RNA as a drug target: chemical, modelling, and evolutionary tools

Effect of hydrophobicity and size of the ligands on the intercalative binding interactions of some metallo-surfactants containing π-conjugated systems with yeast tRNA

The intercalative yeast t-RNA binding behavior of some metallo-surfactant complexes, Co(ip)2(TA)2](ClO4)3 (1) and [Co(dpq)2(TA)2](ClO4)3 (2) where TA = Tetradecylamine (Myristylamine), ip = imidazo[4,5-f][1,10]phenanthroline and dpq = dipyrido[3,2-d:2'-3'-f]quinoxaline containing π-conjugated systems (both below and above critical micelle concentration) have been investigated by means of absorption spectral titration, competitive binding, circular dichroism, cyclic voltammetry, and viscometry measurements. Absorption spectral titration results implicate yeast tRNA has significant effects on the binding behaviors of two surfactant complexes via intercalative mode showed a significant absorption band of hypochromicity with red shift. The intrinsic binding constant values below and above CMC were determined as Kb = 6.12 × 105 M-1, 2.31 × 106 M-1, for complex (1) and 7.23 × 105 M-1, 3.57 × 106 M-1, for complex (2). In both sets of complexes (1) and (2), the complexes bind more strongly to yeast tRNA in the above critical micelle concentration can be hydrophobic and confirm intercalation. Competitive displacement studies confirmed that complexes bind to yeast tRNA via intercalative mode. Cyclic voltammetry studies suggest the increasing amounts of yeast tRNA, the cathodic potential Epc for the two complexes shows a positive shift in peak potential indicated the process of binding via intercalation. These observations were further validated by CD, and hydrodynamic measurements. All these studies suggesting that a surfactant complex binds to yeast tRNA appear to be mainly intercalative because of hydrophobicity due to extending aromaticity of the π system of the ligand and planarity of the complex has a significant effect on tRNA binding affinity increasing in the order of complexes containing ligands ip < dpq.Communicated by Ramaswamy H. Sarma.

Native Mass Spectrometry and Nucleic Acid G-Quadruplex Biophysics: Advancing Hand in Hand

While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of fundamental understanding and with new methodological developments. A first goal was to develop mass spectrometry approaches to detect noncovalent interactions between antitumor drugs and their DNA target. Twenty years ago, our attention turned toward specific DNA structures such as the G-quadruplex (a structure formed by guanine-rich strands). Mass spectrometry allows one to discern which molecules interact with one another by measuring the masses of the complexes, and quantify the affinities by measuring their abundance. The most important findings came from unexpected masses. For example, we showed the formation of higher- or lower-order structures by G-quadruplexes used in traditional biophysical assays. We also derived complete thermodynamic and kinetic description of G-quadruplex folding pathways by measuring cation binding, one at a time. Getting quantitative information requires accounting for nonspecific adduct formation and for the response factors of the different molecular forms. With these caveats in mind, the approach is now mature enough for routine biophysical characterization of nucleic acids. A second goal is to obtain more detailed structural information on each of the complexes separated by the mass spectrometer. One such approach is ion mobility spectrometry, and even today the challenge lies in the structural interpretation of the measurements. We showed that, although structures such as G-quadruplexes are well-preserved in the MS conditions, double helices actually get more compact in the gas phase. These major rearrangements forced us to challenge comfortable assumptions. Further work is still needed to generalize how to deduce structures in solution from ion mobility spectrometry data and, in particular, how to account for the electrospray charging mechanisms and for ion internal energy effects. These studies also called for complementary approaches to ion mobility spectrometry. Recently, we applied isotope exchange labeling mass spectrometry to characterize nucleic acid structures for the first time, and we reported the first ever circular dichroism ion spectroscopy measurement on mass-selected trapped ions. Circular dichroism plays a key role in assigning the stacking topology, and our new method now opens the door to characterizing a wide variety of chiral molecules by mass spectrometry. In summary, advanced mass spectrometry approaches to characterize gas-phase structures work well for G-quadruplexes because they are stiffened by inner cations. The next objective will be to generalize these methodologies to a wider range of nucleic acid structures.

Antibiofilm and anti-quorum sensing activities of eugenol and linalool from Ocimum tenuiflorum against Pseudomonas aeruginosa biofilm

AIMS

The aim of this study is to determine the ability of two bioactive compounds, namely, eugenol and linalool, purified from leaves of Ocimum tenuiflorum for eradication of biofilm produced by Pseudomonas aeruginosa.

