The use of a MITO-Porter to deliver exogenous therapeutic RNA to a mitochondrial disease's cell with a A1555G mutation in the mitochondrial 12S rRNA gene results in an increase in mitochondrial respiratory activity.

We report on validating a mitochondrial gene therapeutic strategy using fibroblasts derived from patients with an A1555G point mutation in mitochondrial DNA coding 12S ribosomal RNA (rRNA (12S)). Wild-type rRNA (12S) as a therapeutic RNA was encapsulated in a mitochondrial targeting liposome, a MITO-Porter (rRNA-MITO-Porter), and an attempt was made to deliver the MITO-Porter to mitochondria of the diseased cells. It was confirmed that the rRNA-MITO-Porter treatment significantly decreased the ratio of the mutant rRNA content. Moreover, it was shown that the mitochondrial respiratory activities of the diseased cells were improved as the result of the mitochondrial transfection of the rRNA-MITO-Porter.

RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges.

RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.

Toll-like receptor 3 activation selectively reverses HIV latency in microglial cells.

BACKGROUND: Multiple toll-like receptors (TLRs) are expressed in cells of the monocytic lineage, including microglia, which constitute the major reservoir for human immunodeficiency virus (HIV) infection in the brain. We hypothesized that TLR receptor mediated responses to inflammatory conditions by microglial cells in the central nervous system (CNS) are able to induce latent HIV proviruses, and contribute to the etiology of HIV-associated neurocognitive disorders. RESULTS: Newly developed human microglial cell lines (hµglia), obtained by immortalizing human primary microglia with simian virus-40 (SV40) large T antigen and the human telomerase reverse transcriptase, were used to generate latently infected cells using a single-round HIV virus carrying a green fluorescence protein reporter (hµglia/HIV, clones HC01 and HC69). Treatment of these cells with a panel of TLR ligands showed surprisingly that two potent TLR3 agonists, poly (I:C) and bacterial ribosomal RNA potently reactivated HIV in hµglia/HIV cells. LPS (TLR4 agonist), flagellin (TLR5 agonist), and FSL-1 (TLR6 agonist) reactivated HIV to a lesser extent, while Pam3CSK4 (TLR2/1 agonist) and HKLM (TLR2 agonist) only weakly reversed HIV latency in these cells. While agonists for TLR2/1, 4, 5 and 6 reactivated HIV through transient NF-κB induction, poly (I:C), the TLR3 agonist, did not activate NF-κB, and instead induced the virus by a previously unreported mechanism mediated by IRF3. The selective induction of IRF3 by poly (I:C) was confirmed by chromatin immunoprecipitation (ChIP) analysis. In comparison, in latently infected rat-derived microglial cells (hT-CHME-5/HIV, clone HC14), poly (I:C), LPS and flagellin were only partially active. The TLR response profile in human microglial cells is also distinct from that shown by latently infected monocyte cell lines (THP-1/HIV, clone HA3, U937/HIV, clone HUC5, and SC/HIV, clone HSCC4), where TLR2/1, 4, 5, 6 or 8, but not for TLR3, 7 or 9, reactivated HIV. CONCLUSIONS: TLR signaling, in particular TLR3 activation, can efficiently reactivate HIV transcription in infected microglia, but not in monocytes or T cells. The unique response profile of microglial cells to TLR3 is fundamental to understanding how the virus responds to continuous microbial exposure, especially during inflammatory episodes, that characterizes HIV infection in the CNS.

Circulating nucleic acids in type 1 diabetes may modulate the thymocyte turnover rate.

The autoimmunity of type 1 diabetes is associated with T-cell hyperactivity. Current study was designed to examine the effect of circulating ribonucleic acids (RNAs), isolated from type 1 diabetic patients on proliferative, apoptotic and inflammatory potential of rat thymocytes. Rat thymocytes were assayed for proliferating nuclear cell antigen (PCNA), Bcl-2, Bax and NF-κB level, using the flow cytometric and fluorometric assays. Cells were allocated into groups, treated with RNAs purified from plasma of juvenile diabetics, adult type 1 diabetic patients, control healthy children, healthy adult persons, nucleic acids and polynucleotide standards (RNA, polyC, PolyA, PolyIC, and CpG). The upregulation of PCNA and Bcl-2 protein and downregulation of Bax protein and NF-κB was shown when the thymocytes where incubated with RNA purified from plasma of juvenile type 1 diabetic patients. The dysregulation of inflammatory cascade and central tolerance may be a defect in autoimmune diseases related to innate immunity leading to corresponding alteration in adaptive immune response.

[Antiherpetic effect of RNA-tilorone molecular complex in cell culture].

