👤 Seda Vatansever H

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo-electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis. Show less

We hypothesize that predictable variations in environmental conditions caused by night/day cycles created opportunities and hazards that initiated information dynamics central to life's origin. Increased daytime temperatures accelerated key chemical reactions but also caused the separation of double-stranded polynucleotides, leading to hydrolysis, particularly of single-stranded RNA. Daytime solar UV radiation promoted the synthesis of organic molecules but caused broad damage to protocell macromolecules. We hypothesize that inter-related simultaneous adaptations to these hazards produced molecular dynamics necessary to store and use information. Self-replicating RNA heritably reduced the hydrolysis of single strands after separation during warmer daytime periods by promoting sequences that formed hairpin loops, generating precursors to transfer RNA (tRNA), and initiating tRNA-directed evolutionary dynamics. Protocell survival during daytime promoted sequences in self-replicating RNA within protocells that formed RNA-peptide hybrids capable of scavenging UV-induced free radicals or catalyzing melanin synthesis from tyrosine. The RNA-peptide hybrids are precursors to ribosomes and the triplet codes for RNA-directed protein synthesis. The protective effects of melanin production persist as melanosomes are found throughout the tree of life. Similarly, adaptations mitigating UV damage led to the replacement of Na+ by K+ as the dominant mobile cytoplasmic cation to promote diel vertical migration and selected for homochirality. We conclude that information dynamics emerged in early life through adaptations to predictably fluctuating opportunities and hazards during night/day cycles, and its legacy remains observable in extant life. Show less

In the healthcare industry, the ever-increasing volume of clinical trial data presents challenges for ensuring drug safety and detecting adverse drug reactions (ADRs). This study aims to address the challenge of accurately detecting Serious Adverse Events (SAEs) in pharmacovigilance, a critical component in ensuring drug safety during and after clinical trials. The key problem lies in the underreporting and delayed detection of Adverse Drug Reactions (ADRs) due to the heterogeneous nature of medical data, class imbalance, and the limited scope of traditional monitoring techniques. This study proposes a hybrid AI-driven framework that integrates structured (e.g., patient demographics, lab results) and unstructured data (e.g., clinical notes) to detect ADRs using advanced deep learning and NLP methods. The objective is to outperform traditional signal detection methods and provide interpretable predictions to aid clinicians in real-time. By leveraging advanced Machine Learning (ML) and Deep Learning (DL) techniques, including Random Forests, Gradient Boosting Machines, and Convolutional Neural Networks (CNNs), our model aims to identify potential ADRs across different patient subgroups. Through meticulous feature engineering and the application of techniques to address data imbalance, our model demonstrates improved accuracy and interpretability in predicting ADRs. The CNN model achieved an accuracy of 85 %, outperforming traditional models, such as Logistic Regression (78 %) and Support Vector Machines (80 %). These findings suggest that specific demographic and clinical factors significantly influence the likelihood of adverse reactions, offering valuable insights for targeted monitoring and risk mitigation strategies[11]. This research underscores the potential of predictive modeling to enhance pharmacovigilance efforts and ensure safer clinical trial outcomes.•The research methodology includes a comparison of supervised learning algorithms, such as Logistic Regression, Random Forest, Gradient Boost, CNN, and genetic algorithms, to identify patterns and anomalies in clinical trial data. BERT and GPT, were also employed to provide the functionality of textual interactions over medical data.•Performance metrics such as accuracy, precision, recall, and F1-score were systematically applied to evaluate each model's performance. Among the models tested, the CNN model with BERT achieved the highest accuracy, providing valuable insights into the potential of deep learning for enhancing pharmacovigilance practices.•These findings suggest that an inclusion of diverse clinical data when supplied to advanced ML and NLP techniques can significantly improve the detection of ADRs, leading to better alignment with the fundamental principles of Good Clinical Practice (GCP). 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

