Trimethylguanosine cap-fluorescent molecular rotor (TMG-FMR) conjugates are potent, specific snurportin1 ligands enabling visualization in living cells.

The trimethylguanosine (TMG) cap is a motif present inter alia at the 5' end of small nuclear RNAs, which are involved in RNA splicing. The TMG cap plays a crucial role in RNA processing and stability as it protects the RNA molecule from degradation by exonucleases and facilitates its export from the nucleus. Additionally, the TMG cap plays a role in the recognition of snRNA by snurportin, a protein that facilitates nuclear import. TMG cap analogs are used in biochemical experiments as molecular tools to substitute the natural TMG cap. To expand the range of available TMG-based tools, here we conjugated the TMG cap to Fluorescent Molecular Rotors (FMRs) to open the possibility of detecting protein-ligand interactions in vitro and, potentially, in vivo, particularly visualizing interactions with snurportin. Consequently, we report the synthesis of 34 differently modified TMG cap-FMR conjugates and their evaluation as molecular probes for snurportin. As FMRs we selected three GFP-like chromophores (derived from green fluorescent protein) and one julolidine derivative. The evaluation of binding affinities for snurportin showed unexpectedly a strong stabilizing effect for TMGpppG-derived dinucleotides containing the FMR at the 2'-O-position of guanosine. These newly discovered compounds are potent snurportin ligands with nanomolar KD (dissociation constant) values, which are two orders of magnitude lower than that of natural TMGpppG. The effect is diminished by ∼50-fold for the corresponding 3'-regioisomers. To deepen the understanding of the structure-activity relationship, we synthesized and tested FMR conjugates lacking the TMG cap moiety. These studies, supported by molecular docking, suggested that the enhanced affinity arises from additional hydrophobic contacts provided by the FMR moiety. The strongest snurportin ligand, which also gave the greatest fluorescence enhancement (Fm/F0) when saturated with the protein, were tested in living cells to detect interactions and visualize complexes by fluorescence lifetime monitoring. This approach has potential applications in the study of RNA processing and RNA-protein interactions.

Fluorescence Anisotropy Assay with Guanine Nucleotides Provides Access to Functional Analysis of Gαi1 Proteins.

Gα proteins as part of heterotrimeric G proteins are molecular switches essential for G protein-coupled receptor- mediated intracellular signaling. The role of the Gα subunits has been examined for decades with various guanine nucleotides to elucidate the activation mechanism and Gα protein-dependent signal transduction. Several approaches describe fluorescent ligands mimicking the GTP function, yet lack the efficient estimation of the proteins' GTP binding activity and the fraction of active protein. Herein, we report the development of a reliable fluorescence anisotropy-based method to determine the affinity of ligands at the GTP-binding site and to quantify the fraction of active Gαi1 protein. An advanced bacterial expression protocol was applied to produce active human Gαi1 protein, whose GTP binding capability was determined with novel fluorescently labeled guanine nucleotides acting as high-affinity Gαi1 binders compared to the commonly used BODIPY FL GTPγS. This study thus contributes a new method for future investigations of the characterization of Gαi and other Gα protein subunits, exploring their corresponding signal transduction systems and potential for biomedical applications.

Molecule Edit Graph Attention Network: Modeling Chemical Reactions as Sequences of Graph Edits.

The central challenge in automated synthesis planning is to be able to generate and predict outcomes of a diverse set of chemical reactions. In particular, in many cases, the most likely synthesis pathway cannot be applied due to additional constraints, which requires proposing alternative chemical reactions. With this in mind, we present Molecule Edit Graph Attention Network (MEGAN), an end-to-end encoder-decoder neural model. MEGAN is inspired by models that express a chemical reaction as a sequence of graph edits, akin to the arrow pushing formalism. We extend this model to retrosynthesis prediction (predicting substrates given the product of a chemical reaction) and scale it up to large data sets. We argue that representing the reaction as a sequence of edits enables MEGAN to efficiently explore the space of plausible chemical reactions, maintaining the flexibility of modeling the reaction in an end-to-end fashion and achieving state-of-the-art accuracy in standard benchmarks. Code and trained models are made available online at https://github.com/molecule-one/megan.

A multicolor riboswitch-based platform for imaging of RNA in live mammalian cells.

RNAs directly regulate a vast array of cellular processes, emphasizing the need for robust approaches to fluorescently label and track RNAs in living cells. Here, we develop an RNA imaging platform using the cobalamin riboswitch as an RNA tag and a series of probes containing cobalamin as a fluorescence quencher. This highly modular 'Riboglow' platform leverages different colored fluorescent dyes, linkers and riboswitch RNA tags to elicit fluorescence turn-on upon binding RNA. We demonstrate the ability of two different Riboglow probes to track mRNA and small noncoding RNA in live mammalian cells. A side-by-side comparison revealed that Riboglow outperformed the dye-binding aptamer Broccoli and performed on par with the gold standard RNA imaging system, the MS2-fluorescent protein system, while featuring a much smaller RNA tag. Together, the versatility of the Riboglow platform and ability to track diverse RNAs suggest broad applicability for a variety of imaging approaches.