METHODS AND RESULTS

The phytoextract of O. tenuiflorum (KT), a common ethno-botanical plant of India, was purified through high-performance liquid chromatography and was analysed using ultraviolet (UV) spectroscopy and gas chromatography-mass spectrometry (GC-MS). Eugenol and linalool were found to be the most active amongst all phytocompounds present in phytoextract and showed a significant reduction in the viability of sessile cells of P. aeruginosa and the minimum revival after withdrawal of phyto-challenge. They could bring about notable reduction in the protein and carbohydrate content of exopolysaccharide of biofilm. Eugenol and linalool could affect the synthesis of quorum sensing (QS) proteins like LasA and LasB as well as virulence factors such as pyocyanin, and rhamnolipids, which seriously hamper the formation of biofilm. The biofilm framework was extremely affected by the phytocompounds through the reduction of protein and carbohydrate content of extracellular polymeric substance (EPS). Another interesting found out was that they brought about maximum inhibition to the genomic DNA and RNA content. The studies were supported by in silico interaction between eugenol and linalool with the QS proteins. The antibiofilm efficacies of eugenol, linalool and phytoextract (KT) were further confirmed by microscopic studies with scanning electron microscopy (SEM), atomic force microscopy and fluorescence confocal microscopy microscopic studies.

CONCLUSIONS

The phytocompounds are proved to be more effective than conventional antibiotics in inhibiting the biofilm forming sessile cells and can be used as a replacement for antibiotic.

SIGNIFICANCE AND IMPACT OF THE STUDY

Pure eugenol extracted from common basil leaves can be used as a safe substitute for common antibiotic for treatment of chronic infections caused by P. aeruginosa. It will be cost effective, devoid of notable side effects and will not generate antibiotic resistance in host body.

Catechin as the Most Efficient Bioactive Compound from Azadirachta indica with Antibiofilm and Anti-quorum Sensing Activities Against Dental Biofilm: an In Vitro and In Silico Study

Neem (Azadirachta indica [AI]) is a unique and traditional source of antioxidant and antibacterial compounds. The GC-MS studies revealed that phytoextract of Azadirachta indica comprises a large number of phytocompounds that possess the efficacy of inhibiting the biofilm. It was observed that phytocompounds like catechin showed maximum eradication of biofilm along with the degradation of EPS structural components like carbohydrates and proteins compared to quercetin, nimbolide, nimbin, and azardirachtin, and hence, catechin was proved to be the best against dental plaque-forming bacteria. It was also observed that catechin was able to bring about a marked reduction in quorum sensing (QS) both in Alcaligenes faecalis and Pseudomonas gingivalis dental biofilm-forming strains. The extent of such reduction was maximum for catechin (94.56±2.56% in P. gingivalis & 96.56±2.5 in A. faecalis) in comparison to other bioactive compounds. It was further observed that the bioactive compounds possess the ability to quickly pass across the membrane and bring about inhibition in the DNA and RNA content of the sessile cells. This was further validated by microscopic and in silico studies. Thus, this study revealed that catechin obtained from the phytoextract of AI showed a marked ability to inhibit the dental biofilm and can be used as a natural drug-like compound in treating biofilm-associated chronic infections.

Quaternized styryl-azinium fluorophores as cellular RNA-binders

The capability of three quaternized styryl-azinium iodides to bind cellular RNA has been tested by means of Fluorescence Confocal Microscopy imaging of stained MCF-7 cells treated with RNase. Their association constants have been estimated through spectrophotometric and fluorimetric titrations with tRNA and compared to their affinity toward DNA. Transient absorption spectroscopy with femtosecond resolution confirmed the binding of the investigated compounds with tRNA and shed new light on the excited state dynamics of their complexes, by revealing a significant lengthening of the lifetime of S₁ upon complexation, which parallels the fluorescence quantum yield enhancement.

The Supramolecular Self-Assembly of Aminoglycoside Antibiotics and their Applications

Aminoglycosides, a class of antibiotics that includes gentamicin, kanamycin, neomycin, streptomycin, tobramycin and apramycin, are derived from various streptomyces species. Despite the significant increase in the antibacterial resistant pathogens, aminoglycosides remain an important class of antimicrobial drugs due to their unique chemical structure which offers a broad spectrum of activity. The modification of antibiotics and their subsequent use in supramolecular chemistry is rarely reported. Given the importance of aminoglycosides, here we give a brief overview on the modification of 4,5- and 4,6-disubstituted deoxystreptamine classes of aminoglycosides through supramolecular chemistry and their potential for real world applications. We also make the case that the work in this area is gaining momentum, and there are significant opportunities to meet the challenges of modern antibiotics through the modification of aminoglycosides by harnessing the advantages of supramolecular chemistry.

An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb

The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat–TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181–TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.

Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data

Molecular dynamics (MD) simulations play an important role in characterizing Ribonucleic Acid (RNA) structure, augmenting information from experimental techniques such as Nuclear Magnetic Resonance (NMR). In this work, we examine the accuracy of structural representation resulting from application of a number of explicit and implicit solvent models and refinement protocols against experimental data ranging from high density of residual dipolar coupling (RDC) restraints to completely unrestrained simulations. For a prototype A-form RNA helix, our results indicate that AMBER RNA force field with either implicit or explicit solvent can produce a realistic dynamic representation of RNA helical structure, accurately cross-validating with respect to a diverse array of NMR observables. In refinement against NMR distance restraints, modern MD force fields are found to be equally adequate, with high fidelity cross-validation to the residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), while slightly over-estimating structural order as monitored via NMR relaxation data. With restraints trimmed to encode only for base pairing information, cross-validation quality significantly deteriorates, now exhibiting a pronounced dependence on the choice of the solvent model. This deterioration is found to be partially reversible by increasing planarity restraints on the nucleobase geometry. For completely unrestrained MD simulations, the choice of water model becomes very important, with the best-performing TIP4P-Ew accurately reproducing both the RDC and RCSA data, while closely matching the NMR-derived order parameters. The information provided here will serve as a foundation for MD-based refinement of solution state NMR structures of RNA.

Revealing the distinct folding phases of an RNA three-helix junction

Remarkable new insight has emerged into the biological role of RNA in cells. RNA folding and dynamics enable many of these newly discovered functions, calling for an understanding of RNA self-assembly and conformational dynamics. Because RNAs pass through multiple structures as they fold, an ensemble perspective is required to visualize the flow through fleetingly populated sets of states. Here, we combine microfluidic mixing technology and small angle X-ray scattering (SAXS) to measure the Mg-induced folding of a small RNA domain, the tP5abc three helix junction. Our measurements are interpreted using ensemble optimization to select atomically detailed structures that recapitulate each experimental curve. Structural ensembles, derived at key stages in both time-resolved studies and equilibrium titrations, reproduce the features of known intermediates, and more importantly, offer a powerful new structural perspective on the time-progression of folding. Distinct collapse phases along the pathway appear to be orchestrated by specific interactions with Mg ions. These key interactions subsequently direct motions of the backbone that position the partners of tertiary contacts for later bonding, and demonstrate a remarkable synergy between Mg and RNA across numerous time-scales.

Study of the Interaction of Ciprofloxacin and Sparfloxacin with Biomolecules by Spectral, Electrochemical and Molecular Docking Methods

Interactions of ciprofloxacin and sparfloxacin with different biomolecules (DNA, RNA and BSA) are investigated by UV–Visible spectroscopy, fluorescence spectroscopy, cyclic voltammetry and molecular docking methods. Upon increasing the concentration of the biomolecules, the absorption maxima of ciprofloxacin and sparfloxacin are red shifted in the aqueous solutions whereas red or blue shift noticed in the fluorescence spectra. The negative free energy changes suggest that the interaction processes are spontaneous. Cyclic voltammetry results suggested that when the drug concentration is increased, the anodic electrode potential increased. Molecular docking results showed that hydrophobic forces, electrostatic interactions, and hydrogen bonds played vital roles in the interaction drugs with biomolecules. The molecular docking calculation clarifies the binding mode and the binding sites are in good accordance with the experiment results.

Cancer transcriptome profiling at the juncture of clinical translation

Methodological breakthroughs over the past four decades have repeatedly revolutionized transcriptome profiling. Using RNA sequencing (RNA-seq), it has now become possible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples. These transcriptomes provide a link between cellular phenotypes and their molecular underpinnings, such as mutations. In the context of cancer, this link represents an opportunity to dissect the complexity and heterogeneity of tumours and to discover new biomarkers or therapeutic strategies. Here, we review the rationale, methodology and translational impact of transcriptome profiling in cancer.

Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets

The emergence of antibiotic resistance mechanisms among bacterial pathogens increases the demand for novel treatment strategies. Lately, the contribution of non-coding RNAs to antibiotic resistance and their potential value as drug targets became evident. RNA attenuator elements in mRNA leader regions couple expression of resistance genes to the presence of the cognate antibiotic. Trans-encoded small RNAs (sRNAs) modulate antibiotic tolerance by base-pairing with mRNAs encoding functions important for resistance such as metabolic enzymes, drug efflux pumps, or transport proteins. Bacteria respond with extensive changes of their sRNA repertoire to antibiotics. Each antibiotic generates a unique sRNA profile possibly causing downstream effects that may help to overcome the antibiotic challenge. In consequence, regulatory RNAs including sRNAs and their protein interaction partners such as Hfq may prove useful as targets for antimicrobial chemotherapy. Indeed, several compounds have been developed that kill bacteria by mimicking ligands for riboswitches controlling essential genes, demonstrating that regulatory RNA elements are druggable targets. Drugs acting on sRNAs are considered for combined therapies to treat infections. In this review, we address how regulatory RNAs respond to and establish resistance to antibiotics in bacteria. Approaches to target RNAs involved in intrinsic antibiotic resistance or virulence for chemotherapy will be discussed.

