Controlled Bio-Orthogonal Catalysis Using Nanozyme-Protein Complexes via Modulation of Electrostatic Interactions.

Bio-orthogonal chemistry provides a powerful tool for drug delivery systems due to its ability to generate therapeutic agents in situ, minimizing off-target effects. Bio-orthogonal transition metal catalysts (TMCs) with stimuli-responsive properties offer possibilities for controllable catalysis due to their spatial-, temporal-, and dosage-controllable properties. In this paper, we fabricated a stimuli-responsive bio-orthogonal catalysis system based on an enhanced green fluorescent protein (EGFP)-nanozyme (NZ) complex (EGFP-NZ). Regulation of the catalytic properties of the EGFP-NZ complex was directly achieved by modulating the ionic strength of the solution. The dielectric screening introduced by salt ions allows the dissociation of the EGFP-NZ complex, increasing the access of substrate to the active site of the NZs and concomitantly increasing nanozyme activity. The change in catalytic rate of the NZ/EGFP = 1:1 complex was positively correlated with salt concentration from 0 mM to 150 mM.

Predicting Natural Evolution in the RBD Region of the Spike Glycoprotein of SARS-CoV-2 by Machine Learning.

Machine learning (ML) is a key focus in predicting protein mutations and aiding directed evolution. Research on potential virus variants is crucial for vaccine development. In this study, the machine learning software PyPEF was employed to conduct mutation analysis within the receptor-binding domain (RBD) of the Spike glycoprotein of SARS-CoV-2. Over 48,960,000 variants were predicted. Eight prospective variants that could surface in the future underwent modeling and molecular dynamics simulations. The study forecasts that the latest variant, ISOY2P5O1, may potentially emerge around 17 November 2023, with an approximate window of uncertainty of ±22 days. The ISOY8P5O2 variant displayed an increased binding capacity in the dry assay, with a total predicted binding energy of -110.306 kcal/mol. This represents an 8.25% enhancement in total binding energy compared to the original SARS-CoV-2 strain discovered in Wuhan (-101.892 kcal/mol). Reverse research confirmed the structural significance of mutation sites using ML models, particularly in the context of protein folding. The study validated regression methods (SVR, RF, and PLS) with different data structures. This study investigates the effectiveness of the "ML-Guided Design Correctly Predicts Combinatorial Effects Strategy" compared to the "ML-Guided Design Correctly Predicts Natural Evolution Prediction Strategy". To enhance machine learning, we created a timestamping algorithm and two auxiliary programs using advanced techniques to rapidly process extensive data, surpassing batch sequencing capabilities. This study not only advances machine learning in guiding protein evolution but also holds potential for forecasting future viruses and vaccine development.

Modulation of Gold Nanoparticle Ligand Structure-Dynamic Relationships Probed Using Solution NMR.

Ligand dynamics plays a critical role in the chemical and biological properties of gold nanoparticles (AuNPs). In this study, ligands featuring hydrophobic alkanethiol interiors and hydrophilic shells were used to systematically examine the effects of ligand headgroups on the ligand dynamics. Solution nuclear magnetic resonance (NMR) spectroscopy provided quantitative insight into the monolayer ligand dynamics. Notably, the introduction of hydrophobic moieties to the cationic headgroups significantly decreased ligand conformational mobility; however, variations in hydrophobicity among these moieties had a limited effect on this reduction. Further examination of ligand dynamics under various physiological conditions, including ionic strength and temperature, showed that ligands bound to the AuNP surface become less conformationally mobile with an increase in ionic strength or decreasing temperature. This exploration of ligand dynamics provides insight into designing nanoparticles tailored to specific biological applications.

Polarization of macrophages to an anti-cancer phenotype through in situ uncaging of a TLR 7/8 agonist using bioorthogonal nanozymes.

