Industrial scale high-throughput screening delivers multiple fast acting macrofilaricides

High-efficiency removal of As(iii) from groundwater using siderite as the iron source in the electrocoagulation process

Electrocoagulation technology, due to its simplicity and ease of operation, is often considered for treating arsenic-contaminated groundwater. However, challenges such as anode wear have hindered its development and application. This study aims to develop a siderite-filled anode electrocoagulation system for efficient removal of As(iii) and investigate its effectiveness. The impact of operational parameters on the removal rate of As(iii) was analyzed through single-factor tests, and the stability and superiority of the device were evaluated. The response surface methodology was employed to analyze the interactions between various factors and determine the optimal operational parameters by integrating data from these tests. Under conditions where the removal rate of As reached 99.3 ± 0.37%, with an initial concentration of As(iii) at 400 μg L-1, current intensity at 30 mA, initial solution pH value at 7, and Na2SO4 concentration at 10 mM. The flocculant used was subjected to characterization analysis to examine its structure, morphology, and elemental composition under these optimal operational parameters. The oxidation pathway for As(iii) within this system relies on integrated results from direct electrolysis as well as ˙O2 -, ˙OH, and Fe(iv) mediated oxidation processes. The elimination of arsenic encompasses two fundamental mechanisms: firstly, the direct adsorption of As(iii) by highly adsorbent flocculants like γ-FeOOH and magnetite (Fe3O4); secondly, the oxidation of As(iii) into As(v), followed by its reaction with siderite or other compounds to generate a dual coordination complex or iron arsenate, thus expediting its eradication. The anodic electrocoagulation system employing siderite as a filler exhibits remarkable efficiency and cost-effectiveness, while ensuring exceptional stability, thereby providing robust theoretical underpinnings for the application of electrocoagulation technology in arsenic removal.

Dual RNA-seq in filarial nematodes and Wolbachia endosymbionts using RNase H based ribosomal RNA depletion

Lymphatic filariasis is caused by parasitic nematodes and is a leading cause of disability worldwide. Many filarial worms contain the bacterium Wolbachia as an obligate endosymbiont. RNA sequencing is a common technique used to study their molecular relationships and to identify potential drug targets against the nematode and bacteria. Ribosomal RNA (rRNA) is the most abundant RNA species, accounting for 80-90% of the RNA in a sample. To reduce sequencing costs, it is necessary to remove ribosomal reads through poly-A enrichment or ribosomal depletion. Bacterial RNA does not contain a poly-A tail, making it difficult to sequence both the nematode and Wolbachia from the same library preparation using standard poly-A selection. Ribosomal depletion can utilize species-specific oligonucleotide probes to remove rRNA through pull-down or degradation methods. While species-specific probes are commercially available for many commonly studied model organisms, there are currently limited depletion options for filarial parasites. Here, we performed total RNA sequencing from Brugia malayi containing the Wolbachia symbiont (wBm) and designed ssDNA depletion probes against their rRNA sequences. We compared the total RNA library to poly-A enriched, Terminator 5'-Phosphate-Dependent Exonuclease treated, NEBNext Human/Bacteria rRNA depleted and our custom nematode probe depleted libraries. The custom nematode depletion library had the lowest percentage of ribosomal reads across all methods, with a 300-fold decrease in rRNA when compared to the total RNA library. The nematode depletion libraries also contained the highest percentage of Wolbachia mRNA reads, resulting in a 16-1,000-fold increase in bacterial reads compared to the other enrichment and depletion methods. Finally, we found that the Brugia malayi depletion probes can remove rRNA from the filarial worm Dirofilaria immitis and the majority of rRNA from the more distantly related free living nematode Caenorhabditis elegans. These custom filarial probes will allow for future dual RNA-seq experiments between nematodes and their bacterial symbionts from a single sequencing library.

One-pot reaction for the preparation of diatom hemostatic particles with effective hemostasis and economic benefits

Effective hemostatic materials have been in demand for rapid pre-hospital hemostasis in emergency situations, which can significantly reduce accidental deaths. The development of emergency hemostatic materials with rapid hemostasis, biosafety, and economical preparation is a great challenge. In this study, Ca(OH)2-complexed diatom powder hemostatic particles (Ca(OH)2-Php) were prepared based on a one-pot reaction by directly mixing various raw materials and by rotary granulation. High-temperature calcination was able to carbonate and consume the organic matter in the hemostatic particles. The crosslinked hydrogen bonds in those particles were converted to silica-oxygen bonds, the particles became more stable, and the porous structure of diatom biosilica (DBs) was exposed. Ca(OH)2-Php has high porosity, can quickly adsorb the water in blood (water absorption: 75.85 ± 6.93%), and exhibits rapid hemostasis capacity (clotting time was shortened by 43% compared with that of the control group), good biocompatibility (hemolysis rate <7%, no cytotoxicity), and simplicity of handling (conveniently debride, no residues, no tissue inflammation). This study provides a new idea for the preparation of emergency hemostatic materials, and Ca(OH)2-Php prepared by one-pot reaction has various high-quality characteristics including rapid hemostasis, wide applicability, economical preparation, and potential for large-scale production.

Single-cell transcriptomics is revolutionizing the improvement of plant biotechnology research: recent advances and future opportunities

Single-cell approaches are a promising way to obtain high-resolution transcriptomics data and have the potential to revolutionize the study of plant growth and development. Recent years have seen the advent of unprecedented technological advances in the field of plant biology to study the transcriptional information of individual cells by single-cell RNA sequencing (scRNA-seq). This review focuses on the modern advancements of single-cell transcriptomics in plants over the past few years. In addition, it also offers a new insight of how these emerging methods will expedite advance research in plant biotechnology in the near future. Lastly, the various technological hurdles and inherent limitations of single-cell technology that need to be conquered to develop such outstanding possible knowledge gain is critically analyzed and discussed.

Improved metagenome assemblies through selective enrichment of bacterial genomic DNA from eukaryotic host genomic DNA using ATAC-seq

Genomics can be used to study the complex relationships between hosts and their microbiota. Many bacteria cannot be cultured in the laboratory, making it difficult to obtain adequate amounts of bacterial DNA and to limit host DNA contamination for the construction of metagenome-assembled genomes (MAGs). For example, Wolbachia is a genus of exclusively obligate intracellular bacteria that live in a wide range of arthropods and some nematodes. While Wolbachia endosymbionts are frequently described as facultative reproductive parasites in arthropods, the bacteria are obligate mutualistic endosymbionts of filarial worms. Here, we achieve 50-fold enrichment of bacterial sequences using ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) with Brugia malayi nematodes, containing Wolbachia (wBm). ATAC-seq uses the Tn5 transposase to cut and attach Illumina sequencing adapters to accessible DNA lacking histones, typically thought to be open chromatin. Bacterial and mitochondrial DNA in the lysates are also cut preferentially since they lack histones, leading to the enrichment of these sequences. The benefits of this include minimal tissue input (<1 mg of tissue), a quick protocol (<4 h), low sequencing costs, less bias, correct assembly of lateral gene transfers and no prior sequence knowledge required. We assembled the wBm genome with as few as 1 million Illumina short paired-end reads with >97% coverage of the published genome, compared to only 12% coverage with the standard gDNA libraries. We found significant bacterial sequence enrichment that facilitated genome assembly in previously published ATAC-seq data sets from human cells infected with Mycobacterium tuberculosis and C. elegans contaminated with their food source, the OP50 strain of E. coli. These results demonstrate the feasibility and benefits of using ATAC-seq to easily obtain bacterial genomes to aid in symbiosis, infectious disease, and microbiome research.