Inhibition of Multimolecular RNA-Protein Interactions Using Multitarget-Directed Nanohybrid System

Multitarget-directed ligands (MTDLs) are hybrid ligands obtained by covalently linking active pharmacophores that can act on different targets. We envision that the concept of MTDLs can also be applied to supramolecular bioinorganic nanohybrid systems. Here, we report the inhibition of multimolecular RNA-protein complexes using multitarget-directed peptide-carbon nanotube hybrids (SPCHs). One of the most well-characterized and important RNA-protein interactions, a Rev-response element (RRE) RNA:Rev protein:Crm1 protein interaction system in human immunodeficiency virus type-1, was used as a model of multimolecular RNA-protein interactions. Although all previous studies have targeted only one of the interaction interfaces, that is, either the RRE:Rev interface or the RRE-Rev complex:Crm1 interface, we here have developed multitarget-directed SPCHs that could target both interfaces because the supramolecular nanosystem could be best suited for inhibiting multimolecular RNA-protein complexes that are characterized by large and complex molecular interfaces. The results showed that the single target-directed SPCHs were inhibitory to the single interface comprised only of RNA and protein in vitro, whereas multitarget-directed SPCHs were inhibitory to the multimolecular RNA-protein interfaces both in vitro and in cellulo. The MTDL nanohybrids represent a novel nanotherapeutic system that could be used to treat complex disease targets.

Alternative splicing: the pledge, the turn, and the prestige : The key role of alternative splicing in human biological systems

Alternative pre-mRNA splicing is a tightly controlled process conducted by the spliceosome, with the assistance of several regulators, resulting in the expression of different transcript isoforms from the same gene and increasing both transcriptome and proteome complexity. The differences between alternative isoforms may be subtle but enough to change the function or localization of the translated proteins. A fine control of the isoform balance is, therefore, needed throughout developmental stages and adult tissues or physiological conditions and it does not come as a surprise that several diseases are caused by its deregulation. In this review, we aim to bring the splicing machinery on stage and raise the curtain on its mechanisms and regulation throughout several systems and tissues of the human body, from neurodevelopment to the interactions with the human microbiome. We discuss, on one hand, the essential role of alternative splicing in assuring tissue function, diversity, and swiftness of response in these systems or tissues, and on the other hand, what goes wrong when its regulatory mechanisms fail. We also focus on the possibilities that splicing modulation therapies open for the future of personalized medicine, along with the leading techniques in this field. The final act of the spliceosome, however, is yet to be fully revealed, as more knowledge is needed regarding the complex regulatory network that coordinates alternative splicing and how its dysfunction leads to disease.

A feedback mechanism between PLD and deadenylase PARN for the shortening of eukaryotic poly(A) mRNA tails that is deregulated in cancer cells

The removal of mRNA transcript poly(A) tails by 3′→5′ exonucleases is the rate-limiting step in mRNA decay in eukaryotes. Known cellular deadenylases are the CCR4-NOT and PAN complexes, and poly(A)-specific ribonuclease (PARN). The physiological roles and regulation for PARN is beginning to be elucidated. Since phospholipase D (PLD2 isoform) gene expression is upregulated in breast cancer cells and PARN is downregulated, we examined whether a signaling connection existed between these two enzymes. Silencing PARN with siRNA led to an increase in PLD2 protein, whereas overexpression of PARN had the opposite effect. Overexpression of PLD2, however, led to an increase in PARN expression. Thus, PARN downregulates PLD2 whereas PLD2 upregulates PARN. Co-expression of both PARN and PLD2 mimicked this pattern in non-cancerous cells (COS-7 fibroblasts) but, surprisingly, not in breast cancer MCF-7 cells, where PARN switches from inhibition to activation of PLD2 gene and protein expression. Between 30 and 300 nM phosphatidic acid (PA), the product of PLD enzymatic reaction, added exogenously to culture cells had a stabilizing role of both PARN and PLD2 mRNA decay. Lastly, by immunofluorescence microscopy, we observed an intracellular co-localization of PA-loaded vesicles (0.1-1 nm) and PARN. In summary, we report for the first time the involvement of a phospholipase (PLD2) and PA in mediating PARN-induced eukaryotic mRNA decay and the crosstalk between the two enzymes that is deregulated in breast cancer cells.

