The discovery and characterization of two novel structural motifs on the carboxy-terminal domain of kinetoplastid RNA editing ligases.

Parasitic protozoans of the Trypanosoma and Leishmania species have a uniquely organized mitochondrial genome, the kinetoplast. Most kinetoplast-transcribed mRNAs are cryptic and encode multiple subunits for the electron transport chain following maturation through a uridine insertion/deletion process called RNA editing. This process is achieved through an enzyme cascade by an RNA editing catalytic complex (RECC), where the final ligation step is catalyzed by the kinetoplastid RNA editing ligases, KREL1 and KREL2. While the amino-terminal domain (NTD) of these proteins is highly conserved with other DNA ligases and mRNA capping enzymes, with five recognizable motifs, the functional role of their diverged carboxy-terminal domain (CTD) has remained elusive. In this manuscript, we assayed recombinant KREL1 in vitro to unveil critical residues from its CTD to be involved in protein-protein interaction and dsRNA ligation activity. Our data show that the α-helix (H)3 of KREL1 CTD interacts with the αH1 of its editosome protein partner KREPA2. Intriguingly, the OB-fold domain and the zinc fingers on KREPA2 do not appear to influence the RNA ligation activity of KREL1. Moreover, a specific KWKE motif on the αH4 of KREL1 CTD is found to be implicated in ligase auto-adenylylation analogous to motif VI in DNA ligases. In summary, we present in the KREL1 CTD a motif VI for auto-adenylylation and a KREPA2 binding motif for RECC integration.

Hammerhead ribozyme-based U-insertion and deletion RNA editing assays for multiplexing in HTS applications.

Untranslatable mitochondrial transcripts in kinetoplastids are decrypted post-transcriptionally through an RNA editing process that entails uridine insertion/deletion. This unique stepwise process is mediated by the editosome, a multiprotein complex that is a validated drug target of considerable interest in addressing the unmet medical needs for kinetoplastid diseases. With that objective, several in vitro RNA editing assays have been developed, albeit with limited success in discovering potent inhibitors. This manuscript describes the development of three hammerhead ribozyme (HHR) FRET reporter-based RNA editing assays for precleaved deletion, insertion, and ligation assays that bypass the rate-limiting endonucleolytic cleavage step, providing information on U-deletion, U-insertion, and ligation activities. These assays exhibit higher editing efficiencies in shorter incubation times while requiring significantly less purified editosome and 10,000-fold less ATP than the previously published full round of in vitro RNA editing assay. Moreover, modifications in the reporter ribozyme sequence enable the feasibility of multiplexing a ribozyme-based insertion/deletion editing (RIDE) assay that simultaneously surveils U-insertion and deletion editing suitable for HTS. These assays can be used to find novel chemical compounds with chemotherapeutic applications or as probes for studying the editosome machinery.

Sulfonated inhibitors of the RNA editing ligases validate the essential role of the MRP1/2 proteins in kinetoplastid RNA editing.

The RNA editing core complex (RECC) catalyzes mitochondrial U-insertion/deletion mRNA editing in trypanosomatid flagellates. Some naphthalene-based sulfonated compounds, such as C35 and MrB, competitively inhibit the auto-adenylylation activity of an essential RECC enzyme, kinetoplastid RNA editing ligase 1 (KREL1), required for the final step in editing. Previous studies revealed the ability of these compounds to interfere with the interaction between the editosome and its RNA substrates, consequently affecting all catalytic activities that comprise RNA editing. This observation implicates a critical function for the affected RNA binding proteins in RNA editing. In this study, using the inhibitory compounds, we analyzed the composition and editing activities of functional editosomes and identified the mitochondrial RNA binding proteins 1 and 2 (MRP1/2) as their preferred targets. While the MRP1/2 heterotetramer complex is known to bind guide RNA and promote annealing to its cognate pre-edited mRNA, its role in RNA editing remained enigmatic. We show that the compounds affect the association between the RECC and MRP1/2 heterotetramer. Furthermore, RECC purified post-treatment with these compounds exhibit compromised in vitro RNA editing activity that, remarkably, recovers upon the addition of recombinant MRP1/2 proteins. This work provides experimental evidence that the MRP1/2 heterotetramer is required for in vitro RNA editing activity and substantiates the hypothesized role of these proteins in presenting the RNA duplex to the catalytic complex in the initial steps of RNA editing.