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

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

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

Cisplatin and its analogs are extensively utilized as metal-based anticancer agents in clinical settings due to their mechanism of action, which involves targeting genomic double-stranded DNA to induce cytotoxicity in cancer cells. However, the associated severe side effects and DNA damage repair-inducing drug resistance present significant challenges. In recent years, G-quadruplex nucleic acids, formed through the self-assembly of guanine-rich nucleic acid sequences, have emerged as a compelling target for the design of novel anticancer therapeutics. The strategic design of platinum complexes that selectively interact with, stabilize, or cleave G-quadruplex structures represents a promising approach for developing effective anticancer agents to overcome cisplatin resistance. This review will emphasize the advancements made over the past decade in interacting G-quadruplexes with platinum complexes as potential anticancer therapeutics. The ongoing development of platinum complexes spans from targeting nuclear DNA G-quadruplexes to mitochondrial DNA and cytoplasmic RNA G-quadruplexes, evolving from monotherapy approaches, such as chemotherapy and photodynamic therapy, to a combination of radiotherapy, immunotherapy, and more, highlighting the dynamic progress of platinum complexes. At the end, we have summarized 4 points of pending issues in this fast-growing field, which we hope can provide some help to the development of this field. Show less

Mitochondria are essential organelles for many aspects of cellular homeostasis. They play an indispensable role in the development and progression of diseases, particularly cancer which is a major cause of death worldwide. We analyzed the scientific research output on mitochondria and cancer via PubMed and Web of Science over the period 1990-2023. Show less

Here, we shed physico-chemical light on major kinase signal transduction cascades in cell proliferation in the Ras network, MAPK and PI3K/AKT/mTOR. The cascades respond to external stimuli. The kinases are allosterically activated and relay the signal, leading to cell growth and division. The pathways are crosslinked, with the output of one pathway influencing the other. The effectiveness of their allosteric signaling relay stems from coordinated speed and precision. These qualities are essential for cell life-yet exactly how they are obtained and regulated has challenged the community over four decades. Here, we define their nature by their kinases' repertoires, substrate specificities and breadth, activation and autoinhibition mechanisms, catalytic rates, interactions, and their dilution state. The cascades are lodged in a dense molecular condensate phase at the membrane adjoining RTK clusters, where their assemblies promote specific, productive signaling. Aiming to shed further physico-chemical light, we ask (i) how starting the cascades with a single substrate and ending with hundreds is still labeled specific; (ii) what we can learn from their different number of mutations; and (iii) why B-Raf unique side-to-side inverse dimerization slows ERK activation and signaling. We point to the (iv) chemical mechanics of the distributions of rates of the crucial MAPK cascade: slower at the top and rapid at the bottom. Finally, the cascades provide inspiration for pharmacological perspectives. Collectively, our updated physico-chemical outlook provides the molecular basis of targeting protein kinases in cancer and spans mechanisms and scales, from conformational landscapes to membraneless organelles, cells and systems levels. 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

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

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

Researchers are increasingly focusing on developing target-specific, highly cytoselective, lipophilic, water-soluble Ru(II) arene complexes to mitigate the side effects of commercially available platinum-based anticancer drugs. In this context, we present novel Ru(II) arene complexes, (Ru1 and Ru1a-f), which are based on a 1,10-phenanthroline-substituted imidazolium core derivatized with alkyl (butyl(a), octyl(b), dodecyl(c)) or benzyl ((benzyl(d), 2,4,6-trimethylbenzyl(e), pentamethylbenzyl(f)) groups. The structures of these complexes were characterized using ¹H, ¹³C, ¹⁹F and, ³¹P nuclear magnetic resonance (NMR) spectroscopy, Fourier transform infrared spectroscopy, mass spectrometry and elemental analysis. The cytotoxic activities of Ru1 and Ru1a-f complexes were tested against the cancer cell lines MCF-7 and MDA-MB-231 and normal cell lines, such as MCF-10 A. The cell cycle distribution in the MCF-7 and MDA-MB-231 breast cancer cell lines after 72 h of incubation with IC₅₀ concentration of the complex Ru1c can validly inhibit cell growth in the G2/M phase. Flow cytometry analysis showed that the complex Ru1c induced apoptosis in MCF-7 and MDA-MB-231 breast cancer cells. Additionally, the binding mode of the complex Ru1c with Fish-Salmon DNA was examined using ultraviolet-visible spectroscopy. Interaction of Ru1c complex with bovine serum albumin was analyzed by absorption study. The stability of all complexes in the solvent was assessed using ¹H NMR spectroscopy. Additionally, quantitative determination of the total ruthenium level within the cells was performed by inductively coupled plasma mass spectrometry (ICP-MS). Molecular docking was performed to evaluate the interaction residues and docking scores of Ru1c and the reference drug cis‑platinum against CDK1, cyclin B1, Bcl-xL and Bcl-2 proteins. 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

