Small molecule approaches to targeting RNA.

The development of innovative methodologies to identify RNA binders has attracted enormous attention in chemical biology and drug discovery. Although antibiotics targeting bacterial ribosomal RNA have been on the market for decades, the renewed interest in RNA targeting reflects the need to better understand complex intracellular processes involving RNA. In this context, small molecules are privileged tools used to explore the biological functions of RNA and to validate RNAs as therapeutic targets, and they eventually are to become new drugs. Despite recent progress, the rational design of specific RNA binders requires a better understanding of the interactions which occur with the RNA target to reach the desired biological response. In this Review, we discuss the challenges to approaching this underexplored chemical space, together with recent strategies to bind, interact and affect biologically relevant RNAs.

Forgotten Perfumery Plants - Part II: New Insights into the Development of Novel Fragrant Ingredients - Hawthorn Case Study.

Naturalness is gaining ground among perfumers and the use of natural raw materials is spreading in perfumery. Forgotten perfumery plants are of concern to develop innovative and natural ingredients for modern perfume industries. The main purpose of this study was to evaluate the potential interest of Crataegus monogyna Jacq. extracts as fragrance ingredient. To this end, various extractions, phytochemical characterizations and organoleptic evaluations of hawthorn were conducted on fresh, frozen, and dried flowering aerial parts, to identify those most likely to be of interest. More than a hundred compounds, anisaldehyde being the predominant one, were characterized for the first time in the volatile fraction, using HS-SPME-GC-MS technology. Impact of plant treatment and harvest year on the extracts were also discussed. From this work, a new and natural hawthorn-based ingredient was developed to complete the perfumers' palette.

Synthesis of Bleomycin-Inspired RNA Ligands Targeting the Biogenesis of Oncogenic miRNAs.

Noncoding RNAs (ncRNAs) play pivotal roles in the regulation of gene expression and represent a promising target for the development of new therapeutic approaches. Among these ncRNAs, microRNAs (miRNAs or miRs) are involved in the regulation of gene expression, and their dysregulation has been linked to several diseases such as cancers. Indeed, oncogenic miRNAs are overexpressed in cancer cells, thus promoting tumorigenesis and maintenance of cancer stem cells that are resistant to chemotherapy and often responsible for therapeutic failure. Here, we describe the design and synthesis of new small-molecule RNA binders able to inhibit the biogenesis of oncogenic miRNAs and target efficiently cancer stem cells. Through the biochemical study of their interaction with the target and thanks to intracellular assays, we describe the structure-activity relationships for this new series of RNA ligands, and we identify compounds bearing a very promising antiproliferative activity against cancer stem cells.

Commiphora wildii Merxm. Essential Oil: Natural Heptane Source and Co-Product Valorization.

As an alternative to fossil volatile hydrocarbon solvents used nowadays in perfumery, investigation on essential oil of Commiphora wildii Merxm. oleo gum resin as a source of heptane is reported here. Heptane, representing up to 30 wt-% of this oleo gum resin, was successfully isolated from the C. wildii essential oil, using an innovative double distillation process. Isolated heptane was then used as a solvent in order to extract some noble plants of perfumery. It was found that extracts obtained with this solvent were more promising in terms of sensory analysis than those obtained from fossil-based heptane. In addition, in order to valorize the essential oil depleted from heptane, chemical composition of this oil was found to obtain, and potential biological activity properties were studied. A total of 172 different compounds were identified by GC-MS in the remaining oil. In vitro tests-including hyaluronidase, tyrosinase, antioxidant, elastase and lipoxygenase, as well as inhibitory tests against two yeasts and 21 bacterial strains commonly found on the skin-were carried out. Overall, bioassays results suggest this heptane-depleted essential oil is a promising active ingredient for cosmetic applications.

Sustainable extraction of antioxidants from out-of-caliber kiwifruits.

Valorisation of discarded kiwifruits is proposed by extracting bioactive compounds using sustainable solvents namely deep eutectic solvents (DES). A screening of fifteen DES and several hydrogen bonding donor solvents was carried out. Extraction efficiency was measured in terms of antioxidant activity using DPPH and FRAP tests. The influence of solvents characteristics in particular DES structure, presence of ethanol or water, and pH of DES/water mixture on the antioxidant properties of the extracts was studied. Results show that kiwi peels extracts obtained with DES based on carboxylic acids exhibit enhanced antioxidant activity compared to conventional solvents and alcohol-based DES with a maximum DPPH scavenging activity of 42.0 mg TE/g DW. Glycerol or ethylene glycol are also efficient at extracting antioxidant compounds with DPPH scavenging activity of 33.1 and 36.7 mg TE/g DW. Finally, a chemical analysis of extracts using HPTLC revealed that most active compounds extracted are polyphenolic compounds, presumably tannins.