Synthesis of Trifluoromethylated Purine Ribonucleotides and Their Evaluation as 19F NMR Probes.

Protected guanosine and adenosine ribonucleosides and guanine nucleotides are readily functionalized with CF3 substituents within the nucleobase. Protected guanosine is trifluoromethylated at the C8 position under radical-generating conditions in up to 95% yield and guanosine 5'-oligophosphates in up to 35% yield. In the case of adenosine, the selectivity of trifluoromethylation depends heavily on the functional group protection strategy and leads to a set of CF3-modified nucleosides with different substitution patterns (C8, C2, or both) in up to 37% yield. Further transformations based on phosphorimidazolide chemistry afford various CF3-substituted mono- and dinucleoside oligophosphates in good yields. The utility of the trifluoromethylated nucleotides as probes for 19F NMR-based real-time enzymatic reaction monitoring is demonstrated with three different human nucleotide hydrolases (Fhit, DcpS, and cNIIIB). Substrate and product(s) resonances were sufficiently separated to enable effective tracking of each enzymatic activity of interest.

Vitamin†B12 Phosphate Conjugation and Its Effect on Binding to the Human B12 -Binding Proteins Intrinsic Factor and Haptocorrin.

The binding of vitamin B12 derivatives to human B12 transporter proteins is strongly influenced by the type and site of modification of the cobalamin original structure. We have prepared the first cobalamin derivative modified at the phosphate moiety. The reaction conditions were fully optimized and its limitations examined. The resulting derivatives, particularly those bearing terminal alkyne and azide groups, were isolated and used in copper-catalyzed alkyne-azide cycloaddition reactions (CuAAC). Their sensitivity towards light revealed their potential as photocleavable molecules. The binding abilities of selected derivatives were examined and compared with cyanocobalamin. The interaction of the alkylated derivatives with haptocorrin was less affected than the interaction with intrinsic factor. Furthermore, the configuration of the phosphate moiety was irrelevant to the binding process.

Vitamin B12 derivatives for orthogonal functionalization.

The synthesis of vitamin B12 derivatives for selective orthogonal conjugation at both the Co center and 5'-OH is reported. Newly developed, reduction-free, direct alkynylation of vitamin B12 at the central cobalt ion proved to be versatile, with the formed acetylides, unlike other metalloorganic derivatives, showing remarkable heat and light stability, thus making them promising candidates as a drug carrier. Subsequently, high-yielding functionalization can be achieved via a sequence of selective [1,3] dipolar azide-alkyne cycloadditions (AACs) or carbamate formation followed by AAC.

Corroles that "click": modular synthesis of azido- and propargyl-functionalized metallocorrole complexes and convergent synthesis of a bis-corrole scaffold.

Bis-corroles have been prepared through a convergent synthesis using a copper-catalyzed azide-alkyne cycloaddition. Synthesis of the final homo- and heterobimetallic complexes has been achieved in three to four steps from commercially available materials in good overall yield. Meso-substituted corroles functionalized with a single azido or propargyl group were used as key starting materials. (C6F5)2(p-O(CH2CCH)Ph)corroleH3 (1) and ((C6F5)2(m-CH2N3)Ph)corroleH3 (3) were metalated with copper or iron and attached by Huisgen azide-alkyne cycloaddition ("click" reaction) first to small substrates and then to each other, demonstrating a convergent synthesis of bimetallic bis-corrole molecules.

"Clickable" vitamin B12 derivative.

A "clickable" vitamin B12 derivative possessing the azide functionality at the 5'-position was synthesized by means of a two-step procedure on the gram scale. The reaction of cobalamin with mesyl chloride (MsCl) afforded the 5'-OMs derivative, which was subsequently transformed to the desired 5'-azide, the structure of which was confirmed using X-ray analysis. It proved to be reactive in the azide-alkyne 1,3-dipolar cycloaddition reaction to give substituted triazoles in high yields. A study of the reaction conditions and the scope of the process are reported.

Protoporphyrin IX/Cobyrinate Derived Hybrids - Novel Activators of Soluble Guanylyl Cyclase.

A new cobyrinate/protoporphyrin IX molecular hybrids were prepared via CuAAC reaction. The synthesis involved selective preparation of cobyrinate and PpIX derived building blocks possessing respectively terminal alkyne and azide moieties followed by the CuOAc catalyzed cycloaddition reaction. Synthesized molecules activated soluble guanylyl cyclase showing strong linker length/activation dependence.

Introducing SuFNucs: Sulfamoyl-Fluoride-Functionalized Nucleosides That Undergo Sulfur Fluoride Exchange Reaction.

The reaction between ribonucleosides and ex situ generated sulfonyl fluoride has been developed. The reaction takes place at the -NH2 groups of nucleobases, and the resulting nucleosides are equipped with a sulfamoyl fluoride moiety, dubbed SuFNucs. These species undergo a selective sulfur fluoride exchange (SuFEx) reaction with various amines, leading to sulfamide-functionalized derivatives of adenosine, guanosine, and cytidine (SulfamNucs). The scope and examples of further SuFNucs fuctionalization leading to nucleotides, oligonucleotides, and peptide-nucleoside conjugates are presented.

