👤 Tan Z

Predicting protein‒protein interactions (PPIs) plays a crucial role in understanding biological processes. Although biological experimental methods can identify PPIs, they are costly, time-consuming, labor-intensive, and often lack stability. In contrast, computational approaches for PPI prediction, particularly deep learning methods, can efficiently learn representations from protein sequences. However, the generalizability, robustness, and stability of computational PPI prediction models still need improvement, especially for species with limited verified PPI data. Protein embeddings generated by protein language models can extract features from protein sequences and reflect hierarchical biological structures, making them suitable for predicting PPIs. Therefore, in this study, we propose a novel protein sequence-based PPI prediction framework designed for generalized PPI assessment by integrating two protein language models (PLMs) and an enhanced deep neural network (MPIDNN-GPPI). Specifically, the sequences are embedded using two protein language models, Ankh and ESM-2. A deep neural network is then used to learn representations from the feature vectors produced by PLMs. Subsequently, a multi-head attention mechanism is introduced to capture long-range dependencies and fuse them with DNN-derived representations. Finally, a deep neural network is applied to assess the probability of interaction between two proteins. To evaluate the performance of MPIDNN-GPPI, nine PPI datasets were collected from the STRING database, covering a diverse set of species: five datasets from mammals (D. melanogaster, C. elegans, S. cerevisiae, H. sapiens, and M. musculus), and four datasets from plants (O. sativa, A. thaliana, G. max, and Z. mays). When trained on H. sapiens, MPIDNN-GPPI achieved AUC values of 0.959, 0.966, 0.954, and 0.916 on independent test sets for M. musculus, D. melanogaster, C. elegans, and S. cerevisiae, respectively. These results represent the best performance among all PPI models compared in this study. Similarly, when trained on O. sativa, the model achieved AUC values of 0.96, 0.95, and 0.913 on independent datasets for A. thaliana, G. max, and Z. mays, respectively. Ablation experiments demonstrated that models combining Ankh and ESM-2 outperformed those relying on a single protein language model. Furthermore, MPIDNN-GPPI, which incorporates multi-head attention and deep neural networks (DNN), achieved superior performance compared to models using DNN alone. These findings indicate that MPIDNN-GPPI possesses strong generalization capability for cross-species PPI prediction. The proposed model, trained on one species, can be effectively applied to accurately predict PPIs in other species. Show less

Ferroptosis is a regulated form of cell death characterized by iron-dependent lipid peroxidation. It plays a crucial role in various pathological conditions, including neurodegenerative diseases, cancer, ischemia-reperfusion injury, and organ failure. This review systematically explores the key mechanisms underlying ferroptosis, including polyunsaturated fatty acid-containing phospholipid (PUFA-PL) peroxidation, iron metabolism, and mitochondrial dysfunction. Additionally, we summarize major endogenous ferroptosis defense systems, including the SLC7A11-glutathione (GSH)-glutathione peroxidase 4 (GPX4) axis, the ferroptosis suppressor protein 1 (FSP1)-ubiquinol (CoQH₂) system, the mitochondrial dihydroorotate dehydrogenase (DHODH)-CoQH₂ pathway, and the guanosine triphosphate cyclohydrolase 1 (GCH1)-tetrahydrobiopterin (BH4) pathway, which act as critical brakes on ferroptosis. Furthermore, we discuss various small-molecule inhibitors targeting ferroptosis, categorized by their mechanisms of action, including iron chelators, lipid peroxidation inhibitors, antioxidants, and regulatory pathway modulators. Recent advances in pharmacological strategies and their potential therapeutic applications are also highlighted. Show less

Ferroptosis suppressor protein 1 (FSP1) has emerged as a critical regulator of ferroptosis, an iron-dependent form of programmed cell death with significant therapeutic potential in cancer treatment. Despite rapidly expanding research, current knowledge on FSP1 remains fragmented across various tumor types and experimental contexts. The aim of this review is to systematically integrate the latest evidence regarding the molecular structure, biological functions, and regulatory mechanisms controlling FSP1 expression, emphasizing its involvement in tumor progression and resistance to therapy. Readers can expect comprehensive coverage of FSP1's structural characteristics, enzymatic roles, transcriptional and post-transcriptional regulation, and its pathological significance in hepatocellular carcinoma, colorectal cancer, pancreatic cancer, gastric cancer, breast cancer, lung cancer, and leukemia. We further evaluate emerging therapeutic strategies targeting FSP1 aimed at overcoming resistance and improving clinical outcomes. Relevant studies were systematically identified by searching PubMed, Web of Science, and Embase databases, focusing particularly on the recent and impactful literature to guide future research directions. Show less

