Motifs Of Interest Research Articles

Motif-Aware miRNA-Disease Association Prediction via Hierarchical Attention Network.

As post-transcriptional regulators of gene expression, micro-ribonucleic acids (miRNAs) are regarded as potential biomarkers for a variety of diseases. Hence, the prediction of miRNA-disease associations (MDAs) is of great significance for an in-depth understanding of disease pathogenesis and progression. Existing prediction models are mainly concentrated on incorporating different sources of biological information to perform the MDA prediction task while failing to consider the fully potential utility of MDA network information at the motif-level. To overcome this problem, we propose a novel motif-aware MDA prediction model, namely MotifMDA, by fusing a variety of high- and low-order structural information. In particular, we first design several motifs of interest considering their ability to characterize how miRNAs are associated with diseases through different network structural patterns. Then, MotifMDA adopts a two-layer hierarchical attention to identify novel MDAs. Specifically, the first attention layer learns high-order motif preferences based on their occurrences in the given MDA network, while the second one learns the final embeddings of miRNAs and diseases through coupling high- and low-order preferences. Experimental results on two benchmark datasets have demonstrated the superior performance of MotifMDA over several state-of-the-art prediction models. This strongly indicates that accurate MDA prediction can be achieved by relying solely on MDA network information. Furthermore, our case studies indicate that the incorporation of motif-level structure information allows MotifMDA to discover novel MDAs from different perspectives.

Screening potential dye sensitizers for water splitting photocatalysts using a genetic algorithm.

Addressing the global fossil energy crisis necessitates the efficient utilization of sustainable energy sources. Hydrogen, a green fuel, can be generated using sunlight, water, and a photocatalyst. Employing sensitizers holds promise for enhancing photocatalyst performance, enabling high rates of hydrogen evolution through increased visible light absorption. However, sifting through millions of diverse molecules to identify suitable dyes for specific photocatalysts poses a significant challenge. In this study, we integrate genetic algorithm and geometry-frequency-noncovalent extended tight binding methods to efficiently screen 2.6 million potential sensitizers with a D-π-A-π-AA structure within a short timeframe. Subsequently, these optimized sensitizers are rigorously reassessed by using DFT/TDDFT methods, elucidating why they may serve as superior dyes compared to the reference dye WS5F, particularly in terms of light absorption, driving force, binding energy, etc. Additionally, our methodology uncovers molecular motifs of particular interest, including the furan π-bridge and the double cyano anchoring acceptor, which are prevalent in the most promising set of molecules. The developed genetic algorithm workflow and dye design principles can be extended to various compelling projects, such as dye-sensitized solar cells, organic photovoltaics, photo-induced redox reactions, pharmaceuticals, and beyond.

Chemical Attachment of 5-Nitrosalicylaldimine Motif to Silatrane Resulting in an Organic-Inorganic Structure with High Medicinal Significance.

Two chemical motifs of interest for medicinal chemistry, silatrane as 1-(3-aminopropyl) silatrane (SIL M), and nitro group attached in position 5 to salicylaldehyde, are coupled in a new structure, 1-(3-{[(2-hydroxy-5-nitrophenyl)methylidene]amino}propyl)silatrane (SIL-BS), through an azomethine moiety, also known as a versatile pharmacophore. The high purity isolated compound was structurally characterized by an elemental, spectral, and single crystal X-ray diffraction analysis. Given the structural premises for being a biologically active compound, different specific techniques and protocols have been used to evaluate their in vitro hydrolytic stability in simulated physiological conditions, the cytotoxicity on two cancer cell lines (HepG2 and MCF7), and protein binding ability-with a major role in drug ADME (Absorption, Distribution, Metabolism and Excretion), in parallel with those of the SIL M. While the latter had a good biocompatibility, the nitro-silatrane derivative, SIL-BS, exhibited a higher cytotoxic activity on HepG2 and MCF7 cell lines, performance assigned, among others, to the known capacity of the nitro group to promote a specific cytotoxicity by a "activation by reduction" mechanism. Both compounds exhibited increased bio- and muco-adhesiveness, which can favor an optimized therapeutic effect by increased drug permeation and residence time in tumor location. Additional benefits of these compounds have been demonstrated by their antimicrobial activity on several fungi and bacteria species. Molecular docking computations on Human Serum Albumin (HSA) and MPRO COVID-19 protease demonstrated their potential in the development of new drugs for combined therapy.

