👤 Lu L

Sequences of tRNAs are highly patterned in easily identifiable RNA repeats and RNA inverted repeats (stem-loop-stems). Because of patterning, the multi-step evolution of tRNA can be described in remarkable detail. To evolve life on Earth or another planet or the moon requires the evolution of tRNA or a tRNA-like molecule to act as a genetic adapter. To replace tRNA with an alternate or improved genetic adapter is a remarkably challenging problem, indicating strong chemical selection of tRNA precursors in pre-life. The genetic code, translation systems, and first proteins coevolved with tRNAomes (all of the tRNAs of an organism). Because the tRNA sequence can be separated into component parts, a simple pathway for chemical evolution of life and genetic coding can be described in sufficient detail to allow the assembly of a living entity in laboratories. Show less

Claudin (CLDN) proteins are extensively studied due to their critical role in maintaining tissue barriers and cell polarity. However, significant gaps remain in understanding the functional mechanisms of their sequence motifs and the molecular mechanisms of their interactions with other tight junction proteins. This review systematically examines the multifunctional properties of the CLDN protein family from the perspectives of sequence and structure. During evolution, CLDN family members have developed highly conserved structural features, particularly key conserved sites within the first extracellular loop (ECL1) and the C-terminal PDZ-binding domain, which play a central role in regulating the barrier function of tight junctions, ion selectivity, and protein-protein interactions. Furthermore, the distribution pattern of acidic and basic amino acids in ECL1 has been shown to directly determine ion selectivity and paracellular permeability. Meanwhile, the assembly and functional stability of tight junctions are precisely regulated by the C-terminal PDZ-binding domain through its interactions with the ZO protein family. Additionally, the study further elucidates how CLDN proteins modulate critical signaling pathways governing cellular proliferation, survival, and permeability, thereby participating in diverse physiological and pathological processes. These insights have deepened the understanding of the functional diversity of CLDN proteins and provided a new theoretical basis for developing disease diagnostic markers and designing targeted treatment strategies based on CLDN proteins. Show less

N6-methyladenosine (m6A) is the most prevalent internal modification of eukaryotic mRNA and has emerged as a pivotal regulator of gene expression at the post-transcriptional level. In the tumor immune microenvironment, tumor-associated macrophages (TAMs) represent a highly plastic and heterogeneous population that profoundly influences cancer progression, immune evasion, and therapeutic response. Recent studies have uncovered that m6A modification, mediated by dynamic "writers," "erasers," and "readers," exerts critical regulatory effects on TAM differentiation, polarization, and functional reprogramming. By modulating the stability, translation, and decay of transcripts involved in inflammatory signaling, metabolic adaptation, and immune checkpoints, m6A shapes the balance between tumor-promoting (M2-like) and tumor-suppressive (M1-like) macrophage phenotypes. Moreover, dysregulation of m6A machinery in TAMs has been linked to the suppression of anti-tumor immunity and resistance to immunotherapy, highlighting its translational potential as a therapeutic target. This review summarizes current advances in understanding the roles and mechanisms of m6A modification in TAM biology, discusses its implications in tumor immunity, and outlines the challenges and opportunities of targeting the m6A-TAM axis for cancer treatment. Show less

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

Deep learning, a cornerstone of artificial intelligence, is driving rapid advancements in computational biology. Protein-protein interactions (PPIs) are fundamental regulators of biological functions. With the inclusion of deep learning in PPI research, the field is undergoing transformative changes. Therefore, there is an urgent need for a comprehensive review and assessment of recent developments to improve analytical methods and open up a wider range of biomedical applications. This review meticulously assesses deep learning progress in PPI prediction from 2021 to 2025. We evaluate core architectures (GNNs, CNNs, RNNs) and pioneering approaches-attention-driven Transformers, multi-task frameworks, multimodal integration of sequence and structural data, transfer learning via BERT and ESM, and autoencoders for interaction characterization. Moreover, we examined enhanced algorithms for dealing with data imbalances, variations, and high-dimensional feature sparsity, as well as industry challenges (including shifting protein interactions, interactions with non-model organisms, and rare or unannotated protein interactions), and offered perspectives on the future of the field. In summary, this review systematically summarizes the latest advances and existing challenges in deep learning in the field of protein interaction analysis, providing a valuable reference for researchers in the fields of computational biology and deep learning. Show less