Ewing sarcoma (EwS) cell line culture largely relies on standard techniques, which do not recapitulate physiological conditions. Here, we report on a feasible and cost-efficient EwS cell culture technique with increased physiological relevance employing an advanced medium composition, reduced fetal calf serum, and spheroidal growth. Improved reflection of the transcriptional activity related to proliferation, hypoxia, and differentiation in EwS patient tumors was detected in EwS cells grown in this refined in vitro condition. Moreover, transcriptional signatures associated with the oncogenic activity of the EwS-specific FET::ETS fusion transcription factors in the refined culture condition were shifted from proliferative toward metabolic gene signatures. The herein-presented EwS cell culture technique with increased physiological relevance provides a broadly applicable approach for enhanced in vitro modeling relevant to advancing EwS research and the validity of experimental results. Show less

Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein question answering systems. To tackle these issues, we propose the Prot2Chat framework. Show less

Despite the vast number of enzymatic kinetic measurements reported across decades of biochemical literature, the majority of relational enzyme kinetic data-linking amino acid sequence, substrate identity, kinetic parameters, and assay conditions-remains uncollected and inaccessible in structured form. This constitutes a significant portion of the "dark matter" of enzymology. Unlocking these hidden data through automated extraction offers an opportunity to expand enzyme dataset diversity and size, critical for building accurate, generalizable models that drive predictive enzyme engineering. To address this limitation, we built EnzyExtract, a large language model-powered pipeline that automates the extraction, verification, and structuring of enzyme kinetics data from scientific literature. By processing 137,892 full-text publications (PDF/XML), EnzyExtract collected more than 218,095 enzyme-substrate-kinetics entries, including 218,095 kcat and 167,794 Km values. These entries are mapped to enzymes spanning 3569 unique four-digit EC numbers, with a total of 84,464 entries assigned at least a first-digit EC number. EnzyExtract identified 89,544 unique kinetic entries (kcat and Km combined) absent from BRENDA, significantly expanding the known enzymology dataset. The newly curated dataset was compiled into a database named EnzyExtractDB. EnzyExtract demonstrates high accuracy when benchmarked against manually curated datasets and strong consistency with BRENDA-derived data. To create model-ready datasets, enzyme and substrate sequences were aligned to UniProt and PubChem, yielding 92,286 high-confidence, sequence-mapped kinetic entries. To assess the practical utility of our dataset, we retrained several state-of-the-art kcat predictors (including MESI, DLKcat, and TurNuP) using EnzyExtractDB. Across held-out test sets, all models demonstrate improved predictive performance in terms of RMSE, MAE, and R2, highlighting the value of high-quality, large-scale, literature-derived EnzyExtractDB for enhancing predictive modeling of enzyme kinetics. The EnzyExtract source code and the database are openly available at https://github.com/ChemBioHTP/EnzyExtract, and an interactive demo can be accessed via Google Colab at https://colab.research.google.com/drive/1MwKSEZzLPNOseksRshbzkkFoO_cgJhva. Show less

LitSense 2.0 (https://www.ncbi.nlm.nih.gov/research/litsense2/) is an advanced biomedical search system enhanced with dense vector semantic retrieval, designed for accessing literature on sentence and paragraph levels. It provides unified access to 38 million PubMed abstracts and 6.6 million full-length articles in the PubMed Central (PMC) Open Access subset, encompassing 1.4 billion sentences and ∼300 million paragraphs, and is updated weekly. Compared to PubMed and PMC, the primary platforms for biomedical information search, LitSense offers cross-platform functionality by searching seamlessly across both PubMed and PMC and returning relevant results at a more granular level. Building on the success of the original LitSense launched in 2018, LitSense 2.0 introduces two major enhancements. The first is the addition of paragraph-level search: users can now choose to search either against sentences or against paragraphs. The second is improved retrieval accuracy via a state-of-the-art biomedical text encoder, ensuring more reliable identification of relevant results across the entire biomedical literature. Show less