Entropy-Driven Enhancement of the Conductivity and Phase Purity of Na4Fe3(PO4)2P2O7 as the Superior Cathode in Sodium-Ion Batteries

Na4Fe3(PO4)2(P2O7) (NFPP) is regarded as a promising cathode material for sodium-ion batteries (SIBs) owing to its low cost, easy manufacture, environmental purity, high structural stability, unique three-dimensional Na-ion diffusion channels, and appropriate working voltage. However, for NFPP, the low conductivity of electrons and ions limits their capacity and power density. The generation of NaFeP2O7 and NaFePO4 inhibits the diffusion of sodium ions and reduces reversible capacity and rate performance during the manufacturing process in synthesis methods. Herein, we report an entropy-driven approach to enhance the electronic conductivity and, concurrently, phase purity of NFPP as the superior cathode in sodium-ion batteries. This approach was realized via Ti ions substituting different ratios of Fe-occupied sites in the NFPP lattice (denoted as NTFPP-X, T is the Ti in the lattice, X is the ratio of Ti-substitution) with the configurational entropic increment of the lattice structures from 0.68 R to 0.79 R. Specifically, 5% Ti-substituted lattice (NTFPP-0.05) inducing entropic augmentation not only improves the electronic conductivity from 7.1 × 10-2 S/m to 8.6 × 10-2 S/m but also generates the pure-phase of NFPP (suppressing the impure phases of the NaFeP2O7 and NaFePO4) of the lattice structure, which is validated by a series of characterizations, including powder X-ray diffraction (XRD), Fourier transform infrared spectra (FT-IR), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT). Benefiting from the Ti replacement in the lattice, the optimal NTFPP-0.05 composite shows a high first discharge capacity (118.5 mAh g-1 at 0.1 C), superior rate performance (70.5 mAh g-1 at 10 C), and excellent long cycling life (1200 cycles at 10 C with capacity retention of 86.9%). This research proposes a new entropy-driven approach to improve the electrochemical performance of NFPP and reports a low-cost, ultrastable, and high-rate cathode material of NTFPP-0.05 for SIBs.

Combinations of the azaquinazoline anti-Wolbachia agent, AWZ1066S, with benzimidazole anthelmintics synergise to mediate sub-seven-day sterilising and curative efficacies in experimental models of filariasis

Lymphatic filariasis and onchocerciasis are two major neglected tropical diseases that are responsible for causing severe disability in 50 million people worldwide, whilst veterinary filariasis (heartworm) is a potentially lethal parasitic infection of companion animals. There is an urgent need for safe, short-course curative (macrofilaricidal) drugs to eliminate these debilitating parasite infections. We investigated combination treatments of the novel anti-Wolbachia azaquinazoline small molecule, AWZ1066S, with benzimidazole drugs (albendazole or oxfendazole) in up to four different rodent filariasis infection models: Brugia malayi-CB.17 SCID mice, B. malayi-Mongolian gerbils, B. pahangi-Mongolian gerbils, and Litomosoides sigmodontis-Mongolian gerbils. Combination treatments synergised to elicit threshold (>90%) Wolbachia depletion from female worms in 5 days of treatment, using 2-fold lower dose-exposures of AWZ1066S than monotherapy. Short-course lowered dose AWZ1066S-albendazole combination treatments also delivered partial adulticidal activities and/or long-lasting inhibition of embryogenesis, resulting in complete transmission blockade in B. pahangi and L. sigmodontis gerbil models. We determined that short-course AWZ1066S-albendazole co-treatment significantly augmented the depletion of Wolbachia populations within both germline and hypodermal tissues of B. malayi female worms and in hypodermal tissues in male worms, indicating that anti-Wolbachia synergy is not limited to targeting female embryonic tissues. Our data provides pre-clinical proof-of-concept that sub-seven-day combinations of rapid-acting novel anti-Wolbachia agents with benzimidazole anthelmintics are a promising curative and transmission-blocking drug treatment strategy for filarial diseases of medical and veterinary importance.

Tranexamic acid (class I drug) reduced and capped gold nanoparticles as a potential hemostatic agent with enhanced performance

External hemostatic agents play a crucial role in stabilizing an impaired process during pathological conditions. The idea is to stabilize thein vivosystem as soon as possible. This study uses a class I hemostatic drug tranexamic acid as a reducing and capping agent for synthesizing the gold nanoparticles (Tr-AuNPs). Being the synthetic analogue of lysine and a biologically inspired alkylamine molecule, the chemistry can be fine-tuned for stable material that can simultaneously target the intrinsic and extrinsic hemostatic pathway, making it promising for hemostatic applications. The Tr-AuNPs of hydrodynamic diameter ∼46 nm were synthesized and evaluated physio-chemically using various analytical techniques wherein they showed hemocompatibility and increased thrombus weight compared to the native drug. The decrease in prothrombin time (PT) and international normalized ratio supported by the dynamic thromboelastography (TEG) study indicates the prepared nano-conjugate's potential in reducing time for attaining hemostasis as compared to the native tranexamic acid drug. At a 9μg ml-1concentration, Tr-AuNPs had a procoagulant effect, shown by decreased reaction time (R) and coagulation time (K) with improvedαangle and MA. There was a significant increase in the rate of coagulationin vivoby Tr-AuNPs, i.e. (52 s) compared to the native tranexamic acid (360 s). Radiolabelling studies ascertained thein vivobiocompatibility (non-invasive distribution, residence, clearance, and stability) of the Tr-AuNPs. The short-term toxicity studies were conducted to establish a proof of concept for the biomedical application of the material. The results highlighted the use of biologically alkyl amine molecules as capping and reducing agents for the synthesis of nanoparticles, which have shown a synergistic effect on the coagulation cascade while holding the potential for also acting as potential theranostic agents.

The cellular lives of Wolbachia

Wolbachia are successful Gram-negative bacterial endosymbionts, globally infecting a large fraction of arthropod species and filarial nematodes. Efficient vertical transmission, the capacity for horizontal transmission, manipulation of host reproduction and enhancement of host fitness can promote the spread both within and between species. Wolbachia are abundant and can occupy extraordinary diverse and evolutionary distant host species, suggesting that they have evolved to engage and manipulate highly conserved core cellular processes. Here, we review recent studies identifying Wolbachia-host interactions at the molecular and cellular levels. We explore how Wolbachia interact with a wide array of host cytoplasmic and nuclear components in order to thrive in a diversity of cell types and cellular environments. This endosymbiont has also evolved the ability to precisely target and manipulate specific phases of the host cell cycle. The remarkable diversity of cellular interactions distinguishes Wolbachia from other endosymbionts and is largely responsible for facilitating its global propagation through host populations. Finally, we describe how insights into Wolbachia-host cellular interactions have led to promising applications in controlling insect-borne and filarial nematode-based diseases.