Summary: Cell signaling enzyme phospholipase D2 (PLD2) and its reaction product, phospholipid phosphatidic acid (PA), are involved in mediating PARN-induced eukaryotic mRNA decay.

BzDANP, a Small-Molecule Modulator of Pre-miR-29a Maturation by Dicer

We here report the synthesis of novel molecule BzDANP having a three-ring benzo[c][1,8]naphthyridine system, the evaluation of its binding properties to a single nucleotide bulge in RNA duplexes, and BzDANP-induced suppression of pre-miR-29a processing by Dicer. BzDANP showed much increased affinity to the bulged RNAs as compared with the parent molecule DANP, which possesses the same hydrogen-bonding surface as BzDANP but in a two-ring [1,8]naphthyridine system. Melting temperature analysis of bulged RNAs showed that BzDANP most effectively stabilized the C-bulged RNA. Dicer-mediated processing of pre-miR-29a was suppressed by BzDANP in a concentration dependent manner. The presence of the C-bulge at the Dicer cleavage site was effective for the suppression of pre-miR-29a processing by BzDANP. These results demonstrated that the small molecule binding to the bulged site in the vicinity of the Dicer cleavage site could be a potential modulator for the maturation of pre-miRNA.

Small molecules targeting viral RNA

Highly conserved noncoding RNA (ncRNA) elements in viral genomes and transcripts offer new opportunities to expand the repertoire of drug targets for the development of antiinfective therapy. Ligands binding to ncRNA architectures are able to affect interactions, structural stability or conformational changes and thereby block processes essential for viral replication. Proof of concept for targeting functional RNA by small molecule inhibitors has been demonstrated for multiple viruses with RNA genomes. Strategies to identify antiviral compounds as inhibitors of ncRNA are increasingly emphasizing consideration of drug‐like properties of candidate molecules emerging from screening and ligand design. Recent efforts of antiviral lead discovery for RNA targets have provided drug‐like small molecules that inhibit viral replication and include inhibitors of human immunodeficiency virus (HIV), hepatitis C virus (HCV), severe respiratory syndrome coronavirus (SARS CoV), and influenza A virus. While target selectivity remains a challenge for the discovery of useful RNA‐binding compounds, a better understanding is emerging of properties that define RNA targets amenable for inhibition by small molecule ligands. Insight from successful approaches of targeting viral ncRNA in HIV, HCV, SARS CoV, and influenza A will provide a basis for the future exploration of RNA targets for therapeutic intervention in other viral pathogens which create urgent, unmet medical needs. Viruses for which targeting ncRNA components in the genome or transcripts may be promising include insect‐borne flaviviruses (Dengue, Zika, and West Nile) and filoviruses (Ebola and Marburg). WIREs RNA 2016, 7:726–743. doi: 10.1002/wrna.1373

This article is categorized under: 1

RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems

2

RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions

3

Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs

A self-assembling RNA aptamer-based nanoparticle sensor for fluorometric detection of Neomycin B in milk

To date, there are few reports regarding the development of RNA aptamer-based biosensors for the detection of small molecules. The possible reason is attributed to the weak nuclease resistance of RNA in biological environments. In this study, we have developed an RNA aptamer-based gold nanoparticle (AuNP) sensor for fluorometric detection of Neomycin B in milk. This aptasensor depends on the self-assembly of the RNA aptamer/Neomycin B complex and fluorescence quenching by AuNPs. This biosensor exhibited a low detection limit of 0.01 μM, with a linear dynamic range from 0.1 to 10 μM in milk, and a good selectivity toward Neomycin B. Specifically, because of the shorter RNA fragments and the nuclease inhibition ability of the RNA-modified AuNPs, the RNA sequences remained stable during the experiments. This work will serve as an example for the development of novel biosensors based on RNA aptamers. Graphical Abstract An RNA aptamer-based nanoparticle sensor, developed for the detection of Neomycin B in milk, shows high binding affinity and selectivity. This aptasensor depends on the self-assembly of the aptamer/ligand complex and fluorescence quenching by gold nanoparticles (AuNPs). Because of the shorter RNA fragments and the nuclease inhibition ability of RNA-modified AuNPs, RNA sequences remain stable during the detection.