Design, Synthesis, and Evaluation of Neomycin-Imidazole Conjugates for RNA Cleavage.

Targeting RNA with synthetic small molecules attracted much interest during recent years as a particularly promising therapeutic approach in a large number of pathologies spanning from genetic disorders, cancers as well as bacterial and viral infections. In this work, we took advantage of a known RNA binder, neomycin, to prepare neomycin-imidazole conjugates mimicking the active site of ribonuclease enzymes able to induce a site-specific cleavage of HIV-1 TAR RNA in physiological conditions. These new conjugates were prepared using a straightforward synthetic methodology and were studied for their ability to bind the target, inhibit Tat/TAR interaction and induce selective cleavage using fluorescence-based assays and molecular docking. We found compounds with nanomolar affinity, promising cleavage activity and the ability to inhibit Tat/TAR interaction with submicromolar IC50 s.

Anti-Aging Potential of a Rosa centifolia Stem Extract with Focus on Phytochemical Composition by Bioguided Fractionation.

Agricultural practices generate huge amounts of by-products, often simply discarded as waste that must be processed at some cost. The natural by-products revalorisation as raw material to produce high-added value ingredients for various industrial sectors may pave the way towards more sustainable industrial practices, via an optimised utilisation of natural resources. Integrating the circular economy precepts to production systems is considered to be a more and more promising management solution to significantly reduce the environmental impact of economic activities. This article discusses the valorisation of Rosa centifolia stem to produce a natural extract with cosmetic anti-aging potential. To do so, the cosmetic potential of 30 extracts obtained by maceration of agricultural by-products in a hydroalcoholic solvent was evaluated: their activities, as well as their inhibitory activities of specific enzymes were assessed in vitro to identify those that could be used effectively as anti-ageing actives while meeting the consumer's expectations in terms of sustainability, naturality, transparency and traceability.[1] A hydroalcoholic extract of R. centifolia stem revealed itself particularly promising due to its valuable anti-hyaluronidase and antioxidant activities, and its interesting anti-elastase and anti-inflammatory potential. The bio-guided fractionation of this extract allows the characterisation of three major compounds, e. g., isoquercitrin, quercitrin and euscaphic acid, never identified in R. centifolia previously.

Development of 2-deoxystreptamine-nucleobase conjugates for the inhibition of oncogenic miRNA production.

The discovery of new original scaffolds for selective RNA targeting is one of the main challenges of current medicinal chemistry since therapeutically relevant RNAs represent potential targets for a number of pathologies. Recent efforts have been devoted to the search for RNA ligands targeting the biogenesis of oncogenic miRNAs whose overexpression has been directly linked to the development of various cancers. In this work, we developed a new series of RNA ligands for the targeting of oncogenic miRNA biogenesis based on the 2-deoxystreptamine scaffold. The latter is part of the aminoglycoside neomycin and is known to play an essential role in the RNA interaction of this class of RNA binders. 2-deoxystreptamine was thus conjugated to natural and artificial nucleobases to obtain new binders of the oncogenic miR-372 precursor (pre-miR-372). We identified some conjugates exhibiting a similar biological activity to previously synthesized neomycin analogs and studied their mode of binding with the target pre-miR-372.

Inhibition of the drug efflux activity of Ptch1 as a promising strategy to overcome chemotherapy resistance in cancer cells.

