Using the structural diversity of RNA: protein interfaces to selectively target RNA with small molecules in cells: methods and perspectives.

In recent years, RNA has gained traction both as a therapeutic molecule and as a therapeutic target in several human pathologies. In this review, we consider the approach of targeting RNA using small molecules for both research and therapeutic purposes. Given the primary challenge presented by the low structural diversity of RNA, we discuss the potential for targeting RNA: protein interactions to enhance the structural and sequence specificity of drug candidates.

Design, synthesis and biological evaluation of quinoline-2-carbonitrile-based hydroxamic acids as dual tubulin polymerization and histone deacetylases inhibitors.

A series of quinoline and quinazoline analogs were designed and synthesized as new tubulin polymerization (TP) and histone deacetylases (HDAC) inhibitors. Compounds 12a and 12d showed the best cytotoxicity activities against a panel of human cancer cell lines with an averaged IC value of 0.6 and 0.

Identification of a small molecule splicing inhibitor targeting UHM domains.

Splicing factor mutations are frequent in myeloid neoplasms, blood cancers, and solid tumors. Cancer cells harboring these mutations present a particular vulnerability to drugs that target splicing factors such as SF3b155 or CAPERα. Still, the arsenal of chemical probes that target the spliceosome is very limited.

Targeting Degradation of EGFR through the Allosteric Site Leads to Cancer Cell Detachment-Promoted Death.

Targeting epidermal growth factor receptor (EGFR) with tyrosine kinase inhibitors (TKI) has been widely exploited to disrupt aberrant phosphorylation flux in cancer. However, a bottleneck of potent TKIs is the acquisition of drug resistance mutations, secondary effects, and low ability to attenuate tumor progression. We have developed an alternative means of targeting EGFR that relies on protein degradation through two consecutive routes, ultimately leading to cancer cell detachment-related death.

YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis.

The structural rearrangements accompanying mRNA during translation in mammalian cells remain poorly understood. Here, we discovered that YB-1 (YBX1), a major partner of mRNAs in the cytoplasm, forms a linear nucleoprotein filament with mRNA, when part of the YB-1 unstructured C-terminus has been truncated. YB-1 possesses a cold-shock domain (CSD), a remnant of bacterial cold shock proteins that have the ability to stimulate translation under the low temperatures through an RNA chaperone activity.

Design and Synthesis of Tubulin and Histone Deacetylase Inhibitor Based on iso-Combretastatin A-4.

Designing multitarget drugs have raised considerable interest due to their advantages in the treatment of complex diseases such as cancer. Their design constitutes a challenge in antitumor drug discovery. The present study reports a dual inhibition of tubulin polymerization and HDAC activity.

Cucurbitacin I elicits the formation of actin/phospho-myosin II co-aggregates by stimulation of the RhoA/ROCK pathway and inhibition of LIM-kinase.

Cucurbitacins are cytotoxic triterpenoid sterols isolated from plants. One of their earliest cellular effect is the aggregation of actin associated with blockage of cell migration and division that eventually lead to apoptosis. We unravel here that cucurbitacin I actually induces the co-aggregation of actin with phospho-myosin II.

Acceleration of an aromatic Claisen rearrangement via a designed spiroligozyme catalyst that mimics the ketosteroid isomerase catalytic dyad.

A series of hydrogen-bonding catalysts have been designed for the aromatic Claisen rearrangement of a 1,1-dimethylallyl coumarin. These catalysts were designed as mimics of the two-point hydrogen-bonding interaction present in ketosteroid isomerase that has been proposed to stabilize a developing negative charge on the ether oxygen in the migration of the double bond.1 Two hydrogen bond donating groups, a phenol alcohol and a carboxylic acid, were grafted onto a conformationally restrained spirocyclic scaffold, and together they enhance the rate of the Claisen rearrangement by a factor of 58 over the background reaction.

Aromatic Claisen Rearrangements of O-prenylated tyrosine and model prenyl aryl ethers: Computational study of the role of water on acceleration of Claisen rearrangements.

