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Using photodynamic therapy (PDT) to trigger nonconventional cell death pathways has provided a new scheme for highly efficient and non-side effects to drug-resistant cancer therapies. Nonetheless, the unclear targets of available photosensitizers leave the manner of PDT-induced tumor cell death relatively unpredictable. Herein, we developed a novel Ru(II)-based photosensitizer, Ru-Poma. Possessing the E3 ubiquitin ligase CRBN-targeting moiety and high singlet oxygen yield of 0.96, Ru-Poma was demonstrated to specifically photodegrade endogenous CRBN, increase lipid peroxide, downregulate GPX4 and GAPDH expression, and consequently induce ferroptosis in cisplatin-resistant cancerous cells. Furthermore, with the deep penetration of two-photon excitation, Ru-Poma achieved drug-resistant circumvention in a 3D tumor cell model. Thus, we describe the first sample of the CRBN-targeting Ru(II) complex active in PDT. Show less

Title: Insights into the anticancer photodynamic activity of Ir(III) and Ru(II) polypyridyl complexes bearing β-carboline ligands. Abstract: Ir(III) and Ru(II) polypyridyl complexes are promising photosensitizers (PSs) for photodynamic therapy (PDT) due to their outstanding photophysical properties. Herein, one series of cyclometallated Ir(III) complexes and two series of Ru(II) polypyridyl derivatives bearing three different thiazolyl-β-carboline N^N' ligands have been synthesized, aiming to evaluate the impact of the different metal fragments ([Ir(C^N)2]+ or [Ru(N^N)2]2+) and N^N' ligands on the photophysical and biological properties. All the compounds exhibit remarkable photostability under blue-light irradiation and are emissive (605 < λem < 720 nm), with the Ru(II) derivatives displaying higher photoluminescence quantum yields and longer excited state lifetimes. The Ir PSs display pKa values between 5.9 and 7.9, whereas their Ru counterparts are less acidic (pKa > 9.3). The presence of the deprotonated form in the Ir-PSs favours the generation of reactive oxygen species (ROS) since, according to theoretical calculations, it features a low-lying ligand-centered triplet excited state (T1 = 3LC) with a long lifetime. All compounds have demonstrated anticancer activity. Ir(III) complexes 1-3 exhibit the highest cytotoxicity in dark conditions, comparable to cisplatin. Their activity is notably enhanced by blue-light irradiation, resulting in nanomolar IC50 values and phototoxicity indexes (PIs) between 70 and 201 in different cancer cell lines. The Ir(III) PSs are also activated by green (with PI between 16 and 19.2) and red light in the case of complex 3 (PI = 8.5). Their antitumor efficacy is confirmed by clonogenic assays and using spheroid models. The Ir(III) complexes rapidly enter cells, accumulating in mitochondria and lysosomes. Upon photoactivation, they generate ROS, leading to mitochondrial dysfunction and lysosomal damage and ultimately cell apoptosis. Additionally, they inhibit cancer cell migration, a crucial step in metastasis. In contrast, Ru(II) complex 6 exhibits moderate mitochondrial activity. Overall, Ir(III) complexes 1-3 show potential for selective light-controlled cancer treatment, providing an alternative mechanism to chemotherapy and the ability to inhibit lethal cancer cell dissemination. Show less

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0’s online interface and API utilize these precomputed entity relations and synonyms to provide advanced Show less

Motivation: Thousands of genomes are publicly available, however, most genes in those genomes have poorly defined functions. This is partly due to a gap between previously published, experimentally characterized protein activities and activities deposited in databases. This activity de­ position is bottlenecked by the time-consuming biocuration process. The emergence of large language models presents an opportunity to speed up the text-mining of protein activities for biocuration. Results: We developed FuncFetch—a workflow that integrates NCBI E-Utilities, OpenAI’s GPT-4, and Zotero—to screen thousands of manu­ Show less

Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterised by antibodies to DNA (anti-DNA) and other nuclear macromolecules. Anti-DNA antibodies are markers for classification and disease activity and promote pathogenesis by forming immune complexes that deposit in the tissue or stimulate cytokine production. Studies on the antibody response to DNA have focused primarily on a conformation of DNA known as B-DNA, the classic right-handed double helix. Among other conformations of DNA, Z-DNA is a left-handed helix with a zig-zag backbone; hence, the term Z-DNA. Z-DNA formation is favoured by certain base sequences, with the energetically unfavourable flip from B-DNA to Z-DNA dependent on conditions. Z-DNA differs from B-DNA in its immunogenicity in animal models. Furthermore, anti-Z-DNA antibodies, but not anti-B-DNA antibodies, can be present in otherwise healthy individuals. In SLE, antibodies to Z-DNA can occur in association with antibodies to B-DNA as a cross-reactive response, rising and falling together. While formed transiently in chromosomal DNA, Z-DNA is stably present in bacterial biofilms; biofilms can provide protection against antibiotics and other challenges including elements of host defence. The high GC content of certain bacterial DNA also favours Z-DNA formation as do DNA-binding proteins of bacterial or host origin. Together, these findings suggest that sources of Z-DNA can enhance the immunogenicity of DNA and, in SLE, stimulate the production of cross-reactive antibodies that bind both B-DNA and Z-DNA. As such, DNA can act as a molecular chameleon that, when stabilised in the Z-DNA conformation, can drive autoimmunity. Show less

Copper is a necessary micronutrient for maintaining the well-being of the human body. The biological activity of organic ligands, especially their anticancer activity, is often enhanced when they coordinate with copper(I) and (II) ions. Copper and its compounds are capable of inducing tumor cell death through various mechanisms of action, including activation of apoptosis signaling pathways by reactive oxygen species (ROS), inhibition of angiogenesis, induction of cuproptosis, and paraptosis. Some of the copper complexes are currently being evaluated in clinical trials for their ability to map tumor hypoxia in various cancers, including locally advanced rectal cancer and bulky tumors. Several studies have shown that copper nanoparticles can be used as effective agents in chemodynamic therapy, phototherapy, hyperthermia, and immunotherapy. Despite the promising anticancer activity of copper-based compounds, their use in clinical trials is subject to certain limitations. Elevated copper concentrations may promote tumor growth, angiogenesis, and metastasis by affecting cellular processes. Show less

PT-112 is a novel immunogenic cell death (ICD)-inducing small molecule currently under Phase 2 clinical development, including in metastatic castration-resistant prostate cancer (mCRPC), an immunologically cold and heterogeneous disease state in need of novel therapeutic approaches. PT-112 has been shown to cause ribosome biogenesis inhibition and organelle stress followed by ICD in cancer cells, culminating in anticancer immunity. In addition, clinical evidence of PT-112-driven immune effects has been observed in patient immunoprofiling. Given the unmet need for immune-based therapies in prostate cancer, along with a Phase I study (NCT#02266745) showing PT-112 activity in mCRPC patients, we investigated PT-112 effects in a panel of human prostate cancer cell lines. PT-112 demonstrated cancer cell selectivity, inhibiting cell growth and leading to cell death in prostate cancer cells without affecting the non-tumorigenic epithelial prostate cell line RWPE-1 at the concentrations tested. PT-112 also caused caspase-3 activation, as well as stress features in mitochondria including ROS generation, compromised membrane integrity, altered respiration, and morphological changes. Moreover, PT-112 induced damage-associated molecular pattern (DAMP) release, the first demonstration of ICD in human cancer cell lines, in addition to autophagy initiation across the panel. Taken together, PT-112 caused selective stress, growth inhibition and death in human prostate cancer cell lines. Our data provide additional insight into mitochondrial stress and ICD in response to PT-112. PT-112 anticancer immunogenicity could have clinical applications and is currently under investigation in a Phase 2 mCRPC study. Show less