A significant challenge in the treatment of melanoma with immune checkpoint blockades (ICBs) is the limited T cells response often observed in immunologically "cold" tumors. By leveraging the immunogenicity of immunogenic cell death (ICD), which increases the susceptibility of tumor cells to ICBs, this study investigated the potential of a nucleus-targeted ruthenium(II) complex (Ru1) as an inducer of ICD. Treatment with Ru1 induced DNA damage in melanoma cells, activating the cyclic GMP-AMP synthase-stimulator of the interferon genes (cGAS-STING) pathway. This triggered endoplasmic reticulum (ER) stress, leading to ICD. Ru1-treated dying melanoma cells exhibited characteristics such as cell exposure of calreticulin (CRT) on the cell surface, release of adenosine triphosphate (ATP), and secretion of high-mobility group box 1 (HMGB1). Vaccination with Ru1-treated, dying melanoma cells elicited robust antitumor immune responses, as evidenced by CD8⁺ T cells activation, reduced Foxp3⁺ T cells count, and the development of a memory immune response that protected mice from subsequent melanoma challenges. Combining Ru1 with anti-PD-1 therapy significantly promoted T cells infiltration, enhanced dendritic cell activation, and reduced tumor-associated immunosuppressive factors, indicating a reprogramming of the tumor microenvironment. These findings suggest that Ru1 is a promising therapeutic agent for treating "cold" tumors in cancer chemoimmunotherapy. Show less

Ruthenium-based metallodrugs have garnered attention as a promising alternative for anticancer therapy, aiming to overcome chemoresistance and severe side effects linked to platinum-based drugs. However, ruthenium complexes tested in clinical trials to date have yielded unsatisfactory results. This study synthesized a positively charged ruthenium complex (Ru-2) that effectively penetrated cancer cells and exhibited superior cytotoxicity to cisplatin in vitro against cancer cell lines and organoids. Ru-2 selectively targeted mitochondria, disrupting their function by depolarizing mitochondrial membrane potential, elevating reactive oxygen species production, and impairing both oxidative phosphorylation and the tricarboxylic acid cycle. Furthermore, Ru-2 triggered endoplasmic reticulum (ER) stress and apoptosis. Integrative transcriptomic and proteomic analyses, performed using RNA sequencing and mass spectrometry, identified key molecular changes in cancer cells treated with Ru-2. For enhanced in vivo application, we developed a transferrin-based nanomedicine formulation, TF/Ru-2, incorporating Ru-2 into transferrin. In vivo studies demonstrated that both Ru-2 and TF/Ru-2 exhibited superior antitumor efficacy and improved biosafety compared to cisplatin. This study presents a novel ruthenium complex and a transferrin-based drug delivery platform with significant potential for future cancer therapies. Show less

Title: Novel Ru(II) Complexes as Type-I/-II Photosensitizers for Multimodal Hypoxia-Tolerant Chemo-Photodynamic/Immune Therapy. Abstract: Photodynamic therapy (PDT) is increasingly regarded as an attractive approach for cancer treatment due to its advantages of low invasiveness, minimal side effects, and high efficiency. Here, two novel Ru(II) complexes 8a,b were designed and synthesized by coordinating phenanthroline and biquinoline ligands with Ru(II) center, and their chemo-photodynamic therapy and immunotherapy were explored. Both 8a and 8b exhibited significant phototoxicity against A549 and 4T1 tumor cells via type-I/-II PDT. Among them, 8b exhibited superior oxygen-independent antitumor effects (IC50s = 1.50-1.76 μM) upon laser irradiation, and displayed micromolar-level chemotherapeutic activities, indicating its potential for chemo/photodynamic dual effects. Furthermore, 8b also initiated an ICD cascade, enhancing recruitment and maturation of antigen-presenting cells, thus triggering a CD8+ T cell antitumor immune response. Finally, in vivo antitumor experiments demonstrated that 8b exhibited significant inhibition of lung and breast tumor growth, with inhibition rates of 94.6% and 97.3%, respectively. Therefore, the Ru(II) complexes we designed, as effective type-I/-II photosensitizers and potential immunoactivators, demonstrate multiple antitumor mechanisms, warranting further study. Show less