It's a loop world - single strands in RNA as structural and functional elements

Unpaired regions in RNA molecules - loops - are centrally involved in defining the characteristic three-dimensional (3D) architecture of RNAs and are of high interest in RNA engineering and design. Loops adopt diverse, but specific conformations stabilised by complex tertiary structural interactions that provide structural flexibility to RNA structures that would otherwise not be possible if they only consisted of the rigid A-helical shapes usually formed by canonical base pairing. By participating in sequence-non-local contacts, they furthermore contribute to stabilising the overall fold of RNA molecules. Interactions between RNAs and other nucleic acids, proteins, or small molecules are also generally mediated by RNA loop structures. Therefore, the function of an RNA molecule is generally dependent on its loops. Examples include intermolecular interactions between RNAs as part of the microRNA processing pathways, ribozymatic activity, or riboswitch-ligand interactions. Bioinformatics approaches have been successfully applied to the identification of novel RNA structural motifs including loops, local and global RNA 3D structure prediction, and structural and conformational analysis of RNAs and have contributed to a better understanding of the sequence-structure-function relationships in RNA loops.

Nonconventional chemical inhibitors of microRNA: therapeutic scope

MicroRNAs (miRNAs) are a class of genomically encoded small RNA molecules (∼22nts in length), which regulate gene expression post transcriptionally. miRNAs are implicated in several diseases, thus modulation of miRNA is of prime importance. Small molecules offer a non-conventional alternative to do so.

Interaction of phenazinium dyes with double-stranded poly(A): spectroscopy and isothermal titration calorimetry studies

A comprehensive study on the binding of phenazinium dyes viz. janus green B, indoine blue, safranine O and phenosafranine with double stranded poly(A) using various spectroscopic and calorimetric techniques is presented. A higher binding of janus green B and indoine blue over safranine O and phenosafranine to poly(A) was observed from all experiments. Intercalative mode of binding of the dyes was inferred from fluorescence polarization anisotropy, iodide quenching and viscosity experiments. Circular dichroism study revealed significant perturbation of the secondary structure of poly(A) on binding of these dyes. Results from isothermal titration calorimetry experiments suggested that the binding was predominantly entropy driven with a minor contribution of enthalpy to the standard molar Gibbs energy. The results presented here may open new opportunities in the application of these dyes as RNA targeted therapeutic agents.

Antibiotic drugs targeting bacterial RNAs

RNAs have diverse structures that include bulges and internal loops able to form tertiary contacts or serve as ligand binding sites. The recent increase in structural and functional information related to RNAs has put them in the limelight as a drug target for small molecule therapy. In addition, the recognition of the marked difference between prokaryotic and eukaryotic rRNA has led to the development of antibiotics that specifically target bacterial rRNA, reduce protein translation and thereby inhibit bacterial growth. To facilitate the development of new antibiotics targeting RNA, we here review the literature concerning such antibiotics, mRNA, riboswitch and tRNA and the key methodologies used for their screening.

Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies

Amikacin is a 2-deoxystreptamine aminoglycoside antibiotic possessing a unique l-HABA (l-(-)-γ-amino-α-hydroxybutyric acid) group and applied in the treatment of hospital-acquired infections. Amikacin influences bacterial translation by binding to the decoding region of the small ribosomal subunit that overlaps with the binding site of aminoacylated-tRNA (A-site). Here, we have characterized thermodynamics of interactions of amikacin with a 27-mer RNA oligonucleotide mimicking the aminoglycoside binding site in the bacterial ribosome. We applied isothermal titration and differential scanning calorimetries, circular dichroism and thermal denaturation experiments, as well as computer simulations. Thermal denaturation studies have shown that amikacin affects only slightly the melting temperatures of the A-site mimicking RNA model suggesting a moderate stabilization of RNA by amikacin. Isothermal titration calorimetry gives the equilibrium dissociation constants for the binding reaction between amikacin and the A-site oligonucleotide in the micromolar range with a favorable enthalpic contribution. However, for amikacin we observe a positive entropic contribution to binding, contrary to other aminoglycosides, paromomycin and ribostamycin. Circular dichroism spectra suggest that the observed increase in entropy is not caused by structural changes of RNA because amikacin binding does not destabilize the helicity of the RNA model. To investigate the origins of this positive entropy change we performed all-atom molecular dynamics simulations in explicit solvent for the 27-mer RNA oligonucleotide mimicking one A-site and the crystal structure of an RNA duplex containing two A-sites. We observed that the diversity of the conformational states of the l-HABA group sampled in the simulations of the complex was larger than for the free amikacin in explicit water. Therefore, the larger flexibility of the l-HABA group in the bound form may contribute to an increase of entropy upon binding.