Cuproptosis, a newly identified copper (Cu)-dependent form of cell death, stands out due to its distinct mechanism that sets it apart from other known cell death pathways. The molecular underpinnings of cuproptosis involve the binding of Cu to lipoylated enzymes in the tricarboxylic acid cycle. This interaction triggers enzyme aggregation and proteotoxic stress, culminating in cell death. The specific mechanism of cuproptosis has yet to be fully elucidated. This newly recognized form of cell death has sparked numerous investigations into its role in tumorigenesis and cancer therapy. In this review, we summarized the current knowledge on Cu metabolism and its link to cancer. Furthermore, we delineated the molecular mechanisms of cuproptosis and summarized the roles of cuproptosis-related genes in cancer. Finally, we offered a comprehensive discussion of the most recent advancements in Cu ionophores and nanoparticle delivery systems that utilize cuproptosis as a cutting-edge strategy for cancer treatment. Show less

Background Hypoxia is a common feature of many solid tumors and causes radiotherapy and immunotherapy resistance. Pharmacological inhibition of oxidative phosphorylation (OXPHOS) has emerged as a therapeutic strategy to reduce hypoxia. However, the OXPHOS inhibitors tested in clinical trials caused only moderate responses in hypoxia alleviation or trials were terminated due to dose-limiting toxicities. To improve the therapeutic benefit, FDA approved OXPHOS inhibitors (e.g. atovaquone) were conjugated to triphenylphosphonium ­( TPP+) to preferentially target Show less

Artificial intelligence (AI) has emerged as a key enabler in optimizing renewable energy systems, significantly contributing to global efforts toward environmental sustainability. This review explores the application of AI technologies in enhancing the efficiency, reliability, and integration of renewable energy sources such as solar, wind, and hydropower. It focuses on how machine learning (ML), deep learning (DL), and other AI-driven algorithms improve energy forecasting, grid management, and storage optimization. Survey data and case studies demonstrate the potential of AI to minimize energy waste, reduce costs, and lower greenhouse gas emissions, reinforcing its role in transitioning to a sustainable energy future. The review concludes with a discussion of challenges and future research directions. Show less

Flavonol-metal complexes can enhance the biological activity of flavonols. Inspired by the potential of ruthenium-based drugs in pharmaceutical applications, seven flavonol-Ru (II) complexes were synthesized to evaluate their biological activities. Among these compounds, compounds 8, 11, and 12 showed potent antioxidant activities. Compound 12 exhibited superior anti-inflammatory activity to natural quercetin, which served as a positive control. This study is the first to report the free radical scavenging abilities and antioxidant activity of flavonol-Ru (II) complexes. Furthermore, compound 12 demonstrated comparable efficacy to 5-FU against human non-small-cell lung cancer cells (A549). These results strongly support the potential of flavonol-Ru (II) agents. Show less

AbstractStructure elucidation plays a critical role across the landscape of medicinal chemistry, including medicinal inorganic chemistry. Herein, we discuss the importance of structure elucidation in drug development and then provide three vignettes that capture key instances of its relevance in the development of biologically active inorganic compounds. In the first, we describe the exploration of the biological activity of the trinuclear Ru compound called ruthenium red and the realization that this activity derived from a dinuclear impurity. We next explore the development of Au‐based antitubercular and antiarthritic drugs, which features a key step whereby ligands were discovered to bind to Au through S atoms. The third exposition traces the development of As‐based antiparasitic drugs, a key step of which was the realization that the reaction of arsenic acid and aniline does not produce an anilide of arsenic acid, as originally thought, but rather an amino arsonic acid. These case studies provide the motivation for an outlook in which the development of Sb‐based antiparasitic drugs is described. Although antileishmanial pentavalent antimonial drugs remain in widespread use to this day, their chemical structures remain unknown. Show less