Title: Systematic Investigation of Coordination Chemistry in Iridium(III) and Ruthenium(II) Complexes Derived from Pyridyl-Amine Ligands and Their Anticancer Evaluation. Abstract: A systematic investigation of the coordination chemistry of iridium(III) and ruthenium(II) complexes synthesized from pyridyl-amine ligands was performed, focusing on how ligand steric hindrance and metal centers affect oxidation behavior, coordination modes, and biological activities. The study revealed that steric hindrance at the ligand's bridge carbon strongly influenced both oxidation behavior and coordination modes. Smaller substituents (e.g., H and Me) facilitated oxidation to form pyridyl-imine species under adventitious oxygen, whereas bulky substituents (e.g., i-Bu and mesityl) suppressed oxidation, yielding stable pyridyl-amine or 16-electron pyridyl-amido complexes. Moreover, iridium(III) complexes were more prone to oxidation than the corresponding ruthenium(II) complexes under similar conditions. The aqueous stability of the newly synthesized complexes was confirmed. Cytotoxicity assays demonstrated that most of the complexes exhibited notable anticancer potency against A549, HeLa and cisplatin-resistant A549/DDP cancer cells. Mechanistic studies suggested a redox-driven pathway involving the catalytic oxidation of NADH to NAD+, the elevation of ROS levels and depolarization of the mitochondrial membrane. Notably, pyridyl-amine complexes induced apoptosis, while 16-electron pyridyl-amido complexes did not, though both caused S phase cell cycle arrest. Additionally these complexes can inhibit A549 cell migration, suggesting their potential to reduce cancer metastasis. Show less

Bioenergetic therapy targeting mitochondrial bioenergy is a promising therapeutic strategy for cancer. However, its clinical efficacy is limited by the metabolic adaptability of tumor cells, as they can switch between glycolytic and oxidative phosphorylation metabolic phenotypes to maintain energy homeostasis. In this study, we discovered 1,8-naphthyridine-piperazine-dithiocarbamate ruthenium(II) polypyridyl complexes (RuL1) that enhanced energy deprivation by inhibiting the activity of mitochondrial complex I and III, thereby disrupting oxidative phosphorylation. Simultaneously, RuL1 inhibits glycolysis while unexpectedly activating antitumor immunity. This dual metabolic-immunological targeting resulted in enhanced anticancer activity against MGC-803 cells. To the best of our knowledge, RuL1 is the first ruthenium polypyridyl complex reported to achieve high anticancer activity through dual metabolic inhibition. Show less

A series of half-sandwich ruthenium^II and iridium^III complexes bearing hybrid sp³-N/sp²-N amine-imine bidentate chelating ligands were strategically designed and synthesized. Their structures were fully characterized by ¹H and ¹³C NMR spectroscopy, mass spectrometry, and single-crystal X-ray diffraction, revealing nonplanar five-membered metallacycles in representative complexes. The complexes exhibited potent cytotoxicity against A549 lung, HeLa cervical, and HepG2 liver cancer cell lines, with IC₅₀ values ranging from 0.88 to 4.98 μM, significantly lower than that of cisplatin. Notably, the amine-imine complexes displayed superior cytotoxicity compared to their α-diimine analogues. Mechanistic studies indicated that DNA binding is not the primary mode of action. Instead, these complexes selectively target mitochondria, induce mitochondrial membrane depolarization, elevate intracellular reactive oxygen species (ROS) levels, and trigger apoptosis. Additionally, they enter A549 cells through an energy-dependent pathway and effectively inhibit cancer cell migration in vitro. Show less

The diversification of ligands provides more opportunities to adjust the photophysical performance as well as the bio-function of Ru(II) complexes as novel photosensitizers. Herein, a kind of Ru(II) complexes carrying resveratrol derivative, amino-Res, as ligand was designed and synthesized. The representative complex (named Ru4) showed potent anticancer activity under the trigger of 520 nm-light. Lipophilicity and cellular accumulation experiments indicated that Ru4 possessed higher LogP_O/W value and cell up-take than Ru1-Ru3 and [Ru(bpy)₃]²⁺. Mechanism study revealed that Ru4 could inhibit cancer cell migration, invasion and cancer stemness. The bio-function of Ru4 was mainly inherited from the amino-Res ligand. The in vivo study demonstrated that Ru4 could inhibit the tumor growth without significant system toxicity. Show less

In this study, we synthesized 12 monofunctional tridentate ONS-donor salicylaldimine ligand (L)-based Ru(II) complexes with general formula [(Ru(L)(p-cymene)]⁺·Cl^- (C1-C12), characterized by ¹H NMR, ¹³C NMR, UV, FT-IR spectroscopy, HR-ESI mass spectrometry, and single-crystal X-ray analysis showing ligand's orientation around the Ru(II) center. All 12 of these 12 complexes were tested for their anticancer activities in multiple cancer cells. The superior antitumor efficacy of C2, C8, and C11 was demonstrated by reduced mitochondrial membrane potential, impaired proliferative capacity, and disrupted redox homeostasis, along with enhanced apoptosis through caspase-3 activation and downregulation of Bcl-2 expression. In the 4T1 breast cancer orthotopic mouse model, assessment of bioluminescence for metastatic spread, tumor burden, histopathological evaluation, immunohistochemistry (IHC), and hematological profiling and tissue Protein expression of caspase-3, cleaved caspase-3, TNF-α, and bcl-2 demonstrated that C8 treatment led to prolonged survival and suppressed tumor progression in triple negative breast cancer. Show less