Palladium-Mediated Synthesis of [Carbonyl-11C]acyl Amidines from Aryl Iodides and Aryl Bromides and Their One-Pot Cyclization to 11C-Labeled Oxadiazoles.

Positron emission tomography (PET) is a highly valuable imaging technique with many clinical applications. The possibility to study physiological and biochemical processes in vivo also makes PET an important tool in drug discovery. Of importance is the possibility of labelling the compound of interest with a positron-emitting radionuclide, such as carbon-11. Carbonylation reactions with [11C]carbon monoxide ([11C]CO) has been used to label a number of molecules containing a carbonyl derivative, such as amides and esters, with carbon-11. Presented herein is the palladium-mediated carbonylative synthesis of [carbonyl-11C]acyl amidines and their subsequent cyclization to 11C-labeled 1,2,4-oxadiazoles. Starting from amidines, [11C]CO, and either aryl iodides or aryl bromides, [carbonyl-11C]acyl amidines were synthesized and isolated in good to very good radiochemical yields (RCY). The 11C-labeled 1,2,4-oxadiazoles were synthesized without the isolation of the intermediate [carbonyl-11C]acyl amidines and isolated in useful RCYs, including the NF-E2-related factor 2 activator DDO-7263. 3-Phenyl-5-(4-tolyl)-1,2,4-(5-11C)oxadiazole was synthesized and isolated with a clinically relevant molar activity. The broadened substrate scope, together with the good RCY and high Am, demonstrates the utility of this method for the incorporation of carbon-11 into acyl amidines and 1,2,4-oxadiazoles, structural motifs of pharmacological interest.

Pharmacophore-Based Discovery of Viral RNA Conformational Modulators.

New RNA-binding small-molecule scaffolds are needed to unleash the pharmacological potential of RNA targets. Here we have applied a pharmacophore-based virtual screening approach, seldom used in the RNA recognition field, to identify novel conformational inhibitors of the hepatitis C virus internal ribosome entry site. The conformational effect of the screening hits was assessed with a fluorescence resonance energy transfer assay, and the affinity, specificity, and binding site of the ligands were determined using a combination of fluorescence intensity and NMR spectroscopy experiments. The results indicate that this strategy can be successfully applied to discover RNA conformational inhibitors bearing substantially less positive charge than the reference ligands. This methodology can potentially be accommodated to other RNA motifs of pharmacological interest, facilitating the discovery of novel RNA-targeted molecules.

RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history.

Alu elements are one of the most successful groups of RNA retrotransposons and make up 11% of the human genome with over 1 million individual loci. They are linked to genetic defects, increases in sequence diversity, and influence transcriptional activity. Still, their RNA metabolism is poorly understood yet. It is even unclear whether Alu elements are mostly transcribed by RNA Polymerase II or III. We have conducted a transcription shutoff experiment by α-amanitin and metabolic RNA labeling by 4-thiouridine combined with RNA fragmentation (TT-seq) and RNA-seq to shed further light on the origin and life cycle of Alu transcripts. We find that Alu RNAs are more stable than previously thought and seem to originate in part from RNA Polymerase II activity, as previous reports suggest. Their expression however seems to be independent of the transcriptional activity of adjacent genes. Furthermore, we have developed a novel statistical test for detecting the expression of quantitative trait loci in Alu elements that relies on the de Bruijn graph representation of all Alu sequences. It controls for both statistical significance and biological relevance using a tuned k-mer representation, discovering influential sequence features missed by regular motif search. In addition, we discover several point mutations using a generalized linear model, and motifs of interest, which also match transcription factor-binding motifs.

