Strong Binding Sites Research Articles

Elucidation of specific binding sites and extraction of toxic Gen X from HSA employing cyclodextrin

The presence of per and poly-fluoroalkyl substances (PFAS), commonly referred to as forever chemicals, in aquatic systems is a serious global health problem. While the remediation of PFAS from aqueous media has been extensively investigated, their interactions with and removal from biological systems have received far less attention. We report herein structural alterations to human serum albumin (HSA) upon addition of perfluoro(2-methyl-3-oxahexanoic) acid (Gen X) monitored by changes to the fluorescence and circular dichroism (CD) spectra of HSA. The equilibrium association constant for Gen X binding to HSA is 7( ± 1) × 103 M−1 determined from changes in HSA fluorescence emission data during titration. Site-specific HSA binding fluorophores, 8-anilinonaphthalene-1-sulfonic acid (1,8-ANS), warfarin and dansyl-L-proline were used to investigate the specific binding sites of Gen X on HSA. A competitive displacement study yields association constants for Gen X to HSA at the 1,8-ANS, warfarin, and dansyl-L-proline binding sites to be 6.25 ( ± 0.5) × 104 M−1, 1.1 × 106 M−1, and 2.5( ± 0.2) × 109 M−1 respectively. Addition of β-cyclodextrin (β-CD) and heptakis(6-deoxy-6-amino)-β-cyclodextrin heptahydrochloride to the HSA:Gen X complex leads to the effective extraction of Gen X from the complex with the return of HSA in its native form. Gen X also leads to displacement of site-specific binding fluorophores bound to HSA, while subsequent addition of β-CD extracts Gen X from HSA with the return of the characteristic fluorescence of the HSA bound site-specific agent. These results illustrate the strong and specific binding sites of Gen X on HSA and demonstrate the principles for the potential application of β-CD for the remediation of PFAS from biological systems.

Weak multivalent biomolecular interactions: a strength versus numbers tug of war with implications for phase partitioning.

In this short Perspective, we discuss how recent dynamic live-cell imaging experiments have challenged our understanding of mechanisms driving functional molecular interactions in vivo. While we have generally considered the formation of functional biomolecular complexes as resulting from the stable assembly of two or more partner molecules, here we entertain the possibility that function may actually be maintained while molecules are rapidly exchanged within a complex. We postulate that at high effective concentrations, even very weak interactions can lead to strong binding site occupancy and thereby mediate function in a highly dynamic fashion. This new perspective in our definition of what represents a functional complex in living cells and in vivo could significantly alter how we define the nature of molecular transactions critical for mediating regulation in the cellular context. These less conventional principles also allow a broadening of the mechanistic options we should explore when interpreting essential biological processes such as gene regulation.

Spatially resolved sorption of Cm(III) on crystalline rock: influence of surface roughness and mineralogy

Abstract. Many countries will use deep geological repositories to dispose of highly active nuclear waste. Crystalline rock is a potential host rock because of its strong geotechnical stability, low permeability and low solubility; however, its inherent mineralogy is heterogeneous, consisting of a wide set of minerals in varying amounts. Therefore, there is a need for using sophisticated techniques that allow spatial resolution to characterize the nanostructure of such crystalline rock surfaces and the speciation of the actinides therein. As a representative for trivalent actinides, such as Am(III), Np(III), and Pu(III), which are expected to be present due to the reducing conditions encountered in a deep geological repository, we have chosen the actinide Cm(III). Cm(III) possesses excellent luminescence properties, which allows us to not only examine the sorption uptake but also the speciation of Cm(III) on the surface. We combined spatially resolved investigation techniques, such as vertical scanning interferometry, calibrated autoradiography, and Raman microscopy coupled to micro-focus time-resolved laser-induced luminescence spectroscopy (µTRLFS) (Molodtsov et al., 2019). Thus, we were able to correlate mineralogy, surface roughness, and grain boundary effects with radionuclide speciation, allowing us to identify important radionuclide retention processes and parameters (see Fig. 1). Investigations focused on granite from Eibenstock (Germany) and migmatised gneiss from Bukov (Czech Republic). Cm(III) sorption on the rock's constituting minerals – primarily feldspar, mica and quartz – was analyzed quantitatively and qualitatively. We observed that Cm(III) sorption uptake and speciation depends not only on the mineral phase but also the surface roughness (Demnitz et al., 2021). An increasing surface roughness leads to higher sorption uptake and a stronger coordination of the sorbed Cm(III). On the same mineral grains sorption differed significantly depending if an area exhibits a low or high surface roughness. In the case that one mineral phase dominates the sorption process, sorption of Cm(III) on other mineral phases will only occur at strong binding sites, typically where surface roughness is high. Areas of feldspar and quartz with high surface roughness additionally showed the formation of sorption species with particularly high sorption strength that could either be interpreted as Cm(III) incorporation species or ternary complexes on the mineral surface (Demnitz et al., 2021). We conclude that in addition to mineral composition, surface roughness needs to be adequately considered to describe interfacial speciation of contaminants and respective retention patterns for the safety assessments of nuclear waste repositories.