Hepatic ischemia-reperfusion injury (HIRI) is one of the main causes of liver insufficiency and failure after liver surgery. However, the effectiveness of current methods of treating HIRI is generally limited. Previous studies have shown that hydrogen sulfide (H₂S) has a beneficial effect on HIRI, and an appropriate concentration of H₂S can significantly reduce HIRI by protecting the mitochondria. Therefore, establishing an accurate imaging platform for monitoring variations in mitochondrial H₂S is an effective strategy for anti-HIRI drug discovery and efficacy evaluation. To this end, a cyclometalated iridium(III) complex-based probe, Cym-Ir-EDB, was developed for detecting mitochondrial H₂S in HIRI. Cym-Ir-EDB possesses good sensitivity, high selectivity, negligible cytotoxicity, and excellent mitochondrial-targeting ability, rendering it a promising imaging tool for analyzing variations in mitochondrial H₂S in HIRI cells. Using Cym-Ir-EDB as a probe, anti-HIRI drugs were screened from isothiocyanates by monitoring variations in mitochondrial H₂S in HIRI cells, for the first time. Moreover, the dynamics of mitochondrial H₂S in HIRI cells were visualized and the response of HIRI to treatment with the screened erucin was monitored. The findings indicate that Cym-Ir-EDB can serve as a useful imaging platform for the precise imaging of mitochondrial H₂S in HIRI, thereby contributing to anti-HIRI drug discovery and efficacy evaluation. Show less

Title: Triphenylphosphine-modified cyclometalated iridium Abstract: This study presents the development and evaluation of triphenylphosphine-modified cyclometalated iridiumIII complexes as selective anticancer agents targeting mitochondria. By leveraging the mitochondrial localization capability of the triphenylphosphine group, these complexes displayed promising cytotoxicity in the micromolar range (3.12-7.24 μM) against A549 and HeLa cancer cells, these complexes exhibit significantly higher activity compared to their unmodified counterparts lacking the triphenylphosphine moiety. Moreover, they demonstrate improved specificity for cancer cells over normal cells, achieving selectivity index in the range of 5.46-14.83. Mechanistic studies confirmed that these complexes selectively target mitochondria rather than DNA, as shown by confocal microscopy and flow cytometry, where they accumulate to induce mitochondrial dysfunction. This disruption leads to mitochondrial membrane depolarization (MMP), elevated reactive oxygen species (ROS) levels, and activation of intrinsic apoptosis pathways. Furthermore, the complexes induce cell cycle arrest at the G2/M phase and suppress the migration of A549 cells. Show less

Site-specific bioconjugation techniques are extensively utilized in biological and biomedical fields to precisely label biomolecules with luminescent tags for direct visualization of their intracellular dynamics or with cytotoxic agents for the development of novel anticancer therapeutics. In this work, a series of cyclometalated iridium-(III) polypyridine complexes featuring a thioester moiety was designed as novel phosphorogenic probes for labeling N-terminal cysteine (N-Cys)-containing biomolecules. These thioester complexes were weakly emissive in solutions due to the presence of a low-lying nonradiative distorted triplet intraligand (³IL) state localized on the thioester unit, as elucidated by computational analyses. However, their emission intensities and singlet oxygen (¹O₂)-photosensitization efficiencies substantially increased upon reaction with l-Cys due to the conversion of the quenching thioester moiety to a nonquenching amide unit. Additionally, the thioester complexes exhibited high selectivity toward N-Cys and displayed significantly enhanced reactivity due to the electron-withdrawing iridium-(III) polypyridine moiety. The remarkable aminothiol-induced emission and ¹O₂-photosensitization turn-on of the thioester complexes were exploited for the development of intracellular Cys sensors and Cys-activatable photosensitizers for cancer-targeted photodynamic therapy. Furthermore, one of the thioester complexes was selected to react with various N-Cys-modified tumor-targeting peptides, yielding photofunctional iridium-(III)-peptide conjugates with high ¹O₂ generation efficiencies. These conjugates retained the tumor-targeting capabilities of the original peptides and showed high specificity for MDA-MB-231 cells compared to MCF-7 and HEK-293 cells, resulting in selective photocytotoxicity toward this triple-negative breast cancer cell line. We believe that our design approach will inspire the development of novel luminogenic thioester-based reagents for bioconjugation, bioimaging, and therapeutic applications. Show less