Improved Electrocatalytic Activity and Stability by Single Iridium Atoms on Iron-based Layered Double Hydroxides for Oxygen Evolution

Full understanding to the origin of the catalytic performance of a supported nanocatalyst from the points of view of both the active component and support is significant for the achievement of high performance. Herein, based on a model electrocatalyst of single-iridium-atom-doped iron (Fe)-based layered double hydroxides (LDH) for oxygen evolution reaction (OER), we reveal the first completed origin of the catalytic performance of such supported nanocatalysts. Specially, besides the activity enhancement of Ir sites by LDH support, the stability of surface Fe sites is enhanced by doped Ir sites: DFT calculation shows that the Ir sites can reduce the activity and enhance the stability of the nearby Fe sites; while further finite element simulations indicate, the stability enhancement of distant Fe sites could be attributed to the much low concentration of OER reactant (hydroxyl ions, OH- ) around them induced by the much fast consumption of OH- on highly active Ir sites. These new findings about the interaction between the main active components and supports are applicable in principle to other heterogeneous nanocatalysts and provide a completed understanding to the catalytic performance of heterogeneous nanocatalysts.

RECOVER identifies synergistic drug combinations in vitro through sequential model optimization

For large libraries of small molecules, exhaustive combinatorial chemical screens become infeasible to perform when considering a range of disease models, assay conditions, and dose ranges. Deep learning models have achieved state-of-the-art results in silico for the prediction of synergy scores. However, databases of drug combinations are biased toward synergistic agents and results do not generalize out of distribution. During 5 rounds of experimentation, we employ sequential model optimization with a deep learning model to select drug combinations increasingly enriched for synergism and active against a cancer cell line-evaluating only ∼5% of the total search space. Moreover, we find that learned drug embeddings (using structural information) begin to reflect biological mechanisms. In silico benchmarking suggests search queries are ∼5-10× enriched for highly synergistic drug combinations by using sequential rounds of evaluation when compared with random selection or ∼3× when using a pretrained model.

The Proteome and Lipidome of Extracellular Vesicles from Haemonchus contortus to Underpin Explorations of Host-Parasite Cross-Talk

Many parasitic worms have a major adverse impact on human and animal populations worldwide due to the chronicity of their infections. There is a growing body of evidence indicating that extracellular vesicles (EVs) are intimately involved in modulating (suppressing) inflammatory/immune host responses and parasitism. As one of the most pathogenic nematodes of livestock animals, Haemonchus contortus is an ideal model system for EV exploration. Here, employing a multi-step enrichment process (in vitro culture, followed by ultracentrifugation, size exclusion and filtration), we enriched EVs from H. contortus and undertook the first comprehensive (qualitative and quantitative) multi-omic investigation of EV proteins and lipids using advanced liquid chromatography-mass spectrometry and informatics methods. We identified and quantified 561 proteins and 446 lipids in EVs and compared these molecules with those of adult worms. We identified unique molecules in EVs, such as proteins linked to lipid transportation and lipid species (i.e., sphingolipids) associated with signalling, indicating the involvement of these molecules in parasite-host cross-talk. This work provides a solid starting point to explore the functional roles of EV-specific proteins and lipids in modulating parasite-host cross-talk, and the prospect of finding ways of disrupting or interrupting this relationship to suppress or eliminate parasite infection.

Dirofilariasis mouse models for heartworm preclinical research

Introduction

Dirofilariasis, including heartworm disease, is a major emergent veterinary parasitic infection and a human zoonosis. Currently, experimental infections of cats and dogs are used in veterinary heartworm preclinical drug research.

Methods

As a refined alternative in vivo heartworm preventative drug screen, we assessed lymphopenic mouse strains with ablation of the interleukin-2/7 common gamma chain (γc) as susceptible to the larval development phase of Dirofilaria immitis.

Results

Non-obese diabetic (NOD) severe combined immunodeficiency (SCID)γc^-/- (NSG and NXG) and recombination-activating gene (RAG)2^-/-γc^-/- mouse strains yielded viable D. immitis larvae at 2-4 weeks post-infection, including the use of different batches of D. immitis infectious larvae, different D. immitis isolates, and at different laboratories. Mice did not display any clinical signs associated with infection for up to 4 weeks. Developing larvae were found in subcutaneous and muscle fascia tissues, which is the natural site of this stage of heartworm in dogs. Compared with in vitro-propagated larvae at day 14, in vivo-derived larvae had completed the L4 molt, were significantly larger, and contained expanded Wolbachia endobacteria titres. We established an ex vivo L4 paralytic screening system whereby assays with moxidectin or levamisole highlighted discrepancies in relative drug sensitivities in comparison with in vitro-reared L4 D. immitis. We demonstrated effective depletion of Wolbachia by 70%-90% in D. immitis L4 following 2- to 7-day oral in vivo exposures of NSG- or NXG-infected mice with doxycycline or the rapid-acting investigational drug, AWZ1066S. We validated NSG and NXG D. immitis mouse models as a filaricide screen by in vivo treatments with single injections of moxidectin, which mediated a 60%-88% reduction in L4 larvae at 14-28 days.

Discussion

Future adoption of these mouse models will benefit end-user laboratories conducting research and development of novel heartworm preventatives via increased access, rapid turnaround, and reduced costs and may simultaneously decrease the need for experimental cat or dog use.

Active therapy based on the byproducts of micro/nanomotors

Different from traditional colloidal particles based on Brownian motion, micro/nanomotors are micro/nanoscale devices capable of performing complex tasks in liquid media via transforming various energy sources into mechanical motion or actuation. Such unique self-propulsion endows motors with fantastic capabilities to access and enter the deep layer of targeted diseased tissue, which in turn breaks through the limitation of the poor permeability of traditional pharmaceutical preparations, thus providing giant prospects for active therapy. It is noteworthy that recently several studies, which utilized the byproducts generated in situ by micro/nanomotors to achieve active therapy, in a truly green zero-waste manner, have been carried out. In this minireview, we highlight the recent efforts with respect to active therapy based on the byproducts of micro/nanomotors, expecting to motivate readers to expand the practical biomedical application scope of micro/nanomotors in a broader horizon. Accompanied by ever booming enthusiasm and persevering exploration, micro/nanomotors are on their way to revolutionize conventional fields.

Multivariate chemogenomic screening prioritizes new macrofilaricidal leads

Development of direct acting macrofilaricides for the treatment of human filariases is hampered by limitations in screening throughput imposed by the parasite life cycle. In vitro adult screens typically assess single phenotypes without prior enrichment for chemicals with antifilarial potential. We developed a multivariate screen that identified dozens of compounds with submicromolar macrofilaricidal activity, achieving a hit rate of >50% by leveraging abundantly accessible microfilariae. Adult assays were multiplexed to thoroughly characterize compound activity across relevant parasite fitness traits, including neuromuscular control, fecundity, metabolism, and viability. Seventeen compounds from a diverse chemogenomic library elicited strong effects on at least one adult trait, with differential potency against microfilariae and adults. Our screen identified five compounds with high potency against adults but low potency or slow-acting microfilaricidal effects, at least one of which acts through a novel mechanism. We show that the use of microfilariae in a primary screen outperforms model nematode developmental assays and virtual screening of protein structures inferred with deep learning. These data provide new leads for drug development, and the high-content and multiplex assays set a new foundation for antifilarial discovery.

