RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder.

Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im-induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im-induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides-dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im-induced transcriptional arrest.

Synthesis of Sulfilimines Enabled by Copper-Catalyzed S-Arylation of Sulfenamides.

Herein, an unprecedented synthetic route to sulfilimines via a copper-catalyzed Chan-Lam-type coupling of sulfenamides is presented. A key to success in this novel transformation is the chemoselective S-arylation of S(II) sulfenamides to form S(IV) sulfilimines, overriding the competitive, and more thermodynamically favored, C-N bond formation that does not require a change in the sulfur oxidation state. Computations reveal that the selectivity arises from a selective transmetallation event where bidentate sulfenamide coordination through the sulfur and oxygen atoms favors the S-arylation pathway. The mild and environmentally benign catalytic conditions enable broad functional group compatibility, allowing a variety of diaryl or alkyl aryl sulfilimines to be efficiently prepared. The Chan-Lam coupling procedure could also tolerate alkenylboronic acids as coupling partners to afford alkenyl aryl sulfilimines, a class of scaffolds that cannot be directly synthesized via conventional imination strategies. The benzoyl-protecting groups could be conveniently removed from the product, which, in turn, could be readily transformed into several S(IV) and S(VI) derivatives.

Biomolecule-Compatible Dehydrogenative Chan-Lam Coupling of Free Sulfilimines.

Inspired by the discovery of a S═N bond in the collagen IV network and its essential role in stabilizing basement membranes, sulfilimines have drawn much attention in the fields of chemistry and biology. However, their further uptake is hindered by the lack of mild, efficient, and environmentally benign protocols by which sulfilimines can be constructed under biomolecule-compatible conditions. Here, we report a terminal oxidant-free copper-catalyzed dehydrogenative Chan-Lam coupling of free diaryl sulfilimines with arylboronic acids with excellent chemoselectivity and broad substrate compatibility. The mild reaction conditions and biomolecule-compatible nature allow the employment of this protocol in the late-stage functionalization of complex peptides, and more importantly, as an effective bioconjugation method as showcased in a model protein. A combined experimental and computational mechanistic investigation reveals that an inner-sphere electron-transfer process circumvents the sacrificial oxidant employed in traditional Chan-Lam coupling reactions. An energetically viable concerted pathway was located wherein a copper hydride facilitates hydrogen-atom abstraction from the isopropanol solvent to produce dihydrogen via a four-membered transition state.

Repression of the transcriptional activity of ERRα with sequence-specific DNA-binding polyamides.

The orphan nuclear receptors estrogen-related receptors (ERRs) bind to the estrogen-related receptor response element (ERRE) to regulate transcriptional programs in cellular metabolism and cancer cell growth. In this study, we evaluated the potential for a pyrrole-imidazole polyamide to block ERRα binding to ERREs to inhibit gene expression. We demonstrated that the ERRE-targeted polyamide 1 blocked the binding of ERRα to the consensus ERRE and reduced the transcriptional activity of ERRα in cell culture. We further showed that inhibiting ERRα transcriptional activity with polyamide 1 led to reduced mitochondrial oxygen consumption, a primary biological effect regulated by ERRα. Finally, our data demonstrated that polyamide 1 is an inhibitor for cancer cell growth.

Palladium-Catalyzed Enantioselective Arylation of Aryl Sulfenate Anions: A Combined Experimental and Computational Study.

A novel approach to produce chiral diaryl sulfoxides from aryl benzyl sulfoxides and aryl bromides via an enantioselective arylation of aryl sulfenate anions is reported. A (JosiPhos)Pd-based catalyst successfully promotes the asymmetric arylation reaction with good functional group compatibility. A wide range of enantioenriched diaryl, aryl heteroaryl, and even diheteroaryl sulfoxides were generated. Many of the sulfoxides prepared herein would be difficult to prepare via classic enantioselective oxidation of sulfides, including Ph(Ph-d5)SO (90% ee, 95% yield). A DFT-based computational study suggested that chiral induction originates from two primary factors: (i) both a kinetic and a thermodynamic preference for oxidative addition that places the bromide trans to the JosiPhos-diarylphosphine moiety and (ii) Curtin-Hammett-type control over the interconversion between O- and S-bound isomers of palladium sulfenate species following rapid interconversion between re- and si-bound transmetalation products, re/si-Pd-OSPh (re/si-PdO-trans).

Birefringent Stable Glass with Predominantly Isotropic Molecular Orientation.