Title: Mitochondrial-targeted iridium(III) complexes suppress tumor growth through inducting immunogenic cell death to activate immune response. Abstract: A new ligand, 2-(2-hydroxyl-4-methyl)phenyl-1H-imidazo[4,5-f][1,10]phenanthroline (IPMP), and [Ir(ppy)2(IPMP)]PF6 (7a), [Ir(bzq)2(IPMP)]PF6 (7b), and [Ir(piq)2(IPMP)]PF6 (7c) have been prepared and characterized by HRMS, NMR spectra. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assays revealed that 7b exhibited excellent activity (IC50 = 4.5 ± 0.4 μM), while 7a and 7c showed good cytotoxicity (IC50 = 8.5 ± 0.9 μM and 8.9 ± 2.2 μM) against non-small cell lung cancer A549 cells. The experiments of cellular uptake and mitochondrial localization demonstrate that these new iridium(III) complexes are readily taken up by A549 cells and accumulate in the mitochondria and damage the structure of the mitochondria, which results in the loss of mitochondrial membrane potential (MMP), elevated lipid peroxidation, as well as DNA damage, the inhibition of microtubule polymerization, hindrance of the cell cycle in the G0/G1 phase, and release of cytochrome c, collectively leading to apoptosis. Furthermore, upregulation of Beclin-1, overexpression of NF-κB and downregulation of GPX4 protein were observed, which resulted in the activation of autophagy, pyroptosis and ferroptosis, respectively. In the C57BL/6 mouse model, the 7b demonstrated promising in vivo antitumor efficacy, with a tumor inhibitory rate of 66.9 %. Additionally, the complexes induce an immunogenic cell death to activate immune response, further enhance CD8+ T cells and efficiently inhibit tumor growth. Collectively, we consider that the complexes may be utilized as potential candidate agents for the treatment of A549 cancer. Show less

Title: Aggregation-Induced Photosensitization of Long-Chain-Substituted Osmium Complexes for Lysosomes Targeting Photodynamic Therapy. Abstract: Photodynamic therapy (PDT) has been demonstrated to be an effective tool for cancer treatment. Seeking organelle-targeting photosensitizers (PSs) with robust reactive oxygen species (ROS) production is extremely in demand. Herein, we propose an aggregation-induced photosensitization strategy for effective PDT with osmium complexes. We designed and synthesized three osmium complexes (Os-Me, Os-tBu, and Os-Nonly) with ligands of different alkyl chains. In phosphate-buffered saline solution, the complex Os-Nonly formed a spherical aggregate with diameters of around 220 nm. The results from ROS assays indicate that Os-Nonly showed the highest efficiency in generating superoxide anions and singlet oxygen, demonstrating its role as a type I/II photosensitizer. Additionally, Os-Nonly specifically targeted lysosomes in 4T1 and MCF-7 cells, producing ROS in a sustained and efficient manner with high phototoxicity (IC50 = 6.999 μM in MCF-7 cells), thereby inducing cancer cell death. In 4T1-tumor-bearing mice models, Os-Nonly effectively inhibited tumor growth with a minimal impact on normal organs. Show less

Although 5-fluorouracil (5-FU) is the primary chemotherapy treatment for colorectal cancer (CRC), its efficacy is limited by drug resistance. Ferroptosis activation is a promising treatment for 5-FU-resistant cancer cells; however, potential therapeutic targets remain elusive. This study investigated ferroptosis vulnerability and dihydroorotate dehydrogenase (DHODH) activity using stable, 5-FU-resistant CRC cell lines and xenograft models. Ferroptosis was characterized by measuring malondialdehyde levels, assessing lipid metabolism and peroxidation, and using mitochondrial imaging and assays. DHODH function is investigated through gene knockdown experiments, tumor behavior assays, mitochondrial import reactions, intramitochondrial localization, enzymatic activity analyses, and metabolomics assessments. Intracellular lipid accumulation and mitochondrial DHODH deficiency led to lipid peroxidation overload, weakening the defense system of 5-FU-resistant CRC cells against ferroptosis. DHODH, primarily located within the inner mitochondrial membrane, played a crucial role in driving intracellular pyrimidine biosynthesis and was redistributed to the cytosol in 5-FU-resistant CRC cells. Cytosolic DHODH, like its mitochondrial counterpart, exhibited dihydroorotate catalytic activity and participated in pyrimidine biosynthesis. This amplified intracellular pyrimidine pools, thereby impeding the efficacy of 5-FU treatment through molecular competition. These findings contribute to the understanding of 5-FU resistance mechanisms and suggest that ferroptosis and DHODH are promising therapeutic targets for patients with CRC exhibiting resistance to 5-FU. Show less