Macrophages are plastic cells of the immune system that can be broadly classified as having pro-inflammatory (M1-like) or anti-inflammatory (M2-like) phenotypes. M2-like macrophages are often associated with cancers and can promote cancer growth and create an immune-suppressive tumor microenvironment. Repolarizing macrophages from M2-like to M1-like phenotype provides a crucial strategy for anticancer immunotherapy. Imiquimod is an FDA-approved small molecule that can polarize macrophages by activating toll-like receptor 7/8 (TLR 7/8) located inside lysosomes. However, the non-specific inflammation that results from the drug has limited its systemic application. To overcome this issue, we report the use of gold nanoparticle-based bioorthogonal nanozymes for the conversion of an inactive, imiquimod-based prodrug to an active compound for macrophage re-education from anti- to pro-inflammatory phenotypes. The nanozymes were delivered to macrophages through endocytosis, where they uncaged pro-imiquimod in situ. The generation of imiquimod resulted in the expression of pro-inflammatory cytokines. The re-educated M1-like macrophages feature enhanced phagocytosis of cancer cells, leading to efficient macrophage-based tumor cell killing.

Nanoparticles with intermediate hydrophobicity polarize macrophages to plaque-specific Mox phenotype via Nrf2 and HO-1 activation.

Mox macrophages were identified recently and are closely associated with atherosclerosis. Considering the potential health risks and the impact on macrophage modulation, this study investigated the Mox polarization of macrophages induced by nanoparticles (NPs) with tunable hydrophobicity. One nanoparticle (C4NP) with intermediate hydrophobicity efficiently upregulated the mRNA expression of Mox-related genes including HO-1, Srxn1, Txnrd1, Gsr, Vegf and Cox-2 through increased accumulation of Nrf2 at a nontoxic concentration in both resting and LPS-challenged macrophages. Additionally, C4NP impaired phagocytic capacity by 20% and significantly increased the secretion of cytokines, including TNFα, IL-6 and IL-10. Mechanistic studies indicated that intracellular reactive oxygen species (ROS) were elevated by 1.5-fold and 2.6-fold in resting and LPS-challenged macrophages respectively. Phosphorylated p62 was increased by 2.5-fold in resting macrophages and maintained a high level in LPS-challenged ones, both of which partially accounted for the significant accumulation of Nrf2 and HO-1. Notably, C4NP depolarized mitochondrial membrane potential by more than 50% and switched macrophages from oxidative phosphorylation-based aerobic metabolism to glycolysis for energy supply. Overall, this study reveals a novel molecular mechanism potentially involving ROS-Nrf2-p62 signaling in mediating macrophage Mox polarization, holding promise in ensuring safer and more efficient use of nanomaterials.

[Research progress on plant-derived exosome-like nanoparticles and their applications].

Plant-derived exosome-like nanoparticles(PELNs) are a class of membranous vesicles with diameters approximately ranging from 30 to 300 nm, isolated from plant tissues. They contain components such as proteins, lipids, and nucleic acids. PELNs play an important role in the metabolism of plant substances and immune defense, and can also cross-regulate the physiological activities of fungi and animal cells, showing significant potential applications. In recent years, research on PELNs has significantly increased, highlighting three main issues:(1) the mixed sources of plant materials for PELNs;(2) the lack of a unified system for isolating and characterizing PELNs;(3) the urgent need to elucidate the molecular mechanisms underlying the cross-regulation of biological functions by PELNs. This article focused on these concerns. It began by summarizing the biological origin and composition of PELNs, discussing the techniques for isolating and characterizing PELNs, and analyzing their biomedical applications and potential future research directions., aiming to promote the establishment of standardized research protocols for PELNs and provide theoretical references for in-depth exploration of the mechanisms underlying PELNs' cross-regulatory effects.

One-Pot Synthesis of Tumor-Microenvironment Responsive Degradable Nanoflower-Medicine for Multimodal Cancer Therapy with Reinvigorating Antitumor Immunity.

