Progress toward the development of the small molecule equivalent of small interfering RNA

Given that many small molecules could bind to structured regions at sites that will not affect function, approaches that trigger degradation of RNA could provide a general way to affect biology. Indeed, targeted RNA degradation is an effective strategy to selectively and potently modulate biology. We describe several approaches to endow small molecules with the power to cleave RNAs. Central to these strategies is Inforna, which designs small molecules targeting RNA from human genome sequence. Inforna deduces the uniqueness of a druggable pocket, enables generation of hypotheses about functionality of the pocket, and defines on- and off-targets to drive compound optimization. RNA-binding compounds are then converted into cleavers that degrade the target directly or recruit an endogenous nuclease to do so. Cleaving compounds have significantly contributed to understanding and manipulating biological functions. Yet, there is much to be learned about how to affect human RNA biology with small molecules.     

A mutation in helicase motif III of E. coli RecG protein abolishes branch migration of Holliday junctions.

The RecG protein of Escherichia coli catalyses branch migration of Holliday junctions made by RecA and dissociates synthetic X junctions into duplex products in reactions that require hydrolysis of ATP. To investigate the mode of action of this enzyme a chromosomal mutation that inactivates recG (recG162) was cloned and sequenced. The recG162 mutation is a G:C to A:T transition, which produces an Ala428 to Val substitution in the protein. This change affects a motif (motif III) in the protein that is highly conserved in DNA and RNA helicases. RecG162 protein was purified and shown to retain the ability to bind synthetic X and Y junctions. However, it does not dissociate these junctions and fails to catalyse branch migration of Holliday junction intermediates purified from a RecA strand exchange reaction. RecG162 retains a DNA-dependent ATPase activity, but this is much reduced relative to the wild-type protein, especially with single-stranded DNA as a co-factor. These results suggest that branch migration by RecG is related to a junction-targeted DNA helicase activity.     

Two distinct binding modes of a protein cofactor with its target RNA

Like most cellular RNA enzymes, the bI5 group I intron requires binding by a protein cofactor to fold correctly. Here, we use single-molecule approaches to monitor the structural dynamics of the bI5 RNA in real time as it assembles with its CBP2 protein cofactor. These experiments show that CBP2 binds to the target RNA in two distinct modes with apparently opposite effects: a "non-specific" mode that forms rapidly and induces large conformational fluctuations in the RNA, and a "specific" mode that forms slowly and stabilizes the native RNA structure. The bI5 RNA folds though multiple pathways toward the native state, typically traversing dynamic intermediate states induced by non-specific binding of CBP2. These results suggest that the protein cofactor-assisted RNA folding involves sequential non-specific and specific protein-RNA interactions. The non-specific interaction potentially increases the local concentration of CBP2 and the number of conformational states accessible to the RNA, which may promote the formation of specific RNA-protein interactions.     

Ergot Alkaloids (Re)generate New Leads as Antiparasitics

Praziquantel (PZQ) is a key therapy for treatment of parasitic flatworm infections of humans and livestock, but the mechanism of action of this drug is unresolved. Resolving PZQ-engaged targets and effectors is important for identifying new druggable pathways that may yield novel antiparasitic agents. Here we use functional, genetic and pharmacological approaches to reveal that serotonergic signals antagonize PZQ action in vivo. Exogenous 5-hydroxytryptamine (5-HT) rescued PZQ-evoked polarity and mobility defects in free-living planarian flatworms. In contrast, knockdown of a prevalently expressed planarian 5-HT receptor potentiated or phenocopied PZQ action in different functional assays. Subsequent screening of serotonergic ligands revealed that several ergot alkaloids possessed broad efficacy at modulating regenerative outcomes and the mobility of both free living and parasitic flatworms. Ergot alkaloids that phenocopied PZQ in regenerative assays to cause bipolar regeneration exhibited structural modifications consistent with serotonergic blockade. These data suggest that serotonergic activation blocks PZQ action in vivo, while serotonergic antagonists phenocopy PZQ action. Importantly these studies identify the ergot alkaloid scaffold as a promising structural framework for designing potent agents targeting parasitic bioaminergic G protein coupled receptors.     