Colorectal cancer (CRC) exhibits significant diversity and heterogeneity, posing a requirement for novel therapeutic targets. Polysulfides are associated with CRC progression and immune evasion, but the underlying mechanisms are not fully understood. Sulfide: quinone oxidoreductase (SQR), a mitochondrial flavoprotein, catalyzes hydrogen sulfide (H2S) oxidation and polysulfides production. Herein, we explored its role in CRC pathogenesis and its potential as a therapeutic target. Our findings revealed that SQR knockout disrupted polysulfides homeostasis, diminished mitochondrial function, impaired cell proliferation, and triggered early apoptosis in HCT116 CRC cells. Moreover, the SQR knockout led to markedly reduced tumor sizes in mice models of colon xenografts. Although the transcription of glycolytic genes remained largely unchanged, metabolomic analysis demonstrated a reprogramming of glycolysis at the fructose-1,6-bisphosphate degradation step, catalyzed by aldolase A (ALDOA). Both Western blot analysis and enzymatic assays confirmed the decrease in ALDOA levels and activity. In conclusion, the study establishes the critical role of SQR in mitochondrial function and metabolic regulation in CRC, with its knockout leading to metabolic reprogramming and diminished tumor growth in HCT116 tumor xenografts. These insights lay a foundation for the development of SQR-targeted therapies for CRC. Show less

Ferroptosis is a distinct form of regulated cell death characterized by iron-dependent lipid peroxidation, which plays a critical role in the pathogenesis of various diseases, including ischemic tissue injury, infectious diseases, neurodegenerative disorders, and cancer. The regulatory mechanisms underlying ferroptosis involve a complex interplay of multiple subcellular organelles, orchestrating iron homeostasis, lipid metabolism, and the generation of reactive oxygen species (ROS) that drive peroxidation processes, ultimately leading to membrane damage and cell death. Numerous antioxidant systems play pivotal roles in regulating and preventing ferroptosis, among which the recently identified mitochondrial inner membrane enzyme dihydroorotate dehydrogenase (DHODH) represents a novel therapeutic target for ferroptosis intervention. This systematic review comprehensively elucidates several key cellular defense mechanisms against ferroptosis that counteract ROS-driven peroxidation and operate through distinct subcellular localizations. We particularly focus on delineating the molecular mechanisms by which DHODH regulates ferroptosis, with special emphasis on its role in suppressing mitochondrial lipid peroxidation. Furthermore, we systematically evaluate the therapeutic potential of DHODH inhibitors in oncology, virology, and immune-inflammatory disorders. By integrating ferroptosis biology with DHODH-mediated cytoprotective networks, this review aims to provide mechanistic insights and novel therapeutic strategies for cancer and oxidative stress-related disorders. Show less

Ferroptosis, a novel form of regulated cell death induced by the excessive accumulation of lipid peroxidation products, plays a pivotal role in the suppression of tumorigenesis. Two prominent mitochondrial ferroptosis defense systems are glutathione peroxidase 4 (GPX4) and dihydroorotate dehydrogenase (DHODH), both of which are localized within the mitochondria. However, the existence of supplementary cellular defense mechanisms against mitochondrial ferroptosis remains unclear. Our findings unequivocally demonstrate that inactivation of mitochondrial respiratory chain complex I (MCI) induces lipid peroxidation and consequently invokes ferroptosis across GPX4 low-expression cancer cells. However, in GPX4 high expression cancer cells, the MCI inhibitor did not induce ferroptosis, but increased cell sensitivity to ferroptosis induced by the GPX4 inhibitor. Overexpression of the MCI alternative protein yeast NADH-ubiquinone reductase (NDI1) not only quells ferroptosis induced by MCI inhibitors but also confers cellular protection against ferroptosis inducers. Mechanically, MCI inhibitors actuate an elevation in the NADH level while concomitantly diminishing the CoQH2 level. The manifestation of MCI inhibitor-induced ferroptosis can be reversed by supplementation with mitochondrial-specific analogues of CoQH2. Notably, MCI operates in parallel with mitochondrial-localized GPX4 and DHODH to inhibit mitochondrial ferroptosis, but independently of cytosolically localized GPX4 or ferroptosis suppressor protein 1(FSP1). The MCI inhibitor IACS-010759, is endowed with the ability to induce ferroptosis while concurrently impeding tumor proliferation in vivo. Our results identified a ferroptosis defense mechanism mediated by MCI within the mitochondria and suggested a therapeutic strategy for targeting ferroptosis in cancer treatment. Show less