The development of inhibitors of key biological mechanisms involved in multidrug resistance (MDR) burden meets an important medical need but still represents a challenging task. Major MDR targets in both bacterial and cancer cells are multidrug efflux systems. Several aspects should be considered in the attempt to design efficient inhibitors of these systems such as toxicity, stability, permeability as a few examples. In order to successfully design promising new compounds, a full understanding of the efflux mechanism is required, from both biological and structural points of view. It is nowadays well established that the success rate in classical drug design and biological evaluation improves when combined with in silico methodologies. In this review, we focus on the biological evaluation and molecular mechanistic insights of inhibitors of the drug efflux activity of the Hedgehog receptor Patched1 (Ptch1). Ptch1 is known to be over-expressed in many types of cancers, but its activity and role in the resistance to chemotherapy of cancer cells have been highlighted only recently. Remarkably, due to its peculiar efflux mechanism, inhibition of Ptch1 was shown to be particularly relevant for improving the efficacy of chemotherapy without concomitant toxicity for healthy cells or potential side effects. To date, three compounds have been identified as efficient Ptch1 inhibitors, namely astemizole, methiothepin and panicein A hydroquinone. Due to the chemical and structural differences of these molecules, the hit-to-lead drug design is not straightforward. This review describes how the merging of in vitro, in vivo and in silico studies provides molecular details that could contribute to the rational design of new Ptch1 inhibitors.

Design and Implementation of Synthetic RNA Binders for the Inhibition of miR-21 Biogenesis.

Targeting RNAs using small molecules is an emerging field of medicinal chemistry and holds promise for the discovery of efficient tools for chemical biology. MicroRNAs are particularly interesting targets since they are involved in a number of pathologies such as cancers. Indeed, overexpressed microRNAs in cancer are oncogenic and various series of inhibitors of microRNAs biogenesis have been developed in recent years. Here, we describe the structure-based design of new efficient inhibitors of microRNA-21. Starting from a previously identified hit, we performed biochemical studies and molecular docking to design a new series of optimized conjugates of neomycin aminoglycoside with artificial nucleobases and amino acids. Investigation about the mode of action and the site of the interaction of the newly synthesized compounds allowed for the description of structure-activity relationships and the identification of the most important parameters for miR-21 inhibition.

Molecular insights into the Patched1 drug efflux inhibitory activity of panicein A hydroquinone: a computational study.

Human Hedgehog receptor Patched1 (PTCH1) is able to efflux chemotherapeutics of different chemical structure out of cancer cells thus contributing to multidrug resistance phenomena in tumor treatment. A screening of natural compounds purified from marine sponges led to the identification of the first PTCH1 efflux inhibitor, panicein A hydroquinone (PAH), demonstrated to increase doxorubicin toxicity in vitro and vemurafenib toxicity in vitro and in vivo. In this work we combined different computational techniques to gain molecular insights of the inhibitory activity of PAH and some of its active and inactive analogues. We first performed a thorough characterization and druggability analysis of the main putative substrate binding pockets known from available cryo-electron microscopy structures. Further, dynamical descriptors of the active and inactive PAH analogues were extracted from microsecond-long all-atom molecular dynamics simulations in water solution. Finally, a blind ensemble docking methodology coupled with the conformational analysis of compounds enabled rationalization of the interaction between PTCH1 and PAH and derivatives in terms of their intrinsic physico-chemical properties. Our results suggest that the Neck pocket is the preferential binding site for PAH analogues on PTCH1, and that compounds assuming an open cylindric-like shape in solution are most likely to be good binders for PTCH1.

Differentiation of Cancer Stem Cells by Using Synthetic Small Molecules: Toward New Therapeutic Strategies against Therapy Resistance.

Despite the existing arsenal of anti-cancer drugs, 10 million people die each year worldwide due to cancers; this highlights the need to discover new therapies based on innovative modes of action against these pathologies. Current chemotherapies are based on the use of cytotoxic agents, targeted drugs, monoclonal antibodies or immunotherapies that are able to reduce or stop the proliferation of cancer cells. However, tumor eradication is often hampered by the presence of resistant cells called cancer stem-like cells or cancer stem cells (CSCs). Several strategies have been proposed to specifically target CSCs such as the use of CSC-specific antibodies, small molecules able to target CSC signaling pathways or drugs able to induce CSC differentiation rendering them sensitive to classical chemotherapy. These latter compounds are the focus of the present review, which aims to report recent advances in anticancer-differentiation strategies. This therapeutic approach was shown to be particularly promising for eradicating tumors in which CSCs are the main reason for therapeutic failure. This general view of the chemistry and mechanism of action of compounds inducing the differentiation of CSCs could be particularly useful for a broad range of researchers working in the field of anticancer therapies as the combination of compounds that induce differentiation with classical chemotherapy could represent a successful approach for future therapeutic applications.

Uptake study in Juncus sp. and Salicornia europaea of six pharmaceuticals by liquid chromatography quadrupole time-of-flight mass spectrometry.