Differences in inhibition by IDF45 (an inhibitory diffusible factor) of early RNA synthesis stimulation induced by pp60 v-src and various mitogens.

Factors inhibiting cell growth have been isolated from different cell types. However, little information is available concerning their mode of action. A novel growth inhibitory factor of 45 kDa (IDF45) was recently purified to homogeneity from medium conditioned by 3T3 cells. This molecule was able to inhibit DNA synthesis and the growth of chick embryo fibroblasts (CEF) in a reversible manner. By contrast, DNA synthesis stimulated by v-src expression in CEF was poorly inhibited by IDF45. In order to gain further insight into the IDF45 mode of action in normal and transformed CEF, we compared the effects of IDF45 on early stimulation of RNA synthesis induced in CEF by different mitogenic factors and by v-src gene expression. Stimulation, by serum, of RNA synthesis was inhibited by IDF45; however, inhibition increased when cells were preincubated with IDF45 before addition of serum and cell labeling for 2 h. IDF45 was also able to inhibit partially the stimulation of RNA synthesis induced by PMA and PDGF but was unable to inhibit stimulation of RNA synthesis induced by insulin and v-src expression. By contrast, stimulation of RNA synthesis induced by IGF-I was rapidly 100% inhibited by IDF45. The effect of IDF45 on DNA synthesis stimulated by the different mitogens was also determined and was correlated with the effect of IDF45 on RNA synthesis. These results suggest that the modes of action of IDF45 on stimulation of RNA synthesis by v-src and by insulin are similar. Our present results agree with others showing the bifunctional activity of IDF45 as an IGF-binding protein and as an inhibitory molecule in DNA stimulation induced by serum.     

Saccharomyces cerevisiae spheroplasts are sensitive to the action of diphtheria toxin.

Diphtheria toxin kills spheroplasts of Saccharomyces cerevisiae but not the intact yeast cells. After 2 h of exposure to ca. 10(-7) M toxin, less than 1% of spheroplasts were able to regenerate into intact cells. The same high levels of toxin inhibited the rate of protein synthesis by more than 90% within 1 h, whereas RNA and DNA synthesis were not inhibited until 4 h or exposure. Both killing and protein synthesis inhibition were dependent on toxin concentration. The nature of the toxin-cell interaction was also studied by using fragments of intact toxin and mutant toxin proteins. Neither toxin fragment A nor CRM45 nor CRM197 affected spheroplasts, but CRM197 and ATP prevented the inhibitory action of intact toxin. These results suggest that toxin acts on S. cerevisiae spheroplasts in much the same manner as it acts on sensitive mammalian cells.     

REVERSIBLE DEGRADATION OF POLYRIBOSOMES IN CHANG CELLS CULTURED IN A GLUTAMINE-DEFICIENT MEDIUM

The effects of temporary glutamine deficiency on the protein and nucleic acid metabolism of Chang's liver cells in suspension cultures have been studied. It was observed that cells maintained in a glutamine-free medium showed a reduced incorporation of labeled precursors into protein and RNA. At the same time, the activity of the ribosomes and the proportion of polyribosomal aggregates in cell extracts diminished. These effects were reversed when the glutamine content of the medium was restored. The restoration of a normal rate of amino acid incorporation by intact cells as well as by cell-free systems was time dependent, and took place within a few hours after glutamine addition without preceding increase in the prevailing low rate of RNA synthesis. The addition of actinomycin D at concentrations that strongly inhibited the RNA metabolism of the cells did not prevent the increase in protein synthesis or the reappearance of polyribosomal aggregates. These facts suggest that the restoration of protein synthesis in the cells after glutamine starvation was not dependent on a production of new messenger RNA. The experimental data are consistent with the hypothesis that previously synthesized messenger RNA, preserved in the cells in a stable form, was brought into action in response to the reestablishment of an adequate cellular environment.     