Expert curation is essential to capture knowledge of enzyme functions from the scientific literature in FAIR open knowledgebases but cannot keep pace with the rate of new discoveries and new publications. In this work we present EnzChemRED, for Enzyme Chemistry Relation Extraction Dataset, a new training and benchmarking dataset to support the development of Natural Language Processing (NLP) methods such as (large) language models that can assist enzyme curation. EnzChemRED consists of 1,210 expert curated PubMed abstracts where enzymes and the chemical reactions they catalyze are annotated using identifiers from the protein knowledgebase UniProtKB and the chemical ontology ChEBI. We show that fine-tuning language models with EnzChemRED significantly boosts their ability to identify proteins and chemicals in text (86.30% F1 score) and to extract the chemical conversions (86.66% F1 score) and the enzymes that catalyze those conversions (83.79% F1 score). We apply our methods to abstracts at PubMed scale to create a draft map of enzyme functions in literature to guide curation efforts in UniProtKB and the reaction knowledgebase Rhea. 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 search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery. Show less

Lysosome-targeted photodynamic therapy, which enhances reactive oxygen species (ROS)-responsive tumor cell death, has emerged as a promising strategy for cancer treatment. Herein, a uridine (dU)-modified Ru(II) complex (RdU) was synthesized by click chemistry. It was found that RdU exhibits impressive photo-induced inhibition against the growth of triple-negative breast cancer (TNBC) cells in normoxic and hypoxic microenvironments through ROS production. It was further revealed that RdU induces ferroptosis of MDA-MB-231 cells under light irradiation (650 nm, 300 mW/cm²). Additional experiments showed that RdU binds to lysosomal integral membrane protein 2 (LIMP-2), which was confirmed by the fact that RdU selectively localizes in the lysosomes of MDA-MB-231 cells and significantly augments the levels of LIMP-2. Molecular docking simulations and an isothermal titration calorimetry assay also showed that RdU has a high affinity to LIMP-2. Finally, in vivo studies in tumor-bearing (MDA-MB-231 cells) nude mice showed that RdU exerts promising photodynamic therapeutic effects on TNBC tumors. In summary, the uridine-modified Ru(II) complex has been developed as a potential LIMP-2 targeting agent for TNBC treatment through enhancing ROS production and promoting ferroptosis. Show less

A diverse set of neutral half-sandwich iminoamido iridium and ruthenium organometallic complexes is synthesized through the utilization of Schiff base pro-ligands with N^˄N donors. Notably, these metal complexes with varying leaving groups (Cl^- or OAc^-) are formed by employing different quantities of the deprotonating agent NaOAc, and exhibit promising cytotoxicity against various cancer cell lines such as A549 and cisplatin-resistant A549/DDP lung cancer cells, as well as HeLa cells, with IC₅₀ values spanning from 9.26 to 15.98 μM. Cytotoxicity and anticancer selectivity (SI: 1.9-2.4) of these metal complexes remain unaffected by variations in the metal center, leaving group, and ligand substitution. Further investigations reveal that these metal complexes specifically target mitochondria, leading to the depolarization of the mitochondrial membrane and instigating the production of intracellular reactive oxygen species. Furthermore, the metal complexes are found to induce late apoptosis and disrupt the cell cycle, leading to G₂/M cell cycle arrest specifically in A549 cancer cells. In light of these findings, it is evident that the primary mechanism contributing to the anticancer effectiveness of these metal complexes is the redox pathway. Show less

Title: Rational design of a red-light absorbing ruthenium polypyridine complex as a photosensitizer for photodynamic therapy. Abstract: Herein, the computer-guided design, chemical synthesis, and biological evaluation of a RuC polypyridine complex, that could eradicate cancerous cells upon excitation with red light at 630 nm, is reported. Show less