Magnet for the Needle in Haystack: "Crystal Structure First" Fragment Hits Unlock Active Chemical Matter Using Targeted Exploration of Vast Chemical Spaces

Fragment-based drug discovery (FBDD) has successfully led to approved therapeutics for challenging and "undruggable" targets. In the context of FBDD, we introduce a novel, multidisciplinary method to identify active molecules from purchasable chemical space. Starting from four small-molecule fragment complexes of protein kinase A (PKA), a template-based docking screen using Enamine's multibillion REAL Space was performed. A total of 93 molecules out of 106 selected compounds were successfully synthesized. Forty compounds were active in at least one validation assay with the most active follow-up having a 13,500-fold gain in affinity. Crystal structures for six of the most promising binders were rapidly obtained, verifying the binding mode. The overall success rate for this novel fragment-to-hit approach was 40%, accomplished in only 9 weeks. The results challenge the established fragment prescreening paradigm since the standard industrial filters for fragment hit identification in a thermal shift assay would have missed the initial fragments.

Current advances of Pichia pastoris as cell factories for production of recombinant proteins

Pichia pastoris (syn. Komagataella spp.) has attracted extensive attention as an efficient platform for recombinant protein (RP) production. For obtaining a higher protein titer, many researchers have put lots of effort into different areas and made some progress. Here, we summarized the most recent advances of the last 5 years to get a better understanding of its future direction of development. The appearance of innovative genetic tools and methodologies like the CRISPR/Cas9 gene-editing system eases the manipulation of gene expression systems and greatly improves the efficiency of exploring gene functions. The integration of novel pathways in microorganisms has raised more ideas of metabolic engineering for enhancing RP production. In addition, some new opportunities for the manufacture of proteins have been created by the application of novel mathematical models coupled with high-throughput screening to have a better overview of bottlenecks in the biosynthetic process.

Thermal proteome profiling reveals Haemonchus orphan protein HCO_011565 as a target of the nematocidal small molecule UMW-868

Parasitic roundworms (nematodes) cause destructive diseases, and immense suffering in humans and other animals around the world. The control of these parasites relies heavily on anthelmintic therapy, but treatment failures and resistance to these drugs are widespread. As efforts to develop vaccines against parasitic nematodes have been largely unsuccessful, there is an increased focus on discovering new anthelmintic entities to combat drug resistant worms. Here, we employed thermal proteome profiling (TPP) to explore hit pharmacology and to support optimisation of a hit compound (UMW-868), identified in a high-throughput whole-worm, phenotypic screen. Using advanced structural prediction and docking tools, we inferred an entirely novel, parasite-specific target (HCO_011565) of this anthelmintic small molecule in the highly pathogenic, blood-feeding barber’s pole worm, and in other socioeconomically important parasitic nematodes. The “hit-to-target” workflow constructed here provides a unique prospect of accelerating the simultaneous discovery of novel anthelmintics and associated parasite-specific targets.

iRaPCA and SOMoC: Development and Validation of Web Applications for New Approaches for the Clustering of Small Molecules

The clustering of small molecules implies the organization of a group of chemical structures into smaller subgroups with similar features. Clustering has important applications to sample chemical datasets or libraries in a representative manner (e.g., to choose, from a virtual screening hit list, a chemically diverse subset of compounds to be submitted to experimental confirmation, or to split datasets into representative training and validation sets when implementing machine learning models). Most strategies for clustering molecules are based on molecular fingerprints and hierarchical clustering algorithms. Here, two open-source in-house methodologies for clustering of small molecules are presented: iterative Random subspace Principal Component Analysis clustering (iRaPCA), an iterative approach based on feature bagging, dimensionality reduction, and K-means optimization; and Silhouette Optimized Molecular Clustering (SOMoC), which combines molecular fingerprints with the Uniform Manifold Approximation and Projection (UMAP) and Gaussian Mixture Model algorithm (GMM). In a benchmarking exercise, the performance of both clustering methods has been examined across 29 datasets containing between 100 and 5000 small molecules, comparing these results with those given by two other well-known clustering methods, Ward and Butina. iRaPCA and SOMoC consistently showed the best performance across these 29 datasets, both in terms of within-cluster and between-cluster distances. Both iRaPCA and SOMoC have been implemented as free Web Apps and standalone applications, to allow their use to a wide audience within the scientific community.

Probiotics synergized with conventional regimen in managing Parkinson's disease

Parkinson's disease (PD) is mainly managed by pharmacological therapy (e.g., Benserazide and dopamine agonists). However, prolonged use of these drugs would gradually diminish their dopaminergic effect. Gut dysbiosis was observed in some patients with PD, suggesting close association between the gut microbiome and PD. Probiotics modulate the host's gut microbiota beneficially. A 3-month randomized, double-blind, placebo-controlled clinical trial was conducted to investigate the beneficial effect of probiotic co-administration in patients with PD. Eighty-two PD patients were recruited and randomly divided into probiotic [n = 48; Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8), Benserazide, dopamine agonists] and placebo (n = 34; placebo, Benserazide, dopamine agonists) groups. Finally, 45 and 29 patients from Probio-M8 and placebo groups provided complete fecal and serum samples for further omics analysis, respectively. The results showed that Probio-M8 co-administration conferred added benefits by improving sleep quality, alleviating anxiety, and gastrointestinal symptoms. Metagenomic analysis showed that, after the intervention, there were significantly more species-level genome bins (SGBs) of Bifidobacterium animalis, Ruminococcaceae, and Lachnospira, while less Lactobacillus fermentum and Klebsiella oxytoca in Probio-M8 group (P < 0.05). Interestingly, Lactobacillus fermentum correlated positively with the scores of UPDRS-III, HAMA, HAMD-17, and negatively with MMSE. Klebsiella oxytoca correlated negatively with feces hardness. Moreover, co-administering Probio-M8 increased SGBs involved in tryptophan degradation, gamma-aminobutyric acid, short-chain fatty acids, and secondary bile acid biosynthesis, as well as serum acetic acid and dopamine levels (P < 0.05). Taken together, Probio-M8 synergized with the conventional regimen and strengthened the clinical efficacy in managing PD, accompanied by modifications of the host's gut microbiome, gut microbial metabolic potential, and serum metabolites.

Current perspective of new anti-Wolbachial and direct-acting macrofilaricidal drugs as treatment strategies for human filariasis

Filarial diseases like lymphatic filariasis and onchocerciasis belong to the Neglected Tropical Diseases and remain a public health problem in endemic countries. Lymphatic filariasis and onchocerciasis can lead to stigmatizing pathologies and present a socio-economic burden for affected people and their endemic countries. Current treatment recommendations by the WHO include mass drug administration with ivermectin for the treatment of onchocerciasis and a combination of ivermectin, albendazole and diethylcarbamazine (DEC) for the treatment of lymphatic filariasis in areas that are not co-endemic for onchocerciasis or loiasis. Limitations of these treatment strategies are due to potential severe adverse events in onchocerciasis and loiasis patients following DEC or ivermectin treatment, respectively, the lack of a macrofilaricidal efficacy of those drugs and the risk of drug resistance development. Thus, to achieve the elimination of transmission of onchocerciasis and the elimination of lymphatic filariasis as a public health problem by 2030, the WHO defined in its roadmap that new alternative treatment strategies with macrofilaricidal compounds are required. Within a collaboration of the non-profit organizations Drugs for Neglected Diseases initiative (DNDi), the Bill & Melinda Gates Foundation, and partners from academia and industry, several new promising macrofilaricidal drug candidates were identified, which will be discussed in this review.