Multimodal cancer therapies show great promise in synergistically enhancing anticancer efficacy through different mechanisms. However, most current multimodal therapies either rely on complex assemblies of multiple functional nanomaterials and drug molecules or involve the use of nanomedicines with poor in vivo degradability/metabolizability, thus restricting their clinical translatability. Herein, a nanoflower-medicine using iron ions, thioguanine (TG), and tetracarboxylic porphyrin (TCPP) are synthesized as building blocks through a one-step hydrothermal method for combined chemo/chemodynamic/photodynamic cancer therapy. The resulting nanoflowers, consisting of low-density Fe2 O3 core and iron complex (Fe-TG and Fe-TCPP compounds) shell, exhibit high accumulation at the tumor site, desirable degradability in the tumor microenvironment (TME), robust suppression of tumor growth and metastasis, as well as effective reinvigoration of host antitumor immunity. Triggered by the low pH in tumor microenvironment, the nanoflowers gradually degrade after internalization, contributing to the effective drug release and initiation of high-efficiency catalytic reactions precisely in tumor sites. Moreover, iron ions can be eliminated from the body through renal clearance after fulfilling their mission. Strikingly, it is also found that the multimodal synergistic therapy effectively elicits the host antitumor immunity without inducing additional toxicity. This easy-manufactured and degradable multimodal therapeutic nanomedicine is promising for clinical precision oncology.

Impact of COVID-19 and lockdown on COPD admissions to Christchurch Hospital, New Zealand 2020-2021: a combined quantitative and qualitative study.

BACKGROUND: During the year following New Zealand's first COVID-19 lockdown, a 33% reduction in chronic obstructive pulmonary disease (COPD)-related admissions occurred and persisted beyond this period at Christchurch Hospital. AIM: To identify contributing factors which may have resulted in a persistent decrease in COPD hospitalisation rates at Christchurch Hospital following the 2020 COVID-19 lockdown. METHODS: Using an explanatory sequential mixed-methods research design, we (i) retrospectively analysed hospital admissions and primary healthcare access by people with COPD (n = 1358) in Canterbury before, during and after COVID lockdown (24 March 2019 to 2021) and (ii) undertook individual interviews from a sample of patients (n = 14). RESULTS: Patients who were not re-admitted following the COVID-19 lockdown had fewer general practice encounters, acute primary care access, antibiotic and prednisone prescriptions. Proportionally fewer Maori and more Pacific patients were admitted with COPD following lockdown. Positive contributing factors at a primary care level included improvements in primary care interactions and medication management. At a patient and community level, there were improvements in lifestyle, self-management practices, social support and contact precautions. However, a subgroup of patients described negative effects such as social isolation. CONCLUSION: A combination of patient, primary care and community-level factors led to an overall persistent decrease in COPD admissions following the COVID-19 lockdown. Future targeted and individualised measures focusing on these modifiable factors may decrease future COPD-related hospital admissions. The study design facilitated further explanation about factors that contributed to the persistent decrease in hospital admissions among people living with COPD and has underscored the importance of social support, patient empowerment and reduction in barriers in accessing care in admission reduction.

Biodegradable nanoemulsion-based bioorthogonal nanocatalysts for intracellular generation of anticancer therapeutics.

Bioorthogonal catalysis mediated by transition metal catalysts (TMCs) provides controlled in situ activation of prodrugs through chemical reactions that do not interfere with cellular bioprocesses. The direct use of 'naked' TMCs in biological environments can have issues of solubility, deactivation, and toxicity. Here, we demonstrate the design and application of a biodegradable nanoemulsion-based scaffold stabilized by a cationic polymer that encapsulates a palladium-based TMC, generating bioorthogonal nanocatalyst "polyzymes". These nanocatalysts enhance the stability and catalytic activity of the TMCs while maintaining excellent mammalian cell biocompatibility. The therapeutic potential of these nanocatalysts was demonstrated through efficient activation of a non-toxic prodrug into an active chemotherapeutic drug, leading to efficient killing of cancer cells.

Sensor Array-Enabled Identification of Drugs for Repolarization of Macrophages to Anti-Inflammatory Phenotypes.

Macrophages are key components of the innate immune system that have essential functions in physiological processes and diseases. The phenotypic plasticity of macrophages allows cells to be polarized into a multidimensional spectrum of phenotypes, broadly classed as pro-inflammatory (M1) and anti-inflammatory (M2) states. Repolarization of M1 to M2 phenotypes alters the immune response to ameliorate autoimmune and inflammation-associated diseases. Detection of this repolarization, however, is challenging to execute in high-throughput applications. In this work, we demonstrate the ability of a single polymer fabricated to provide a six-channel sensor array that can determine macrophage polarization phenotypes. This sensing platform provides a sensitive and high-throughput tool for detecting drug-induced M1-to-M2 repolarization, allowing the identification of new therapeutic leads for inflammatory diseases. The ability of this sensor array to discriminate different M2 subtypes induced by drugs can also improve the efficacy evaluation of anti-inflammatory drugs and avoid adverse effects.