LynF, an enzyme from the TruF family, O-prenylates tyrosines in proteins; subsequent Claisen rearrangements give C-prenylated tyrosine products. These reactions in tyrosines and model phenolic systems have been explored with DFT and SCS-MP2 calculations. Various benchmarks have been computed (CBS-QB3, MP2, SCS-MP2) to examine the accuracy of commonly used density functionals, such as B3LYP and M06-2X.

Elucidation of the ATP7B N-domain Mg2+-ATP coordination site and its allosteric regulation.

The diagnostic of orphan genetic disease is often a puzzling task as less attention is paid to the elucidation of the pathophysiology of these rare disorders at the molecular level. We present here a multidisciplinary approach using molecular modeling tools and surface plasmonic resonance to study the function of the ATP7B protein, which is impaired in the Wilson disease. Experimentally validated in silico models allow the elucidation in the Nucleotide binding domain (N-domain) of the Mg(2+)-ATP coordination site and answer to the controversial role of the Mg(2+) ion in the nucleotide binding process.

Ordered and oriented supramolecular n/p-heterojunction surface architectures: completion of the primary color collection.

In this study, we describe synthesis, characterization, and zipper assembly of yellow p-oligophenyl naphthalenediimide (POP-NDI) donor-acceptor hybrids. Moreover, we disclose, for the first time, results from the functional comparison of zipper and layer-by-layer (LBL) assembly as well as quartz crystal microbalance (QCM), atomic force microscopy (AFM), and molecular modeling data on zipper assembly. Compared to the previously reported blue and red NDIs, yellow NDIs are more pi-acidic, easier to reduce, and harder to oxidize.

Site-dependent excited-state dynamics of a fluorescent probe bound to avidin and streptavidin.

The excited-state dynamics of biotin-spacer-Lucifer-Yellow (LY) constructs bound to avidin (Avi) and streptavidin (Sav) was investigated using femtosecond spectroscopy. Two different locations in the proteins, identified by molecular dynamics simulations of Sav, namely the entrance of the binding pocket and the protein surface, were probed by varying the length of the spacer. A reduction of the excited-state lifetime, stronger in Sav than in Avi, was observed with the long spacer construct.

Enantioselective organocatalytic conjugate addition of aldehydes to vinyl sulfones and vinyl phosphonates as challenging Michael acceptors.

Chiral framework: Chiral amines with pyrrolidine frameworks catalyze the enantioselective conjugate addition of a wide range of aldehydes to various vinyl sulfones and vinyl phosphonates in high yields and with enantioselectivities up to >99 % ee (see scheme). The high versatility of the Michael adducts is exemplified by various functionalizations with conservation of the optical purity.Chiral amines with a pyrrolidine framework catalyze the enantioselective conjugate addition of a broad range of aldehydes to various vinyl sulfones and vinyl phosphonates in high yields and with enantioselectivities up to >99 % ee.

Screening of pi-basic naphthalene and anthracene amplifiers for pi-acidic synthetic pore sensors.

Synthetic ion channels and pores attract current attention as multicomponent sensors in complex matrixes. This application requires the availability of reactive signal amplifiers that covalently capture analytes and drag them into the pore. pi-Basic 1,5-dialkoxynaphthalenes (1,5-DAN) are attractive amplifiers because aromatic electron donor-acceptor (AEDA) interactions account for their recognition within pi-acidic naphthalenediimide (NDI) rich synthetic pores.

Rigid-rod anion-pi slides for multiion hopping across lipid bilayers.

Shape-persistent oligo-p-phenylene-N,N-naphthalenediimide (O-NDI) rods are introduced as anion-pi slides for chloride-selective multiion hopping across lipid bilayers. Results from end-group engineering and covalent capture as O-NDI hairpins suggested that self-assembly into transmembrane O-NDI bundles is essential for activity. A halide topology VI (Cl > F > Br approximately I, Cl/Br approximately Cl/I > 7) implied strong anion binding along the anion-pi slides with relatively weak contributions from size exclusion (F >or= OAc).

Synthetic pores with reactive signal amplifiers as artificial tongues.