To effectively inhibit the growth and metastasis of triple-negative breast cancer (TNBC), we developed a high-efficiency and low-toxicity arene ruthenium (Ru) complex based on apoferritin (AFt). To achieve this, we optimized a series of Ru(II) 1,10-phenanthroline-2,9-diformaldehyde thiosemicarbazone complexes by studying their structure-activity relationships to obtain an arene binuclear Ru(II) complex (C5) with significant cytotoxicity and high accumulation in the mitochondria of tumor cells. Subsequently, a C5-AFt nanoparticle (NPs) delivery system was constructed. We found that the C5/C5-AFt NPs effectively inhibited TNBC growth and metastasis with few side effects. The C5-AFt NPs improved the anticancer and targeting abilities of C5 in vivo. Moreover, we confirmed the mechanism by which C5/C5-AFt NPs inhibit tumor growth and metastasis via mitochondrial damage-mediated ferroptosis and activation of the cGAS-STING pathway. Show less

Title: Antitumor Cream: Transdermal Hydrogel Containing Liposome-Encapsulated Ruthenium Complex for Infrared-Controlled Multimodal Synergistic Therapy. Abstract: A transdermal drug delivery cream, which is non-invasive and painless, containing a liposome-encapsulated Ru(II) complex (LipoRu) is created for the treatment of skin cancer. This formulation capitalizes on the synergistic antitumor effects of two-photon excited photodynamic therapy (PDT), photothermal therapy (PTT), and chemotherapy. LipoRu exhibits effective tumor accumulation, efficient cellular uptake, pH-sensitive and infrared-accelerated release, and dual localization to the nucleus and mitochondria. The released Ru(II) complexes within cells exert multiple antitumor mechanisms, such as DNA topoisomerase and RNA polymerase inhibition, Type I and II PDT, PTT, DNA photodamage, and apoptosis and ferroptosis induction. The biodistribution and therapeutic efficacy of LipoRu in vivo are systematically compared via three distinct administration routes: intratumoral injection, intravenous injection, and transdermal delivery through topical cream application. The positive therapeutic effects of the LipoRu cream fabricated here in subcutaneous tumor-bearing mice offer optimistic potential for the painless and non-invasive treatment of both early-stage and advanced skin cancers, as well as superficially located solid tumors. Show less

Chemoresistance remains an arduous challenge in oncology, but ferroptosis shows potential for overcoming it by stimulating the immune system. Herein, a novel high-performance ruthenium(II)-based arene complex [Ru(η⁶-p-cym)(BTBpy)Cl] (RuBTB) is developed for ferroptosis-enhanced antitumor immunity and drug resistance reversal via glutathione (GSH) metabolism imbalance. RuBTB shows significantly enhanced antiproliferation activity against cisplatin (CDDP)-resistant lung cancer cells (A549R), with 26.35-fold better anticancer effects than CDDP. Immunogenic ferroptosis is induced by GSH depletion/glutathione peroxidase 4 (GPX4) inactivation, mitochondrial dysfunction, and endoplasmic reticulum (ER) stress in RuBTB-treated cells. Mechanism studies indicate that RuBTB regulates ferroptosis and immune-related pathways, coordinating with GSH metabolism-mediated glutathione S-transferase (GST) inhibition to reverse drug resistance in platinum-combined therapy. Tumor vaccination experiments demonstrate the intensified antitumor effects endowed by highly immunogenic ferroptosis in vivo. This study provides the first example of a metal-arene complex for achieving satisfactory ferroptosis therapeutic effects with efficient immunogenicity to overcome drug resistance in metal-based immunochemotherapy. Show less

Transition metal complexes with characteristics of unique packaging in nanoparticles and remarkable cancer cell cytotoxicity have emerged as potential alternatives to platinum-based antitumor drugs. Here we report the synthesis, characterization, and antitumor activities of three new Ruthenium complexes that introduce 5-fluorouracil-derived ligands. Notably, encapsulation of one such metal complex, Ru3, within pluronic^® F-127 micelles (Ru3-M) significantly enhanced Ru3 cytotoxicity toward A549 cells by a factor of four. To determine the mechanisms underlying Ru3-M cytotoxicity, additional in vitro experiments were conducted that revealed A549 cell treatment with lysosome-targeting Ru3-M triggered oxidative stress, induced mitochondrial membrane potential depolarization, and drastically reduced intracellular ATP levels. Taken together, these results demonstrated that Ru3-M killed cells mainly via a non-apoptotic pathway known as oncosis, as evidenced by observed Ru3-M-induced cellular morphological changes including cytosolic flushing, cell swelling, and cytoplasmic vacuolation. In turn, these changes together caused cytoskeletal collapse and activation of porimin and calpain1 proteins with known oncotic functions that distinguished this oncotic process from other cell death processes. In summary, Ru3-M is a potential anticancer agent that kills A549 cells via a novel mechanism involving Ru(II) complex triggering of cell death via oncosis. Show less