Interaction of spermidine with viral RNA and its influence on protein synthesis

Addition of spermidine to a cell-free protein synthesizing system from wheat germ programmed with total brome mosaic virus (BMV) RNA resulted in a several-fold stimulation of amino acid incorporation. Increasing the spermidine concentration in the system led to inhibition of the overall protein synthesis, but the production of longer polypeptides was inhibited much more than that of the coat protein (shorter product). Analysis of the products synthesized under direction of BMV RNA 3 (longer product) and RNA 4 (coat protein) revealed that optimal translation of RNA 3 occurred at a much lower concentration of spermidine than that of RNA 4. Binding experiments with radioactive spermidine and BMV RNAs showed that the saturation of spermidine binding is achieved at a lower concentration of spermidine for RNA 3 than for RNA 4, which may suggest that the structure of RNA 4 is more compact than that of RNA 3. Taking into account the binding obtained at a spermidine concentration corresponding to optimal conditions of protein synthesis, it may be concluded that the optimum translation of these two mRNAs occurs when there is a similar level of RNA charge neutralisation, which implies a similar level of RNA structure stabilisation.     

Targeting of T7 RNA polymerase to tobacco nuclei mediated by an SV40 nuclear location signal

We have expressed two T7 RNA polymerase genes by electroporation into tobacco protoplasts. One of the genes was modified by inserting nucleotides encoding a viral nuclear localization signal (NLS) from the large T antigen of SV40. Both T7 RNA polymerase genes directed synthesis of a ca. 100 kDa protein in the electroporated protoplasts. T7 RNA polymerase activity was detected in extracts of protoplasts electroporated with both genes. Immunofluorescence analysis of these protoplasts indicated that only the polymerase carrying the NLS accumulated in the cell nucleus. These experiments suggest that mechanisms involved in the transport from the cytoplasm to the nucleus are similar in plant and animal cells. This system demonstrates the feasibility of T7 RNA polymerase-based approaches for the high-level expression of introduced genes in plant cells.     

Ribonucleic acid synthesis termination protein rho function: effects of conditions that destabilize ribonucleic acid secondary structure

The dependence fo rate of adenosine 5'-triphosphate (ATP) hydrolysis catalyzed by ribonucleic acid (RNA) synthesis termination protein rho from Escherichia coli with T7 RNA as cofactor is used to probe the nature of the interaction between rho and RNA. In general, reaction conditions that destabilize the secondary structure of the RNA enhance its cofactor activity. This is indicated by the effects of MgCl2 concentration, spermidine, temperature, dimethyl sulfoxide, and pretreatment of the RNA with formaldehyde. These results suggest that a functional interaction between rho and RNA depends either on the presence of a sufficiently large single-stranded region in the RNA or on the ability of rho to unwind double helices in the RNA. It is also shown that changes in reaction conditions that increase RNA secondary structure and decrease the rho protein adenosine triphosphate phosphohydrolase (rhoATPase) activity with isolated T7 RNA also decrease the stringency of rho action in RNA synthesis termination. On the other hand, monovalent salts decrease rhoATPase activity with isolated T7 RNA and binding of rho to T7 RNA independently of the MgCl2 concentration and thus the relative stability of the RNA secondary structure.     

Toxicity of methylglyoxal towards rat enterocytes and colonocytes.

Effect of methylglyoxal, a bacterial metabolic product, on protein, DNA, and RNA synthesis in rat enterocytes and colonocytes was investigated. Results showed that 1 mM methylglyoxal inhibited protein, DNA, and RNA synthesis to the extent of 65-85, 65-80, and 10-20 per cent, respectively, in villus and crypt cells and colonocytes. The inhibitory pattern was similar in these various cell types. The inhibitory effect on protein and DNA synthesis was more marked than that on RNA synthesis. Inclusion of thiol compounds up to 4 mM concentration did not protect the cells from the inhibitory effect of methylglyoxal. No alteration in the level of cellular reduced glutathione and glyoxalase enzyme activity was observed when cells were incubated with 2 mM methylglyoxal. These results suggest that the antiproliferative action of methylglyoxal on eukaryotic cells may be through the inhibition of macromolecular synthesis.     

Effect of transforming RNA on the synthesis of a protein with a secretory signal sequence in vitro.