Whole-organism phenotypic screening methods used in early-phase anthelmintic drug discovery

Diseases caused by parasitic helminths (worms) represent a major global health burden in both humans and animals. As vaccines against helminths have yet to achieve a prominent role in worm control, anthelmintics are the primary tool to limit production losses and disease due to helminth infections in both human and veterinary medicine. However, the excessive and often uncontrolled use of these drugs has led to widespread anthelmintic resistance in these worms - particularly of animals - to almost all commercially available anthelmintics, severely compromising control. Thus, there is a major demand for the discovery and development of new classes of anthelmintics. A key component of the discovery process is screening libraries of compounds for anthelmintic activity. Given the need for, and major interest by the pharmaceutical industry in, novel anthelmintics, we considered it both timely and appropriate to re-examine screening methods used for anthelmintic discovery. Thus, we reviewed current literature (1977-2021) on whole-worm phenotypic screening assays developed and used in academic laboratories, with a particular focus on those employed to discover nematocides. This review reveals that at least 50 distinct phenotypic assays with low-, medium- or high-throughput capacity were developed over this period, with more recently developed methods being quantitative, semi-automated and higher throughput. The main features assessed or measured in these assays include worm motility, growth/development, morphological changes, viability/lethality, pharyngeal pumping, egg hatching, larval migration, CO₂- or ATP-production and/or enzyme activity. Recent progress in assay development has led to the routine application of practical, cost-effective, medium- to high-throughput whole-worm screening assays in academic or public-private partnership (PPP) contexts, and major potential for novel high-content, high-throughput platforms in the near future. Complementing this progress are major advances in the molecular data sciences, computational biology and informatics, which are likely to further enable and accelerate anthelmintic drug discovery and development.

Anti-Wolbachia drugs for filariasis

The mutualistic association between Wolbachia endosymbionts and their filarial nematode hosts has been exploited as a validated drug target delivering macrofilaricidal outcomes. Limitations of existing antibiotics to scale-up have driven the search for new drugs, which are effective in shorter regimens of 7 days or less. Here, we review the last 14 years of anti-Wolbachia drug discovery by the anti-Wolbachia (A·WOL) consortium, which has screened more than two million compounds, delivering thousands of hit compounds. Refined screening models integrated with robust pharmacokinetic/pharmacodynamic (PK/PD) driven optimisation and selection strategies have delivered the first two drug candidates specifically designed to target Wolbachia. AWZ1066S and ABBV-4083 are currently progressing through clinical trials with the aim of delivering safe and effective macrofilaricides to support the elimination of onchocerciasis and lymphatic filariasis.

Human filariasis-contributions of the Litomosoides sigmodontis and Acanthocheilonema viteae animal model

Filariae are vector-borne parasitic nematodes that are endemic worldwide, in tropical and subtropical regions. Important human filariae spp. include Onchocerca volvulus, Wuchereria bancrofti and Brugia spp., and Loa loa and Mansonella spp. causing onchocerciasis (river blindness), lymphatic filariasis (lymphedema and hydrocele), loiasis (eye worm), and mansonelliasis, respectively. It is estimated that over 1 billion individuals live in endemic regions where filarial diseases are a public health concern contributing to significant disability adjusted life years (DALYs). Thus, efforts to control and eliminate filarial diseases were already launched by the WHO in the 1970s, especially against lymphatic filariasis and onchocerciasis, and are mainly based on mass drug administration (MDA) of microfilaricidal drugs (ivermectin, diethylcarbamazine, albendazole) to filarial endemic areas accompanied with vector control strategies with the goal to reduce the transmission. With the United Nations Sustainable Development Goals (SDGs), it was decided to eliminate transmission of onchocerciasis and stop lymphatic filariasis as a public health problem by 2030. It was also requested that novel drugs and treatment strategies be developed. Mouse models provide an important platform for anti-filarial drug research in a preclinical setting. This review presents an overview about the Litomosoides sigmodontis and Acanthocheilonema viteae filarial mouse models and their role in immunological research as well as preclinical studies about novel anti-filarial drugs and treatment strategies.

CO2 Footprint of Thermal Versus Photothermal CO2 Catalysis

Transformation of CO₂ into value-added products via photothermal catalysis has become an increasingly popular route to help ameliorate the energy and environmental crisis derived from the continuing use of fossil fuels, as it can integrate light into well-established thermocatalysis processes. The question however remains whether negative CO₂ emission could be achieved through photothermal catalytic reactions performed in facilities driven by electricity mainly derived from fossil energy. Herein, we propose universal equations that describe net CO₂ emissions generated from operating thermocatalysis and photothermal reverse water-gas shift (RWGS) and Sabatier processes for batch and flow reactors. With these reactions as archetype model systems, the factors that will determine the final amount of effluent CO₂ can be determined. The results of this study could provide useful guidelines for the future development of photothermal catalytic systems for CO₂ reduction.

Recent advances in materials for hemostatic management

Traumatic hemorrhage can be a fatal event, particularly when large quantities of blood are lost in a short period of time. Therefore, hemostasis has become a crucial part of emergency treatment. For small wounds, hemostasis can be achieved intrinsically depending on the body's own blood coagulation mechanism; however, for large-area wounds, particularly battlefield and complex wounds, materials delivering rapid and effective hemostasis are required. In parallel with the constant progress in science, technology, and society, advances in hemostatic materials have also undergone various iterations by integrating new ideas with old concepts. There are various natural and synthetic hemostatic materials, including hemostatic powders, adhesives, hydrogels, and tourniquets, for the treatment of severe external trauma. This review covers the differences among the currently available hemostatic materials and comprehensively describes the hemostatic effects of different materials based on the underlying mechanisms. Finally, solutions for current issues related to trauma bleeding are discussed, and the prospects of hemostatic materials are proposed.

Facile fabrication of soy protein isolate-functionalized nanofibers with enhanced biocompatibility and hemostatic effect on full-thickness skin injury

Extensive full-thickness skin defect lacks self-healing ability. Tissue engineering wound dressing is considered as the most promising approach to promote wound healing. In this study, a series of biocompatible and hemostatic nanofiber dressings were fabricated. Soy protein isolate (SPI) and poly(L-lactic acid) (PLLA) solutions were mixed in certain proportions for high-voltage electrospinning. The obtained products were coded as SPNF-n (n = 100, 80, 60 and 40, corresponding to the weight percentage of PLLA solution). We found that SPNF-n (n = 100, 80, 60 and 40) could facilitate the adhesion and spread of L929 cells. In particular, SPNF-80 was capable of promoting fibroblast proliferation and diminishing inflammation. Compared with the neat PLLA film (SPNF-100), the biosafety and hemostatic effect of SPNF-80 got significantly improved. The hemostatic effect of SPNF-80 was comparable with that of a commercial gelatin sponge. In vivo wound healing assay demonstrated that SPNF-80 could accelerate the wound healing process by enhancing vascularization, re-epithelization and collagen formation. In conclusion, our results reveal that SPNF-n has good biocompatibility and hemostatic effect, and exhibits great application potential in wound healing.