Fluorinated Phosphoadenosine 5'-Phosphosulfate Analogues for Continuous Sulfotransferase Activity Monitoring and Inhibitor Screening by 19F NMR Spectroscopy.

Sulfotransferases (STs) are ubiquitous enzymes that participate in a vast number of biological processes involving sulfuryl group (SO3) transfer. 3'-phosphoadenosine 5'-phosphosulfate (PAPS) is the universal ST cofactor, serving as the "active sulfate" source in cells. Herein, we report the synthesis of three fluorinated PAPS analogues that bear fluorine or trifluoromethyl substituents at the C2 or C8 positions of adenine and their evaluation as substitute cofactors that enable ST activity to be quantified and real-time-monitored by fluorine-19 nuclear magnetic resonance (19F NMR) spectroscopy. Using plant AtSOT18 and human SULT1A3 as two model enzymes, we reveal that the fluorinated PAPS analogues show complementary properties with regard to recognition by enzymes and the working 19F NMR pH range and are attractive versatile tools for studying STs. Finally, we developed an 19F NMR assay for screening potential inhibitors against SULT1A3, thereby highlighting the possible use of fluorinated PAPS analogues for the discovery of drugs for ST-related diseases.

Selective modifications of hydrophobic vitamin B12 derivatives at c-and d-positions.

The acid-sensitivity of vitamin B(12) derived mono- and diamides was studied. It was found that the use of reductive ring-opening of the lactone moiety deactivated undesired decomposition of c-mono- and c,d-diamides under acidic conditions. As a result, reactions gave respectively c- or d-acids which were further functionalized via coupling with amino acids. Though mono- and diamides exhibited acid sensitivity, they were used for the preparation of several highly functionalized molecules showing their stability under various reaction conditions.

Efficient Synthesis of Trifluoromethylated Purine Ribonucleosides and Ribonucleotides.

The protocols presented in this article describe highly detailed synthesis of trifluoromethylated purine nucleotides and nucleosides (G and A). The procedure involves trifluoromethylation of properly protected (acetylated) nucleosides, followed by deprotection leading to key CF3 -containing nucleosides. This gives synthetic access to 8-CF3 -substituted guanosine derivatives and three adenosine derivatives (8-CF3 , 2-CF3 , and 2,8-diCF3 ). In further steps, phosphorylation and phosphate elongation (for selected examples) result in respective trifluoromethylated nucleoside mono-, di-, and triphosphates. Support protocols are included for compound handling, purification procedures, analytical sample preparation, and analytical techniques used throughout the performance of the basic protocols. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of trifluoromethylated guanosine and adenosine derivatives Basic Protocol 2: Synthesis of trifluoromethylated guanosine and adenosine monophosphates Basic Protocol 3: Synthesis of phosphorimidazolides of 8-CF3 GMP and 8-CF3 AMP Basic Protocol 4: Synthesis of trifluoromethylated guanosine and adenosine oligophosphates Support Protocol 1: TLC sample preparation and analysis Support Protocol 2: Purification protocol for Basic Protocol 1 Support Protocol 3: HPLC analysis and preparative HPLC Support Protocol 4: Ion-exchange chromatography.

Reduction-free synthesis of stable acetylide cobalamins.

A straightforward, reduction-free method for the synthesis of organometallic cobalamins has been developed. Stable phenylacetylide derivatives were characterized by X-ray analysis, showing a pronounced influence of the electronic nature of substituents on their structure.

Synthesis and evaluation of bifunctional sGC regulators: optimization of a connecting linker.

Hybrid molecules composed of PpIX and cobyrinic acid derivatives conjugated through linkers of varying length and composition were prepared via 1,3-dipolar cycloaddition (CuAAC) or amidation/esteryfication reactions. They were tested for activation of soluble guanylyl cyclase (sGC), a key enzyme in the NO/cGMP signaling pathway, by an in vitro GTP→cGMP conversion assay. Using purified heme-deficient sGC and truncated sGC variants lacking a heme-binding domain, we demonstrated that such hybrid molecules may activate sGC by targeting heme-binding and/or catalytic domain. While all conjugates activated sGC, only selected compounds served as bifunctional regulators and were capable of simultaneous targeting both heme and catalytic domains of sGC. The length and type of a linker connecting both components had a profound effect on the extent of sGC activation, indicating that the linker's type is crucial for their binding affinities with regulatory and catalytic domains. Only hybrids with the conjugated linker of 13-16 atom length synergistically target both domains and displayed the lowest EC50 and highest activating potency. Compounds with shorter connecting linkers were much less potent and were no more active than the cobyrinic acid component alone. The most active conjugate, which showed a 60-fold activation of sGC, was compound 11, in which PpIX and cobyrinic acid components are separated by 11 atoms chain with the triazole moiety in between.