The sensation of taste is mediated by activation or deactivation of transmembrane pores. Artificial stimulus-responsive pores are enormously appealing as sensor components because changes in their activity are readily detectable in many different ways. However, the detection of multiple components in complex matrices (such as foods) with one pore sensor has so far remained elusive because the specificity necessary for sensing a target compound in complex mixtures is incompatible with the broad applicability needed for the detection of multiple components.

Synthetic pores with sticky pi-clamps.

In this report, we describe design, synthesis, evaluation and molecular dynamics simulations of synthetic multifunctional pores with pi-acidic naphthalenediimide clamps. Experimental evidence is provided for the formation of unstable but inert, heterogeneous and acid-insensitive dynamic tetrameric pores that are sensitive to base and ionic strength. Blockage experiments reveal that the introduction of aromatic electron donor-acceptor interactions provides access to the selective recognition of pi-basic intercalators within the pore.

Adhesive pi-clamping within synthetic multifunctional pores.

We report the design, synthesis, and evaluation of synthetic multifunctional pores with adhesive, that is, electron-deficient naphthalenediimide (NDI) pi-clamps at their inner surface. We find that, in lipid bilayer membranes, comparable synthetic pores with and without pi-clamps have similar, nanomolar activity. Functional relevance of adhesive pi-clamping within synthetic pores is demonstrated by means of an innovative in situ blocker screening method.

Rigid oligonaphthalenediimide rods as transmembrane anion-pi slides.

We report the design, synthesis, and evaluation of rigid oligonaphthalenediimide (O-NDI) rods that are expected to act as transmembrane anion-pi slides. Studies in fluorogenic large unilamellar egg yolk phosphatidylcholine vesicles reveal that rigid O-NDI rods mediate anion-selective transport with a rare halide VI selectivity sequence (Cl- > F- > Br- > I-). This and decreasing activity, selectivity, and halide sequence with increasing positive charge of the rod termini support the occurrence of anion-pi interactions.

Photoproduction of proton gradients with pi-stacked fluorophore scaffolds in lipid bilayers.

Rigid p-octiphenyl rods were used to create helical tetrameric pi-stacks of blue, red-fluorescent naphthalene diimides that can span lipid bilayer membranes. In lipid vesicles containing quinone as electron acceptors and surrounded by ethylenediaminetetraacetic acid as hole acceptors, transmembrane proton gradients arose through quinone reduction upon excitation with visible light. Quantitative ultrafast and relatively long-lived charge separation was confirmed as the origin of photosynthetic activity by femtosecond fluorescence and transient absorption spectroscopy.

Ligand-gated synthetic ion channels.

Supramolecular pi-stack architecture is fundamental in DNA chemistry but absent in biological and synthetic ion channels and pores. Here, a novel rigid-rod pi-stack architecture is introduced to create synthetic ion channels with characteristics that are at the forefront of rational design, that is, ligand gating by a conformational change of the functional supramolecule. Namely, the intercalation of electron-rich aromatics is designed to untwist inactive electron-poor helical pi-stacks without internal space into open barrel-stave ion channels.

Synthetic multifunctional pores that open and close in response to chemical stimulation.

Studies on synthetic multifunctional pores with external and internal active sites for ligand gating and noncompetitive blockage are presented, with emphasis on the contribution of external ligands to the characteristics of pore. A comparison between different synthetic multifunctional pores reveals that the location of functional groups in rigid-rod beta-barrel pores is precisely reflected in the function: molecular recognition at the outer barrel surface results in pore opening, while molecular recognition at the inner barrel surface results in pore closing. Negligible nonspecific leakage, disappearance of pH gating, inhibition of intervesicular pore transfer, and maybe also the flickering of currents of single open pores characterize external ligands as adhesive cushions that liberate the pore from lateral pressure exerted by the surrounding membrane.

Synthetic ion channels with rigid-rod pi-stack architecture that open in response to charge-transfer complex formation.

We describe the design, synthesis, and evaluation of synthetic ion channels with a new rigid-rod pi-stack architecture that open in response to guest binding by aromatic electron donor-acceptor interactions. Highly cooperative and highly selective ligand gating is shown to yield anion selective, small ion channels that have the characteristic plum color of the charge-transfer complexes formed between the dialkoxynaphthalene ligands and the stacked naphthalenediimide acceptors of the channel.