Reactive molecules, including oxygen and nitrogen species, serve dual roles in human physiology. While they function as essential signaling molecules under normal physiological conditions, they contribute to cellular dysfunction and damage when produced in excess by normal metabolism or in response to stressors. Oxidative/nitrosative stress is a pathological state, resulting from the overproduction of reactive species exceeding the antioxidant capacity of the body, which is implicated in several chronic human diseases. Antioxidant therapies aimed at restoring redox balance and preventing oxidative/nitrosative stress have demonstrated efficacy in preclinical models. However, their clinical applications have met with inconsistent success owing to efficacy, safety, and bioavailability concerns. This summative review analyzes the role of reactive species in human pathophysiology, the mechanisms of action of antioxidant protection, and the challenges that hinder their translation into effective clinical therapies in order to evaluate potential emerging strategies such as targeted delivery systems, precision medicine, and synergistic therapeutic approaches, among others, to overcome current limitations. By integrating recent advances, this review highlights the value of targeting reactive species in the prevention and management of chronic diseases. Show less

As two pivotal regulatory factors in cancer biology, oxidative stress and inflammation interact dynamically through complex network mechanisms to influence tumor initiation, progression, and treatment resistance. Oxidative stress induces genomic instability, oncogenic signaling activation, and tumor microenvironment (TME) remodeling via the abnormal accumulation of reactive oxygen species (ROS) or reactive nitrogen species (RNS). Conversely, inflammation sustains malignant phenotypes by releasing pro-inflammatory cytokines and chemokines and promoting immune cell infiltration. These processes create a vicious cycle via positive feedback loops whereby oxidative stress initiates inflammatory signaling, while the inflammatory milieu further amplifies ROS/RNS production, collectively promoting proliferation, migration, angiogenesis, drug resistance, and immune evasion in tumor cells. Moreover, their crosstalk modulates DNA damage repair, metabolic reprogramming, and drug efflux pump activity, significantly impacting the sensitivity of cancer cells to chemotherapy, radiotherapy, and targeted therapies. This review systematically discusses these advances and the molecular mechanisms underlying the interplay between oxidative stress and inflammation in cancer biology. It also explores their potential as diagnostic biomarkers and prognostic indicators and highlights novel therapeutic strategies targeting the oxidative stress-inflammation axis. The goal is to provide a theoretical framework and translational roadmap for developing synergistic anti-tumor therapies. Show less

The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we describe ongoing changes to our production pipeline to limit the sequences available in UniProtKB to high-quality, non-redundant reference proteomes. We continue to manually curate the scientific literature to add the latest functional data and use machine learning techniques. We also encourage community curation to ensure key publications are not missed. We provide an update on the automatic annotation methods used by UniProtKB to predict information for unreviewed entries describing unstudied proteins. Finally, updates to the UniProt website are described, including a new tab linking protein to genomic information. In recognition of its value to the scientific community, the UniProt database has been awarded Global Core Biodata Resource status. 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