The authors studied the antiviral effect of an interferonogenic yeast RNA-tilorone molecular complex (MC) compared to the Virolex, videly used antiherpetic drug, and standard interferon (IFN) alpha/beta inducer poly(I)poly(C) in Vero cells culture infected with herpes simplex type I virus (HSV-1). The tilorone contained by MC has been shown to be twice less toxic and twice more active against HSV than its free molecules. The value of chemotherapeutic index (CI) of Virolex in experiments with Vero cells reaches 2500, CI poly(I)poly(C) and MC being 324; the last value meets the requirements for promising drugs.

Stimulation of ATG12-ATG5 conjugation by ribonucleic acid.

The ubiquitin-like conjugation reactions, ATG8/microtubule-associated protein 1 light chain 3/MAP1LC3 (LC3) to phosphatidylethanolamine (PE) and ATG12 to ATG5, are biochemical hallmarks for autophagy, a cellular process that degrades bulk cellular proteins and organelles. The two conjugation reactions share the same E1-like enzyme ATG7 but have different E2-like enzymes, ATG3 for LC3-PE and ATG10 for ATG12-ATG5. In cells, ATG12-ATG5 conjugation appears to be required for LC3-PE conjugation. Previously, in vitro reconstitution of LC3-PE conjugation, but not the upstream ATG12-ATG5 conjugation, was reported. In this study, we describe for the first time the de novo reconstitution of mammalian ATG12-ATG5 conjugation by using purified recombinant proteins. We show that ATG7, ATG10 and ATP as an energy source are all essential for ATG12-ATG5 conjugation, and mutation of the specific lysine residue of ATG5 for ATG12 conjugation abrogates the reaction. Furthermore, a potent stimulating activity for ATG12-ATG5 conjugation was detected in mammalian cell extracts, and was surprisingly identified as ribosomes. Our detail biochemical analyses indicate that the ribonucleic acid (RNA) component of ribosomes is both necessary and sufficient for this stimulation.

The dNTPase enzyme activity is inhibited by nucleic acids and contains a heat-insensitive component.

The dNTpase enzyme has previously been shown to specifically hydrolyse monodeoxyribonucleoside triphosphates (dNTPs). The remnant nucleotide resulting from this hydrolysis lacks the terminal phosphate and is covalently attached as part of a 3 kDa species, which we have termed the product nucleotide binding particle or "PNBP." PNBP is resistant to numerous nucleases and RNases, suggesting that it is not a nucleic acid polymer. Given that the exclusive specificity of dNTPase for dNTPs suggests some associative cellular role for the enzyme in polynucleotide maintenance, the interaction of dNTPase with various nucleic acids has now been examined. It is demonstrated that dNTPase activity is significantly inhibited by addition of single-stranded DNA or tRNA, but not rRNA. The data presented also suggest that thio-dATP can substitute for conventional phosphoester dATP in the enzymatic reaction. It is also demonstrated that the dNTPase enzyme comprises both heat/proteolysis/denaturant stable and heat/proteolysis/denaturant-sensitive components and we propose that this stable component may be the precursor to liganded PNBP.

RNA-protein interactions in the ribonucleoprotein T-complexes in a mitochondrial extract from Leishmania tarentolae.

We have investigated protein-RNA interactions and the incorporation of [alpha-32P]UTP into the guide RNA and mRNA components of the 'T-complexes' in a mitochondrial extract from Leishmania tarentolae. The terminal uridylyl transferase-containing complex T-IV is probably involved in the maturation of the 3'-oligo(U) tail of the gRNAs, but the biological function and biochemical nature of the remaining T-complexes is not known. We have found that the relative extent of labeling of the RNA components is dependent on the UTP concentration: at low levels, the main endogenous RNA components labeled are the gRNAs in T-IV; at higher levels, the mRNAs in all of the T-complexes are preferentially labeled. We also show a tentative correlation in the migration pattern of UTP-labeled T-complexes and complexes which bind exogenous labeled RNA. The relative extent of binding to specific complexes is dependent upon the type of RNA. Most of the interactions between the labeled RNAs and proteins can be disrupted by heparin or a large excess of rRNA, but two labeled complexes were resistant to competition. Most of the binding of labeled exogenous gRNA is disrupted by competition with a large excess of rRNA, but predigestion of the extract with micrococcal nuclease and saturation with rRNA uncovered a high affinity complex, which involves at least two proteins interacting with the bound gRNAs. A knowledge of the RNA and protein components may aid in understanding the biological roles of these RNP complexes.

Ribozymes as potential anti-HIV-1 therapeutic agents.