Birefringence in stable glasses produced by physical vapor deposition often implies molecular alignment similar to liquid crystals. As such, it remains unclear whether these glasses share the same energy landscape as liquid-quenched glasses that have been aged for millions of years. Here, we produce stable glasses of 9-(3,5-di(naphthalen-1-yl)phenyl)anthracene molecules that retain three-dimensional shapes and do not preferentially align in a specific direction. Using a combination of angle- and polarization-dependent photoluminescence and ellipsometry experiments, we show that these stable glasses possess a predominantly isotropic molecular orientation while being optically birefringent. The intrinsic birefringence strongly correlates with increased density, showing that molecular ordering is not required to produce stable glasses or optical birefringence, and provides important insights into the process of stable glass formation via surface-mediated equilibration. To our knowledge, such novel amorphous packing has never been reported in the past.

Organocatalytic Synthesis of Alkynes.

Carbon-carbon triple bonds of alkynes are ubiquitous. They serve as valuable starting materials that can be transformed into a vast array of diverse materials, with applications ranging from medicinal chemistry to electronic materials. The methods used to prepare alkynes involve stoichiometric reactions and the most popular install only a single carbon rather than uniting larger fragments. These methods are useful, but they are limited by harsh conditions or the need to prepare reagents. Introduced herein is the first catalytic method to prepare carbon-carbon triple bonds from precursors that do not contain such linkages. By coupling benzaldehyde and benzyl chloride derivatives under basic conditions with an organocatalyst, good yields of alkynes are obtained. The catalyst, a highly reactive sulfenate anion, is readily generated under the reaction conditions from air-stable precursors. This method represents an attractive organocatalytic alternative to well-established stoichiometric approaches to alkynes and to transition-metal-based alkyne functionalization methods in various applications.

Palladium-Catalyzed Arylation of Alkyl Sulfenate Anions.

A unique palladium-catalyzed arylation of alkyl sulfenate anions is introduced that affords aryl alkyl sulfoxides in high yields. Due to the base sensitivity of the starting sulfoxides, sulfenate anion intermediates, and alkyl aryl sulfoxide products, the use of a mild method to generate alkyl sulfenate anions was crucial to the success of this process. Thus, a fluoride triggered elimination strategy was employed with alkyl 2-(trimethylsilyl)ethyl sulfoxides to liberate the requisite alkyl sulfenate anion intermediates. In the presence of palladium catalysts with bulky monodentate phosphines (SPhos and Cy-CarPhos) and aryl bromides or chlorides, alkyl sulfenate anions were readily arylated. Moreover, the thermal fragmentation and the base promoted elimination of alkyl sulfoxides was overridden. The alkyl sulfenate anion arylation exhibited excellent chemoselectivity in the presence of functional groups, such as anilines and phenols, which are also known to undergo palladium catalyzed arylation reactions.

NiXantphos: a deprotonatable ligand for room-temperature palladium-catalyzed cross-couplings of aryl chlorides.

Although the past 15 years have witnessed the development of sterically bulky and electron-rich alkylphosphine ligands for palladium-catalyzed cross-couplings with aryl chlorides, examples of palladium catalysts based on either triarylphosphine or bidentate phosphine ligands for efficient room temperature cross-coupling reactions with unactivated aryl chlorides are rare. Herein we report a palladium catalyst based on NiXantphos, a deprotonatable chelating aryldiphosphine ligand, to oxidatively add unactivated aryl chlorides at room temperature. Surprisingly, comparison of an extensive array of ligands revealed that under the basic reaction conditions the resultant heterobimetallic Pd-NiXantphos catalyst system outperformed all the other mono- and bidentate ligands in a deprotonative cross-coupling process (DCCP) with aryl chlorides. The DCCP with aryl chlorides affords a variety of triarylmethane products, a class of compounds with various applications and interesting biological activity. Additionally, the DCCP exhibits remarkable chemoselectivity in the presence of aryl chloride substrates bearing heteroaryl groups and sensitive functional groups that are known to undergo 1,2-addition, aldol reaction, and O-, N-, enolate-α-, and C(sp(2))-H arylations. The advantages and importance of the Pd-NiXantphos catalyst system outlined herein make it a valuable contribution for applications in Pd-catalyzed arylation reactions with aryl chlorides.

A General and Practical Palladium-Catalyzed Direct α-Arylation of Amides with Aryl Halides.