Dynamic Polymer Amphiphiles for Efficient Intracellular and In Vivo Protein Delivery.

Intracellular delivery of proteins is receiving considerable attention in biotherapeutics for various diseases by replacing dysfunctional proteins. Successful intracellular protein delivery highly relies on the development of efficient and safe polymeric carriers, which remains a grand challenge due to the lack of strong binding sites on proteins and their distinct molecular sizes and polarities. In this work, a strategy is proposed for efficient intracellular protein delivery by using dynamic polymer supra-amphiphiles, which are prepared by grafting boronated polylysine with a series of lipidated catechols via dynamic covalent catechol-boronate ester bonds. The prepared supra-amphiphiles can coassemble with proteins to form stable nanoparticles in water and also enable the release of bound proteins in cells due to their dynamic features, thereby strongly promoting the intracellular delivery process. The lead supra-amphiphiles screened in the library demonstrate high efficiency in the delivery of various proteins including bovine serum albumin, β-galactosidase, α-chymotrypsin, saporin, R-phycoerythrin, ovalbumin, catalase, and superoxide dismutase, and show great potency in delivering superoxide dismutase to treat ulcerative colitis in vivo. This work provides new opportunities for rational design and facile construction of robust intracellular protein delivery materials by the integration of polymer chemistry and supramolecular engineering strategies.

Breaking the trade-off between selectivity and adsorption capacity for gas separation

SummaryThe trade-off between selectivity and adsorption capacity with porous materials is a major roadblock to reducing the energy footprint of gas separation technologies. To address this matter, we report herein a systematic crystal engineering study of C2H2 removal from CO2 in a family of hybrid ultramicroporous materials (HUMs). The HUMs are composed of the same organic linker ligand, 4-(3,5-dimethyl-1H-pyrazol-4-yl)pyridine, pypz, three inorganic pillar ligands, and two metal cations, thereby affording six isostructural pcu topology HUMs. All six HUMs exhibited strong binding sites for C2H2 and weaker affinity for CO2. The tuning of pore size and chemistry enabled by crystal engineering resulted in benchmark C2H2/CO2 separation performance. Fixed-bed dynamic column breakthrough experiments for an equimolar (v/v = 1:1) C2H2/CO2 binary gas mixture revealed that one sorbent, SIFSIX-21-Ni, was the first C2H2 selective sorbent that combines exceptional separation selectivity (27.7) with high adsorption capacity (4 mmol·g−1).

The zinc finger protein CLAMP promotes long-range chromatin interactions that mediate dosage compensation of the Drosophila male X-chromosome

BackgroundDrosophila dosage compensation is an important model system for defining how active chromatin domains are formed. The male-specific lethal dosage compensation complex (MSLc) increases transcript levels of genes along the length of the single male X-chromosome to equalize with that expressed from the two female X-chromosomes. The strongest binding sites for MSLc cluster together in three-dimensional space largely independent of MSLc because clustering occurs in both sexes. CLAMP, a non-sex specific, ubiquitous zinc finger protein, binds synergistically with MSLc to enrich the occupancy of both factors on the male X-chromosome.ResultsHere, we demonstrate that CLAMP promotes the observed three-dimensional clustering of MSLc binding sites. Moreover, the X-enriched CLAMP protein more strongly promotes longer-range three-dimensional interactions on the X-chromosome than autosomes. Genome-wide, CLAMP promotes three-dimensional interactions between active chromatin regions together with other insulator proteins.ConclusionOverall, we define how long-range interactions which are modulated by a locally enriched ubiquitous transcription factor promote hyper-activation of the X-chromosome to mediate dosage compensation.