Global identification of conserved post-transcriptional regulatory programs in trypanosomatids.

While regulatory programs are extensively studied at the level of transcription, elements that are involved in regulation of post-transcriptional processes are largely unknown, and methods for systematic identification of these elements are in early stages. Here, using a novel computational framework, we have integrated sequence information with several functional genomics data sets to characterize conserved regulatory programs of trypanosomatids, a group of eukaryotes that almost entirely rely on post-transcriptional processes for regulation of mRNA abundance. This analysis revealed a complex network of linear and structural RNA elements that potentially govern mRNA abundance across different life stages and environmental conditions. Furthermore, we show that the conserved regulatory network that we have identified is responsive to chemical perturbation of several biological functions in trypanosomatids. We have further characterized one of the most abundant regulatory RNA elements that we discovered, an AU-rich element (ARE) that can be found in 3' untranslated region of many trypanosomatid genes. Using bioinformatics approaches as well as in vitro and in vivo experiments, we have identified three ELAV-like homologs, including the developmentally critical protein TbRBP6, which regulate abundance of a large number of trypanosomatid ARE-containing transcripts. Together, these studies lay out a roadmap for characterization of mechanisms that modulate development and metabolic pathways in trypanosomatids.

Transition metal-catalyzed C-C bond formation via C-S bond cleavage: an overview.

Transition metal-catalyzed C-C bond formations have been well studied over the last four decades. An improved mechanistic understanding of such reactions has helped chemists to develop further improvements, modifications and even new reactions. In the area of transition metal-catalyzed cross-coupling reactions the C-S bond cleaving reactions have attracted a lot of attention in the last decade as they provide a good alternative to the use of organo-halide reagents in traditional cross-coupling reactions. The availability of a wide range of organo-sulfur species provides the opportunity for developing different transformations for the synthesis of interesting organic compounds. This tutorial review focuses on recent examples of the transition metal-catalyzed C-C bond forming reactions using organo-sulfur species.

Ruthenium-catalyzed cascade C-H functionalization of phenylacetophenones.

Three orthogonal cascade CH functionalization processes are described, based on ruthenium-catalyzed CH alkenylation. 1-Indanones, indeno indenes, and indeno furanones were accessed through cascade pathways by using arylacetophenones as substrates under conditions of catalytic [{Ru(p-cymene)Cl2 }2 ] and stoichiometric Cu(OAc)2 . Each transformation uses CH functionalization methods to form CC bonds sequentially, with the indeno furanone synthesis featuring a CO bond formation as the terminating step. This work demonstrates the power of ruthenium-catalyzed alkenylation as a platform reaction to develop more complex transformations, with multiple CH functionalization steps taking place in a single operation to access novel carbocyclic structures.

High-throughput screening of compounds targeting RNA editing in Trypanosoma brucei: Novel molecular scaffolds with broad trypanocidal effects.

Mitochondrial uridine insertion/deletion RNA editing, catalyzed by a multiprotein complex (editosome), is essential for gene expression in trypanosomes and Leishmania parasites. As this process is absent in the human host, a drug targeting this mechanism promises high selectivity and reduced toxicity. Here, we successfully miniaturized our FRET-based full-round RNA editing assay, which replicates the complete RNA editing process, adapting it into a 1536-well format. Leveraging this assay, we screened over 100,000 compounds against purified editosomes derived from Trypanosoma brucei, identifying seven confirmed primary hits. We sourced and evaluated various analogs to enhance the inhibitory and parasiticidal effects of these primary hits. In combination with secondary assays, our compounds marked inhibition of essential catalytic activities, including the RNA editing ligase and interactions of editosome proteins. Although the primary hits did not exhibit any growth inhibitory effect on parasites, we describe eight analog compounds capable of effectively killing T. brucei and/or Leishmania donovani parasites within a low micromolar concentration. Whether parasite killing is - at least in part - due to inhibition of RNA editing in vivo remains to be assessed. Our findings introduce novel molecular scaffolds with the potential for broad antitrypanosomal effects.