In this work, we have carefully designed and synthesized two Ru(II) metal complexes: [Ru(phen)₂(HMPIP)](PF₆)₂ (6a, where phen = 1,10-phenanthroline, HMPIP = 2-(2-hydroxy-3-methylphenyl-1H-imidazo[4,5-f][1,10]phenanthroline) and [Ru(bpy)₂(HMPIP)](PF₆)₂ (6b, where bpy = 2,2'-bipyridine). Using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to explore the cytotoxicity of 6a and 6b towards HepG2, B16, A549, SGC-7901, HCT116 and non-cancer LO2. The complexes exhibited cytotoxicity activity against HepG2 cells. The capacity of 6a and 6b to impede the proliferation and dissemination of cancer cells was evaluated by conducting proliferation and migration experiments and 3D model. The anticancer mechanism was investigated in detail. The utilization of cycle blocking assays revealed that 6a and 6b induced a G0/G1 phase arrest in HepG2 cells. The cellular uptake experiments show that the complexes enter the cell nuclei, then escape from the cell nuclei into the cytoplasm, finally accumulate in the mitochondria. Apoptosis assays and the examination of proteins indicated that the complexes were capable of efficiently inducing apoptosis in HepG2 cells. Additionally, the potential induction of autophagy-mediated cell death was explored. The observed reduction in glutathione (GSH) levels and glutathione peroxidase 4 (GPX4) expression suggested a disruption of redox homeostasis within cancer cells, an increment in malondialdehyde (MDA) amount, together with BODIPY staining experiment, confirm that 6a and 6b can induce ferroptosis. Interestingly, in a nude mouse model, 6a showed a significant suppression of tumor growth with an inhibition rate of 63.4 %, without causing any weight loss of mice. The studies on the mechanism show that 6a causes immune cell death, increase the amount of TNF-α and IFN-γ, reduce IL-10 content, which further activates immune response to increase CD8⁺ T cells to prevent tumor growth. Therefore, 6a inhibits the tumor growth through stimulating the immune response to increase CD8⁺ T cells. In addition, the experiments in vitro show that the complexes through inhibition of PI3K/AKT/mTOR signaling pathway and intrinsic mitochondria pathway to cause cell apoptosis. These results demonstrate that Ru(II) complexes may be potent anticancer candidates for HepG2 tumor. 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

In recent years, photodynamic therapy (PDT) has emerged as a promising alternative to classical chemotherapy for treating cancer. PDT is based on a nontoxic prodrug called photosensitizer (PS) activated by light at the desired location. Upon irradiation, the PS reacts with the oxygen present in the tumor, producing cytotoxic reactive oxygen species (ROS). Compounds with highly conjugated π-bond systems, such as porphyrins and chlorins, have proven to be excellent light scavengers, and introducing a metal atom in their structure improved the generation of ROS. In this work, a series of tetrapyrrole-ruthenium(II) complexes derived from protoporphyrin IX and the commercial drug verteporfin were designed as photosensitizers for PDT. The complexes were almost nontoxic on human gastric cancer cells under dark conditions, revealing remarkable cytotoxicity upon irradiation with light. The ruthenium atom in the central cavity of the chlorin ligand allowed combined mechanisms in photodynamic therapy, as both singlet oxygen and superoxide radicals were detected. Additionally, one complex produced large amounts of singlet oxygen under hypoxic conditions. Biological assays demonstrated that the ruthenium derivatives caused cell death through a caspase 3 mediated apoptotic pathway and via CHOP, an endoplasmic reticulum stress-inducible transcription factor involved in apoptosis and growth arrest. Show less