SMMRNA: a database of small molecule modulators of RNA

We have developed SMMRNA, an interactive database, available at http://www.smmrna.org, with special focus on small molecule ligands targeting RNA. Currently, SMMRNA consists of ∼770 unique ligands along with structural images of RNA molecules. Each ligand in the SMMRNA contains information such as Kd, Ki, IC50, ΔTm, molecular weight (MW), hydrogen donor and acceptor count, XlogP, number of rotatable bonds, number of aromatic rings and 2D and 3D structures. These parameters can be explored using text search, advanced search, substructure and similarity-based analysis tools that are embedded in SMMRNA. A structure editor is provided for 3D visualization of ligands. Advance analysis can be performed using substructure and OpenBabel-based chemical similarity fingerprints. Upload facility for both RNA and ligands is also provided. The physicochemical properties of the ligands were further examined using OpenBabel descriptors, hierarchical clustering, binning partition and multidimensional scaling. We have also generated a 3D conformation database of ligands to support the structure and ligand-based screening. SMMRNA provides comprehensive resource for further design, development and refinement of small molecule modulators for selective targeting of RNA molecules.

The size of the aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs. ds-DNA

Aryl-linked (pyridine- vs. phenanthroline-) bis-polyaza pyridinophane scorpiands PYPOD and PHENPOD strongly bind to the double stranded DNA and RNA, whereby very intriguing RNA over DNA selectivity is finely tuned by aryl-linker length and aromatic surface. Moreover, PYPOD and PHENPOD dimer formation at high compound/polynucleotide ratios is highly sensitive to the fine interplay between the steric and binding properties of compound-dimers and the DNA minor groove/RNA major groove. That is demonstrated by significantly different induced CD spectra, which allow spectroscopic differentiation between various DNA/RNA secondary structures. A significantly higher (micromolar) antiproliferative effect of PYPOD and PHENPOD on human cell lines with respect to previously reported pyridine-based tripodal aliphatic polyamines is attributed to masked positive charges and increased hydrophobicity of novel compounds, resulting in more efficient membrane permeation and cellular uptake.

The promise of riboswitches as potential antibacterial drug targets

Riboswitches represent promising novel RNA structures for developing compounds that artificially regulate gene expression and, thus, bacterial growth. The past years have seen increasing efforts to identify metabolite-analogues which act on riboswitches and which reveal antibacterial activity. Here, we summarize the current inventory of riboswitch-targeting compounds, their characteristics and antibacterial potential.

Binding of the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs to tRNA(phe.)

Background

Three new analogs of berberine with aryl/arylalkyl amino carbonyl methyl substituent at the 9-position of the isoquinoline chromophore along with berberrubine were studied for their binding to tRNA^phe by wide variety of biophysical techniques like spectrophotometry, spectrofluorimetry, circular dichroism, thermal melting, viscosity and isothermal titration calorimetry.

Methodology/Principal Findings

Scatchard binding isotherms revealed that the cooperative binding mode of berberine was propagated in the analogs also. Thermal melting studies showed that all the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs stabilized the tRNA^phe more in comparison to berberine. Circular dichroism studies showed that these analogs perturbed the structure of tRNA^phe more in comparison to berberine. Ferrocyanide quenching studies and viscosity results proved the intercalative binding mode of these analogs into the helical organization of tRNA^phe. The binding was entropy driven for the analogs in sharp contrast to the enthalpy driven binding of berberine. The introduction of the aryl/arylalkyl amino carbonyl methyl substituent at the 9-position thus switched the enthalpy driven binding of berberine to entropy dominated binding. Salt and temperature dependent calorimetric studies established the involvement of multiple weak noncovalent interactions in the binding process.

Conclusions/Significance

The results showed that 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs exhibited almost ten folds higher binding affinity to tRNA^phe compared to berberine whereas the binding of berberrubine was dramatically reduced by about twenty fold in comparison to berberine. The spacer length of the substitution at the 9-position of the isoquinoline chromophore appears to be critical in modulating the binding affinities towards tRNA^phe.

A dimeric form of N-methoxycarbonyl-2-amino-1,8-naphthyridine bound to the A-A mismatch in the CAG/CAG base triad in dsRNA

A dimeric form of N-methoxycarbonyl-2-amino-1,8-naphthyridine (MCND) connected at the C2 position with a three-atom linker was examined for the binding to mismatches in double stranded RNA. Despite the fully complementary hydrogen bonding groups to guanine, MCND did not bind to guanine-guanine mismatch but did to adenine-adenine mismatch. The base pairs flanking the mismatch had weak effect on the binding, with showing the strongest binding to the A-A mismatch in the CAG/CAG sequence. The A-A mismatch in the GAC/GAC sequence was a poor substrate for the MCND binding. A monomeric derivative of MCND and another derivative lacking a methylcarbamate group showed negligilble binding to the A-A mismatch and the sequence selectivity. These results are important clues for the better molecular design of RNA binding small molecules.