The Origins of the Personal Type of Narrative in D. N. Mamin-Sibiryak’s Shorter Prose

Based on D. N. Mamin-Sibiryak’s shorter prose (essays, stories), the author distinguishes various types of narrative, i.e. first and third person narration and a personal type of narration. In several stories of the essay type, special markers of the presence of the personal narrator stand out expressed in characteristic motifs of admiration, interest, and curiosity. The author proves that during the period of the so-called “second debut” (1881–1882), Mamin began with the development of the form of a personal narrator, most characteristic of the genre of the essay, and gradually switched to the auctorial type of narrative, typical already of the genre of the story and assuming the form of an objective narrator author. It is also noted that in the form of an auctorial narration, Mamin successfully mastered the device of non-personal direct speech, or the speech interference of the character and the narrator author, which brings us to the rudimentary forms of “personal” narrative. From about the mid-1880s, the tendency towards a personal narrative became apparent, which is most noticeable in the stories Korobkin, Doctor Osokin’s Amendment and Simply, which focus on the state of the split consciousness of the character who finds himself in a situation of “man in front of a mirror” (M. M. Bakhtin) and acts as a direct subject of cognition. In the works of the same period (stories Between Us, The Old Fife, and others) a personal type of narration emerges clearly, which continues logically in the stories of the 1900s (Influenza. Monologue, A Dumpling and a Blot). The writer pays attention to the situation of the relationship between the character and the stereotyped nickname imposed on him, a certain “foreign” word-nomination, which leads to an increase in the act of self-awareness of the character and an intensification of the personal narrative. Finally, the article concludes that the development of a personal point of view in the narrative structure of the story leads Mamin-Sibiryak to the emergence of a new genre form, i.e. a personal “monologue” or “diary”, as well as to focus on the aesthetic potential of receptive poetics, which reveals points of convergence with genre variation of Chekhov’s “discovery story”.

Asymmetric Transfer Hydrogenation of gem-Difluorocyclopropenyl Esters: Access to Enantioenriched gem-Difluorocyclopropanes.

Catalytic enantioselective access to disubstituted functionalized gem-difluorocyclopropanes, which are emerging fluorinated motifs of interest in medicinal chemistry, was achieved through asymmetric transfer hydrogenation of gem-difluorocyclopropenyl esters, catalyzed by a Noyori-Ikariya (p-cymene)-ruthenium(II) complex, with (N-tosyl-1,2-diphenylethylenediamine) as the chiral ligand and isopropanol as the hydrogen donor. The resulting cis-gem-difluorocyclopropyl esters were obtained with moderate to high enantioselectivity (ee=66-99 %), and post-functionalization reactions enable access to valuable building blocks incorporating a cis- or trans-gem-difluorocyclopropyl motif.

Asymmetric Transfer Hydrogenation of gem‐Difluorocyclopropenyl Esters: Access to Enantioenriched gem‐Difluorocyclopropanes

AbstractCatalytic enantioselective access to disubstituted functionalized gem‐difluorocyclopropanes, which are emerging fluorinated motifs of interest in medicinal chemistry, was achieved through asymmetric transfer hydrogenation of gem‐difluorocyclopropenyl esters, catalyzed by a Noyori–Ikariya (p‐cymene)‐ruthenium(II) complex, with (N‐tosyl‐1,2‐diphenylethylenediamine) as the chiral ligand and isopropanol as the hydrogen donor. The resulting cis‐gem‐difluorocyclopropyl esters were obtained with moderate to high enantioselectivity (ee=66–99 %), and post‐functionalization reactions enable access to valuable building blocks incorporating a cis‐ or trans‐gem‐difluorocyclopropyl motif.

Functionalization of 8-17 DNAzymes modulates catalytic efficiency and divalent metal ion preference.

8-17 and 17E DNAzyme are being explored as biosensors for metal ions and RNA motifs of interest, more sensitive and efficient DNAzymes are required to meet the practical applications. Their similarity in the catalytic cores and differences in catalytic efficiency and metal ion dependence initiated great interest about the contribution of the catalytic residues. Functionalization of four adenine residues in the catalytic cores of 8-17 DNAzyme and 17E was conducted with amino, guanidinium, and imidazolyl groups. In the bulge loops of 8-17 and 17E, N6-(3-aminopropyl)-2'-deoxyadenosine (residue 1) at A15 led to new DNAzymes 8-17DZ-A15-1 and 17E-A15-1, with much more efficient cleavage ability in the Ca2+-mediated reaction and the greater preference for Ca2+ over Mg2+ than 8-17 DNAzyme and 17E, respectively, especially with a concentration-dependent increase of the selectivity, which is different from most DNAzymes with the similar dependence on both Mg2+ and Ca2+. With this kind of post-selection modification on 8-17 DNAzymes, for the first time, the catalytic efficiency and metal ion selectivity could be positively modulated. It is also helpful for the catalyic mechanistic studies of these DNAzymes, especially, the role of the unconserved A15 should be emphasized.