Reduction of pollution loads based on sewage treatment projects around a lake: A case study on Erhai Lake.

Erhai Lake is a highland freshwater lake in Dali, China. Rapid tourism development has generated large amounts of pollutants. Since 2015, six wastewater treatment plants (WWTPs) have been built to treat wastewater collected through sewage interception projects. In this study, reductions in the pollution load of wastewater from different sources were evaluated by considering the effects of groundwater leakage, microbial degradation, and rainfall-runoff. The results showed that the systems reduced the chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) loads by 85, 83, and 85%, respectively. Discharge wastewater has the characteristics of a low concentration of domestic sewage discharge, large tourist sewage discharge, and high concentration of livestock wastewater. Due to the high groundwater level, there is groundwater infiltration in the influent water of WWTPs, which dilutes the pollutant concentration of the influent and, therefore, results in a lower treatment efficiency. Further treatment of tailwater also reduced the pollution loads discharged into the lake as well as the COD and TN by 10.25 and 22.90%, respectively. The results indicate that groundwater infiltration in the sewer network system is the primary target to be addressed in future developments.

Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between?

The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.

Identification of Proteins Using Supramolecular Gold Nanoparticle-Dye Sensor Arrays.

The rapid detection of proteins is very important in the early diagnosis of diseases. Gold nanoparticles (AuNPs) can be engineered to bind biomolecules efficiently and differentially. Cross-reactive sensor arrays have high sensitivity for sensing proteins using differential interactions between sensor elements and bioanalytes. A new sensor array was fabricated using surface-charged AuNPs with dyes supramolecularly encapsulated into the AuNP monolayer. The fluorescence of dyes is partially quenched by the AuNPs and can be restored or further quenched due to the differential interactions between AuNPs with proteins. This sensing system enables the discrimination of proteins in both buffer and human serum, providing a potential tool for real-world disease diagnostics.

Genome-wide identification and expression analysis of MADS-box transcription factors reveal their involvement in sex determination of hardy rubber tree (Eucommia ulmoides oliv.).

Eucommia ulmoides is a famous rubber-producing and medicinal tree species that produces unisexual flowers on separate individuals from the earliest stage of stamen/pistil primordium formation. To explore the genetic regulation pathway of sex in E. ulmoides, comprehensive genome-wide analyses and tissue-/sex-specific transcriptome comparisons of MADS-box transcription factors were performed for the first time in this work. Quantitative real-time PCR technique was employed to further validate the expression of genes that are assigned to floral organ ABCDE model. A total of 66 non-redundant E. ulmoides MADS-box (EuMADS) genes were identified, they were classified into Type I (M-type, 17 genes) and Type II (MIKC, 49 genes). Complex protein-motif composition, exon-intron structure and phytohormone-response cis-elements were detected in MIKC-EuMADS genes. Furthermore, 24 differentially-expressed EuMADS genes (DEGs) between male and female flowers, and two DEGs between male and female leaves were revealed. Amongst the 14 floral organ ABCDE model-related genes, there were 6 (A/B/C/E-class) and 5 (A/D/E-class) genes displayed male- and female-biased expression respectively. In particular, one B-class gene EuMADS39 and one A-class gene EuMADS65 were almost exclusively expressed in male trees, no matter in flower or leaf tissues. Collectively, these results suggested a critical role of MADS-box transcription factors in sex determination of E. ulmoides, which is conducive to decoding the molecular regulation mechanism of sex in E. ulmoides.

Biodegradable Antibacterial Bioorthogonal Polymeric Nanocatalysts Prepared by Flash Nanoprecipitation.