Acute leukemia, a cancer originating in the bone marrow and blood-forming tissues, poses a significant threat to human health. Chemotherapy may cause a range of side effects and further cause greater suffering to the patients. Thus, reducing the toxicity of the drugs for treating leukemia has become a significant challenge. In this study, we developed two non‑platinum anticancer agents, ole-Ru and ole-Ir, by fusing the natural product oleanolic acid as the ligand into two metal (ruthenium and iridium) precursors. Ole-Ru and ole-Ir not only exhibited remarkable selectivity and cytotoxicity against NB4 cells through the apoptosis pathway, but also demonstrated low toxicity towards normal lung fibroblast cells, suggesting their potential for targeted treatment of acute leukemia cells. This work presents a rational design strategy for metal-based anticancer complexes aimed at inhibiting NB4 cells and expanded the scope of metallodrugs used in the treatment of leukemia. 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

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

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: Radiosensitization effect of iridium (III) complex on lung cancer cells via mitochondria apoptosis pathway. Abstract: BACKGROUND: Lung cancer is the leading cause of cancer-related death in the worldwide. Although cisplatin and other platinum-based drugs are widely used as radiosensitizers in radiotherapy and considered the first-line treatment for advanced lung cancer, their clinical utility is often limited by drug resistance and severe cytotoxic side effects. In recent years, iridium-based complexes and other transition metal cation complexes with similar structural properties have garnered increasing research interest due to their potential anticancer properties. METHODS: Recently, we synthesized a novel iridium (III) complex (Ir-1) and evaluated its safety and stability. The present study aimed to identify Ir-1 with potent anticancer activity by assessing its cytotoxic effects on lung cancer cells in vitro. Additionally, it investigated Ir-1's radiosensitizing efficacy and the underlying mechanisms. RESULTS: The results demonstrated that Ir-1 exhibited significant radiosensitizing effects on lung cancer cells. Ir-1 effectively reduced cell viability and colony formation, arrested the cell cycle at the G2/M phase, inhibited cell migration and invasion, decreased mitochondrial membrane potential, and increased reactive oxygen species (ROS) generation in lung cancer cells. Importantly, these cytotoxic effects were selective, with minimal impact on normal cells. Mechanistic studies showed that Ir-1 enhanced radiation-induced cancer cell death by disrupting mitochondrial function and activating the mitochondrial apoptotic pathway. This was evidenced by upregulated expression levels of Bax, Cytochrome c (Cyt-C), and Caspase9 proteins, along with reduced level of Bcl-2 protein. Notably, the addition of a Cyt-C inhibitor significantly reduced the expression of Cyt-C and Caspase9 proteins. Similarly, treatment with the Caspase9 inhibitor Z-LEHD-FMK also reduced Caspase9 protein level. CONCLUSION: This study provides robust evidence that Ir-1 is a promising and safe radiosensitizer for lung cancer therapy. Its ability to enhance radiation-induced cytotoxicity through mitochondrial dysfunction and activation of apoptotic pathways highlights its potential for clinical application. Show less