In order to discover new dual-active agents, novel ruthenium (η⁶-p-cymene) complexes of the general formula [(η⁶-p-cym)Ru(OO)Cl] with O,O-diketo ester ligands ethyl 2-hydroxy-4-aryl-4-oxobut-2-enoate (1-3), were synthesized. The complexes 1-3 were characterized by spectral techniques (UV-Vis, IR, ¹H and ¹³C NMR, and ESI-HRMS), elemental analysis, and X-ray crystallography. Based on in vitro DNA/HSA experiments, complex 1 exhibited the highest DNA/HSA-activity, suggesting that the presence of an alkene chain contributes to increased activity. The cytotoxic activity of 1-3 was evaluated in a panel of human cancer cell lines (A549, MDA-MB-231, LS-174, HeLa), and in one normal cell line (MRC-5), both in the absence and presence of biocompatible ionic liquids (BIO-ILs) such as cholinium glycinate (Cho-Gly), cholinium β-alaninate (Cho-Ala), and cholinium glutamate (Cho-Glu). Complex 1 exhibited the highest cytotoxicity and demonstrated selectivity toward HeLa cells. Additionally, its cytotoxicity was enhanced when combined with the BIO-ILs Cho-Gly and Cho-Ala. This study suggests that ionic liquids can influence the efficacy and selectivity of cancer treatments, highlighting the potential for enhancing therapeutic outcomes. However, it also emphasizes the need for a deeper understanding of BIO-IL interactions with cellular processes. Furthermore, compound 1 displayed strong antimicrobial activity against Staphylococcus aureus and Escherichia coli (MIC = 0.078 mg/mL). Among the assessed species, Candida albicans showed the highest sensitivity to antifungal activity. These results suggest that investigated compounds may have potential for further development as clinical candidates, pending additional studies. 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

Title: Ruthenium(II) and copper(II) polyamine complexes as promising antitumor agents: synthesis, characterization, and biological evaluation. Abstract: Ruthenium or copper complexes have emerged as some of the most promising alternatives for the treatment of many types of cancer. They have enhanced activity, greater selectivity and reduced side effects compared to their predecessors, cisplatin and its analogues. On the other hand, polyamine metabolism is often deregulated in cancer, leading to increased intracellular concentrations of polyamines that promote cell proliferation, differentiation, and tumorigenesis. In the present work, we report the synthesis and characterization of a family of mono- and binuclear Ru(II) and Cu(II) complexes functionalized with polyamine ligands derived from norspermine. The computer-aided analysis of the electron paramagnetic resonance (EPR) spectra provided magnetic and dynamic parameters, which helped to identify prevalent Cu-N2 coordination in a partially distorted square planar geometry of the Cu(II) complexes and the flexibility of the complexes in solution, slowed down by both the complex size and the hydrophobic interactions between chains. In vitro studies focused on advanced prostate cancer have demonstrated that these new metal complexes present a high level of cytotoxicity against PC3 cells. Furthermore, these metallic compounds exhibit the ability to inhibit cell adhesion and migration while reducing intracellular reactive oxygen species levels, which are key factors of metastasis. Show less

We introduce ruthenosomes, a fusion of liposomal and reactive oxygen species (ROS)-generating properties meticulously engineered as potent ferroptosis inducers (FINs), marking a significant advancement in metallodrug design for cancer therapy. Formed through the self-assembly of oleate-conjugated ruthenium complexes, these ruthenosomes exhibit exceptional cellular uptake, selectively accumulating in mitochondria and causing substantial disruption. This targeted mitochondrial damage significantly elevates ROS levels, triggering autophagy and selectively activating ferritinophagy. Together, these processes sensitize cancer cells to ferroptosis. In vivo, ruthenosomes effectively suppress colorectal tumor growth, underscoring their therapeutic potential. Our study pioneers a design strategy that transforms ruthenium complexes into liposome-like structures capable of inducing ferroptosis independent of light activation. By leveraging ruthenosomes as multifunctional nanocarriers, this research offers a versatile and powerful platform for ROS-mediated, ferroptosis-driven cancer cell eradication. Show less