Adsorption and desorption behaviors of hydroxyurea drug on delivery systems of B12N12 fullerene and its Al-, Si- and P-dopings from theoretical perspective

The nano-based drug delivery system has become a promising strategy for improving the efficiency of therapy. In this work, the adsorption and desorption behaviours of hydroxyurea (HU) drug on the delivery system of B12N12 fullerene and its Al-, Si- and P-dopings were systematically investigated by density functional theory (DFT). We found the most stable configuration is HU drug adsorbed on B12N12 through the strong nucleophilic binding site (–C=O group). Then the doping effects on B12N12 were examined and found Al dopant dramatically improves the strength of drug-carrier interaction. The simulations in body condition show the proposed drug delivery systems of HU/B12N12 and HU/AlB11N12 can be stable in the aqueous phase but will separate in the acidic environment of tumours. We hope this comprehensive work can provide new insights for the potential application of B12N12 and its Al-doped derivative as vehicles of HU drug.

ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach

BackgroundChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still regions bound by proteins weakly, with a relatively low ChIP-seq signal enrichment. These weak binding sites, especially those at promoters and enhancers, are functionally important because they also regulate nearby gene expression. Yet, it remains a challenge to accurately identify weak binding sites in ChIP-seq data due to the ambiguity in differentiating these weak binding sites from the amplified background DNAs.ResultsChIP-BIT2 (http://sourceforge.net/projects/chipbitc/) is a software package for ChIP-seq peak detection. ChIP-BIT2 employs a mixture model integrating protein and control ChIP-seq data and predicts strong or weak protein binding sites at promoters, enhancers, or other genomic locations. For binding sites at gene promoters, ChIP-BIT2 simultaneously predicts their target genes. ChIP-BIT2 has been validated on benchmark regions and tested using large-scale ENCODE ChIP-seq data, demonstrating its high accuracy and wide applicability.ConclusionChIP-BIT2 is an efficient ChIP-seq peak caller. It provides a better lens to examine weak binding sites and can refine or extend the existing binding site collection, providing additional regulatory regions for decoding the mechanism of gene expression regulation.

Role of support in tuning the properties of single atom catalysts: Cu, Ag, Au, Ni, Pd, and Pt adsorption on SiO2/Ru, SiO2/Pt, and SiO2/Si ultrathin films.

The role of the support in tuning the properties of transition metal (TM) atoms is studied by means of density functional theory calculations. We have considered the adsorption of Cu, Ag, Au, Ni, Pd, and Pt atoms on crystalline silica bilayers, either free-standing or supported on Ru(0001) and Pt(111) metal surfaces. These systems have been compared with an hydroxylated SiO2/Si(100) film simulating the native oxide formed on a silicon wafer. The properties of the TM atoms change significantly on the various supports. While the unsupported silica bilayer weakly binds some of the TM atoms studied, the SiO2/Ru(0001) or SiO2/Pt(111) supports exhibit enhanced reactivity, sometimes resulting in a net electron transfer with the formation of charged species. Differences in the behavior of SiO2/Ru(0001) and SiO2/Pt(111) are rationalized in terms of different work functions and metal/oxide interfacial distances. No electron transfer is observed on the SiO2/Si(100) films. Here, the presence of hydroxyl groups on the surface provides relatively strong binding sites for the TM atoms that can be stabilized by the interaction with one or two OH groups. The final aspect that has been investigated is the porosity of the silica bilayer, at variance with the dense SiO2/Si(100) film. Depending on the atomic size, some TM atoms can penetrate spontaneously through the six-membered silica rings and become stabilized in the pores of the bilayer or at the SiO2/metal interface. This study shows how very different chemical properties can be obtained by depositing the same TM atom on different silica supports.

Fluoroarene Separations in Metal-Organic Frameworks with Two Proximal Mg2+ Coordination Sites.

Fluoroarenes are widely used in medicinal, agricultural, and materials chemistry, and yet their production remains a critical challenge in organic synthesis. Indeed, the nearly identical physical properties of these vital building blocks hinders their purification by traditional methods, such as flash chromatography or distillation. As a result, the Balz-Schiemann reaction is currently employed to prepare fluoroarenes instead of more atom-economical C-H fluorination reactions, which produce inseparable mixtures of regioisomers. Herein, we propose an alternative solution to this problem: the purification of mixtures of fluoroarenes using metal-organic frameworks (MOFs). Specifically, we demonstrate that controlling the interaction of fluoroarenes with adjacent coordinatively unsaturated Mg2+ centers within a MOF enables the separation of fluoroarene mixtures with unparalleled selectivities. Liquid-phase multicomponent equilibrium adsorption data and breakthrough measurements coupled with van der Waals-corrected density functional theory calculations reveal that the materials Mg2(dobdc) (dobdc4- = 2,5-dioxidobenzene-1,4-dicarboxylate) and Mg2(m-dobdc) (m-dobdc4- = 2,4-dioxidobenzene-1,5-dicarboxylate) are capable of separating the difluorobenzene isomers from one another. Additionally, these frameworks facilitate the separations of fluoroanisoles, fluorotoluenes, and fluorochlorobenzenes. In addition to enabling currently unfeasible separations for the production of fluoroarenes, our results suggest that carefully controlling the interaction of isomers with not one but two strong binding sites within a MOF provides a general strategy for achieving challenging liquid-phase separations.