An efficient system for the direct catalytic intermolecular α-arylation of acetamide derivatives with aryl bromides and chlorides is presented. The palladium catalyst is supported by Kwong's indole-based phosphine ligand and provides monoarylated amides in up to 95% yield. Excellent chemoselectivities (>10:1) in the mono- and diarylation with aryl bromides were achieved by careful selection of bases, solvents, and stoichiometry. Under the coupling conditions, the weakly acidic α-protons of amides (pKa up to 35) were reversibly depotonated by LiO t Bu, NaO t Bu, or NaN(SiMe3)2.

Diaryl sulfoxides from aryl benzyl sulfoxides: a single palladium-catalyzed triple relay process.

A novel approach to produce diaryl sulfoxides from aryl benzyl sulfoxides is reported. Optimization of the reaction conditions was performed using high-throughput experimentation techniques. The [Pd(dba)2 ]/NiXantPhos catalyst system successfully promotes a triple relay process involving sulfoxide α-arylation, CS bond cleavage, and CS bond formation. The byproduct benzophenone is formed by an additional palladium-catalyzed process. It is noteworthy that palladium-catalyzed benzylative CS bond cleavage of sulfoxides is unprecedented. A wide range of aryl benzyl sulfoxides, as well as alkyl benzyl sulfoxides with various (hetero)aryl bromides were employed in the triple relay process in good to excellent yields (85-99 %). Moreover, aryl methyl sulfoxides, dibenzyl sulfoxides, and dimethylsulfoxide could be utilized to generate diaryl sulfoxides involving multiple catalytic cycles by a single catalyst.

A new class of organocatalysts: sulfenate anions.

Sulfenate anions are known to act as highly reactive species in the organic arena. Now they premiere as organocatalysts. Proof of concept is offered by the sulfoxide/sulfenate-catalyzed (1-10 mol%) coupling of benzyl halides in the presence of base to generate trans-stilbenes in good to excellent yields (up to 99%). Mechanistic studies support the intermediacy of sulfenate anions, and the deprotonated sulfoxide was determined to be the resting state of the catalyst.

A combined experimental and computational study of ligand-controlled Chan-Lam coupling of sulfenamides.

The unique features of the sulfenamides' S(II)-N bond lead to interesting stereochemical properties and significant industrial functions. Here we present a chemoselective Chan-Lam coupling of sulfenamides to prepare N-arylated sulfenamides. A tridentate pybox ligand governs the chemoselectivity favoring C-N bond formation, and overrides the competitive C-S bond formation by preventing the S,N-bis-chelation of sulfenamides to copper center. The Cu(II)-derived resting state of catalyst is captured by UV-Vis spectra and EPR technique, and the key intermediate is confirmed by the EPR isotope response using 15N-labeled sulfenamide. A computational mechanistic study reveals that N-arylation is both kinetically and thermodynamically favorable, with deprotonation of the sulfenamide nitrogen atom occurring prior to reductive elimination. The origin of ligand-controlled chemoselectivity is explored, with the interaction between the pybox ligand and the sulfenamide substrate controlling the energy of the S-arylation and the corresponding product distribution, in agreement with the EPR studies and kinetic results.

Palladium-catalyzed direct arylation of methyl sulfoxides with aryl halides.

The palladium-catalyzed α-arylation of unactivated sulfoxides has been developed. The weakly acidic α-protons of sulfoxides are reversibly deprotonated by LiOtBu, and a palladium phosphine complex facilitates the arylation. A variety of aryl methyl sulfoxides were coupled with aryl bromides. More challenging coupling partners, such as alkyl methyl sulfoxides (including dimethyl sulfoxide) and aryl chlorides proved to be suitable under the optimized conditions. This method was utilized to synthesize bioactive benzyl sulfoxide intermediates.

Photocatalytic N-Alkylation of NH-Diaryl Sulfondiimines via Anti-Markovnikov Hydroamination with Styrenes.

Sulfondiimines, which are isoelectronic with sulfones and sulfoximines, represent a neglected yet intriguing pharmacophore in the discovery program. Herein, we present a facile and mild photocatalytic anti-Markovnikov hydroamination of styrenes for the construction of N-alkylated sulfondiimines with primary, secondary, and tertiary alkyl substituents. A sulfondiimine-derived analogue of the marketed drug Vioxx was synthesized using this method as the key step.

Potentiometric Determination of Acid Dissociation Constants (pK a) for an Anticancer Pyrrole-Imidazole Polyamide.