In this work, eight plants of Juncus sp. and ten of Salicornia europaea were used for an uptake assay of pharmaceuticals (flumequine, cirpofloxacin, enrofloxacin, carbamazepine, diclofenac and ibuprofen) by irrigation at three concentration levels: 10 ng mL-1 (low level); 700 ng mL-1 (medium level) and 10 µg mL-1 (high level). Two plants irrigated with pharmaceutical-free water were set up as controls. For each level, two plants were watered every day with 50 mL (Juncus sp.) and every two days with 20 mL (Salicornia europaea) of aqueous solutions containing all the analytes at the described concentrations. Plants irrigated at 10 µg mL-1 were significantly the most affected, whereas the rest of the plants remained, in general, largely displayed no apparent physiological effects throughout the 30 days (Juncus sp.) and 21 days (Salicornia europaea) assays. Leaves and stems were cut every seven days and roots were collected at the end of the assay. The samples were lyophilized, submitted to a microwave assisted extraction using 5 mL of acetonitrile:water mixture (1:1, v/v) and they were analyzed (in triplicate) in a liquid chromatography-quadrupole time of flight mass spectrometry instrument. Most of the analytes were quantified in many of the samples corresponding to the three exposure levels with the highest concentrations obtained at high exposure levels. Ibuprofen was not detected in any sample and enrofloxacin, ciprofloxacin and diclofenac were not detected in the samples from Salicornia europaea.

Inhibition of Patched Drug Efflux Increases Vemurafenib Effectiveness against Resistant BrafV600E Melanoma.

Melanoma patients harboring the BRAFV600E mutation are treated with vemurafenib. Almost all of them ultimately acquire resistance, leading to disease progression. Here, we find that a small molecule from a marine sponge, panicein A hydroquinone (PAH), overcomes resistance of BRAFV600E melanoma cells to vemurafenib, leading to tumor elimination in corresponding human xenograft models in mice. We report the synthesis of PAH and demonstrate that this compound inhibits the drug efflux activity of the Hedgehog receptor, Patched. Our SAR study allowed identifying a key pharmacophore responsible for this activity. We showed that Patched is strongly expressed in metastatic samples from a cohort of melanoma patients and is correlated with decreased overall survival. Patched is a multidrug transporter that uses the proton motive force to efflux drugs. This makes its function specific to cancer cells, thereby avoiding toxicity issues that are commonly observed with inhibitors of ABC multidrug transporters. Our data provide strong evidence that PAH is a highly promising lead for the treatment of vemurafenib resistant BRAFV600E melanoma.

Resveratrol and HIV-protease inhibitors control UCP1 expression through opposite effects on p38 MAPK phosphorylation in human adipocytes.

Brown and brown-like adipocytes (BBAs) control thermogenesis and are detected in adult humans. They express UCP1, which transforms energy into heat. They appear as promising cells to fight obesity. Deciphering the molecular mechanisms leading to the browning of human white adipocytes or the whitening of BBAs represents a goal to properly and safely control the pathways involved in these processes. Here, we analyzed how drugs endowed with therapeutic potential affect the differentiation of human adipose progenitor-cells into BBAs and/or their phenotype. We showed that HIV-protease inhibitors (PI) reduced UCP1 expression in BBAs modifying their metabolic profile and the mitochondria functionality. Lopinavir (LPV) was more potent than darunavir (DRV), a last PI generation. PPARγ and PGC-1α were decreased in a PI or cell-specific manner, thus altering UCP1's constitutive expression. In addition, LPV altered p38 MAPK phosphorylation, blunting then the ß-adrenergic responses. In contrast, low doses of resveratrol stimulated the activatable expression of UCP1 in a p38 MAPK-dependent manner and counteracted the LPV induced loss of UCP1. This effect was independent of the resveratrol-induced sirtuin-1 expression. Altogether our results uncover how drugs impact crucial components of the networks regulating the expression of the thermogenic signature. They provide important information to control the relevant pathways involved in energy expenditure.

Forgotten Perfumery Plants - Part I: Balm of Judea.