Structural analysis and binding sites of inhibitors targeting the CD47/SIRPα interaction in anticancer therapy

Cluster of differentiation 47 (CD47)/signal regulatory protein alpha (SIRPα) is a negative innate immune checkpoint signaling pathway that restrains immunosurveillance and immune clearance, and thus has aroused wide interest in cancer immunotherapy. Blockade of the CD47/SIRPα signaling pathway shows remarkable antitumor effects in clinical trials. Currently, all inhibitors targeting CD47/SIRPα in clinical trials are biomacromolecules. The poor permeability and undesirable oral bioavailability of biomacromolecules have caused researchers to develop small-molecule CD47/SIRPα pathway inhibitors. This review will summarize the recent advances in CD47/SIRPα interactions, including crystal structures, peptides and small molecule inhibitors. In particular, we have employed computer-aided drug discovery (CADD) approaches to analyze all the published crystal structures and docking results of small molecule inhibitors of CD47/SIRPα, providing insight into the key interaction information to facilitate future development of small molecule CD47/SIRPα inhibitors.

Dynamic responses of neurons in different states under magnetic field stimulation

Transcranial magnetic stimulation (TMS) is an effective method to treat neurophysiological disorders by modulating the electrical activities of neurons. Neurons can exhibit complex nonlinear behaviors underlying the external stimuli. Currently, we do not know how stimulation interacts with endogenous neural activity. In this paper, the effects of magnetic field on spiking neuron, bursting neuron and bistable neuron are studied based on the Hodgkin-Huxley (HH) neuron model. The results show that the neurons in three different states can exhibit different dynamic responses under magnetic field stimulation. The magnetic field stimulation could increase or decrease the firing frequencies of spiking neuron, bursting neuron and bistable neuron. The transitions between different firing patterns of neurons can be promoted by changing the parameters of the magnetic field. Magnetic field stimulation has a minimal impact on the firing temporal sequence sequences in bursting neuron than that in spiking neuron and bistable neuron. These results provided an insight into the impact of neuronal states on neuronal dynamic responses under brain stimulation and show that subtle changes in external conditions and stimuli can cause complex neuronal responses. This study can help us understand the state-dependent coding mechanism of neurons under electromagnetic stimulation.

Development of Pyrazolopyrimidine Anti-Wolbachia Agents for the Treatment of Filariasis

Anti-Wolbachia therapy has been identified as a viable treatment for combating filarial diseases. Phenotypic screening revealed a series of pyrazolopyrimidine hits with potent anti-Wolbachia activity. This paper focuses on the exploration of the SAR for this chemotype, with improvement of metabolic stability and solubility profiles using medicinal chemistry approaches. Organic synthesis has enabled functionalization of the pyrazolopyrimidine core at multiple positions, generating a library of compounds of which many analogues possess nanomolar activity against Wolbachia in vitro with improved DMPK parameters. A lead compound, 15f, was selected for in vivo pharmacokinetics (PK) profiling in mice. The combination of potent anti-Wolbachia activity in two in vitro assessments plus the exceptional oral PK profiles in mice puts this lead compound in a strong position for in vivo proof-of-concept pharmacodynamics studies and demonstrates the strong potential for further optimization and development of this series for treatment of filariasis in the future.

Practical High-Throughput Method to Screen Compounds for Anthelmintic Activity against Caenorhabditis elegans

In the present study, we established a practical and cost-effective high throughput screening assay, which relies on the measurement of the motility of Caenorhabditis elegans by infrared light-interference. Using this assay, we screened 14,400 small molecules from the "HitFinder" library (Maybridge), achieving a hit rate of 0.3%. We identified small molecules that reproducibly inhibited the motility of C. elegans (young adults) and assessed dose relationships for a subset of compounds. Future work will critically evaluate the potential of some of these hits as candidates for subsequent optimisation or repurposing as nematocides or nematostats. This high throughput screening assay has the advantage over many previous assays in that it is cost- and time-effective to carry out and achieves a markedly higher throughput (~10,000 compounds per week); therefore, it is suited to the screening of libraries of tens to hundreds of thousands of compounds for subsequent evaluation and development. The present phenotypic whole-worm assay should be readily adaptable to a range of socioeconomically important parasitic nematodes of humans and animals, depending on their dimensions and motility characteristics in vitro, for the discovery of new anthelmintic candidates. This focus is particularly important, given the widespread problems associated with drug resistance in many parasitic worms of livestock animals globally.

High-Throughput Phenotypic Assay to Screen for Anthelmintic Activity on Haemonchus contortus

Parasitic worms cause very significant diseases in animals and humans worldwide, and their control is critical to enhance health, well-being and productivity. Due to widespread drug resistance in many parasitic worms of animals globally, there is a major, continuing demand for the discovery and development of anthelmintic drugs for use to control these worms. Here, we established a practical, cost-effective and semi-automated high throughput screening (HTS) assay, which relies on the measurement of motility of larvae of the barber’s pole worm (Haemonchus contortus) using infrared light-interference. Using this assay, we screened 80,500 small molecules and achieved a hit rate of 0.05%. We identified three small molecules that reproducibly inhibited larval motility and/or development (IC₅₀ values of ~4 to 41 µM). Future work will critically assess the potential of selected hits as candidates for subsequent optimisation or repurposing against parasitic nematodes. This HTS assay has a major advantage over most previous assays in that it achieves a ≥ 10-times higher throughput (i.e., 10,000 compounds per week), and is thus suited to the screening of libraries of tens of thousands to hundreds of thousands of compounds for subsequent hit-to-lead optimisation or effective repurposing and development. The current assay should be adaptable to many socioeconomically important parasitic nematodes, including those that cause neglected tropical diseases (NTDs). This aspect is of relevance, given the goals of the World Health Organization (WHO) Roadmap for NTDs 2021–2030, to develop more effective drugs and drug combinations to improve patient outcomes and circumvent the ineffectiveness of some current anthelmintic drugs and possible drug resistance.