Prevalence and Determinants of Low Birth Weight among the Newborns in Dadra and Nagar Haveli: A Community-based Study.

Background: The world is not on track to meet the World Health Assembly (WHA) global target on Low Birth Weight (LBW). To estimate the prevalence and to identify the associated determinants of LBW among the newborns. Material and Methods: We conducted a cross-sectional study among the 364 mothers registered under the all government health facilities of Dadra & Nagar Haveli (DNH) during November 2021 to January 2022. Results: The prevalence of LBW was found to be 39%. On uni-variable logistic regression, live in relationship, caste, weight of mother, Body Mass Index (BMI), weight gain <5 kg in 2nd and 3rd trimester, high-risk pregnancy, complication present in previous pregnancy and preterm delivery, while on multi-variable logistic regression, weight gain <5 kg in 2nd and 3rd trimester (AOR 2, 95% CI 1.007-4.2) and having high-risk pregnancy (AOR 2, 95% CI 1.1-3.0) were found to be the significant predictors of LBW among the newborns. Conclusions: We conclude from the study that the prevalence of low birth weight among the newborn was high. There is a need to address maternal and child health issues like low birth weight, malnutrition and high-risk pregnancy under the RMNCAH+N program through various effective interventions. Future research should evaluate the feasibility of collaborative activities between RMNCAH+N program and the UNICEF in India.

Synthesis and HIV-1 RT inhibitory action of novel (4/6-substituted benzo[d]thiazol -2-yl)thiazolidin-4-ones. Divergence from the non-competitive inhibition mechanism.

Reverse transcriptase (RT) inhibitors play a major role in the therapy of human immunodeficiency virus type 1 (HIV-1) infection. Although, many compounds are already used as anti-HIV drugs, research on development of novel inhibitors continues, since drug resistant strains appear because of prolonged therapy. In this paper, we present the synthesis and evaluation of HIV-1 RT inhibitory action of eighteen novel (4/6-halogen/MeO/EtO-substituted benzo[d]thiazol-2-yl)thiazolidin-4-ones. The two more active compounds (IC50 : 0.04 µM and 0.25 µM) exhibited better inhibitory action than the reference compound, nevirapine. Docking analysis supports a stable binding of the most active derivative to the allosteric centre of RT. Kinetic analysis of two of the most active compounds indicate an uncompetitive inhibition mode. This is a desired characteristic, since mutations that affect activity of traditional non-competitive NNRTIs may not affect activity of compounds of this series. Interestingly, the less active derivatives (IC50 > 40 µM) exhibit a competitive mode of action.

Microwave-assisted C-C bond forming cross-coupling reactions: an overview.

Among the fundamental transformations in the field of synthetic organic chemistry, transition-metal-catalyzed reactions provide some of the most attractive methodologies for the formation of C-C and C-heteroatom bonds. As a result, the application of these reactions has increased tremendously during the past decades and cross-coupling reactions became a standard tool for synthetic organic chemists. Furthermore, a tremendous upsurge in the development of new catalysts and ligands, as well as an increased understanding of the mechanisms, has contributed substantially to recent advances in the field. Traditionally, organic reactions are carried out by conductive heating with an external heat source (for example, an oil bath). However, the application of microwave irradiation is a steadily gaining field as an alternative heating mode since its dawn at the end of the last century. This tutorial review focuses on some of the recent developments in the field of cross-coupling reactions assisted by microwave irradiation.

N-heterocyclic carbene catalyzed aroylation of 3,5-dichloro-2(1H)-pyrazinones.

The N-heterocyclic carbene catalyzed chemoselective C3-aroylation of 3,5-dichloro-2(1H)-pyrazinones with various aldehydes is reported. We herein describe results of this remarkable mild and efficient procedure.

An expeditious route toward pyrazine-containing nucleoside analogues.

An improved and convenient methodology for the synthesis of asymmetrically substituted pyrazines starting from 3,5-dichloropyrazin-2(1H)-ones has been elaborated. Several nucleoside analogues have been synthesized containing the pyrazine core as the organic base coupled with the sugar via a triazole linkage. The beneficial effect of microwave irradiation throughout the sequence has been demonstrated.