Perfumes have always been products of great importance, mainly composed of natural, valuable and vegetal raw materials. Today, some of them have completely disappeared in perfumery, even though they are part of our cultural heritage and were commonly used in the past. Balm of Judea is one of the most noble, rare and fascinating ingredient long used in perfumery and medicine, that is missing today. After years of research, we collected a resin and an essential oil (steam distillation of fresh aerial parts) from Commiphora gileadensis (L.) C.Chr. native from Saudi Arabia and cultivated in Israel. The aims of this study were to i) identify the main reasons of the loss of the balm of Judea, ii) characterize the volatile composition of the resin and the essential oil and iii) evaluate their olfactory profile and assess their biological activity. Eighty-three compounds were identified in the resin, by a combination of GC-MS and GC/FID techniques, using direct injection and HS-SPME. α-Pinene (24.0 %), sabinene (43.8 %), ß-pinene (6.3 %) and cymene (3.6 %) were the main identified compounds, giving an intense, terpenic and lemony smell to the resin. Anti-inflammatory, wound-healing and whitening activities were highlighted. Sabinene (22.7 %), terpinen-4-ol (18.7 %), α-pinene (14.4 %) and cymene (13.6 %) were identified as the main components of the essential oil, giving a spicy, woody and lemony fragrance. Anti-inflammatory and whitening activities were emphasized.

Involvement of Phosphodiesterase 2A Activity in the Pathophysiology of Fragile X Syndrome.

The fragile X mental retardation protein (FMRP) is an RNA-binding protein involved in translational regulation of mRNAs that play key roles in synaptic morphology and plasticity. The functional absence of FMRP causes the fragile X syndrome (FXS), the most common form of inherited intellectual disability and the most common monogenic cause of autism. No effective treatment is available for FXS. We recently identified the Phosphodiesterase 2A (Pde2a) mRNA as a prominent target of FMRP. PDE2A enzymatic activity is increased in the brain of Fmr1-KO mice, a recognized model of FXS, leading to decreased levels of cAMP and cGMP. Here, we pharmacologically inhibited PDE2A in Fmr1-KO mice and observed a rescue both of the maturity of dendritic spines and of the exaggerated hippocampal mGluR-dependent long-term depression. Remarkably, PDE2A blockade rescued the social and communicative deficits of both mouse and rat Fmr1-KO animals. Importantly, chronic inhibition of PDE2A in newborn Fmr1-KO mice followed by a washout interval, resulted in the rescue of the altered social behavior observed in adolescent mice. Altogether, these results reveal the key role of PDE2A in the physiopathology of FXS and suggest that its pharmacological inhibition represents a novel therapeutic approach for FXS.

Liquid chromatography quadrupole time-of-flight mass spectrometry determination of six pharmaceuticals in vegetal biota. Uptake study in Lavandula dentata.

A procedure based on microwave assisted extraction for the determination of 6 pharmaceuticals in samples of Lavandula dentata, Salicornia ramosissima and Juncus sp. by liquid chromatography-quadrupole time of flight mass spectrometry (LC-QTOF/MS) was optimized and validated. Best results were obtained using microwave assisted extraction of 1.0g of homogeneous lyophilized samples and 5mL of a mixture ACN:H2O (1:1 v/v) as extracting solvent. Analytical recoveries ranged from 60 to 107% with relative standard deviation (RSD) lower than 15%. Limits of quantitation (LOQ) for the 6 pharmaceuticals flumequine (FLM), carbamazepine (CBZ), ciprofloxacin (CPR), enrofloxacin (ENR), diclofenac (DCL), and ibuprofen (IBU) were in the range 20.8-125ngg-1. The method was satisfactory applied for an uptake study in Lavandula dentata samples finding quantifying concentrations of FLM and CBZ in roots, leaf and stem.

Cosmetic potentials of Prunus domestica L. leaves.

BACKGROUND: The current study presents new insight on the phytochemical content and biological activities of five Prunus domestica L. varieties ('Quetsche blanche de Létricourt', 'Mirabelle de Nancy', 'Perdrigon violet', 'Mirabelle de Provence', 'Reine-claude dorée'). RESULTS: The plum leaves were found to possess promising anti-aging activities by their capacity to inhibit 1,1-diphenyl-2-picrylhydrazyl (DPPH), elastase, hyaluronidase and lipoxygenase. After solid phase extraction (SPE), chlorogenic acid, rutin, quercetin and their derivatives were putatively identified by high-performance liquid chromatography coupled with tandem mass spectrometry using an electrospray ionization source (HPLC/ESI-MS/MS). CONCLUSION: The plum leaf, a by-product, provides an interesting valuable resource for use as a natural cosmetic product or as a food supplement. © 2017 Society of Chemical Industry.