Structure-activity studies on the fluorescent indicator in a displacement assay for the screening of small molecules binding to RNA

A series of xanthone and thioxanthone derivatives with aminoalkoxy substituents were synthesized as fluorescent indicators for a displacement assay in the study of small-molecule-RNA interactions. The RNA-binding properties of these molecules were investigated in terms of the improved binding selectivity to the loop region in the RNA secondary structure relative to 2,7-bis(2-aminoethoxy)xanthone (X2S) by fluorimetric titration and displacement assay. An 11-mer double-stranded RNA and a hairpin RNA mimicking the stem loop IIB of Rev response element (RRE) RNA of HIV-1 mRNA were used. The X2S derivatives with longer aminoalkyl substituents showed a higher affinity to the double-stranded RNA than the parent molecule. Introduction of a methyl group on the aminoethoxy moiety of X2S effectively modulated the selectivity to the RNA secondary structure. Methyl group substitution at the C1' position suppressed the binding to the loop regions. Substitution with two methyl groups on the amino nitrogen atom resulted in reducing the affinity to the double-stranded region by a factor of 40%. The effect of methyl substitution on the amino nitrogen atom was also observed for a thioxanthone derivative. Titration experiments, however, suggested that thioxanthone derivatives showed a more prominent tendency of multiple binding to RNA than xanthone derivatives. The selectivity index calculated from the affinity to the double-stranded and loop regions suggested that the N,N-dimethyl derivative of X2S would be suitable for the screening of small molecules binding to RRE.

Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA

Binding of proteins and small molecules to RNA involves many electrostatic interactions, which may alter the distribution of ions around the RNA molecule. Here, we use molecular dynamics simulations to investigate how binding of a cyclic peptide mimic of the HIV-1 Tat protein affects the ionic distribution around the HIV-1 TAR RNA element. The calculations reproduce the structural properties observed in NMR studies of TAR and its complex. They also provide insight into the rearrangement of counterions during the molecular recognition events leading to the formation of the protein/RNA complex.

Identification of protein-RNA interaction sites using the information of spatial adjacent residues

BACKGROUND

Protein-RNA interactions play an important role in numbers of fundamental cellular processes such as RNA splicing, transport and translation, protein synthesis and certain RNA-mediated enzymatic processes. The more knowledge of Protein-RNA recognition can not only help to understand the regulatory mechanism, the site-directed mutagenesis and regulation of RNA-protein complexes in biological systems, but also have a vitally effecting for rational drug design.

RESULTS

Based on the information of spatial adjacent residues, novel feature extraction methods were proposed to predict protein-RNA interaction sites with SVM-KNN classifier. The total accuracies of spatial adjacent residue profile feature and spatial adjacent residues weighted accessibility solvent area feature are 78%, 67.07% respectively in 5-fold cross-validation test, which are 1.4%, 3.79% higher than that of sequence neighbour residue profile feature and sequence neighbour residue accessibility solvent area feature.

CONCLUSIONS

The results indicate that the performance of feature extraction method using the spatial adjacent information is superior to the sequence neighbour information approach. The performance of SVM-KNN classifier is little better than that of SVM. The feature extraction method of spatial adjacent information with SVM-KNN is very effective for identifying protein-RNA interaction sites and may at least play a complimentary role to the existing methods.

Molecular recognition of RNA: challenges for modelling interactions and plasticity

There is growing interest in molecular recognition processes of RNA because of RNA's widespread involvement in biological processes. Computational approaches are increasingly used for analysing and predicting binding to RNA, fuelled by encouraging progress in developing simulation, free energy and docking methods for nucleic acids. These developments take into account challenges regarding the energetics of RNA-ligand binding, RNA plasticity, and the presence of water molecules and ions in the binding interface. Accordingly, we will detail advances in force field and scoring function development for molecular dynamics (MD) simulations, free energy computations and docking calculations of nucleic acid complexes. Furthermore, we present methods that can detect moving parts within RNA structures based on graph-theoretical approaches or normal mode analysis (NMA). As an example of the successful use of these developments, we will discuss recent structure-based drug design approaches that focus on the bacterial ribosomal A-site RNA as a drug target.

Acid-base properties of functionalised tripodal polyamines and their interaction with nucleotides and nucleic acids

Novel, highly positively charged tripodal polyamines with appended heterocyclic moieties revealed an intriguing panel of protonation species within the biologically relevant range. Studied compounds bind nucleotide monophosphates by mostly electrostatic interactions but only the imidazole analogue showed selectivity toward UMP in respect to other nucleotides. Strong binding of all the studied compounds to both ds-DNA and ds-RNA is to some extent selective toward the latter, showing rather rare RNA over DNA preference.