A microwave-assisted diastereoselective multicomponent reaction to access dibenzo[c,e]azepinones: synthesis and biological evaluation.

An unprecedented microwave-assisted multicomponent strategy has been elaborated for the fast, efficient, and diastereoselective generation of the dibenzo[c,e]azepinone scaffold. The generated compounds were evaluated for their bioactivity.

Microwave-assisted cycloaddition reactions.

Cycloaddition reactions belong to one of the most well-investigated and widely used reactions in synthetic organic chemistry for the construction of (hetero)cyclic compounds in a single-step operation. In this tutorial review, a select number of examples of some [3+2] cycloadditions, i.e. for 1,2,3-triazole formation, as well as of some [4+2] and [2+2] cycloadditions are reviewed, where it has been proven that the application of microwave irradiation has a profound influence on the outcome of the reaction.

Microwave-assisted palladium-catalyzed phosphonium coupling of 2(1H)-pyrazinones.

An expedient route for the synthesis of differently substituted 2(1H)-pyrazinones applying a microwave-assisted palladium-catalyzed phosphonium coupling procedure is reported. The method has also been successfully extended to some other tautomerizable heterocycles for efficient C-C cross-coupling.

Microwave-assisted synthesis of a novel class of imidazolylthiazolidin-4-ones and evaluation of its biological activities.

The synthesis and biological activity of a hitherto unknown class of compounds, the imidazolylthiazolidin-4-ones, are described. A two-step procedure has been elaborated starting from our previously described 2-aminoimidazoles. The application of microwave irradiation has been proven to be beneficial for the condensation of the imine with mercaptoacetic acid leading to the formation of imidazolylthiazolidin-4-ones. None of the compounds showed antiviral activity at subtoxic concentrations. Several compounds displayed a moderate cytostatic activity. These data form the basis for further improvement of the potential antiproliferative activity of this class of compounds.

Mild room-temperature palladium-catalyzed C3-arylation of 2(1H)-pyrazinones via a desulfitative Kumada-type cross-coupling reaction.

An efficient desulfitative Kumada-type cross-coupling protocol is reported for the C3-arylation of 5-chloro-3-(phenylsulfanyl)pyrazin-2(1H)-ones. The method has also been successfully extended to the arylation of some (hetero)aryl thioethers and thioesters.

Synthesis and fungicidal activity of 3,5-dichloropyrazin-2(1H)-one derivatives.

We synthesized a family of 3,5-dichloropyrazin-2(1H)-one derivatives and assessed their in vitro fungicidal activity against Candida albicans. Compounds 11 and 20 were most active against C. albicans and induced accumulation of reactive oxygen species in this pathogen. Using a genome-wide approach in the yeast Saccharomyces cerevisiae, we demonstrated that genes involved in vacuolar functionality and DNA-related functions play an important role in cellular mechanisms underlying the fungicidal activity of these compounds.

Pd-catalyzed cascade reactions involving skipped dienes: from double carbopalladation to remote C-C cleavage.

We report two ligand-controlled cascade reactions relying on the intramolecular carbopalladation of skipped dienes. The use of a bulky monodentate phosphine ligand affords [4,5]-spirocycles via sequential double carbopalladation, however bidentate phosphines promote a remote ß-C-elimination process which does not rely on the use of strained or sterically hindered substrates.

Scale Effect of a Fluorescent Waveguide in Organic Micromaterials: A Case Study Based on Coumarin Microfibers.

The classical method for evaluating the waveguide ability only focuses on the optical loss coefficient. However, for the micro- or submicroscale, an organic waveguide is demonstrated by the present study whose scale effect should not be neglected. We found that the optical loss coefficient increased remarkably when decreasing the sectional size of the microfibers. Furthermore, simulations based on Finite-Difference Time-Domain also demonstrated the size-dependent effect of the waveguide. Both the experimental and simulating results showed that the optical loss coefficient converges to a certain value, which means that the scale effect can be neglected as the sectional size is large enough. On the basis of the present study, we suggest that the scale-dependent effect on the sectional size of the waveguide should be investigated by evaluating the waveguide ability by the optical loss coefficient.