A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections.

Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N2), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expression of viral sequences is expected to increasingly sequester RBPs - SRSF1 and RNPS1. Ordinarily, RBPs bound to nascent host transcripts prevents their annealing to complementary DNA. Their depletion induces destabilizing R-loops. Chromosomal breakage occurs when an excess of unresolved R-loops collide with incoming replication forks, overwhelming the DNA repair machinery. We estimated stoichiometry of inhibition of RBPs in host nuclear RNA by counting competing binding sites in replicating viral genomes and host RNA. Results: Host RBP binding sites are frequent and conserved among different strains of RNA viral genomes. Similar binding motifs of SRSF1 and RNPS1 explain why DNA damage resulting from SRSF1 depletion is complemented by expression of RNPS1. Clustering of strong RBP binding sites coincides with the distribution of RNA-DNA hybridization sites across the genome. SARS-CoV-2 replication is estimated to require 32.5-41.8 hours to effectively compete for binding of an equal proportion of SRSF1 binding sites in host encoded nuclear RNAs. Significant changes in expression of transcripts encoding DNA repair and apoptotic proteins were found in an analysis of influenza A and Dengue-infected cells in some individuals. Conclusions: R-loop-induced apoptosis indirectly resulting from viral replication could release significant quantities of membrane-associated virions into neighboring alveoli. These could infect adjacent pneumocytes and other tissues, rapidly compromising lung function, causing multiorgan system failure and other described symptoms.

New computational model for miRNA-mediated repression reveals novel regulatory roles of miRNA bindings inside the coding region.

MicroRNAs (miRNAs) are short (∼24nt), non-coding RNAs, which downregulate gene expression in many species and physiological processes. Many details regarding the mechanism which governs miRNA-mediated repression continue to elude researchers. We elucidate the interplay between the coding sequence and the 3'UTR, by using elastic net regularization and incorporating translation-related features to predict miRNA-mediated repression. We find that miRNA binding sites at the end of the coding sequence contribute to repression, and that weak binding sites are linked to effective de-repression, possibly as a result of competing with stronger binding sites. Furthermore, we propose a recycling model for miRNAs dissociated from the open reading frame (ORF) by traversing ribosomes, explaining the observed link between increased ribosome density/traversal speed and increased repression. We uncover a novel layer of interaction between the coding sequence and the 3'UTR (untranslated region) and suggest the ORF has a larger role than previously thought in the mechanism of miRNA-mediated repression. The code is freely available at https://github.com/aescrdni/miRNA_model. Supplementary data are available at Bioinformatics online.

A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections

Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N2), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expression of viral sequences is expected to increasingly sequester RBPs - SRSF1 and RNPS1. Ordinarily, RBPs bound to nascent host transcripts prevents their annealing to complementary DNA. Their depletion induces destabilizing R-loops. Chromosomal breakage occurs when an excess of unresolved R-loops collide with incoming replication forks, overwhelming the DNA repair machinery. We estimated stoichiometry of inhibition of RBPs in host nuclear RNA by counting competing binding sites in replicating viral genomes and host RNA. Results: Host RBP binding sites are frequent and conserved among different strains of RNA viral genomes. Similar binding motifs of SRSF1 and RNPS1 explain why DNA damage resulting from SRSF1 depletion is complemented by expression of RNPS1. Clustering of strong RBP binding sites coincides with the distribution of RNA-DNA hybridization sites across the genome. SARS-CoV-2 replication is estimated to require 32.5-41.8 hours to effectively compete for binding of an equal proportion of SRSF1 binding sites in host encoded nuclear RNAs. Significant changes in expression of transcripts encoding DNA repair and apoptotic proteins were found in an analysis of influenza A and Dengue-infected cells in some individuals. Conclusions: R-loop-induced apoptosis indirectly resulting from viral replication could release significant quantities of membrane-associated virions into neighboring alveoli. These could infect adjacent pneumocytes and other tissues, rapidly compromising lung function, causing multiorgan system failure and other described symptoms.

