryl oxidase 1 isoform a ( QSOX1-a ), not present in isoform b. Additional studies show that F1 specifically bound RNA over DNA and protein; that is, we studied the entire DNA, RNA, and protein interactome. This interaction was used to design a ribonuclease targeting chimera (RIBOTAC) to locally recruit Ribonuclease L to degrade QSOX1 mRNA in an isoform-specific manner, as QSOX1-a , but not QSOX1-b , mRNA and protein levels were reduced. The RIBOTAC alleviated QSOX1 -mediated phenotypes in cancer cells. This approach can be broadly applied to discover ligands that bind RNA in cells, which could be bioactive themselves or augmented with functionality such as targeted degradation.

A stereoselective total synthesis of (+)-marrubiin has been accomplished starting from a chiral building block via the CyNH2-promoted Pauson-Khand reaction (PKR) followed by oxidative cleavage of the resultant cyclopentenone ring. Two successive oxidations and internal transacetalization culminated in the total synthesis of the antispasmodic labdane diterpenoid (-)-marrulibacetal.

A stereoselective synthesis of the CDE ring portion of the antitumor saponin scillascilloside E-1 has been achieved, utilizing an Ireland-Claisen rearrangement to construct the contiguous tetrasubstituted stereocenters at C13 and C17 simultaneously and intramolecular nitrile oxide cycloaddition to form the five-membered ring as key steps.

Methods for highly stereocontrolled syntheses of chiral building blocks with a triad of contiguous stereocenters, including two quaternary ones, have been developed. Ireland-Claisen rearrangement of the (Z)-silyl ketene acetal generated stereoselectively from the (R)-3-methylcyclohex-2-enyl ester derived from an acyclic carboxylic acid proceeded through a chairlike transition state to give the rearranged product with an S configuration at the position α to the carboxyl group. Introduction of a cyclic conformational constraint in the acid component completely switched the transition state of the rearrangement to a boatlike one, leading to the predominant formation of a product with an R configuration, from which pseudodiastereomeric α-hydroxy esters were obtained in a four-step sequence. The enyne obtained through a base-mediated double eliminative ring-opening reaction was successfully converted into advanced intermediates for the synthesis of 9-oxygenated labdane diterpenoids through a Heck reaction and a regioselective transformation of the resultant diene.

The preparations of two new phosphinothiophene ligands, 3,3'-bis(diphenylphosphino)-2,2'-bithiophene (dppbt; 1) and 3,3' "-dihexyl-3',3' '-bis(diphenylphosphino)-2,5':2',2' ':5' ',2' "-quaterthiophene (hdppqt; 2) are reported. Oxidation of 1 gives 3,3'-bis(diphenylphosphine oxide)-2,2'-bithiophene (3), and the crystal structure of this compound was determined. Pd(II) and Au(I) complexes of these ligands have been synthesized and characterized. Crystal structures of [(dppbt)PdCl(2)] (1-Pd), [(hdppqt)PdCl(2)] (2-Pd), [(dppbt)(AuCl)(2)] (1-Au), and [(hdppqt)(AuCl)(2)] (2-Au) were obtained. [(dppbt)(AuCl)(2)] crystallized in two solid-state forms; crystals grown from CH(2)Cl(2)/Et(2)O show a gold-gold interaction of 3.3221(4) A, but from CH(2)Cl(2)/toluene, the molecule crystallizes as a toluene adduct (1-Au-tol) and does not show any gold-gold interaction. All the complexes were characterized via UV-vis spectroscopy and cyclic voltammetry, and the effect of the metal on the energy of the pi-pi transition and oxidation potential was determined. These data are correlated to the interannular torsion angles in the oligothienyl groups from the crystal structure studies.