Certain RNA molecules, called ribozymes, possess enzymatic, self-cleaving activity. The cleavage reaction is catalytic and no energy source is required. Ribozymes of the "hammerhead" motif were identified in plant RNA pathogens. These ribozymes possess unique secondary (and possibly tertiary) structures critical for their cleavage ability. The present study shows precise cleavage of human immunodeficiency virus type 1 (HIV-1) sequences in a cell-free system by hammerhead ribozymes. In addition to the cell-free studies, human cells stably expressing a hammerhead ribozyme targeted to HIV-1 gag transcripts have been constructed. When these cells were challenged with HIV-1, a substantial reduction in the level of HIV-1 gag RNA relative to that in nonribozyme-expressing cells, was observed. The reduction in gag RNA was reflected in a reduction in antigen p24 levels. These results suggest the feasibility of developing ribozymes as therapeutic agents against human pathogens such as HIV-1.

Restoration of pole-cell-forming ability to u.v.-irradiated Drosophila embryos by injection of mitochondrial lrRNA.

Screening a cDNA library generated from poly(A) +RNA of Drosophila cleavage embryos, we selected a cDNA clone (pDE20.6). The cDNA hybridized specifically with a poly(A) +RNA that is capable of restoring embryos from u.v.-caused inability of pole cell formation. The RNA hybrid-selected by pDE20.6 was also able to induce pole cells in the anterior region of embryos, if it was coinjected with u.v.-irradiated polar plasm, although the RNA or irradiated polar plasm alone was not effective. Pole cells thus formed in the anterior or in the u.v.-irradiated posterior region were identified by polar granules and nuclear bodies, morphological markers for normal pole cells. Furthermore, the RNA-induced pole cells were able to migrate into gonadal rudiments. The nucleotide sequence of pDE20.6 cDNA insert was highly homologous with the mitochondrial large rRNA (lrRNA) gene, but not with any nuclear DNA sequences. Using pDE20.6 as a primer, a full-length cDNA of mitochondrial lrRNA was generated and cloned. The RNA transcribed in vitro from the cDNA was able to restore pole cell formation. The cDNA hybridized only with a 1.5 kb poly(A) +RNA on a Northern blot. The 1.5 kb RNA sedimented more with the post-mitochondrial (P3) fraction than with the mitochondrial (P2) fraction, while the majority of transcripts from another mitochondrial gene was detected in the P2 fraction.

Interaction of Cibacron blue F3GA and polynucleotides with ricin A-chain, 60 S ribosomal subunit-inactivating protein.

Cibacron blue F3GA, a sulfonated polyaromatic blue dye, inhibited the ability of ricin A-chain to inactivate ribosomes. Difference-spectroscopic study revealed that the dye bound to the A-chain (Kd = 0.72 microM), producing a difference spectrum with a single maximum at 688 nm and two minima at 585 and 628 nm. Such a significant difference spectrum was not observed in the presence of ricin B-chain or intact ricin, neither of which can inactivate ribosomes. Modification of arginine residues in the A-chain with phenylglyoxal showed a correlation between the loss of inhibitory activity on protein synthesis and the loss of difference absorbance produced by the dye-A-chain interaction. Both losses occurred significantly at an early stage of the modification. Furthermore, the dye protected the A-chain against a loss of its inhibitory activity resulting from the modification of arginine residues. These results suggest that the same arginine residues participate both in the interaction with the dye and in the inactivation of ribosomes. Based on these data, the dye appears to interact with the active site of the A-chain. Addition of several polynucleotides, namely rRNA, tRNA, poly(U) and DNA, to the dye-A-chain complex resulted in a marked displacement of the dye, whereas mono- and dinucleotides had little or no effect on the dye-A-chain interaction. These findings indicate the possible existence of a polynucleotide binding site in the active site of the A-chain. A combination of these and other results suggests that the A-chain recognizes and acts on some part of RNA of the 60 S ribosomal subunit.

A new 'sense' RNA approach to block viral RNA replication in vitro.

The use of "antisense" RNA is being widely considered to block specific steps in viral infection. We propose here a new "sense" RNA approach to block viral RNA replication in vitro and possibly in vivo. In the turnip yellow mosaic virus (TYMV) system, the recognition site of the viral replicase (RNA-dependent RNA polymerase) is assumed to be located within the 3' end of the RNA genome. Small "sense" RNAs have been obtained by in vitro transcription of the corresponding cloned cDNAs. Replication of TYMV RNA in vitro is shown here to be blocked only by those RNAs that contain the 3' terminal region of the genome.

T-cell-independent macrophage activation in mice induced with rRNA from Listeria monocytogenes and dimethyldioctadecylammonium bromide.