Abstract Ferroptosis is a new form of regulated cell death featuring iron‐dependent lipid peroxides accumulation to kill tumor cells. A growing body of evidence has shown the potential of ferroptosis‐based cancer therapy in eradicating refractory malignancies that are resistant to apoptosis‐based conventional therapies. In recent years, studies have reported a number of ferroptosis inducers that can increase the vulnerability of tumor cells to ferroptosis by regulating ferroptosis‐related signaling pathways. Encouraged by the rapid development of ferroptosis‐driven cancer therapies, interdisciplinary fields that combine ferroptosis, pharmaceutical chemistry, and nanotechnology are focused. First, the prerequisites and metabolic pathways for ferroptosis are briefly introduced. Then, in detail emerging ferroptosis inducers designed to boost ferroptosis‐induced tumor therapy, including metal complexes, metal‐based nanoparticles, and metal‐free nanoparticles are summarized. Subsequently, the application of synergistic strategies that combine ferroptosis with apoptosis and other regulated cell death for cancer therapy, with emphasis on the use of both cuproptosis and ferroptosis to induce redox dysregulation in tumor and intracellular bimetallic copper/iron metabolism disorders during tumor treatment is discussed. Finally, challenges associated with clinical translation and potential future directions for potentiating cancer ferroptosis therapies are highlighted. Show less

Indexing articles by their publication type and study design is essential for efficient search and filtering of the biomedical literature, but is understudied compared to indexing by MeSH topical terms. In this study, we leveraged the human-curated publication types and study designs in PubMed to generate a dataset of more than 1.2M articles (titles and abstracts) and used state-of-the-art Transformer-based models for automatic tagging of publication types and study designs. Specifically, we trained PubMedBERT-based models using a multi-label classification approach, and explored undersampling, feature verbalization, and contrastive learning to improve model performance. Our results show that PubMedBERT provides a strong baseline for publication type and study design indexing; undersampling, feature verbalization, and unsupervised constrastive loss have a positive impact on performance, whereas supervised contrastive learning degrades the performance. We obtained the best overall performance with 80% undersampling and feature verbalization (0.632 macro-F1, 0.969 macro-AUC). The model outperformed previous models (MultiTagger) across all metrics and the performance difference was statistically significant (p < 0.001). Despite its stronger performance, the model still has room for improvement and future work could explore features based on full-text as well as model interpretability. We make our data and code available at https://github.com/ScienceNLP-Lab/MultiTagger-v2/tree/main/AMIA. Show less

ConspectusThe study of the origin of life requires a multifaceted approach to understanding where and how life arose on Earth. One of the most compelling hypotheses is the chemosynthetic origin of life at hydrothermal vents, as this condition has been considered viable for early forms of life. The continuous production of H2 and heat by serpentinization generates reductive conditions at hydrothermal vents, in which CO2 can be used to build large biomolecules. Although this involves surface catalysis and an autocatalytic process, in which solid minerals act as catalysts in the conversion of CO2 to metabolically important organic molecules, the systematic investigation of heterogeneous catalysis to comprehend prebiotic chemistry at hydrothermal vents has not been undertaken.In this Account, we discuss geochemical CO2 fixation to metabolic intermediates by synthetic minerals at hydrothermal vents from the perspective of heterogeneous catalysis. Ni and Fe are the most abundant transition metals at hydrothermal vents and occur in the active site of the enzymes carbon monoxide dehydrogenases/acetyl coenzyme A synthases (CODH/ACS). Synthetic free-standing NiFe alloy nanoparticles can convert CO2 to acetyl coenzyme A pathway intermediates such as formate, acetate, and pyruvate. The same alloy can further convert pyruvate to citramalate, which is essential in the biological citramalate pathway. Thermal treatment of Ni3Fe nanoparticles under NH3, which can occur in hydrothermal vents, results in Ni3FeN/Ni3Fe heterostructures. This catalyst has been demonstrated to produce prebiotic formamide and acetamide from CO2 and H2O using Ni3FeN/Ni3Fe as both substrate and catalyst. In the process of serpentinization, Co can be reduced in the vicinity of olivine, a Mg-Fe silicate mineral. This produces CoFe and CoFe2 with serpentine in nature, representing SiO2-supported CoFe alloys. In mimicking these natural minerals, synthetic SiO2-supported CoFe alloys demonstrate the same liquid products as NiFe alloys, namely, formate, acetate, and pyruvate under mild hydrothermal vent conditions. In contrast to the NiFe system, hydrocarbons up to C6 were detected in the gas phase, which is also present in hydrothermal vents. The addition of alkali and alkaline-earth metals to the catalysts results in enhanced formate concentration, playing a promotional role in CO2 reduction. Finally, Co was loaded onto ordered mesoporous SiO2 after modification with cations to simulate the minerals found in hydrothermal vents. These catalysts were then investigated under diminished H2O concentration, revealing the conversion of CO2 to CO, CH4, methanol, and acetate. Notably, the selectivity to metabolically relevant methanol was enhanced in the presence of cations that could generate and stabilize the methoxy intermediate. Calculation using the machine learning approach revealed the possibility of predicting the selectivity of CO2 fixation when modifying mesoporous SiO2 supports with heterocations. Our research demonstrates that minerals at hydrothermal vents can convert CO2 into metabolites under a variety of prebiotic conditions, potentially paving the way for modern biological CO2 fixation processes. Show less