Gauging Molecular Orientation through Time Domain Simulations of Surface-Enhanced Raman Scattering.

Molecular reorientation dynamics modulate the physical and chemical properties of molecules at interfaces. This is particularly the case for organic molecules interacting with metallic surfaces-structural motifs of current interest to ultrasensitive chemical/biological detection/imaging. In this context, surface-enhanced Raman scattering (SERS) can be used to gauge the orientation of molecules in the immediate vicinity of plasmonic metals. Herein, we analyze SERS spectra of two aromatic thiols (4-mercaptobenzonitrile and thiophenol) chemisorbed onto silver substrates using ab initio molecular dynamics-based Raman spectral simulations that account for the optical response of molecules in the bulk and oriented molecules at the surface. Through a comparison with prior works aimed at gauging the orientation of our two model systems on metallic substrates, we describe the advantages and discuss the limitations of our described models and approach to gauging the orientation of molecules on metals through time domain simulations of their SERS signatures.

Computational and experimental analysis of bioactive peptide linear motifs in the integrin adhesome.

Therapeutic modulation of protein interactions is challenging, but short linear motifs (SLiMs) represent potential targets. Focal adhesions play a central role in adhesion by linking cells to the extracellular matrix. Integrins are central to this process, and many other intracellular proteins are components of the integrin adhesome. We applied a peptide network targeting approach to explore the intracellular modulation of integrin function in platelets. Firstly, we computed a platelet-relevant integrin adhesome, inferred via homology of known platelet proteins to adhesome components. We then computationally selected peptides from the set of platelet integrin adhesome cytoplasmic and membrane adjacent protein-protein interfaces. Motifs of interest in the intracellular component of the platelet integrin adhesome were identified using a predictor of SLiMs based on analysis of protein primary amino acid sequences (SLiMPred), a predictor of strongly conserved motifs within disordered protein regions (SLiMPrints), and information from the literature regarding protein interactions in the complex. We then synthesized peptides incorporating these motifs combined with cell penetrating factors (tat peptide and palmitylation for cytoplasmic and membrane proteins respectively). We tested for the platelet activating effects of the peptides, as well as their abilities to inhibit activation. Bioactivity testing revealed a number of peptides that modulated platelet function, including those derived from α-actinin (ACTN1) and syndecan (SDC4), binding to vinculin and syntenin respectively. Both chimeric peptide experiments and peptide combination experiments failed to identify strong effects, perhaps characterizing the adhesome as relatively robust against within-adhesome synergistic perturbation. We investigated in more detail peptides targeting vinculin. Combined experimental and computational evidence suggested a model in which the positively charged tat-derived cell penetrating part of the peptide contributes to bioactivity via stabilizing charge interactions with a region of the ACTN1 negatively charged surface. We conclude that some interactions in the integrin adhesome appear to be capable of modulation by short peptides, and may aid in the identification and characterization of target sites within the complex that may be useful for therapeutic modulation.

Iron‐Catalyzed C(sp2)−C(sp3) Cross‐Coupling of Chlorobenzamides with Alkyl Grignard Reagents: Development of Catalyst System, Synthetic Scope, and Application

AbstractDirect preparation of alkylated amide‐derivatives by cross‐coupling chemistry using sustainable protocols is challenging due to sensitivity of the amide functional group to reaction conditions. Herein, we report the synthesis of alkyl‐substituted amides by iron‐catalyzed C(sp2)−C(sp3) cross‐coupling of Grignard reagents with aryl chlorides. The products of these reactions are broadly used in the synthesis of pharmaceuticals, agrochemicals and other biologically‐active molecules. Furthermore, amides are used as versatile intermediates that can participate in the synthesis of valuable ketones and amines, providing access to motifs of broad synthetic interest. The reaction is characterized by its good substrate scope, tolerating a range of amide substitution, including sterically‐bulky, sensitive and readily modifiable amides. The reaction is compatible with challenging organometallics possessing β‐hydrogens, and proceeds under very mild, operationally‐simple conditions. Optimization of the catalyst system demonstrated the beneficial effect of O‐coordinating ligands on the cross‐coupling. The reaction was found to be fully chemoselective for the mono‐substitution at the less sterically‐hindered position. Mechanistic studies establish the order of reactivity and provide insight into the role of amide to control mono‐selectivity of the alkylation. The protocol provides the possibility for convenient access to alkyl‐amide structural building blocks using sustainable cross‐coupling conditions with high efficiency.magnified image

Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling

Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS–MODEL were used to generate the 40S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation (RMSD) value of 3.9Å relative to the template׳s crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying this approach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.

High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum.

Phage display is a prominent screening technique with a multitude of applications including therapeutic antibody development and mapping of antigen epitopes. In this study, phages were selected based on their interaction with patient serum and exhaustively characterised by high-throughput sequencing. A bioinformatics approach was developed in order to identify peptide motifs of interest based on clustering and contrasting to control samples. Comparison of patient and control samples confirmed a major issue in phage display, namely the selection of unspecific peptides. The potential of the bioinformatic approach was demonstrated by identifying epitopes of a prominent peanut allergen, Ara h 1, in sera from patients with severe peanut allergy. The identified epitopes were confirmed by high-density peptide micro-arrays. The present study demonstrates that high-throughput sequencing can empower phage display by (i) enabling the analysis of complex biological samples, (ii) circumventing the traditional laborious picking and functional testing of individual phage clones and (iii) reducing the number of selection rounds.

Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity

Wrapping, crossover, and braiding of DNA are the motifs of fundamental interest in genome packaging, gene regulation, and enzyme recognition. This study explores elastic mechanisms for the selection of chirality in wrapping, crossover, and braiding of DNA based on a coarse-grained model. The DNA model consists of two elastic chains that mutually intertwine in a right-handed manner forming a double-stranded helix with the distinction between major and minor grooves. Although individual potential energy functions of the DNA model have no asymmetry in terms of left and right twist, the model as a whole exhibits an asymmetric propensity to writhe in the left direction upon bending due to the right-handed helical geometry. Monte Carlo simulations of this model suggest that DNA has a propensity to prefer left-handed wrapping around a spherical core particle and also around a uniform rod due to the asymmetric elastic coupling between bending and writhing. This result indicates an elastic origin of the uniform left-handed wrapping of DNA in nucleosomes and also has implications on the wrapping of double-stranded DNA around rod-like molecules. Monte Carlo simulations of the DNA model also suggest that two juxtaposed DNA molecules can braid each other spontaneously under moderate attractive interactions with the preference for left-handed braiding due to the asymmetric coupling between bending and writhing. This result suggests the importance of asymmetric elasticity in the selection of chirality in braiding of a pair of DNA molecules.

Rare time series motif discovery from unbounded streams

The detection of time series motifs , which are approximately repeated subsequences in time series streams, has been shown to have great utility as a subroutine in many higher-level data mining algorithms. However, this detection becomes much harder in cases where the motifs of interest are vanishingly rare or when faced with a never-ending stream of data. In this work we investigate algorithms to find such rare motifs. We demonstrate that under reasonable assumptions we must abandon any hope of an exact solution to the motif problem as it is normally defined; however, we introduce algorithms that allow us to solve the underlying problem with high probability.

Simulations and Modelling of Biomimetic Nanopores

Nanopores are fast becoming a major scientific tool in molecular analysis and detection due to their ability to detect polynucleotides, proteins, and small molecules. Previous work has included the manipulation of α-hemolysin into a DNA sequencing pore however further development is needed for the use of a simple, monomeric pore for this purpose.Biomimetic modelling of nanopores allows for a specific function to be built into the model based on the replication and analysis of existing selectivity present in proteins.An initial analysis of known porin structures using computational techniques (pore radius profiles and electrostatic calculations) has identified potential structures for manipulation. Steered Molecular Dynamics simulations on a select number of membrane proteins have given insight into possible residue motifs of interest. With this, “simple protein” pores have been made with varying number of beta strands based on models of existing barrel proteins. Motifs have been modelled for exploration via MD simulations.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

BackgroundOne of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function.ResultsHere, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM.ConclusionsOur findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.