Purified rRNA from Listeria monocytogenes or Pseudomonas aeruginosa injected in combination with dimethyldioctadecylammonium bromide (DDA), protects mice nonspecifically against a lethal challenge of various extra- and intracellular bacteria. In the present study vaccination of BALB/c as well as C57BL/Ka mice with listerial RNA-DDA resulted in activation of fixed-tissue macrophages, as measured by an enhanced in vivo L. monocytogenes killing in spleen and liver. Evidence was found that macrophage activation by vaccination with rRNA-DDA occurred by a T-cell-independent mechanism. Treatment of mice with cyclosporin A had no effect on the enhanced L. monocytogenes killing induced with RNA-DDA; in vitro exposure of RNA-DDA to spleen cell cultures did not give rise to any lymphocyte proliferation. No evidence could be found for a possible adjuvant activity for RNA-DDA in cellular responses; in fact, RNA-DDA had an inhibitory effect on lymphocyte proliferative responses to Listeria antigen and to concanavalin A.

Antibacterial resistance, macrophage influx, and activation induced by bacterial rRNA with dimethyldioctadecylammonium bromide.

Intraperitoneally injected rRNA from Pseudomonas aeruginosa combined with dimethyldioctadecylammonium bromide (DDA) increased nonspecifically the resistance of mice against an intraperitoneal challenge with extracellular (P. aeruginosa, Escherichia coli) and intracellular (Listeria monocytogenes) bacteria. This study concerns the mechanism underlying the nonspecific resistance. RNA with DDA (RNA-DDA) induced a cell influx and activated peritoneal macrophages (M phi) as judged by the decreased 5'-nucleotidase and alkaline phosphodiesterase activities in M phi lysates, the enhanced O2- release, and the increased antitumor activity in comparison with unstimulated M phi. RNA without DDA did not enhance the resistance and did not influence the peritoneal cell numbers or M phi properties. DDA without RNA enhanced the resistance of mice only slightly; it induced a cell influx, yielding elicited M phi as judged by the decreased 5'-nucleotidase activity and increased alkaline phosphodiesterase activity, the slightly enhanced O2- release, and the absence of increased antitumor activity. Both RNA-DDA and DDA M phi showed an enhanced capacity to ingest and kill L. monocytogenes in vitro, DDA M phi being slightly less effective than RNA-DDA M phi with respect to killing. We conclude that the enhanced killing capacity of M phi for L. monocytogenes is characteristic of both elicited DDA M phi and activated RNA-DDA M phi. The relationship between nonspecific resistance, peritoneal cell numbers, and antibacterial M phi activity is discussed. In addition, it is shown that RNA and DDA retain their activity when they are injected apart, suggesting that they activate M phi by sequential action.

Superhelical DNA-dependent ATPase from calf thymus.

Two physically and catalytically distinct DNA-dependent ATPases were isolated from a purified preparation of calf thymus poly(ADP-ribose) polymerase. A unique feature of these two ATPases was the high stimulation by supercoiled DNA. Other nucleic acids (including denatured DNA and ribosomal RNA) and certain polynucleotides differentially stimulated the two enzymes. We have not detected any other DNA-related activity associated with these ATPases.

Effect of polycations and polyanions on cell division of cultured mammalian cells.

The polycations (H1 histone and polylysine) and polyanions (heparin and various RNA preparations) stimulate cell division of cultured mammalian cells. The mechanisms by which both polycations (H1 histone and polylysine) and polyanions (heparin and RNA) may increase the rate of cell division are discussed.

[No effect of particular r-RNA fragments on cytostatic-induced myelosuppression in a rat transplanted tumor model]. / Kein Einfluss partikulärer r-RNS-Fragmente auf Zytostatika-induzierte Myelosuppression an einem transplantierten Rattentumormodell.

Particular r-RNA fragments of E. coli (BLR = Beljanski leukocyte restorer) were given together with a high dose combination chemotherapy of a transplanted neurogenic rat tumor. A restoring effect on the myelopoesis that could be exploited therapeutically was not observed after BLR.

Biosynthesis of vitamin B-12. Part I. Role of the ribosomal proteins in vitamin B-12 biosynthesis.

1. 70 S ribosomes isolated from strains of Escherichia coli 113-3, K12 and B take part in vitamin B-12 biosynthesis from AdoCbi-GDP, NAD and dimethylbenzimidazole in the presence of enzymes of the cytosol fraction. 2. 70 S ribosomes from E.coli 113-3 bind Ado[58Co]Cbi-GDP. This reaction is independent of fusidic acid. 3. Proteins from 5 S RNA complex as well as l3 protein isolated from E.coli 113-3 ribosomes catalyze vitamin B-12 biosynthesis. The main catalytic function in this reaction is preformed by protein L18. 4. Vitamin B-12 biosynthesis proceeding in the presence of isolated ribosomal proteins is inhibited by fusidic acid, chloramphenicol and vernamycin but not by erythromycin. 5. Vitamin B-12 synthesized in the presence of isolated ribosomal proteins is biologically active.