Cancer remains a significant global health challenge, necessitating continuous advancements in therapeutic strategies. Chemotherapeutic agents have long been pivotal in cancer treatment, with platinum(Pt)-based drugs holding a prominent place. Oxaliplatin, a third-generation Pt(II) compound, has gathered attention for its efficacy towards several cisplatin-resistant cancer cells and has become the front-line therapy for metastatic colorectal cancer. However, inherent limitations such as resistance development and dose-dependent side effects like oxaliplatin-induced peripheral neuropathy (OIPN) prompt the exploration of novel derivatives. Pt(IV) prodrugs have emerged as a promising avenue in cancer therapy, exploiting the intrinsic cytotoxicity of platinum while offering enhanced stability and tunable pharmacokinetics. However, the majority of Pt(IV) prodrugs reported in the literature, for their in vitro or in vivo anticancer properties, are cisplatin-based. This comprehensive review gathers, to our knowledge, the recent advances on oxaliplatin-based Pt(IV) derivatives and how they can strategically address the aforementioned challenges. Show less

Anti-PD-L1 immunotherapy, a new lung cancer treatment, is limited to a few patients due to low PD-L1 expression and tumor immunosuppression. To address these challenges, the upregulation of PD-L1 has the potential to elevate the response rate and efficiency of anti-PD-L1 and alleviate the immunosuppression of the tumor microenvironment. Herein, we developed a novel usnic acid-derived Iridium(III) complex, Ir-UA, that boosts PD-L1 expression and converts "cold tumors" to "hot". Subsequently, we administered Ir-UA combined with anti-PD-L1 in mice, which effectively inhibited tumor growth and promoted CD4⁺ and CD8⁺ T cell infiltration. To our knowledge, Ir-UA is the first iridium-based complex to stimulate the expression of PD-L1 by explicitly regulating its transcription factors, which not only provides a promising platform for immune checkpoint blockade but, more importantly, provides an effective treatment strategy for patients with low PD-L1 expression. Show less

Title: Mitochondrial Viscosity Probes: Iridium(III) Complexes Induce Apoptosis in HeLa Cells. Abstract: Mitochondrial viscosity has emerged as a promising biomarker for diseases such as cancer and neurodegenerative disorders, yet accurately measuring viscosity at the subcellular level remains a significant challenge. In this study, we synthesized and characterized three cyclometalated iridium(III) complexes (Ir1-Ir3) containing 5-fluorouracil derivatives as ligands. Among these, Ir1 selectively induced apoptosis in HeLa cells by increasing mitochondrial production of reactive oxygen species (ROS), which triggered a cascade of events leading to mitochondrial dysfunction. Additionally, the fluorescence lifetime of Ir1 demonstrated high sensitivity to intracellular viscosity changes, enabling real-time fluorescence lifetime imaging microscopy (FLIM) of cellular micro-viscosity during apoptosis. These findings underscore the potential of cyclometalated Ir(III) complexes for both therapeutic and diagnostic applications at the subcellular level. Show less