To optimize the pharmacological properties of an anticancer pyrrole-imidazole (Py-Im) polyamide (PIP-1), we characterized the acid dissociation constants of PIP-1, three other structurally related hairpin-shaped polyamides, and a cyclic polyamide bearing the same core sequence as PIP-1 via potentiometric titration. The acidities of the carboxylic acid at the C-terminus and the tertiary amine in the triamine linker remained very similar among the polyamides tested, whereas the pK a of the N-methylimidazole (Im) moieties varied with the peptide sequence and molecular architecture. A nearly 0.2 pH unit pK a shift of terminal Im toward the neutral state compared to internal Im was observed. Furthermore, according to the dissociation constants, a speciation diagram of PIP-1 as a function of pH is presented, which allows an assessment of the net charge and distribution of protonated species in the range of physiological pH.

Tagging Peptides with a Redox Responsive Fluorescent Probe Enabled by Photoredox Difunctionalization of Phenylacetylenes with Sulfinates and Disulfides.

Herein, we describe a photoredox three-component atom-transfer radical addition (ATRA) reaction of aryl alkynes directly with dialkyl disulfides and alkylsulfinates, circumventing the utilization of chemically unstable and synthetically challenging S-alkyl alkylthiosulfonates as viable addition partners. A vast array of (E)-ß-alkylsulfonylvinyl alkylsulfides was prepared with great regio- and stereoselectivity. Moreover, this powerful tactic could be employed to tag cysteine residues of complex polypeptides in solution or on resin merging with solid phase peptide synthesis (SPPS) techniques. A sulfonyl-derived redox responsive fluorescent probe could be conveniently introduced on the peptide, which displays green fluorescence in cells while showing blue fluorescence in medium. The photophysical investigations reveal that the red shift of the emission fluorescence is attested to reduction of carbonyl group to the corresponding hydroxyl moiety. Interestingly, the fluorescence change of tagged peptide could be reverted in cells by treatment of H2O2, arising from the reoxidation of hydroxyl group back to ketone by the elevated level of reactive oxygen species (ROS).

Atom Transfer Radical Addition to Styrenes with Thiosulfonates Enabled by Synergetic Copper/Photoredox Catalysis.

A synergetic copper/photoredox catalyzed ATRA of styrenes and thiosulfonates is developed. Besides aryl ethylenes, the challenging α-substituted styrenes were employed to construct the benzylic quaternary carbon centers. Owing to the mild conditions as well as the high level of substrate compability, this ATRA could be applied to derivatize bioactive natural products in late stage, and to install fluorophores across alkenes. The mechanistic studies reveal sulfonyl radicals as the key intermediate in the transformation.

Radical Anion Promoted Chemoselective Cleavage of Csp2-S Bond Enables Formal Cross-Coupling of Aryl Methyl Sulfones with Alcohols.

A novel formal cross-coupling of aryl methyl sulfones and alcohols affording alkyl aryl ethers via an SRN1 pathway is developed. Two marketed antitubercular drugs were efficiently prepared employing this approach as the key step. A dimsyl-anion initiated radical chain process was revealed as the major pathway. DFT calculations indicate that the formation of a radical anion via nucleophilic addition of alkoxide to the aryl radical is the key step in determining the observed chemoselectivity.

Autocatalytic photoredox Chan-Lam coupling of free diaryl sulfoximines with arylboronic acids.

N-Arylation of NH-sulfoximines represents an appealing approach to access N-aryl sulfoximines, but has not been successfully applied to NH-diaryl sulfoximines. Herein, a copper-catalyzed photoredox dehydrogenative Chan-Lam coupling of free diaryl sulfoximines and arylboronic acids is described. This neutral and ligand-free coupling is initiated by ambient light-induced copper-catalyzed single-electron reduction of NH-sulfoximines. This electron transfer route circumvents the sacrificial oxidant employed in traditional Chan-Lam coupling reactions, increasing the environmental friendliness of this process. Instead, dihydrogen gas forms as a byproduct of this reaction. Mechanistic investigations also reveal a unique autocatalysis process. The C-N coupling products, N-arylated sulfoximines, serve as ligands along with NH-sulfoximine to bind to the copper species, generating the photocatalyst. DFT calculations reveal that both the NH-sulfoximine substrate and the N-aryl product can ligate the copper accounting for the observed autocatalysis. Two energetically viable stepwise pathways were located wherein the copper facilitates hydrogen atom abstraction from the NH-sulfoximine and the ethanol solvent to produce dihydrogen. The protocol described herein represents an appealing alternative strategy to the classic oxidative Chan-Lam reaction, allowing greater substrate generality as well as the elimination of byproduct formation from oxidants.