Eluting mode of photodynamic nanofibers without photosensitizer leakage for one-stop treatment of outdoor hemostasis and sterilizing superbacteria

Bleeding in outdoor environments is often accompanied by bacterial infection. Due to poor outdoor conditions, it is essential to use the same materials to achieve one-stop treatment of fast hemostasis and simultaneously sterilizing bacteria, especially multidrug-resistant bacteria. Photodynamic therapy (PDT) can kill superbacteria, and local PDT through a nanofiber platform can effectively reduce damage to normal tissue. However, current photosensitizers whether in the interior or on the surface of fibers would leak into the wound and inhibit collagen regeneration. Herein, we use a battery-powered handheld electrospinning device that can work outdoors. It directly spins fibers onto the wound, which facilitates fast hemostasis due to its excellent adhesion to the wound. Eluting holes in the hydrophobic fibers by wound tissue fluid are also proposed to accelerate the escape of reactive oxygen species (ROS) from the interior of the fibers to the wound. After photosensitizers were coated on upconverting nanoparticles (UCNPs), they formed clusters whose size (∼55 nm) was much larger than the uniform elution hole (∼4 nm), which prevented photosensitizers from leaking out into the wound tissue. This cluster structure can also tailor the photosensitizers to be triggered by near infrared (NIR) light, whose deeper penetration depth in tissue can facilitate treating deep infections. Because of the combination of the in situ fiber deposition method with the designed elution mode, ROS is effectively poured out onto the fiber surface and is quickly delivered to the wound. Thus, after rapid hemostasis (<7 s), this one-stop treatment followed by photodynamic sterilizing of superbacteria can promote collagen regeneration and reduce wound healing time from 24 to 16 days.

Small molecule screening identified cepharanthine as an inhibitor of porcine reproductive and respiratory syndrome virus infection in vitro by suppressing integrins/ILK/RACK1/PKCα/NF-κB signalling axis

Porcine Reproductive and Respiratory Syndrome (PRRS) is a devastating disease among the most notorious threats to the swine industry worldwide and is characterized by respiratory distress and reproductive failure. Highly evolving porcine reproductive and respiratory syndrome virus (PRRSV) strains with complicated genetic diversity make the current vaccination strategy far from cost-effective and thus urge identification of potent lead candidates to provide prevention and treatment approaches. From an in vitro small molecule screening with the TargetMol Natural Compound Library comprising 623 small molecules, cytopathic effect (CPE) observations and RT-qPCR analysis of viral ORF7 gene expression identified cepharanthine (CEP) to be one of the most protent inhibitors of PRRSV infection in Marc-145 cells. When compared with tilmicosin, which is one of the most commonly used antibiotics in swine industry to inhibit infections, CEP more prominently inhibited PRRSV infection represented by both RNA and protein levels, further reduced the TCID₅₀ by 5.6 times, and thus more remarkably protected Marc-145 cells against PRRSV infection. Mechanistically, western blot analyses of the Marc-145 cells and the porcine alveolar macrophages (PAMs) with or without CEP treatment and PRRSV infection at various time points revealed that CEP can inhibit the expression of integrins β1 and β3, integrin-linked kinase (ILK), RACK1 and PKCα, leading to NF-κB suppression and consequent alleviation of PRRSV infection. Collectively, our small molecule screening identified cepharanthine as an inhibitor of PRRSV infection in vitro by suppressing Integrins/ILK/RACK1/PKCα/NF-κB signalling axis, which may enlighten the deeper understanding of the molecular pathogenesis of PRRSV infection and more importantly, suggested CEP as a potential promising drug for PRRS control in veterinary clinics.

A Machine Learning Strategy for Drug Discovery Identifies Anti-Schistosomal Small Molecules

Schistosomiasis is a chronic and painful disease of poverty caused by the flatworm parasite Schistosoma. Drug discovery for antischistosomal compounds predominantly employs in vitro whole organism (phenotypic) screens against two developmental stages of Schistosoma mansoni, post-infective larvae (somules) and adults. We generated two rule books and associated scoring systems to normalize 3898 phenotypic data points to enable machine learning. The data were used to generate eight Bayesian machine learning models with the Assay Central software according to parasite’s developmental stage and experimental time point (≤24, 48, 72, and >72 h). The models helped predict 56 active and nonactive compounds from commercial compound libraries for testing. When these were screened against S. mansoni in vitro, the prediction accuracy for active and inactives was 61% and 56% for somules and adults, respectively; also, hit rates were 48% and 34%, respectively, far exceeding the typical 1–2% hit rate for traditional high throughput screens.

NMR as a "Gold Standard" Method in Drug Design and Discovery

Studying disease models at the molecular level is vital for drug development in order to improve treatment and prevent a wide range of human pathologies. Microbial infections are still a major challenge because pathogens rapidly and continually evolve developing drug resistance. Cancer cells also change genetically, and current therapeutic techniques may be (or may become) ineffective in many cases. The pathology of many neurological diseases remains an enigma, and the exact etiology and underlying mechanisms are still largely unknown. Viral infections spread and develop much more quickly than does the corresponding research needed to prevent and combat these infections; the present and most relevant outbreak of SARS-CoV-2, which originated in Wuhan, China, illustrates the critical and immediate need to improve drug design and development techniques. Modern day drug discovery is a time-consuming, expensive process. Each new drug takes in excess of 10 years to develop and costs on average more than a billion US dollars. This demonstrates the need of a complete redesign or novel strategies. Nuclear Magnetic Resonance (NMR) has played a critical role in drug discovery ever since its introduction several decades ago. In just three decades, NMR has become a "gold standard" platform technology in medical and pharmacology studies. In this review, we present the major applications of NMR spectroscopy in medical drug discovery and development. The basic concepts, theories, and applications of the most commonly used NMR techniques are presented. We also summarize the advantages and limitations of the primary NMR methods in drug development.

Stress-resilient electrode materials for lithium-ion batteries: strategies and mechanisms

Next-generation high-performance lithium-ion batteries (LIBs) with high energy and power density, long cycle life and uncompromising safety standards require new electrode materials beyond conventional intercalation compounds. However, these materials face a tradeoff between the high capacity and stable cycling because more Li stored in the materials also brings instability to the electrode. Stress-resilient electrode materials are the solution to balance this issue, where the decoupling of strong chemomechanical effects on battery cycling is a prerequisite. This review covers the (de)lithiation behaviors of the alloy and conversion-type anodes and their stress mitigation strategies. We highlight the reaction and degradation mechanisms down to the atomic scale revealed by in situ methods. We also discuss the implications of these mechanistic studies and comment on the effectiveness of the electrode structural and chemical designs that could potentially enable the commercialization of the next generation LIBs based on high-capacity anodes.

A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts

Wolbachia is a genus containing obligate, intracellular endosymbionts with arthropod and nematode hosts. Numerous studies have identified differentially expressed transcripts in Wolbachia endosymbionts that potentially inform the biological interplay between these endosymbionts and their hosts, albeit with discordant results. Here, we re-analyze previously published Wolbachia RNA-Seq transcriptomics data sets using a single workflow consisting of the most up-to-date algorithms and techniques, with the aim of identifying trends or patterns in the pan-Wolbachia transcriptional response. We find that data from one of the early studies in filarial nematodes did not allow for robust conclusions about Wolbachia differential expression with these methods, suggesting the original interpretations should be reconsidered. Across datasets analyzed with this unified workflow, there is a general lack of global gene regulation with the exception of a weak transcriptional response resulting in the upregulation of ribosomal proteins in early larval stages. This weak response is observed across diverse Wolbachia strains from both nematode and insect hosts suggesting a potential pan-Wolbachia transcriptional response during host development that diverged more than 700 million years ago.