Crosstalk between vrille transcripts, proteins, and regulatory elements controlling circadian rhythms and development in Drosophila.

SummaryThe vrille (vri) gene encodes a transcriptional repressor required for Drosophila development as well as circadian behavior in adults. Alternate first exons produce vri transcripts predicted to produce a short VRI isoform during development and long VRI in adults. A vri mutant (vriΔ679) lacking long VRI transcripts is viable, confirming that short VRI is sufficient for developmental functions, yet behavioral rhythms in vriΔ679 flies persist, showing that short VRI is sufficient for clock output. E-box regulatory elements that drive rhythmic long VRI transcript expression are required for developmental expression of short VRI transcripts. Surprisingly, long VRI transcripts primarily produce short VRI in adults, apparently due to a poor Kozak sequence context, demonstrating that short VRI drives circadian behavior. Thus, E-box-driven long VRI transcripts primarily control circadian rhythms via short VRI, whereas the same E-boxes drive short VRI transcripts that control developmental functions using short VRI.

Developing understanding of the fate and behaviour of silver in fresh waters and waste waters

The Windermere Humic Aqueous Model (WHAM) is often used for risk assessment of metals; WHAM can be used to estimate the potential bioavailability of dissolved metals, where metals complexed to dissolved organic matter (DOM) are expected to be less toxic than ionic forms. Silver is a potential metal of concern but WHAM has not been rigorously tested against experimental measurements. This study compares WHAM predictions to measured ionic silver during fixed pH (4, 8 or 10) argentometric titrations of DOM from diverse origins. There were almost two orders of magnitude variation in free silver between sources but, within model uncertainty, WHAM captured this variability. This agreement, between measurements and models, suggests that WHAM is an appropriate tool for silver risk assessment in surface receiving waters when DOM is predominantly in the form of humic/fulvic acids. In sewage samples WHAM dramatically underestimated silver binding by approximately 3 orders of magnitude. Simulations with additional specific strong silver binding sulphide-like binding sites could explain Ag binding at low loadings, but not at higher loadings. This suggests the presence of additional intermediate strength binding sites. These additional ligands would represent components of the raw sewage largely absent in natural waters unimpacted by sewage effluents. A revised empirical model was proposed to account for these sewage-specific binding sites. Further, it is suspected that as sewage organic matter is degraded, either by natural attenuation or by engineered treatment, that sewage organic matter will degrade to a form more readily modelled by WHAM; i.e., humic-like substances. These ageing experiments were performed starting from raw sewage, and the material did in fact become more humic-like, but even after 30 days of aerobic incubation still showed greater Ag+ binding than WHAM predictions. In these incubation experiments it was found that silver (up to 1000 μg/L) had minimal impact on ammonia oxidation kinetics.

Power Law Behavior in Protein Desorption Kinetics Originating from Sequential Binding and Unbinding

The study of protein adsorption at the single molecule level has recently revealed that the adsorption is reversible, but with a long-tailed residence time distribution which can be approximated with a sum of exponential functions putatively related to distinct adsorption sites. Here it is proposed that the shape of the residence time distribution results from an adsorption process with sequential and reversible steps that contribute to overall binding strength resembling "zippering". In this model, the survival function of the residence time distribution of single proteins varies from an exponential distribution for a single adsorption step to a power law distribution with exponent -1/2 for a large number of adsorption steps. The adsorption of fluorescently labeled fibrinogen to glass surfaces is experimentally studied with single molecule imaging. The experimental residence time distribution can be readily fit by the proposed model. This demonstrates that the observed long residence times can arise from stepwise adsorption rather than rare but strong binding sites and provides guidance for the control of protein adsorption to biomaterials.

Rational Design of Aptamer-Tagged tRNAs.

Reprogramming of the genetic code system is limited by the difficulty in creating new tRNA structures. Here, I developed translationally active tRNA variants tagged with a small hairpin RNA aptamer, using Escherichia coli reporter assay systems. As the tRNA chassis for engineering, I employed amber suppressor variants of allo-tRNAs having the 9/3 composition of the 12-base pair amino-acid acceptor branch as well as a long variable arm (V-arm). Although their V-arm is a strong binding site for seryl-tRNA synthetase (SerRS), insertion of a bulge nucleotide in the V-arm stem region prevented allo-tRNA molecules from being charged by SerRS with serine. The SerRS-rejecting allo-tRNA chassis were engineered to have another amino-acid identity of either alanine, tyrosine, or histidine. The tip of the V-arms was replaced with diverse hairpin RNA aptamers, which were recognized by their cognate proteins expressed in E. coli. A high-affinity interaction led to the sequestration of allo-tRNA molecules, while a moderate-affinity aptamer moiety recruited histidyl-tRNA synthetase variants fused with the cognate protein domain. The new design principle for tRNA-aptamer fusions will enhance radical and dynamic manipulation of the genetic code.