Bioorthogonal activation of pro-dyes and prodrugs using transition-metal catalysts (TMCs) provides a promising strategy for imaging and therapeutic applications. TMCs can be loaded into polymeric nanoparticles through hydrophobic encapsulation to generate polymeric nanocatalysts with enhanced solubility and stability. However, biomedical use of these nanostructures faces challenges due to unwanted tissue accumulation of nonbiodegradable nanomaterials and cytotoxicity of heavy-metal catalysts. We report here the creation of fully biodegradable nanocatalysts based on an engineered FDA-approved polymer and the naturally existing catalyst hemin. Stable nanocatalysts were generated through kinetic stabilization using flash nanoprecipitation. The therapeutic potential of these nanocatalysts was demonstrated through effective treatment of bacterial biofilms through the bioorthogonal activation of a pro-antibiotic.

Bioorthogonal nanozymes for breast cancer imaging and therapy.

Bioorthogonal catalysis via transition metal catalysts (TMCs) enables the generation of therapeutics locally through chemical reactions not accessible by biological systems. This localization can enhance the efficacy of anticancer treatment while minimizing off-target effects. The encapsulation of TMCs into nanomaterials generates "nanozymes" to activate imaging and therapeutic agents. Here, we report the use of cationic bioorthogonal nanozymes to create localized "drug factories" for cancer therapy in vivo. These nanozymes remained present at the tumor site at least seven days after a single injection due to the interactions between cationic surface ligands and negatively charged cell membranes and tissue components. The prodrug was then administered systemically, and the nanozymes continuously converted the non-toxic molecules into active drugs locally. This strategy substantially reduced the tumor growth in an aggressive breast cancer model, with significantly reduced liver damage compared to traditional chemotherapy.

Inorganic nanoparticles as scaffolds for bioorthogonal catalysts.

Bioorthogonal transition metal catalysts (TMCs) transform therapeutically inactive molecules (pro-drugs) into active drug compounds. Inorganic nanoscaffolds protect and solubilize catalysts while offering a flexible design space for decoration with targeting elements and stimuli-responsive activity. These "drug factories" can activate pro-drugs in situ, localizing treatment to the disease site and minimizing off-target effects. Inorganic nanoscaffolds provide structurally diverse scaffolds for encapsulating TMCs. This ability to define the catalyst environment can be employed to enhance the stability and selectivity of the TMC, providing access to enzyme-like bioorthogonal processes. The use of inorganic nanomaterials as scaffolds TMCs and the use of these bioorthogonal nanozymes in vitro and in vivo applications will be discussed in this review.

All-natural gelatin-based bioorthogonal catalysts for efficient eradication of bacterial biofilms.

Bioorthogonal catalysis mediated by transition metal catalysts (TMCs) presents a versatile tool for in situ generation of diagnostic and therapeutic agents. The use of 'naked' TMCs in complex media faces numerous obstacles arising from catalyst deactivation and poor water solubility. The integration of TMCs into engineered inorganic scaffolds provides 'nanozymes' with enhanced water solubility and stability, offering potential applications in biomedicine. However, the clinical translation of nanozymes remains challenging due to their side effects including the genotoxicity of heavy metal catalysts and unwanted tissue accumulation of the non-biodegradable nanomaterials used as scaffolds. We report here the creation of an all-natural catalytic "polyzyme", comprised of gelatin-eugenol nanoemulsion engineered to encapsulate catalytically active hemin, a non-toxic iron porphyrin. These polyzymes penetrate biofilms and eradicate mature bacterial biofilms through bioorthogonal activation of a pro-antibiotic, providing a highly biocompatible platform for antimicrobial therapeutics.

Enhanced Design of Gold Catalysts for Bioorthogonal Polyzymes.

Bioorthogonal chemistry introduces nonbiogenic reactions that can be performed in biological systems, allowing for the localized release of therapeutic agents. Bioorthogonal catalysts can amplify uncaging reactions for the in situ generation of therapeutics. Embedding these catalysts into a polymeric nanoscaffold can protect and modulate the catalytic activity, improving the performance of the resulting bioorthogonal "polyzymes". Catalysts based on nontoxic metals such as gold(I) are particularly attractive for therapeutic applications. Herein, we optimized the structural components of a metal catalyst to develop an efficient gold(I)-based polyzyme. Tailoring the ligand structure of gold phosphine-based complexes, we improved the affinity between the metal complex and polymer scaffold, resulting in enhanced encapsulation efficiency and catalytic rate of the polyzyme. Our findings show the dependence of the overall polyzyme properties on the structural properties of the encapsulated metal complex.