U5 small nuclear RNA itself can act as a clastogenic and transforming agent when transfected into cells. In the previous work, the 3' half of the U5 small nuclear RNA first stem structure (designated RNA3S) was capable of driving normal cells into tumorigenic cells when expressed with a poly(A) tail (RNA3S+). This transformation critically depended upon the polypurine sequence GGAGAGGAA in RNA3S+. In this work, we first examined the pre-beta-lactamase and luciferase (model secretory and nonsecretory proteins) translation with the in vitro synthesized RNA3S in rabbit reticulocyte lysate. The capped RNA3S with a poly(A) tail suppressed the translation. In addition, the polypurine sequence played a crucial role in affecting the secretory protein synthesis, indicating a primary action of RNA3S+. Further studies revealed that the oligodeoxynucleotides, corresponding to the polypurine and its antisense sequences, directly contacted 28 S rRNA in ribosome and 7SL RNA in signal recognition particle, respectively, and differentially affected the nascent chain elongation of secretory protein synthesis. These results suggest that RNA3S+ blocks a physiological regulatory function played by signal recognition particle and the ribosome in the secretory protein synthesis and support the idea that the transformation might result from a repressed cellular activity.     

The Incorporation of Leucine-C14 into Microsomal Particles and other Subcellular Components of the Pea Epicotyl

Incorporation of leucine-C¹⁴ into subcellular fractions of the apical section of pea seedlings has been studied as a function of the length of incubation. The specific activity of the microsomes was higher than that of the supernatant for short but not for long incubations, in agreement with observations on other systems. In this developing tissue the nuclei and especially the mitochondria appear to incorporate amino acid very rapidly. An insoluble fraction of the microsome pellet, which is presumably a liponucleoprotein complex, was found to possess, after 1 hour of incubation, a specific activity much greater than that of the purified microsomal particles or the supernatant fraction. Ninety-eight per cent of the leucine-C¹⁴ in the purified microsomal particles has been shown to possess bound amino groups, presumably in peptide linkages, by the DNP-end group method. These particles liberate but little peptide or protein of very high specific activity when they are destroyed by removal of Mg or by hydrolysis of RNA. Microsomal particles were fractionated into an RNA fraction and five protein fractions by means of density gradient centrifugation. By this method 95 per cent of the RNA can be separated from 90 per cent of the protein of the particle. Furthermore, the RNA fraction has been shown to contain very little protein of high specific activity. A particular protein fraction which contains the remaining 5 per cent of the RNA, possessed after 1 hour of incubation a specific activity 2 to 9 times higher than the protein of the other fractions.     

Do polyphenols enter the brain and does it matter? Some theoretical and practical considerations

Although several epidemiological and intervention studies suggest that polyphenols (PPs) and PP-rich foods may improve memory and cognition in animals and humans, PPs' mode of action is only poorly understood. To help distinguish between the different modes of action that have been proposed for PPs, it is obviously important to know how much PPs can accumulate in the brain, if any at all. However, reliable data on PP uptake into the brain of animals are limited as many studies failed to report important control procedures during data acquisition. In this paper, we summarize published data on the penetration of PPs into animal brain and review some hypotheses to explain the biological basis of potentially health-beneficial effects of PPs to the brain. Finally, we highlight promising new approaches, especially those of a hormetic dose-response and gut microbiota-brain interaction, which may allow a better understanding of PPs' mode of action in animals and humans.     

Superinduction of human interleukin-2 messenger RNA by inhibitors of translation

Stimulation of human lymphocytes with phytohemagglutinin results in the induction of messenger RNA encoding interleukin-2 (IL-2), a lymphokine possessing immuno-regulatory properties. We have previously demonstrated a dramatic superinduction of the formation of IL-2 and of biologically active IL-2 mRNA in the presence of cycloheximide, an inhibitor of translation. These findings suggested the involvement of a labile protein repressor in the regulation of human IL-2 gene expression. Here, we show a commensurate superinduction of IL-2 mRNA sequences by three additional inhibitors of protein synthesis with distinct modes of action: T-2 toxin, pactamycin, and sparsomycin. These results strengthen the concept that a labile protein controls the formation of mature IL-2 mRNA. They tend to eliminate the possibility that the superinduction phenomenon observed in the presence of cycloheximide is due to its action on a process other than translation.