Comparative study between adsorption and membrane technologies for the removal of mercury

Mercury is one of the most detrimental by-products of industrial activities, such as mining and fossil fuel combustion. What differentiates this contaminant from other pollutants is its bioaccumulation and rapid distribution in the food chain. This review paper provides a comprehensive comparison between two competing wastewater treatment technologies for the removal of mercury in aqueous systems. Adsorption and membrane separation technologies both yield high percentage removals and high selectivity distinguishing them from other treatment options. This review offers a critical summary of recent research works dedicated to developing unique adsorbents and membranes for the removal of mercury from wastewaters. The assessment of the two technologies is based on the removal performance, regeneration efficiency, selectivity and effect of experimental conditions. This work reveals that both techniques can be further enhanced by the addition of functional groups such as thiols where sulfur serves as a strong binding site for mercury ions. However, the main issues that normally entail adsorption and membrane separation are waste disposal and fouling respectively. Given that the adsorption process offers several benefits in comparison to membrane technologies including low capital and operating costs, ease of operation in addition to the potential application of a wide range of solid media for the removal of hazardous substances, the adsorption process is the feasible option.

Butterfly Structure: A Privileged Scaffold Targeting Tubulin-Colchicine Binding Site.

Butterfly-shaped structure, as a novel scaffold with an attractive and certain shape, has been widely used in new drug discovery. Tubulin, composing of α- and β-tubulin heterodimers, plays a key role in mitosis and cell division which are regarded as an excellent target for cancer therapy. Currently, a series of butterfly shape diaryl heterocyclic compounds have been reported with strong potential against the tubulin-colchicine binding site. It is with one ring buried in the β subunit, another ring interacts with the α subunit and the main body is located in the flat pocket. Here, we firstly introduce the concept of butterfly structure for the tubulin inhibitors, focusing on the latest advancements in a variety of molecules bearing butterfly structure, and then highlight the challenges and future direction of butterfly structure- based tubulin-colchicine binding site inhibitors.

A proposed molecular mechanism for pathogenesis of severe RNA-viral pulmonary infections.

Background: Certain riboviruses can cause severe pulmonary complications leading to death in some infected patients. We propose that DNA damage induced-apoptosis accelerates viral release, triggered by depletion of host RNA binding proteins (RBPs) from nuclear RNA bound to replicating viral sequences. Methods: Information theory-based analysis of interactions between RBPs and individual sequences in the Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2), Influenza A (H3N1), HIV-1, and Dengue genomes identifies strong RBP binding sites in these viral genomes. Replication and expression of viral sequences is expected to increasingly sequester RBPs - SRSF1 and RNPS1. Ordinarily, RBPs bound to nascent host transcripts prevents their annealing to complementary DNA. Their depletion induces destabilizing R-loops. Chromosomal breakage occurs when an excess of unresolved R-loops collide with incoming replication forks, overwhelming the DNA repair machinery. We estimated stoichiometry of inhibition of RBPs in host nuclear RNA by counting competing binding sites in replicating viral genomes and host RNA. Results: Host RBP binding sites are frequent and conserved among different strains of RNA viral genomes. Similar binding motifs of SRSF1 and RNPS1 explain why DNA damage resulting from SRSF1 depletion is complemented by expression of RNPS1. Clustering of strong RBP binding sites coincides with the distribution of RNA-DNA hybridization sites across the genome. SARS-CoV-2 replication is estimated to require 32.5-41.8 hours to effectively compete for binding of an equal proportion of SRSF1 binding sites in host encoded nuclear RNAs. Significant changes in expression of transcripts encoding DNA repair and apoptotic proteins were found in an analysis of influenza A and Dengue-infected cells in some individuals. Conclusions: R-loop-induced apoptosis indirectly resulting from viral replication could release significant quantities of membrane-associated virions into neighboring alveoli. These could infect adjacent pneumocytes and other tissues, rapidly compromising lung function, causing multiorgan system failure and other described symptoms.