Title: A Bioactive Benzimidazole-Cyclometalated Iridium(III) Complex as an Epigenetic Regulator through Effectively Interrupting the EED-EZH2 Interaction. Abstract: Epigenetic regulation plays a fundamental role in controlling gene expression and maintaining cellular identity. Among epigenetic processes, the translocation of methyltransferases is critical for the modification of chromatin structure and transcriptional activity. The regulation of these translocation events and the mechanisms involved are complex, yet critical for understanding and manipulating epigenetic states. Therefore, novel strategies are required for detecting and visualizing the movement and interaction of methyltransferases within cells. Using enhancer of zeste homolog 2 (EZH2) methyltransferase as an example, a bifunctional compound capable of both monitoring and disrupting its translocation process is developed by targeting the protein-protein interaction (PPI) between embryonic ectoderm development (EED) and EZH2. The Ir(III) complex 1 bound enthalpically to EED and effectively inhibited the methyltransferase activity of EZH2. Moreover, disruption of the EED-EZH2 PPI led to increased transcriptional activity of P21 and P27, resulting in the suppression of triple-negative breast cancer (TNBC) cell proliferation. Excitingly, 1 suppressed tumor metastasis in a TNBC mouse model in vivo. To our knowledge, complex 1 is the first metal-based bifunctional therapeutic agent designed to probe and inhibit the EED-EZH2 PPI, highlighting the feasibility and significance of using metal complexes to monitor and influence methyltransferase translocations for therapeutic applications. Show less

A novel bioorganometallic PNA conjugate (Ir-PNA) was synthesized by covalently bonding a model PNA tetramer to a luminescent bis-cyclometalated Ir(III) complex that acted as a photosensitizer under light irradiation to generate singlet oxygen (¹O₂). The conjugate was prepared using an Ir complex bearing the 1,10-phenanthroline ligand functionalized with either a free primary amine (Ir-NH₂) or a carboxyl group (Ir-COOH) for the conjugation to PNA. The photophysical studies on the Ir-COOH and the Ir-PNA demonstrated that the luminescent properties were maintained after the conjugation of the Ir fragment to PNA. Furthermore, the abilities to produce ¹O₂ of Ir-COOH and Ir-PNA were confirmed in a cuvette under visible light irradiation employing 1,5-dihydroxynaphthalene as a reporter, and the measured singlet oxygen quantum yield (Φ_Δ) supported the Ir-PNA conjugate efficacy as a photosensitizer (Φ_Δ = 0.54). Two-photon absorption microscopy on HeLa cells revealed that Ir-PNA localized in both the cytosol and nucleus, suggesting its potential as an intracellular carrier for PNA. Cytotoxicity assays by MTT tests showed that Ir-PNA was nontoxic in the absence of light, but induced cell death (EC₅₀ = 18 μM) after UV irradiation. Overall, the Ir-PNA conjugate represents a promising system for the intracellular delivery of the PNA and its application in PDT. 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

Photoactivatable systems have received considerable attention in the development of diagnostics and therapeutics due to their noninvasive nature and precise spatiotemporal control. Of particular interest is the 3,6-dithio-1,2,4,5-tetrazine (S,S-tetrazine) unit, which can not only act as a photolabile protecting group for constructing photoactivatable systems but also as a bioorthogonal scaffold that enables the inverse electron-demand Diels-Alder (IEDDA) cycloaddition reaction with strained alkynes. In this study, we designed and synthesised a cyclometallated iridium(iii) complex modified with a 3-chloro-6-thio-1,2,4,5-tetrazine moiety (1) for cysteine conjugation. The complex was conjugated with an integrin-targeting peptide c(RGDfC) to afford a tumour-targeting conjugate (1-RGD) for bioimaging and photoactivated therapy. An RGD-free analogue (2) was also prepared for comparison studies. Unlike common iridium(iii) complexes, excitation of conjugate 1-RGD and complex 2 resulted in weak emission and negligible singlet oxygen (¹O₂) generation due to the quenching effect of the tetrazine unit. Upon continuous light irradiation, the S,S-tetrazine moiety in conjugate 1-RGD and complex 2 underwent efficient photodissociation, yielding thiocyanate (3) and amide (4) complexes as photoproducts with increased emission intensities and enhanced ¹O₂ generation efficiencies. Interestingly, the IEDDA cycloaddition reaction of the S,S-tetrazine-containing conjugate 1-RGD and complex 2 with (1R,8S,9s)-bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN-OH) led to significant emission enhancement. Notably, conjugate 1-RGD showed higher cellular uptake and (photo)cytotoxicity (IC_50,dark = 26 μM, IC_50,light = 0.08 μM) in U87-MG cells, which overexpress integrin, compared to MCF-7 (IC_50,dark = 52 μM, IC_50,light = 0.22 μM) and HEK293 cells (IC_50,dark > 50 μM, IC_50,light = 1.3 μM) with lower integrin levels. This work will contribute to the development of photoactivatable transition metal complexes for cancer-targeted imaging and therapy. Show less