Machine learning classification can reduce false positives in structure-based virtual screening

With the recent explosion in the size of libraries available for screening, virtual screening is positioned to assume a more prominent role in early drug discovery's search for active chemical matter. In typical virtual screens, however, only about 12% of the top-scoring compounds actually show activity when tested in biochemical assays. We argue that most scoring functions used for this task have been developed with insufficient thoughtfulness into the datasets on which they are trained and tested, leading to overly simplistic models and/or overtraining. These problems are compounded in the literature because studies reporting new scoring methods have not validated their models prospectively within the same study. Here, we report a strategy for building a training dataset (D-COID) that aims to generate highly compelling decoy complexes that are individually matched to available active complexes. Using this dataset, we train a general-purpose classifier for virtual screening (vScreenML) that is built on the XGBoost framework. In retrospective benchmarks, our classifier shows outstanding performance relative to other scoring functions. In a prospective context, nearly all candidate inhibitors from a screen against acetylcholinesterase show detectable activity; beyond this, 10 of 23 compounds have IC₅₀ better than 50 μM. Without any medicinal chemistry optimization, the most potent hit has IC₅₀ 280 nM, corresponding to K_i of 173 nM. These results support using the D-COID strategy for training classifiers in other computational biology tasks, and for vScreenML in virtual screening campaigns against other protein targets. Both D-COID and vScreenML are freely distributed to facilitate such efforts.

Secretome-Based Screening in Target Discovery

Secreted proteins and their cognate plasma membrane receptors regulate human physiology by transducing signals from the extracellular environment into cells resulting in different cellular phenotypes. Systematic use of secretome proteins in assays enables discovery of novel biology and signaling pathways. Several secretome-based phenotypic screening platforms have been described in the literature and shown to facilitate target identification in drug discovery. In this review, we summarize the current status of secretome-based screening. This includes annotation, production, quality control, and sample management of secretome libraries, as well as how secretome libraries have been applied to discover novel target biology using different disease-relevant cell-based assays. A workflow for secretome-based screening is shared based on the AstraZeneca experience. The secretome library offers several advantages compared with other libraries used for target discovery: (1) screening using a secretome library directly identifies the active protein and, in many cases, its cognate receptor, enabling a rapid understanding of the disease pathway and subsequent formation of target hypotheses for drug discovery; (2) the secretome library covers significant areas of biological signaling space, although the size of this library is small; (3) secretome proteins can be added directly to cells without additional manipulation. These factors make the secretome library ideal for testing in physiologically relevant cell types, and therefore it represents an attractive approach to phenotypic target discovery.

Novel anti-Wolbachia drugs, a new approach in the treatment and prevention of veterinary filariasis?

Filarial nematodes are tissue-dwelling parasitic worms that can cause a range of disfiguring pathologies in humans and potentially lethal infections of companion animals. The bacterial endosymbiont, Wolbachia, is present within most human and veterinary filarial pathogens, including the causative agent of heartworm disease, Dirofilaria immitis. Doxycycline-mediated drug targeting of Wolbachia leads to sterility, clearance of microfilariae and gradual death of adult filariae. This mode of action is attractive in the treatment of filariasis because it avoids severe host inflammatory adverse reactions invoked by rapid-killing anthelmintic agents. However, doxycycline needs to be taken for four weeks to exert curative activity. In this review, we discuss the evidence that Wolbachia drug targeting is efficacious in blocking filarial larval development as well as in the treatment of chronic filarial disease. We present the current portfolio of next-generation anti-Wolbachia candidates discovered through phenotypic screening of chemical libraries and validated in a range of in vitro and in vivo filarial infection models. Several novel chemotypes have been identified with selected narrow-spectrum anti-Wolbachia specificity and superior time-to-kill kinetics compared with doxycycline. We discuss the opportunities of developing these novel anti-Wolbachia agents as either cures, adjunct therapies or new preventatives for the treatment of veterinary filariasis.

Single atomic site catalysts: synthesis, characterization, and applications

Single atomic site catalysts (SASCs) have attracted great attention in heterogenous catalysis due to their maximized atomic utilization and unique electronic structure. This feature article summarizes the recent contributions of the authors in the synthesis, characterization, and applications of SASCs. Firstly, we disclose the tricks of our recent progress in the synthesis of SASCs, including impregnation of metal precursors on defect-rich supports, pyrolysis of polymer-encapsulated metals and isolation of contiguous atoms by alloying. Then, we show several key characterization technologies to identify the geometric and electronic structure of SASCs, and reveal the advantages and disadvantages of these characterization technologies. Finally, the applications of the SASCs in heterogenous catalysis are presented, which are classified into electrocatalysis and thermocatalysis, and the structure-function relationships are disclosed.

Uniform yolk–shell structured Si–C nanoparticles as a high performance anode material for the Li-ion battery

Uniform yolk–shell Si–C nanoparticles with a well-defined void space allowing large volume expansion of the Si anode for the Li-ion battery.

Drug Repurposing of Bromodomain Inhibitors as Potential Novel Therapeutic Leads for Lymphatic Filariasis Guided by Multispecies Transcriptomics

The current treatment regimen for lymphatic filariasis is mostly microfilaricidal. In an effort to identify new drug candidates for lymphatic filariasis, we conducted a three-way transcriptomics/systems biology study of one of the causative agents of lymphatic filariasis, Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host Aedes aegypti at 16 distinct B. malayi life stages. B. malayi upregulates the expression of bromodomain-containing proteins in the adult female, embryo, and microfilaria stages. In vitro, we find that the existing cancer therapeutic JQ1(+), which is a bromodomain and extraterminal protein inhibitor, has adulticidal activity in B. malayi.

To better understand the transcriptomic interplay of organisms associated with lymphatic filariasis, we conducted multispecies transcriptome sequencing (RNA-Seq) on the filarial nematode Brugia malayi, its Wolbachia endosymbiont wBm, and its laboratory vector Aedes aegypti across the entire B. malayi life cycle. In wBm, transcription of the noncoding 6S RNA suggests that it may be a regulator of bacterial cell growth, as its transcript levels correlate with bacterial replication rates. For A. aegypti, the transcriptional response reflects the stress that B. malayi infection exerts on the mosquito with indicators of increased energy demand. In B. malayi, expression modules associated with adult female samples consistently contained an overrepresentation of genes involved in chromatin remodeling, such as the bromodomain-containing proteins. All bromodomain-containing proteins encoded by B. malayi were observed to be upregulated in the adult female, embryo, and microfilaria life stages, including 2 members of the bromodomain and extraterminal (BET) protein family. The BET inhibitor JQ1(+), originally developed as a cancer therapeutic, caused lethality of adult worms in vitro, suggesting that it may be a potential therapeutic that can be repurposed for treating lymphatic filariasis.

IMPORTANCE The current treatment regimen for lymphatic filariasis is mostly microfilaricidal. In an effort to identify new drug candidates for lymphatic filariasis, we conducted a three-way transcriptomics/systems biology study of one of the causative agents of lymphatic filariasis, Brugia malayi, its Wolbachia endosymbiont wBm, and its vector host Aedes aegypti at 16 distinct B. malayi life stages. B. malayi upregulates the expression of bromodomain-containing proteins in the adult female, embryo, and microfilaria stages. In vitro, we find that the existing cancer therapeutic JQ1(+), which is a bromodomain and extraterminal protein inhibitor, has adulticidal activity in B. malayi.