While molecular isomers exhibit nearly identical compositions, their spatial arrangement often dictates distinct physicochemical properties. We present a regioisomer engineering strategy to construct two iridium(III) complexes (Ir1 and Ir2) through precise positioning of triphenylamine electron donors relative to the metal chelation core. Compared to Ir1, Ir2 features strategically displaced donors that create a contracted bandgap, reduced oxidation potential, and amplified spin-orbit coupling (SOC). These electronic modifications synergistically enable Ir2 to achieve superior type I photodynamic activity and thus generate O₂^•- and •OH radicals after 633 nm irradiation even under hypoxic conditions. The sustained reactive oxygen species (ROS) production induces potent immunogenic cell death (ICD), ultimately stimulating dendritic cell maturation and antitumor immunity. This regioisomeric design paradigm establishes a molecular blueprint for oxygen-tolerant photosensitizers, addressing the critical challenge of hypoxia in photoimmunotherapy applications. 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

Modulating mitochondrial activity to regulate cancer cell homeostatic recycling presents a promising approach to overcome tumor resistance. Consequently, there is an urgent need for novel mitochondria-targeting agents and innovative strategies. We have developed [((η⁵-Cp∗)Ir(rhod)]²⁺2PF₆^- (Ir-rhod), a new mitochondria-targeted iridium complex that exhibits greater cytotoxicity towards A549R (cisplatin-resistant human lung cancer) cells compared to the ligand rhod. Ir-rhod's mitochondrial targeting ability stems from both rhodamine's inherent mitochondrial affinity and the complex's positive bivalent nature. The positively charged Ir-rhod enters cells and is drawn to mitochondria due to the high transmembrane potential in tumor cells. Notably, rhodamine enables real-time observation of Ir-rhod's dynamic distribution in vivo. Ir-rhod influences mitochondrial function, triggering tumor cell ferroptosis and apoptosis by modulating ACSL4 and GPX4. The targeting effect of Ir-rhod reduces its systemic toxicity in vivo, enhancing its biosafety profile. To our knowledge, Ir-rhod is an effective mitochondria-targeted Ir complex capable of inducing tumor cell death by disrupting mitochondrial function, offering a potent strategy to suppress cisplatin resistance in non-small cell lung cancer. 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

Drug-drug interactions (DDIs) can produce unpredictable pharmacological effects and lead to adverse events that have the potential to cause irreversible damage to the organism. Traditional methods to detect DDIs through biological or pharmacological analysis are time-consuming and expensive, therefore, there is an urgent need to develop computational methods to effectively predict drug-drug interactions. Currently, deep learning and knowledge graph techniques which can effectively extract features of entities have been widely utilized to develop DDI prediction methods. In this research, we aim to systematically review DDI prediction researches applying deep learning and graph knowledge. The available biomedical data and public databases related to drugs are firstly summarized in this review. Then, we discuss the existing drug-drug interactions prediction methods which have utilized deep learning and knowledge graph techniques and group them into three main classes: deep learning-based methods, knowledge graph-based methods, and methods that combine deep learning with knowledge graph. We comprehensively analyze the commonly used drug related data and various DDI prediction methods, and compare these prediction methods on benchmark datasets. Finally, we briefly discuss the challenges related to drug-drug interactions prediction, including asymmetric DDIs prediction and high-order DDI prediction. Show less

Hydrogen sulfide (H2S) played a pivotal role in the early evolution of life on Earth before the predominance of atmospheric oxygen. The legacy of a persistent role for H2S in life's processes recently emerged through its discovery in modern biochemistry as an endogenous cellular signalling modulator involved in numerous biological processes. One major mechanism through which H2S signals is protein cysteine persulfidation, an oxidative post-translational modification. In recent years, chemoproteomic technologies have been developed to allow the global scanning of protein persulfidation targets in mammalian cells and tissues, providing a powerful tool to elucidate the broader impact of altered H2S in organismal physiological health and human disease states. While hundreds of proteins were confirmed to be persulfidated by global persulfidome methodologies, the targeting of specific proteins of interest and the investigation of further mechanistic studies are still underdeveloped due to a lack of stringent specificity of the methods and the inherent instability of persulfides. This review provides an overview of the processes of endogenous H2S production, oxidation, and signalling and highlights the application and limitations of current persulfidation labelling approaches for investigation of this important evolutionarily conserved biological switch for protein function. Show less