Title: Monomer Versus Dimer of Cationic Ir(III) Complexes for Photodynamic Therapy by Two-Photon Activation: A Comparative Study. Abstract: Iridium(III) complexes have been recognized as promising candidates for two-photon sensitized photodynamic therapy (PDT). In this context, we report on the study of two complexes: a monomer (IrL1) and a dimer (Ir2L2). Both complexes possess 2-phenylpyridine cyclometallating ligands and a pyridylbenzimidazole derivative as an ancillary ligand. In the dimer, the two Ir(III) centers are connected by a non-conjugated bridged bis(pyridylbenzimidazole). We compare the photophysical properties of these complexes. Both display phosphorescent emission in the orange-red part of the visible spectrum, with emissions centered at 610 nm for IrL1 and 625 nm for Ir2L2, both exhibiting quantum yields of ∼24%. However, Ir2L2 proves to be much brighter than the monomer, making the dimer four times brighter than IrL1. This trend is consistent under two-photon excitation (TPE), and the singlet oxygen generation quantum yields, with the dimer displaying a figure of merit (σTPA × ΦΔ) of 40, compared to only 5 for the monomer. Both complexes generate intracellular ROS and exhibit strong phototoxicity upon blue light activation (λ = 420 nm), achieving submicromolar IC50 values in HT29 and A549 cell lines after 24 h of incubation. Moreover, with TPE (λ = 800 nm), both complexes also generate intracellular ROS and induce cancer cell death. Show less

Life is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent. Show less

The gasotransmitter hydrogen sulfide (H2S) is thought to be involved in the post-translational modification of cysteine residues to produce reactive persulfides. A persulfide-specific chemoselective proteomics approach with mammalian cells has identified a broad range of zinc finger (ZF) proteins as targets of persulfidation. Parallel studies with isolated ZFs show that persulfidation is mediated by ZnII, O2, and H2S, with intermediates involving oxygen- and sulfur-based radicals detected by mass spectrometry and optical spectroscopies. A small molecule ZnII complex exhibits analogous reactivity with H2S and O2, giving a persulfidated product. These data show that ZnII is not just a biological structural element, but also plays a critical role in mediating H2S-dependent persulfidation. ZF persulfidation appears to be a general post-translational modification and a possible conduit for H2S signaling. This work has implications for our understanding of H2S-mediated signaling and the regulation of ZFs in cellular physiology and development. 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

The versatility of cellular response arises from the communication, or crosstalk, of signaling pathways in a complex network of signaling and transcriptional regulatory interactions. Understanding the various mechanisms underlying crosstalk on a global scale requires untargeted computational approaches. We present a network-based statistical approach, MuXTalk, that uses high-dimensional edges called multilinks to model the unique ways in which signaling and regulatory interactions can interface. We demonstrate that the signaling-regulatory interface is located primarily in the intermediary region between signaling pathways where crosstalk occurs, and that multilinks can differentiate between distinct signaling-transcriptional mechanisms. Using statistically over-represented multilinks as proxies of crosstalk, we infer crosstalk among 60 signaling pathways, expanding currently available crosstalk databases by more than five-fold. MuXTalk surpasses existing methods in terms of model performance metrics, identifies additions to manual curation efforts, and pinpoints potential mediators of crosstalk. Moreover, it accommodates the inherent context-dependence of crosstalk, allowing future applications to cell type- and disease-specific crosstalk. 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